Bio Book
Bio Book
Bio Book
HOW
LIFE
WORKS
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BIOLO GY
HOW
LIFE
WORKS
SECOND EDITION
James Morris
BRANDEIS UNIVERSIT Y
Daniel Hartl
H A R VA R D U N I V E RS I T Y
Andrew Knoll
H A R VA R D U N I V E RS I T Y
Robert Lue
H A R VA R D U N I V E RS I T Y
Melissa Michael
U N I V E R S I T Y O F I L L I N O I S AT U R B A N A - C H A M PA I G N
H A R VA R D U N I V E RS I T Y
PUBLISHER Kate Ahr Parker ART AND MEDIA DIRECTOR Robert Lue, Harvard University
ACQUISITIONS EDITOR Beth Cole EXECUTIVE MEDIA EDITOR Amanda Nietzel
LEAD DEVELOPMENTAL EDITOR Lisa Samols SENIOR DEVELOPMENT EDITOR FOR TEACHING & LEARNING STRATEGIES Elaine Palucki
SENIOR DEVELOPMENTAL EDITOR Susan Moran SENIOR MEDIA PRODUCER Keri DiManigold
DEVELOPMENTAL EDITOR Erica Champion PROJECT EDITOR Robert Errera
EDITORIAL ASSISTANTS Jane Taylor, Alexandra Garrett, Abigail Fagan MANUSCRIPT EDITOR Nancy Brooks
REVIEW COORDINATOR Donna Brodman DIRECTOR OF DESIGN, CONTENT MANAGEMENT Diana Blume
PROJECT MANAGER Karen Misler DESIGN Tom Carling, Carling Design Inc.
DIRECTOR OF MAR KET DEVELOPMENT Lindsey Jaroszewicz ART MANAGER Matt McAdams
EXECUTIVE MAR KETING MANAGER Will Moore ILLUSTRATIONS Imagineering
ISBN-13: 978-1-4641-2609-3
ISBN-10: 1-4641-2609-7
First printing
Macmillan Learning
W. H. Freeman and Company
One New York Plaza
Suite 4500
New York, NY 10004-1562
www.macmillanhighered.com
DEDICATION
To all who are curious about life and how it works
ABOUT THE AUTHORS
JAMES R. MORRIS is Professor of Biology at Brandeis University. He ROBERT A. LUE is Professor of Molecular and Cellular Biology at
teaches a wide variety of courses for majors and non-majors, including Harvard University and the Richard L. Menschel Faculty Director
introductory biology, evolution, genetics and genomics, epigenetics, of the Derek Bok Center for Teaching and Learning. Dr. Lue has a
comparative vertebrate anatomy, and a first-year seminar on Darwin’s longstanding commitment to interdisciplinary teaching and research,
On the Origin of Species. He is the recipient of numerous teaching and chaired the faculty committee that developed the first integrated
awards from Brandeis and Harvard. His research focuses on the rapidly science foundation in the country to serve science majors as well as
growing field of epigenetics, making use of the fruit fly Drosophila pre-medical students. The founding director of Life Sciences Education
melanogaster as a model organism. He currently pursues this research at Harvard, Dr. Lue led a complete redesign of the introductory
with undergraduates in order to give them the opportunity to do curriculum, redefining how the university can more effectively foster
genuine, laboratory-based research early in their scientific careers. new generations of scientists as well as science-literate citizens.
Dr. Morris received a PhD in genetics from Harvard University and Dr. Lue has also developed award-winning multimedia, including
an MD from Harvard Medical School. He was a Junior Fellow in the the animation “The Inner Life of the Cell.” He has coauthored
Society of Fellows at Harvard University, and a National Academies undergraduate biology textbooks and chaired education conferences
Education Fellow and Mentor in the Life Sciences. He also writes short on college biology for the National Academies and the National
essays on science, medicine, and teaching at his Science Whys blog Science Foundation and on diversity in science for the Howard Hughes
(http://blogs.brandeis.edu/sciencewhys). Medical Institute and the National Institutes of Health. In 2012, Dr.
Lue’s extensive work on using technology to enhance learning took
a new direction when he became faculty director of university-wide
online education initiative HarvardX; he now helps to shape Harvard’s
DANIEL L. HARTL is Higgins Professor of Biology in the Department
engagement in online learning to reinforce its commitment to
of Organismic and Evolutionary Biology at Harvard University and
teaching excellence. Dr. Lue earned his PhD from Harvard University.
Professor of Immunology and Infectious Diseases at the Harvard
Chan School of Public Health. He has taught highly popular courses
in genetics and evolution at both the introductory and advanced
levels. His lab studies molecular evolutionary genetics and population MELISSA MICHAEL is Director for Core Curriculum and Assistant
genetics and genomics. Dr. Hartl is the recipient of the Samuel Director for Undergraduate Instruction for the School of Molecular
Weiner Outstanding Scholar Award as well as the Gold Medal of the and Cellular Biology at the University of Illinois at Urbana-Champaign.
Stazione Zoologica Anton Dohrn, Naples. He is a member of the A cell biologist, she primarily focuses on the continuing development
National Academy of Sciences and the American Academy of Arts of the School’s undergraduate curricula. She is currently engaged in
and Sciences. He has served as President of the Genetics Society several projects aimed at improving instruction and assessment at
of America and President of the Society for Molecular Biology and the course and program levels. Her research focuses primarily on how
Evolution. Dr. Hartl’s PhD is from the University of Wisconsin, and creative assessment strategies affect student learning outcomes, and
he did postdoctoral studies at the University of California, Berkeley. how outcomes in large-enrollment courses can be improved through
Before joining the Harvard faculty, he served on the faculties of the use of formative assessment in active classrooms.
the University of Minnesota, Purdue University, and Washington
University Medical School. In addition to publishing more than 400
scientific articles, Dr. Hartl has authored or coauthored 30 books.
ANDREW BERRY is Lecturer in the Department of Organismic and
Evolutionary Biology and an undergraduate advisor in the Life Sciences
at Harvard University. With research interests in evolutionary biology
ANDREW H. KNOLL is Fisher Professor of Natural History in the and history of science, he teaches courses that either focus on one
Department of Organismic and Evolutionary Biology at Harvard of the areas or combine the two. He has written two books: Infinite
University. He is also Professor of Earth and Planetary Sciences. Dr. Knoll Tropics, a collection of the writings of Alfred Russel Wallace, and, with
teaches introductory courses in both departments. His research focuses James D. Watson, DNA: The Secret of Life, which is part history, part
on the early evolution of life, Precambrian environmental history, and exploration of the controversies surrounding DNA-based technologies.
the interconnections between the two. He has also worked extensively
on the early evolution of animals, mass extinction, and plant evolution.
He currently serves on the science team for NASA’s mission to Mars.
ANDREW A. BIEWENER is Charles P. Lyman Professor of Biology in
Dr. Knoll received the Phi Beta Kappa Book Award in Science for Life on
the Department of Organismic and Evolutionary Biology at Harvard
a Young Planet. Other honors include the Paleontological Society Medal
University and Director of the Concord Field Station. He teaches
and Wollaston Medal of the Geological Society, London. He is a member
both introductory and advanced courses in anatomy, physiology, and
of the National Academy of Sciences and a foreign member of the Royal
biomechanics. His research focuses on the comparative biomechanics
Society of London. He received his PhD from Harvard University and
and neuromuscular control of mammalian and avian locomotion, with
then taught at Oberlin College before returning to Harvard.
relevance to biorobotics. He is currently Deputy Editor-in-Chief for
the Journal of Experimental Biology. He also served as President of the
American Society of Biomechanics.
vi
BRIAN D. FARRELL is Director of the David Rockefeller Center for students receive general education credit on the sixteen campuses of
Latin American Studies and Professor of Organismic and Evolutionary the University of North Carolina system.
Biology and Curator in Entomology at the Museum of Comparative
Zoology at Harvard University. He is an authority on coevolution
between insects and plants and a specialist on the biology of beetles.
JOHN MERRILL is Director of the Biological Sciences Program in the
He is the author of many scientific papers and book chapters on the
College of Natural Science at Michigan State University. This program
evolution of ecological interactions between plants, beetles, and
administers the core biology course sequence required for all science
other insects in the tropics and temperate zone. Professor Farrell also
majors. He is a National Academies Education Mentor in the Life
spearheads initiatives to repatriate digital information from scientific
Sciences. In recent years he has focused his research on teaching and
specimens of insects in museums to their tropical countries of origin.
learning with emphasis on classroom interventions and enhanced
In 2011–2012, he was a Fulbright Scholar to the Universidad Autónoma
assessment. A particularly active area is the NSF-funded development
de Santo Domingo in the Dominican Republic. Professor Farrell
of computer tools for automatic scoring of students’ open-ended
received a BA degree in Zoology and Botany from the University of
responses to conceptual assessment questions, with the goal of making
Vermont and MS and PhD degrees from the University of Maryland.
it feasible to use open-response questions in large-enrollment classes.
N. MICHELE HOLBROOK is Charles Bullard Professor of Forestry in RANDALL PHILLIS is Associate Professor of Biology at the University
the Department of Organismic and Evolutionary Biology at Harvard of Massachusetts Amherst. He has taught in the majors introductory
University. She teaches an introductory course on biodiversity as biology course at this institution for 19 years and is a National
well as advanced courses in plant biology. She studies the physics and Academies Education Mentor in the Life Sciences. With help from
physiology of vascular transport in plants with the goal of understanding the Pew Center for Academic Transformation (1999), he has been
how constraints on the movement of water and solutes between soil and instrumental in transforming the introductory biology course to an
leaves influences ecological and evolutionary processes. active learning format that makes use of classroom communication
systems. He also participates in an NSF-funded project to design model-
based reasoning assessment tools for use in class and on exams. These
ASSESSMENT AUTHORS tools are being designed to develop and evaluate student scientific
reasoning skills, with a focus on topics in introductory biology.
JEAN HEITZ is a Distinguished Faculty Associate at the University of
Wisconsin in Madison, WI. She has worked with the two-semester
introductory sequence for biological sciences majors for over 30 years. DEBRA PIRES is an Academic Administrator at the University of
Her primary roles include developing both interactive discussion/ California, Los Angeles. She teaches the introductory courses in the Life
recitation activities designed to uncover and modify misconceptions Sciences Core Curriculum. She is also the Instructional Consultant for
in biology and open-ended process-oriented labs designed to give the Center for Education Innovation & Learning in the Sciences (CEILS).
students a more authentic experience with science. The lab experience Many of her efforts are focused on curricular redesign of introductory
includes engaging all second-semester students in independent biology courses. Through her work with CEILS, she coordinates faculty
research, either mentored research or a library-based meta-analysis of development workshops across several departments to facilitate
an open question in the literature. She is also the advisor to the Peer pedagogical changes associated with curricular developments. Her
Learning Association and is actively involved in TA training. She has current research focuses on what impact the experience of active
taught a graduate course in “Teaching College Biology,” has presented learning pedagogies in lower division courses may have on student
active-learning workshops at a number of national and international performance and concept retention in upper division courses.
meetings, and has published a variety of lab modules, workbooks, and
articles related to biology education.
ASSESSMENT CONTRIBUTORS
MARK HENS is Associate Professor of Biology at the University of
ELENA R. LOZOVSKY, Principal Staff Scientist, Department of
North Carolina Greensboro, where he has taught introductory biology
Organismic and Evolutionary Biology, Harvard University
since 1996. He is a National Academies Education Mentor in the Life
Sciences and is the director of his department’s Introductory Biology FULTON ROCKWELL, Research Associate, Department of Organismic
Program. In this role, he guided the development of a comprehensive and Evolutionary Biology, Harvard University
set of assessable student learning outcomes for the two-semester
introductory biology course required of all science majors at UNCG. In
various leadership roles in general education, both on his campus and
statewide, he was instrumental in crafting a common set of assessable
student learning outcomes for all natural science courses for which
vii
VISION AND STORY OF
BIOLOGY: HOW LIFE WORKS
Dear students and instructors,
One of the most frequent questions we get about the second edition of Biology: How Life
Works is, “Has science really changed that much in three years?”
O
ngoing discoveries in biology mean that a new edition Instructors have told us that they especially like the activities
of an introductory biology textbook will certainly have that can be used in class to foster active learning among
some new science content. But, more importantly, our students. In response, the second edition includes a rich set of
second edition is new in the sense that we had the opportunity, activities across the introductory biology curriculum. Some are
for the first time, to listen to students and instructors who used short, taking just a couple of minutes to explore a specific topic
HLW in the classroom. The second edition is responsive to this or concept. Others are longer, spanning several class periods and
group and their input has proven invaluable. exploring topics and concepts across many chapters.
What we heard from this community is that the philosophy of Although students and instructors appreciated a streamlined
HLW resonates with students and instructors. They appreciate text, we also heard that more attention was needed in ecology.
a streamlined text that rigorously focuses on introductory In response, we added a chapter that focuses on physical
biology, an emphasis on integration, a modern treatment of processes and global ecology. This new chapter also had a ripple
biology, and equal attention to text, assessment, and media. effect throughout the later chapters of Part 2, giving us more
These elements haven’t changed—they are the threads that space to explore other ecological concepts more deeply as well.
connect the first and second editions. In fact, all of the
changes of the second edition are integrated within the The media in HLW is many layered, so that a static visual
framework of the first edition; they are not simply add-ons. synthesis on the page becomes animated online — and even
interactive — through visual synthesis maps and simulations,
We are particularly excited about the work we’ve done in using a consistent visual language and supported by assessment.
assessment. In the first edition, we worked with a creative and Media resources for this new edition have been expanded to
dedicated team of assessment authors to create something reflect its increased emphasis on global ecology — for example,
wholly new: not a standard test bank, but a thoughtful, there is a new Visual Synthesis figure and online map on the
curated, well-aligned set of questions that can be used for flow of matter and energy in ecosystems. We also developed
teaching as well as testing. These questions are written at a additional media resources that focus on viruses, cells, and
variety of cognitive levels. In addition, they can be used in a tissues.
variety of contexts, including pre-class, in-class, homework,
and exam, providing a learning path for students. We feel that this edition is a wonderful opportunity for us to
continue to develop an integrated set of resources to support
Our approach was so well received that we took it a step further instructor teaching and student learning in introductory biology.
in the second edition. The HLW team is excited to have Melissa Thank you for taking the time to use it in the classroom.
Michael, our lead assessment author in the first edition, join us
as a lead author in the second edition. Her new role allows her Sincerely,
to work more closely with the text and media, which makes for The Biology: How Life Works Author Team
an even tighter alignment among these various components.
viii
RETHINKING The Biology: How Life Works team set out to create a resource for today’s
biology students that would reimagine how content is created and
BIOLOGY delivered. With this second edition, we’ve refined that vision using
feedback from the many dedicated instructors and students who have
become a part of the How Life Works community.
Thematic Selective
We wrote How Life Works with six themes in mind. We used It is unrealistic to expect the majors course to cover every-
these themes as a guide to make decisions about which thing. We envision How Life Works not as a reference for all of
concepts to include and how to organize them. The themes biology, but as a resource focused on foundational concepts,
provide a framework that helps students see biology as a set of terms, and experiments. We explain fundamental topics care-
connected concepts rather than disparate facts. fully, with an appropriate amount of supporting detail, so that
students leave an introductory biology class with a framework
• The scientific method is a deliberate way of asking and on which to build.
answering questions about the natural world.
• Life works according to fundamental principles of
chemistry and physics. Integrated
• The fundamental unit of life is the cell.
How Life Works moves away from minimally related chapters
• Evolution explains the features that organisms share and to provide guidance on how concepts connect to one another
those that set them apart. and the bigger picture. Across the book, key concepts such
• Organisms interact with one another and with their as chemistry are presented in context and Cases and Visual
physical environment, shaping ecological systems that Synthesis figures throughout the text provide a framework
sustain life. for connecting and assimilating information.
• In the 21st century, humans have become major agents in
ecology and evolution.
Visual Synthesis Figures and Online Maps on the A rich collection of in-class activities provides active learn-
Flow of Matter and Energy through Ecosystems, Cellular ing materials for instructors to use in a variety of settings.
Communities, and Viruses allow students to explore Learn more about the new in-class activities on page xvii.
connections between concepts through dynamic
visualizations. Learn more about the new media on page xix. Improved LaunchPad functionality makes it easier
to search and filter within our expansive collection of
assessment questions. Learn more about new LaunchPad
functionality on page xii.
ix
TABLE OF CONTENTS
The table of contents is arranged in a familiar way to allow its easy use in a range of EVOLUTION COVERAGE: Chapter 1 introduces
introductory biology courses. On closer look, there are significant differences that evolution as a major theme of the book before
discussing gene expression in Chapters 3 and 4 as a
aim to help biology teachers incorporate the outlooks and research of biology today.
foundation for later discussions of the conservation
Key differences are identified by and unique chapters by . of metabolic pathways and enzyme structure
(Chapters 6–8) and genetic and phenotypic
variation (Chapters 14 and 15). After the chapters
on the mechanisms and patterns of evolution
(Chapters 21–24), we discuss the diversity of all
organisms in terms of adaptations and comparative
CHAPTER 1 Life: Chemical, Cellular, and Evolutionary Foundations features, culminating in ecology as the ultimate
illustration of evolution in action.
CASE 1 THE FIRST CELL: LIFE’S ORIGINS
CASE 4 MALARIA: COEVOLUTION OF HUMANS AND A PARASITE UNIQUE CHAPTERS: Biology: How Life Works,
Second Edition includes chapters that don’t
traditionally appear in introductory biology texts,
CHAPTER 21 Evolution: How Genotypes and Phenotypes Change over Time one in almost every major subject area. These
novel chapters represent shifts toward a more
CHAPTER 22 Species and Speciation
modern conception of certain topics in biology
CHAPTER 23 Evolutionary Patterns: Phylogeny and Fossils and are identified by .
CHAPTER 24 Human Origins and Evolution
x
“The approach to teaching is something my colleagues and I had To hear the authors talk about the table
been waiting for in a textbook. However, the text is flexible of contents in more depth, visit
enough to accommodate a traditional teaching style.” biologyhowlifeworks.com
xi
RETHINKING THE TEXTBOOK
THROUGH LAUNCHPAD
O
rdinarily, textbooks are developed by first writing The text, visuals, and assessments come together most
chapters, then making decisions about art and effectively through LaunchPad, Macmillan’s integrated
images, and finally assembling a test bank and learning management system. In LaunchPad, students and
ancillary media. Biology: How Life Works develops the text, instructors can access all components of Biology: How Life Works.
visual program, and assessment at the same time. These
three threads are tied to the same set of core concepts, LaunchPad resources for How Life Works are flexible and aligned.
share a common language, and use the same visual palette, Instructors have the ability to select the visuals, assessments, and
which ensures a seamless learning experience for students activities that best suit their classroom and students.
throughout the course. All resources are aligned to one another as well as to the text
to ensure effectiveness in helping students build skills and develop
knowledge necessary for a foundation in biology.
NEW IN LAUNCHPAD
FOR BIOLOGY: HOW
LIFE WORKS, SECOND
EDITION
Functionality to search the question
database and filter questions for a
number of variables including Core
Concept, difficulty level, Bloom’s level,
and class setting allows instructors to
make best use of the robust assessment
assets of How Life Works.
xii
LAUNCHPAD LAUNCHPADWORKS.COM
Where content counts.
Where service matters. Powerful, Simple, and Inviting
Where students learn. LaunchPad for How Life Works includes: e-Book to encourage students to use the
resources at hand.
The complete Biology: How Life
Works interactive e-Book
Pre-built units that are easy to adapt
Carefully curated multimedia visuals and augment to fit your course.
and assessments, assignable by the
instructor and easily accessible by A Gradebook that provides clear
students. feedback to students and instructors on
performance in the course as a whole
LearningCurve adaptive quizzing and individual assignment.
that puts “testing to learn” into action,
with individualized question sets and LMS integration allows LaunchPad
feedback for each student based on his to be easily integrated into your school’s
or her correct and incorrect responses. learning management system so your
All the questions are tied back to the Gradebook and roster are always in sync.
LEARNINGCURVE LEARNINGCURVEWORKS.COM
Improve knowledge of
course material Recommend LearningCurve
to other students
Earn better grades
Percentage of students
xiii
RETHINKING The art in the text of How Life Works and the associated
media in LaunchPad were developed in coordination with
This Visual Synthesis figure on Speciation brings together multiple concepts from the chapters on evolution.
xiv
Online, the Visual Synthesis figures turn
into zoomable, dynamic Visual Synthesis
Maps where students can explore both
the big picture and the details.
xv
RETHINKING Well-designed assessment is a tremendous tool for instructors in gauging
student understanding, actively teaching students, and preparing students
ASSESSMENT for exams. The Biology: How Life Works assessment author team applied
decades of experience researching and implementing assessment practices
to create a variety of questions and activities for pre-class, in-class,
homework, and exam settings. All assessment items are carefully aligned
with the text and media and have the flexibility to meet the needs of
instructors with any experience level, classroom size, or teaching style.
Alignment Flexibility
If the questions, exercises, and activities in the course aren’t The How Life Works assessment authors teach in a variety
aligned with course objectives and materials, practice with of classroom sizes and styles, and recognize that there is a
these resources may not help students succeed in their exam wide diversity of course goals and circumstances. Each set of
or in future biology courses. Each How Life Works assessment materials, from in-class activities to exam questions, includes
item is carefully aligned to the goals and content of the text, a spectrum of options for instructors. All the assessment items
and to the assessment items used in other parts of the course. are housed in the LaunchPad platform, which is designed to
Students are guided through a learning path that provides allow instructors to assign and organize assessment items to
them with repeated and increasingly challenging practice suit the unique needs of their course and their students.
with the important concepts illustrated in the text and media.
Which of the following reactions would you predict could be coupled to ATP
synthesis from ADP + Pi? Select all that apply.
a.) creatine phosphate + H2O b creatine + Pi, ∆G -10.3 kcal/mol
b.) phosphoenolpyruvate + H2O b pyruvate + Pi, ∆G -14.8 kcal/mol
c.) glucose 6-phosphate + H2O b glucose + Pi, ∆G -3.3 kcal/mol
d.) glucose 1-phosphate + H2O b glucose + Pi, ∆G -5.0 kcal/mol
Answer the following questions about the reactions
e.) glutamic acid + NH3 b glutamine, ∆G +3.4 kcal/mol
shown in the graph.
xvi
RETHINKING Active learning exercises are an important component of the learning
pathway and provide students with hands-on exploration of challenging
ACTIVITIES topics and misconceptions. The second edition of Biology: How Life Works
includes a new collection of over 40 in-class activities crafted to address the
concepts that students find most challenging.
T
he activities collection was designed to cover a range of
classroom sizes and complexity levels, and many can be
easily adapted to suit the available time and preferred
teaching style. Each activity includes a detailed activity guide
for instructors. The activity guide introduces the activity,
outlines learning objectives, and provides guidance on how to
implement and customize the activity.
xvii
WHAT’S NEW IN
THE SECOND EDITION?
F
rom the start, Biology: How Life Works was envisioned not as a reference book for all of biology, but as a resource
focused on foundational concepts, terms, and experiments, all placed in a framework that motivates student
interest through a coherent and authentic presentation of current science. In preparing this edition, we
carefully considered the latest breakthroughs and incremental, but nevertheless significant, changes across the fields
of biology. We also reached out to adopters, instructors not using our book, and primary literature to determine what
concepts and details are relevant, important, and necessary additions. Our integrated approach to text, media, and
assessment means that all changes are carefully reflected in each of these areas.
xviii
NEW MEDIA
Cell Communities Visual Synthesis Map to accompany
the printed Visual Synthesis figure
New Animations
Virus Visual Synthesis Map to accompany the printed Chapter 9: Basic Principles of Cell Signaling Chapter 10: Dynamic Nature of Actin Filaments
Visual Synthesis figure
Chapter 9: G protein-coupled Receptor Signaling Chapter 19: Lac Operon
New Visual Synthesis figure and map on the Flow of
Matter and Energy in Ecosystems Chapter 9: Signal Amplification Chapter 20: ABC Model of Floral Development
Virus Video featuring author Rob Lue
Chapter 10: Dynamic Nature of Microtubules Chapter 40: Glucose Absorption in the Small Intestine
Cell Membrane simulation
Chapter 10: Motor Proteins Chapter 42: Gastrulation
NEW TOPICS AND The following is a detailed list of content changes in this edition. These range from the very small
(nucleotides shown at physiological pH) to quite substantial (an entire new chapter in the ecology
OTHER REVISIONS section). Especially important changes are indicated with an asterisk ( ).
New coverage of functional groups (Chapter 2) New branching order of the eukaryote tree to A new introduction to the immune system (Chapter 43)
reflect new research in the past three years
Nucleotides now shown at physiological pH (Chapter 3) (Chapter 27 and onward) A new discussion of nematodes (Chapter 44)
Amino acids now shown at physiological pH (Chapter 4) A new paragraph on ciliates (Chapter 27) Introduction of a newly discovered species,
Dendrogramma enigmatica (Chapter 44)
The story of the evolution of photosynthesis now A new explanation of protist diversity (Chapter 27)
brought together in a single major section at the end A simplified population growth equation (Chapter 46)
of Chapter 8 (section 8.5) A new discussion of plant nutrients with a table
(Chapter 29) A new discussion of facilitation (Chapter 47)
Chapters 9 and 10 streamlined to better match our
An enhanced discussion of seeds, including the An expanded discussion of herbivory (Chapter 47)
mission statement
development of the embryo and dispersal structures
(Chapter 30) A new example of microbial symbionts (Chapter 47)
A new discussion of cellular response and what
determines it (Chapter 9) New coverage of the genetic advantages of alternation A new discussion of biodiversity and its importance
of generations, and how it allows inbreeding (Chapter (Chapter 47)
New inclusion of the trombone model of DNA 30)
replication (Chapter 12) An entirely new chapter on physical processes that
Addition of apomixis (Chapter 30) underlie different biomes (Chapter 48)
Addition of CRISPR technology (Chapter 12)
• Differential solar energy around the globe
The section on the role of plant sensory systems in and seasonality
Expanded coverage of retrotransposons and reverse the timing of plant reproduction moved from Chapter
• Wind and ocean currents
transcriptase (Chapter 13) 30 to Chapter 31
• Effects of circulation and topography on rainfall
A new How Do We Know? figure explaining Mendel’s Completely revised explanation of the basis for • Expanded discussion of terrestrial biomes
experimental results (Chapter 16) angiosperm diversity (Chapter 33) • Freshwater and marine biomes
• Integration of concepts of biogeochemical cycles
New coverage of the mechanism of X-inactivation Brief descriptions of unfamiliar organisms and the from Chapters 25 and 26 with ecological concepts
(Chapter 19) major groups of organisms layered in the animal phys- • Global patterns of primary production
iology chapters to make it easier to teach physiology
• Global biodiversity
before diversity (Chapters 35-42)
An expanded discussion of non-random mating
and inbreeding depression (Chapter 21)
Brief review of organismal form and function in the A new exploration of the effect of fracking on the
plant and animal diversity chapters (Chapters 33 carbon cycle (Chapter 49)
Addition of the effect of mass extinctions on and 44), allowing these chapters to be used on their
species diversity (Chapter 23) own or before the physiology chapters and giving New coverage of habitat loss and biodiversity
instructors maximum flexibility (Chapter 49)
Updated discussion of the relationship between
Neanderthals and Homo sapiens, as well as A new section on the composition of blood New coverage of overexploitation of resources and its
Denisovans (Chapter 24) (Chapter 39) effects on community ecology (Chapter 49)
Significantly revised link between the carbon cycle, New diagrams of hormone feedback loops in the A new Core Concept and discussion of conservation
biodiversity, and ecology (Chapter 25) menstrual cycle (Chapter 42) biology (Chapter 49)
xix
PRAISE FOR
HOW LIFE WORKS
I have taught botany and then Biology II for over We have all seen an improvement in our students’
20 years and have been very frustrated when I have understanding of the material this year, the first year
realized how little knowledge students retained. Since that we used the Morris text.
we have gone to this textbook, I find that the questions – ANUPAMA SESHAN, Emmanuel College
students are asking in class are much more probing
than those in the past, and the students seem much
more engaged in the topics. I am hopeful that this I like the figures, especially the 3D ones — we focus
approach will help our students be deeper thinkers and on “perceptual ability” training in our classes and
better scientists. figures that encourage students to think about cells in
3D are excellent!
– GLORIA CADDELL, University of Central Oklahoma
– KIRKWOOD LAND, University of the Pacific
xx
Good questions are just as important as a good I think HLW does a better job of presenting
textbook. The available variety of assessment tools introductory material than our current text, which
was very important for our adoption of this text. tends to overwhelm students.
If the whole book reads like this I would love to use it! With the quick checks and the experiments the first
This is the way I like to teach! I want students to chapter already has the learners thinking about
understand rather than memorize and this chapter experiments and critical analysis.
seems aimed at this. – JOHN KOONTZ, University of Tennessee Knoxville
The writing style is excellent, it makes a great – PAUL MOORE, Bowling Green State University
xxi
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ACKNOWLEDGMENTS
Biology: How Life Works is not only a book. Instead, it is an integrated and cover designer, and Sheridan Sellers, our compositor. Together,
set of resources to support student learning and instructor teaching they managed the look and feel of the book, coming up with creative
in introductory biology. As a result, we work closely with an entire solutions for page layout.
community of authors, publishers, instructors, reviewers, and
students. We would like to thank this dedicated group. In digital media, we thank Amanda Nietzel for her editorial insight in
making pedagogically useful media tools, and Keri deManigold and Chris
First and foremost, we thank the thousands of students we have Efstratiou for managing and coordinating the media and websites. They
collectively taught. Their curiosity, intelligence, and enthusiasm have each took on this project with dedication, persistence, enthusiasm,
been sources of motivation for all of us. and attention to detail that we deeply appreciate.
Our teachers and mentors have provided us with models of patience, We are extremely grateful to Elaine Palucki for her insight into
creativity, and inquisitiveness that we strive to bring into our own teaching and learning strategies, Donna Brodman for coordinating the
teaching and research. They encourage us to be life-long learners, many reviewers, and Jane Taylor, Alexandra Garrett, and Abigail Fagan
teachers, and scholars. for their consistent and tireless support.
We feel very lucky to be a partner with W. H. Freeman and Macmillan Imagineering under the patient and intelligent guidance of Mark
Learning. From the start, they have embraced our project, giving us the Mykytuik provided creative, insightful art to complement, support,
space and room to achieve something unique, while at the same time and reinforce the text. We also thank our illustration coordinator, Matt
providing guidance, support, and input from the broader community of McAdams, for skillfully guiding our collaboration with Imagineering.
instructors and students. Christine Buese, our photo editor, and Lisa Passmore and Richard Fox,
our photo researchers, provided us with a steady stream of stunning
Beth Cole, our acquisitions editor, deserves thanks for taking on the photos, and never gave up on those hard-to-find shots. Paul Rohloff,
second edition and becoming our leader. She keeps a watchful eye our production manager, ensured that the journey from manuscript to
on important trends in science, education, and technology, carefully printing was seamless.
listens to what we want to do, and helps us put our aspirations in a
larger context. We would also like to acknowledge Kate Parker, Publisher of Sciences,
Chuck Linsmeier, Vice President of Editorial, Susan Winslow,
Lead developmental editor Lisa Samols continues to have just the Managing Director, and Ken Michaels, Chief Executive Officer, for
right touch — the ability to listen as well as offer intelligent their support of How Life Works and our unique approach.
suggestions, serious with a touch of humor, quiet but persistent. Senior
developmental editor Susan Moran has an eye for detail and the uncanny We also sincerely thank Erin Betters, Jere A. Boudell, Donna Koslowsky,
ability to read the manuscript like a student. Developmental editor Erica and Jon Stoltzfus for thoughtful and insightful contributions to the
Champion brings intelligence and thoughtfulness to her edits. assessment materials.
Karen Misler kept us all on schedule in a clear and firm but always We are extremely grateful for all of the hard work and expertise of the
understanding and compassionate way. sales representatives, regional managers, and regional sales specialists. We
have enjoyed meeting and working with this dedicated sales staff, who
Lindsey Jaroszewicz, our market development manager, is remarkable are the ones that ultimately put the book in the hands of instructors.
for her energy and enthusiasm, her attention to detail, and her
creativity in ways to reach out to instructors and students. Will Moore, Countless reviewers made invaluable contributions to this book and
our marketing manager, refined the story of How Life Works 2e and deserve special thanks. From catching mistakes to suggesting new and
works tirelessly with our sales teams to bring the second edition to innovative ways to organize the content, they provided substantial
instructors and students everywhere. input to the book. They brought their collective years of teaching to
the project, and their suggestions are tangible in every chapter.
We thank Robert Errera for coordinating the move from manuscript
to the page, and Nancy Brooks for helping to even out the prose. We Finally, we would like to thank our families. None of this would have
also thank Diana Blume, our design director, Tom Carling, our text been possible without their support, inspiration, and encouragement.
xxiii
Contributors, First Edition
Thank you to all the instructors who worked in collaboration with the authors and assessment authors to write Biology: How
Life Works assessments, activities, and exercises.
Allison Alvarado, University of California, Los Angeles Kerry Kilburn, Old Dominion University
Peter Armbruster, Georgetown University Jo Kurdziel, University of Michigan
Zane Barlow-Coleman, formerly of University of David Lampe, Duquesne University
Massachusetts, Amherst Brenda Leady, University of Toledo
James Bottesch, Brevard Community College Sara Marlatt, Yale University*
Jessamina Blum, Yale University Kelly McLaughlin, Tufts University
Jere Boudell, Clayton State University Brad Mehrtens, University of Illinois at Urbana-
David Bos, Purdue University Champaign
Laura Ciaccia West, Yale University* Nancy Morvillo, Florida Southern College
Laura DiCaprio, Ohio University Jennifer Nauen, University of Delaware
Tod Duncan, University of Colorado, Denver Kavita Oommen, Georgia State University
Cindy Giffen, University of Wisconsin, Madison Patricia Phelps, Austin Community College
Paul Greenwood, Colby College Melissa Reedy, University of Illinois at Urbana-
Stanley Guffey, The University of Tennessee, Knoxville Champaign
Alison Hill, Duke University Lindsay Rush, Yale University*
Meg Horton, University of North Carolina at Sukanya Subramanian, Collin College
Greensboro Michelle Withers, West Virginia University
First Edition Michael Angilletta, Arizona State Charles Baer, University of Florida
Thomas Abbott, University of University Brian Bagatto, University of
Connecticut Jonathan Armbruster, Auburn Akron
Tamarah Adair, Baylor University University Alan L. Baker, University of New
Sandra Adams, Montclair State Jessica Armenta, Lone Star Hampshire
University College System Ellen Baker, Santa Monica College
Jonathon Akin, University of Brian Ashburner, University of Mitchell Balish, Miami University
Connecticut Toledo Teri Balser, University of Florida
Eddie Alford, Arizona State Andrea Aspbury, Texas State Paul Bates, University of
University University Minnesota, Duluth
Chris Allen, College of the Nevin Aspinwall, Saint Louis Michel Baudry, University of
Mainland University Southern California
Sylvester Allred, Northern Felicitas Avendano, Grand View Jerome Baudry, The University of
Arizona University University Tennessee, Knoxville
Shivanthi Anandan, Drexel Yael Avissar, Rhode Island College Mike Beach, Southern
University Ricardo Azpiroz, Richland College Polytechnic State University
Andrew Andres, University of Jessica Baack, Southwestern Andrew Beall, University of North
Nevada, Las Vegas Illinois College Florida
xxiv
Gregory Beaulieu, University Heather Bruns, Ball State Catharina Coenen, Allegheny
of Victoria University College
John Bell, Brigham Young Jill Buettner, Richland Mary Colavito, Santa Monica
University College College
Michael Bell, Richland Stephen Burnett, Clayton State Craig Coleman, Brigham Young
College University University
Rebecca Bellone, University Steve Bush, Coastal Carolina Alex Collier, Armstrong Atlantic
of Tampa University State University
Anne Bergey, Truman State David Byres, Florida State College Sharon Collinge, University of
University at Jacksonville Colorado, Boulder
Laura Bermingham, University of James Campanella, Montclair Jay Comeaux, McNeese State
Vermont State University University
Aimee Bernard, University of Darlene Campbell, Cornell Reid Compton, University of
Colorado, Denver University Maryland
Annalisa Berta, San Diego State Jennifer Campbell, North Ronald Cooper, University of
University Carolina State University California, Los Angeles
Joydeep Bhattacharjee, University John Campbell, Northwest Victoria Corbin, University of
of Louisiana, Monroe College Kansas
Arlene Billock, University of David Canning, Murray State Asaph Cousins, Washington State
Louisiana, Lafayette University University
Daniel Blackburn, Trinity Richard Cardullo, University of Will Crampton, University of
College California, Riverside Central Florida
Mark Blackmore, Valdosta State Sara Carlson, University of Kathryn Craven, Armstrong
University Akron Atlantic State University
Justin Blau, New York University Jeff Carmichael, University of Scott Crousillac, Louisiana State
Andrew Blaustein, Oregon State North Dakota University
University Dale Casamatta, University of Kelly Cude, College of the
Mary Bober, Santa Monica North Florida Canyons
College Anne Casper, Eastern Michigan Stanley Cunningham, Arizona
Robert Bohanan, University of University State University
Wisconsin, Madison David Champlin, University of Karen Curto, University of
Jim Bonacum, University of Southern Maine Pittsburgh
Illinois at Springfield Rebekah Chapman, Georgia State Bruce Cushing, The University of
Laurie Bonneau, Trinity University Akron
College Samantha Chapman, Villanova Rebekka Darner, University of
David Bos, Purdue University University Florida
James Bottesch, Brevard Mark Chappell, University of James Dawson, Pittsburg State
Community College California, Riverside University
Jere Boudell, Clayton State P. Bryant Chase, Florida State Elizabeth De Stasio, Lawrence
University University University
Nancy Boury, Iowa State Young Cho, Eastern New Mexico Jennifer Dechaine, Central
University University Washington University
Matthew Brewer, Georgia State Tim Christensen, East Carolina James Demastes, University of
University University Northern Iowa
Mirjana Brockett, Georgia Steven Clark, University of D. Michael Denbow, Virginia
Institute of Technology Michigan Polytechnic Institute and State
Andrew Brower, Middle Ethan Clotfelter, Amherst University
Tennessee State University College Joseph Dent, McGill University
xxv
Terry Derting, Murray State John Elder, Valdosta State J. Yvette Gardner, Clayton State
University University University
Jean DeSaix, University of North William Eldred, Boston Gillian Gass, Dalhousie University
Carolina at Chapel Hill University Jason Gee, East Carolina
Donald Deters, Bowling Green David Eldridge, Baylor University University
State University Inge Eley, Hudson Valley Topher Gee, University of North
Hudson DeYoe, The University of Community College Carolina at Charlotte
Texas, Pan American Lisa Elfring, University of Arizona Vaughn Gehle, Southwest
Leif Deyrup, University of the Richard Elinson, Duquesne Minnesota State University
Cumberlands University Tom Gehring, Central Michigan
Laura DiCaprio, Ohio University Kurt Elliott, Northwest Vista University
Jesse Dillon, California State College John Geiser, Western Michigan
University, Long Beach Miles Engell, North Carolina State University
Frank Dirrigl, The University of University Alex Georgakilas, East Carolina
Texas, Pan American Susan Erster, Stony Brook University
Kevin Dixon, Florida State University Peter Germroth, Hillsborough
University Joseph Esdin, University of Community College
Elaine Dodge Lynch, Memorial California, Los Angeles Arundhati Ghosh, University of
University of Newfoundland Jean Everett, College of Pittsburgh
Hartmut Doebel, George Charleston Carol Gibbons Kroeker,
Washington University Brent Ewers, University of University of Calgary
Jennifer Doll, Loyola University, Wyoming Phil Gibson, University of
Chicago Melanie Fierro, Florida State Oklahoma
Logan Donaldson, York College at Jacksonville Cindee Giffen, University of
University Michael Fine, Virginia Wisconsin, Madison
Blaise Dondji, Central Commonwealth University Matthew Gilg, University of
Washington University Jonathan Fingerut, St. Joseph’s North Florida
Christine Donmoyer, Allegheny University Sharon Gillies, University of the
College Ryan Fisher, Salem State Fraser Valley
James Dooley, Adelphi University University Leonard Ginsberg, Western
Jennifer Doudna, University of David Fitch, New York University Michigan University
California, Berkeley Paul Fitzgerald, Northern Virginia Florence Gleason, University of
John DuBois, Middle Tennessee Community College Minnesota
State University Jason Flores, University of North Russ Goddard, Valdosta State
Richard Duhrkopf, Baylor Carolina at Charlotte University
University Matthias Foellmer, Adelphi Miriam Golbert, College of the
Kamal Dulai, University of University Canyons
California, Merced Barbara Frase, Bradley University Jessica Goldstein, Barnard
Arthur Dunham, University of Caitlin Gabor, Texas State College, Columbia University
Pennsylvania University Steven Gorsich, Central Michigan
Mary Durant, Lone Star College Michael Gaines, University of University
System Miami Sandra Grebe, Lone Star College
Roland Dute, Auburn University Jane Gallagher, The City College System
Andy Dyer, University of South of New York, The City Robert Greene, Niagara
Carolina, Aiken University of New York University
William Edwards, Niagara Kathryn Gardner, Boston Ann Grens, Indiana University,
University University South Bend
xxvi
Theresa Grove, Valdosta State David Hicks, The University of Jonghoon Kang, Valdosta State
University Texas at Brownsville University
Stanley Guffey, The University of Karen Hicks, Kenyon College George Karleskint, St. Louis
Tennessee, Knoxville Alison Hill, Duke University Community College at
Nancy Guild, University of Kendra Hill, South Dakota State Meramec
Colorado, Boulder University David Karowe, Western Michigan
Lonnie Guralnick, Roger Williams Jay Hodgson, Armstrong Atlantic University
University State University Judy Kaufman, Monroe
Laura Hake, Boston College John Hoffman, Arcadia University Community College
Kimberly Hammond, University Jill Holliday, University of Florida Nancy Kaufmann, University of
of California, Riverside Sara Hoot, University of Pittsburgh
Paul Hapeman, University of Wisconsin, Milwaukee John Kauwe, Brigham Young
Florida Margaret Horton, University of University
Luke Harmon, University of North Carolina at Greensboro Elena Keeling, California
Idaho Lynne Houck, Oregon State Polytechnic State University
Sally Harmych, University of University Jill Keeney, Juniata College
Toledo Kelly Howe, University of New Tamara Kelly, York University
Jacob Harney, University of Mexico Chris Kennedy, Simon Fraser
Hartford William Huddleston, University University
Sherry Harrel, Eastern Kentucky of Calgary Bretton Kent, University of
University Jodi Huggenvik, Southern Illinois Maryland
Dale Harrington, Caldwell University Jake Kerby, University of South
Community College and Melissa Hughes, College of Dakota
Technical Institute Charleston Jeffrey Kiggins, Monroe
J. Scott Harrison, Georgia Randy Hunt, Indiana University Community College
Southern University Southeast Scott Kight, Montclair State
Diane Hartman, Baylor University Tony Huntley, Saddleback University
Mary Haskins, Rockhurst College Stephen Kilpatrick, University of
University Brian Hyatt, Bethel College Pittsburgh, Johnstown
Bernard Hauser, University of Jeba Inbarasu, Metropolitan Kelly Kissane, University of
Florida Community College Nevada, Reno
David Haymer, University of Colin Jackson, The University of David Kittlesen, University of
Hawaii Mississippi Virginia
David Hearn, Towson University Eric Jellen, Brigham Young Jennifer Kneafsey, Tulsa
Marshal Hedin, San Diego State University Community College
University Dianne Jennings, Virginia Jennifer Knight, University of
Paul Heideman, College of Commonwealth University Colorado, Boulder
William and Mary Scott Johnson, Wake Technical Ross Koning, Eastern
Gary Heisermann, Salem State Community College Connecticut State University
University Mark Johnston, Dalhousie David Kooyman, Brigham Young
Brian Helmuth, University of University University
South Carolina Susan Jorstad, University of Olga Kopp, Utah Valley
Christopher Herlihy, Middle Arizona University
Tennessee State University Stephen Juris, Central Michigan Anna Koshy, Houston
Albert Herrera, University of University Community College
Southern California Julie Kang, University of Todd Kostman, University of
Brad Hersh, Allegheny College Northern Iowa Wisconsin, Oshkosh
xxvii
Peter Kourtev, Central Michigan Janet Loxterman, Idaho State Richard Merritt, Houston
University University Community College
William Kroll, Loyola University, Ford Lux, Metropolitan State Jennifer Metzler, Ball State
Chicago College of Denver University
Dave Kubien, University of New José-Luis Machado, Swarthmore James Mickle, North Carolina
Brunswick College State University
Allen Kurta, Eastern Michigan C. Smoot Major, University of Brian Miller, Middle Tennessee
University South Alabama State University
Ellen Lamb, University of North Charles Mallery, University of Allison Miller, Saint Louis
Carolina at Greensboro Miami University
Troy Ladine, East Texas Baptist Mark Maloney, Spelman Yuko Miyamoto, Elon University
University College Ivona Mladenovic, Simon Fraser
David Lampe, Duquesne Carroll Mann, Florida State University
University College at Jacksonville Marcie Moehnke, Baylor
Evan Lampert, Gainesville State Carol Mapes, Kutztown University
College University of Pennsylvania Chad Montgomery, Truman State
James Langeland, Kalamazoo Nilo Marin, Broward College University
College Diane Marshall, University of Jennifer Mook, Gainesville State
John Latto, University of New Mexico College
California, Santa Barbara Heather Masonjones, University Daniel Moon, University of North
Brenda Leady, University of of Tampa Florida
Toledo Scott Mateer, Armstrong Atlantic Jamie Moon, University of North
Jennifer Leavey, Georgia Institute State University Florida
of Technology Luciano Matzkin, The University Jeanelle Morgan, Gainesville State
Hugh Lefcort, Gonzaga University of Alabama in Huntsville College
Brenda Leicht, University of Iowa Robert Maxwell, Georgia State David Morgan, University of West
Craig Lending, The College at University Georgia
Brockport, The State University Meghan May, Towson University Julie Morris, Armstrong Atlantic
of New York Michael McGinnis, Spelman State University
Nathan Lents, John Jay College of College Becky Morrow, Duquesne
Criminal Justice, The City Kathleen McGuire, San Diego University
University of New York State University Mark Mort, University of Kansas
Michael Leonardo, Coe College Maureen McHale, Truman State Nancy Morvillo, Florida Southern
Army Lester, Kennesaw State University College
University Shannon McQuaig, St. Petersburg Anthony Moss, Auburn University
Cynthia Littlejohn, University of College Mario Mota, University of Central
Southern Mississippi Susan McRae, East Carolina Florida
Zhiming Liu, Eastern New Mexico University Alexander Motten, Duke
University Lori McRae, University of Tampa University
Jonathan Lochamy, Georgia Mark Meade, Jacksonville State Tim Mulkey, Indiana State
Perimeter College University University
Suzanne Long, Monroe Brad Mehrtens, University of John Mull, Weber State
Community College Illinois at Urbana-Champaign University
Julia Loreth, University of North Michael Meighan, University of Michael Muller, University of
Carolina at Greensboro California, Berkeley Illinois at Chicago
Jennifer Louten, Southern Douglas Meikle, Miami Beth Mullin, The University of
Polytechnic State University University Tennessee, Knoxville
xxviii
Paul Narguizian, California State John Peters, College of Peggy Rolfsen, Cincinnati State
University, Los Angeles Charleston Technical and Community
Jennifer Nauen, University of Chris Petrie, Brevard Community College
Delaware College Mike Rosenzweig, Virginia
Paul Nealen, Indiana University of Patricia Phelps, Austin Polytechnic Institute and State
Pennsylvania Community College University
Diana Nemergut, University of Steven Phelps, The University Doug Rouse, University of
Colorado, Boulder of Texas at Austin Wisconsin, Madison
Kathryn Nette, Cuyamaca College Kristin Picardo, St. John Fisher Yelena Rudayeva, Palm Beach
Jacalyn Newman, University of College State College
Pittsburgh Aaron Pierce, Nicholls State Ann Rushing, Baylor
James Nienow, Valdosta State University University
University Debra Pires, University of Shereen Sabet, La Sierra
Alexey Nikitin, Grand Valley State California, Los Angeles University
University Thomas Pitzer, Florida Rebecca Safran, University of
Tanya Noel, York University International University Colorado
Fran Norflus, Clayton State Nicola Plowes, Arizona State Peter Sakaris, Southern
University University Polytechnic State University
Celia Norman, Arapahoe Crima Pogge, City College of Thomas Sasek, University of
Community College San Francisco Louisiana, Monroe
Eric Norstrom, DePaul University Darren Pollock, Eastern New Udo Savalli, Arizona State
Jorge Obeso, Miami Dade College Mexico University University
Kavita Oommen, Georgia State Kenneth Pruitt, The University H. Jochen Schenk, California State
University of Texas at Brownsville University, Fullerton
David Oppenheimer, University Sonja Pyott, University of North Gregory Schmaltz, University of
of Florida Carolina at Wilmington the Fraser Valley
Joseph Orkwiszewski, Villanova Rajinder Ranu, Colorado State Jean Schmidt, University of
University University Pittsburgh
Rebecca Orr, Collin College Philip Rea, University of Andrew Schnabel, Indiana
Don Padgett, Bridgewater State Pennsylvania University, South Bend
College Amy Reber, Georgia State Roxann Schroeder, Humboldt
Joanna Padolina, Virginia University State University
Commonwealth University Ahnya Redman, West Virginia David Schultz, University of
One Pagan, West Chester University Missouri, Columbia
University Melissa Reedy, University of Andrea Schwarzbach, The
Kathleen Page, Bucknell Illinois at Urbana-Champaign University of Texas at
University Brian Ring, Valdosta State Brownsville
Daniel Papaj, University of University Erik Scully, Towson University
Arizona David Rintoul, Kansas State Robert Seagull, Hofstra University
Pamela Pape-Lindstrom, Everett University Pramila Sen, Houston
Community College Michael Rischbieter, Presbyterian Community College
Bruce Patterson, University of College Alice Sessions, Austin
Arizona, Tucson Laurel Roberts, University of Community College
Shelley Penrod, Lone Star College Pittsburgh Vijay Setaluri, University of
System George Robinson, The University Wisconsin
Roger Persell, Hunter College, The at Albany, The State University Jyotsna Sharma, The University of
City University of New York of New York Texas at San Antonio
xxix
Elizabeth Sharpe-Aparicio, Blinn Barbara Stegenga, University of Terry Trier, Grand Valley State
College North Carolina, Chapel Hill University
Patty Shields, University of Patricia Steinke, San Jacinto Stephen Trumble, Baylor
Maryland College, Central Campus University
Cara Shillington, Eastern Asha Stephens, College of the Jan Trybula, The State University
Michigan University Mainland of New York at Potsdam
James Shinkle, Trinity Robert Steven, University of Alexa Tullis, University of Puget
University Toledo Sound
Rebecca Shipe, University of Eric Strauss, University of Marsha Turell, Houston
California, Los Angeles Wisconsin, La Crosse Community College
Marcia Shofner, University of Sukanya Subramanian, Collin Mary Tyler, University of Maine
Maryland College Marcel van Tuinen, University
Laurie Shornick, Saint Louis Mark Sugalski, Southern of North Carolina at
University Polytechnic State University Wilmington
Jill Sible, Virginia Polytechnic Brad Swanson, Central Michigan Dirk Vanderklein, Montclair State
Institute and State University University University
Allison Silveus, Tarrant County Ken Sweat, Arizona State Jorge Vasquez-Kool, Wake
College University Technical Community College
Kristin Simokat, University of David Tam, University of North William Velhagen, New York
Idaho Texas University
Sue Simon-Westendorf, Ohio Ignatius Tan, New York University Dennis Venema, Trinity Western
University William Taylor, University of University
Sedonia Sipes, Southern Illinois Toledo Laura Vogel, North Carolina State
University, Carbondale Christine Terry, Lynchburg University
John Skillman, California State College Jyoti Wagle, Houston Community
University, San Bernardino Sharon Thoma, University of College
Marek Sliwinski, University of Wisconsin, Madison Jeff Walker, University of
Northern Iowa Pamela Thomas, University of Southern Maine
Felisa Smith, University of New Central Florida Gary Walker, Appalachian State
Mexico Carol Thornber, University of University
John Sollinger, Southern Oregon Rhode Island Andrea Ward, Adelphi University
University Patrick Thorpe, Grand Valley State Fred Wasserman, Boston
Scott Solomon, Rice University University University
Morvarid Soltani-Bejnood, The Briana Timmerman, University of Elizabeth Waters, San Diego State
University of Tennessee South Carolina University
Vladimir Spiegelman, University Chris Todd, University of Douglas Watson, The University
of Wisconsin, Madison Saskatchewan of Alabama at Birmingham
Chrissy Spencer, Georgia Institute Gail Tompkins, Wake Technical Matthew Weand, Southern
of Technology Community College Polytechnic State University
Kathryn Spilios, Boston Martin Tracey, Florida Michael Weber, Carleton
University International University University
Ashley Spring, Brevard Randall Tracy, Worcester State Cindy Wedig, The University of
Community College University Texas, Pan American
Bruce Stallsmith, The University James Traniello, Boston Brad Wetherbee, University of
of Alabama in Huntsville University Rhode Island
Jennifer Stanford, Drexel Bibit Traut, City College of San Debbie Wheeler, University of the
University Francisco Fraser Valley
xxx
Clay White, Lone Star College Kelly Young, California State David Baum, University of
System University, Long Beach Wisconsin, Madison
Lisa Whitenack, Allegheny James Yount, Brevard Community Kevin S. Beach, The University of
College College Tampa
Maggie Whitson, Northern Min Zhong, Auburn University Philip Becraft, Iowa State
Kentucky University University
Stacey Wild East, Tennessee State Second Edition Alexandra Bely, University of
University Barbara J. Abraham, Hampton Maryland
Herbert Wildey, Arizona State University Lauryn Benedict, University of
University and Phoenix Jason Adams, College of DuPage Northern Colorado
College Sandra D. Adams, Montclair State Anne Bergey, Truman State
David Wilkes, Indiana University, University University
South Bend Richard Adler, University of Joydeep Bhattacharjee,
Lisa Williams, Northern Virginia Michigan, Dearborn University of Louisiana,
Community College Nancy Aguilar-Roca, University of Monroe
Elizabeth Willott, University of California, Irvine Todd Bishop, Dalhousie
Arizona Shivanthi Anandan, Drexel University
Mark Wilson, Humboldt State University Catherine Black, Idaho State
University Lynn Anderson-Carpenter, University
Ken Wilson, University of University of Michigan Andrew R. Blaustein, Oregon
Saskatchewan Christine Andrews, The State University
Bob Winning, Eastern Michigan University of Chicago James Bolton, Georgia Gwinnett
University Peter Armbruster, Georgetown College
Candace Winstead, California University Jim Bonacum, University of
Polytechnic State University Jessica Armenta, Austin Illinois at Springfield
Robert Wise, University of Community College Laurie J. Bonneau, Trinity College
Wisconsin, Oshkosh Brian Ashburner, University of James Bottesch, Eastern Florida
D. Reid Wiseman, College of Toledo State College
Charleston Ann J. Auman, Pacific Lutheran Lisa Boucher, The University of
MaryJo Witz, Monroe University Texas at Austin
Community College Nicanor Austriaco, Providence Nicole Bournias-Vardiabasis,
David Wolfe, American River College California State University,
College Felicitas Avendano, Grand View San Bernardino
Kevin Woo, University of Central University Nancy Boury, Iowa State
Florida J. P. Avery, University of North University
Denise Woodward, Penn State Florida Matthew Brewer, Georgia State
Shawn Wright, Central New Jim Bader, Case Western Reserve University
Mexico Community College University Christoper G. Brown, Georgia
Grace Wyngaard, James Madison Ellen Baker, Santa Monica College Gwinnett College
University Andrew S. Baldwin, Mesa Jill Buettner, Richland College
Aimee Wyrick, Pacific Union Community College Sharon K. Bullock, University of
College Stephen Baron, Bridgewater North Carolina at Charlotte
Joanna Wysocka-Diller, Auburn College Lisa Burgess, Broward College
University Paul W. Bates, University of Jorge Busciglio, University of
Ken Yasukawa, Beloit College Minnesota, Duluth California, Irvine
John Yoder, The University of Janet Batzli, University of Stephen Bush, Coastal Carolina
Alabama Wisconsin, Madison University
xxxi
David Byres, Florida State College Janice Countaway, University of Meghan Duffy, University of
at Jacksonville Central Oklahoma Michigan
Gloria Caddell, University of Joseph A. Covi, University of Richard E. Duhrkopf, Baylor
Central Oklahoma North Carolina at Wilmington University
Guy A. Caldwell, The University Will Crampton, University of Jacquelyn Duke, Baylor
of Alabama Central Florida University
Kim A. Caldwell, The University Kathryn Craven, Armstrong State Kamal Dulai, University of
of Alabama University California, Merced
John S. Campbell, Northwest Lorelei Crerar, George Mason Rebecca K. Dunn, Boston
College University College
Jennifer Capers, Indian River Kerry Cresawn, James Madison Jacob Egge, Pacific Lutheran
State College University University
Joel Carlin, Gustavus Adolphus Richard J. Cristiano, Houston Kurt J. Elliott, Northwest Vista
College Community College Northwest College
Sara G. Carlson, University of Cynthia K. Damer, Central Miles Dean Engell, North
Akron Michigan University Carolina State University
Dale Casamatta, University of David Dansereau, Saint Mary’s Susan Erster, Stony Brook
North Florida University University
Merri Lynn Casem, California Mark Davis, Macalester College Barbara I. Evans, Lake Superior
State University, Fullerton Elizabeth A. De Stasio, Lawrence State University
Anne Casper, Eastern Michigan University Lisa Felzien, Rockhurst
University Tracy Deem, Bridgewater College University
David Champlin, University of Kimberley Dej, McMaster Ralph Feuer, San Diego State
Southern Maine University University
Rebekah Chapman, Georgia State Terrence Delaney, University of Ginger R. Fisher, University of
University Vermont Northern Colorado
P. Bryant Chase, Florida State Tracie Delgado, Northwest John Flaspohler, Concordia
University University College
Thomas T. Chen, Santa Monica Mark S. Demarest, University of Sam Flaxman, University of
College North Texas Colorado, Boulder
Young Cho, Eastern New Mexico D. Michael Denbow, Virginia Nancy Flood, Thompson Rivers
University Polytechnic Institute and State University
Sunita Chowrira, University of University Arthur Frampton, University of
British Columbia Jonathan Dennis, Florida State North Carolina at Wilmington
Tim W. Christensen, East Carolina University Caitlin Gabor, Texas State
University Brandon S. Diamond, University University
Steven Clark, University of of Miami Tracy Galarowicz, Central
Michigan AnnMarie DiLorenzo, Montclair Michigan University
Beth Cliffel, Triton College State University Raul Galvan, South Texas College
Liane Cochran-Stafira, Saint Frank J. Dirrigl, Jr., University of Deborah Garrity, Colorado State
Xavier University Texas, Pan American University
John G. Cogan, The Ohio State Christine Donmoyer, Allegheny Jason Mitchell Gee, East Carolina
University College University
Reid Compton, University of Samuel Douglas, Angelina College T.M. Gehring, Central Michigan
Maryland John D. DuBois, Middle University
Ronald H. Cooper, University of Tennessee State University John Geiser, Western Michigan
California, Los Angeles Janet Duerr, Ohio University University
xxxii
Carol A. Gibbons Kroeker, David Haymer, University of John S. K. Kauwe, Brigham Young
Ambrose University Hawaii at Manoa University
Susan A. Gibson, South Dakota Chris Haynes, Shelton State Lori J. Kayes, Oregon State
State University Community College University
Cynthia J. Giffen, University of Christiane Healey, University of Todd Kelson, Brigham Young
Michigan Massachusetts, Amherst University, Idaho
Matthew Gilg, University of David Hearn, Towson University Christopher Kennedy, Simon
North Florida Marshal Hedin, San Diego State Fraser University
Sharon L. Gillies, University of the University Jacob Kerby, University of South
Fraser Valley Triscia Hendrickson, Morehouse Dakota
Leslie Goertzen, Auburn College Stephen T. Kilpatrick, University
University Albert A. Herrera, University of of Pittsburgh, Johnstown
Marla Gomez, Nicholls State Southern California Mary Kimble, Northeastern
University Bradley Hersh, Allegheny College Illinois University
Steven Gorsich, Central Michigan Anna Hiatt, East Tennessee State Denice D. King, Cleveland State
University University Community College
Daniel Graetzer, Northwest Laura Hill, University of Vermont David Kittlesen, University of
University Jay Hodgson, Armstrong State Virginia
James Grant, Concordia University Ann Kleinschmidt, Allegheny
University James Horwitz, Palm Beach State College
Linda E. Green, Georgia Institute College Kathryn Kleppinger-Sparace,
of Technology Sarah Hosch, Oakland University Tri-County Technical College
Sara Gremillion, Armstrong State Kelly Howe, University of New Daniel Klionsky, University of
University Mexico Michigan
Ann Grens, Indiana University, Kimberly Hruska, Langara Ned Knight, Reed College
South Bend College Benedict Kolber, Duquesne
John L. Griffis, Joliet Junior William Huddleston, University University
College of Calgary Ross Koning, Eastern
Nancy A. Guild, University of Carol Hurney, James Madison Connecticut State University
Colorado, Boulder University John Koontz, The University of
Lonnie Guralnick, Roger Williams Brian A. Hyatt, Bethel University Tennessee, Knoxville
University Bradley C. Hyman, University of Peter Kourtev, Central Michigan
Valerie K. Haftel, Morehouse California, Riverside University
College Anne Jacobs, Allegheny College Elizabeth Kovar, The University
Margaret Hanes, Eastern Robert C. Jadin, Northeastern of Chicago
Michigan University Illinois University Nadine Kriska, University of
Sally E. Harmych, University of Rick Jellen, Brigham Young Wisconsin, Whitewater
Toledo University Tim L. Kroft, Auburn University at
Sherry Harrel, Eastern Kentucky Dianne Jennings, Virginia Montgomery
University Commonwealth University William Kroll, Loyola University
J. Scott Harrison, Georgia L. Scott Johnson, Towson of Chicago
Southern University University Dave Kubien, University of New
Pat Harrison, University of the Russell Johnson, Colby College Brunswick
Fraser Valley Susan Jorstad, University of Jason Kuehner, Emmanuel
Diane Hartman, Baylor University Arizona College
Wayne Hatch, Utah State Matthew Julius, St. Cloud State Josephine Kurdziel, University of
University Eastern University Michigan
xxxiii
Troy A. Ladine, East Texas Baptist Peter B. McIntyre, University of Jennifer S. O’Neil, Houston
University Wisconsin, Madison Community College
Diane M. Lahaise, Georgia Iain McKinnell, Carleton Kavita Oommen, Georgia State
Perimeter College University University
Janice Lai, Austin Community Krystle McLaughlin, Lehigh Nathan Opolot Okia, Auburn
College, Cypress Creek University University at Montgomery
Kirk Land, University of the Susan B. McRae, East Carolina Robin O’Quinn, Eastern
Pacific University Washington University
James Langeland, Kalamazoo Mark Meade, Jacksonville State Sarah A. Orlofske, Northeastern
College University Illinois University
Neva Laurie-Berry, Pacific Richard Merritt, Houston Don Padgett, Bridgewater State
Lutheran University Community College Northwest University
Brenda Leady, University of James E. Mickle, North Carolina Lisa Parks, North Carolina State
Toledo State University University
Adrienne Lee, University of Chad Montgomery, Truman State Nilay Patel, California State
California, Fullerton University University, Fullerton
Chris Levesque, John Abbott Scott M. Moody, Ohio University Markus Pauly, University of
College Daniel Moon, University of California, Berkeley
Bai-Lian Larry Li, University of North Florida Daniel M. Pavuk, Bowling Green
California, Riverside Jamie Moon, University of North State University
Cynthia Littlejohn, University of Florida Marc Perkins, Orange Coast
Southern Mississippi Jonathan Moore, Virginia College
Jason Locklin, Temple College Commonwealth University Beverly Perry, Houston
Xu Lu, University of Findlay Paul A. Moore, Bowling Green Community College
Patrice Ludwig, James Madison State University John S. Peters, College of
University Tsafrir Mor, Arizona State Charleston
Ford Lux, Metropolitan State University Chris Petrie, Eastern Florida State
University of Denver Jeanelle Morgan, University of College
Morris F. Maduro, University of North Georgia John M. Pleasants, Iowa State
California, Riverside Mark Mort, University of Kansas University
C. Smoot Major, University of Anthony Moss, Auburn Michael Plotkin, Mt. San Jacinto
South Alabama University College
Barry Margulies, Towson Karen Neal, Reynolds Community Mary Poffenroth, San Jose State
University College University
Nilo Marin, Broward College Kimberlyn Nelson, Pennsylvania Dan Porter, Amarillo College
Michael Martin, John Carroll State University Sonja Pyott, University of North
University Hao Nguyen, California State Carolina at Wilmington
Heather D. Masonjones, University, Sacramento Mirwais Qaderi, Mount Saint
University of Tampa John Niedzwiecki, Belmont Vincent University
Scott C. Mateer, Armstrong State University Nick Reeves, Mt. San Jacinto
University Alexey G. Nikitin, Grand Valley College
Robert Maxwell, Georgia State State University Adam J. Reinhart, Wayland
University Matthew Nusnbaum, Georgia Baptist University
Joseph McCormick, Duquesne State University Stephanie Richards, Bates
University Robert Okazaki, Weber State College
Lori L. McGrew, Belmont University David A. Rintoul, Kansas State
University Tiffany Oliver, Spelman College University
xxxiv
Trevor Rivers, University of Pramila Sen, Houston Bruce Stallsmith, The University
Kansas Community College of Alabama in Huntsville
Laurel Roberts, University of Anupama Seshan, Emmanuel Maria L. Stanko, New Jersey
Pittsburgh College Institute of Technology
Casey Roehrig, Harvard University Alice Sessions, Austin Nancy Staub, Gonzaga University
Jennifer Rose, University of North Community College Barbara Stegenga, University of
Georgia Vijay Setaluri, University of North Carolina
Michael S. Rosenzweig, Virginia Wisconsin Robert Steven, University of
Polytechnic Institute and State Timothy E. Shannon, Francis Toledo
University Marion University Lori Stevens, University of
Caleb M. Rounds, University of Wallace Sharif, Morehouse Vermont
Massachusetts, Amherst College Mark Sturtevant, Oakland
Yelena Rudayeva, Palm Beach Mark Sherrard, University of University
State College Northern Iowa Elizabeth B. Sudduth, Georgia
James E. Russell, Georgia Cara Shillington, Eastern Gwinnett College
Gwinnett College Michigan University Mark Sugalski, Kennesaw State
Donald Sakaguchi, Iowa State Amy Siegesmund, Pacific University, Southern
University Lutheran University Polytechnic State University
Thomas Sasek, University of Christine Simmons, Southern Fengjie Sun, Georgia Gwinnett
Louisiana at Monroe Illinois University, Edwardsville College
Leslie J. Saucedo, University of S. D. Sipes, Southern Illinois Bradley J. Swanson, Central
Puget Sound University, Carbondale Michigan University
Udo M. Savalli, Arizona State John Skillman, California State Brook O. Swanson, Gonzaga
University West Campus University, San Bernardino University
Smita Savant, Houston Daryl Smith, Langara College Ken Gunter Sweat, Arizona
Community College Southwest Julie Smith, Pacific Lutheran State University West
Leena Sawant, Houston University Campus
Community College Southwest Karen Smith, University of British Annette Tavares, University of
H. Jochen Schenk, California State Columbia Ontario Institute of
University, Fullerton Leo Smith, University of Kansas Technology
Aaron E. Schirmer, Northeastern Ramona Smith-Burrell, Eastern William R. Taylor, University of
Illinois University Florida State College Toledo
Mark Schlueter, Georgia Joel Snodgrass, Towson University Samantha Terris Parks, Georgia
Gwinnett College Alan J. Snow, University of Akron– State University
Gregory Schmaltz, University of Wayne College Jessica Theodor, University of
the Fraser Valley Judith Solti, Houston Community Calgary
Jennifer Schramm, Chemeketa College, Spring Branch Sharon Thoma, University of
Community College Ann Song, University of Wisconsin, Madison
Roxann Schroeder, Humboldt California, Fullerton Sue Thomson, Auburn University
State University C. Kay Song, Georgia State at Montgomery
Tim Schuh, St. Cloud State University Mark Tiemeier, Cincinnati State
University Chrissy Spencer, Georgia Institute Technical and Community
Kevin G. E. Scott, University of of Technology College
Manitoba Rachel Spicer, Connecticut Candace Timpte, Georgia
Erik P. Scully, Towson University College Gwinnett College
Sarah B. Selke, Three Rivers Ashley Spring, Eastern Florida Nicholas Tippery, University of
Community College State College Wisconsin, Whitewater
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Chris Todd, University of William Velhagen, Caldwell Charles Welsh, Duquesne
Saskatchewan University University
Kurt A. Toenjes, Montana State Sara Via, University of Naomi L. B. Wernick,
University, Billings Maryland University of Massachusetts,
Jeffrey L. Travis, The University at Christopher Vitek, University of Lowell
Albany, The State University of Texas, Pan American Mary E. White, Southeastern
New York Neal J. Voelz, St. Cloud State Louisiana University
Stephen J. Trumble, Baylor University David Wilkes, Indiana University,
University Mindy Walker, Rockhurst South Bend
Jan Trybula, The State University University Frank Williams, Langara College
of New York at Potsdam Andrea Ward, Adelphi Kathy S. Williams, San Diego
Cathy Tugmon, Georgia Regents University State University
University Jennifer Ward, University of Lisa D. Williams, Northern
Alexa Tullis, University of Puget North Carolina at Asheville Virginia Community College
Sound Pauline Ward, Houston Christina Wills, Rockhurst
Marsha Turell, Houston Community College University
Community College Alan Wasmoen, Metropolitan Brian Wisenden, Minnesota State
Pat Uelmen Huey, Georgia Community College University, Moorhead
Gwinnett College Elizabeth R. Waters, San Diego David Wolfe, American River
Steven M. Uyeda, Pima State University College
Community College Matthew Weand, Southern Ramakrishna Wusirika, Michigan
Rani Vajravelu, University of Polytechnic State Technological University
Central Florida University G. Wyngaard, James Madison
Moira van Staaden, Bowling K. Derek Weber, Raritan Valley University
Green State University Community College James R. Yount, Eastern Florida
Dirk Vanderklein, Montclair State Andrea Weeks, George Mason State College
University University Min Zhong, Auburn University
xxxvi
BIOLOGY
HOW
LIFE
WORKS
CONTENTS Evolution predicts a nested pattern of relatedness among
species, depicted as a tree. 16
Evolution can be studied by means of experiments. 17
HOW DO WE KNOW? Can evolution be demonstrated in the
laboratory? 18
About the Authors vi
1.5 Ecological Systems 19
Preface viii
Basic features of anatomy, physiology, and behavior shape
Acknowledgments xxiii ecological systems. 19
Ecological interactions play an important role in evolution. 20
PART 1 FROM CELLS TO ORGANISMS
1.6 The Human Footprint 20
CHAPTER 1 LIFE
? CASE 1 The First Cell: Life’s Origins 25
Chemical, Cellular, and Evolutionary Foundations 3
1.2 Chemical and Physical Principles 8 A covalent bond results when two atoms share electrons. 33
The living and nonliving worlds share the same chemical A polar covalent bond is characterized by unequal sharing of
foundations and obey the same physical laws. 8 electrons. 33
The scientific method shows that living organisms come from An ionic bond forms between oppositely charged ions. 34
other living organisms. 10 A chemical reaction involves breaking and forming chemical
HOW DO WE KNOW? Can living organisms arise from bonds. 35
nonliving matter? 10
2.3 Water: The Medium of Life 35
HOW DO WE KNOW? Can microscopic life arise from
Water is a polar molecule. 35
nonliving matter? 11
A hydrogen bond is an interaction of a hydrogen atom and
1.3 The Cell 12 an electronegative atom. 35
Nucleic acids store and transmit information needed for Hydrogen bonds give water many unusual properties. 36
growth, function, and reproduction. 12
pH is a measure of the concentration of protons in solution. 37
Membranes define cells and spaces within cells. 14
Metabolism converts energy from the environment into a form 2.4 Carbon: Life’s Chemical Backbone 37
that can be used by cells. 14 Carbon atoms form four covalent bonds. 38
A virus is genetic material in need of a cell. 15 Carbon-based molecules are structurally and functionally
diverse. 38
1.4 Evolution 15
Variation in populations provides the raw material for 2.5 Organic Molecules 39
evolution. 15 Functional groups add chemical character to carbon chains. 39
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Proteins are composed of amino acids. 40 The RNA polymerase complex is a molecular machine that
opens, transcribes, and closes duplex DNA. 63
Nucleic acids encode genetic information in their nucleotide
sequence. 40 3.4 Fate of the RNA Primary Transcript 63
Complex carbohydrates are made up of simple sugars. 42 Messenger RNA carries information for the synthesis of a
Lipids are hydrophobic molecules. 43 specific protein. 63
Primary transcripts in eukaryotes undergo several types of
? 2.6 How Did the Molecules of Life Form? 45
chemical modification. 64
The building blocks of life can be generated in the laboratory. 45
Some RNA transcripts are processed differently from protein-
HOW DO WE KNOW? Could the building blocks of organic coding transcripts and have functions of their own. 65
molecules have been generated on the early Earth? 46
Experiments show how life’s building blocks can form
macromolecules. 46 CHAPTER 4 TRANSLATION AND PROTEIN STRUCTURE 69
The three-dimensional structure of DNA gave important clues Translation uses many molecules found in all cells. 77
about its functions. 56 The genetic code shows the correspondence between codons
Cellular DNA is coiled and packaged with proteins. 58 and amino acids. 79
HOW DO WE KNOW? How was the genetic code
3.3 Retrieval of Genetic Information Stored in DNA:
deciphered? 80
Transcription 58
Translation consists of initiation, elongation, and
? What was the first nucleic acid molecule, and how did it
termination. 81
arise? 59
? How did the genetic code originate? 83
RNA is a polymer of nucleotides in which the 5-carbon sugar
is ribose. 59 VISUAL SYNTHESIS Gene Expression 84
In transcription, DNA is used as a template to make 4.3 Protein Evolution and the Origin of New Proteins 86
complementary RNA. 60
Most proteins are composed of modular folding
Transcription starts at a promoter and ends at a terminator. 60 domains. 86
RNA polymerase adds successive nucleotides to the 3� end of Amino acid sequences evolve through mutation and
the transcript. 62 selection. 86
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Mitochondria provide the eukaryotic cell with most of its
CHAPTER 5 ORGANIZING PRINCIPLES
usable energy. 111
Lipids, Membranes, and Cell Compartments 89
Chloroplasts capture energy from sunlight. 111
Passive transport involves diffusion. 96 Kinetic and energy potential energy are two forms of energy. 118
Primary active transport uses the energy of ATP. 97 Chemical energy is a form of potential energy. 118
Secondary active transport is driven by an electrochemical ATP is a readily accessible form of cellular energy. 119
gradient. 98
6.3 The Laws of Thermodynamics 119
Many cells maintain size and composition using active
The first law of thermodynamics: Energy is conserved. 119
transport. 99
The second law of thermodynamics: Energy transformation
The cell wall provides another means of maintaining cell
always results in an increase of disorder in the universe. 119
shape. 100
6.4 Chemical Reactions 120
5.3 The Internal Organization of Cells 100
A chemical reaction occurs when molecules interact. 120
Eukaryotes and prokaryotes differ in internal organization. 101
The laws of thermodynamics determine whether a chemical
Prokaryotic cells lack a nucleus and extensive internal
reaction requires or releases energy available to do work. 121
compartmentalization. 101
The hydrolysis of ATP releases energy. 122
Eukaryotic cells have a nucleus and specialized internal
structures. 101 Non-spontaneous reactions are often coupled to
spontaneous reactions. 123
5.4 The Endomembrane System 104
6.5 Enzymes and the Rate of Chemical Reactions 124
The endomembrane system compartmentalizes the cell. 104
The nucleus houses the genome and is the site of RNA Enzymes reduce the activation energy of a chemical reaction. 124
synthesis. 105 Enzymes form a complex with reactants and products. 125
The endoplasmic reticulum is involved in protein and lipid Enzymes are highly specific. 126
synthesis. 105
HOW DO WE KNOW? Do enzymes form complexes with
The Golgi apparatus modifies and sorts proteins and lipids. 105 substrates? 126
Lysosomes degrade macromolecules. 107 Enzyme activity can be influenced by inhibitors and activators. 127
Protein sorting directs proteins to their proper location in or Allosteric enzymes regulate key metabolic pathways. 127
out of the cell. 108
? What naturally occurring elements might have spurred
5.5 Mitochondria and Chloroplasts 111 the first reactions that led to life? 128
xl
Fatty acids and proteins are useful sources of energy. 148
CHAPTER 7 CELLULAR RESPIRATION
Harvesting Energy from Carbohydrates and Other Fuel Molecules 131 The intracellular level of ATP is a key regulator of cellular
respiration. 149
Exercise requires several types of fuel molecules and the
coordination of metabolic pathways. 150
CHAPTER 8 PHOTOSYNTHESIS
Using Sunlight to Build Carbohydrates 153
7.4 The Citric Acid Cycle 138 8.2 The Calvin Cycle 157
The citric acid cycle produces ATP and reduced electron The incorporation of CO2 is catalyzed by the enzyme rubisco. 157
carriers. 138 NADPH is the reducing agent of the Calvin cycle. 158
? What were the earliest energy-harnessing reactions? 139 The regeneration of RuBP requires ATP. 158
7.5 The Electron Transport Chain and Oxidative The steps of the Calvin cycle were determined using
Phosphorylation 140 radioactive CO2. 158
The electron transport chain transfers electrons and pumps Carbohydrates are stored in the form of starch. 158
protons. 140 HOW DO WE KNOW? How is CO2 used to synthesize
The proton gradient is a source of potential energy. 142 carbohydrates? 159
ATP synthase converts the energy of the proton gradient 8.3 Capturing Sunlight into Chemical Forms 160
into the energy of ATP. 142
Chlorophyll is the major entry point for light energy in
HOW DO WE KNOW? Can a proton gradient drive the
photosynthesis. 160
synthesis of ATP? 143
Photosystems use light energy to drive the photosynthetic
7.6 Anaerobic Metabolism and the Evolution of Cellular electron transport chain. 161
Respiration 144 The photosynthetic electron transport chain connects two
Fermentation extracts energy from glucose in the absence photosystems. 162
of oxygen. 145 HOW DO WE KNOW? Do chlorophyll molecules operate on
? How did early cells meet their energy requirements? 146 their own or in groups? 163
The accumulation of protons in the thylakoid lumen drives
7.7 Metabolic Integration 147
the synthesis of ATP. 164
Excess glucose is stored as glycogen in animals and starch
Cyclic electron transport increases the production of ATP. 166
in plants. 147
Sugars other than glucose contribute to glycolysis. 147 8.4 Challenges to Photosynthetic Efficiency 166
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Excess light energy can cause damage. 166 9.5 Receptor Kinases and Long-Term Responses 191
Photorespiration leads to a net loss of energy and carbon. 168 Receptor kinases phosphorylate each other, activate
intercellular signaling pathways, lead to a response, and
Photosynthesis captures just a small percentage of incoming
are terminated. 192
solar energy. 169
? How do cell signaling errors lead to cancer? 192
8.5 The Evolution of Photosynthesis 170
Signaling pathways are integrated to produce a response
? How did early cells use sunlight to meet their energy in a cell. 193
requirements? 170
The ability to use water as an electron donor in photosynthesis
evolved in cyanobacteria. 170 CHAPTER 10 CELL AND TISSUE ARCHITECTURE 197
Eukaryotic organisms are believed to have gained
photosynthesis by endosymbiosis. 171
VISUAL SYNTHESIS Harnessing Energy: Photosynthesis
and Cellular Respiration 172
9.1 Principles of Cell Communication 180 Motor proteins associate with microtubules and micro-
filaments to cause movement. 202
Cells communicate using chemical signals that bind to specific
receptors. 180 Intermediate filaments are polymers of proteins that vary
according to cell type. 204
Signaling involves receptor activation, signal transduction,
response, and termination. 181 The cytoskeleton is an ancient feature of cells. 205
xlii
Tumor suppressors block specific steps in the development
CHAPTER 11 CELL DIVISION
of cancer. 238
Variations, Regulation, and Cancer 219
Most cancers require the accumulation of multiple mutations. 238
VISUAL SYNTHESIS Cellular Communities 240
Prometaphase: Chromosomes attach to the mitotic spindle. 224 During DNA replication, the parental strands separate and
new partners are made. 248
Metaphase: Chromosomes align as a result of dynamic
changes in the mitotic spindle. 224 HOW DO WE KNOW? How is DNA replicated? 249
Anaphase: Sister chromatids fully separate. 224 New DNA strands grow by the addition of nucleotides to the
3� end. 250
Telophase: Nuclear envelopes re-form around newly
segregated chromosomes. 225 In replicating DNA, one daughter strand is synthesized
continuously and the other in a series of short pieces. 251
The parent cell divides into two daughter cells by cytokinesis. 225
A small stretch of RNA is needed to begin synthesis of a
11.3 Meiotic Cell Division 226 new DNA strand. 252
Pairing of homologous chromosomes is unique to meiosis. 226 Synthesis of the leading and lagging strands is coordinated. 252
Crossing over between DNA molecules results in exchange DNA polymerase is self-correcting because of its proof-
of genetic material. 227 reading function. 254
The first meiotic division brings about the reduction in
chromosome number. 227 12.2 Replication of Chromosomes 254
The second meiotic division resembles mitosis. 228 Replication of DNA in chromosomes starts at many places
almost simultaneously. 254
Division of the cytoplasm often differs between the sexes. 231
Telomerase restores tips of linear chromosomes shortened
Meiosis is the basis of sexual reproduction. 231
during DNA replication. 255
11.4 Regulation of the Cell Cycle 233
12.3 Isolation, Identification, and Sequencing of DNA
Protein phosphorylation controls passage through the cell Fragments 257
cycle. 233
The polymerase chain reaction selectively amplifies regions
HOW DO WE KNOW? How is progression through the cell of DNA. 257
cycle controlled? 234
Electrophoresis separates DNA fragments by size. 259
Different cyclin–CDK complexes regulate each stage of the
Restriction enzymes cleave DNA at particular short
cell cycle. 235
sequences. 260
Cell cycle progression requires successful passage through
DNA strands can be separated and brought back together
multiple checkpoints. 235
again. 261
? 11.5 What Genes Are Involved in Cancer? 236 DNA sequencing makes use of the principles of DNA
Oncogenes promote cancer. 236 replication. 263
HOW DO WE KNOW? Can a virus cause cancer? 237 ? What new technologies are being developed to sequence
your personal genome? 264
Proto-oncogenes are genes that when mutated may cause
cancer. 238 12.4 Genetic Engineering 264
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Recombinant DNA combines DNA molecules from two or Organelle DNA forms nucleoids that differ from those in
more sources. 264 bacteria. 285
Recombinant DNA is the basis of genetically modified 13.5 Viruses and Viral Genomes 285
organisms. 266
Viruses can be classified by their genomes. 286
DNA editing can be used to alter gene sequences almost at will. 267
The host range of a virus is determined by viral and host
surface proteins. 287
CHAPTER 13 GENOMES 271 Viruses have diverse sizes and shapes. 287
Viruses are capable of self-assembly. 288
Genome annotation includes searching for sequence motifs. 276 Mutations are random with regard to an organism’s needs. 295
Comparison of genomic DNA with messenger RNA reveals HOW DO WE KNOW? Do mutations occur randomly, or are
the intron–exon structure of genes. 276 they directed by the environment? 296
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Early theories of heredity predicted the transmission of
CHAPTER 15 GENETIC VARIATION 309
acquired characteristics. 326
Belief in blending inheritance discouraged studies of
hereditary transmission. 326
16.1 Early Theories of Inheritance 326 17.1 The X and Y Sex Chromosomes 346
xlv
In many animals, sex is genetically determined and associated The relative importance of genes and environment can be
with chromosomal differences. 346 determined by differences among individuals. 367
Segregation of the sex chromosomes predicts a 1:1 ratio Genetic and environmental effects can interact in
of females to males. 347 unpredictable ways. 367
17.2 Inheritance of Genes in the X Chromosome 348 18.2 Resemblance Among Relatives 368
X-linked inheritance was discovered through studies of male For complex traits, offspring resemble parents but show
fruit flies with white eyes. 348 regression toward the mean. 369
Genes in the X chromosome exhibit a “crisscross” inheritance Heritability is the proportion of the total variation due to
pattern. 348 genetic differences among individuals. 370
X-linkage provided the first experimental evidence that genes
18.3 Twin Studies 371
are in chromosomes. 350
Twin studies help separate the effects of genes and
Genes in the X chromosome show characteristic patterns in
environment in differences among individuals. 371
human pedigrees. 351
HOW DO WE KNOW? What is the relative importance of
17.3 Genetic Linkage and Recombination 353 genes and of the environment for common traits? 372
Nearby genes in the same chromosome show linkage. 353
18.4 Complex Traits in Health and Disease 373
The frequency of recombination s a measure of the distance
Most common diseases and birth defects are affected by
between linked genes. 355
many genes that each have relatively small effects. 373
Genetic mapping assigns a location to each gene along a
Human height is affected by hundreds of genes. 374
chromosome. 355
HOW DO WE KNOW? Can recombination be used to construct
? Can personalized medicine lead to effective treatments of
common diseases? 375
a genetic map of a chromosome? 356
18.1 Heredity and Environment 364 ? How do lifestyle choices affect expression of your personal
genome? 386
Complex traits are affected by the environment. 365
Complex traits are affected by multiple genes. 366 19.3 Transcriptional Regulation in Prokaryotes 386
xlvi
Transcriptional regulation can be positive or negative. 387 20.5 Cell Signaling in Development 415
Lactose utilization in E. coli is the pioneering example of A signaling molecule can cause multiple responses in the cell. 415
transcriptional regulation. 388 Developmental signals are amplified and expanded. 416
HOW DO WE KNOW? How does lactose lead to the
VISUAL SYNTHESIS Genetic Variation and Inheritance 418
production of active β-galactosidase enzyme? 388
The repressor protein binds with the operator and prevents ? CASE 4 Malaria: Coevolution of Humans and a Parasite 422
transcription, but not in the presence of lactose. 389
The function of the lactose operon was revealed by genetic
studies. 390 CHAPTER 21 EVOLUTION
The lactose operon is also positively regulated by How Genotypes and Phenotypes Change over Time 425
CRP–cAMP. 390
Transcriptional regulation determines the outcome of
infection by a bacterial virus. 391
VISUAL SYNTHESIS Virus: A Genome in Need of a Cell 394
HOW DO WE KNOW? How do stem cells lose their ability to DNA sequencing is the gold standard for measuring genetic
differentiate into any cell type? 402 variation. 428
? Can cells with your personal genome be reprogrammed for HOW DO WE KNOW? How is genetic variation measured? 429
new therapies? 403
21.3 Evolution and the Hardy–Weinberg Equilibrium 430
20.2 Hierarchical Control of Development 404 Evolution is a change in allele or genotype frequency over
Drosophila development proceeds through egg, larval, and time. 430
adult stages. 404 The Hardy–Weinberg equilibrium describes situations in
The egg is a highly polarized cell. 405 which allele and genotype frequencies do not change. 430
Development proceeds by progressive regionalization and The Hardy–Weinberg equilibrium relates allele frequencies
specification. 406 and genotype frequencies. 431
Homeotic genes determine where different body parts The Hardy–Weinberg equilibrium is the starting point for
develop in the organism. 408 population genetic analysis. 432
20.3 Evolutionary Conservation of Key Transcription Factors 21.4 Natural Selection 432
in Development 410 Natural selection brings about adaptations. 432
Animals have evolved a wide variety of eyes. 410 The Modern Synthesis combines Mendelian genetics and
Pax6 is a master regulator of eye development. 410 Darwinian evolution. 434
Natural selection increases the frequency of advantageous
20.4 Combinatorial Control in Development 412 mutations and decreases the frequency of deleterious
Floral differentiation is a model for plant development. 412 mutations. 434
The identity of the floral organs is determined by ? What genetic differences have made some individuals more
combinatorial control. 413 and some less susceptible to malaria? 434
xlvii
Natural selection can be stabilizing, directional, or disruptive. 435 ? How did malaria come to infect humans? 455
HOW DO WE KNOW? How far can artificial selection be Sympatric populations—those not geographically separated—
taken? 436 may undergo speciation. 456
Sexual selection increases an individual’s reproductive Speciation can occur instantaneously. 458
success. 437
22.4 Speciation and Selection 459
21.5 Migration, Mutation, Genetic Drift, and Non-Random
Speciation can occur with or without natural selection. 459
Mating 438
Natural selection can enhance reproductive isolation. 459
Migration reduces genetic variation between populations. 438
VISUAL SYNTHESIS Speciation 460
Mutation increases genetic variation. 438
Genetic drift has a large effect in small populations. 438
Non-random mating alters genotype frequencies without CHAPTER 23 EVOLUTIONARY PATTERNS
affecting allele frequencies. 439
Phylogeny and Fossils 463
21.6 Molecular Evolution 440
The molecular clock relates the amount of sequence difference
between species and the time since the species diverged. 440
The rate of the molecular clock varies. 440
Species are reproductively isolated from other species. 446 23.2 Building a Phylogenetic Tree 468
The BSC is more useful in theory than in practice. 447 Homology is similarity by common descent. 468
The BSC does not apply to asexual or extinct organisms. 447 Shared derived characters enable biologists to reconstruct
evolutionary history. 469
Ring species and hybridization complicate the BSC. 448
The simplest tree is often favored among multiple possible
Ecology and evolution can extend the BSC. 448
trees. 469
22.2 Reproductive Isolation 449 Molecular data complement comparative morphology in
Pre-zygotic isolating factors occur before egg fertilization. 450 reconstructing phylogenetic history. 471
Post-zygotic isolating factors occur after egg fertilization. 450 Phylogenetic trees can help solve practical problems. 472
HOW DO WE KNOW? Did an HIV-positive dentist spread
22.3 Speciation 450
the AIDS virus to his patients? 473
Speciation is a by-product of the genetic divergence of
separated populations. 451 23.3 The Fossil Record 474
Allopatric speciation is speciation that results from the Fossils provide unique information. 474
geographical separation of populations. 451 Fossils provide a selective record of past life. 474
Dispersal and vicariance can isolate populations from Geological data indicate the age and environmental setting
each other. 451 of fossils. 476
HOW DO WE KNOW? Can vicariance cause speciation? 452 Fossils can contain unique combinations of characters. 479
Co-speciation is speciation that occurs in response to HOW DO WE KNOW? Can fossils bridge the evolutionary
speciation in another species. 455 gap between fish and tetrapod vertebrates? 481
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xlviii
Rare mass extinctions have altered the course of evolution. 481 Some human differences have likely arisen by natural
selection. 500
23.4 Comparing Evolution’s Two Great Patterns 482
? What human genes are under selection for resistance to
Phylogeny and fossils complement each other. 482 malaria? 501
Agreement between phylogenies and the fossil record
provides strong evidence of evolution. 482 24.5 Culture, Language, and Consciousness 502
Culture changes rapidly. 502
Is culture uniquely human? 503
CHAPTER 24 HUMAN ORIGINS AND EVOLUTION 485 Is language uniquely human? 503
Is consciousness uniquely human? 503
The fossil record gives us direct information about our Photosynthesis and respiration are key processes in
evolutionary history. 488 short-term carbon cycling. 511
HOW DO WE KNOW? How much CO2 was in the atmosphere
24.2 African Origins 491 1000 years ago? 512
Studies of mitochondrial DNA reveal that modern humans The regular oscillation of CO2 reflects the seasonality of
evolved in Africa relatively recently. 491 photosynthesis in the Northern Hemisphere. 512
HOW DO WE KNOW? When and where did the most recent Human activities play an important role in the modern
common ancestor of all living humans live? 492 carbon cycle. 513
Studies of the Y chromosome provide independent evidence Carbon isotopes show that much of the CO2 added to air
for a recent origin of modern humans. 494 over the past half century comes from burning fossil fuels. 513
Neanderthals disappear from the fossil record as modern
HOW DO WE KNOW? What is the major source of the
humans appear, but have contributed to the modern human
CO2 that has accumulated in Earth’s atmosphere over the
gene pool. 494
past two centuries? 514
24.3 Distinct Features of Our Species 495 25.2 The Long-Term Carbon Cycle 515
Bipedalism was a key innovation. 495 Reservoirs and fluxes are key in long-term carbon cycling. 515
Adult humans share many features with juvenile Physical processes add and remove CO2 from the atmosphere. 516
chimpanzees. 496
Records of atmospheric composition over 400,000 years
Humans have large brains relative to body size. 496 show periodic shifts in CO2 content. 517
The human and chimpanzee genomes help us identify genes Variations in atmospheric CO2 over hundreds of millions
that make us human. 498 of years reflect plate tectonics and evolution. 520
24.4 Human Genetic Variation 498 25.3 The Carbon Cycle: Ecology, Biodiversity, and Evolution 521
The prehistory of our species has had an impact on the Food webs trace the cycling of carbon through communities
distribution of genetic variation. 499 and ecosystems. 521
The recent spread of modern humans means that there are Biological diversity reflects the many ways that organisms
few genetic differences between groups. 500 participate in the carbon cycle. 522
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The carbon cycle weaves together biological evolution and Thaumarchaeota may be the most abundant cells in the oceans. 546
environmental change through Earth history. 522 HOW DO WE KNOW? How abundant are archaeons in
the oceans? 547
? CASE 5 The Human Microbiome: Diversity Within 525
26.6 The Evolutionary History of Prokaryotes 548
Life originated early in our planet’s history. 548
CHAPTER 26 BACTERIA AND ARCHAEA 529 Prokaryotes have coevolved with eukaryotes. 549
? How do intestinal bacteria influence human health? 550
Proteobacteria are the most diverse bacteria. 543 ? How did the eukaryotic cell originate? 560
The gram-positive bacteria include organisms that cause How did the eukaryotic cell originate? 560
and cure disease. 543 In the oceans, many single-celled eukaryotes harbor
Photosynthesis is widely distributed on the bacterial tree. 544 symbiotic bacteria. 562
The archaeal tree has anaerobic, hyperthermophilic Our own group, the opisthokonts, is the most diverse
organisms near its base. 545 eukaryotic superkingdom. 563
The Archaea include several groups of acid-loving Amoebozoans include slime molds that produce multicellular
microorganisms. 546 structures. 564
Only Archaea produce methane as a by-product of energy Archaeplastids, which include land plants, are photosynthetic
metabolism. 546 organisms. 566
One group of the Euryarchaeota thrives in extremely salty Stramenopiles, alveolates, and rhizarians dominate eukaryotic
environments. 546 diversity in the oceans. 568
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Photosynthesis spread through eukaryotes by repeated Regulatory genes have played an important role in the
endosymbioses involving eukaryotic algae. 570 evolution of complex multicellular organisms. 592
HOW DO WE KNOW? How did photosynthesis spread through HOW DO WE KNOW? What controls color pattern in
the Eukarya? 571 butterfly wings? 593
Complex multicellularity requires communication 29.3 The Stem: Transport of Water Through Xylem 606
between cells. 584
Xylem provides a low-resistance pathway for the movement
HOW DO WE KNOW? How do bacteria influence the life of water. 607
cycles of choanoflagellates? 584
HOW DO WE KNOW? How large are the forces that allow
Complex multicellularity requires a genetic program leaves to pull water from the soil? 608
for coordinated growth and cell differentiation. 585
Water is pulled through xylem by an evaporative pump. 609
28.4 Variations on a Theme: Plants versus Animals 587 Xylem transport is at risk of conduit collapse and cavitation. 610
Cell walls shape patterns of growth and development
29.4 The Stem: Transport of Carbohydrates Through Phloem 610
in plants. 587
Phloem transports carbohydrates from sources to sinks. 611
Animal cells can move relative to one another. 588
Carbohydrates are pushed through phloem by an osmotic
28.5 The Evolution of Complex Multicellularity 589 pump. 611
Fossil evidence of complex multicellular organisms is first Phloem feeds both the plant and the rhizosphere. 612
observed in rocks deposited 579 –555 million years ago. 589
29.5 The Root: Uptake of Water and Nutrients from the Soil 612
Oxygen is necessary for complex multicellular life. 590
Plants obtain essential mineral nutrients from the soil. 613
Land plants evolved from green algae that could carry out
photosynthesis on land. 591 Nutrient uptake by roots is highly selective. 614
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Nutrient uptake requires energy. 614
CHAPTER 31 PLANT GROWTH AND DEVELOPMENT 641
Mycorrhizae enhance nutrient uptake. 615
Symbiotic nitrogen-fixing bacteria supply nitrogen to both
plants and ecosystems. 616
30.3 Flowering Plants 628 Wood has both mechanical and transport functions. 652
Flowers are reproductive shoots specialized for the 31.4 Root Growth and Development 654
production, transfer, and receipt of pollen. 628
Roots grow by producing new cells at their tips. 654
The diversity of floral morphology is related to modes of
Root elongation and vascular development are coordinated. 654
pollination. 631
The formation of new root apical meristems allows roots
Angiosperms have mechanisms to increase outcrossing. 632 to branch. 655
HOW DO WE KNOW? Are pollinator shifts associated with The structures and functions of root systems are diverse. 655
the formation of new species? 633
31.5 The Environmental Context of Growth and Development 656
Angiosperms delay provisioning their ovules until after
fertilization. 635 Plants orient the growth of their stems and roots by light
and gravity. 656
Fruits enhance the dispersal of seeds. 636
HOW DO WE KNOW? How do plants grow toward light? 657
? How did scientists increase crop yields during the Green
Revolution? 637 HOW DO WE KNOW? How do seeds detect the presence
of plants growing overhead? 659
30.4 Asexual Reproduction 638 Seeds can delay germination if they detect the presence of
Asexually produced plants disperse with and without seeds. 638 plants overhead. 659
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Plants grow taller and branch less when growing in the Nutrient-rich environments select for plants that allocate
shade of other plants. 660 more resources to growth than to defense. 681
Roots elongate more and branch less when water is scarce. 661 Exposure to multiple threats can lead to trade-offs. 682
Exposure to wind results in shorter and stronger stems. 661
32.4 Defense and Plant Diversity 682
31.6 Timing of Developmental Events 661 The evolution of new defenses may allow plants to diversify. 682
Flowering time is affected by day length. 661 Pathogens, herbivores, and seed predators can increase plant
Plants use their internal circadian clock and photoreceptors to biodiversity. 683
determine day length. 662 ? Can modifying plants genetically protect crops from
Vernalization prevents plants from flowering until winter herbivores and pathogens? 683
has passed. 663
Plants use day length as a cue to prepare for winter. 664
CHAPTER 33 PLANT DIVERSITY 687
Some defenses are always present, whereas others are Fern diversity has been strongly affected by the evolution
turned on in response to a threat. 679 of angiosperms. 698
Plants can sense and respond to herbivores. 679 An aquatic fern contributes to rice production. 698
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Conifers are woody plants that thrive in dry and cold climates. 700 34.3 Diversity 726
Gnetophytes are gymnosperms that have independently Fungi are highly diverse. 726
evolved xylem vessels and double fertilization. 702 Fungi evolved from aquatic, unicellular, and flagellated
33.5 Angiosperms 702 ancestors. 727
Angiosperms may have originated in the shady understory Zygomycetes produce hyphae undivided by septa. 728
of tropical forests. 702 Glomeromycetes form endomycorrhizae. 728
Angiosperm diversity results from flowers and xylem vessels, The Dikarya produce regular septa during mitosis. 728
among other traits, as well as interactions with animals and
Ascomycetes are the most diverse group of fungi. 729
other organisms. 704
HOW DO WE KNOW? Can a fungus influence the behavior
Monocots are diverse in shape and size despite not forming
of an ant? 731
a vascular cambium. 704
Basidiomycetes include smuts, rusts, and mushrooms. 731
HOW DO WE KNOW? When did grasslands expand over
the land surface? 706 ? How do fungi threaten global wheat production? 733
Eudicots are the most diverse group of angiosperms. 707
? CASE 7 Predator–Prey: A Game of Life and Death 736
? What can be done to protect the genetic diversity of crop
species? 708
CHAPTER 34 FUNGI
Structure, Function, and Diversity 715
The fungal life cycle often includes a stage in which haploid HOW DO WE KNOW? What is the resting membrane
cells fuse, but nuclei do not. 723 potential? How does electrical activity change during
an action potential? 750
HOW DO WE KNOW? What determines the shape of fungal
spores that are ejected into the air? 724 Signals between neurons can be excitatory or inhibitory. 752
Genetically distinct mating types promote outcrossing. 725 35.4 Nervous System Organization 754
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Nervous systems are organized into peripheral and central The brain is divided into lobes with specialized functions. 778
components. 754 Information is topographically mapped into the vertebrate
Peripheral nervous systems have voluntary and involuntary cerebral cortex. 780
components. 755
36.6 Memory and Cognition 780
The nervous system helps to maintain homeostasis. 756
The brain serves an important role in memory and learning. 780
Simple reflex circuits provide rapid responses to stimuli. 757
Cognition involves brain information processing and decision
making. 781
CHAPTER 36 ANIMAL SENSORY SYSTEMS AND BRAIN
FUNCTION 761
CHAPTER 37 ANIMAL MOVEMENT
Muscles and Skeletons 785
36.2 Smell and Taste 766 Muscles contract by the sliding of myosin and actin
filaments. 789
Smell and taste depend on chemoreception of molecules
carried in the environment and in food. 766 Calcium regulates actin–myosin interaction through
excitation–contraction coupling. 791
36.3 Gravity, Movement, and Sound 767
Calmodulin regulates Ca activation and relaxation of
2+
Hair cells sense gravity and motion. 767 smooth muscle. 792
Hair cells detect the physical vibrations of sound. 768
37.2 Muscle Contractile Properties 792
? How have sensory systems evolved in predators
and prey? 771 Muscle length affects actin–myosin overlap and generation
of force. 792
36.4 Vision 771
HOW DO WE KNOW? How does filament overlap affect force
Animals see the world through different types of eyes. 771 generation in muscles? 793
The structure and function of the vertebrate eye underlie Muscle force and shortening velocity are inversely related. 793
image processing. 773
Antagonist pairs of muscles produce reciprocal motions at
Vertebrate photoreceptors are unusual because they
a joint. 794
hyperpolarize in response to light. 774
Muscle force is summed by an increase in stimulation
Color vision detects different wavelengths of light. 774
frequency and the recruitment of motor units. 795
Local sensory processing of light determines basic features
of shape and movement. 775 Skeletal muscles have slow-twitch and fast-twitch fibers. 796
HOW DO WE KNOW? How does the retina process visual ? How do different types of muscle fiber affect the speed
information? 776 of predators and prey? 797
36.5 Brain Organization and Function 777 37.3 Animal Skeletons 797
The brain processes and integrates information received from Hydrostatic skeletons support animals by muscles that act
different sensory systems. 777 on a fluid-filled cavity. 797
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Exoskeletons provide hard external support and protection. 798 Local chemical signals regulate neighboring target cells. 823
The rigid bones of vertebrate endoskeletons are jointed for Pheromones are chemical compounds released into the
motion and can be repaired if damaged. 799 environment to signal physiological and behavioral changes
in other species members. 823
37.4 Vertebrate Skeletons 800
HOW DO WE KNOW? How are growth and development Voluntary and involuntary mechanisms control breathing. 835
controlled in insects? 810
39.3 Oxygen Transport by Hemoglobin 835
The endocrine system underlies homeostasis. 811
Blood is composed of fluid and several types of cell. 835
38.2 Properties of Hormones 813
HOW DO WE KNOW? What is the molecular structure of
Hormones act specifically on cells that bind the hormone. 813 hemoglobin and myoglobin? 837
Two main classes of hormone are peptides and amines, Hemoglobin is an ancient molecule with diverse roles
and steroid hormones. 813 related to oxygen binding and transport. 837
Hormonal signals are to strengthen their effect. 815 Hemoglobin reversibly binds oxygen. 837
Hormones are evolutionarily conserved molecules with Myoglobin stores oxygen, enhancing delivery to muscle
diverse functions. 818 mitochondria. 838
38.3 The Vertebrate Endocrine System 818 Many factors affect hemoglobin–oxygen binding. 839
The pituitary gland integrates diverse bodily functions 39.4 Circulatory Systems 840
by secreting hormones in response to signals from the
hypothalamus. 819 Circulatory systems have vessels of different sizes to
facilitate bulk flow and diffusion. 841
Many targets of pituitary hormones are endocrine tissues
that also secrete hormones. 820 Arteries are muscular, elastic vessels that carry blood
away from the heart under high pressure. 841
Other endocrine organs have diverse functions. 821
Veins are thin-walled vessels that return blood to the
? How does the endocrine system influence predators heart under low pressure. 843
and prey? 821
Compounds and fluid move across capillary walls by
38.4 Other Forms of Chemical Communication 822 diffusion, filtration, and osmosis. 843
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? How do hormones and nerves provide homeostatic 40.4 Digestion and Absorption of Food 864
regulation of blood flow as well as allow an animal to respond The digestive tract has regional specializations. 864
to stress? 843
Digestion begins in the mouth. 864
39.5 The Evolution, Structure, and Function of the Heart 844 Further digestion and storage of nutrients take place in
Fish have two-chambered hearts and a single circulatory the stomach. 865
system. 845 Final digestion and nutrient absorption take place in the
Amphibians and reptiles have more three-chambered hearts small intestine. 866
and partially divided circulations. 845 The large intestine absorbs water and stores waste. 869
Mammals and birds have four-chambered hearts and fully The lining of the digestive tract is composed of distinct layers. 869
divided pulmonary and systemic circulations. 846 Plant-eating animals have specialized digestive tracts that
Cardiac muscle cells are electrically connected to contract in reflect their diets. 870
synchrony. 847
40.3 Adaptations for Feeding 861 41.3 Structure and Function of the Mammalian Kidney 886
Suspension filter feeding is common in many aquatic The mammalian kidney has an outer cortex and inner
animals. 861 medulla. 886
Large aquatic animals apprehend prey by suction feeding Glomerular filtration isolates wastes carried by the blood
and active swimming. 862 along with water and small solutes. 887
Jaws and teeth provide specialized food capture and The proximal convoluted tubule reabsorbs solutes by active
mechanical breakdown of food. 862 transport. 888
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The loop of Henle acts as a countercurrent multiplier to create a VISUAL SYNTHESIS Reproduction and Development 916
concentration gradient from the cortex to the medulla. 888 Childbirth is initiated by hormonal changes. 918
HOW DO WE KNOW? How does the mammalian kidney
produce concentrated urine? 890
The distal convoluted tubule secretes additional wastes. 891 CHAPTER 43 ANIMAL IMMUNE SYSTEMS 921
The final concentration of urine is determined in the
collecting ducts and is under hormonal control. 891
The kidneys help regulate blood pressure and blood volume. 892
Exclusive asexuality is often an evolutionary dead end. 901 Inflammation is a coordinated response to tissue injury. 926
HOW DO WE KNOW? Do bdelloid rotifers reproduce The complement system participates in the innate and adaptive
only asexually? 902 immune systems. 927
42.2 Movement onto Land and Reproductive Adaptations 903 43.3 Adaptive Immunity: B Cells and Antibodies 928
Fertilization can take place externally or internally. 903 B cells produce antibodies. 929
r-strategists and K-strategists differ in number of offspring Mammals produce five classes of antibody with different
and parental care. 904 biological functions. 929
Animals either lay eggs or give birth to live young. 904 Clonal selection is the basis for antibody specificity. 930
Clonal selection also explains immunological memory. 931
42.3 Human Reproductive Anatomy and Physiology 905
Genomic rearrangement creates antibody diversity. 931
The male reproductive system is specialized for the
production and delivery of sperm. 905 HOW DO WE KNOW? How is antibody diversity generated? 932
The female reproductive system produces eggs and supports 43.4 Adaptive Immunity: T cells and Cell-Mediated Immunity 934
the developing embryo. 907
T cells include helper and cytotoxic cells. 934
Hormones regulate the human reproductive system. 908
T cells have T cell receptors on their surface that recognize an
42.4 Gamete Formation to Birth in Humans 911 antigen in association with MHC proteins. 934
Male and female gametogenesis have both shared and The ability to distinguish between self and nonself is
distinct features. 911 acquired during T cell maturation. 936
Fertilization occurs when a sperm fuses with an oocyte. 912 43.5 Three Pathogens: A Virus, Bacterium, and Eukaryote 936
The first trimester includes cleavage, gastrulation, and The flu virus evades the immune system by antigenic drift
organogenesis. 913 and shift. 937
The second and third trimesters are characterized by Tuberculosis is caused by a slow-growing, intracellular
fetal growth. 915 bacterium. 937
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The malaria parasite changes surface molecules by antigenic Amniotes evolved terrestrial eggs. 970
variation. 938
44.5 The Evolutionary History of Animals 972
? CASE 8 Biodiversity Hotspots: Rain Forests and Reefs 941 Fossils and phylogeny show that animal forms were initially
simple but rapidly evolved complexity. 972
The animal body plans we see today emerged during
the Cambrian Period. 973
CHAPTER 44 ANIMAL DIVERSITY 945
Tabulations of described fossils show that animal diversity
has been shaped by both radiation and mass extinction over
the part 500 million years. 974
Animals began to colonize the land 420 million years ago. 974
44.1 A Tree of Life for More than a Million Animal Species 946 CHAPTER 45 ANIMAL BEHAVIOR 981
Cnidarians are the architects of life’s largest constructions: 45.2 Dissecting Behavior 983
coral reefs. 950
The fixed action pattern is a stereotyped behavior. 983
Ctenophores and placozoans represent the extremes of body The nervous system processes stimuli and evokes behaviors. 984
organization among early-branching animals. 952
Hormones can trigger certain behaviors. 985
The order of early branches on the animal tree remains
Breeding experiments can help determine the degree to
uncertain. 953
which a behavior is genetic. 986
The discovery of new animals with a unique body plan
Molecular techniques provide new ways of testing the role
complicates phylogenetic hypotheses still further. 954
of genes in behavior. 987
44.3 Bilaterian Animals 956 HOW DO WE KNOW? Can genes influence behavior? 988
Lophotrozochoans make up nearly half of all animal phyla,
45.3 Learning 989
including the diverse and ecologically important annelids and
mollusks. 956 Non-associative learning occurs without linking two events. 990
Ecdysozoans include nematodes, the most numerous animals, Associative learning occurs when two events are linked. 990
and arthropods, the most diverse. 959 Learning is an adaptation. 990
HOW DO WE KNOW? How did the diverse feeding HOW DO WE KNOW? To what extent are insects capable
appendages of arthropods arise? 961 of learning? 991
Deuterostomes include humans and other chordates, and 45.4 Orientation, Navigation, and Biological Clocks 992
also acorn worms and sea stars. 963
Orientation involves a directed response to a stimulus. 992
Chordates include vertebrates, cephalochordates,
and tunicates. 964 Navigation is demonstrated by the remarkable ability of
homing in birds. 993
44.4 Vertebrate Diversity 966 Biological clocks provide important time cues for many
Fish are the earliest-branching and most diverse vertebrate behaviors. 993
animals. 967 HOW DO WE KNOW? Does a biological clock play a role
The common ancestor of tetrapods had four limbs. 969 in birds’ ability to orient? 994
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45.5 Communication 995 Patterns of survivorship vary among organisms. 1013
Communication is the transfer of information between Reproductive patterns reflect the predictability of a species’
a sender and receiver. 995 environment. 1014
Some forms of communication are complex and learned The life history of an organism shows trade-offs among
during a sensitive period. 996 physiological functions. 1014
Other forms of communication convey specific information. 997 46.4 Metapopulation Dynamics 1015
46.2 Population Growth and Decline 1007 ? Can competition drive species diversification? 1025
Population size is affected by birth, death, immigration, Species compete for resources other than food. 1025
and emigration. 1007 Predation, parasitism, and herbivory are interactions in
Exponential growth is characterized by a constant per which one species benefits at the expense of another. 1025
capital growth rate. 1008 HOW DO WE KNOW? Can predators and prey coexist stably
Carrying capacity is the maximum number of individuals in certain environments? 1026
a habitat can support. 1008 Facilitation can occur when two species prey on a third
Logistic growth produces an S-shaped curve and describes species. 1027
the growth of many natural populations. 1009
47.3 Mutualistic Interactions Between Species 1028
Factors that influence population growth can be dependent
Mutualisms are interactions between species that benefit
on or independent of its density. 1009
both participants. 1028
46.3 Age-Structured Population Growth 1010 Mutualisms may evolve increasing interdependence. 1028
Birth and death rates vary with age and environment. 1011 HOW DO WE KNOW? Have aphids and their symbiotic
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Mutualisms may be obligate or facultative. 1030 The biological carbon cycle shapes ecological interactions
and reflects evolution. 1060
The costs and benefits of species interactions can change
over time. 1030 The nitrogen cycle also reflects the interplay between
ecology and evolution. 1062
47.4 Ecological Communities 1031
Phosphorus cycles through ecosystems, supporting primary
Species that live in the same place make up communities. 1031 production. 1062
? How is biodiversity measured? 1032 Global patterns of primary production reflect variations in
One species can have a great effect on all other members climate and nutrient availability. 1063
of the community. 1032 HOW DO WE KNOW? Does iron limit primary production
Keystone species have disproportionate effects on in some parts of the oceans? 1065
communities. 1033
48.4 Global Biodiversity 1066
Disturbance can modify community composition. 1034
? Why does biodiversity decrease from the equator toward
Succession describes the community response to new
the poles? 1066
habitats or disturbance. 1035
Evolutionary and ecological history underpins diversity. 1068
47.5 Ecosystems 1036
Species interactions result in food webs that cycle carbon
and other elements through ecosystems. 1036
CHAPTER 49 THE ANTHROPOCENE
Species interactions form trophic pyramids that transfer Humans as a Planetary Force 1071
energy through ecosystems. 1037
Light, water, nutrients, and diversity all influence rates
of primary production. 1038
HOW DO WE KNOW? Does species diversity promote
primary productivity? 1039
48.2 Biomes 1049 Nitrogen fertilizer transported to lakes and the sea causes
eutrophication. 1082
Terrestrial biomes reflect the distribution of climate. 1050
Phosphate fertilizer is also used in agriculture, but has
Aquatic biomes reflect climate, and also the availability of
finite sources. 1082
nutrients and oxygen and the depth to which sunlight
penetrates through water. 1052 What can be done? 1083
48.3 Global Ecology: Cycling Bioessential Elements 1060 49.4 Human Influence on Evolution 1084
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Human activities have reduced the quality and size of many Conservation biologists have a diverse toolkit for
habitats, decreasing the number of species they can support. 1084 confronting threats to biodiversity. 1092
Overexploitation threatens species and disrupts ecological Global change provides new challenges for conservation
relationships within communities. 1085 biology in the 21st century. 1092
VISUAL SYNTHESIS Flow of Matter and Energy Sustainable development provides a strategy for
Through Ecosystems 1086 conserving biodiversity while meeting the needs of the
human population. 1093
Humans play an important role in the dispersal of species. 1088
Humans have altered the selective landscape for many 49.6 Scientists and Citizens in the 21st Century 1094
pathogens. 1089
Quick Check Answers Q-1
Are amphibians ecology’s “canary in the coal mine”? 1090
Glossary G-1
49.5 Conservation Biology 1091
? What are our conservation priorities? 1091 Index I-1
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BIOLOGY
HOW
LIFE
WORKS
PA RT 1 CHAPTER 1
Life
FROM Chemical, Cellular, and
CELLS TO
Evolutionary Foundations
ORGANISMS
” Nothing in biology
makes sense except
in the light of evolution.”
—THEODOSIUS DOBZHANSKY
1
CH
C HA
APPTTEERR 11
Life
Chemical, Cellular, and
Evolutionary Foundations
Core Concepts
1.1 The scientific method is a
deliberate way of asking and
answering questions about the
natural world.
1.2 Life works according to
fundamental principles of
chemistry and physics.
1.3 The fundamental unit of life is
the cell.
1.4 Evolution explains the features
that organisms share and those
that set them apart.
1.5 Organisms interact with
one another and with their
physical environment, shaping
ecological systems that sustain
life.
1.6 In the 21st century, humans
have become major agents in
ecology and evolution.
Giovanna Griffo/Gallery Stock.
1
4 SECTION 1.1 THE SCIENTIFIC METHOD
Every day, remarkable things happen within and around you. we know about life? And we hope you will develop a basis for
Strolling through a local market, you come across a bin full of crisp making informed decisions about your life, career, and the actions
apples, pick one up, and take a bite. Underlying this unremarkable you take as a citizen.
occurrence is an extraordinary series of events. Your eyes sense the
apple from a distance, and nerves carry that information to your
brain, permitting identification. Biologists call this cognition, an 1.1 THE SCIENTIFIC METHOD
area of biological study. Stimulated by the apple and recognizing
it as ripe and tasty, your brain transmits impulses through nerves How do we go about trying to understand the vastness and
to your muscles. How we respond to external cues motivates complexity of nature? For most scientists, studies of the natural
behavior, another biological discipline. Grabbing the apple requires world involve the complementary processes of observation and
the coordinated activities of dozens of muscles that move your experimentation. Observation is the act of viewing the world
arm and hand to a precise spot. These movements are described around us. Experimentation is a disciplined and controlled way
by biomechanics, yet another area of biological research. And, as of asking and answering questions about the world in an unbiased
you bite down on the apple, glands in your mouth secrete saliva, manner.
starting to convert energy stored in the apple as sugar into energy
that you will use to fuel your own activities. Physiology, like Observation allows us to draw tentative explanations
biomechanics, lies at the heart of biological function. called hypotheses.
The study of cognition, behavior, biomechanics, and physiology Observations allow us to ask focused questions about nature. Let’s
are all ways of approaching biology, the science of how life works. say you observe a hummingbird like the one pictured in Fig. 1.1
Biologists, scientists who study life, have come to understand a hovering near a red flower, occasionally dipping its long beak into
great deal about these and other processes at levels that run from the bloom. What motivates this behavior? Is the bird feeding on
molecular mechanisms within the cell, through the integrated some substance within the flower? Is it drawn to the flower by its
actions of many cells within an organ or body, to the interactions vivid color? What benefit, if any, does the flower derive from this
among different organisms in nature. We don’t know everything busy bird?
about how life works—in fact, it seems as if every discovery raises Observations such as these, and the questions they raise,
new questions. But biology provides us with an organized way of allow us to propose tentative explanations, or hypotheses. We
understanding ourselves and the world around us. might, for example, hypothesize that the hummingbird is carrying
Why study biology? The example of eating an apple was pollen from one flower to the next, facilitating reproduction in
deliberately chosen because it is an everyday occurrence that we the plant. Or we might hypothesize that nectar produced deep
ordinarily wouldn’t think about twice. The scope of modern biology, within the flower provides nutrition for the hummingbird—that
however, is vast, raising questions that can fire our imaginations, the hummingbird’s actions reflect the need to take in food. Both
affect our health, and influence our future. How, for example, will hypotheses provide a reasonable explanation of the behavior we
our understanding of the human genome change the way that observed, but they may or may not be correct. To find out, we have
we fight cancer? How do bacteria in our digestive system help to test them.
determine health and well-being? Will expected increases in the Charles Darwin’s classic book, On the Origin of Species,
temperature and acidity of seawater doom coral reefs? Is there, or published in 1859, beautifully illustrates how we can piece
has there ever been, life on Mars? And, to echo the great storyteller together individual observations to construct a working
Rudyard Kipling, why do leopards have spots, and tigers stripes? hypothesis. In this book, Darwin discussed a wide range of
We can describe six grand themes that connect and unite the observations, from pigeon breeding to fossils and from embryology
many dimensions of life science, from molecules to the biosphere. to the unusual animals and plants found on islands. Darwin noted
These six themes are stated as Core Concepts for this chapter and the success of animal breeders in selecting specific individuals for
are introduced in the following sections. Throughout the book, reproduction and thereby generating new breeds for agriculture or
these themes will be visited again and again. We view them as the show. He appreciated that selective breeding is successful only if
keys to understanding the many details in subsequent chapters specific features of the animals can be passed from one generation
and relating them to one another. Our hope is that by the time to the next by inheritance. Reading economic treatises by the
you finish this book, you will have an understanding of how life English clergyman Thomas Malthus, he understood that limiting
works, from the molecular machines inside cells and the metabolic environmental resources could select among the variety of
pathways that cycle carbon through the biosphere to the process of different individuals in populations in much the way that breeders
evolution, which has shaped the living world that surrounds (and select among cows or pigeons.
includes) us. You will, we hope, see the connections among these Gathering together all these seemingly disparate pieces of
different ways of understanding life, and come away with a greater information, Darwin argued that life has evolved over time by
understanding of how scientists think about and ask questions means of natural selection. Since its formulation, Darwin’s initial
about the natural world. How, in fact, do we know what we think hypothesis has been tested by experiments, many thousands of
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO L U T I O N A RY F O U N DAT I O N S 5
Using observations to generate a hypothesis and then Working in Italy, the American geologist Walter Alvarez
making predictions based on that hypothesis that can be tested collected samples from the precise point in the rock layers that
experimentally are the first two steps in the scientific method, corresponds to the time of the extinction. Careful chemical
outlined in Fig. 1.2. The scientific method is a deliberate and analysis showed that rocks at this level are unusually enriched in
careful way of asking questions about the unknown. We make the element iridium. Iridium is rare in most rocks on continents
observations, collect field or laboratory samples, and design and and the seafloor, but is relatively common in rocks that fall from
carry out experiments or analyses to make sense of things we space—that is, in meteorites. From these observations, Alvarez
initially do not understand. The scientific method has proved to and his colleagues developed a remarkable hypothesis: 66 million
be spectacularly successful in helping us to understand the years ago, a large (11-km diameter) meteor slammed into Earth,
world around us. We explore several aspects of the scientific and in the resulting environmental havoc, dinosaurs and many
method, including experimental design, data and data other species became extinct. This hypothesis makes specific
presentation, probability and statistics, and scale and predictions, described in Fig. 1.3, which turned out to be supported
approximation on . by further observations. Thus, observational tests support the
To emphasize the power of the scientific method, we turn hypothesis that nearly 150 million years of dinosaur evolution
to a famous riddle drawn from the fossil record (Fig. 1.3). Since were undone in a moment.
the nineteenth century, paleontologists have known that before
mammals expanded to their current ecological importance, other General explanations of natural phenomena
large animals dominated Earth. Dinosaurs evolved about supported by many experiments and observations
210 million years ago and disappeared abruptly 66 million years are called theories.
ago, along with many other species of plants, animals, and As already noted, a hypothesis may initially be tentative.
microscopic organisms. In many cases, the skeletons and shells of Commonly, in fact, it will provide only one of several possible
these creatures were buried in sediment and became fossilized. ways of explaining existing data. With repeated observation and
Layers of sedimentary rock therefore record the history of Earth. experimentation, however, a good hypothesis gathers strength,
FIG. 1.3
HOW DO WE KNOW?
OBSERVATION
274
Paleogene
276
Depth (m)
discovered in rock layers 280
corresponding to the
time of extinction.
282
Cretaceous
Photo Source: Kirk Johnson, Denver 284
Museum of Nature & Science.
286
0 0.5 1 1.5 2 2.5 3 3.5 4
Amount of Iridium (parts per billion)
HYPOTHESIS The impact of a large meteorite disrupted communities on land and in the sea, causing the extinction of the dinosaurs
and many other species.
PREDICTIONS Independent evidence of a meteor impact should be found in rock layers corresponding to the time of the extinction
and be rare or absent in older and younger beds.
FURTHER OBSERVATIONS
U.S.A.
CONCLUSION A giant meteor struck Earth 66 million years ago, causing the extinction of the dinosaurs and many other species.
FOLLOW-UP WORK Researchers have documented other mass extinctions, but the event that eliminated the dinosaurs appears to be the only
one associated with a meteorite impact.
SOURCE Alvarez, W. 1998. T. rex and the Crater of Doom. New York: Vintage Press.
7
8 SECTION 1.2 C H E M I C A L A N D P H YS I C A L P R I N C I P L E S
HOW DO WE KNOW?
is harnessed by cells, only some is used to do work; the rest is
FIG. 1.8
dissipated as heat (Fig. 1.6). That is, conversion of energy from
one form to another is never 100% efficient. Heat is a form of
energy, so the total amount of energy is conserved, as dictated by Can living organisms arise
the first law. In addition, heat corresponds to the motion of small
molecules—the greater the heat, the greater the motion, and the from nonliving matter?
greater the motion, the greater the degree of disorder. Therefore,
the release of heat as organisms harness energy means that the
BACKGROUND Until the 1600s, many people believed that
total entropy for the combination of the cell and its surroundings
increases, in keeping with the second law (Fig. 1.7). rotting meat spontaneously generates maggots (fly larvae).
As simple
compounds are of the scientific method settled the issue. In the 1600s, the
combined into Italian physician and naturalist Francesco Redi hypothesized that
more complex Some of the energy maggots (and hence flies) in rotting meat come only from other
molecules, the is released as heat,
entropy inside increasing the flies that laid their eggs in the meat.
the cell decreases, entropy (motion of To test his hypothesis, Redi set up an experiment in which
requiring energy. molecules) in the he placed meat in three glass jars (Fig. 1.8). One jar was left open,
environment. The
total entropy of the a second was covered with gauze, and the third was sealed with
cell plus the a cap. The jars were left in a room with flies. Note that in this
environment
increases.
experiment, the three jars were subject to the same conditions—
the only difference was the opening of the jar. The open jar allowed
HOW DO WE KNOW?
FIG. 1.9
HYPOTHESIS Pasteur hypothesized that if microbes were generated spontaneously from nonliving matter, they should reappear in
sterilized broth without the addition of microbes.
EXPERIMENT Pasteur used two flasks, one with a straight neck and one with a swan neck. The straight-neck flask allowed dust particles
with microbes to enter. The swan-neck flask did not.
RESULTS
Broth
Broth remains clear
and sterile—no
microbes appear.
Straight- Swan-
neck neck
flask flask Boiling kills all the Dust particles carrying microbes Broth becomes
microbes, thereby enter the straight-neck flask, cloudy because of
sterilizing the broth. but not the swan-neck flask. growth of microbes.
CONCLUSION The presence of microbes in the straight-neck flask and the absence of microbes in the swan-neck flask supported the
hypothesis that microbes come from other microbes and are not spontaneously generated.
DISCUSSION Redi’s and Pasteur’s research illustrate classic attributes of well-designed experiments. Multiple treatments are set up, and
nearly all conditions are the same in them all—they are constant, and therefore cannot be the cause of different outcomes of the experiment.
One key feature—the variable—is changed by the experimenter from one treatment to the next. This is a place to look for explanations of
different experimental outcomes.
for the passage of flies and air; the jar with the gauze allowed for flask. The straight-neck flask allowed airborne dust particles
the passage of air but not flies; and the sealed jar did not allow air carrying microbes to fall into the sterile broth, while the swan-
or flies to enter. Over time, Redi observed that maggots appeared neck flask prevented dust from getting inside. Over time, Pasteur
only on the meat in the open jar. No maggots appeared in the observed that microbes grew in the broth inside the straight-neck
other two jars, which did not allow access to the meat by flies. flask but not in the swan-neck flask. From these observations,
These observations supported Redi’s hypothesis that flies come Pasteur rejected the hypothesis that microbes arise spontaneously
from other flies, and did not provide support for the alternative from sterile broth. Instead, exposure to microbes carried on
hypothesis that maggots arise spontaneously from meat. airborne dust particles is necessary for microbial growth.
Redi demonstrated that living organisms come from other Redi’s and Pasteur’s experiments demonstrated that living
organisms, but some argued that his conclusion might apply only organisms come from other living organisms and are not generated
to larger organisms—microscopic life might be another matter spontaneously from chemical components. But this raises the
entirely. It was not until the nineteenth century that the French question of how life arose in the first place. If life comes from life,
chemist and biologist Louis Pasteur tested the hypothesis that where did the first living organisms come from? Although today
microorganisms can arise by spontaneous generation (Fig. 1.9). all organisms are produced by parental organisms, early in Earth’s
Pasteur filled two glass flasks with broth that had first been history this was not the case. Scientists hypothesize that life
sterilized over heat—one with a straight vertical neck and the initially emerged from chemical compounds about 4 billion years
other with a curved swan neck. As in Redi’s experiments, there ago. That is, chemical systems capable of evolution arose from
was only one variable, in this case the shape of the neck of the chemical reactions that took place on the early Earth. We’ll return
11
12 SECTION 1.3 THE CELL
to the great question of life’s origin in Case 1: The First Cell and in pictured in Fig. 1.11b, extend slender projections known as axons
Chapters 2 through 8. for distances as great as a meter, and the cannonball-size egg of an
ostrich in Fig. 1.11c is a single giant cell.
The types of cell just mentioned—bacteria, yeasts, skin cells,
1.3 THE CELL nerve cells, and an egg—seem very different, but all are organized
along broadly similar lines. In general, all cells contain a stable
The cell is the simplest entity that can exist as an independent blueprint of information in molecular form; they have a discrete
unit of life. Every known living organism is either a single cell boundary that separates the interior of the cell from its external
or an ensemble of a few to many cells (Fig. 1.10). Most bacteria environment; and they have the ability to harness materials and
(like those in Pasteur’s experiment), yeasts, and the tiny algae energy from the environment.
that float in oceans and ponds spend their lives as single cells. In
contrast, plants and animals contain billions to trillions of cells Nucleic acids store and transmit information needed
that function in a coordinated fashion. for growth, function, and reproduction.
Most cells are tiny, their dimensions well below the threshold The first essential feature of a cell is its ability to store and
of detection by the naked eye (Fig. 1.11). The cells that make up transmit information. To accomplish this, cells require a stable
the layers of your skin (Fig. 1.11a) average about 100 microns (μm) archive of information that encodes and helps determine their
or 0.1 mm in diameter, which means that about 10 would fit in a physical attributes. Just as the construction and maintenance of
row across the period at the end of this sentence. Many bacteria a house requires a blueprint that defines the walls, plumbing,
are less than a micron long. Certain specialized cells, however, and electrical wiring, organisms require an accessible and reliable
can be quite large. Some nerve cells in humans, like the ones archive of information that helps determine their structure
FIG. 1.10 Unicellular and multicellular organisms. All living organisms are made up of cells: (a) bacteria; (b) brewer’s yeast; (c) algae;
(d) cheetahs; (e) humans. Sources: a. Steve Gschmeissner/Science Source; b. Steve Gschmeissner/Science Source; c. Michael Abbey/Getty Images;
d. Sven-Olof Lindblad/Science Source; e. Megapress/Alamy.
a b c
d e
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO LU T I O N A RY F O U N DAT I O N S 13
Translation
Protein
14 SECTION 1.3 THE CELL
information to be passed from cell to cell or from an organism contributions from their surroundings, both simple ions and the
to its progeny. Each organism’s DNA archive can be stably and building blocks required to manufacture macromolecules. They also
reliably passed from generation to generation in large part because release waste products into the environment. As discussed more
of its double-stranded helical structure. During replication, each fully in Chapter 5, the plasma membrane controls the movement of
strand of the double helix serves as a template for a new strand. materials into and out of the cell.
Replication is necessarily precise and accurate because mistakes In addition to the plasma membrane, many cells have internal
introduced into the cell’s information archive may be lethal to the membranes that divide the cell into discrete compartments,
cell. That said, errors in DNA can and do occur during the process each specialized for a particular function. A notable example
of replication, and environmental insults can damage DNA as is the nucleus, which houses the cell’s DNA. Like the plasma
well. Such changes are known as mutations; they can spell death membrane, the nuclear membrane selectively controls movement
for the cell, or they can lead to the variations that underlie the of molecules into and out of it. As a result, the nucleus occupies a
diversity of life and the process of evolution. discrete space within the cell, separate from the space outside the
nucleus, called the cytoplasm.
j Quick Check 3 How does the central dogma help us to
Not all cells have a nucleus. In fact, cells can be grouped
understand how mutations in DNA can result in disease?
into two broad classes depending on whether or not they have a
nucleus. Cells without a nucleus are called prokaryotes, and cells
Membranes define cells and spaces within cells. with a nucleus are eukaryotes.
The second essential feature of all cells is a plasma membrane that The first cells that emerged about 4 billion years ago were
separates the living material within the cell from the nonliving prokaryotic. Their descendants include the familiar bacteria, found
environment around it (Fig. 1.14). This boundary between today nearly everywhere that life can persist. Some prokaryotes
inside and outside does not mean that cells are closed systems live in peaceful coexistence with humans, inhabiting our gut and
independent of the environment. On the contrary, there is an active aiding digestion. Others cause disease—salmonella, tuberculosis,
and dynamic interplay between cells and their surroundings that and cholera are familiar examples. The success of these cells
is mediated by the plasma membrane. All cells require sustained depends in part on their small size, their ability to reproduce
rapidly, and their ability to obtain energy and nutrients from
diverse sources. Most prokaryotes live as single-celled organisms,
but some have simple multicellular forms.
FIG. 1.14 The plasma membrane. The plasma membrane
Eukaryotes evolved much later, roughly 2 billion years ago,
surrounds every cell and controls the exchange of
from prokaryotic ancestors. They include familiar groups such as
material with the environment. Sources: (top) Dr. Gopal Murti/
animals, plants, and fungi, along with a wide diversity of single-
SPL/Science Source; (bottom) Don W. Fawcett/Science Source.
celled microorganisms called protists. Eukaryotic organisms
exist as single cells like yeasts or as multicellular organisms
Plasma
membrane Outside of cell like humans. In multicellular organisms, cells may specialize to
perform different functions. For example, in humans, muscle
cells contract; red blood cells carry oxygen to tissues; and skin cells
Cytoplasm
provide an external barrier.
The terms “prokaryotes” and “eukaryotes” are useful in drawing
attention to a fundamental distinction between these two groups
of cells. However, today, biologists recognize three domains of life—
Bacteria, Archaea, and Eukarya (Chapters 26 and 27). Bacteria and
Archaea both lack a nucleus and are therefore prokaryotes, whereas
Eukarya are eukaryotic. Archaea are single-celled microorganisms,
many of which flourish under seemingly hostile conditions, such as
the hot springs of Yellowstone National Park.
Organisms acquire energy from just two sources—the sun and displays a remarkable degree of diversity. We don’t really know
chemical compounds. The term metabolism describes chemical how many species share our planet, but reasonable estimates run
reactions by which cells convert energy from one form to another to 10 million or more. Both the unity and the diversity of life are
and build and break down molecules. These reactions are required explained by the process of evolution, or change over time.
to sustain life. Regardless of their source of energy, all organisms
use chemical reactions to break down molecules, releasing energy Variation in populations provides the raw material
in the process that is stored in a chemical form called adenosine for evolution.
triphosphate, or ATP. This molecule enables cells to carry out all Described in detail, evolution by natural selection calls on
sorts of work, including growth, division, and moving substances complex mathematical formulations, but at heart its main
into and out of the cell. principles are simple, indeed unavoidable. When there is variation
Many metabolic reactions are highly conserved between within a population of organisms, and when that variation can be
organisms, meaning the same reactions are found in many inherited (that is, when it can be passed from one generation to
different organisms. This observation suggests that the reactions the next), the variants best suited for growth and reproduction
evolved early in the history of life and have been maintained in a given environment will contribute disproportionately to the
for billions of years because of their fundamental importance to next generation. As Darwin recognized, farmers have used this
cellular biochemistry. principle for thousands of years to select for crops with high yield
or improved resistance to drought and disease. It is how people
A virus is genetic material in need of a cell. around the world have developed breeds of dog ranging from
It’s worth taking a moment to consider viruses. A virus is an agent terriers to huskies (Fig. 1.15). And it is why antibiotic resistance
that infects cells. It is smaller and simpler than cells. Why, then, is on the rise in many disease-causing microorganisms. Life has
aren’t viruses the smallest unit of life? We just considered three been shaped by evolution since its origin, and the capacity for
essential features of cells—the capacity to store and transmit Darwinian evolution may be life’s most fundamental property.
information, a membrane that selectively controls movement in
and out, and the ability to harness energy from the environment.
Viruses have a stable archive of genetic information, which can FIG. 1.15 Artificial selection. Selection over many centuries has
be RNA or DNA, surrounded by a protein coat and sometimes resulted in remarkable variations among dogs. Charles
a lipid envelope. But viruses cannot harness energy from the Darwin called this “selection under domestication” and
environment. Therefore, on their own viruses cannot read and use noted that it resembles selection that occurs in nature.
the information contained in their genetic material, nor can they Source: © Rob Brodman 2011.
regulate the passage of substances across their protein coats or lipid
envelopes the way that cells do. To replicate, they require a cell.
A virus infects a cell by binding to the cell’s surface, inserting
its genetic material into the cell, and, in most cases, using the
cellular machinery to produce more viruses. In this way, it is often
said that a virus “hijacks” a cell. The infected cell may produce
more viruses, sometimes by lysis, or breakage, of the cell, and the
new viruses can then infect more cells. In some cases, the genetic
material of the virus integrates into the DNA of the host cell.
We discuss viruses many times throughout the book. Each
species of Bacteria, Archaea, and Eukarya is susceptible to many
types of virus that are specialized to infect its cells. Several hundred
types of virus are known to infect humans, and the catalog is
still incomplete. Useful tools in biological research, viruses have
provided a model system for many problems in biology, including
how genes are turned on and off and how cancer develops.
1.4 EVOLUTION
The themes introduced in the last two sections stress life’s unity:
Cells form the basic unit of all life; DNA, RNA, and proteins
carry out the molecular functions of all cells; and metabolic
reactions build and break down macromolecules. We need only
look around us, however, to recognize that for all its unity, life
16 SECTION 1.4 E VO L U T I O N
The apples in the bin from which you made your choice didn’t some of the flowers of another, enabling the sperm inside pollen
all look alike. Had you picked your apple in an orchard, you would grains to fertilize egg cells within that single flower. All the seeds
have seen that different apples on the same tree looked different— on an apple tree contain shared genes from one parent, the tree
some smaller, some greener, some misshapen, a few damaged by on which they developed. But they contain distinct sets of genes
worms. Such variation is so commonplace that we scarcely pay contributed by sperm transported in pollen from other trees. In
attention to it. Variation is observed among individuals in virtually all sexual organisms, fertilization produces unique combinations
every species of organism. Variation that can be inherited provides of genes, which explains in part why sisters and brothers with the
the raw material on which evolution acts. same parents can be so different from one another.
The causes of variation among individuals within a species Genetic variation arises ultimately from mutations. Mutations
are usually grouped into two broad categories. Variation among arise either from random errors during DNA replication or from
individuals is sometimes due to differences in the environment; this environmental factors such as ultraviolet (UV) radiation, which
is called environmental variation. Among apples on the same tree can damage DNA. If these mutations are not corrected, they are
some may have good exposure to sunlight; some may be hidden in passed on to the next generation. To put a human face on this,
the shade; some were lucky enough to escape the female codling consider that lung cancer can result from an environmental
moth, whose egg develops into a caterpillar that eats its way into the insult, such as cigarette smoking, or from a genetic susceptibility
fruit. These are all examples of environmental variation. inherited from the parents.
The other main cause of variation among individuals is In nature, most mutations that harm growth and reproduction
differences in the genetic material that is transmitted from parents die out after a handful of generations. Those that are neither
to offspring; this is known as genetic variation. Differences among harmful nor beneficial can persist for hundreds or thousands
individuals’ DNA can lead to differences among the individuals’ of generations. And those that are beneficial to growth and
RNA and proteins, which affect the molecular functions of the cell reproduction can gradually become incorporated into the genetic
and ultimately can lead to physical differences that we can observe. makeup of every individual in the species. That is how evolution
Genetic differences among apples produce varieties whose mature works: The genetic makeup of a population changes over time.
fruits differ in taste and color, such as the green Granny Smith, the
yellow Golden Delicious, and the scarlet Red Delicious. Evolution predicts a nested pattern of relatedness
But even on a single tree, each apple contains seeds that are among species, depicted as a tree.
genetically distinct because the apple tree is a sexual organism. Evolutionary theory predicts that new species arise by the
Bees carry pollen from the flowers of one tree and deposit it in divergence of populations through time from a common ancestor.
As a result, closely related species are
likely to resemble each other more
closely than they do more distantly
FIG. 1.16 Phylogenetic relationships among primates. (a) Humans share many features with related species. You know this to be
chimpanzees. (b) Humans and chimpanzees, in turn, share more features with gorillas true from common experience. All of
than they do with other species, and so on down through the evolutionary tree of us recognize the similarity between
primates. Treelike patterns of nested similarities are the predicted result of evolution. a chimpanzee’s face and body and
Source: AP Photo/Bela Szandelszky. our own (Fig. 1.16a), and biologists
have long known that we share more
a. b. features with chimpanzees than we
Lemurs do with any other species.
Tarsiers Humans and chimpanzees,
in turn, share more features with
New World monkeys
gorillas than they do with any other
Old World monkeys species. And humans, chimpanzees,
and gorillas share more features
Gibbons
with orangutans than they do with
Orangutans any other species. And so on. We
can continue to include a widening
Nodes Gorillas
indicate a diversity of species, successively
common Chimpanzees adding monkeys, lemurs, and other
ancestor.
primates, to construct a set of
Humans
evolutionary relationships that can
Time be depicted as a tree (Fig. 1.16b). In
this tree, the tips or branches on the
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO L U T I O N A RY F O U N DAT I O N S 17
BACTERIA
EUKARYOTES
Plants All land plants lie
on this branch.
Animals
Animal diversity
Proposed position of root lies on this branch
Time runs from the of the tree.
root to the branches.
right represent different groups of organisms, nodes (where lines comparisons of DNA sequences and fossils show that the close
split) represent the most recent common ancestor, and time runs similarity between humans and chimpanzees reflects descent
from left to right. from a common ancestor that lived about 6 million years ago.
Evolutionary theory predicts that primates should show a Their differences reflect what Darwin called “descent with
nested pattern of similarity, and this is what morphological and modification”—evolutionary changes that have accumulated
molecular observations reveal. We can continue to add other over time since the two lineages split. For example, as discussed
mammals and then other vertebrate animals to our comparison, in Chapter 24, the flat face of humans, our small teeth, and
in the process generating a pattern of evolutionary relationships our upright posture all evolved within our ancestors after they
that forms a larger tree, with the primates confined to one limb. diverged from the ancestors of chimpanzees. At a broader
And using comparisons of DNA among species, we can generate scale, the fundamental features shared by all organisms reflect
still larger trees, ones that include plants as well as animals and the inheritance from a common ancestor that lived billions of years
full diversity of microscopic organisms. Biologists call the full set of ago. And the differences that characterize the many branches
evolutionary relationships among all organisms the tree of life. on the tree of life have formed through the continuing action of
This tree, illustrated in Fig. 1.17, has three major branches evolution since the time of our earliest ancestors.
representing the three domains mentioned earlier and is made up Four decades ago, the geneticist Theodosius Dobzhansky
mostly of microorganisms. The last common ancestor of all living wrote, “Nothing in biology makes sense except in the light of
organisms, which form a root to the tree, is thought to lie between evolution.” For this reason, evolution permeates discussions
the branch leading to Bacteria and the branch leading to Archaea throughout this book, whether we are explaining the molecular
and Eukarya. The plants and animals so conspicuous in our daily biology of cells, how organisms function and reproduce, how
existence make up only two branches on the eukaryotic limb of species interact in nature, or the remarkable biological diversity of
the tree. our planet.
The tree of life makes predictions for the order of appearance
of different life-forms in the fossil record. For example, Fig. Evolution can be studied by means of experiments.
1.16—one small branch on the greater tree—predicts that humans Both the nested patterns of similarity among living organisms
should appear later than monkeys, and that primates more akin and the succession of fossils in the geologic record fit the
to lemurs and tarsiers should appear even earlier. The greater tree predictions of evolutionary theory. Can we actually capture
also predicts that all records of animal life should be preceded by a evolutionary processes in action? One way to accomplish this is
long interval of microbial evolution. As we will see in subsequent in the laboratory. Bacteria are ideal for these experiments because
chapters, these predictions are confirmed by the geologic record. they reproduce rapidly and can form populations with millions of
Shared features, then, sometimes imply inheritance from individuals. Large population size means that mutations are likely
a common ancestor. In combination, molecular studies such as to form in nearly every generation, even though the probability
18 SECTION 1.4 E VO L U T I O N
that any individual cell will acquire a mutation is small. (In from those of earlier generations—that is, did evolution occur?—
contrast to bacteria, think about trying evolutionary experiments and did the bacteria evolve an improved ability to use succinate?
on elephants!) In fact, the bacteria did evolve an improved ability to use
One such experiment is illustrated in Fig. 1.18. The succinate, demonstrated by the results shown in Fig. 1.18. This
microbiologists Santiago Elena and Richard Lenski grew experiment illustrates how experiments can be used to test
populations of the common intestinal bacterium Escherichia coli hypotheses and it shows evolution in action. Furthermore,
in liquid medium, with the organic acid succinate as the only follow-up studies of the bacterial DNA identified differences in
source of food. In general, E. coli cells feed on succinate poorly if genetic makeup that resulted in the improved ability of E. coli
at all, leading the researchers to hypothesize that any bacterium to use succinate. Many experiments of this general type have
with a mutation that increased its ability to use succinate would been carried out, applying the scientific method to demonstrate
reproduce at a faster rate than other bacteria in the population. how bacteria adapt through mutation and natural selection to any
The key questions were: Did bacteria from later generations differ number of environments.
HOW DO WE KNOW?
demonstrated in the
laboratory? Later
Ancestral
BACKGROUND Escherichia coli is an intestinal bacterium
Later
commonly used in the laboratory. It grows poorly in liquid media
where the only source of food is succinate. Santiago Elena and
Richard Lenski wondered whether E. coli grown for 20,000 Source: Neerja Hajela, Michigan State University.
increase in frequency relative to other types of bacteria, thereby Later strains grew more rapidly
demonstrating evolution in a bacterial population. than ancestral strains at each
generation.
EXPERIMENT Cells of E. coli can be frozen in liquid nitrogen,
which keeps them in a sort of suspended animation in which
no biological processes take place, but the cells survive. At the
beginning of the experiment, the researchers froze a large number
of samples of the starting bacteria (“Ancestral”). As the experiment Generation
progressed, they took samples of the bacterial populations at
CONCLUSION Evolution occurred in the population: The bacteria
intervals (“Later”) and grew them together with a thawed sample
evolved an improved ability to metabolize succinate.
of the starting bacteria in succinate. They then compared the rate
of growth of the ancestral bacteria with that of the bacteria taken at FOLLOW-UP WORK Other experimental studies have shown
later time points. that bacteria are able to evolve adaptations to a wide variety of
environmental conditions.
RESULTS At each time interval, the cells from later time
points grew more rapidly than the ancestral cells when the two SOURCE (top) Elena, S. F., and R. E. Lenski. 2003. “Evolution Experiments with
populations were grown together in succinate. Microorganisms.” Nature Review Genetics 4:457– 469.
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO L U T I O N A RY F O U N DAT I O N S 19
Experiments in laboratory evolution help us to understand tolerances. They are also strongly influenced by interactions with
how life works, and they have an immensely important practical other species, including other plants that compete for the limited
side as well. They allow biologists to develop new and beneficial resources available for growth, animals that feed on them or
strains of microorganisms that, for example, remove toxins from spread their pollen, and microorganisms that infest their tissues.
lakes and rivers. And they show how some of our worst pathogens Ecology is the study of how organisms interact with one another
develop resistance to drugs designed to eliminate them. and with their physical environment in nature.
FIG. 1.20 Ecological relationships. (a) The trees in a rain forest all require water and nutrients. Neighboring plants compete for the limited
supplies of these materials. (b) Plants provide food for many animals. Leaf-cutter ants cut slices of leaves from tropical plants and
transport them to their nests, where the leaves grow fungi that the ants eat. Sources: a. Louise Murray/Getty Images; b. Gail Shumway/Getty Images.
a b
In short, ecological relationships reflect the biomechanical, avoid predation by synthesizing toxic compounds in their leaves
physiological, and behavioral traits of organisms in nature. Form may gain the upper hand. In each case, interactions between
and function, in turn, arise from molecular processes within cells, organisms lead to the evolution of particular traits.
governed by the expression of genes. To take another example from mammal–plant interactions:
Selection for fleshy fruits improved the dispersal of apples
Ecological interactions play an important role because it increased the attractiveness of these seed-bearing
in evolution. structures to hungry mammals. Tiny yeasts make a meal on
G. Evelyn Hutchinson, one of the founders of modern ecology, sugary fruits as well, in the process producing alcohol that deters
wrote a book called The Ecological Theater and the Evolutionary potential competitors for the food. Already in prehistoric times,
Play (1965). This wonderful title succinctly captures a key humans had learned to harness this physiological capability of
feature of biological relationships. It suggests that ecological yeasts, and for this reason the total abundance and distribution of
communities provide the stage on which the play of evolution Vitis vinifera, the wine grape, has increased dramatically through
takes place. time.
As an example, let’s look again at plants competing for
resources. As a result of this competition, natural selection may
favor plants that have more efficient uptake of nutrients or 1.6 THE HUMAN FOOTPRINT
water. In the example of animals eating plants, natural selection
may favor animals with greater jaw strength or more efficient The story of life has a cast of millions, with humans playing only
extraction of nutrients in the digestive system. In turn, plants that one of many roles in an epic 4 billion years in the making. Our
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO L U T I O N A RY F O U N DAT I O N S 21
own species, Homo sapiens, has existed for only the most recent in the 21st century human activities have taken on special
1/200 of 1% of life’s history, yet there are compelling reasons to importance because our numbers and technological abilities make
pay special attention to ourselves. We want to understand how our footprint on Earth’s ecology so large. Human activities now
our own bodies work and how humans came to be: Curiosity about emit more carbon dioxide than do volcanoes, through industrial
ourselves is after all a deeply human trait. processes we convert more atmospheric nitrogen to ammonia than
We also want to understand how biology can help us conquer nature does, and we commandeer, either directly or indirectly, as
disease and improve human welfare. Epidemics have decimated much as 25% of all photosynthetic production on land. To chart
human populations throughout history. The Black Death— our environmental future, we need to understand our role in the
bubonic plague caused by the bacterium Yersinia pestis—is Earth system as a whole.
estimated to have killed half the population of Europe in the And, as we have become major players in ecology, humans
fourteenth century. Casualties from the flu pandemic of 1918 have become important agents of evolution. As our population
exceeded those of World War I. Even King Tut, we now know, has expanded, some species have expanded along with us. We’ve
suffered from malaria in his Egyptian palace approximately seen how agriculture has sharply increased the abundance and
3300 years ago. Throughout this book, we discuss how basic distribution of grapes, and the same is true for corn, cows, and
biological principles are helping scientists to prevent and cure apple trees. At the same time, we have inadvertently helped
the great diseases that have persisted since antiquity, as well as other species to expand—the crowded and not always clean
modern ones such as AIDS and Ebola. environments of cities provide excellent habitats for cockroaches
Furthermore, we need to understand the evolutionary and and rats (Fig. 1.21).
ecological consequences of a human population that now exceeds Other species, however, are in decline, their populations
7 billion. All species affect the world around them. However, reduced by hunting and fishing, changes in land use, and other
FIG. 1.21 Species that have benefited from human activity, including (a) corn, (b) rats, and (c) cockroaches.
Sources: a. Fred Dimmick/iStockphoto; b. Arndt Sven-Erik/age footstock; c. Nigel Cattlin/Alamy.
a b
c
22 SECTION 1.6 T H E H U M A N F O OT P R I N T
FIG. 1.22 Extinct and endangered species. Humans have caused many organisms to become extinct, such as (a) the dodo, (b) passenger pigeon,
(c) Bali tiger, and (d) dusky seaside sparrow. Burgeoning human populations have diminished the ranges of many others, including
(e) the white rhinoceros. Sources: a. Science Source; b. G. I. Bernard/Science Source; c. Look and Learn/Bridgeman Images; d. P.W. Sykes/U.S. Fish and Wildlife
Service; e. James Warwick/Science Source.
a b c
d e
human activities. When Europeans first arrived on the Indian Throughout this book, we return to the practical issues of
Ocean island of Mauritius, large flightless birds called dodos were life science. How can we use the principles of biology to improve
plentiful (Fig. 1.22). Within a century, the dodo was extinct. Early human welfare, and how can we live our lives in ways that control
Europeans in North America were greeted by vast populations our impact on the world around us? The answers to the questions
of passenger pigeons, more than a million in a single flock. By critically depend on understanding biology in an integrated fashion.
the early twentieth century, the species was extinct, a victim of While it is tempting to consider molecules, cells, organisms, and
hunting and habitat change through expanding agriculture. Other ecosystems as separate entities, they are inseparable in nature.
organisms both great (the Bali tiger) and small (the dusky seaside To tackle biological problems, whether building an artificial cell,
sparrow) have become extinct in recent decades. Still others are stopping the spread of infectious diseases such as HIV or malaria,
imperiled by human activities; the magnificent white rhinoceros feeding a growing population, or preserving endangered habitats
of Africa is threatened by both habitat destruction and poaching. and species, we need an integrated perspective. In decisively
Whether any rhinos will exist at the end of this century will important ways, our future welfare depends on improving our
depend almost entirely on decisions we make today. knowledge of how life works. •
CHAPTER 1 L I F E : C H E M I C A L , C E L LU L A R , A N D E VO L U T I O N A RY F O U N DAT I O N S 23
Observations are used to generate a hypothesis, a tentative When there is variation within a population of organisms, and
explanation that makes predictions that can be tested. when that variation can be inherited, the variants best able to
page 4 grow and reproduce in a particular environment will contribute
disproportionately to the next generation, leading to a change
On the basis of a hypothesis, scientists design experiments
in the population over time, or evolution. page 15
and make additional observations that test the
hypothesis. page 5 Variation can be genetic or environmental. The ultimate source
of genetic variation is mutation. page 16
A controlled experiment typically involves several groups
in which all the conditions are the same and one group Organisms show a nested pattern of similarity, with humans
where a variable is deliberately introduced in order to more similar to primates than other organisms, primates more
determine if that variable has an effect. page 5 similar to mammals, mammals more similar to vertebrates, and
so on. page 16
If a hypothesis is supported through continued
Evolution can be demonstrated by laboratory experiments.
observation and experiments over long periods of time, it
page 18
is elevated to a theory, a sound and broad explanation of
some aspect of the world. page 6
1.5 Organisms interact with one another and with their
physical environment, shaping ecological systems that
1.2 Life works according to fundamental principles
sustain life.
of chemistry and physics.
Ecology is the study of how organisms interact with one another
The living and nonliving worlds follow the same chemical
and with their physical environment in nature. page 19
rules and obey the same physical laws. page 8
These interactions are driven in part by the anatomy,
Experiments by Redi in the 1600s and Pasteur in the 1800s
physiology, and behavior of organisms, that is, the basic
demonstrated that organisms come from other organisms
features of organisms shaped by evolution. page 19
and are not spontaneously generated. page 10
Life originated on Earth about 4 billion years ago, arising 1.6 In the 21st century, humans have become major
from nonliving matter. page 11 agents in ecology and evolution.
Humans have existed for only the most recent 1/200 of 1% of
1.3 The fundamental unit of life is the cell.
life’s 4-billion-year history. page 20
The cell is the simplest biological entity that can exist
In spite of our recent arrival, our growing numbers are leaving
independently. page 12
a large ecological and evolutionary footprint. page 21
Information in a cell is stored in the form of the nucleic Solving biological problems requires an integrated
acid DNA. page 12 understanding of life, with contributions from all the fields
The central dogma describes the usual flow of information of biology, including molecular biology, cell biology, genetics,
in a cell, from DNA to RNA to protein. page 13 organismal biology, and ecology, as well as from chemistry,
physics, and engineering. page 22
The plasma membrane is the boundary that separates the
cell from its environment. page 14
4. State the first and second laws of thermodynamics and 8. Name and describe several features that determine the shape
describe how they apply to living organisms. of ecological systems.
5. Describe what it means to say that a cell is life’s functional 9. Name three ways that humans have affected life on Earth.
unit.
10. Summarize the six themes that are discussed in this chapter.
6. Describe the experimental evidence that demonstrates
that living organisms come from other living organisms.
Log in to to check your answers to the Self-
7. Explain how evolution accounts for both the unity and the Assessment questions, and to access additional learning tools.
diversity of life.
CHAPTER 1 LIFE 25
CASE 1
Deep underground, in Mexico’s Cueva de Villa Luz, the have evolved into the millions of different species that
cave walls drip with slime. The rocky surfaces are teeming populate the planet today.
with colonies of mucus-producing bacteria. No sunlight How did the first living cell arise? Scientists generally
reaches these organisms far beneath Earth’s surface. accept that life arose from nonliving materials—a
Instead, the bacteria survive by capturing energy released process called abiogenesis—and thousands of laboratory
as they oxidize hydrogen sulfide gas that exists within experiments performed over the past sixty years provide
the cave. As a by-product of that reaction, the microbes glimpses of how this might have occurred. In our modern
produce sulfuric acid, making the slime that oozes from world, the features that separate life from nonlife are
the cave walls—dubbed “snottites” by researchers—as relatively easy to discern. But Earth’s first organisms were
corrosive as battery acid. almost certainly much less complicated than even the
Snottites might be stomach turning, but they’re simplest bacteria alive today. And before those first truly
intriguing, too. The organisms that produce snottites are living things appeared, molecular systems presumably
called extremophiles because they live in places where existed that hovered somewhere between the living and
humans and most other animals cannot survive. Such the nonliving.
microorganisms may tell us something about life when All cells require an archive of information, a
Earth was young. membrane to separate the inside of the cell from its
From cave-dwelling surroundings, and the ability to gather materials and
All cells require an bacteria to 100-ton blue harness energy from the environment. In modern
whales, the diversity of life organisms, the cell’s information archive is DNA, the
archive of information, on Earth is astounding. Yet double-stranded molecule that contains the instructions
a membrane to separate all of our planet’s organisms, needed for cells to grow, differentiate, and reproduce.
living and extinct, exist on Without that molecular machinery, life as we know it
the inside of the cell branches of the same family would not exist.
from its surroundings, tree. Bacteria that produce DNA is critical, and it’s complex. Among the
snottites, swordfish, humans, organisms alive today, the smallest known genome
and the ability to hydrangeas—all evolved from belongs to the bacterium Carsonella rudii. Even that
gather materials and a single common ancestor. genome contains nearly 160,000 DNA base pairs. How
When and how life could such sophisticated molecular systems have arisen?
harness energy from the originated are some of the The likely answer to that question is: step by step.
environment. biggest questions in biology. Laboratory experiments have shown how precursors to
Earth is nearly 4.6 billion nucleic acids might have come together under chemical
years old. Chemical evidence from 3.5-billion-year-old conditions present on the young Earth. It’s exceedingly
rocks in Australia suggests that biologically driven carbon unlikely that a molecule as complex as DNA was employed
and sulfur cycles existed at the time those rocks were by the very first living cells. As you’ll see in the chapters
formed. In the eons since, the first primitive life-forms that follow, scientists have gathered evidence suggesting
25
Snottites deep
underground in a
Mexican cave. These
stalactite-like slime
formations are produced by
bacteria that gain energy by
reacting hydrogen sulfide
gas with oxygen. Source:
Kenneth Ingham Photography.
environments, scientists may uncover clues about how of life’s origins produces many more questions than
Earth’s first cells came together and functioned. answers—and not just for biologists. The mystery of
Did life arise just once? Or could it have started up life spans the fields of biology, chemistry, physics, and
and died out several times before it finally got a foothold? planetary science. Though the questions are vast, our
If, given Earth’s early chemistry, life here was inevitable, understanding of life’s origins is likely to come about the
could it have arisen elsewhere in the universe? The study same way life itself arose: step by step.
? CASE 1 QUESTIONS
Special sections in Chapters 2–8 discuss the following questions related to Case 1.
The Molecules
of Life
Core Concepts
2.1 The atom is the fundamental
unit of matter.
2.2 Atoms can combine to form
molecules linked by chemical
bonds.
2.3 Water is essential for life.
2.4 Carbon is the backbone of
organic molecules.
2.5 Organic molecules include
proteins, nucleic acids,
carbohydrates, and lipids, each
of which is built from simpler
units.
2.6 Life likely originated on Earth
by a set of chemical reactions
that gave rise to the molecules
of life.
Science Photo Library/Alamy.
29
30 SECTION 2.1 P RO P E RT I E S O F ATO M S
FIG. 2.2 Electron orbitals and energy levels (shells) for hydrogen and carbon. The orbital of an electron can be visualized as a cloud of points
that is more dense where the electron is more likely to be. The hydrogen atom contains a single orbital, in a single energy level (a and c).
The carbon atom has five orbitals, one in the first energy level and four in the second energy level (b and c).
1e-
x y y y y
Hydrogen
(1 electron)
Spherical orbitals Dumbbell-shaped orbitals Carbon (6 electrons)
be known, but it is possible to identify a region in space, called dumbbell-shaped orbitals is empty. Because a full orbital contains
an orbital, where an electron is present most of the time. For two electrons, it would take a total of four additional electrons to
example, Fig. 2.2a shows the orbital for hydrogen, which is simply completely fill all of the orbitals at this energy level. Therefore,
a sphere occupied by a single electron. Most of the time, the after the first shell, the maximum number of electrons per energy
electron is found within the space defined by the sphere, although level is eight. Fig. 2.2c shows simplified diagrams of atoms in
its exact location at any instant is unpredictable. which the highest energy level, or shell, of hydrogen, represented
The maximum number of electrons in any orbital is two. Most by the outermost circle, contains one electron, and that of carbon
atoms have more than two electrons and so have several orbitals contains four electrons.
positioned at different distances from the nucleus. These orbitals
j Quick Check 1 In the early 1900s, Ernest Rutherford produced
differ in size and shape. Electrons in orbitals close to the nucleus
a beam of very small positive particles and directed it at a thin
have less energy than do electrons in orbitals farther away, so
piece of gold foil just a few atoms thick. Most of the particles
electrons fill up orbitals close to the nucleus before occupying
passed through the foil without changing their path; very rarely, a
those farther away. Several orbitals can exist at a given energy
particle was deflected. What conclusions can you draw from this
level, or shell. The first shell consists of the spherical orbital
experiment about the structure of an atom?
shown in Fig. 2.2a.
Fig. 2.2b shows electron orbitals for carbon. Of carbon’s six
electrons, two occupy the small spherical orbital representing the Elements have recurring, or periodic, chemical
lowest energy level. The remaining four are distributed among properties.
four possible orbitals at the next highest energy level: One of these The chemical elements are often arranged in a tabular form known
four orbitals is a sphere (larger in diameter than the orbital at the as the periodic table of the elements, shown in Fig. 2.3 and
lowest energy level) and three are dumbbell-shaped. In carbon, generally credited to the nineteenth-century Russian chemist
the outermost spherical orbital has two electrons, two of the Dmitri Mendeleev. The table provides a way to organize all the
dumbbell-shaped orbitals have one electron each, and one of the chemical elements in terms of their chemical properties.
32 SECTION 2.2 MOLECULES AND CHEMICAL BONDS
1 2
FIG. 2.3 The periodic table of the
H Abundance in cells He
elements. Elements are
3 4 5 6 7 8 9 10
Li Be High Low Trace None
B C N O F Ne arranged by increasing
11 12 13 14 15 16 17 18 number of protons, the
Na Mg Al Si P S Cl Ar atomic number. The
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 elements in a column share
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr similar chemical properties.
37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
55 56 57-71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86
Cs Ba La-Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
87 88 89-103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118
Fr Ra Ac-Lr Rf Db Sg Bh Hs Mt Ds Rg Cn Uut Uuq Uup Uuh Uus Uuo
57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
89 90 91 92 93 94 95 96 97 98 99 100 101 102 103
Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
In the periodic table, the elements are indicated by their interact with other elements to form a diversity of molecules, as
chemical symbols and arranged in order of increasing atomic we will see in the next section.
number. For example, the second row of the periodic table begins
with lithium (Li) with 3 protons and ends with neon (Ne) with 10
protons. 2.2 MOLECULES AND CHEMICAL
For the first three horizontal rows in the periodic table, BONDS
elements in the same row have the same number of shells, and
so also have the same number and types of orbitals available to Atoms can combine with other atoms to form molecules, which
be filled by electrons. Across a row, therefore, electrons fill the are groups of two or more atoms attached together. that act as
shell until a full complement of electrons is reached on the right- a single unit. When two atoms form a molecule, the individual
hand side of the table. Fig. 2.4 shows the filling of the shells for atoms interact through what is called a chemical bond, a form of
elements in the second row of the periodic table. attraction between atoms that holds them together. The ability of
The elements in a vertical column are called a group or family. atoms to form bonds with other atoms explains in part why just a
Members of a group all have the same number of electrons in their few types of element can come together in many different ways to
outermost shell. For example, carbon (C) and lead (Pb) both have make a variety of molecules that can carry out diverse functions in
four electrons in their outermost shell. The number of electrons a cell. There are several ways in which atoms can interact with one
in the outermost shell determines in large part how elements another, and therefore many different types of chemical bond.
FIG. 2.4 Energy levels (shells) of row 2 of the periodic table. The complete complement of electrons in the outer shell of this row of elements
is eight.
Across the row, electrons are added until the outer shell
contains its complete complement of eight electrons.
FIG. 2.6 Four molecules. Atoms tend to combine in such a way as to complete the complement of electrons in the outer shell.
H H
The electrons in an
H H C H N H O atom’s outermost
shell are the valence
electrons.
H H H H
H
FIG. 2.8 An ionic bond. (a) Sodium chloride (salt) is formed by the attraction of two ions. (b) In solution, the ions are surrounded by water
molecules.
a.
+ +
Cl–
+ +
NaCl H2O
CHAPTER 2 THE MOLECULES OF LIFE 35
paired with an atom of very low electronegativity, the difference the same time, each oxygen atom forms new covalent bonds with
in electronegativity is so great that the electronegative atom two hydrogen atoms, forming two molecules of water. In fact,
“steals” the electron from its less electronegative partner. In this this reaction is the origin of the name “hydrogen,” which literally
case, the atom with the extra electron has a negative charge and means “water former.” The reaction releases a good deal of energy;
is a negative ion. The atom that has lost an electron has a positive it was used in the main engine of the space shuttle.
charge and is a positive ion. The two ions are not covalently bound, In biological systems, chemical reactions provide a way to
but because opposite charges attract they associate with each build and break down molecules for use by the cell, as well as to
other in what is called an ionic bond. An example of a compound harness energy, which can be held in chemical bonds (Chapter 6).
formed by the attraction of a positive ion and a negative ion is
table salt, or sodium chloride (NaCl) (Fig. 2.8a).
When sodium chloride is placed in water, the salt dissolves to 2.3 WATER: THE MEDIUM OF LIFE
form sodium ions (written as “Na1”) that have lost an electron and
so are positively charged, and chloride ions (Cl2) that have gained On Earth, all life depends on water. Indeed, life originated in water,
an electron and so are negatively charged. In solution, the two and the availability of water strongly influences the environmental
ions are pulled apart and become surrounded by water molecules: distributions of different species. Furthermore, water is the single
The negatively charged ends of water molecules are attracted to most abundant molecule in cells, so water is the medium in which
the positively charged sodium ion, and the positively charged ends the molecules of life interact. So important to life is water that, in
of other water molecules are attracted to the negatively charged the late 1990s, the National Aeronautic and Space Administration
chloride ion (Fig. 2.8b). Only as the water evaporates do the (NASA) announced that the search for extraterrestrial life would be
concentrations of Na1 and Cl2 increase to the point where the ions based on a simple strategy: Follow the water. NASA’s logic makes
join and precipitate as salt crystals. sense because, within our own solar system, Earth stands out both
for its abundance of water and the life it supports. What makes
A chemical reaction involves breaking and forming water so special as the medium of life?
chemical bonds.
The chemical bonds that link atoms in molecules can change in Water is a polar molecule.
a chemical reaction, a process by which atoms or molecules, As we saw earlier, water molecules have polar covalent bonds,
called reactants, are transformed into different molecules, called characterized by an uneven distribution of electrons. A molecule
products. During a chemical reaction, atoms keep their identity like water that has regions of positive and negative charge is
but change which atoms they are bonded to. called a polar molecule. Molecules, or even different regions of
For example, two molecules of hydrogen gas (2H2) and one the same molecule, fall into two general classes, depending on
molecule of oxygen gas (O2) can react to form two molecules of how they interact with water: hydrophilic (“water loving”) and
water (2H2O), as shown in Fig. 2.9. In this reaction, the numbers hydrophobic (“water fearing”).
of each type of atom are conserved, but their arrangement is Hydrophilic compounds are polar; they dissolve readily in
different in the reactants and the products. Specifically, the H–H water. That is, water is a good solvent, capable of dissolving many
bond in hydrogen gas and the O5O bond in oxygen are broken. At substances. Think of what happens when you stir a teaspoon of
sugar into water: The sugar seems to disappear as it dissolves. What
is happening is that the sugar molecules are dispersing through
the water and becoming separated from one another, forming a
FIG. 2.9 A chemical reaction. During a chemical reaction, atoms
solution in the watery, or aqueous, environment.
retain their identity, but their connections change as bonds
By contrast, hydrophobic compounds are nonpolar. Nonpolar
are broken and new bonds are formed.
compounds do not have regions of positive and negative charge. As
+ + + +
H H a result, they arrange themselves to minimize their contact with
H H
O O water. For example, oil molecules are hydrophobic, and when oil
– – and water are mixed, the oil molecules organize themselves into
2H2 + O2 2H2O droplets that limit the oil–water interface. This hydrophobic
Hydrogen gas Oxygen Water
effect, in which polar molecules like water exclude nonpolar
ones, drives such biological processes as the folding of proteins
H H (Chapter 4) and the formation of cell membranes (Chapter 5).
H H O O O
H H
A hydrogen bond is an interaction between a hydrogen
H H atom and an electronegative atom.
O
Because the oxygen and hydrogen atoms have slight charges,
Reactants Products water molecules orient themselves to minimize the repulsion of
36 SECTION 2.3 WAT E R : T H E M E D I U M O F L I F E
FIG. 2.11 Liquid water and ice. Hydrogen bonds create (a) a dense structure in water, and (b) a highly ordered, less dense, crystalline structure
in ice.
a. Liquid water b. Ice
CHAPTER 2 THE MOLECULES OF LIFE 37
evaporates from leaves, water is pulled upward, sometimes as high pH of blood is slightly basic, with a pH around 7.4. This value is
as 100 meters above the ground in giant sequoia and coast redwood sometimes referred to in medicine as physiological pH. Freshwater
trees, which are among the tallest trees on Earth. lakes, ponds, and rivers tend to be slightly acidic because carbon
The hydrogen bonds of water also influence how water dioxide from the air dissolves in the water and forms carbonic acid
responds to heating. Molecules are in constant motion, and this (Chapter 6).
motion increases as the temperature increases. When water is
heated, some of the energy added by heating is used to break
hydrogen bonds instead of causing more motion among the 2.4 CARBON: LIFE’S CHEMICAL
molecules, so the temperature increases less than if there were no BACKBONE
hydrogen bonding. The abundant hydrogen bonds make water more
resistant to temperature changes than other substances, a property Hydrogen and helium are far and away the most abundant
that is important for living organisms on a variety of scales. In the elements in the universe. In contrast, the solid Earth is dominated
cell, water resists temperature variations that would otherwise by silicon, oxygen, aluminum, iron, and calcium (Chapter 1). In
result from numerous biochemical reactions. On a global scale, other words, Earth is not a typical sample of the universe. Nor
the oceans minimize temperature fluctuations, stabilizing the is the cell a typical sample of the solid Earth. Fig. 2.12 shows
temperature on Earth in a range compatible with life. the relative abundance by mass of chemical elements present
In short, water is clearly the medium of life on Earth, but is in human cells after all the water has been removed. Note that
this because water is uniquely suited for life, or is it because life just four elements—carbon (C), oxygen (O), hydrogen (H), and
on Earth has adapted through time to a watery environment? nitrogen (N)—constitute 94% of the total dry mass, and that the
We don’t know the answer, but probably both explanations are most abundant element is carbon. The elemental composition
partly true. Chemists have proposed that under conditions of of human cells is typical of all cells. Human life, and all life as
high pressure and temperature, other small molecules, among we know it, is based on carbon. Carbon molecules play such
them ammonia (NH3) and some simple carbon-containing an important role in living organisms that carbon-containing
molecules, might display similar characteristics friendly to life. molecules have a special name—they are called organic
However, under the conditions that exist on Earth, water is the molecules. Their central role in life implies that there must be
only molecule uniquely suited to life. Water is a truly remarkable something very special about carbon, and there is. Carbon has
substance, and life on Earth would not be possible without it. the ability to combine with many other elements to form a wide
pH 5 –log [H1]
Oxygen (O)
30%
The pH of a solution can range from 0 to 14. Since the pH scale
is logarithmic, a difference of one pH unit corresponds to a tenfold
difference in hydrogen ion concentration. A solution is neutral
Hydrogen (H)
(pH 5 7) when the concentrations of protons (H1) and hydroxide 9%
ions (OH2) are equal. When the concentration of protons is Carbon (C)
higher than that of hydroxide ions, the pH is lower than 7 and 47%
the solution is acidic. When the concentration of protons is
Nitrogen (N)
lower than that of hydroxide ions, the pH is higher than 7 and the 8%
solution is basic. An acid can therefore be described as a molecule
that releases a proton (H1), and a base is a molecule that accepts a Phosphorus (P)
3%
proton in aqueous solution.
Sulfur (S)
Pure water has a pH of 7—that is, it is neutral, with an equal Others Potassium (K)
concentration of protons and hydroxide ions. The pH of most 1% Calcium (Ca)
cells is approximately 7 and is tightly regulated, as most chemical Sodium (Na)
Chlorine (Cl)
reactions can be carried out only in a narrow pH range. Certain Magnesium (Mg)
cellular compartments, however, have a much lower pH. The 2%
38 SECTION 2.4 C A R B O N : L I F E' S C H E M I C A L B AC K B O N E
FIG. 2.13 A carbon atom with four covalent bonds. One carbon
atom combines with four hydrogen atoms to form carbon atoms can link with each other by covalent bonds to form
methane. long chains. These chains can be branched, or two carbons at the
ends of the chain or within the chain can link to form a ring.
Chemical CH4 Among the simplest chains is ethane, shown in Fig. 2.14a.
formula Methane H
Ethane is formed when two carbon atoms become connected by
a covalent bond. In this case, the orbitals of unpaired electrons
in two carbon atoms form the covalent bond. Each carbon atom
H is also bound to three hydrogen atoms. Some more complex
Structural examples of carbon-containing molecules are shown in Fig. 2.14b,
formula H C H
C
H as both structural formulas and in simplified form.
H
H Two adjacent carbon atoms can also share two pairs of
electrons, forming a double bond, as shown in Fig. 2.15. Note
that each carbon atom has exactly four covalent bonds, but in this
The molecular orbitals of
methane point to the four case two are shared between adjacent carbon atoms. The double
corners of a tetrahedron. H bond is shorter than a single bond and is not free to rotate, so all
of the covalent bonds formed by the carbon atoms connected by
CHAPTER 2 THE MOLECULES OF LIFE 39
more atoms that have particular chemical properties on their own, functions. Since proteins consist of amino acids linked covalently
regardless of what they are attached to. Among the functional to form a chain, we need to examine the chemical features of
groups frequently encountered in biological molecules are amine amino acids to understand the diversity and versatility of proteins.
(5NH), amino (–NH2), carboxyl (–COOH), hydroxyl (–OH), ketone The general structure of an amino acid is shown in Fig. 2.17a.
(5O), phosphate (–O–PO3H2), sulfhydryl (–SH), and methyl Each amino acid contains a central carbon atom, called the
(–CH3). The nitrogen, oxygen, phosphorus, and sulfur atoms in a (alpha) carbon, covalently linked to four groups: an amino
these functional groups are more electronegative than the carbon group (–NH2; blue), a carboxyl group (–COOH; brown), a
atoms, and functional groups containing these atoms are polar. hydrogen atom (H), and an R group, or side chain, (green) that
The methyl group (–CH3), on the other hand, is nonpolar. differs from one amino acid to the next. The identity of each
Because many functional groups are polar, otherwise nonpolar amino acid is determined by the structure and composition of the
molecules containing these groups become polar and so become side chain. The side chain of the amino acid glycine is simply H, for
soluble in the cell’s aqueous environment. In other words, they example, and that of alanine is CH3. In most amino acids, the
disperse in solution throughout the cell. Moreover, because many a carbon is covalently linked to four different groups. Glycine is
functional groups are polar, they are also reactive. Notice in the the exception, since its R group is a hydrogen atom.
following sections that the reactions joining simpler molecules At the pH commonly found in a cell (pH 7.4), the amino and
into polymers usually take place between functional groups. carboxyl groups are ionized (charged), with the amino group
gaining a proton (–NH13 ; blue) and the carboxyl group losing a
Proteins are composed of amino acids. proton (–COO2; brown), as shown in Fig. 2.17b.
Proteins do much of the cell’s work. Some function as catalysts Amino acids are linked in a chain to form a protein
that accelerate the rates of chemical reactions (in which case they (Fig. 2.17c). The carbon atom in the carboxyl group of one amino
are called enzymes), and some act as structural components acid is joined to the nitrogen atom in the amino group of the next
necessary for cell shape and movement. Your body contains many by a covalent linkage called a peptide bond. In Fig. 2.17c, the chain
thousands of distinct types of protein that perform a wide range of of amino acids includes four amino acids, and the peptide bonds are
indicated in red. The formation of a peptide bond involves the loss of
a water molecule since in order to form a C–N bond, the carbon atom
of the carboxyl group must release an oxygen atom and the nitrogen
FIG. 2.17 Amino acids and peptide bonds. (a) An amino acid atom of the amino group must release two hydrogen atoms. These
contains four groups attached to a central carbon atom. can then combine to form a water molecule (H2O). The loss of
(b) In the environment of a cell, the amino group gains a a water molecule also occurs in the linking of subunits to form
proton and the carboxyl group loses a proton. (c) Peptide polymers such as nucleic acids and complex carbohydrates.
bonds link amino acids to form a protein. Cellular proteins are composed of combinations of 20 different
amino acids, each of which can be classified according to the
a. Amino acid
H chemical properties of its R group. The particular sequence, or
O
order, in which amino acids are present in a protein determines
H2N C C Carboxyl
Amino group
how it folds into its three-dimensional structure. The three-
group OH
R dimensional structure, in turn, determines the protein’s function.
carbon R group In Chapter 4, we examine how the sequence of amino acids in a
particular protein is specified and discuss how proteins fold into
b. Ionized amino acid their three-dimensional shapes.
H
O
H3N+ C C Carboxyl Nucleic acids encode genetic information in their
Amino
group R
O– group nucleotide sequence.
Nucleic acids are examples of informational molecules—that is,
carbon R group
they are large molecules that carry information in the sequence
of nucleotides that make them up. This molecular information is
c. Polypeptide chain (protein)
much like the information carried by the letters in an alphabet, but
Peptide bond
in the case of nucleic acids, the information is in chemical form.
H O H
O The nucleic acid deoxyribonucleic acid (DNA) is the
O R2 O R4
C N C C N C genetic material in all organisms. It is transmitted from parents
H NH+ C C N C C O– to offspring, and it contains the information needed to specify
R1 H R3 H
H H H H the amino acid sequence of all the proteins synthesized in an
organism. The nucleic acid ribonucleic acid (RNA) has multiple
Amino Amino Amino Amino functions; it is a key player in protein synthesis and the regulation
acid acid acid acid of gene expression.
CHAPTER 2 THE MOLECULES OF LIFE 41
H H H H
N O N O N O
3’
O H
Cytosine (C) Thymine (T) Uracil (U)
Phosphodiester -O P O
bond
b. Purine bases O
O
O NH2 In a nucleic acid, each 5’ CH2 Base
N N base is attached to
NH N either a ribose or a H H
H H
deoxyribose by the
3’
bond indicated in red.
N N NH2 N N OH H
Deoxyribose
Guanine (G) Adenine (A) sugar
42 SECTION 2.5 O RG A N I C M O L E C U L E S
a. b.
A simple sugar is also called a monosaccharide
(mono means “one”), and two simple sugars
Adenine (A) Thymine (T)
linked together by a covalent bond is called a
Guanine (G) Cytosine (C) disaccharide (di means “two”). Sucrose (C12H22O11),
or table sugar, is a disaccharide that combines
one molecule each of glucose and fructose.
c. Simple sugars combine in many ways to form
H polymers called polysaccharides (poly means
N N H O CH3 “many”) that provide long-term energy storage
Base
pairs (starch and glycogen) or structural support
N A N H N T (cellulose in plant cell walls). Long, branched
Deoxyribose
N N chains of monosaccharides are called complex
O carbohydrates.
Deoxyribose
Let’s take a closer look at monosaccharides,
Sugar– H
phosphate the simplest sugars. Monosaccharides are
N
backbone O H N unbranched carbon chains with either an
N
aldehyde (HC5O) or a ketone (C5 O) group
G N H N C (Fig. 2.22). Monosaccharides with an aldehyde
Deoxyribose
N N group are called aldoses and those with a ketone
N H O
Deoxyribose group are known as ketoses. In both types of
H monosaccharide, the other carbons each carry one
Hydrogen bond hydroxyl (–OH) group and one hydrogen (H) atom.
CHAPTER 2 THE MOLECULES OF LIFE 43
FIG. 2.24 Glycosidic bonds. Glycosidic bonds link carbohydrate molecules together; in this example they link glucose monomers together to
form the polysaccharide starch.
6
CH2OH CH2OH CH2OH CH2OH
5
C O C O C O C O
H H H H H H H H
4 H H H H
C C C C C C C C
OH H 1 OH H OH H OH H
OH
OH O O O
3C C C C C C C C
2
H OH H OH H OH H OH
Glycosidic bonds
44 SECTION 2.5 O RG A N I C M O L E C U L E S
HOW DO WE KNOW?
Miller and others conducted many variations on his original
FIG. 2.28
experiment, all with similar results. Today, many scientists
doubt that the early atmosphere had the composition found
Could the building blocks in Miller’s experimental apparatus, but amino acids and other
biologically important molecules can form in a variety of
of organic molecules have simulated atmospheric compositions. If oxygen gas (O2) is
absent and hydrogen is more common in the mixture than
been generated on the early carbon, the addition of energy generates diverse amino acids.
The absence of oxygen gas is critical since these types of
Earth? reactions cannot run to completion in modern air or seawater.
Here, however, geology supports the experiments: Chemical
analyses of Earth’s oldest sedimentary rocks indicate that,
BACKGROUND In the 1950s, Earth’s early atmosphere was
for its first 2 billion years, Earth’s surface contained little or
widely believed to have been rich in water vapor, methane,
no oxygen.
ammonia, and hydrogen gas, with no free oxygen.
Later experiments have shown that other chemical
EXPERIMENT Stanley Miller built an apparatus, shown below, reactions can generate simple sugars, the bases found
designed to simulate Earth’s early atmosphere. Then he passed a in nucleotides, and the lipids needed to form primitive
spark through the mixture to simulate lightning. membranes. Independent evidence that simple chemistry can
form the building blocks of life comes from certain meteorites,
which provide samples of the early solar system and contain
diverse amino acids, lipids, and other organic molecules.
Electrodes
Experiments show how life’s building blocks can
form macromolecules.
Spark From the preceding discussion, we have seen that life’s simple
Gas inlet
H2O, CH4, CH4, NH3 building blocks can be generated under conditions likely to
NH3, H2 have been present on the early Earth, but can these simple
Direction of units be linked together to form polymers? Once again, careful
circulation
Cold experiments have shown how polymers could have formed
water Condenser
for cooling in the conditions of the early Earth. Clay minerals that form
from volcanic rocks can bind nucleotides on their surfaces
Sampling (Fig. 2.29a). The clays provide a surface that places the
valve nucleotides near one another, making it possible for them to
join to form chains or simple strands of nucleic acid.
In a classic experiment, biochemist Leslie Orgel placed
H2O
Heating a short nucleic acid sequence into a reaction vessel and
source then added individual chemically modified nucleotides. The
nucleotides spontaneously joined into a polymer, forming the
RESULTS As the experiment proceeded, reddish material sequence complementary to the nucleic acid already present
accumulated on the walls of the flask. Analysis showed that the (Fig. 2.29b).
brown matter included a number of amino acids. Such experiments show that nucleic acids can be
synthesized experimentally from nucleotides, but until
CONCLUSION Amino acids can be generated in conditions that
recently the synthesis of nucleotides themselves presented a
mimic those of the early Earth.
formidable problem for research on the origins of life. Many
FOLLOW-UP WORK Recent analysis of the original extracts, tried to generate nucleotides from their sugar, base, and
saved by Miller, shows that the experiment actually produced phosphate components, but no one succeeded until 2009.
about 20 different amino acids, not all of them found in That year, John Sutherland and his colleagues showed that
organisms. nucleotides can be synthesized under conditions thought to
be like those on the young Earth. These chemists showed how
SOURCES Miller, S. L. 1953. “Production of Amino Acids Under Possible simple organic molecules likely to have formed in abundance
Primitive Earth Conditions.” Science 117:528–529; Johnson, A. P., et al. 2008.
“The Miller Volcanic Spark Discharge Experiment.” Science 322:404.
on the early Earth react in the presence of phosphate
molecules, yielding the long-sought nucleotides.
46
CHAPTER 2 THE MOLECULES OF LIFE 47
The number of protons determines the identity of A polar covalent bond results when two atoms do not
an atom. page 30 share electrons equally as a result of a difference in the
ability of the atoms to attract electrons, a property called
The number of protons and neutrons together determines
electronegativity. page 33
the mass of an atom. page 30
An ionic bond results from the attraction of oppositely
The number of protons versus the number of electrons
charged ions. page 34
determines the charge of an atom. page 30
Negatively charged electrons travel around the nucleus in 2.3 Water is abundant and essential for life.
regions called orbitals. page 30
Water is a polar molecule because shared electrons are
The periodic table of the elements reflects a regular distributed asymmetrically between the oxygen and
and repeating pattern in the chemical behavior of hydrogen atoms. page 35
elements. page 31 Hydrophilic molecules dissolve readily in water, whereas
hydrophobic molecules in water tend to associate with one
2.2 Atoms can combine to form molecules linked another, minimizing their contact with water. page 35
by chemical bonds.
A hydrogen bond results when a hydrogen atom covalently
Valence electrons occupy the outermost energy level bonded to an electronegative atom interacts with an
(shell) of an atom and determine the ability of an electronegative atom of another molecule. page 35
48 SSEECLT
F I-O
ANS S1E.S1S MTEH
NET S C I E N T I F I C M E T H O D
Water forms hydrogen bonds, which help explain its The tight packing of fatty acids in lipids is the result of van
high cohesion, surface tension, and resistance to rapid der Waals forces, a type of weak, noncovalent bond.
temperature change. page 36 page 44
Nucleic
Acids and
Transcription
Core Concepts
3.1 Deoxyribonucleic acid
(DNA) stores and transmits
genetic information.
3.2 DNA is a polymer of
nucleotides and forms a
double helix.
3.3 Transcription is the process
by which RNA is synthesized
from a DNA template.
3.4 The primary transcript
is processed to become
messenger RNA (mRNA).
Pasieka/Science Source.
49
50 SECTION 3.1 M A J O R B I O LO G I C A L F U N C T I O N S O F D N A
So much in biology depends on shape. Take your hand, for example. In this chapter, we examine the structure of DNA in more
You can pick up a pin, text on a smartphone, or touch your pinky to detail and show how its structure is well suited to its biological
your thumb. These activities are made possible by the coordinated function as the carrier and transmitter of genetic information.
movement of dozens of bones, muscles, nerves, and blood vessels
that give shape to your hand. The functional abilities of your hand
emerge from its structure. A causal connection between structure 3.1 MAJOR BIOLOGICAL
and function exists in many molecules, too. Proteins are a good FUNCTIONS OF DNA
example. Composed of long, linear strings of 20 different kinds
of amino acids in various combinations, each protein folds into DNA is the molecule by which hereditary information is
a specific three-dimensional shape due to chemical interactions transmitted from generation to generation. Today the role of DNA
between the amino acids along the chain. The three-dimensional is well known, but at one time hardly any biologist would have bet
structure of the protein determines its functional properties, such on it. Any poll of biologists before about 1950 would have shown
as what other molecules it can bind with, and enables the protein overwhelming support for the idea of proteins as life’s information
to carry out its job in the cell. molecule. Compared with the seemingly monotonous, featureless
Another notable example is the macromolecule structure of DNA, the three-dimensional structures of proteins are
deoxyribonucleic acid (DNA), a linear polymer of four different highly diverse. Proteins carry out most of the essential activities in
subunits. DNA molecules from all cells and organisms have a the life of a cell, and so it seemed logical to assume that they would
very similar three-dimensional structure, reflecting their play a key role in heredity, too. But while proteins do play a role in
shared ancestry. This structure, called a double helix, is heredity, they play a supporting role in looking after the DNA—
composed of two strands coiled around each other to form a rather like the way worker bees are essential in maintaining the
sort of spiral staircase. The banisters of the spiral staircase are queen bee, who alone is able to reproduce.
formed by the linear backbone of the paired strands, and the
steps are formed by the pairing of the subunits at the same level in DNA can transfer biological characteristics from one
each strand. organism to another.
The spiral-staircase structure is common to all cellular DNA The first experiments to demonstrate that molecules can transfer
molecules, and its structure gave immediate clues to its function. genetic information from one organism to another were carried
First, DNA stores information. Some of the information in out in 1928 by Frederick Griffith, working with the bacterium
DNA encodes for proteins that provide structure and do much Streptococcus pneumoniae. This organism causes a variety of
of the work of the cell. Information in DNA is called genetic infections in humans and a deadly form of pneumonia in mice. In
information, and it is organized in the form of genes, as textual the original experiments, illustrated in Fig. 3.1, Griffith studied
information is organized in the form of words. Genes can exist two strains of the bacterium, one a virulent (harmful) strain that
in different forms in different individuals, even within a single caused pneumonia and death when injected into mice, and the
species. Differences in genes can affect the shape of the hand, other a mutant, nonvirulent strain that allowed injected mice to
for example, yielding long or short fingers or extra or missing survive. When the debris of dead virulent cells was mixed with live
fingers. As we will see, it is the order of individual subunits (bases) nonvirulent cells, some of the nonvirulent cells became virulent.
of DNA that accounts for differences in genes. Genes usually Griffith concluded that some type of molecule in the debris carried
have no effect on the organism unless they are “turned on” and the genetic information for virulence, but he did not identify the
their product is made. The turning on of a gene is called gene molecule.
expression. The molecular processes that control whether Experiments carried out in 1944 by Oswald Avery, Colin
gene expression occurs at a given time or in a given cell constitute MacLeod, and Maclyn McCarty showed that the molecule
gene regulation. responsible for the conversion, or transformation, of nonvirulent
Second, DNA transmits genetic information from one cells into virulent cells is DNA (Fig. 3.2). These scientists killed
generation to the next. The transmission of genetic information virulent cells with heat, and then purified the remains to make
from parents to their offspring enables species of organisms to a solution, or preparation. They found that the preparation could
maintain their identity through time. The genetic information carry out transformation. When the preparation was treated
in DNA guides the development of the offspring, ensuring that with enzymes that destroy any trace of protein or RNA, the
parental apple trees give rise to apple seedlings and parental geese transforming ability of the preparation remained. But when the
give rise to goslings. As we will see, determining the double-helical preparation was treated with an enzyme that destroys DNA, the
structure of DNA provided one of the first hints of how genetic transforming ability was lost.
information could be faithfully copied from cell to cell, and from These experiments, along with others, established that DNA
one generation to the next. is the genetic material. Today, transformation is widely used in
HOW DO WE KNOW?
FIG.3.1 and died (Fig. 3.1d). Furthermore, when he isolated bacteria from
the dead mice, they had the appearance of the virulent strain, even
genetic material?
RESULTS
c. d.
Killed Killed
virulent virulent
BACKGROUND In the 1920s, it was not clear what biological molecule bacteria and live
nonvirulent
carries genetic information. Fred Neufeld, a German microbiologist,
bacteria
identified several strains of the bacterium Streptococcus pneumoniae,
one of which was virulent and caused death when injected into mice
(Fig. 3.1a), and another which was nonvirulent and did not cause
illness when injected into mice (Fig. 3.1b).
a. b.
Virulent Nonvirulent
bacteria bacteria
biological research and in the genetic modification of agricultural An unrepaired error in DNA replication results in a mutation,
plants and animals (Chapter 12). which is a change in the genetic information in DNA. A mutation
in DNA causes the genetic difference between virulent and
DNA molecules are copied in the process of nonvirulent Streptococcus pneumoniae. While most mutations in
replication. genes are harmful, rare favorable mutations are essential in the
DNA can serve as the genetic material because it is unique process of evolution because they allow populations of organisms
among cellular molecules in being able to specify exact copies to change through time and adapt to their environment.
of itself. This copying process, known as replication, discussed
in detail in Chapter 12, allows the genetic information from one Genetic information flows from DNA to RNA
DNA molecule to be copied into that of another DNA molecule. to protein.
Faithful replication is critical in that it allows DNA to pass genetic Biologists often say that genetic information in DNA directs the
information from cell to cell and from parent to offspring. The activities in a cell or guides the development of an organism, but
copying must reproduce the sequence of subunits almost exactly these effects of DNA are indirect. Most of the active molecules in
because, as we will see in Chapter 14, mistakes in DNA replication cells and development are proteins, including the enzymes that
that go unrepaired may be harmful to the cell or organism. convert energy into usable forms and the proteins that provide
51
FIG.3.2
H OW DO WE KNOW?
structural support for the cell. DNA acts indirectly
What is the nature of the genetic by specifying the sequence of amino acid subunits of
which each protein is composed, and this sequence in
material? turn determines the three-dimensional structure of
the protein, its chemical properties, and its biological
BACKGROUND Oswald Avery, Colin MacLeod, and Maclyn McCarty also activities.
studied virulence in pneumococcal bacteria. They recognized the significance In specifying the amino acid sequence of proteins,
of Griffith’s experiments (see Fig. 3.1) and wanted to identify the molecule DNA acts through an intermediary molecule
responsible for transforming nonvirulent bacteria into virulent ones. known as ribonucleic acid (RNA), another type of
linear polymer. As we saw in Chapter 1, the flow of
EXPERIMENT Avery, MacLeod, and McCarty prepared an extract from information from DNA to RNA to protein has come
virulent bacteria that could transform nonvirulent bacteria into virulent to be known as the central dogma of molecular
ones. This extract allowed them to perform a series of tests and controlled biology (Fig. 3.3). The central dogma states that
experiments. To identify what caused transformation, they separated the genetic information can be transferred from DNA to
extract into its macromolecular components. The transforming activity RNA to protein. Through the years, some exceptions
remained associated with the DNA; however, the DNA preparation also to this “dogma” have been discovered, including the
contained trace amounts of RNA and protein. They treated this preparation transfer of genetic information from RNA to DNA (as
with enzymes that destroyed one of the three molecules. Their hypothesis was in HIV, which causes AIDS), from RNA to RNA (as in
that transformation would not occur if they destroyed the molecule responsible replication of the genetic material of influenza virus),
for it. and even from protein to protein (in the unusual
Virulent bacteria
RESULTS
(killed) DNA is extracted case of disease-causing molecules called prions).
from heat-killed Nevertheless, the central dogma still conveys the
virulent cells, along
with trace amounts
basic idea that in most cases the flow of information
of RNA and protein. is from DNA to RNA to protein.
The first step in this process is transcription,
in which the genetic information in a molecule of
RNase Protease DNase
DNA is used as a template, or pattern, to generate a
molecule of RNA. The term “transcription” is used
because it emphasizes that both molecules use the
same language of nucleic acids. Transcription is the
first step in gene expression, which is the production
Nonvirulent Nonvirulent Nonvirulent Nonvirulent
bacteria bacteria bacteria bacteria of a functional gene product. The second step in
the readout of genetic information is translation,
in which a molecule of RNA is used as a code for
the sequence of amino acids in a protein. The term
“translation” is used to indicate a change of languages,
Virulent and Virulent and Virulent and Nonvirulent from nucleotides that make up nucleic acids to amino
nonvirulent nonvirulent nonvirulent bacteria only acids that make up proteins.
bacteria bacteria bacteria
The processes of transcription and translation
The untreated Only extracts treated with the enzyme that are regulated, meaning that they do not occur at all
extract can destroys DNA were unable to transform times in all cells, even though all cells in an individual
transform nonvirulent bacteria.
nonvirulent contain the same DNA. Genes are expressed, or
cells into “turned on,” only at certain times and places, and not
virulent cells.
expressed, or “turned off,” at other times and places.
In multicellular organisms, for instance, cells are
CONCLUSION DNA is the molecule responsible for transforming nonvirulent
specialized for certain functions, and these different
bacteria into virulent bacteria. This experiment provided a key piece of
functions depend on which genes are on and which
evidence that DNA is the genetic material.
genes are off in specific cells. Muscle cells express
FOLLOW-UP WORK These experiments were followed up by Alfred Hershey genes that encode for proteins involved in muscle
and Martha Chase, who used a different system to confirm that DNA is the contraction, but these genes are not expressed in
genetic material. skin cells or liver cells, for example. Similarly, during
SOURCE Avery, O., C. MacLeod, and M. McCarty. 1944. “Studies on the Chemical Nature development of a multicellular organism, genes may
of the Substance Inducing Transformation of Pneumococcal Types.” Journal of Experimental
Medicine 79:137–158.
52
CHAPTER 3 N U C L E I C AC I D S A N D T R A N S C R I P T I O N 53
indicated by the vertical red lines that connect the 3� carbon of one left is the 5� end. Hence, we could say the sequence in Fig. 3.7 is
nucleotide to the 5� carbon of the next nucleotide in line through AGCT, which means 5�-AGCT-3�.
the 5�-phosphate group. This C–O–P–O–C linkage is known as a
phosphodiester bond, which in DNA is a relatively stable bond Cellular DNA molecules take the form of a double
that can withstand stress like heat and substantial changes in pH helix.
that would break weaker bonds. The succession of phosphodiester To the knowledge of the chemical makeup of the nucleotides
bonds traces the backbone of the DNA strand. and their linkages in a DNA strand, Watson and Crick added
The phosphodiester linkages in a DNA strand give it polarity, results from earlier physical studies indicating that DNA is a
which means that one end differs from the other. In Fig. 3.7, the long molecule. They also relied on important information from
nucleotide at the top has a free 5� phosphate, and is known as the X-ray diffraction studies by Rosalind Franklin implying that DNA
5� end of the molecule. The nucleotide at the bottom has a free molecules form a helix with a simple repeating structure. Analysis
3� hydroxyl and is known as the 3� end. The DNA strand in of the pattern of X-rays diffracted from a crystal of a molecule can
Fig. 3.7 has the sequence of bases AGCT from top to bottom, but indicate the arrangement of atoms in the molecules.
because of strand polarity we need to specify which end is which. With these critical pieces of information in hand, Watson
For this strand of DNA, we could say that the base sequence is and Crick set out to build a model of DNA that could account for
5�-AGCT-3� or equivalently 3�-TCGA-5�. When a base sequence is the results of all previous chemical and physical experiments,
stated without specifying the 5� end, by convention the end at the using sheet metal cutouts of the bases and wire ties for the
sugar–phosphate backbone. After many false
starts and much disappointment, they finally
found a structure that worked. They realized
immediately that they had made one of the
FIG. 3.8 Structure of DNA. The DNA double helix can be shown with (a) the atoms as
most important discoveries in all of biology,
solid spheres or (b) the backbones as ribbons.
and that day, February 28, 1953, they lunched
a. b.
at the Eagle, a pub across the street from their
3’ 5’
laboratory, where Crick loudly pronounced,
“We have discovered the secret of life.” The
Sugar–
phosphate Eagle is still there in Cambridge, England, and
backbone sports on its wall a commemorative plaque
marking the table where the two ate.
Why all the fuss (and why the Nobel
Prize nine years later)? First, let’s look at the
structure, and you will see that the structure
itself tells you how DNA carries and transmits
genetic information. The Watson–Crick
34 Å = 3.4 nm Major
(10 base pairs) structure, now often called the double helix,
groove
per complete is shown in Fig. 3.8. Fig. 3.8a is a space-filling
turn
model, in which each atom is represented as
a color-coded sphere. The big surprise of the
Minor structure is that it consists of two DNA strands
Major
groove groove like those in Fig. 3.7, each wrapped around
the other in the form of a helix coiling to the
right, with the sugar–phosphate backbones
winding around the outside of the molecule
Minor and the bases pointing inward. In the double
groove
helix, there are 10 base pairs per complete turn,
and the diameter of the molecule is 2 nm, a
measurement that is hard to relate to everyday
objects, but it might help to know that the cross
section of a bundle of 100,000 DNA molecules
would be about the size of the period at the end
3’ 5’ of this sentence. The outside contours of
the twisted strands form an uneven pair of
Diameter 20 Å = 2 nm
T A G C grooves, called the major groove and the
56 SECTION 3.2 C H E M I C A L CO M P O S I T I O N A N D S T RU C T U R E O F D N A
then relieve the strain and help to preserve the 10 base pairs per
FIG. 3.11 DNA replication.The structure of the double helix gave turn in the double helix.
an important clue to how it replicates. In eukaryotic cells, most DNA molecules in the nucleus are
5’ linear, and each individual molecule forms one chromosome.
There is a packaging problem here, too, which you can appreciate
by considering that the length of the DNA molecule contained in
Parental strands serve
as the templates for a single human chromosome is roughly 6000 times greater than
3’
the daughter strands. the average diameter of the cell nucleus. Double-stranded DNA
molecules in eukaryotes are usually packaged with proteins called
3’
5’ histones, and others, to form a complex of DNA and proteins
referred to as chromatin (Chapter 13).
Parental Daughter
strands strands Histone proteins are found in all eukaryotes, and they interact
5’ 3’ with double-stranded DNA without regard to sequence. The
reason for this ability is that these proteins are evolutionarily
conserved, which means that they are very similar in sequence
5’
from one organism to the next. Conserved DNA, RNA, or protein
sequences indicate that they serve an essential function and
therefore have not changed very much over long stretches of
3’
evolutionary time. The more distantly related two organisms are
that share conserved sequences, the more highly conserved the
sequence is.
there are technical details that make the actual process more
complex. These are discussed in Chapter 12.
Cellular DNA is coiled and packaged with proteins. 3.3 RETRIEVAL OF GENETIC
The DNA molecules inside cells are highly convoluted. They have INFORMATION STORED IN
to be because DNA molecules in cells have a length far greater DNA: TRANSCRIPTION
than the diameter of the cell itself. The DNA of a bacterium
known as Mycoplasma, for example, if stretched to its full linear Although the three-dimensional structure of DNA gave important
extent would be about 1000 times longer than the diameter of clues about how DNA stores and transmits information, it left
the bacterial cell. Many of the double-stranded DNA molecules open many questions about how the genetic information in DNA
in prokaryotic cells are circular and form supercoils in which is read out to control cellular processes. In 1953, when the double
the circular molecule coils upon itself, much like what happens helix was discovered, virtually nothing was known about these
to a rubber band when you twist it between your thumb and processes. Within a few years, however, evidence was already
forefinger (Fig. 3.12). Supercoiling is caused by enzymes called accumulating that DNA carries the genetic information for proteins,
topoisomerases that cleave, partially unwind, and reattach a and that proteins are synthesized on particles called ribosomes.
DNA strand, which puts strain on the DNA double helix. Supercoils But in eukaryotes, DNA is located in the nucleus and ribosomes are
FIG. 3.12 Supercoils. A highly twisted rubber band forms coils of coils (supercoils), much as a circular DNA molecule does when it contains too
many base pairs per helical turn.
Supercoil Coil
CHAPTER 3 N U C L E I C AC I D S A N D T R A N S C R I P T I O N 59
located in the cytoplasm. There must therefore be an intermediary catalyzed the reaction more efficiently, and after only a few dozen
molecule by which the genetic information is transferred from rounds of the procedure, very efficient RNA catalysts had evolved.
the DNA in the nucleus to ribosomes in the cytoplasm, and some Experiments such as this one suggest that RNA molecules can
researchers began to suspect that this intermediary was another evolve over time and act as catalysts. Therefore, many scientists
type of nucleic acid called ribonucleic acid (RNA). believe that RNA, with its dual functions of information storage
The hypothesis of an RNA intermediary that carries genetic and catalysis, was a key molecule in the very first forms of life.
information from DNA to the ribosomes was supported by a clever If RNA played a key role in the origin of life, why do cells now
experiment carried out in 1961 by Sydney Brenner, François Jacob, use DNA for information storage and proteins to carry out other
and Matthew Meselson. They used the virus T2, which infects cells cellular processes? RNA is much less stable than DNA, and proteins
of the bacterium Escherichia coli and hijacks the cellular machinery are more versatile, so a plausible explanation is that life evolved
to produce viral proteins. The researchers found that while T2 from an RNA-based world to one in which DNA, RNA, and proteins
DNA never associates with bacterial ribosomes, the infected cells are specialized for different functions.
produce a burst of RNA molecules shortly after infection and
before viral proteins are made. This finding and others suggested RNA is a polymer of nucleotides in which the 5-carbon
that RNA retrieves the genetic information stored in DNA for sugar is ribose
use in protein synthesis. The transfer of genetic information RNA is a polymer of nucleotides linked by phosphodiester bonds
from DNA to RNA constitutes the key step of transcription in the similar to those in DNA (see Fig. 3.7). Each RNA strand therefore
central dogma of molecular biology (see Fig. 3.2). In this section, has a polarity determined by which end of the chain carries the
we examine RNA and the process of transcription. 3� hydroxyl (–OH) and which end carries the 5� phosphate. There
are a number of important differences that distinguish RNA from
DNA, however (Fig. 3.13). First, the sugar in RNA is ribose, which
? CASE 1 THE FIRST CELL: LIFE’S ORIGINS carries a hydroxyl group on the 2� carbon (highlighted in pink
What was the first nucleic acid molecule, and how in Fig. 3.13a). Hydroxyls are reactive functional groups, so the
did it arise? additional hydroxyl group on ribose in part explains why RNA is
RNA is a remarkable molecule. Like DNA, it can store information a less stable molecule than DNA. Second, the base uracil in RNA
in its sequence of nucleotides. In addition, some RNA molecules
can actually act as enzymes that facilitate chemical reactions.
Because RNA has properties of both DNA (information storage)
and proteins (enzymes), many scientists think that RNA, not FIG. 3.13 RNA. RNA differs from DNA in that (a) RNA contains
DNA, was the original information-storage molecule in the earliest the sugar ribose rather than deoxyribose and (b) the base
forms of life on Earth. This idea, sometimes called the RNA world uracil rather than thymine.
hypothesis, is supported by other evidence as well. Notably, as we a.
will see, RNA is involved in key cellular processes, including DNA OH OH
replication, transcription, and translation. Many scientists believe O O
5’ CH2 OH 5’ CH2 OH
that this involvement is a remnant of a time when RNA played a 4’ 4’
Ribose 1’ Deoxyribose 1’
more central role in life’s fundamental processes. H H H H H H H H
Ingenious experiments carried out by Jack W. Szostak and 2’ 2’
collaborators show how RNA could have evolved the ability to 3’ 3’
OH OH OH H
catalyze a simple reaction. A strand of RNA was synthesized in
the laboratory and then replicated many times to produce a large Ribose has a hydroxyl (–OH) group
population of identical RNA molecules. Next, the RNA was exposed where deoxyribose has a hydrogen (–H).
to a chemical that induced random changes in the identity of some
of the nucleotides in these molecules. These random changes were
b.
mutations that created a population of diverse RNA molecules,
Uracil has a hydrogen (–H) where
much in the way that mutation builds genetic variation in cells.
thymine has a methyl (–CH3) group.
Next, all of these RNA molecules were placed into a container,
and those RNA variants that successfully catalyzed a simple O O
reaction—cleaving a strand of RNA, for example, or joining two H CH3
strands together—were isolated, and the cycle was repeated. In H N H N
Uracil Thymine
each round of the experiment, the RNA molecules that functioned (U) (T)
best were retained, replicated, subjected to treatments that O O
induced additional mutations, and then tested for the ability N N
to catalyze the same reaction. With each generation, the RNA Ribose Deoxyribose
60 SECTION 3.3 R E T R I E VA L O F G E N E T I C I N F O R M AT I O N S TO R E D I N D N A : T R A N S C R I P T I O N
replaces thymine in DNA (Fig. 3.13b). The groups that participate j Quick Check 2 A segment of one strand of a double-stranded
in hydrogen bonding (highlighted in pink in Fig. 3.13b) are DNA molecule has the sequence 5�-ACTTTCAGCGAT-3�. What
identical so that uracil pairs with adenine (U–A) just as thymine is the sequence of an RNA molecule synthesized from this DNA
pairs with adenine (T–A). Third, while the 5� end of a DNA strand template?
is typically a monophosphate, the 5� end of an RNA molecule is
typically a triphosphate. Transcription starts at a promoter and ends at a
Two other features that distinguish RNA from DNA are terminator.
physical rather than chemical. One is that RNA molecules are A long DNA molecule typically contains thousands of genes, most
usually much shorter than DNA molecules. A typical RNA of them coding for proteins or RNA molecules with specialized
molecule used in protein synthesis consists of a few thousand functions, and hence thousands of different transcripts are
nucleotides, whereas a typical DNA molecule consists of millions produced. For example, the DNA molecule in the bacterium
or tens of millions of nucleotides. The other major distinction is E. coli has about 4 million base pairs and produces about 4000 RNA
that most RNA molecules in the cell are single stranded, whereas transcripts, most of which code for proteins. A typical map of a
DNA molecules, as we saw, are double stranded. Single-stranded small part of a long DNA molecule is shown in Fig. 3.15. Each green
RNA molecules often form complex three-dimensional structures segment indicates the position where a transcription is initiated,
by folding back upon themselves, which enhances their stability. and each purple segment indicates the position where it ends.
The green segments are promoters, regions of typically a
In transcription, DNA is used as a template to make few hundred base pairs where RNA polymerase and associated
complementary RNA. proteins bind to the DNA duplex. Many eukaryotic and archaeal
Conceptually, the process of transcription is straightforward. As a promoters contain a sequence similar to 5�-TATAAA-3�, which
region of the DNA duplex unwinds, one strand is used as a template is known as a TATA box because the TATA sequence is usually
for the synthesis of an RNA transcript that is complementary present. The first nucleotide to be transcribed is usually positioned
in sequence to the template according to the base-pairing rules, about 25 base pairs from the TATA box, and transcription takes
except that the transcript contains U (uracil) where the template place as the RNA polymerase moves along the template strand in
has an A (Fig. 3.14). The transcript is produced by polymerization the 3�-to-5� direction.
of ribonucleoside triphosphates. The enzyme that carries out the Transcription continues until the RNA polymerase encounters
polymerization is known as RNA polymerase, which acts by adding a sequence known as a terminator (shown in purple in Fig. 3.15).
successive nucleotides to the 3� end of the growing transcript Transcription stops at the terminator, and the transcript is released.
(Fig. 3.14). Only the template strand of DNA is transcribed. Its A long DNA molecule contains the genetic information for
partner, called the nontemplate strand, is not transcribed. hundreds or thousands of genes. For any one gene, usually only one
It is important to keep in mind the direction of growth of the DNA strand is transcribed; however, different genes in the same
RNA transcript and the direction that the DNA template is read. double-stranded DNA molecule can be transcribed from opposite
All nucleic acids are synthesized by addition of nucleotides to the strands. Which strand is transcribed depends on the position of
3� end. That is, they grow in a 5�-to-3� direction, also described the promoter. As shown in Fig. 3.15, promoters in opposite strands
simply as the 3� direction. Just like two strands of DNA in a double result in transcription occurring in opposite directions. The DNA
helix, the DNA template and the RNA strand transcribed from it strand that contains the promoter sequence matters because, as
are antiparallel, meaning the DNA template runs in the opposite noted earlier, transcription can proceed only by successive addition
direction from the RNA (Fig. 3.14). of nucleotides to the 3� end of the transcript.
Transcription does not take place indiscriminately
from promoters but is a regulated process. For genes
called housekeeping genes, whose products are
FIG. 3.14 Transcription.The DNA double helix unwinds for transcription, and
needed at all times in all cells, transcription takes place
usually only one strand, the template strand, is transcribed.
continually. But most genes are transcribed only at
Template strand certain times, under certain conditions, or in certain
5’ cell types. In E. coli, for example, the genes that encode
G A A T C C G T C A C G T T G proteins needed to utilize the sugar lactose (milk sugar)
ACG
G T T A UGCC U U A G G C A G U G are transcribed only when lactose is present in the
3’ C G AA U
A C AG 3’ environment. For such genes, regulation of transcription
T AAC GCC A T TC G T
A T T GC GGT AA GC A T G 5’ RNA transcript often depends on whether the RNA polymerase and
T CG
5’ CC associated proteins are able to bind with the promoter
AA
T TGC
CT T AGG CAG TGC AAC (Chapter 19).
3’ In bacteria, promoter recognition is mediated by
Nontemplate strand a protein called sigma factor, which associates with
CHAPTER 3 N U C L E I C AC I D S A N D T R A N S C R I P T I O N 61
FIG. 3.16 The eukaryotic transcription complex, composed of many different proteins.
Transcriptional
Enhancer sequences start site
Promoter
3’ 5’ DNA
5’ 3’
5’
3’
Promoter
RNA polymerase
complex (Pol II)
Promoter region
62 SECTION 3.3 R E T R I E VA L O F G E N E T I C I N F O R M AT I O N S TO R E D I N D N A : T R A N S C R I P T I O N
FIG. 3.19 The RNA polymerase complex in prokaryotes. This 3.4 FATE OF THE RNA
molecular machine has channels for DNA input and PRIMARY TRANSCRIPT
output, nucleotide input, and RNA output, and features
that disrupt the DNA double helix, stabilize the RNA– The RNA transcript that comes off the template DNA strand is
DNA duplex, and allow the DNA double helix to re-form. known as the primary transcript, and it contains the genetic
information of the gene that was transcribed. For protein-coding
genes, this means that the primary transcript includes the
information needed to direct the ribosome to produce the protein
RNA transcript corresponding to the gene (Chapter 4). The RNA molecule that
combines with the ribosome to direct protein synthesis is known
RNA polymerase
as the messenger RNA (mRNA) because it serves to carry the
acts here
genetic “message” (information) from the DNA to the ribosome.
As we will see in this section, there is a major difference between
prokaryotes and eukaryotes in the manner in which the primary
transcript relates to the mRNA. We will also see that some
DNA already
transcribed Incoming RNA genes do not code for proteins, but for RNA molecules that have
nucleotides functions of their own.
RNA displaced and Messenger RNA carries information for the synthesis
DNA strands rejoin DNA still to
DNA strands be transcribed of a specific protein.
separated In prokaryotes, the relation between the primary transcript and
the mRNA is as simple as can be: The primary transcript is the
mRNA. Even as the 3� end of the primary transcript is still being
synthesized, ribosomes bind with special sequences near its
5� end and begin the process of protein synthesis (Fig. 3.20). This
shown at the lower right in Fig. 3.18, which also has a high-energy intimate connection between transcription and translation can
phosphate bond that is cleaved by another enzyme. Cleavage of take place because prokaryotes have no nuclear envelope
the pyrophosphate molecule makes the polymerization reaction to spatially separate transcription from translation; the two
irreversible, and the next ribonucleoside triphosphate that processes are coupled, which means that they are connected in
complements the template is brought into line. space and time.
the lariat is released (Fig. 3.23d). The lariat making up the intron is
FIG. 3.23 RNA splicing. quickly broken down into its constituent nucleotides.
a. About 90% of all human genes contain at least one intron.
Primary Exon Intron Although most genes contain 6 to 9 introns, the largest number is
transcript 147, found in a muscle gene. Most introns are just a few thousand
nucleotides in length, but about 10% are longer than 10,000
Spliceosome components nucleotides. The presence of multiple introns in most genes allows
b.
for a process known as alternative splicing, in which primary
transcripts from the same gene can be spliced in different ways to
5’ 3’ yield different mRNAs and therefore different protein products
A site within the intron (Fig. 3.24). More than 80% of human genes are alternatively
attacks the 5’ splice site. spliced. In most cases, the alternatively spliced forms differ in
whether a particular exon is or is not removed from the primary
c. transcript along with its flanking introns. Alternative splicing
allows the same transcript to be processed in diverse ways to
produce mRNA molecules with different combinations of exons
coding for different proteins.
eukaryotes often contain regions of protein-coding sequence, FIG. 3.24 Alternative splicing. A single primary transcript can be
called exons, interspersed with noncoding regions called introns. spliced in different ways.
The third type of modification of the primary transcript is the
removal of the noncoding introns (see Fig. 3.21). The process of Intron Exon
Gene
intron removal is known as RNA splicing, which is catalyzed by a
complex of RNA and protein known as the spliceosome.
The mechanism of splicing is outlined in Fig. 3.23. In the first
step, the spliceosome brings a specific sequence within the intron Primary
transcription E1 E2 E3 E4
into proximity with the 5� end of the intron, at a site known as
the 5� splice site (Fig. 3.23a). The proximity enables a reaction that
cuts the RNA at the 5� splice site, and the cleaved end of the intron Alternative splicing
connects back on itself forming a loop and tail called a lariat
(Fig. 3.23b). In the next step, the spliceosome brings the E3 E4
mRNA
5� splice site close to the splice site at the 3� end of the intron. The E1 E2 E4 E1 E2 E3
5� splice site attacks the 3� splice site (Fig. 3.23c), cleaving the bond
that holds the lariat on the transcript and attaching the ends of the
exons to each other. The result is that the exons are connected and Protein A Protein B
66 CO R E CO N C E P T S S U M M A RY
Pol II. These primary transcripts undergo different types of RNA * Small, regulatory RNA molecules that can inhibit translation
processing, and their processed forms include such important or cause destruction of an RNA transcript. Two major types
noncoding RNA types as: of small regulatory RNA are known as microRNA (miRNA)
and small interfering RNA (siRNA).
* Ribosomal RNA (rRNA), found in all ribosomes that aid in
translation. In eukaryotic cells, the genes and transcripts
By far, the most abundant transcripts in mammalian cells
for ribosomal RNA are concentrated in the nucleolus, a
are those for ribosomal RNA and transfer RNA. In a typical
distinct, dense, non–membrane-bound spherical structure
mammalian cell, about 80% of all of the RNA consists of ribosomal
observed within the nucleus.
RNA, and another approximately 10% consists of transfer RNA.
* Transfer RNA (tRNA) that carries individual amino acids for Why are these types of RNA so abundant? The answer is that they
use in translation. are needed in large amounts to synthesize the proteins encoded
in the messenger RNA. The roles of mRNA, tRNA, and rRNA in
* Small nuclear RNA (snRNA), found in eukaryotes and
involved in splicing, polyadenylation, and other processes in
protein synthesis are discussed in the next chapter. •
the nucleus.
Core Concepts Summary Cellular DNA molecules consist of a helical spiral of two
paired, antiparallel strands called a double helix. page 55
3.1 Deoxyribonucleic acid (DNA) stores and
In a DNA double helix, A pairs with T, and G pairs with C.
transmits genetic information.
page 56
Experiments carried out by Griffith in 1928 demonstrated
The structure of DNA relates to its function. Information is
that bacteria can transmit genetic information from one
coded in the sequence of bases, and the structure suggests
strain to another. page50
a mechanism for replication, in which each parental strand
Experiments performed by Avery, MacLeod, and McCarty serves as a template for a daughter strand. page 56
in 1944 showed that DNA is the molecule that transmits
DNA in eukaryotic cells is packaged with evolutionarily
genetic information. page 50
conserved proteins called histones. page 58
DNA is copied in the process of replication. page 51
Translation
and Protein
Structure
Core Concepts
4.1 Proteins are linear polymers of
amino acids that form three-
dimensional structures with
specific functions.
4.2 Translation is the process in
which the sequence of bases in
messenger RNA specifies the
order of successive amino acids
in a newly synthesized protein.
4.3 Proteins evolve through
mutation and selection and by
combining functional units.
Pasieka/SPL/Getty Images.
69
70 SECTION 4.1 M O L E C U L A R S T RU C T U R E O F P ROT E I N S
Hardly anything happens in the life of a cell that does not require Amino acids differ in their side chains.
proteins. They are the most versatile of macromolecules, each The general structure of an amino acid was discussed in Chapter 2
with its own built-in ability to carry out a cellular function. Some and is shown again in Fig. 4.1. It consists of a central carbon atom,
proteins aggregate to form relatively stiff filaments that help define called the a (alpha) carbon, connected by covalent bonds to four
the cell’s shape and hold organelles in position. Others span the different chemical groups (Fig. 4.1a): an amino group (–NH2,
cell membrane and form channels or pores through which ions and shown in dark blue), a carboxyl group (–COOH, shown in
small molecules can move. Many others are enzymes that catalyze brown), a hydrogen atom (–H, shown in light blue), and a variable
the thousands of chemical reactions needed to maintain life. Still side chain or R group (shown in green). In the environment of a
others are signaling proteins that enable cells to coordinate their cell, where the pH is in the range 7.35–7.45 (called physiological
internal activities or to communicate with other cells. pH), the amino group gains a proton to become –NH13 and the
Want to see some proteins? Look at the white of an egg. Apart carboxyl group loses a proton to become –COO2 (Fig. 4.1b). The
from the 90% or so that is water, most of what you see is protein. four covalent bonds from the a carbon are at equal angles. As a
The predominant type of protein is ovalbumin. Easy to obtain in result, an amino acid forms a tetrahedron, a pyramid with four
large quantities, ovalbumin was one of the first proteins studied triangular faces (Fig. 4.1c).
by the scientific method (Chapter 1). In the 1830s, ovalbumin The R groups of the amino acids differ from one amino acid
was shown to consist largely of carbon, hydrogen, nitrogen, and to the next. They are what make the “letters” of the amino acid
oxygen. Each molecule of ovalbumin was estimated to contain at “alphabet” distinct from one another. Just as letters differ in their
least 400 carbon atoms. Leading chemists of the time scoffed at shapes and sounds—vowels like E, I, and O and hard consonants
this number, believing that no organic molecule could possibly like B, P, and T—amino acids differ in their chemical and physical
be so large. Little did they know: The number of carbon atoms in properties.
ovalbumin is actually closer to 2000 than to 400! The chemical structures of the 20 amino acids commonly
The reason that proteins can be such large organic molecules found in proteins are shown in Fig. 4.2. The R groups (shown
began to become clear only about a hundred years ago, when in green) are chemically diverse and are grouped according to
scientists hypothesized that proteins are polymers (large their properties, with a particular emphasis on whether they
molecules made up of repeated subunits). Now we know that are hydrophobic or hydrophilic, or have special characteristics
proteins are linear polymers of any combination of 20 amino that might affect a protein’s structure. These properties strongly
acids, each of which differs from the others in its chemical
characteristics. In size, ovalbumin is actually an average protein,
consisting of a chain of 385 amino acids.
In Chapter 3, we discussed how genetic information flows FIG. 4.1 Structure of an amino acid. The central carbon atom is
from the sequence of bases of DNA into the sequence of bases attached to an amino group, a carboxyl group, an R group
in a transcript of RNA. For protein-coding genes, the transcript or side chain, and a hydrogen atom.
is processed into messenger RNA (mRNA). In this chapter, we
a. H b. H
examine how amino acid polymers are assembled by ribosomes
by means of a template of messenger RNA and transfer RNAs.
carbon
We also discuss how the amino acid sequences of proteins
C C
help determine their three-dimensional structures and diverse Amino +
HN H3N
group 2 COOH COO–
chemical activities, as well as how proteins change through
evolutionary time. Carboxyl
R R
group
c.
4.1 MOLECULAR STRUCTURE
OF PROTEINS
If you think of a protein as analogous to a word in the English
language, then the amino acids are like letters. The comparison
is not altogether fanciful, as there are about as many amino acids
in proteins as letters in the alphabet, and the order of both amino
acids and letters is important. For example, the word PROTEIN has
the same letters as POINTER, but the two words have completely The corners of this structure
different meanings. Similarly, the exact order of amino acids in a form a tetrahedral shape
around the carbon.
protein determines the protein’s shape and function.
CHAPTER 4 T R A N S L AT I O N A N D P ROT E I N S T RU C T U R E 71
Polar
– – +
+H N
3 CH COO +H N
3 CH COO H3N CH COO– +H
3N CH COO
– +H N
3 CH COO
–
Acidic
COO–
+H N +H N –
CH CH COO
SPECIAL AMINO ACIDS 3 3
CH2 CH2
COO– –
+H N
3 CH HN CH COO +H N
3 CH COO–
C CH2
H H2C CH2 CH2 –
O O
C
CH2
SH –
O O
Glycine Proline Cysteine Aspartic acid Glutamic acid
(Gly, G) (Pro, P) (Cys, C) (Asp, D) (Glu, E)
influence how a polypeptide folds, and hence the three- create temporary charges in the interacting molecules,
dimensional shape of the protein. which are then attracted to each other. The tendency for
Hydrophobic amino acids are those that do not readily interact hydrophilic water molecules to interact with each other and for
with water or form hydrogen bonds. Most hydrophobic amino hydrophobic molecules to interact with each other is the very
acids have nonpolar R groups composed of hydrocarbon chains or same tendency that leads to the formation of oil droplets in water.
uncharged carbon rings. Because water molecules in the cell form This is also the reason why most hydrophobic amino acids tend to
hydrogen bonds with each other instead of with the hydrophobic be buried in the interior of folded proteins, where they are kept
R groups, the hydrophobic R groups tend to aggregate with each away from water.
other. Their aggregation is also stabilized by weak van der Waals Amino acids with polar R groups have a permanent charge
forces (Chapter 2), in which asymmetries in electron distribution separation, in which one end of the R group is slightly more
72 SECTION 4.1 M O L E C U L A R S T RU C T U R E O F P ROT E I N S
FIG. 4.5 the proteins. A film or other detector records the pattern as a series
of spots, which is known as a diffraction pattern. The locations
What are the shapes of and intensities of these spots can be used to infer the position and
arrangement of the atoms in the molecule.
proteins? RESULTS The X-ray diffraction pattern for hemoglobin looks like
this:
BACKGROUND The three-dimensional shapes of proteins can be
Source: Courtesy
determined by X-ray crystallography. One of the pioneers in this of William E. From this two-
Royer, University of dimensional pattern,
field was Dorothy Crowfoot Hodgkin, who used this technique Massachusetts Medical researchers can use
to define the structures of cholesterol, vitamin B12, penicillin, and School and Vukica mathematical methods
Srajer, BioCARS, to determine the three-
insulin. She was awarded the Nobel Prize in Chemistry in 1964 for Center for Advanced dimensional shape of
her early work. Max Perutz and John Kendrew shared the Nobel Radiation Sources, The
the protein.
University of Chicago.
Prize in Chemistry in 1962 for defining the structures of myoglobin
and hemoglobin using this method.
FOLLOW-UP WORK Linus Pauling and Robert Corey used X-ray
METHOD X-ray crystallography can be used to determine the
crystallography to determine two types of secondary structures
shape of proteins, as well as other types of molecules. The first
commonly found in proteins—the a helix and the b sheet. Today,
step, which can be challenging, is to make a crystal of the protein
this technique is a common method for determining the shape of
molecules. A crystal is a solid structure in which the atoms of a
proteins.
protein (or any other molecule) are in an ordered and repeating
pattern in three dimensions. Then X-rays are aimed at the crystal
SOURCES Crowfoot, D. 1935. “X-Ray Single Crystal Photographs of Insulin.”
while it is rotated. Some X-rays pass through the crystal, while Nature 135:591–592; Kendrew, J. C., et al. 1958. “A Three-Dimensional Model of
others are scattered in different directions when they hit atoms of the Myoglobin Molecule Obtained by X-Ray Analysis.” Nature 181:662–666.
localized regions of the polypeptide chain to fold. This localized positioned in the folded protein, and how it might interact with
folding is a major contributor to the secondary structure of the other molecules.
protein. In the early 1950s, American structural biologists Linus The other secondary structure that Pauling and Corey found is
Pauling and Robert Corey used X-ray crystallography to study the the b sheet, depicted in Fig. 4.7. In a b sheet, the polypeptide folds
structure of proteins. This technique was pioneered by British back and forth on itself, forming a pleated sheet that is stabilized by
biochemists Dorothy Crowfoot Hodgkin, Max Perutz, and John hydrogen bonds between carbonyl groups in one chain and amide
Kendrew, among others (Fig. 4.5). Pauling and Corey studied groups in the other chain across the way (dashed lines). The R groups
crystals of highly purified proteins and discovered that two types project alternately above and below the plane of the b sheet. b sheets
of secondary structure are found in many different proteins. typically consist of 4 to 10 polypeptide chains aligned side by side,
These are the a (alpha) helix and the b (beta) sheet. Both these with the amides in each chain hydrogen-bonded to the carbonyls on
secondary structures are stabilized by hydrogen bonding along the either side (except for those at the ends of each strand).
polypeptide backbone. b sheets are typically denoted by broad arrows, where the
In a helices, like the one shown in Fig. 4.6, the polypeptide direction of the arrow runs from the amino end of the polypeptide
backbone is twisted tightly in a right-handed coil with 3.6 amino segment to the carboxyl end. In Fig. 4.7, the arrows run in
acids per complete turn. The helix is stabilized by hydrogen bonds opposite directions, and the polypeptide chains are said to be
that form between each amino acid’s carbonyl group (C5O) and antiparallel. b sheets can also be formed by hydrogen bonding
the amide group (N–H) four residues ahead in the sequence, as between polypeptide chains that are parallel (pointing in the same
indicated by the dashed lines in Fig. 4.6. Note that the R groups direction). However, the antiparallel configuration is more stable
project outward from the a helix. The chemical properties of because the carbonyl and amide groups are more favorably aligned
the projecting R groups largely determine where the a helix is for hydrogen bonding.
74
CHAPTER 4 T R A N S L AT I O N A N D P ROT E I N S T RU C T U R E 75
FIG. 4.7 A β sheet. Hydrogen bonds between neighboring strands stabilize the structure.
␣ carbon
H O Carbonyl group (C=O)
Amide group (N–H)
O H R group (side chain)
H atom
Single bond
Peptide bond
Hydrogen bond
76 SECTION 4.1 M O L E C U L A R S T RU C T U R E O F P ROT E I N S
FIG. 4.8 Three ways of showing the structure of the protein tubulin: (a) ball-and-stick model; (b) ribbon model; (c) space-filling model.
a. b. c.
the inside—that enables the protein to serve as structural support, Polypeptide subunits can come together to form
membrane channel, enzyme, or signaling molecule. Fig. 4.9 shows quaternary structures.
the tertiary structure of a bacterial protein that contains a pocket Although many proteins are complete and fully functional as a
in the center in which certain R groups can form hydrogen bonds single polypeptide chain with a tertiary structure, there are many
with a specific small molecule and hold it in place. other proteins that are composed of two or more polypeptide
The principle that structure determines function can be chains or subunits with a tertiary structure that come together
demonstrated by many observations. For example, most proteins to form a higher-order quaternary structure. In the case of a
can be unfolded, or denatured, by chemical treatment or high multi-subunit protein, the activity of the complex depends on the
temperature that disrupts the hydrogen and ionic bonds holding quaternary structure formed by the combination of the various
the tertiary structure together. Under these conditions, the tertiary structures.
proteins lose their functional activity. Similarly, mutant proteins In a protein with quaternary structure, the polypeptide
containing an amino acid that prevents proper folding are often subunits may be identical or different (Fig. 4.10). Fig. 4.10a
inactive or don’t function properly. shows an example of a protein produced by HIV that consists of
two identical polypeptide subunits. By contrast, many proteins,
j Quick Check 1 A mutation leads to a change in one amino acid in
such as hemoglobin (shown in Fig. 410b), are composed of
a protein. The result is that the protein no longer functions properly.
different subunits. In either case, the subunits can influence each
How is this possible?
other in subtle ways and influence their function. For example,
the hemoglobin in red blood cells that carries oxygen has four
subunits. When one of these binds oxygen, a slight change in its
structure is transmitted to the other subunits, making it easier for
FIG. 4.9 Tertiary structure determines function. This bacterial
them to take up oxygen. In this way, oxygen transport from the
protein has a cavity that can bind with a small molecule
lungs to the tissues is improved.
(shown as a ball-and-stick model in the center).
FIG. 4.10 Quaternary structure. Polypeptide units of proteins may be identical, as in (a) an enzyme from HIV, or different, as in (b) hemoglobin.
a. b.
Cells have evolved proteins called chaperones that help shown in Fig. 4.11. What are these needed components? First,
protect slow-folding or denatured proteins until they can attain the cell needs ribosomes, which are complex structures of RNA
their proper three-dimensional structure. Chaperones bind with and protein that bind with mRNA and are the site of translation.
hydrophobic groups and nonpolar R groups to shield them from In prokaryotes, translation occurs as soon as the mRNA comes off
inappropriate aggregation, and in repeated cycles of binding and the DNA template. In eukaryotes, the processes of transcription
release they give the polypeptide time to find its correct shape. and translation are physically separated: Transcription takes
place in the nucleus, and translation takes place in the cytoplasm.
In both eukaryotes and prokaryotes, the ribosome consists
of a small subunit and a large subunit, each composed of 1 to
4.2 TRANSLATION: HOW PROTEINS 3 types of ribosomal RNA and 20 to 50 types of ribosomal protein.
ARE SYNTHESIZED
The three-dimensional structure of a protein determines what
it can do and how it works, and the immense diversity in the
tertiary and quaternary structures among proteins explains FIG. 4.11 The central dogma, showing how information flows
their wide range of functions in cellular processes. Yet it is the from DNA to RNA to protein. Note the large number of
sequence of amino acids along a polypeptide chain—its primary cellular components required for translation.
structure—that governs how the molecule folds into a stable
Messenger RNA
three-dimensional configuration. How is the sequence of amino (mRNA)
DNA
acids specified? It is specified by the sequence of nucleotides in the
DNA, in coded form. The decoding of the information takes Initiation factors
Transcription
place according to the central dogma of molecular biology, Elongation factors
which defines information flow in a cell from DNA to RNA to
Release factors
protein (Fig. 4.11). In transcription, the sequence of bases along RNA
part of a DNA strand is used as a template in the synthesis of Aminoacyl
a complementary sequence of bases in a molecule of RNA, as Translation tRNA
synthetases
described in Chapter 3. In translation, the sequence of bases in Met
Arg
specify the order in which successive amino acids are added to a (tRNA) U
U A C C
A
UC U
The large subunit includes FIG. 4.13 Transfer RNA structure depicted in (a) a cloverleaf
three binding sites for
tRNAs.
configuration and (b) a more realistic three-
dimensional structure.
a. 3’ end
Amino acid
5’ end A attachment
Eukaryotic ribosomes are larger than prokaryotic ribosomes. C
C site
As indicated in Fig. 4.12, the large subunit of the ribosome
A
includes three binding sites for molecules of transfer RNA, which GC
CG
are called the A (aminoacyl) site, the P (peptidyl) site, and the GC
GU T⌿C loop
E (exit) site. AU
DHU loop UA
A major role of the ribosome is to ensure that, when the
UA
mRNA is in place on the ribosome, the sequence in the mRNA U
GACAC
coding for amino acids is read in successive, non-overlapping CUC A UGUG
GAGC
groups of three nucleotides, much as you would read the sentence
THEBIGBOYSAWTHEBADMANRUN CG
CG
AU
Each non-overlapping group of three adjacent nucleotides (like G
A
THE or BIG or BOY in our sentence analogy) constitutes a codon,
and each codon in the mRNA codes for a single amino acid in the Anticodon loop
polypeptide chain.
In the example above, it is clear that the sentence begins with
THE. However, in a long linear mRNA molecule, the ribosome Anticodon
could begin at any nucleotide. As an analogy, if we knew that the
letters THE were the start of the phrase, then we would know b.
FIG. 4.14 Function of aminoacyl tRNA synthetase enzymes. Aminoacyl tRNA synthetases
attach specific amino acids to tRNAs and are therefore responsible for translating base in the anticodon because, as noted in
the codon sequence in an mRNA into an amino acid sequence in a protein. Chapter 3, nucleic acid strands that undergo
Aminoacyl
base pairing must be antiparallel.
Val
tRNA
Gln Ile synthetase The genetic code shows the
Free amino acids
Each aminoacyl correspondence between codons
tRNA synthetase and amino acids.
Ile binds to one Fig. 4.15 shows how the codon AUG
uncharged tRNA
and its specifies the amino acid methionine (Met)
corresponding by base pairing with the anticodon of a
C A amino acid.
C charged tRNA, denoted tRNAMet. Most
U A G
GUU G codons specify an amino acid according to a
A
Uncharged tRNA U genetic code. This code is sometimes called
the “standard” genetic code because, while
it is used by almost all cells, some minor
Gln
differences are found in a few organisms as
Val There is a specific
enzyme for each well as in mitochondria.
amino acid. The codon at which translation begins is
GUU called the initiation codon, and it is coded by
AUG, which specifies Met. The polypeptide
C A C
is synthesized from the amino end to the
Ile
carboxyl end, and so Met forms the amino
The enzyme attaches end of any polypeptide being synthesized;
the amino acid to the
3’ end of the tRNA. however, in many cases the Met is
U A G cleaved off by an enzyme after synthesis
Charged tRNA is complete. The AUG codon is also used
80 SECTION 4.2 T R A N S L AT I O N : H O W P ROT E I N S A R E S Y N T H E S I Z E D
to specify the incorporation of Met at internal sites within the codon, and the amino acid on that tRNA is attached to the
polypeptide chain. growing chain to become the new carboxyl end of the polypeptide
As is apparent in Fig. 4.15, the AUG codon that initiated chain. This process continues until one of three “stop” codons is
translation is preceded by a region in the mRNA that is not encountered: UAA, UAG, or UGA. (The stop codons are also called
translated. The position of the initiator AUG codon in the termination codons or sometimes nonsense codons.) At this point,
mRNA establishes the reading frame that determines how the the polypeptide is finished and released into the cytosol.
downstream codons (those following the AUG) are to be read. The standard genetic code was deciphered in the 1960s by a
Once the initial Met creates the amino end of a new combination of techniques, but among the most ingenious were
polypeptide chain, the downstream codons are read one by one in chemical methods for making synthetic RNAs of known sequence
non-overlapping groups of three bases. At each step, the ribosome by American biochemist Har Gobind Khorana and his colleagues.
binds to a tRNA with an anticodon that can base pair with the This experiment is illustrated in Fig. 4.16.
HOW DO WE KNOW?
CHAPTER 3 N U C L E I C AC I D S A N D T R A N S C R I P T I O N 8 0
FIG. 4.16
deciphered? Ser Leu Ser Leu Ser Leu Ser Leu Ser Leu
BACKGROUND The genetic code is the correspondence between CONCLUSION Here again there are three reading frames, but each
three-letter nucleotide codons in RNA and amino acids in a of them has alternating UCU and CUC codons. The researchers
protein. American biochemist Har Gobind Khorana performed key could not deduce from this result whether UCU corresponds to Ser
experiments that helped to crack the code. For this work he shared and CUC to Leu or the other way around; the correct assignment
the Nobel Prize in Physiology or Medicine in 1968 with Robert W. came from experiments using other synthetic mRNA molecules.
Holley and Marshall E. Nirenberg. EXPERIMENT 3 AND RESULTS When a synthetic mRNA
METHOD Khorana and his group made RNAs of known sequence. with repeating UCA was used, three different polypeptides
They then added these synthetic RNAs to a solution containing all were produced—polyserine (Ser), polyhistidine (His), and
of the other components needed for translation. By adjusting the polyisoleucine (Ile).
concentration of magnesium and other factors, the researchers c.
could get the ribosome to initiate synthesis with any codon, even if 5’ – U C A U C A U C A U C A U C A U C A U C A U C A U C A U C A – 3’
not AUG.
Ser Ser Ser Ser Ser Ser Ser Ser Ser Ser
EXPERIMENT 1 AND RESULTS When a synthetic poly(U)
was used as the mRNA, the resulting polypeptide was 5’ – U C A U C A U C A U C A U C A U C A U C A U C A U C A U C A – 3’
polyphenylalanine (Phe–Phe–Phe…):
His His His His His His His His His
a.
5’ – U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U – 3’
5’ – U C A U C A U C A U C A U C A U C A U C A U C A U C A U C A – 3’
Phe Phe Phe Phe Phe Phe Phe Phe Phe Phe
Ile Ile Ile Ile Ile Ile Ile Ile Ile
alternating U and C was used, the resulting polypeptide had Code.” In Nobel Lectures, Physiology or Medicine 1963–1970. Amsterdam:
Elsevier.
alternating serine (Ser) and leucine (Leu):
CHAPTER 4 T R A N S L AT I O N A N D P ROT E I N S T RU C T U R E 81
U C A G
The standard genetic code shown in Table 4.1 has 20 amino j Quick Check 2 What polypeptide sequences would you expect
acids specified by 64 codons. Many amino acids are therefore to result from a synthetic mRNA with the repeating sequence
specified by more than one codon, and hence the genetic code is 5�-UUUGGGUUUGGGUUUGGG-3�.
redundant, or degenerate. The redundancy has strong patterns,
however: Translation consists of initiation, elongation,
and termination.
• The redundancy results almost exclusively from the third Translation is usually divided into three separate processes. The
codon position. first is initiation, in which the initiator AUG codon is recognized
and Met is established as the first amino acid in the new
• When an amino acid is specified by two codons, they differ
polypeptide chain. The second process is elongation, in which
either in whether the third position is a U or a C (both
successive amino acids are added one by one to the growing chain.
pyrimidine bases), or in whether the third position is an A or
And the third process is termination, in which the addition of
a G (both purine bases).
amino acids stops and the completed polypeptide chain is released
• When an amino acid is specified by four codons, the identity from the ribosome.
of the third codon position does not matter; it could be U, C, Initiation of translation (Fig. 4.17) requires a number of
A, or G. protein initiation factors that bind to the mRNA. In eukaryotes,
one group of initiation factors binds to the 5� cap that is added to
The chemical basis of these patterns results from two features the mRNA during processing. These recruit a small subunit of the
of translation. First, in many tRNA anticodons the 5� base that ribosome, and other initiation factors bring up a transfer
pairs with the 3� (third) base in the codon is chemically modified RNA charged with Met (Fig. 4.17a). The initiation complex then
into a form that can pair with two or more bases at the third moves along the mRNA until it encounters the first AUG triplet.
position in the codon. Second, in the ribosome, there is less than The position of this AUG establishes the translational reading
perfect alignment between the third position of the codon and frame.
the base that pairs with it in the anticodon, so the requirements When the first AUG codon is encountered, a large ribosomal
for base pairing are somewhat relaxed; this feature of the codon– subunit joins the complex, the initiation factors are released, and
anticodon interaction is referred to as wobble. the next tRNA is ready to join the ribosome (Fig. 4.17b). Note
82 SECTION 4.2 T R A N S L AT I O N : H O W P ROT E I N S A R E S Y N T H E S I Z E D
FIG. 4.18 Initiation in eukaryotes and in prokaryotes. (a) In eukaryotes, translation is initiated only at the 5� cap. (b) In prokaryotes, initiation
takes place at any Shine–Dalgarno sequence; this mechanism allows a single mRNA to include coding sequences for multiple
polypeptides.
(Fig. 4.18a). In prokaryotes, the mRNA molecules have no 5� cap. ? CASE 1 THE FIRST CELL: LIFE’S ORIGINS
Instead, the initiation complex is formed at one or more internal
How did the genetic code originate?
sequences present in the mRNA known as a Shine–Dalgarno
During transcription and translation, proteins and nucleic
sequence (Figure 4.18b). In E. coli, the Shine–Dalgarno sequence
acids work together to convert the information stored in DNA
is 5�-AGGAGGU-3�, and it is followed by an AUG codon eight
into proteins. If we think about how such a system might
nucleotides farther downstream that serves as an initiation codon
have originated, however, we immediately confront a chicken-
for translation. The ability to initiate translation internally allows
and-egg problem: Cells need nucleic acids to make proteins, but
prokaryotic mRNAs to code for more than one protein. Such an
proteins are required to make nucleic acids. Which came first? In
mRNA is known as a polycistronic mRNA. In Fig. 4.18b, the
Chapter 3, we discussed the special features that make RNA an
polycistronic mRNA codes for three different polypeptide chains,
attractive candidate for both information storage and catalysis
each with its own AUG initiation codon preceded eight nucleotides
in early life. Early in evolutionary history, then, proteins had to
upstream by its own Shine–Dalgarno sequence. Each Shine–
be added to the mix. No one fully understands how they were
Dalgarno sequence can serve as an initiation site for translation, and
incorporated, but researchers are looking closely at tRNA, the
so all three polypeptides can be translated.
molecule involved in the “translating” step of translation.
A polycistronic mRNA results from transcription of a group of
In modern cells, tRNA shuttles amino acids to the ribosome,
functionally related genes located in tandem along the DNA and
but an innovative hypothesis suggests that in early life tRNA-
transcribed as a single unit from one promoter. This type of gene
like molecules might have served a different function. This
organization is known as an operon. Prokaryotes have many of
proposal holds that the early precursors of the ribosome were
their genes organized into operons because the production of a
RNA molecules that facilitated the replication of other RNAs,
polycistronic mRNA allows all the protein products to be expressed
not proteins. In this version of an RNA world, precursors to
together whenever they are needed. Typically, the genes organized
tRNA would have shuttled nucleotides to growing RNA strands.
into operons are those whose products are needed either for
Researchers hypothesize that tRNAs bound to amino acids
successive steps in the synthesis of an essential small molecule,
may have acted as simple catalysts, facilitating more accurate
such as an amino acid, or else for successive steps in the breakdown
RNA synthesis. Through time, amino acids brought into close
of a source of energy, such as a complex carbohydrate.
proximity in the process of building RNA molecules might have
j Quick Check 3 Bacterial DNA containing an operon encoding polymerized to form polypeptide chains. From there, natural
three enzymes is introduced into chromosomal DNA in yeast (a selection would favor the formation of polypeptides that
eukaryote) in such a way that it is properly flanked by a promoter enhanced replication of RNA molecules, bringing proteins into
and a transcriptional terminator. The bacterial DNA is transcribed the chemistry of life.
and the RNA correctly processed, but only the protein nearest the All of the steps in gene expression, including transcription
promoter is produced. Can you suggest why? and translation, are summarized in Fig. 4.19 on the next pages.
V I S UA L S Y N T H E S I S Gene Expression
FIG. 4.19 Integrating concepts from Chapters 3 and 4
tRNA
Exon Intron AA
AAA
5’ cap
Primary Spliceosome
RNA
transcript
polymerase
(RNA)
AA
AAA
RNA
transcript
5’
RNA–DNA Template
mplate
Promoter duplex DNA
A Terminator
region sequence AAAA
A
3’ 5’
3’
5’ 3’
Gene
Polymerase
movement
Nucleus
84
Transport Translation
mRNA travels through Ribosomes translate mRNA in the cytosol,
nuclear pores into the producing polypeptide chains. The resulting
cytoplasm. proteins carry out vital cellular functions.
mRNA Protein
Met
Glu Glu Proteins have many different
p
Pr roles in the cell. They
As
u
o
Le
provide structural support,
Ser
Val
Thr Arg Growing act as enzymes that facilitate
polypeptide chemical reactions, and are
Phe
chain involved in cell signaling and
communication.
During elongation, the
Ala
appropriate tRNA anticodon
matches with the available
Me codon on the mRNA, bringing
t
Gly the next amino acid to the
Va polypeptide chain.
l
Ar
g Growing
Glu actin
tRNA Thr
filament
U Incoming
UC E P A tRNA charged
CU with amino acid
site site U
Ribosome UGG Anticodon
AGA A C C GA A
5’ 3’
Codon mRNA
Ribosome moves
along mRNA in a
5’ to 3’ direction.
Actin
protein
Ribosomes
85
86 SECTION 4.3 P ROT E I N E VO L U T I O N A N D T H E O R I G I N O F N E W P ROT E I N S
folding domain called a TIM barrel (Fig. 4.20a) is named after the
4.3 PROTEIN EVOLUTION AND THE enzyme triose phosphate isomerase, in which it is a prominent
ORIGIN OF NEW PROTEINS feature. The TIM barrel consists of alternating a helices and
parallel b sheets connected by loops. In many enzymes with a
The amino acid sequences of more than a million proteins are TIM barrel, the active site is formed by the loops at the carboxyl
known, and the particular three-dimensional structure has been ends of the sheets. Fig. 4.20b is a b barrel formed from antiparallel
determined for each of more than 10,000 proteins. While few of b sheets. b barrel structures occur in proteins in some types of
the sequences and structures are identical, many are sufficiently bacteria, usually in proteins that span the cell membrane, where
similar that the proteins can be grouped into about 25,000 the b barrel provides a channel that binds hydrophilic molecules.
protein families. A protein family is a group of structurally and The number of known folding domains is only about 2500,
functionally related proteins as a result of shared evolutionary which is far fewer than the number of protein families. The reason
history. for the discrepancy is that different protein families contain
Why are there not more types of proteins? The number different combinations of folding domains. Modern protein
of possible sequences is unimaginably large. For example, for families are composed of different combinations of a number of
a polypeptide of only 62 amino acids, there are 2062 possible folding domains, each of which contributes some structural or
sequences (because each of the 62 positions could be occupied by functional feature of the protein. Different types of protein folds
any of the 20 amino acids). The number 2062 equals approximately occur again and again in different contexts and combinations. The
1080; this number is also the estimated total number of electrons, earliest proteins may have been little more than single folding
protons, and neutrons in the entire universe! So why are there so domains that could aggregate to form more complex functional
few protein families? The most likely answer is that the chance units. As life evolved, the proteins became longer by joining the
that any random sequence of amino acids would fold into a stable DNA coding for the individual folding units together into a single
configuration and carry out some useful function in the cell is very molecule.
close to zero. For example, human tissue plasminogen activator, a protein
that is used in treating strokes and heart attacks because it
Most proteins are composed of modular folding dissolves blood clots, contains domains shared with cell-surface
domains. receptors, a domain shared with cellular growth factors, and a
If functional proteins are so unlikely, how could life have evolved? domain that folds into large loops facilitating protein–protein
The answer is that the earliest proteins were probably much interactions. Hence, novel proteins do not always evolve from
shorter than modern proteins and needed only a trace of function. random combinations of amino acids; instead, they often
Only as proteins evolved through billions of years did they become evolve by joining already functional folding domains into novel
progressively longer and more specialized in their functions. Many combinations.
protein families that exist today exhibit small regions of three-
dimensional structure in which the protein folding is similar. Amino acid sequences evolve through mutation and
These regions range in length from 25 to 100 or more amino selection.
acids. A region of a protein that folds in a similar way relatively Another important reason that complex proteins can evolve
independently of the rest of the protein is known as a folding against seemingly long odds is that evolution proceeds stepwise
domain. through the processes of mutation and selection. A mutation
Two examples of folding domains are illustrated in Fig. 4.20. is a change in the sequence of a gene. The process of mutation
Many folding domains are functional units in themselves. The is discussed in Chapter 14, but for now all you need to know is
that mutations affecting proteins occur at random in regard to
their effects on protein function. In protein-coding genes, some
mutations may affect the amino acid sequence; others might
FIG. 4.20 Examples of folding domains: (a) TIM barrel; change the level of protein expression or the time in development
(b) b barrel. or type of cell in which the protein is produced. Here, we will
a. b.
consider only those mutations that change the amino acid
sequence.
By way of analogy, we can use a simple word game. The object
of the game is to change an ordinary English word into another
meaningful English word by changing exactly one letter. Consider
the word GONE. To illustrate “mutations” of the word that are
random with respect to function (that is, random with respect to
whether the change will yield a meaningful new word), we wrote
a computer program that would choose one letter in GONE at
CHAPTER 4 T R A N S L AT I O N A N D P ROT E I N S T RU C T U R E 87
random and replace it with a different random letter. The first GONE will be gone. In a similar way that one meaningful word
24 “mutants” of GONE are: may replace another, one amino acid sequence may be replaced
with a different one in the course of evolution.
UONE GNNE GONJ GOZE
A real-world example that mirrors the word game is found
GONH GOLE GFNE XONE
in the evolution of resistance of the malaria parasite to the
NONE GKNE GJNE DONE
drug pyrimethamine. This drug inhibits an enzyme known as
GCNE GONB GOIE GGNE
dihydrofolate reductase, which the parasite needs to survive and
GONI GFNE GPNE GENE
reproduce inside red blood cells. Resistance to pyrimethamine is
BONE GOWE OONE GYNE
known to have evolved through a stepwise sequence of four amino
Most of the mutant words are gibberish, corresponding to acid replacements. In the first replacement, serine (S)
the biological reality that most random amino acid replacements at the 108th amino acid in the polypeptide sequence (position
impair protein function to some extent. On the other hand, 108) was replaced with asparagine (N); then cysteine (C) at
some mutant proteins function just as well as the original, and position 59 was replaced with arginine (R); asparagine (N)
a precious few change function. In the word-game analogy, the at position 51 was then replaced with isoleucine (I); finally,
mutants that can persist correspond to meaningful words, those isoleucine (I) at position 164 was replaced with leucine (L). If we
words shown in red. list the amino acids according to their single-letter abbreviation
In a population of organisms, random mutations are retained in the order of their occurrence in the protein, the evolution of
or eliminated through the process of selection among individuals resistance followed this pathway:
on the basis of their ability to survive and reproduce. This process
was introduced in Chapter 1 and is considered in greater detail in NCSI ➛ NCNI ➛ NRNI ➛ IRNI ➛ IRNL
Chapter 21, but the principle is straightforward. Most mutations where the mutant amino acids are shown in red. Each successive
that impair protein function will be eliminated because, if the amino acid replacement increased the level of resistance so that a
function of the nonmutant protein contributes to survival and greater concentration of drug was needed to treat the disease. The
reproduction, the individuals carrying these mutations will leave quadruple mutant IRNL is resistant to such high levels that the
fewer offspring than others. Mutations that do not impair function drug is no longer useful.
may remain in the population for long periods because their carriers Depicted according to stepwise amino acid replacements, the
survive and reproduce in normal numbers; a mutation of this type analogy between the evolution of pyrimethamine resistance and
has no tendency to either increase or decrease in frequency over the word game is clear. It should also be clear from our earlier
time. In contrast, individuals that carry the occasional mutation discussion that hundreds of other mutations causing amino acid
that improves protein function will reproduce more successfully replacements in the enzyme must have occurred in the parasite
than others. Because of the enhanced reproduction, the mutant during the course of evolution, but only these amino acid changes
gene encoding the improved protein will gradually increase in occurring in this order persisted and increased in frequency
frequency and spread throughout the entire population. because they conferred greater survival and reproduction of the
In the word game, any of the mutants in red may persist in parasite under treatment with the drug.
the population, but suppose that one of them, GENE for example,
is actually superior to GONE (considered more euphonious, j Quick Check 4 What do you think happened to the mutations
perhaps). Then GENE will gradually displace GONE, and eventually that decreased survival or reproduction of the parasites? •
The tertiary structure of a protein is its three-dimensional sequence of amino acids will fold properly to carry out a
shape, which results from long-range interactions of amino specific function is very small. page 86
acid R groups. page 75
A region of a protein that folds in a particular way and that
Some proteins are made up of several polypeptide carries out a specific function is called a folding domain.
subunits; this group of subunits is the protein’s quaternary page 86
structure. page 76
Proteins evolve by combining different folding domains.
Chaperones help some proteins fold properly. page 76 page 86
Translation consists of three steps: initiation, elongation, 7. Describe the steps of translation initiation,
and termination. page 81 elongation, and termination.
There are far fewer protein families than the total number
of possible proteins because the probability that a random
CHAPTER 5
Organizing
Principles
Lipids, Membranes,
and Cell Compartments
Core Concepts
5.1 Cell membranes are
composed of lipids, proteins,
and carbohydrates.
5.2 The plasma membrane is a
selective barrier that controls
the movement of molecules
between the inside and the
outside of the cell.
5.3 Cells can be classified as
prokaryotes or eukaryotes,
which differ in the degree of
internal compartmentalization.
5.4 The endomembrane system is
an interconnected system of
membranes that includes the
nuclear envelope, endoplasmic
reticulum, Golgi apparatus,
lysosomes, vesicles, and plasma
membrane.
5.5 Mitochondria and chloroplasts
are organelles involved in
harnessing energy, and likely
evolved from free-living
prokaryotes.
Dr. Jeremy Burgess/Science Source.
89
90 SECTION 5.1 S T RU C T U R E O F C E L L M E M B R A N E S
“With the discovery of the cell, biologists found their atom.” So in separating a cell from the external environment and defining
stated François Jacob, the French biologist who shared the Nobel structural and functional spaces within cells.
Prize in Physiology or Medicine in 1965. Just as the atom is the
smallest, most basic unit of matter, the cell is the smallest, most
basic unit of living organisms. All organisms, from single-celled 5.1 STRUCTURE OF CELL MEMBRANES
algae to complex multicellular organisms like humans, are made
up of cells. Therefore, essential properties of life, including growth, Cells are defined by membranes. After all, membranes physically
reproduction, and metabolism, must be understood in terms of cell separate cells from their external environment. In addition,
structure and function. membranes define spaces within many cells that allow them to
Cells were first seen sometime around 1665, when the English carry out their diverse functions.
scientist Robert Hooke built a microscope that he used to observe Lipids are the main component of cell membranes. They have
thin sections of dried cork tissue derived from plants. In these properties that allow them to form a barrier in an aqueous (watery)
sections, Hooke observed arrays of small cavities and named environment. Proteins are often embedded in or associated with
them “cells” (Fig. 5.1). Although Hooke was probably looking at the membrane, where they perform important functions such as
the cell walls of empty (rather than living) cells, his observations transporting molecules. Carbohydrates can also be found in cell
nevertheless led to the concept that cells are the fundamental membranes, usually attached to lipids (glycolipids) and proteins
unit of life. Later in the seventeenth century, the Dutch (glycoproteins).
microbiologist Anton van Leeuwenhoek greatly improved the
magnifying power of microscope lenses, enabling him to see and Cell membranes are composed of two layers of lipids.
describe unicellular organisms, including bacteria, protists, and The major types of lipid found in cell membranes are phospholipids,
algae. Today, modern microscopy provides unprecedented detail introduced in Chapter 2. Most phospholipids are made up of a
and a deeper understanding of the inner architecture of cells. glycerol backbone attached to a phosphate group and two fatty
Cells differ in size and shape, but they share many features. acids (Fig. 5.2). The phosphate head group is hydrophilic (“water-
This similarity in the microscopic organization of all living loving”) because it is polar, enabling it to form hydrogen bonds
organisms led to the development in the middle of the nineteenth with water. By contrast, the two fatty acid tails are hydrophobic
century of one of the pillars of modern biology: the cell theory. (“water-fearing”) because they are nonpolar and do not form
Based on the work and ideas of Matthias Schlieden, Theodor hydrogen bonds with water. Molecules with both hydrophilic and
Schwann, Rudolf Virchow, and others, the cell theory states that hydrophobic regions in a single molecule are termed amphipathic.
all organisms are made up of cells, that the cell is the fundamental In an aqueous environment, amphipathic molecules such as
unit of life, and that cells come from preexisting cells. There is no phospholipids behave in an interesting way. They spontaneously
life without cells, and the cell is the smallest unit of life. arrange themselves into various structures in which the polar
This chapter focuses on cells and their internal organization. head groups on the outside interact with water and the nonpolar
We pay particular attention to the key role that membranes play tail groups come together on the inside away from water. This
arrangement results from the tendency of polar
molecules like water to exclude nonpolar molecules
or nonpolar groups of molecules.
FIG. 5.1 The first observation of cells. Robert Hooke used a simple microscope The shape of the structure is determined by
to observe small chambers in a sample of cork tissue that he described as the bulkiness of the head group relative to the
“cells.” Sources: (left) Science Museum/SSPL/The Image Works; (right) Ted Kinsman/ hydrophobic tails. For example, lipids with bulky
Science Source. heads and a single hydrophobic fatty acid tail are
wedge-shaped and pack into spherical structures
Drawing by Hooke Cork tissue
called micelles (Fig. 5.3a). By contrast, lipids with
less bulky head groups and two hydrophobic tails
form a bilayer (Fig. 5.3b). A lipid bilayer is a structure
formed of two layers of lipids in which the hydrophilic
heads are the outside surfaces of the bilayer and the
hydrophobic tails are sandwiched in between, isolated
from contact with the aqueous environment.
The bilayers form closed structures with an inner
space since free edges would expose the hydrophobic
chains to the aqueous environment. This organization
in part explains why bilayers are effective cell
membranes. It also explains why membranes are
self-healing. Small tears in a membrane are rapidly
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 91
CH2
the action of an enzyme, as long as the
O
concentration of free phospholipids is high
O P O ⴚ
Phosphate
enough and the pH of the solution is similar
Polar O
head to that of a cell. The pH is important because
CH2 CH CH2
group
Glycerol
O O
it ensures that the head groups are in their
Phospholipids backbone
have hydrophilic
C O C O
ionized (charged) form and thus suitably
and hydrophobic
components. CH2 CH2
hydrophilic. Thus, if phospholipids are added
CH2 CH2 to a test tube of water at neutral pH, they
CH2 CH2 spontaneously form spherical bilayer structures
CH2 CH2 called liposomes that surround a central
CH2 CH2 space (Fig. 5.3c). As the liposomes form,
CH2 CH2 they may capture macromolecules present in
CH2 CH solution.
HYDROPHOBIC
Fatty
acid
CH2 HC CH2 Such a process may have been at work
chains CH2 H2C CH2 in the early evolution of life on Earth.
CH2 H2C CH2 Experiments show that liposomes can
CH2 H2C CH2
form, break, and re-form in environments
H2C CH3
CH2 like tidal flats that are repeatedly dried and
CH2 flooded with water. The liposomes can even
CH2
grow, incorporating more and more lipids
CH2
from the environment, and capture nucleic
CH2
acids and other molecules in their interiors.
CH3
Depending on their chemical composition,
Phospholipids can be represented in a
variety of ways to emphasize overall early membranes might have been either
structure, different domains, and 3D shape.
leaky or almost impervious to the molecules
of life. Over time, they evolved in such a way
as to allow at least limited molecular traffic
sealed by the spontaneous rearrangement of the lipids surrounding between the environment and cell interior. At some point, new
the damaged region because of the tendency of water to exclude lipids no longer had to be incorporated from the environment.
nonpolar molecules. Instead, proteins guided lipid synthesis within the cell, although
FIG. 5.3 Phospholipid structures. Phospholipids can form (a) micelles, (b) bilayers, or (c) liposomes when placed in water.
Nonpolar tails
(hydrophobic)
92 SECTION 5.1 S T RU C T U R E O F C E L L M E M B R A N E S
FIG. 5.4 Saturated and unsaturated fatty acids in phospholipids. The composition of cell membranes affects the tightness of packing.
how this switch to protein-mediated synthesis happened remains mobility. Likewise, saturated fatty acid tails, which have no double
uncertain. bonds, are straight and tightly packed—again reducing mobility
All evidence suggests that membranes formed originally by (Fig. 5.4a). The double bonds in unsaturated fatty acids introduce
straightforward physical processes, but that their composition kinks in the fatty acid tails, reducing the tightness of packing and
and function evolved over time. François Jacob once said that enhancing lipid mobility in the membrane (Fig. 5.4b).
evolution works more like a tinkerer than an engineer, modifying
j Quick Check 1 Most animal fats are solid at room temperature,
already existing materials rather than designing systems from
whereas plant and fish oils tend to be liquid. Both contain fatty
scratch. It seems that the evolution of membranes is no exception
acids. Can you predict which type of fat contains saturated fatty
to this pattern.
acids, and which type contains unsaturated fatty acids?
Cell membranes are dynamic. In addition to phospholipids, cell membranes often contain
Lipids freely associate with one another because of extensive other types of lipid, and these can also influence membrane
van der Waals forces between their fatty acid tails (Chapter 2). fluidity. For example, cholesterol is a major component of
These weak interactions are easily broken and re-formed, so lipid animal cell membranes, representing about 30% by mass of the
molecules are able to move within the plane of the membrane, membrane lipids. Like phospholipids, cholesterol is amphipathic,
sometimes very rapidly: A single phospholipid can move across with both hydrophilic and hydrophobic groups in the same
the entire length of a bacterial cell in less than a second. Lipids can molecule. In cholesterol, the hydrophilic region is simply a
also rapidly rotate around their vertical axis, and individual fatty hydroxyl group (–OH) and the hydrophobic region consists of four
acid chains are able to flex, or bend. As a result, membranes are interconnected carbon rings with an attached hydrocarbon chain
dynamic: they are continually moving, forming, and re-forming (Fig. 5.5). This structure allows cholesterol to insert into the lipid
during the lifetime of a cell. bilayer so that its head group interacts with the hydrophilic head
Because membrane lipids are able to move in the plane of group of phospholipids, while the ring structure participates in
the membrane, the membrane is said to be fluid. The degree of van der Waals interactions with the fatty acid chains.
membrane fluidity depends on which types of lipid make up the Cholesterol increases or decreases membrane fluidity
membrane. In a single layer of the lipid bilayer, the strength of the depending on temperature. At temperatures typically found
van der Waals interactions between the lipids’ tails depends on in a cell, cholesterol decreases membrane fluidity because
the length of the fatty acid tails and the presence of double bonds the interaction of the rigid ring structure of cholesterol with
between neighboring carbon atoms. The longer the fatty acid the phospholipid fatty acid tails reduces the mobility of the
tails, the more surface is available to participate in van der Waals phospholipids. However, at low temperatures, cholesterol
interactions. The tighter packing that results tends to reduce lipid increases membrane fluidity because it prevents phospholipids
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 93
FIG. 5.5 Cholesterol in the lipid bilayer. Cholesterol molecules embedded in the lipid bilayer affect the fluidity of the membrane.
Hydrophilic OH
head group
Polar
head CH3
The amphipathic groups
structure of cholesterol Hydrophobic,
allows it to pack tightly rigid planar
with phospholipids. group of rings CH3
CH3
Hydrophobic
hydrocarbon
tail
H3C CH3
Cholesterol
from packing tightly with other phospholipids. Thus, cholesterol flip-flop requires the hydrophilic head group to pass through
helps maintain a consistent state of membrane fluidity by the hydrophobic interior of the membrane. As a result, there
preventing dramatic transitions from a fluid to solid state. is little exchange of components between the two layers of
For many decades, it was thought that the various types of lipid the membrane, which in turn allows the two layers to differ in
found in the membrane were randomly distributed throughout composition. In fact, in many membranes, different types of lipid
the bilayer. However, more recent studies show that specific types are present primarily in one layer or the other.
of lipid, such as sphingolipids, sometimes assemble into defined
patches called lipid rafts. Cholesterol and other membrane Proteins associate with cell membranes in
components such as proteins also appear to accumulate in some different ways.
of these regions. Thus, membranes are not always a uniform fluid Most membranes contain proteins as well as lipids. For example,
bilayer, but instead can contain regions with discrete components. proteins represent as much as 50% by mass of the membrane of a
Although lipids are free to move in the plane of the membrane, red blood cell. Membrane proteins serve different functions
the spontaneous transfer of a lipid between layers of the bilayer, (Fig. 5.6). Some act as transporters, moving ions or other
known as lipid flip-flop, is very rare. This is not surprising since molecules across the membrane. Other membrane proteins
Extracellular
fluid
FIG. 5.7 Integral and peripheral membrane proteins. Integral membrane proteins are permanently associated with the membrane. Peripheral
membrane proteins are temporarily associated with one or other of the two lipid bilayers or with an integral membrane protein.
act as receptors that allow the cell to receive signals from the proteins to move within the membrane and assist proteins in
environment. Still others are enzymes that catalyze chemical clustering in lipid rafts.
reactions or anchors that attach to other proteins and help to Proteins, like lipids, are free to move in the membrane. How do
maintain cell structure and shape. we know this? The mobility of proteins in the cell membrane can
These various membrane proteins can be classified into two be demonstrated using an elegant experimental technique called
groups depending on how they associate with the membrane fluorescence recovery after photobleaching, or FRAP (Fig. 5.8).
(Fig. 5.7). Integral membrane proteins are permanently In this technique, proteins embedded in the cell membrane are
associated with cell membranes and cannot be separated from the labeled with fluorescent dye molecules. Labeling all the proteins
membrane experimentally without destroying the membrane in a membrane creates a fluorescent cell that can be visualized
itself. Peripheral membrane proteins are temporarily associated with a fluorescence microscope. A laser is then used to bleach the
with the lipid bilayer or with integral membrane proteins through fluorescent dye molecules in a small area of the cell membrane,
weak noncovalent interactions. They are easily separated from leaving a nonfluorescent spot on the surface of the cell. If
the membrane by simple experimental procedures that leave the proteins in the cell membrane were not capable of movement,
structure of the membrane intact. the bleached area would remain nonfluorescent. However, over
Most integral membrane proteins are transmembrane time, fluorescence appears in the bleached area, telling us that
proteins that span the entire lipid bilayer, as shown in Fig. 5.7. fluorescent proteins that were not bleached moved into the
These proteins are composed of three regions: two hydrophilic bleached area.
regions, one protruding from each face of the membrane, and a The idea that lipids and proteins coexist in the membrane,
connecting hydrophobic region that spans the membrane. This and that both are able to move in the plane of the membrane,
structure allows for separate functions and capabilities of each end led American biologists S. Jonathan Singer and Garth Nicolson to
of the protein. For example, the hydrophilic region on the external propose the fluid mosaic model in 1972. According to this model,
side of a receptor can interact with signaling molecules, whereas the lipid bilayer is a fluid structure within which molecules move
the hydrophilic region on the internal side of the membrane often laterally, and is a mosaic (a mixture) of two types of molecules,
interacts with other proteins in the cytoplasm of the cell to pass lipids and proteins.
along the message.
Peripheral membrane proteins may be associated with either
the internal or external side of the membrane (Fig. 5.7). These 5.2 THE PLASMA MEMBRANE
proteins interact either with the polar heads of lipids or with AND CELL WALL
integral membrane proteins by weak noncovalent interactions
such as hydrogen bonds. Peripheral membrane proteins are only Phospholipids with embedded proteins make up the membrane
transiently associated with the membrane and can play a role in surrounding all cells. This membrane, called the plasma
transmitting information received from external signals. Other membrane, is a fundamental, defining feature of all cells. It is the
peripheral membrane proteins limit the ability of transmembrane boundary that defines the space of the cell, separating its internal
95 SECTION 5.1 M
HOW DO WE KNOW?
FIG. 5.8
Before bleaching
Laser Recovery
bleaching
Time
CONCLUSION The gradual recovery of fluorescence in the bleached area indicates that proteins move in the plane of the
membrane.
SOURCE Peters, R., et al. 1974. “A Microfluorimetric Study of Translational Diffusion in Erythrocyte Membranes.” Biochim Biophys Acta 367:282–294.
95
96 SECTION 5.2 T H E P L A S M A M E M B R A N E A N D C E L L WA L L
Concentration gradient
known as osmosis. As in any form of diffusion, water moves from
regions of higher water concentration to regions of lower water
concentration (Fig. 5.11). Because water is a solvent within which
nutrients such as glucose or ions such as sodium or potassium are
dissolved, water concentration drops as solute concentration rises.
Therefore, it is sometimes easier to think about water moving from
regions of lower solute concentration toward regions of higher solute
Simple Channel concentration. Either way, the direction of water movement is the
diffusion Carrier same. During osmosis, the net movement of water toward the side
Cytoplasm Facilitated diffusion of the membrane with higher solute concentration continues until
it is opposed by another force. This force could be pressure due to
gravity (in the case of Fig. 5.11) or the cell wall (in the case of plants,
fungi, and bacteria, as described below).
of signal, which may be chemical or electrical (Chapter 9). The j Quick Check 2 A container is divided into two compartments
second type of transporter is a carrier, which binds to and then by a membrane that is fully permeable to water and small ions.
transports specific molecules. Membrane carriers exist in two Water is added to one side of the membrane (side A), and a 5%
conformations, one that is open to one side of the cell, and another solution of sodium chloride (NaCl) is added to the other (side B). In
that is open to the other side of the cell. Binding of the transported which direction will water molecules move? In which direction will
molecule induces a conformational change in the membrane sodium and chloride ions move? When the concentration is equal
protein, allowing the molecule to be transported across the lipid on both sides, will diffusion stop?
bilayer, as shown on the right in Fig. 5.10.
Up to this point, we have focused our attention on the Primary active transport uses the energy of ATP.
movement of molecules (the solutes) in water (the solvent). Passive transport works to the cell’s advantage only if the
We can take a different perspective and focus instead on water concentration gradient is in the right direction, from higher
movement. Water itself also moves into and out of cells by passive on the outside to lower on the inside for nutrients that the cell
Osmosis Water
Selectively permeable
membrane
FIG. 5.12 Primary active transport. The sodium-potassium pump is a membrane protein that uses the energy stored in ATP to move sodium and
potassium ions against their concentration gradients.
Extracellular
fluid
Na
Na Concentration gradient
K Concentration gradient
Na 1 2 3 4 K
binding binding
site site
Na movement
Lower Na Higher K
ATP ADP
K
Cytoplasm
needs to take in, and from higher on the inside and lower on the molecules in the same direction, and are referred to as symporters
outside for wastes that the cell needs to export. However, many or cotransporters.
of the molecules that cells require are not highly concentrated
in the environment. Although some of these molecules can Secondary active transport is driven by an
be synthesized by the cell, others must be taken up from the electrochemical gradient.
environment. In other words, cells have to move these substances Active transport can also work in another way. Because small
from areas of lower concentration to areas of higher concentration. ions cannot cross the lipid bilayer, many cells use a transport
The “uphill” movement of substances against a concentration protein to build up the concentration of a small ion on one side
gradient, called active transport, requires energy. The transport of the membrane. The resulting concentration gradient stores
of many kinds of molecules across membranes requires energy, potential energy that can be harnessed to drive the movement
either directly or indirectly. In fact, most of the energy used of other substances across the membrane against their
by a cell goes into keeping the inside of the cell different from concentration gradient.
the outside, a function carried out by proteins in the plasma For example, some cells actively pump protons (H1) across the
membrane. cell membrane using ATP (Fig. 5.13a). As a result, in these cells
During active transport, cells move substances through the concentration of protons is higher on one side of the
transport proteins embedded in the cell membrane. Some of these membrane and lower on the other side. In other words, the pump
proteins act as pumps, using energy directly to move a substance generates a concentration gradient, also called a chemical gradient
into or out of a cell. A good example is the sodium-potassium because the entity forming the gradient is a chemical (Fig. 5.13b).
pump (Fig. 5.12). Within cells, sodium is kept at concentrations We have already seen that concentration differences favor the
much lower than in the exterior environment; the opposite is true movement of protons back to the other side of the membrane.
of potassium. Therefore, both sodium and potassium have to be However, the lipid bilayer blocks the movement of protons to the
moved against a concentration gradient. The sodium-potassium other side and therefore stores potential energy, just like a dam
pump actively moves sodium out of the cell and potassium into or battery.
the cell. This movement of ions takes energy, which comes In addition to the chemical gradient, another force favors the
from the chemical energy stored in ATP. Active transport that movement of protons back across the membrane: a difference in
uses energy directly in this manner is called primary active charge. Because protons carry a positive charge, the side of the
transport. Note that the sodium ions and potassium ions move membrane with more protons is more positive than the other side.
in opposite directions. Protein transporters that work in this This difference in charge is called an electrical gradient. Protons
way are referred to as antiporters. Other transporters move two (and other ions) move from areas of like charge to areas of unlike
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 99
a. b. c.
FIG. 5.13 Secondary active transport.
Extracellular
Protons are pumped across
fluid a membrane by (a) primary
active transport, resulting
Proton
in (b) an electrochemical
gradient, which drives
Electrical gradient
1 2 3 its concentration gradient.
–
–
–
–
–
–
– –
ADP
ATP
Cytoplasm
Protons are pumped across The proton pump generates An antiporter uses the proton
membrane by primary an electrochemical gradient, electrochemical gradient to move
active transport. with a higher concentration a different molecule out of the cell
of protons outside the cell against its concentration gradient.
and a lower concentration
of protons inside the cell.
charge, driven by an electrical gradient. A gradient that has both solutions (Fig. 5.14). If a red blood cell is placed in a hypertonic
charge and chemical components is known as an electrochemical solution (one with a higher solute concentration than that
gradient (Fig. 5.13b). inside the cell), water leaves the cell by osmosis and the cell
If protons are then allowed to pass through the cell membrane shrinks. By contrast, if a red blood cell is placed in a hypotonic
by a transport protein, they will move down their electrochemical solution (one with a lower solute concentration than that inside
gradient toward the region of lower proton concentration. These the cell), water moves into the cell by osmosis and the cell lyses,
transport proteins can use the movement of protons to drive the or bursts. Animal cells solve the problem of water movement
movement of other molecules against their concentration gradient in part by keeping the intracellular fluid isotonic (that is, at the
(Fig. 5.13c). The movement of protons is always from regions same solute concentration) as the extracellular fluid. Cells use
of higher to lower concentration, whereas the movement of the the active transport of ions to maintain equal concentrations
coupled molecule is from regions of lower to higher concentration.
Because the movement of the coupled molecule is driven by
the movement of protons and not by ATP directly, this form of
transport is called secondary active transport. Secondary active FIG. 5.14 Changes in red blood cell shape due to osmosis. Red
transport uses the potential energy of an electrochemical gradient
blood cells shrink, swell, or burst because of net water
to drive the movement of molecules; by contrast, primary active
movement driven by differences in solute concentration
transport uses the chemical energy of ATP directly.
between the inside and the outside of the cell.
The use of an electrochemical gradient as a temporary energy
source is a common cellular strategy. For example, cells use a sodium
Shrunk Normal Swollen Lysed
electrochemical gradient generated by the sodium-potassium pump
to transport glucose and amino acids into cells. In addition, cells use H2O H2O H2O H 2O
a proton electrochemical gradient to move other molecules and, as
we discuss below and in Chapter 7, to synthesize ATP.
functions. Fig. 5.17a shows a macrophage, a type of animal cell, such as proteins, nucleic acids, lipids, and complex carbohydrates.
with various organelles. The endoplasmic reticulum (ER) is the Peroxisomes also contain many different enzymes and are
organelle in which proteins and lipids are synthesized. The Golgi involved in important metabolic reactions, including the breakdown
apparatus modifies proteins and lipids produced by the ER and of fatty acids and the synthesis of certain types of phospholipid.
acts as a sorting station as they move to their final destinations. Mitochondria are specialized organelles that harness energy for
Lysosomes contain enzymes that break down macromolecules the cell. Many cell membranes that define these organelles are
FIG. 5.17 An animal cell and a plant cell. Animal and plant cells have many cell components in common.
2 μm
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 103
associated with a protein scaffold called the cytoskeleton that and chloroplasts that convert energy of sunlight into chemical
helps cells to maintain their shape and serves as a network of tracks energy.
for the movement of substances within cells (Chapter 10). The entire contents of a cell other than the nucleus make up
Fig. 5.17b shows a typical plant cell. In addition to the the cytoplasm. The jelly-like internal environment of the cell that
organelles described above, plant cells have a cell wall outside the surrounds the organelles inside the plasma membrane is referred
plasma membrane, vacuoles specialized for water uptake, to as the cytosol.
Plasma membrane
Mitochondria
Endoplasmic
reticulum
Cytoskeleton
104 SECTION 5.4 T H E E N D O M E M B R A N E S YS T E M S
In the next two sections, we consider these organelles in more with another organelle or the plasma membrane, re-forming a
detail, focusing on the role of membranes in forming distinct continuous membrane and unloading their contents.
compartments within the cell. In total, these interconnected membranes make up the
endomembrane system. The endomembrane system includes
the nuclear envelope, endoplasmic reticulum, Golgi apparatus,
5.4 THE ENDOMEMBRANE SYSTEM lysosomes, the plasma membrane, and the vesicles that move
between them (Fig. 5.18). In plants, the endomembrane system is
In eukaryotes, the total surface area of intracellular membranes actually continuous between cells through connecting pores called
is about tenfold greater than that of the plasma membrane. This plasmodesmata (see Fig. 5.17; Chapters 10 and 28).
high ratio of internal membrane area to plasma membrane area Extensive internal membranes are not common in
underscores the significant degree to which a eukaryotic cell prokaryotic cells. However, photosynthetic bacteria have internal
is divided into internal compartments. Many of the organelles membranes that are specialized for harnessing light energy
inside cells are not isolated entities, but instead communicate (Chapters 8 and 26).
with one another. In fact, the membranes of these organelles are
either physically connected by membrane “bridges” or they are The endomembrane system compartmentalizes
transiently connected by vesicles, small membrane-enclosed the cell.
sacs that transport substances within a cell or from the interior Because many types of molecules are unable to cross cell
to the exterior of the cell. These vesicles form by budding off an membranes on their own, the endomembrane system divides the
organelle, taking with them a piece of the membrane and internal interior of a cell into two distinct “worlds,” one inside the spaces
contents of the organelle from which they derive. They then fuse defined by these membranes and one outside these spaces. A
molecule within the interior of the ER
can stay in the ER or end up in the interior
of the Golgi apparatus or even outside
FIG. 5.18 The endomembrane system. The endomembrane system is a series of
the cell by the budding off and fusing
interconnected membrane-bound compartments in eukaryotic cells.
of a vesicle between these organelles.
Similarly, a molecule associated with
the ER membrane can move to the Golgi
membrane or the plasma membrane
by vesicle transport. Molecules in
the cytosol are in a different physical
space, separated by membranes of the
endomembrane system. This physical
separation allows specific functions to
take place within the spaces defined
by the membranes and also within the
membrane itself.
Nuclear envelope In spite of forming a continuous
and interconnected system, the various
Endoplasmic compartments have unique properties
reticulum and maintain distinct identities
determined in part by which lipids and
proteins are present in their membranes.
Golgi apparatus
Vesicles not only bud off from and
fuse with organelles but also with the
Vesicle plasma membrane. When a vesicle fuses
Lysosome with the plasma membrane, the process
Plasma membrane is called exocytosis. It provides a way
Exocytosis for a vesicle to empty its contents to the
extracellular space or to deliver proteins
Endocytosis embedded in the vesicle membrane to
the plasma membrane (Fig. 5.18). The
process also works in reverse: A vesicle
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 105
can bud off from the plasma membrane, enclosing material from the sites of protein synthesis, in which amino acids are assembled
outside the cell and bringing it into the cell interior. This process is into polypeptides guided by the information stored in mRNA
called endocytosis. Together, exocytosis and endocytosis provide (Chapter 4). In this way, the nuclear envelope and its associated
a way to move material into and out of cells without passing protein pores regulate which molecules move into and out of
through the cell membrane. the nucleus.
The nucleus houses the genome and is the site The endoplasmic reticulum is involved in protein
of RNA synthesis. and lipid synthesis.
The innermost organelle of the endomembrane system is the The outer membrane of the nuclear envelope is physically
nucleus, which stores DNA, the genetic material that encodes continuous with the endoplasmic reticulum (ER), an organelle
the information for all the activities and structures of the cell. bounded by a single membrane (Fig. 5.20). The ER is a
The nuclear envelope defines the boundary of the nucleus conspicuous feature of many eukaryotic cells, accounting in some
(Fig. 5.19). It actually consists of two membranes, the inner and cases for as much as half of the total amount of membrane. The
outer membranes, and each is a lipid bilayer with associated proteins. ER produces and transports many of the lipids and proteins used
These two membranes are continuous with each other at inside and outside the cell, including all transmembrane proteins,
openings called nuclear pores. These pores are large protein as well as proteins destined for the Golgi apparatus, lysosomes, or
complexes that allow molecules to move into and out of the export out of the cell. The ER is also the site of production of most
nucleus, and thus are essential for the nucleus to communicate of the lipids that make up the various internal and external cell
with the rest of the cell. For example, some proteins that are membranes.
synthesized in the cytosol, such as transcription factors, move Unlike the nucleus, which is a single spherical structure in
through nuclear pores to enter the nucleus, where they control the cell, the ER consists of a complex network of interconnected
how and when genetic information is expressed. tubules and flattened sacs. The interior of the ER is continuous
In addition, the transfer of information encoded by DNA throughout and is called the lumen. As shown in Fig. 5.20,
depends on the movement of mRNA (messenger RNA) molecules the ER has an almost mazelike appearance when sliced and
out of the nucleus through these pores. After exiting the nucleus, viewed in cross section. Its membrane is extensively convoluted,
mRNA binds to free ribosomes in the cytosol or ribosomes allowing a large amount of membrane surface area to fit within
associated with the endoplasmic reticulum (ER). Ribosomes are the cell.
When viewed through an electron microscope, ER membranes
have two different appearances (Fig. 5.20). Some look rough
because they are studded with ribosomes. This portion of the ER is
FIG. 5.19 A surface view of the nuclear envelope. The nucleus is referred to as rough endoplasmic reticulum (RER). The rough
surrounded by a double membrane and houses the cell’s ER synthesizes transmembrane proteins, proteins that end up in
DNA. Source: Don W. Fawcett/Science Source. the interior of organelles, and proteins destined for secretion. As a
result, cells that secrete large quantities of protein have extensive
Nucleus
rough ER, including cells of the gut that secrete digestive enzymes
Nuclear and cells of the pancreas that produce insulin. All cells have at
pores
least some rough ER for the production of transmembrane and
organelle proteins.
There is a small amount of ER membrane in most cells that
appears smooth because it lacks ribosomes. This portion of the
ER is therefore called smooth endoplasmic reticulum (SER)
(Fig. 5.20). Smooth ER is the site of fatty acid and phospholipid
biosynthesis. Thus, this type of ER predominates in cells
specialized for the production of lipids. For example, cells that
synthesize steroid hormones have a well-developed SER that
1 µm produces large quantities of cholesterol. Enzymes within the SER
convert cholesterol into steroid hormones.
The nuclear envelope is perforated by
membrane protein openings called nuclear The Golgi apparatus modifies and sorts proteins
pores. Small molecules and ions can passively and lipids.
diffuse through the pores, but large proteins
and RNA require active transport.
Although it is not physically continuous with the ER, the Golgi
apparatus is often the next stop for vesicles that bud off the ER.
106 SECTION 5.4 T H E E N D O M E M B R A N E S YS T E M S
FIG. 5.20 The endoplasmic reticulum (ER). The ER is a major site for lipid and protein synthesis. (Proteins are also synthesized in the
cytoplasm.) Sources: (top left) Biophoto Associates/Science Source; (bottom left) David M. Phillips/Science Source.
Protein
Ribosome
free in
cytoplasm
Protein
These vesicles carry lipids and proteins, either within the vesicle plasma membrane or other organelles. Vesicles are therefore the
interior or embedded in their membranes. The movement of these primary means by which proteins and lipids move through the
vesicles from the ER to the Golgi apparatus and then to the rest Golgi apparatus to their final destinations.
of the cell is part of a biosynthetic pathway in which lipids and Enzymes within the Golgi apparatus chemically modify
proteins are sequentially modified and delivered to their final proteins and lipids as they pass through it. These modifications
destinations. The Golgi apparatus has three primary roles: take place in a sequence of steps, each performed in a different
(1) It further modifies proteins and lipids produced by the ER; region of the Golgi apparatus, since each region contains a
(2) it acts as a sorting station as these proteins and lipids move to different set of enzymes that catalyzes specific reactions.
their final destinations; and (3) it is the site of synthesis of most of As a result, there is a general movement of vesicles from the
the cell’s carbohydrates. ER through the Golgi apparatus and then to their final
Under the microscope, the Golgi apparatus looks like stacks destinations.
of flattened membrane sacs, called cisternae, surrounded by An example of a chemical modification that occurs
many small vesicles (Fig. 5.21). These vesicles transport proteins predominantly in the Golgi apparatus is glycosylation, in which
and lipids from the ER to the Golgi apparatus, and then between sugars are covalently linked to lipids or specific amino acids of
the various cisternae, and finally from the Golgi apparatus to the proteins. As these lipids and proteins move through the Golgi
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 107
FIG. 5.21 The Golgi apparatus. The Golgi apparatus sorts proteins and lipids to other organelles, the plasma membrane, or the cell exterior.
Source: Biophoto Associates/Science Source.
Vesicle
Cisternae
Golgi
apparatus
Transmembrane
Soluble
protein
protein
Carbohydrate
apparatus, they encounter different enzymes in each region that Lysosomes degrade macromolecules.
add or trim sugars. Glycoproteins are important components of The ability of the Golgi apparatus to sort and dispatch proteins to
the eukaryotic cell surface. The sugars attached to the protein can particular destinations is dramatically illustrated by lysosomes.
protect the protein from enzyme digestion by blocking access Lysosomes are specialized vesicles derived from the Golgi
to the peptide chain. As a result, glycoproteins form a relatively apparatus that degrade damaged or unneeded macromolecules
flexible and protective coating over the plasma membrane. The (Fig. 5.22). They contain a variety of enzymes that break down
distinctive shapes that sugars contribute to glycoproteins and macromolecules such as proteins, nucleic acids, lipids, and
glycolipids also allow them to be recognized specifically by other complex carbohydrates. Macromolecules destined for degradation
cells and molecules in the external environment. For example, are packaged by the Golgi apparatus into vesicles. The vesicles then
human blood types (A, B, AB, and O) are defined by the particular fuse with lysosomes, delivering their contents to the lysosome
sugars that are linked to proteins and lipids on the surface of red interior.
blood cells. The formation of lysosomes also illustrates the ability of
While traffic usually travels from the ER to the Golgi the Golgi apparatus to sort key proteins. The enzymes inside
apparatus, a small amount of traffic moves in the reverse the lysosomes are synthesized in the RER, sorted in the Golgi
direction, from the Golgi apparatus to the ER. This reverse apparatus, and then packaged into lysosomes. In addition, the
pathway is important to retrieve proteins in the ER or Golgi Golgi apparatus sorts and delivers specialized proteins that become
that were accidentally moved forward and to recycle membrane embedded in lysosomal membranes. These include proton pumps
components. that keep the internal environment at an acidic pH of about 5,
108 SECTION 5.4 T H E E N D O M E M B R A N E S YS T E M S
Enzymes
Protons Broken-down
macromolecules
the optimum pH for the activity of the enzymes inside. Other membrane. Protein sorting is the process by which proteins
proteins in the lysosomal membranes transport the breakdown end up where they need to be to perform their function. Protein
products of macromolecules, such as amino acids and simple sorting directs proteins to the cytosol, the lumen of organelles, the
sugars, across the membrane to the cytosol for use by the cell. membranes of the endomembrane system, or even out of the cell
The function of lysosomes underscores the importance entirely.
of having separate compartments within the cell bounded by Recall that proteins are produced in two places: free ribosomes
selectively permeable membranes. Lysosomal enzymes cannot in the cytosol and membrane-bound ribosomes on the rough ER.
function in the normal cellular environment, which has a pH of Proteins produced on free ribosomes are sorted after they are
about 7, and many of a cell’s enzymes and proteins would unfold translated. These proteins often contain amino acid sequences,
and degrade if the entire cell were at the pH of the inside of a called signal sequences, that allow them to be recognized and
lysosome. By restricting the activity of these enzymes to the sorted. As shown in Fig. 5.23, there are several types of signal
lysosome, the cell protects proteins and organelles in the cytosol sequences that direct proteins synthesized on free ribosomes
from degradation. to different cellular compartments. Proteins with no signal
sequence remain in the cytosol (Fig. 5.23a). Proteins destined for
Protein sorting directs proteins to their proper mitochondria or chloroplasts often have a signal sequence at their
location in or out of the cell. amino ends (Fig. 5.23b). Proteins targeted to the nucleus usually
As we have seen, eukaryotic cells have many compartments, and have signal sequences located internally (Fig. 5.23c). These
different proteins function in different places, such as enzymes nuclear signal sequences, called nuclear localization signals,
in lysosomes or transmembrane proteins embedded in the plasma enable proteins to move through pores in the nuclear envelope.
CHAPTER 5 O RG A N I Z I N G P R I N C I P L E S : L I P I D S , M E M B R A N E S , A N D C E L L CO M PA RT M E N T S 109
FIG. 5.23 Signal sequences on proteins synthesized by free FIG. 5.24 Pathways for proteins destined (left) to be secreted
ribosomes. (a) Most proteins with no signal peptide or (right) transported to the plasma membrane.
remain in the cytosol. Other signal sequences direct
proteins to (b) mitochondria and chloroplasts or to
(c) the nucleus.
a. No signal peptide
To cyt
osol Rough
endoplasmic
b. Amino-terminal signal reticulum
To chloroplast
To mitochondrion
c. Internal signal
us
cle
nu
To Golgi apparatus
FIG. 5.25 Interaction of a signal sequence, signal-recognition particle (SRP), and SRP receptor. Binding of a signal sequence with a signal-
recognition particle (SRP) halts translation, followed by docking of the ribosome on the ER membrane, release of the SRP, and
continuation of translation.
a. b. c. d.
The signal-recognition particle The SRP The SRP receptor brings the The protein ends up in the
(SRP) binds to a signal sequence binds to the ribosome to a transmembrane lumen of the ER, where it may
in the amino-terminal end of the SRP receptor channel; the SRP dissociates; remain, be transported to the
growing polypeptide and halts on the ER protein synthesis resumes; and lumen of another organelle, or
translation. membrane. the growing polypeptide chain be secreted out of the cell.
is threaded through the channel.
Cytosol
Ribosome
SRP
Signal
sequence
Proteins destined for cell membranes contain a signal-anchor ER membrane until the signal-anchor sequence is encountered
sequence in addition to the amino-terminal signal sequence (Fig. 5.26a). The signal-anchor sequence is hydrophobic and is
(Fig. 5.26). After the growing polypeptide chain and its ribosome therefore able to diffuse laterally in the lipid bilayer (Fig. 5.26b).
are brought to the ER, it is threaded through the channel in the At this point, the ribosome dissociates from the channel while
a. b. c.
Channel in
rough ER
Signal-anchor
sequence
Rough NH⫹
3 NH⫹ NH⫹
3
3
ER lumen
translation continues. When translation is completed, the carboxyl Mitochondria provide the eukaryotic cell with most
end of the chain remains on the cytosolic side of the ER membrane, of its usable energy.
the amino end is in the ER lumen, and the region between them Mitochondria are organelles that harness energy from chemical
resides in the membrane (Fig. 5.26c). Transmembrane proteins such compounds like sugars and convert it into ATP, which serves as the
as these may stay in the membrane of the ER or end up in other universal energy currency of the cell. ATP is able to drive the many
internal membranes or the plasma membrane, where they serve as chemical reactions in the cell. Mitochondria are present in nearly
transporters, pumps, receptors, or enzymes. all eukaryotic cells.
Mitochondria are rod-shaped organelles with an outer
membrane and a highly convoluted inner membrane whose folds
5.5 MITOCHONDRIA project into the interior (Fig. 5.27). A proton electrochemical
AND CHLOROPLASTS gradient is generated across the inner mitochondrial membrane,
and the energy stored in the gradient is used to synthesize ATP
The membranes of two organelles, mitochondria and for use by the cell. In the process of breaking down sugar and
chloroplasts, are not part of the endomembrane system. Both synthesizing ATP, oxygen is consumed and carbon dioxide is
of these organelles are specialized to harness energy for the cell. released. Does this process sound familiar? It also describes your
Interestingly, they are both semi-autonomous organelles that own breathing, or respiration. Mitochondria are the site of cellular
grow and multiply independently of the other membrane-bound respiration, and the oxygen that you take in with each breath
compartments, and they contain their own genomes. As we is used by mitochondria to produce ATP. Cellular respiration is
discuss in Chapter 27, the similarities between the DNA of these discussed in greater detail in Chapter 7.
organelles and the DNA of certain bacteria have led scientists to
conclude that these organelles originated as bacteria that were Chloroplasts capture energy from sunlight.
captured by a eukaryotic cell and, over time, evolved to their Both animal and plant cells have mitochondria to provide
current function. them with life-sustaining ATP. In addition, plant cells and
FIG. 5.27 Mitochondria. Mitochondria synthesize most of the ATP required to meet the cell’s energy needs. Source: Keith R. Porter/Science Source.
Mitochondria have a
double membrane, Outer membrane
consisting of an inner Inner membrane
and outer membrane
and an aqueous
compartment in between.
112 CO R E CO N C E P T S S U M M A RY
FIG. 5.28 Chloroplasts. Chloroplasts capture energy from sunlight and use it to synthesize sugars. Source: Dr. Jeremy Burgess/Science Source.
Chloroplasts are
Outer membrane
surrounded by a
double membrane Inner membrane
like mitochondria
and in addition have Thylakoid
a third membrane in membrane
the interior, the
thylakoid membrane.
green algae have organelles called chloroplasts that capture molecules called pigments, of which chlorophyll is the most
the energy of sunlight to synthesize simple sugars (Fig. 5.28). important. The green color of chlorophyll explains why so many
This process, called photosynthesis, results in the release of plants have green leaves.
oxygen as a waste product. Like the nucleus and mitochondria, Chlorophyll plays a key role in the chloroplast’s ability to
chloroplasts are surrounded by a double membrane. They also capture energy from sunlight. Using the light energy collected
have a third, internal membrane. This membrane defines a by this pigment, enzymes present in the chloroplast use
separate internal compartment called the thylakoid. The carbon dioxide as a carbon source to produce carbohydrates.
thylakoid membrane contains specialized light-collecting Photosynthesis is discussed in greater detail in Chapter 8. •
5.2 The plasma membrane is a selective barrier that The endoplasmic reticulum is continuous with the outer
controls the movement of molecules between the inside nuclear envelope and manufactures proteins and lipids for
and the outside of the cell. use by the cell or for export out of the cell. page 105
Selective permeability results from the combination of The Golgi apparatus communicates with the endoplasmic
lipids and proteins that makes up cell membranes. reticulum by transport vesicles. It receives proteins and
page 96 lipids from the endoplasmic reticulum and directs them
to their final destinations. page 105
Passive transport is the movement of molecules by
diffusion, the random movement of molecules. There Lysosomes break down macromolecules like proteins
is a net movement of molecules from regions of higher to simpler compounds that can be used by the cell. page 107
concentration to regions of lower concentration.
page 96
Protein sorting directs proteins to their final destinations
in or out of the cell. page 108
Passive transport can occur by the diffusion of molecules
directly through the plasma membrane (simple diffusion) Proteins synthesized on free ribosomes are sorted after
or be aided by protein transporters (facilitated translation and proteins synthesized on ribosomes associated
diffusion). page 96 with the rough endoplasmic reticulum are sorted during
translation. page 108
Active transport moves molecules from regions of lower
concentration to regions of higher concentration and Proteins synthesized on free ribososomes are often
requires energy. page 97 sorted by means of a signal sequence and are destined for
the cytosol, mitochondria, chloroplasts, or nucleus.
Primary active transport uses energy stored in ATP;
page 108
secondary active transport uses the energy stored in an
electrochemical gradient. page 98 Proteins synthesized on ribosomes on the rough endoplasmic
reticulum have a signal sequence that is recognized by a
Animal cells often maintain size and shape by protein
signal-recognition particle. These proteins end up as
pumps that actively move ions in and out of the cell.
transmembrane proteins, in the interior of various organelles,
page 99
or secreted. page 109
Plants, fungi, and bacteria have a cell wall outside the
plasma membrane that maintains cell size and shape. 5.5 Mitochondria and chloroplasts are organelles
page 100 involved in harnessing energy, and likely evolved from
free-living prokaryotes.
5.3 Cells can be classified as prokaryotes or Mitochondria harness energy from chemical compounds for
eukaryotes, which differ in the degree of internal use by both animal and plant cells. page 111
compartmentalization.
Chloroplasts harness the energy of sunlight to build
Prokaryotic cells lack a nucleus and other internal sugars. page 111
membrane-enclosed compartments. page 101
Eukaryotes include animals, plants, fungi, and protists. 2. Describe two types of association between proteins and
page 102 membranes.
The nucleus, which is enclosed by a double membrane 5. Explain the role of lipids and proteins in maintaining the
called the nuclear envelope, houses the genome. page 105 selective permeability of membranes.
114 SELF-ASSESSMENT
6. Distinguish between passive and active transport 10. Explain how a protein ends up free in the cytosol,
mechanisms across cell membranes. embedded in the plasma membrane, or secreted from the cell.
Making Life
Work
Capturing and Using Energy
Core Concepts
6.1 Metabolism is the set of
biochemical reactions that
transforms biomolecules and
transfers energy.
6.2 Kinetic energy is energy of
motion, and potential energy is
stored energy.
6.3 The laws of thermodynamics
govern energy flow in
biological systems.
6.4 Chemical reactions involve the
breaking and forming of bonds.
6.5 The rate of biochemical
reactions is increased by
protein catalysts called
Purestock/Getty Images. enzymes.
115
116 SECTION 6.1 A N OV E RV I E W O F M E TA B O L I S M
We have seen that cells require a way to encode and transmit chemical compounds (Fig. 6.1). Organisms that capture energy
information and a membrane to separate inside from out. The from sunlight are called phototrophs. Plants are the most familiar
third requirement of a cell is energy, which cells need to do work. example. Plants use the energy of sunlight to convert carbon
Cells grow and divide, move, change shape, pump ions in and out, dioxide and water into sugar and oxgen (Chapter 8). Sugars, such
transport vesicles, and synthesize macromolecules such as DNA, as glucose, contain energy in their chemical bonds that can be used
RNA, proteins, and complex carbohydrates. All of these activities to synthesize ATP, which in turn can power the work of the cell.
are considered work, and they therefore require energy. Other organisms derive their energy directly from chemical
We are all familiar with different forms of energy—the sun compounds. These organisms are called chemotrophs, and animals
and wind provide sources of energy, as do fossil fuels such as oil are familiar examples. Animals ingest other organisms, obtaining
and natural gas. We have learned to harness the energy from organic molecules such as glucose that they break down in the
these sources and convert it to other forms, such as electricity, to presence of oxygen to produce carbon dioxide and water. In this
provide needed power to our homes and cities. process, the energy in the chemical bonds of the organic molecule
Cells are faced with similar challenges. They must harness is converted to energy carried in the bonds of ATP (Chapter 7).
energy from the environment and convert it to a form that allows In drawing this distinction between plants and animals, we have
them to do the work necessary to sustain life. Cells harness to be careful. Although sunlight provides the energy that plants
energy from the sun and from chemical compounds, including use to synthesize glucose, plants still power most cellular processes
carbohydrates, lipids, and proteins. Although the source of energy by breaking down the sugar they make, just as animals do. And
may differ among cells, all cells convert energy to a form that can although chemotrophs harness energy from organic molecules, the
be easily used to drive cellular processes. All cells use energy in the energy in these organic molecules is generally derived from the sun.
form of a molecule called adenosine triphosphate (ATP). Bearing these two points in mind, we use the terms “phototroph”
ATP is often called the universal “currency” of cellular energy to and “chemotroph” because they call our attention to the flow of
indicate that ATP provides energy in a form that all cells can readily energy from the sun to organisms and then from one organism to
use to perform the work of the cell. Although “currency” provides the next (discussed more fully in Chapter 25).
a useful analogy for the role that ATP plays, keep in mind an Organisms can also be classified in terms of where they get their
important distinction between actual currency, such as a dollar bill, carbon (Fig. 6.1). Some organisms are able to convert carbon dioxide
and ATP. A dollar bill represents a certain value but does not in fact (an inorganic form of carbon) into glucose (an organic form of
have any value in itself. By contrast, ATP does not represent energy; carbon). These organisms are autotrophs, or “self feeders,” because
it actually contains energy in its chemical bonds. Nevertheless, the they make their own organic carbon using inorganic carbon as the
analogy is useful because ATP, like a dollar bill, engages in a broad starting material. Plants again are an example, so plants are both
range of energy “transactions” in the cell, as we discuss below. phototrophs and autotrophs, or photoautotrophs.
In this chapter, we consider energy in the context of cells. Other organisms do not have the ability to convert carbon
What exactly is energy? What principles govern its flow in dioxide into organic forms of carbon. Instead, they obtain their
biological systems? And how do cells make use of it? carbon from organic molecules synthesized by other organisms,
called preformed organic molecules. In other words, these
organisms eat other organisms or molecules derived from other
6.1 AN OVERVIEW OF METABOLISM organisms. Such organisms are heterotrophs, or “other feeders,”
as they rely on other organisms for their organic forms of carbon.
When considering a cell’s use of energy, it is helpful to also consider Animals obtain carbon in this way, and so animals are both
the cell’s sources of carbon because carbon is the backbone of chemotrophs and heterotrophs, or chemoheterotrophs. In fact,
the organic molecules that make up cells and because cells often animals get their energy and carbon from the same molecule. That
use carbon-based compounds as a stable form of energy storage. is, a molecule of glucose supplies both energy and carbon.
How organisms obtain the energy and carbon needed for growth As we move away from the familiar examples of plants
and other vital functions is so fundamental that it is sometimes and animals and begin in Part 2 to explore the diversity of life,
used to provide a metabolic classification of life (Fig. 6.1). Simply we will see that not all organisms fit into the two categories
put, organisms have two ways of harvesting energy from their of photoautotrophs and chemoheterotrophs (Fig. 6.1). Some
environment and two sources of carbon. Together, this means that microorganisms gain energy from sunlight but obtain their carbon
there are four principal ways in which organisms acquire the energy from preformed organic molecules; such organisms are called
and materials needed to grow, function, and reproduce. photoheterotrophs. Other microorganisms extract energy from
inorganic sources but build their own organic molecules; these
Organisms can be classified according to their energy organisms are called chemoautotrophs. They are often found in
and carbon sources. extreme environments, such as deep-sea vents, where sunlight
Organisms have two ways of harvesting energy from their is absent and inorganic compounds such as hydrogen sulfide
environment: They can obtain energy either from the sun or from are plentiful.
CHAPTER 6 M A K I N G L I F E W O R K : C A P T U R I N G A N D U S I N G E N E RG Y 117
FIG. 6.1 A metabolic classification of organisms. Organisms can be classified according to their energy and carbon sources. Photo sources:
(clockwise from top-left) Dr. Tony Brain/Science Source; ScienceFoto.DE/Dr. Andre Kemp/Getty Images; Copyright 1997 Microbial Diversity, Rolf Schauder; Martin
Oeggerli/Science Source; DNY59/iStockphoto; David J. Patterson; EM image by Manfred Rohde, Helmholtz Centre for Infection Research, Braunschweig, Germany;
Anna Omelchenko/Dreamstime.com.
All organisms
An a b o l i s m
release energy stored in their chemical bonds. The synthesis of than at the bottom (Fig. 6.3). If it were not blocked by the floor,
macromolecules such as carbohydrates and proteins, by contrast, it would move from the position of higher potential energy (the
is anabolic. top of the stairs) to the position of lower potential energy (the
bottom of the stairs) because of the force of gravity. Similarly, an
electrochemical gradient of molecules across a cell membrane is a
6.2 KINETIC AND POTENTIAL ENERGY form of potential energy. Given a pathway through the membrane,
the molecules move down their concentration and electrical
There are many different sources of energy, including sunlight, gradients from higher to lower potential energy (Chapter 5).
wind, electricity, and fossil fuels. The food we eat also contains Energy can be converted from one form to another. The ball
energy. Energy can be defined as the capacity to do work. For a at the top of the stairs has a certain amount of potential energy
cell, work involves processes we discussed in earlier chapters, such because of its position. As it rolls down the stairs, this potential
as synthesizing DNA, RNA, and proteins, pumping substances energy is converted to kinetic energy associated with movement
across the plasma membrane, and moving vesicles between of the ball and the surrounding air. When the ball reaches the
various compartments of a cell. bottom of the stairs, the remaining energy is stored as potential
Although there are many different sources of energy, energy energy. Conversely, it takes an input of energy to move the ball
comes in just two major forms. In this section, we consider these back to the top of the stairs, and this input of energy is stored as
two forms of energy. In addition, we focus on how energy is held in potential energy.
chemical bonds of molecules such as glucose and ATP.
Chemical energy is a form of potential energy.
Kinetic energy and potential energy are two forms We obtain the energy we need from the food we eat, which
of energy. contains chemical energy. Chemical energy is a form of potential
Energy can be classified as one of two forms: kinetic energy or energy held in the chemical bonds between pairs of atoms in a
potential energy (Fig. 6.3). Kinetic energy is the energy of motion, molecule. Recall from Chapter 2 that a covalent bond results from
and it is perhaps the most familiar form of energy. A moving the sharing of electrons between two atoms. Covalent bonds form
object, such as a ball bouncing down a set of stairs, possesses kinetic when the sharing of electrons between two atoms results in a
energy. Kinetic energy is associated with any kind of movement, more stable configuration than if the orbitals of the two atoms did
such as a person running or a muscle contracting. Similarly, light not overlap.
is associated with the movement of photons, electricity with the The more stable configuration will always be the one with
movement of electrons, and thermal energy (perceived as heat) lower potential energy. As a result, energy is required to break a
with the movement of molecules, so these, too, are forms of covalent bond because going from a lower energy state to a higher
kinetic energy. one requires an input of energy. Conversely, energy is released
Energy is not always associated with motion. An immobile when a covalent bond forms.
object can still possess a form of energy called potential energy, Some bonds are stronger than other ones. A strong bond
or stored energy. Potential energy depends on the structure of the is hard to break because the arrangement of orbitals in these
object or its position relative to its surroundings, and it is released molecules is much more stable than the two atoms would be on
by a change in the object’s structure or position. For example, the their own. As a result, strong bonds do not contain very much
potential energy of a ball is higher at the top of a flight of stairs chemical energy, similar to the potential energy of a ball at
the bottom of a flight of stairs (Fig. 6.3). This may at first seem
counterintuitive, but makes sense when you consider that strong
FIG. 6.3 Potential and kinetic energy. Some of the high potential bonds have a very stable arrangement of orbitals and therefore do
energy of a ball at the top of a set of stairs is transformed to not require a lot of energy to remain intact. Examples of molecules
kinetic energy as the ball rolls down the stairs. with strong covalent bonds that contain relatively little chemical
energy are carbon dioxide (CO2) and water (H2O).
Conversely, some covalent bonds are relatively weak. These
bonds are easily broken because the arrangement of orbitals in
these molecules is only somewhat more stable than if the two
atoms did not share any electrons. As a result, weak covalent
bonds require a lot of energy to stay intact and contain a lot
of chemical energy, similar to the potential energy of a ball at
the top of a flight of stairs (Fig. 6.3). Organic molecules such
as carbohydrates, lipids, and proteins contain relatively weak
High potential energy Kinetic energy Low potential energy covalent bonds, including many carbon–carbon (C–C) bonds and
CHAPTER 6 M A K I N G L I F E W O R K : C A P T U R I N G A N D U S I N G E N E RG Y 119
Free energy
Amount of Amount of
concentrations of reactants and products. For example, increasing
energy energy
the concentration of the reactants or decreasing the concentration required (+∆G) released (–∆G)
of the products favors the forward reaction. This effect explains
how many reactions in metabolic pathways proceed: The products Reactants Products
of many reactions are quickly consumed by the next reaction,
helping to drive the first reaction forward. Course of reaction Course of reaction
122 SECTION 6.4 C H E M I C A L R E AC T I O N S
∆G 5 ∆H 2 T∆S
Catabolism
An a bo l i s m
depends on both the change in enthalpy and the change in disorder.
–∆G +∆G
Catabolic reactions are those in which the products have less
chemical energy (lower enthalpy) in their bonds than the reactants ATP + H2O ATP + H2O
have, and the products are more disordered (higher entropy) than
the reactants are. In other words, such reactions have a negative
value of ∆H and a positive value of ∆S. Notice that, in the equation
∆G 5 ∆H 2 T∆S, there is a negative sign in front of ∆S, so both the
negative ∆H and positive ∆S contribute to a negative ∆G. Therefore,
these reactions proceed spontaneously (Fig. 6.9).
The reverse is also true: Increasing chemical energy (positive More disorder (+∆S),
less chemical energy
∆H) and decreasing disorder (negative ∆S), as in the synthesis of in bonds (–∆H).
proteins from individual amino acids and other anabolic reactions,
results in a positive value of ∆G and requires a net input of energy
(Fig. 6.9).
There are also cases in which the change in enthalpy and the
The reaction of ATP with water is an exergonic reaction
change in entropy are both positive or both negative. In these
because there is less free energy in the products compared to the
cases, the absolute value of these parameters determines whether
reactants. The free energy difference can be explained by referring
∆G is positive or negative and therefore whether a reaction is
to the formula we derived in the last section. Recall that the
spontaneous or not.
phosphate groups of ATP are negatively charged at physiological
j Quick Check 2 How does increasing the temperature affect the pH and repel each other. ATP has three phosphate groups, and ADP
change in free energy (∆G ) of a chemical reaction? has two. Therefore, ADP is more stable (contains less chemical
energy in its bonds) than ATP, resulting in a negative value of ∆H.
In addition, a single molecule of ATP is broken down into two
The hydrolysis of ATP is an exergonic reaction. molecules, ADP and Pi. Therefore, the reaction is also associated
Let’s apply these concepts to a specific chemical reaction.
with an increase in entropy, or a positive value of ∆S. Since
Earlier, we introduced ATP, the molecule that drives many
∆G 5 ∆ H 2 T∆ S, ∆ G is negative and the reaction is a spontaneous
cellular processes using the chemical potential energy in its
one that releases energy available to do work.
chemical bonds. ATP reacts with water to form ADP and inorganic
The free energy difference for ATP hydrolysis is approximately
phosphate, Pi (HPO422), as shown here and in Fig. 6.10:
–7.3 kcal per mole (kcal/mol) of ATP. This value is influenced
ATP 1 H2O → ADP 1 Pi by several factors, including the concentration of reactants and
products, the pH of the solution in which the reaction occurs,
This is an example of a hydrolysis reaction, a chemical reaction in and the temperature and pressure. The value –7.3 kcal/mol is
which a water molecule is split into a proton (H1) and a hydroxyl the value under standard laboratory conditions in which the
group (OH2). Hydrolysis reactions often break down polymers into concentrations of reactants and products are equal and pressure
their subunits, and in the process one product gains a proton and is held constant. In a cell, it is likely higher, on the order of
the other gains a hydroxyl group. –12 kcal/mol.
CHAPTER 6 M A K I N G L I F E W O R K : C A P T U R I N G A N D U S I N G E N E RG Y 123
FIG. 6.10 ATP hydrolysis. ATP hydrolysis is an exergonic reaction that releases free energy.
OH OH OH OH
Keep in mind that the release of free energy during ATP for the two reactions is negative. So ATP hydrolysis provides the
hydrolysis comes from breaking weaker bonds (with more thermodynamic driving force for the non-spontaneous reaction,
chemical energy) in the reactants and forming more stable bonds and the shared phosphate group couples the two reactions
(with less chemical energy) in the products. The release of free together.
energy then drives chemical reactions and other processes that Following ATP hydrolysis, the cell needs to replenish its
require a net input of energy, as we discuss next. ATP so that it can carry out additional chemical reactions. The
synthesis of ATP from ADP and Pi is an endergonic reaction with a
Non-spontaneous reactions are positive ∆G, requiring an input of energy. In some cases, exergonic
often coupled to spontaneous reactions. reactions can drive the synthesis of ATP by energetic coupling
If the conversion of reactant A into product B is spontaneous, the (Fig. 6.11b). The sum of the ∆G’s of the two reactions is negative
reverse reaction converting reactant B into product A is not. The and the reactions share a phosphate group, allowing the two
∆ G’s for the forward and reverse reactions have the same absolute reactions to proceed.
value but opposite signs. You might expect that the direction Like ATP, other phosphorylated molecules can be hydrolyzed,
of the reaction would always be from A to B. However, in living releasing free energy. Hydrolysis reactions can be ranked by their
organisms, not all chemical reactions
are spontaneous. Anabolic reactions are
a good example; they require an input
of energy to drive them in the right FIG. 6.11 Energetic coupling. A spontaneous (exergonic) reaction drives a non-spontaneous
direction. This raises the question: What (endergonic) reaction. (a) The hydrolysis of ATP drives the formation of glucose
drives non-spontaneous reactions? 6-phosphate from glucose. (b) The hydrolysis of phosphoenolpyruvate drives the
Energetic coupling is a process in synthesis of ATP.
which a spontaneous reaction (negative The coupled reaction
∆ G) drives a non-spontaneous reaction proceeds because ∆G is
(positive ∆ G). It requires that the net negative and Pi is shared
between the two reactions.
∆ G of the two reactions be negative. In
a.
addition, the two reactions must occur
ATP + H2O ADP + Pi ∆G1 = –7.3 kcal/mol Exergonic reaction
together. In some cases, this coupling
Glucose + Pi Glucose + H2O ∆G2 = +3.3 kcal/mol Endergonic reaction
can be achieved if the two reactions
6-phosphate
share an intermediate.
For example, ATP hydrolysis can Glucose + ATP Glucose + ADP ∆G = –4 kcal/mol Coupled reaction
6-phosphate
be used to drive a non-spontaneous
reaction, as shown in Fig. 6.11a. In this b.
case, the phosphate group released Phosphoenolpyruvate + H2O Pyruvate + Pi ∆G1 = –14.8 kcal/mol Exergonic reaction
during ATP hydrolysis is transferred
ADP + Pi ATP + H2O ∆G2 = +7.3 kcal/mol Endergonic reaction
to glucose to produce glucose
6-phosphate. In addition, the net ∆G Phosphoenolpyruvate + ADP Pyruvate + ATP ∆G = –7.5 kcal/mol Coupled reaction
124 SECTION 6.5 E N Z Y M E S A N D T H E R AT E O F C H E M I C A L R E AC T I O N S
S1E ES EP E1P
All reactions require an input of
energy, called activation energy
(EA), to proceed. The formation of this complex is critical for accelerating the
rate of a chemical reaction. Recall from Chapter 4 that proteins
Transition state adopt three-dimensional shapes and that the shape of a protein is
An enzyme linked to its function. Enzymes are folded into three-dimensional
accelerates
EA the reaction shapes that bring particular amino acids into close proximity to
Free energy
by reducing form an active site. The active site of the enzyme is the portion
EA E A.
of the enzyme that binds substrate and catalyzes its conversion
Reactants to the product (Fig. 6.14). In the active site, the enzyme and
∆G is the same substrate form transient covalent bonds and/or weak noncovalent
∆G with and
Uncatalyzed reaction without an interactions. Together, these interactions stabilize the transition
Catalyzed reaction enzyme. state and decrease the activation energy.
Products
Enzymes also reduce the energy of activation by positioning
Course of reaction two substrates to react. The formation of the enzyme–substrate
complex promotes the reaction between two substrates by
aligning their reactive chemical groups and limiting their motion
relative to each other.
Although an enzyme accelerates a reaction by reducing The size of the active site is extremely small compared with
the activation energy, the difference in free energy between the size of the enzyme. If only a small fraction of the enzyme
reactants and products (∆G) does not change. In other words, an is necessary for the catalysis of a reaction, why are enzymes so
enzyme changes the path of the reaction between reactants and large? Of the many amino acids that form the active site, only a
products, but not the starting or end point (Fig. 6.13). Consider few actively contribute to catalysis. Each of these amino acids has
the breakdown of glucose into carbon dioxide and water. The ∆G to occupy a very specific spatial position to align with the correct
of the reaction is the same whether it proceeds by combustion reactive group on the substrate. If the few essential amino acids
or by the action of multiple enzymes in a metabolic pathway in were part of a short peptide, the alignment of chemical groups
a cell. between the peptide and the substrate would be difficult or
even impossible because the length of the bonds and the bond
j Quick Check 3 Which of the following do enzymes change? ∆G ;
angles in the peptide would constrain its three-dimensional
reaction rate; types of product generated; activation energy; the
structure. In fact, in many cases the catalytic amino acids are spaced
laws of thermodynamics.
far apart in the primary structure of the enzyme, but brought close
S P
FIG. 6.16
Do enzymes form complexes enzyme b-galactosidase binds b-thiogalactoside but cannot cleave
or release it.
HO O HO O
BACKGROUND The idea that enzymes form complexes with H O R H S R
OH H OH H
substrates to catalyze a chemical reaction was first proposed in
H H H H
1888 by the Swedish chemist Svante Arrhenius. One of the earliest
experiments that supported this idea was performed by American H OH H OH
β-galactoside β-thiogalactoside
chemist Kurt Stern in the 1930s. He studied an enzyme called
catalase, which is very abundant in animal and plant tissues. In the
conclusion of his paper, he wrote, “It remains to be seen to which METHOD A container is separated into two compartments by a
extent the findings of this study apply to enzyme action in general.” selectively permeable membrane. The membrane is permeable
Therefore, another experiment that analyzes a different enzyme and to b-galactoside and b-thiogalactoside, but not permeable to the
technique are described here. enzyme.
orientations within a molecule. The specificity of enzymes can Inhibitors can act in many different ways, two of which are
be attributed to the structure of their active sites. The enzyme shown in Fig. 6.17. In some cases, an inhibitor is similar in structure
active site interacts only with substrates having a precise three- to the substrate and therefore is able to bind to the active site of the
dimensional structure. enzyme (Fig. 6.17a). Binding of the inhibitor prevents the binding
of the substrate. In other words, the inhibitor competes with the
Enzyme activity can be influenced by inhibitors and substrate for the active site of the enzyme. These types of inhibitors
activators. can often be overcome by increasing the concentration of substrate.
The activity of enzymes can be influenced by inhibitors and Other inhibitors bind to a site other than the active site of the
activators. Inhibitors decrease the activity of enzymes, whereas enzyme, but still inhibit the activity of the enzyme (Fig. 6.17b). In
activators increase the activity of enzymes. Enzyme inhibitors are this case, binding of the inhibitor changes the shape and activity
quite common. They are synthesized naturally by many plants and of the enzyme. This type of inhibitor usually has a structure very
animals as a defense against predators. Similarly, pesticides and different from that of the substrate.
herbicides often target enzymes to inactivate them. Many drugs Enzymes that are regulated by molecules that bind at sites
used in medicine are enzyme inhibitors, including drugs used to other than their active sites are called allosteric enzymes. The
treat infections as well as drugs used to treat cancer and other activity of allosteric enzymes can be influenced by both inhibitors
diseases. Given the importance of chemical reactions and the and activators. They play a key role in metabolic pathways, as we
role of enzymes in metabolism, it is not surprising that enzyme discuss next.
inhibitors have such widespread applications.
There are two classes of inhibitors. Irreversible inhibitors Allosteric enzymes regulate key metabolic pathways.
usually form covalent bonds with enzymes and irreversibly Enzyme activators and inhibitors are sometimes important in the
inactivate them. Reversible inhibitors form weak bonds with normal operation of a cell—for example, to regulate a metabolic
enzymes and therefore easily dissociate from them. pathway. Consider the synthesis of isoleucine from threonine,
EXPERIMENT 1 Radioactively labeled b-thiogalactoside (S) is RESULT Over time, the level of radioactivity is greater in
added to compartment 1 and the movement of S is followed by compartment 2 than in compartment 1.
measuring the level of radioactivity in the two compartments.
Substrate Time
CONCLUSION These results can be explained if the substrate
diffuses from compartment 1 to compartment 2, forms a complex
with the enzyme, and is not released because the enzyme cannot
catalyze the conversion of substrate to product. In other words,
E and S form a complex.
EXPERIMENT 2 Radioactively labeled b-thiogalactoside (S) is
added to compartment 1, enzyme (E) is added to compartment SOURCES Adapted from Doherty, D. G., and F. Vaslow. 1952. “Thermodynamic
2, and the movement of S is followed by measuring the level of Study of an Enzyme–Substrate Complex of Chymotrypsin.” J. Am. Chem. Soc. 74:
931–936. Stern, K. G. 1936. “On the Mechanism of Enzyme Action: A Study
radioactivity in the two compartments. of the Decomposition of Monoethyl Hydrogen Peroxide by Catalase and of an
Intermediate Enzyme–Substrate Compound.” J. Biol. Chem. 114:473–494.
128 SECTION 6.5 E N Z Y M E S A N D T H E R AT E O F C H E M I C A L R E AC T I O N S
FIG. 6.17 Two mechanisms of inhibitor function. (a) Some inhibitors bind to the active site of the enzyme and (b) other inhibitors bind to a site that
is different from the active site. Both types of inhibitor reduce the activity of an enzyme and therefore decrease the rate of the reaction.
a. b.
Substrate Product Substrate
Product
Active site
Enzyme
Enzyme
Inhibitor site In this case, the inhibitor binds to a site
In this case, the inhibitor binds to the other than the active site, changing the
active site of the enzyme, competing shape of the enzyme and reducing the
Inhibitor with the substrate and reducing the rate of the reaction.
rate of the reaction. Inhibitor
a pathway found in some bacteria. This conversion requires five of the five reactions. Isoleucine binds to the first enzyme in the
reactions, each catalyzed by a different enzyme (Fig. 6.18). pathway, threonine dehydratase, at a site distinct from the active
Once the bacterium has enough isoleucine for its needs, it site. As a result, threonine dehydratase is an example of an allosteric
would be a waste of energy to continue synthesizing the amino acid. enzyme. The binding of isoleucine changes the shape of the enzyme
To shut down the pathway once it is no longer needed, the cell relies and in this way inhibits its function.
on an enzyme inhibitor. The inhibitor is isoleucine, the final product The isoleucine pathway also provides an example of negative
feedback, in which the final product inhibits the first step of the
reaction. This is a common mechanism used widely in organisms
FIG. 6.18 Regulation of threonine dehdyratase, an allosteric to maintain homeostasis, that is, the active maintenance of stable
enzyme. The enzyme is inhibited by the final product, conditions or steady levels of a substance (Chapter 5).
isoleucine, which binds to a site distinct from the Threonine dehydratase can also adjust the rate of the
active site. reaction, depending on the concentration of substrate. At a low
concentration of threonine, the rate of the reaction is very slow.
Threonine As the concentration of threonine increases, the activity of
the enzyme increases. At a particular threshold, a small increase
Threonine in threonine concentration results in a large increase in reaction
dehydratase rate. Finally, when there is excess substrate, the reaction rate
P1
slows down.
In the next two chapters, we examine more closely two key
metabolic processes, cellular respiration and photosynthesis. Both
of these processes require many chemical reactions acting in a
coordinated fashion. Allosteric enzymes catalyze key reactions
P2
in these and other metabolic pathways. These enzymes are
usually found at or near the start of a metabolic pathway or at the
crossroads between two metabolic pathways. Allosteric enzymes
– Allosteric
inhibitor are one way that the cell coordinates the activity of multiple
P3
metabolic pathways.
Metallic cofactors, especially iron, magnesium, manganese, cobalt, mid-ocean hydrothermal vent systems and other environments
copper, zinc, and molybdenum, bind to diverse proteins, including where oxygen is absent. It has been proposed that reactions now
enzymes used in DNA synthesis and nitrogen metabolism. With carried out in cells by iron–sulfur proteins are the evolutionary
this in mind, scientists have asked whether metal ions might, by descendants of chemical reactions that took place spontaneously
themselves, catalyze chemical reactions thought to have played on the early Earth.
a role in the origin of life. They do. For example, magnesium The idea that your cells preserve an evolutionary memory
and zinc ions added to solutions can accelerate the linking of of ancient hydrothermal environments may seem like science
nucleotides to form RNA and DNA molecules. fiction, but it finds support in laboratory experiments. For
Metallic cofactors also bind to enzymes used in the transport example, the reaction of H2S and FeS to form pyrite has been
of electrons for cellular respiration and photosynthesis, processes shown to catalyze a number of plausibly pre-biotic chemical
that are discussed in the next two chapters. Enzymes that contain reactions, including the formation of pyruvate (a key intermediate
iron and sulfur clustered together are particularly important in in energy metabolism discussed in Chapter 7). Thus, the metals in
the transport of electrons within cells. Iron–sulfur minerals, enzymes help connect the chemistry of life to the chemistry of
especially pyrite (or fool’s gold, FeS2), form commonly in Earth. •
Core Concepts Summary The second law of thermodynamics states that there is an
increase in entropy in the universe over time. page 120
6.1 Metabolism is the set of biochemical reactions
that transforms biomolecules and transfers energy. 6.4 Chemical reactions involve the breaking and
forming of bonds.
Organisms can be grouped according to their source of
energy: Phototrophs obtain energy from sunlight and In a chemical reaction, atoms themselves do not change,
chemotrophs obtain energy from chemical compounds. but which atoms are linked to each other changes, forming
page 116 new molecules. page 121
Organisms can also be grouped according to the source of The direction of a chemical reaction is influenced by the
carbon they use to build organic molecules: Heterotrophs concentration of reactants and products. page 121
obtain carbon from organic molecules, and autotrophs
Gibbs free energy (G) is the amount of energy available to
obtain carbon from inorganic sources, such as carbon
do work. page 121
dioxide. page 116
Three thermodynamic parameters define a chemical
Catabolism is the set of reactions that break down
reaction: Gibbs free energy (G), enthalpy (H), and
molecules and release energy, and anabolism is the set of
entropy (S). page 121
reactions that build molecules and require energy.
page 117 Exergonic reactions are spontaneous (ΔG < 0) and release
energy. page 121
6.2 Kinetic energy is energy of motion and potential Endergonic reactions are non-spontaneous (ΔG > 0) and
energy is stored energy. require energy. page 121
Kinetic energy is due to motion. page 118
The change of free energy in a chemical reaction is
Potential energy depends on the structure of an object or described by ΔG 5 ΔH – TΔS. page 122
its position relative to its surroundings. page 118
The hydrolysis of ATP is an exergonic reaction that drives
Chemical energy is a form of potential energy held in the many endergonic reactions in a cell. page 122
bonds of molecules. page 118
In living systems, non-spontaneous reactions are often
coupled to spontaneous ones. page 123
6.3 The laws of thermodynamics govern energy flow
in biological systems.
The first law of thermodynamics states that energy cannot
be created or destroyed. page 119
130 S E LCFT-IAOSNS E5S. S
1M EMN T
An enzyme is highly specific for its substrate and for the 7. If the difference between the enthalpy of the products
types of reaction it catalyzes. page 126 and that of the reactants is positive and the difference
between the entropy of the products and reactants is
Inhibitors reduce the activity of enzymes and can act
negative, predict whether the reaction is spontaneous
irreversibly or reversibly. page 127
or not.
Activators increase the activity of enzymes. page 127
8. Describe how the hydrolysis of ATP can drive non-
Allosteric enzymes bind activators and inhibitors at sites spontaneous reactions in a cell.
other than the active site, resulting in a change in their
9. Give three characteristics of enzymes and describe
shape and activity. page 127
how they permit chemical reactions to occur in cells.
Allosteric enzymes are often found at or near the start
10. Explain how protein folding allows for enzyme specificity.
of a metabolic pathway or at the crossroads of multiple
pathways. page 128
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CHAPTER 7
Cellular
Respiration
Harvesting Energy from
Carbohydrates and Other
Fuel Molecules
Core Concepts
7.1 Cellular respiration is a series
of catabolic reactions that
convert the energy in fuel
molecules into ATP.
7.2 Glycolysis is the partial
oxidation of glucose and results
in the production of pyruvate,
as well as ATP and reduced
electron carriers.
7.3 Pyruvate is oxidized to acetyl-
CoA, connecting glycolysis to
the citric acid cycle.
7.4 The citric acid cycle results in
the complete oxidation of fuel
molecules and the generation
of ATP and reduced electron
carriers.
7.5 The electron transport
chain transfers electrons
from electron carriers to
oxygen, using the energy
released to pump protons and
synthesize ATP by oxidative
phosphorylation.
7.6 Glucose can be broken down
in the absence of oxygen by
fermentation, producing a
modest amount of ATP.
7.7 Metabolic pathways are
integrated, allowing control of
Image Source/Getty Images.
131
132 SECTION 7.1 A N OV E RV I E W O F C E L LU L A R R E S P I R AT I O N
The ability to harness energy from the environment is a key as glucose, fatty acids, and proteins are catabolized into smaller
attribute of life. We have seen that energy is needed for all kinds units, releasing the energy stored in their chemical bonds to power
of tasks—among them cell movement and division, muscle the work of the cell.
contraction, growth and development, and the synthesis of
macromolecules. Organic molecules such as carbohydrates, lipids, Cellular respiration uses chemical energy stored
and proteins are good sources of chemical energy. Some organisms, in molecules such as carbohydrates and lipids to
like humans and other heterotrophs, obtain organic molecules produce ATP.
by consuming them in their diet. Others, like plants and other Cellular respiration is a series of catabolic reactions that converts
autotrophs, synthesize these molecules from inorganic molecules the energy stored in food molecules, such as glucose, into the
like carbon dioxide, as we saw in Chapter 6. Regardless of how energy stored in ATP, and produces carbon dioxide as a waste or
organic molecules are obtained, nearly all organisms—animals, by-product. It can occur in the presence of oxygen (termed
plants, fungi, and microbes—break them down in the process aerobic respiration) or in the absence of oxygen (termed anaerobic
of cellular respiration, releasing energy that can be used to do respiration). Most organisms that you are familiar with are capable
the work of the cell. Cellular respiration is a series of chemical of aerobic respiration; some bacteria respire anaerobically
reactions that convert the chemical energy in fuel molecules into (Chapter 26). Here we focus on aerobic respiration. Oxygen is
the chemical energy of adenosine triphosphate (ATP), which can consumed in aerobic respiration, and carbon dioxide and water are
be readily used by cells. produced, as follows:
It is tempting to think that organic molecules are converted
into energy in this process, but this is not the case. Recall from C6H12O6 1 6O2 → 6CO2 1 6H2O 1 energy
Chapter 6 that the first law of thermodynamics (the law of Glucose Oxygen Carbon Water
conservation of energy) states that energy cannot be created or dioxide
destroyed. Biological processes, like all processes, are subject to
the laws of thermodynamics. As a result, the process of cellular In Chapter 6, we saw that molecules such as carbohydrates and
respiration converts the chemical potential energy stored in lipids have a large amount of potential energy in their chemical
organic molecules to chemical potential energy that is useful to bonds. In contrast, molecules like carbon dioxide and water have
cells: the chemical potential energy in ATP. ATP is the universal less potential energy in their bonds. Cellular respiration releases a
energy currency for all cells. large amount of energy because the sum of the potential energy in
It is also easy to forget that organisms other than animals, all of the chemical bonds of the reactants (glucose and oxygen) is
such as plants, use cellular respiration. If plants use sunlight as a higher than that of the products (carbon dioxide and water). The
source of energy, why would they need cellular respiration? As we maximum amount of free energy—energy available to do work—
will see in the next chapter, plants use the energy of sunlight to released during cellular respiration is –686 kcal per mole of glucose.
make carbohydrates. Plants then break down these carbohydrates Recall from Chapter 6 that when ∆G < 0, energy is released.
in the process of cellular respiration to produce ATP. The overall reaction for cellular respiration helps us focus
In this chapter, we discuss the metabolic pathways that on the starting reactants, final products, and release of energy.
supply the energy needs of a cell: the breakdown, storage, and However, it misses the many intermediate steps that take place
mobilization of sugars such as glucose, the synthesis of ATP, and as the cell catabolizes glucose. Tossing a match into the gas tank
the coordination and regulation of these metabolic pathways. of a car releases a tremendous amount of energy in the form of
an explosion, but this energy is not used to do work. Instead, it
is released as light and heat. Similarly, if all the energy stored in
glucose were released at once, most of it would be released as heat
7.1 AN OVERVIEW OF CELLULAR and the cell would not be able to harness it to do work.
RESPIRATION In cellular respiration, energy is released gradually in a series
of chemical reactions (Fig. 7.1). This allows some of this energy to
In the last chapter, we saw that catabolism describes the set of be used to form ATP. On average, 32 molecules of ATP are produced
chemical reactions that break down molecules into smaller units. from the aerobic respiration of a single molecule of glucose. The
In the process, these reactions release chemical energy that can energy needed (∆G of the reaction) to form one mole of ATP from
be stored in molecules of ATP. Anabolism, by contrast, is the set ADP and Pi is at least 7.3 kcal. Thus, cellular respiration harnesses
of chemical reactions that build molecules from smaller units. at least 32 7.3 5 233.6 kcal of energy in ATP for every mole of
Anabolic reactions require an input of energy, usually in the form glucose that is broken down in the presence of oxygen.
of ATP. About 34% of the total energy released by aerobic respiration
Cellular respiration is one of the major sets of catabolic is harnessed in the form of ATP (233.6/686 5 34%), with the
reactions in a cell. During cellular respiration, fuel molecules such remainder of the energy given off as heat. This degree of efficiency
CHAPTER 7 C E L L U L A R R E S P I R AT I O N : H A RV E S T I N G E N E RG Y F RO M C A R B O H Y D R AT E S A N D OT H E R F U E L M O L E C U L E S 133
FIG. 7.2 Oxidation and reduction in the overall reaction for FIG. 7.3 The four stages of cellular respiration. Cellular
cellular respiration. Electrons are partially lost or gained respiration consists of glycolysis, pyruvate oxidation, the
in the formation of polar covalent bonds. citric acid cycle, and oxidative phosphorylation.
a. Oxidation
Glucose Amino Fatty Glucose
CH2OH acids acids Stage 1
C O Glycolysis Glycolysis
H OH
H
C C Carbon dioxide
OH H ATP Stages 1 & 2:
HO H Fuel molecules
C C O C O are partially
H OH broken down,
producing ATP
Dark Pyruvate and electron
shading carriers.
represents
increased
electron CO2 Stage 2
C C C O density.
Pyruvate
Acetyl-CoA oxidation
Carbon atoms share Carbon atom has partially lost
electrons equally. electrons (and is oxidized) because the
oxygen atom is more electronegative Stage 3
than the carbon atom.
Citric acid
cycle
b. Reduction Citric acid
Oxygen Water cycle
Stage 3:
H H CO2 Fuel molecules
O O
O are fully broken
down, producing
ATP and electron
ATP carriers.
Electron
O O H O carriers Stage 4
Oxidative
e- phosphorylation
Oxygen atoms share Oxygen atom has partially gained
electrons equally. electrons (and is reduced) because the
oxygen atom is more electronegative O2 Stage 4:
than the hydrogen atom. Electron transport chain Electron carriers
donate electrons
H2O to the electron
transport chain,
leading to the
respiration, glucose is oxidized, releasing carbon dioxide, and at synthesis of ATP.
the same time oxygen is reduced, forming water: ATP
Oxidation
C6H12O6 1 6O2 → 6CO2 1 6H2O 1 energy oxygen atom is more electronegative than the carbon atom, so the
electrons are more likely to be found near the oxygen atom.
Reduction As a result, carbon has partially lost electrons to oxygen and is
oxidized.
Let’s first consider the oxidation reaction (Fig. 7.2a). In Let’s now consider the reduction reaction (Fig. 7.2b). In
glucose, there are many C–C and C–H covalent bonds, in which oxygen gas, electrons are shared equally between two oxygen
electrons are shared about equally between the two atoms. By atoms. In water, the electrons that are shared between hydrogen
contrast, in carbon dioxide, electrons are not shared equally. The and oxygen are more likely to be found near oxygen because
CHAPTER 7 C E L L U L A R R E S P I R AT I O N : H A RV E S T I N G E N E RG Y F RO M C A R B O H Y D R AT E S A N D OT H E R F U E L M O L E C U L E S 135
FIG. 7.5 Glycolysis. Glucose is partially oxidized to pyruvate, with the net production of 2 ATP and 2 NADH.
Glucose C O
Glycolysis
H H
ATP H
C C
OH H
ATP
HO OH
First
1
Pyruvate
C C
ATP-consuming
CO2
reaction ADP H OH
Acetyl-CoA Phase 1
ATP
2
Electron
carriers
Fructose 6-phosphate
e-
molecules OH H
Phase 2
Glyceraldehyde 3-phosphate
+ Cleavage phase
Dihydroxyacetone phosphate
5 O
Glyceraldehyde 3-phosphate Glyceraldehyde 3-phosphate P O CH2 CH C
Pi Pi H
OH
NADH- NAD+ NAD+
producing
reaction
6 6
NADH H NADH H
1,3-Bisphosphoglycerate 1,3-Bisphosphoglycerate
First ADP ADP
ATP-producing 7 7
reaction ATP ATP
Phase 3
3-Phosphoglycerate 3-Phosphoglycerate
Payoff phase,
8 8 with production of
4 ATP and 2 NADH
2-Phosphoglycerate 2-Phosphoglycerate
9 9
Phosphoenolpyruvate Phosphoenolpyruvate
ADP ADP
Second
ATP-producing 10 10
reaction ATP ATP O
CH3 C C
Pyruvate Pyruvate
O O
CHAPTER 7 C E L L U L A R R E S P I R AT I O N : H A RV E S T I N G E N E RG Y F RO M C A R B O H Y D R AT E S A N D OT H E R F U E L M O L E C U L E S 137
FIG. 7.7 Pyruvate oxidation. Pyruvate is oxidized in the mitochondrial matrix, forming
acetyl-CoA, the first substrate in the citric acid cycle.
Amino Fatty Glucose
acids acids
Glycolysis
ATP
Pyruvate
CO2
Acetyl-CoA
Cytosol Intermembrane space Matrix
Citric acid
cycle NAD+ NADH H
CO2
Pyruvate Acetyl-CoA
ATP O
CH3 C C CH3 C CoA
Electron
carriers
O O O
e-
Coenzyme A
O2
Electron transport chain
CO2
H2O
ATP
dioxide and one molecule of NADH. Recall, however, that a the variant names “citric acid cycle” and “tricarboxylic acid
single molecule of glucose forms two molecules of pyruvate cycle”). The molecule of citric acid is then oxidized in a series of
during glycolysis. Therefore, two molecules of carbon dioxide, reactions. The last reaction of the cycle regenerates a molecule of
two molecules of NADH, and two molecules of acetyl-CoA are oxaloacetate, joining to a new acetyl group and allowing the cycle
produced from a single starting glucose molecule in this stage of to continue.
cellular respiration. Acetyl-CoA is the substrate of the first step in The citric acid cycle results in the complete oxidation of
the citric acid cycle. the acetyl group of acetyl-CoA. Since the first reaction creates
a molecule with six carbons and the last reaction regenerates a
4-carbon molecule, two carbons are eliminated during the cycle.
7.4 THE CITRIC ACID CYCLE These carbons are released as carbon dioxide. Along with the
release of carbon dioxide from pyruvate during pyruvate oxidation,
The citric acid cycle is the stage in cellular respiration in which these reactions are the sources of carbon dioxide released during
fuel molecules are completely oxidized. Specifically, the acetyl cellular respiration and therefore the sources of the carbon dioxide
group of acetyl-CoA is completely oxidized to carbon dioxide that we exhale when we breathe.
and the chemical energy is transferred to ATP by substrate-level The oxidation reactions that produce carbon dioxide are
phosphorylation and to the reduced electron carriers NADH and coupled with the reduction of the electron carrier NAD1 to NADH
FADH2. In this way, the citric acid cycle supplies electrons to the (Fig. 7.8). In this way, energy released in the oxidation reactions is
electron transport chain, leading to the production of much more transferred to NADH. More reduced electron carriers (NADH and
energy in the form of ATP than is obtained by glycolysis alone. FADH2) are produced in two additional redox reactions. In fact,
the citric acid cycle produces a large quantity of reduced electron
The citric acid cycle produces ATP and reduced carriers: three molecules of NADH and one molecule of FADH2 per
electron carriers. turn of the cycle. These electron carriers donate electrons to the
Like the synthesis of acetyl-CoA, the citric acid cycle takes place electron transport chain, which leads to the production of ATP by
in the mitochondrial matrix. It is composed of eight reactions and oxidative phosphorylation.
is called a cycle because the starting molecule, oxaloacetate, is One of the reactions of the citric acid cycle is a substrate-level
regenerated at the end (Fig. 7.8). phosphorylation reaction that generates a molecule of GTP
In the first reaction, the 2-carbon acetyl group of acetyl-CoA (Fig. 7.8). GTP can transfer its terminal phosphate to a molecule of
is transferred to a 4-carbon molecule of oxaloacetate to form ADP to form ATP. This is the only substrate-level phosphorylation
the 6-carbon molecule citric acid or tricarboxylic acid (hence in the citric acid cycle.
CHAPTER 7 C E L L U L A R R E S P I R AT I O N : H A RV E S T I N G E N E RG Y F RO M C A R B O H Y D R AT E S A N D OT H E R F U E L M O L E C U L E S 139
FIG. 7.8 The citric acid cycle. The acetyl group of acetyl-CoA is completely oxidized, with the net production of one ATP, three NADH,
and one FADH2.
Glycolysis
Acetyl-coenzyme A
2C
ATP
CH3 C CoA CoA SH
Pyruvate O
H2O
CO2
Acetyl-CoA
H NADH
O C COO CH2 COO
Electron
carriers
e- Malate
O2
4C Isocitrate
Electron transport chain
6C
H2O
ATP
NAD+
Citric acid
cycle NADH H
H2O
CO2
Fumarate
4C -Ketoglutarate
5C
NAD+
Succinate
4C Succinyl-CoA
FADH2 FAD CoA SH
4C
NADH H
GDP Pi
CO2
CoA SH GTP
ADP Pi ATP
Overall, two molecules of acetyl-CoA produced from a single ? CASE 1 THE FIRST CELL: LIFE’S ORIGINS
molecule of glucose yield two molecules of ATP, six molecules of
What were the earliest energy-harnessing reactions?
NADH, and two molecules of FADH2 in the citric acid cycle.
Some bacteria run the citric acid cycle in reverse, incorporating
j Quick Check 3 At the end of the citric acid cycle, but before the carbon dioxide into organic molecules instead of liberating it.
subsequent steps of cellular respiration, which molecules contain Running the citric acid cycle in reverse requires energy, which is
the energy held in the original glucose molecule? supplied by sunlight (Chapter 8) or chemical reactions (Chapter 26).
140 SECTION 7.5 T H E E L E C T RO N T R A N S P O RT C H A I N A N D O X I DAT I V E P H O S P H O RY L AT I O N
FIG. 7.10 The electron transport chain. (a) The electron transport chain consists of four complexes (I to IV) in the inner mitochondrial membrane.
(b) Electrons flow from electron carriers to oxygen, the final electron acceptor. (c) The proton gradient formed from the electron
transport chain has potential energy that is used to synthesize ATP.
H⫹ Mitochondrial matrix
NADH
4 H⫹
H⫹ ADP + Pi ATP
NAD+ + 2 H 2O
Complex I
2H⫹
FADH2 FAD +
H⫹ ATP synthase H⫹
O2
⫹
H H⫹
H
Complex III
e-
e-
Complex
Co
Com
omp
om lex II
ple
le I
e- e-
b. Electron transport
H⫹ ATP synthase H⫹
H⫹ H⫹
Complex III
Co
Complex
omp x IIII
Complex
FIG. 7.12
Calculated proton
BACKGROUND Peter Mitchell’s hypothesis that a proton gradient
inside vesicles
concentration
can drive the synthesis of ATP was met with skepticism because it
was proposed before experimental evidence supported it. In the
1970s, biochemist Efraim Racker and his collaborator Walther
Stoeckenius tested the hypothesis.
Dark 23
synthesizes ATP. Proton flow through the channel (Fo) makes it Direct experimental evidence for Mitchell’s idea, called the
possible for the enzyme (F1) to synthesize ATP. chemiosmotic hypothesis, did not come for over a decade.
Proton flow through the Fo channel causes it to rotate, One of the key experiments that provided support for his idea is
converting the energy of the proton gradient into mechanical illustrated in Fig. 7.12.
rotational energy, a form of kinetic energy. The rotation of the Fo
subunit leads to rotation of the F1 subunit in the mitochondrial j Quick Check 5 Uncoupling agents are proteins spanning
matrix (Fig. 7.11). The rotation of the F1 subunit in turn causes the inner mitochondrial membrane that allow protons to pass
conformational changes that allow it to catalyze the synthesis of through the membrane and bypass the channel of ATP synthase.
ATP from ADP and Pi. In this way, mechanical rotational energy is Describe the consequences to the proton gradient and ATP
converted into the chemical energy of ATP. production.
143
144 SECTION 7.6 A N A E RO B I C M E TA B O L I S M A N D T H E E VO L U T I O N O F C E L L U L A R R E S P I R AT I O N
TABLE 7.1 Approximate Total ATP Yield in Cellular Respiration. FIG. 7.13 The flow of energy in cellular respiration. A
single glucose molecule yields 32 ATP molecules.
SUBSTRATE-LEVEL OXIDATIVE TOTAL
PATHWAY PHOSPHORYLATION PHOSPHORYLATION ATP Cell membrane
Total: 32 ATP
path. We saw this earlier in the discussion of the citric acid cycle,
where intermediates in the cycle often feed into other metabolic FIG. 7.14 Lactic acid and ethanol fermentation pathways.
pathways.
One of the major forks in the metabolic road occurs at a. Lactic acid fermentation
pyruvate, the end product of glycolysis (section 10.2). When HO CH2
the whole body, able to release glucose into the bloodstream when
7.7 METABOLIC INTEGRATION it is needed elsewhere. Glycogen provides a source of glucose
6-phosphate to feed glycolysis when the level of blood glucose is
In this chapter, we have focused on the breakdown of glucose. low. Glucose molecules located at the end of glycogen chains can
What happens if there is more glucose than is needed by the cell? be cleaved one by one, and they are released in the form of glucose
As well as glucose, you probably consume diverse carbohydrates, 1-phosphate. Glucose 1-phosphate is then converted into glucose
lipids, and proteins. How are these broken down? And how 6-phosphate, an intermediate in glycolysis. One glucose molecule
are these various metabolic pathways coordinated so that the cleaved offa glycogen chain produces three and not two molecules
intracellular level of ATP is maintained in a narrow range? In of ATP by glycolysis because the ATP-consuming step 1 of glycolysis
this final section, we consider how the cell responds to these is bypassed.
challenges.
Sugars other than glucose contribute to glycolysis.
Excess glucose is stored as glycogen in animals and The carbohydrates in your diet are digested to produce a
starch in plants. variety of sugars (Fig. 7.17). Some of these are disaccharides
Glucose is a readily available form of energy in organisms, but (maltose, lactose, and sucrose) with two sugar units; others are
it is not always broken down immediately. Excess glucose can monosaccharides (fructose, mannose, and galactose) with a single
be stored in cells and then mobilized—that is, broken down— sugar unit. The disaccharides are hydrolyzed into monosaccharides,
when necessary. Glucose can be stored in two major forms: as which are transported into cells.
glycogen in animals and as starch in plants (Fig. 7.16). Both these The hydrolysis of some disaccharides produces glucose
molecules are large branched polymers of glucose. molecules that directly enter glycolysis. What happens to other
Carbohydrates that are consumed by animals are broken down monosaccharides? They, too, enter glycolysis, although not
into simple sugars and circulate in the blood. The level of glucose as glucose. Instead, they are converted into intermediates of
in the blood is tightly regulated. When the blood glucose level is glycolysis that come later in the pathway. For example, fructose
high, as it is after a meal, glucose molecules that are not consumed is produced by the hydrolysis of sucrose (table sugar) and receives
by glycolysis are linked together to form glycogen in liver and a phosphate group to form either fructose 6-phosphate or
muscle. Glycogen stored in muscle is used to provide ATP for fructose 1-phosphate. In the liver, fructose 1-phosphate is cleaved
muscle contraction. By contrast, the liver does not store glycogen and converted into glyceraldehyde 3-phosphate, which enters
primarily for its own use, but is a central glycogen storehouse for glycolysis at reaction 6 (see Fig. 7.5).
FIG. 7.16 Storage forms of glucose. (a) Glycogen is a storage form of glucose in animal cells, and (b) starch is a storage form of glucose in
plant cells.
a. Glycogen b. Starch
CH2OH
Lactose OH Galactose
O
OH
CH2OH CH2OH
Maltose HO O O HO O OH Fructose
CH2OH CH2OH OH OH OH
O O CH2OH O OH
OH OH OH OH HO
HO O OH CH2OH
Milk
OH OH OH
Mannose
Sucrose
CH2OH CH2OH
H O H CH2OH O H O
OH H H HO Barley OH HO
HO O CH2OH OH OH
H OH OH H
Candy Apple
Electron carriers transfer electrons to an electron transport Citric acid cycle intermediates are starting points for
chain, which harnesses the energy of these electrons to the synthesis of many different organic molecules.
generate ATP. page 133 page 140
The movement of protons back into the mitochondrial Phosphofructokinase-1 controls a key step in glycolysis. It
matrix through the Fo subunit of ATP synthase is coupled has many allosteric activators, including ADP and AMP, and
with the formation of ATP, a reaction catalyzed by the F1 allosteric inhibitors, including ATP and citrate. page 149
subunit of ATP synthase. page 142
The ATP in muscle cells used to power exercise is generated
by lactic acid fermentation, aerobic respiration, and
7.6 Glucose can be broken down in the absence of
b-oxidation. page 150
oxygen by fermentation, producing a modest amount
of ATP.
Pyruvate, the end product of glycolysis, is processed Self-Assessment
differently in the presence and the absence of oxygen.
1. Name and describe the four major stages of cellular
page 145
respiration.
In the absence of oxygen, pyruvate enters one of several
2. Explain what an oxidation–reduction reaction is and why
fermentation pathways. page145
the breakdown of glucose in the presence of oxygen to
In lactic acid fermentation, pyruvate is reduced to lactic produce carbon dioxide and water is an example of an
acid. page 145 oxidation–reduction reaction.
In ethanol fermentation, pyruvate is converted to 3. Describe two different ways in which ATP is generated in
acetaldehyde, which is reduced to ethanol. page 145 cellular respiration.
During fermentation, NADH is oxidized to NAD1, allowing 4. Write the overall chemical equation for glycolysis, noting
glycolysis to proceed. page 145 the starting and ending products and highlighting the
energy-storing molecules that are produced.
Glycolysis and fermentation are ancient biochemical
pathways and were likely used in the common ancestor of 5. Describe two different metabolic pathways that pyruvate
all organisms living today. page 146 can enter.
Photosynthesis
Using Sunlight to Build
Carbohydrates
Core Concepts
8.1 Photosynthesis is the major
pathway by which energy and
carbon are incorporated into
carbohydrates.
8.2 The Calvin cycle is a three-step
process that uses carbon dioxide
to synthesize carbohydrates.
8.3 The light-harvesting reactions
use sunlight to produce the ATP
and NADPH required by the
Calvin cycle.
8.4 Challenges to the efficiency of
photosynthesis include excess
light energy and the oxygenase
activity of rubisco.
8.5 The evolution of photosynthesis
had a profound impact on life on
Earth.
Imagewerks Japan/Getty Images .
153
154 SECTION 8.1 P H OTO S Y N T H E S I S : A N OV E RV I E W
Walk through a forest and you will be struck, literally if you aren’t direct consumption of plant material and its indirect consumption
careful, by the substantial nature of trees. Where does the material as meat. It is also the source of all the oxygen that we breathe, as
to construct these massive organisms come from? Because trees well as fuels for heating and transportation. Fossil fuels are the
grow upward from a firm base in the ground, a reasonable first legacy of ancient photosynthesis: Oil has its origin in the bodies
guess is the soil. In the first recorded experiment on this question, of marine algae and the organisms that graze on them, while
the Flemish chemist and physiologist Jan Baptist van Helmont coal represents the geologic remains of terrestrial (land) plants.
(1580–1644) found that the 200 pounds of dry soil into which he Thus, one motivation to understand photosynthesis is the sheer
had planted a small willow tree decreased by only 2 ounces over a magnitude and importance of this process for life on Earth. Before
5-year period. During this same period, the tree gained 164 pounds. exploring the details of how photosynthesis actually occurs, let’s
Van Helmont concluded that water must be responsible for the look at what types of organism carry out photosynthesis and
tree’s growth. He was, in fact, half right: A tree is roughly half liquid where they live, as well as what structural components are needed
water. But what he missed completely is that the other half of his to allow cells to capture energy in this remarkable way.
tree had been created almost entirely out of thin air.
The process that allowed Van Helmont’s tree to increase in Photosynthesis is widely distributed.
mass using material pulled from the air is called photosynthesis. The photosynthesis that is most evident to us is carried out by
Photosynthesis is a biochemical process for building carbohydrates plants on land. Trees, grasses, and shrubs are all examples of
using energy from sunlight and carbon dioxide (CO2) taken from photosynthetic organisms. However, photosynthesis occurs among
the air. These carbohydrates are used both as starting points for the prokaryotic as well as eukaryotic organisms, on land as well as in
synthesis of other molecules and as a means of storing energy that the sea. Approximately 60% of global photosynthesis is carried out
can be converted into ATP through cellular respiration. by terrestrial organisms, with the remaining 40% taking place in
the ocean. The majority of photosynthetic organisms in marine
environments are unicellular. About half of oceanic photosynthesis
8.1 PHOTOSYNTHESIS: AN OVERVIEW is carried out by single-celled marine eukaryotes, while the other
half is carried out by photosynthetic bacteria.
Photosynthesis is the major entry point for energy into biological Photosynthesis takes place almost everywhere sunlight
systems. It is the source of all of the food we eat, both through the is available to serve as a source of energy. In the ocean,
FIG. 8.1 Photosynthesis in extreme environments. (a) Desert crust in the Colorado Plateau formed by photosynthetic bacteria and algae.
(b) A hot spring in Yellowstone National Park. The yellow color is due to photosynthetic bacteria. (c) The surface of a permanent snow
pack. The red color is due to photosynthetic algae. Sources: a. Jayne Belnap/USGS; b. f11photo/Shutterstock; c. Shattil & Rozinski/Naturepl.com.
a c
b
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 155
HOW DO WE KNOW?
FIG. 8.3
electron transport chain is located in
Does the oxygen released by membranes within the cytoplasm or, in some
cases, directly in the plasma membrane. In
photosynthesis come from H2O or CO2? eukaryotic cells, photosynthesis takes place in
chloroplasts. In the center of the chloroplast is
BACKGROUND The reactants in photosynthesis are water and carbon dioxide. Both the highly folded thylakoid membrane
contain oxygen, so it is unclear which one is the source of the oxygen that is produced in the (Fig. 8.4). The photosynthetic electron
reaction. transport chain is located in the thylakoid
membrane.
METHOD Most of the oxygen in the atmosphere is 16O, a stable isotope containing The name “thylakoid” is derived from
8 protons and 8 neutrons. A small amount (0.2%) is 18O, a stable isotope with 8 protons thylakois, the Greek word for “sac.” Thylakoid
and 10 neutrons. The relative abundance of molecules containing 16O versus 18O can be membranes form structures that resemble
measured using a mass spectrometer. H2O and CO2 containing a high percentage of 18O can flattened sacs, and these sacs are grouped into
be used to determine whether the oxygen produced in photosynthesis comes from water or structures called grana (singular, granum) that
carbon dioxide. look like stacks of interlinked pancakes. Grana
EXPERIMENT are connected to one another by membrane
bridges in such a way that the thylakoid
membrane encloses a single interconnected
compartment called the lumen. The region
surrounding the thylakoid membrane is called
Source: Sinclair
Stammers/ the stroma. Carbohydrate synthesis takes place
Science Source.
in the stroma, whereas sunlight is captured
1 Place
Chlorella, a and transformed into chemical energy by the
green alga, into photosynthetic electron transport chain in the
two test tubes. thylakoid membrane.
Initial Although photosynthetic organisms are
correctly described as autotrophs because
This test tube has This test tube has they can form carbohydrates from CO2, they
H218O and CO2. H2O and C18O2. also require a constant supply of ATP to meet
each cell’s energy requirements. Although
ATP is produced within chloroplasts, only
2 Wait 2 hours
carbohydrates (and not ATP) are exported
to allow from chloroplasts to the cytosol. This explains
Final
photosynthesis why cells that have chloroplasts also contain
to occur.
mitochondria. In mitochondria, carbohydrates
are broken down to generate ATP (Chapter 7).
RESULTS Cellular respiration is therefore one of several
1.2 features that heterotrophic organisms like
1.0 3 ourselves share with photosynthetic organisms.
Percent 18O2
0.8 Measure
0.6
percentage of We now consider the underlying
dissolved 18O2
0.4 biochemistry of photosynthesis. Though in this
in test tubes.
0.2 chapter we focus on photosynthesis as carried
Initial Final Initial Final out by eukaryotic cells, there is a remarkable
diversity in the way photosynthesis is carried
out in bacteria. We discuss this diversity in
CONCLUSION The percentage of 18O increases only when water contains 18O, but not Chapter 26. Because carbohydrates are the major
when carbon dioxide contains 18O. This finding indicates that the oxygen produced in product of photosynthesis, we first examine
photosynthesis comes from water, not carbon dioxide. the Calvin cycle, the biochemical pathway used
FOLLOW-UP WORK Carbon also has several isotopes, and their measurements have been
in photosynthesis to synthesize carbohydrates
used to determine the source of increased CO2 in the atmosphere today (Chapter 25). from CO2. Once we understand what energy
forms are needed to drive this autotrophic
SOURCE Adapted from Ruben, S., M. Randall, M. Kamen, and J. L. Hyde. 1941. “Heavy Oxygen (O18) as a pathway, we turn our attention to how energy is
Tracer in the Study of Photosynthesis.” Journal of the American Chemical Society 63:877–879.
captured from sunlight. We then examine some
156
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 157
FIG. 8.5 The Calvin cycle. CO2 is the input and triose phosphate is the output of the Calvin Cycle.
Regeneration
ADP ATP
+
adds CO2 to another molecule is called a carboxylase, explaining A large number of reactions is needed to rearrange the carbon
part of rubisco’s long name. atoms from five 3-carbon triose phosphate molecules into three
Before rubisco can act as a carboxylase, RuBP and CO2 must 5-carbon RuBP molecules. ATP is required for the regeneration
diffuse into its active site. Once the active site is occupied, the of RuBP, raising the Calvin cycle’s total energy requirements to
addition of CO2 to RuBP proceeds spontaneously in the sense two molecules of NADPH and three molecules of ATP for each
that no addition of energy is required. The product is a 6-carbon molecule of CO2 incorporated by rubisco.
compound that immediately breaks into two molecules of The Calvin cycle does not use sunlight directly. For this reason,
3-phosphoglycerate (3-PGA). These 3-carbon molecules are the this pathway is sometimes referred to as the light-independent
first stable products of the Calvin cycle. or even the “dark” reactions of photosynthesis. However, this
pathway cannot operate without the energy input provided
NADPH is the reducing agent of the Calvin cycle. by a steady supply of NADPH and ATP. Both are supplied by
Rubisco is responsible for the addition of the carbon atoms the photosynthetic electron transport chain, in which light is
needed for the formation of carbohydrates, but by itself rubisco captured and transformed into chemical energy. In addition,
does not increase the amount of energy stored within the newly several Calvin cycle enzymes are regulated by cofactors that must
formed bonds. For this energy increase to take place, the carbon be activated by the photosynthetic electron transport chain. Thus,
compounds formed by rubisco must be reduced. Nicotinamide in a photosynthetic cell, the Calvin cycle occurs only in the light.
adenine dinucleotide phosphate (NADPH) is the reducing
j Quick Check 2 The Calvin cycle requires both ATP and
agent used in the Calvin cycle. NADPH transfers the electrons that
NADPH. Which of these molecules provides the major input of
allow carbohydrates to be synthesized from CO2 (Fig. 8.5).
energy needed to synthesize carbohydrates?
Like all components of the Calvin cycle, NADPH can move
freely within the stroma of the chloroplast. Although NADPH is
a powerful reducing agent, energy and electrons are transferred The steps of the Calvin cycle were determined using
from NADPH only under the catalysis of a specific enzyme, thus radioactive CO2.
providing a high degree of control over the fate of these electrons. In a series of experiments conducted between 1948 and 1954, the
In the Calvin cycle, the reduction of 3-PGA involves two steps: American chemist Melvin Calvin and colleagues identified the
(1) ATP donates a phosphate group to 3-PGA, and (2) NADPH carbon compounds produced during photosynthesis (Fig. 8.6). They
transfers two electrons plus one proton (H1) to the phosphorylated supplied radioactively labeled CO2 (14CO2) to the unicellular green
compound, which releases one phosphate group (Pi). Because two alga Chlorella and then plunged the cells into boiling alcohol, thereby
molecules of 3-PGA are formed each time rubisco catalyzes the halting all enzymatic reactions. The carbon compounds produced
incorporation of one molecule of CO2 , two ATP and two NADPH during photosynthesis were thus radioactively labeled and could be
are required for each molecule of CO2 incorporated by rubisco. identified by their radioactivity (Experiment 1 in Fig. 8.6).
NADPH provides most of the energy incorporated in the bonds Figuring out the chemical reactions that connected these
of the carbohydrate molecules produced by the Calvin cycle. labeled compounds, however, required additional experiments.
Nevertheless, ATP plays an essential role in preparing 3-PGA for the For example, by using a very short exposure to 14CO2, Calvin and
addition of energy and electrons from NADPH. colleagues determined that 3-PGA was the first stable product of
These energy transfer steps result in the formation of 3-carbon the Calvin cycle (Experiment 2 in Fig. 8.6).
carbohydrate molecules known as triose phosphates. Triose To determine how 3-PGA is formed, they first supplied
phosphates are the true products of the Calvin cycle and they 14
CO2 so that all of the molecules in the Calvin cycle became
are the principal form in which carbohydrates are exported from radioactively labeled. When they then cut off the supply of CO2,
the chloroplast during photosynthesis. Larger sugars, such as the amount of RuBP increased relative to the amount seen in the
glucose and sucrose, are assembled from triose phosphates in the first experiment. Based on this buildup of RuBP, they concluded
cytoplasm. that the first step in the Calvin cycle was the addition of CO2 to
If every triose phosphate molecule produced by the Calvin RuBP (Experiment 3 in Fig. 8.6).
cycle were exported from the chloroplast, RuBP could not
be regenerated and the Calvin cycle would grind to a halt. In Carbohydrates are stored in the form of starch.
fact, most of the triose phosphate molecules must be used to The Calvin cycle is capable of producing more carbohydrates than
regenerate RuBP. For every six triose phosphate molecules that are the cell needs or, in a multicellular organism, more than the cell is
produced, only one can be withdrawn from the Calvin cycle. able to export. If carbohydrates accumulated in the cell, they would
cause water to enter the cell by osmosis, perhaps damaging the cell.
The regeneration of RuBP requires ATP. Instead, excess carbohydrates are converted to starch, a storage
Of the 15 chemical reactions that make up the Calvin cycle, form of carbohydrates discussed in Chapter 2. Because starch
12 occur in the last step, the regeneration of RuBP (Fig. 8.5). molecules are not soluble, they provide a means of carbohydrate
HOW DO WE KNOW?
FIG. 8.6
14CO
Experiment 1: 2
Use 14CO2 to label all
the products of the RuBP
Calvin cycle.
Triose phosphates
3-PGA
2D paper chromatography
separates molecules according
to factors such as size and
charge that affect their mobility.
Experiment 2:
Shorten exposure to
14CO enough so that Experiment 3:
2
only one compound Following exposure to
14CO as in Experiment 1,
is labeled. 2
3-PGA prevent carboxylation by RuBP
withholding CO2 and see Triose phosphates
which labeled product
increases and which 3-PGA
decreases.
Thus, 3-PGA is the initial
product of carboxylation.
Because RuBP increases, while
3-PGA decreases relative to the
amounts in Experiment 1, RuBP is
the other substrate involved in
the carboxylation step.
CONCLUSION The initial step in the Calvin cycle unites the 5-carbon RuBP with CO2, resulting in the production of two molecules of 3-PGA.
FOLLOW-UP WORK In the 1950s, Marshall Hatch and colleagues showed that some plants, including corn and sugarcane, accumulate
a 4-carbon compound as the first product in photosynthesis. In Chapter 29, we explore how C4 photosynthesis allows plants to avoid the
oxygenase reaction of rubisco.
SOURCE Calvin, M., and H. Benson. 1949. “The Path of Carbon in Photosynthesis IV: The Identity and Sequence of the Intermediates in Sucrose Synthesis.” Science 109:140–142.
159
160 SECTION 8.3 C A P T U R I N G S U N L I G H T I N TO C H E M I C A L F O R M S
FIG. 8.8 Light absorbed by leaves. The graph shows the extent
to which wavelengths of visible light are absorbed by
pigments in an intact leaf.
Electromagnetic spectrum
High energy Low energy
Photosystems contain pigments other than chlorophyll, called play an important role in protecting the photosynthetic electron
accessory pigments. The most notable are the orange-yellow transport chain from damage.
carotenoids, which can absorb light from regions of the visible
spectrum that are poorly absorbed by chlorophyll. Thus, the Photosystems use light energy to drive the
presence of these accessory pigments allows photosynthetic cells to photosynthetic electron transport chain.
absorb a broader range of visible light than would be possible with When visible light is absorbed by a chlorophyll molecule, one of
just chlorophyll alone. As we will see in section 8.4, carotenoids its electrons is elevated to a higher energy state (Fig. 8.10). For
FIG. 8.9 Chemical structure of chlorophyll. Shown is FIG. 8.10 Absorption of light energy by chlorophyll. Absorption of
chlorophyll a, found in all photosynthetic eukaryotes and light energy by (a) an isolated chlorophyll molecule in the
cyanobacteria. lab and (b) an antenna chlorophyll molecule.
CH CH3
H
C C C
C C Light Heat Fluorescence
H3C C C CH2CH3
Light-absorbing C N N C
region HC Mg CH
Chlorophyll e- e- e-
molecule
C N N C
H2C C C C C CH3 Ground-state Excited-state Ground-state
H electron electron electron
CH C C
CH2 HC C O
CH2 C O
C O O
O CH3
CH2
CH
Energy
C CH3
CH2 Absorption of visible light by an
CH2 isolated chlorophyll molecule
results in the release of heat and
CH2 fluorescence when the electron
Hydrocarbon returns to its ground energy state.
side chain HC CH3
b. In the plant cell
CH2
CH2
CH2 Light
HC CH3
e- e- e-
CH2
CH2
Energy
CH2 transfer
CH
H3C CH3
e- e-
Ground-state Excited-state
electron electron
chlorophyll molecules that have been extracted from chloroplasts Without the antennae to gather light energy, reaction centers
in the laboratory, this absorbed light energy is rapidly released, would sit idle much of the time, even in bright sunlight.
allowing the electron to return to its initial “ground” energy state The reaction center chlorophylls have a configuration
(Fig. 8.10a). Most of the energy (>95%) is converted into heat; a distinct from that of the antenna chlorophylls. As a result, when
small amount is reemitted as light (fluorescence). excited, the reaction center transfers an electron to an adjacent
By contrast, for chlorophyll molecules within an intact molecule that acts as an electron acceptor (Fig. 8.11a). When the
chloroplast, energy can be transferred to an adjacent chlorophyll transfer takes place, the reaction center becomes oxidized and
molecule instead of being lost as heat (Fig. 8.10b). When this the adjacent electron-acceptor molecule is reduced. The result is
happens, the energy released as an excited electron returns to its the conversion of light energy into a chemical form. This electron
ground state raises the energy level of an electron in an adjacent transfer initiates a light-driven chain of redox reactions that leads
chlorophyll molecule. This mode of energy transfer is extremely ultimately to the formation of NADPH.
efficient (that is, very little energy is lost as heat), allowing Once the reaction center has lost an electron, it can no longer
energy initially absorbed from sunlight to be transferred from one absorb light or contribute additional electrons. Thus, for the
chlorophyll molecule to another and then on to another. photosynthetic electron transport chain to continue, another
Most of the chlorophyll molecules in the thylakoid electron must be delivered to take the place of the one that has
membrane function as an antenna: Energy is transferred between entered the transport chain (Fig. 8.11b). As we will see below,
chlorophyll molecules until it is finally transferred to a specially these replacement electrons ultimately come from water.
configured pair of chlorophyll molecules known as the reaction
j Quick Check 3 How do antenna chlorophylls differ from
center (Fig. 8.11).
reaction center chlorophylls?
The reaction center is where light energy is converted into
chemical energy as a result of the excited electron’s transfer to
an adjacent molecule. This division of labor among chlorophyll The photosynthetic electron transport chain connects
molecules was discovered in the 1940s in a series of experiments two photosystems.
by the American biophysicists Robert Emerson and William Arnold, In many ways, water is an ideal source of electrons for photo-
who showed that only a small fraction of chlorophyll molecules synthesis. Water is so abundant within cells that it is always
are directly involved in electron transport (Fig. 8.12). We now available to serve as an electron donor in photosynthesis. In
know that several hundred antenna chlorophyll molecules transfer addition, O2, the by-product of pulling electrons from water,
energy to each reaction center. The antenna chlorophylls allow diffuses readily away rather than accumulates. However, from an
the photosynthetic electron transport chain to operate efficiently. energy perspective, water is a challenging electron donor: It takes
FIG. 8.11 The reaction center. (a) Antenna chlorophylls deliver absorbed light energy to the reaction center, allowing electrons to be transferred
to an electron acceptor molecule. (b) After the reaction center has lost an electron, it is reduced by gaining an electron, so it is ready to
absorb additional light energy.
Light
Antenna
chlorophylls
Electron Electron
e- e-
acceptor donor
Measurement 1 (rate of
Do chlorophyll molecules O2 production):
was the pigment responsible for absorbing light energy in Measurement 2 (chlorophyll concentration):
photosynthesis. However, it was unclear how these pigments
2
contributed to the reduction of CO2. The American physiologists Solution 1 3
a great deal of energy to pull electrons from water. The amount transport chain. To run these reactions in the opposite direction
of energy that a single photosystem can capture from sunlight is would require an input of energy. Because the overall energy
not enough both to pull an electron from water and produce an trajectory has an up-down-up configuration resembling a “Z,” the
electron donor capable of reducing NADP1. The solution is to use photosynthetic electron transport chain is sometimes referred to
two photosystems arranged in series. The energy supplied by the as the Z scheme.
first photosystem allows electrons to be pulled from water, and the For the two photosystems to work together to move electrons
energy supplied by the second photosystem step allows electrons from water to NADPH, they must have distinct chemical
to be transferred to NADP1. properties. Photosystem II supplies electrons to the beginning
If you follow the flow of electrons from water through both of the electron transport chain. When photosystem II loses
photosystems and on to NADP1, as shown in Fig. 8.13, you can an electron (that is, when it is itself oxidized), it is able to pull
see a large increase in energy as the electrons pass through each electrons from water. In contrast, photosystem I energizes
of the two photosystems. You can also see that at every other electrons with a second input of light energy so they can be used
step along the photosynthetic electron transport chain there to reduce NADP1. The key point here is that photosystem I when
is a small decrease in energy. This decrease in energy indicates oxidized is not a sufficiently strong oxidant to split water, whereas
that these are exergonic reactions (Chapter 6) and thus explains photosystem II is not a strong enough reductant to form NADPH.
why electrons move in one “direction” through the series of The major protein complexes of the photosynthetic electron
redox reactions that make up the photosynthetic electron transport chain include the two photosystems as well as the
163
164 SECTION 8.3 C A P T U R I N G S U N L I G H T I N TO C H E M I C A L F O R M S
Fig. 8.14c.
How do protons accumulate in the thylakoid
Absorption of light energy A second input of light lumen? Two features of the photosynthetic
by PS II allows electrons energy by PS I produces
electron transport chain are responsible for
pulled from water to enter electron donor molecules
the photosynthetic capable of reducing the buildup of protons in the thylakoid lumen
electron transport chain. NADP+. (Fig. 8.14c). First, the oxidation of water
releases protons and O2 into the lumen. Second,
the cytochrome–b6 f complex, the protein
complex situated between photosystem II and
cytochrome–b6 f complex (cyt), through which electrons pass photosystem I, and plastoquinone together function as a proton
between photosystem II and photosystem I (Fig. 8.14). Small, pump that is functionally and evolutionarily related to proton
relatively mobile compounds convey electrons between these pumping in the electron transport chain of cellular respiration
protein complexes. Plastoquinone (Pq), a lipid-soluble compound (Chapter 7).
similar in structure to coenzyme Q (Chapter 7), carries electrons In photosynthesis, the proton pump involves: (1) the transport
from photosystem II to the cytochrome–b6 f complex by diffusing of two electrons and two protons, by the diffusion of
through the membrane, while plastocyanin (Pc), a water-soluble plastoquinone, from the stroma side of photosystem II to the
protein, carries electrons from the cytochrome–b6 f complex to lumen side of the cytochrome–b6 f complex and (2) the transfer
photosystem I by diffusing through the thylakoid lumen. of electrons within the cytochrome–b6 f complex to a different
Water donates electrons to one end of the photosynthetic molecule of plastoquinone, which results in additional protons
electron transport chain, whereas NADP accepts electrons at the being picked up from the stroma and subsequently released into
other end. The enzyme that pulls electrons from water, releasing the lumen.
both H and O2, is located on the lumen side of photosystem Together, these mechanisms are quite powerful. When the
II. The mechanism by which water splitting occurs is not photosynthetic electron transport chain is operating at full
known, despite the considerable industrial value of developing capacity, the concentration of protons in the lumen can be more
a way to use sunlight to generate hydrogen gas (H2). NADPH than 1000 times greater than their concentration in the stroma
is formed when electrons are passed from photosystem I to a (equivalent to a difference of 3 pH units). This accumulation of
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 165
FIG. 8.14 The photosynthetic electron transport chain. (a) An overview of the production of NADPH and ATP. (b) The linear flow of electrons
from H2O to NADPH. (c) The use of a proton electrochemical gradient to synthesize ATP.
H e-
Fd N
NADP + ATP synthase H
e- d ase
reductase
red e
PS
SI
Cy
Cyt
y
PS II
e- e-
e-
Pq H
e- H
O2 Pc
H2O
H
Lumen H
e-
Fd NADP+
e- reductase
PS I
Cyt
PS II
e- e- e-
Pq
e-
H2O Pc
Lumen
H ATP synthase
H
PS II Cyt
Pq H
O2 H
H2O
H
Lumen H
166 SECTION 8.4 C H A L L E N G E S TO P H OTO S Y N T H E T I C E F F I C I E N C Y
FIG. 8.15 Cyclic electron transport. To increase ATP production, some electrons from photosystem I cycle back into the electron transport chain.
NADPH
ADP Pi ATP
NADP+ H
Stroma Light
H e-
Fd H
NADP+
e- ATP synthase
reductase
PS I
Cyt
e- e-
Pq H
e-
Pc H
Lumen H
protons on one side of the thylakoid membrane can then be used to the lumen. As a result, there are more protons in the lumen that
to power the synthesis of ATP by oxidative phosphorylation as can be used to drive the synthesis of ATP.
described in Chapter 7.
FIG. 8.16 Defenses against reactive oxygen species. (a) Reactive oxygen species are generated when light energy or electrons are transferred to
oxygen. (b) Defenses against the reactive oxygen species include antioxidants that neutralize reactive oxygen species and xanthophylls
that convert excess light energy into heat.
H 2O e-
Pc
O2
H H
Antioxidants detoxify
reactive oxygen species.
b. The solution: Xanthophylls and antioxidants reduce the amount of reactive oxygen species. O2 Reactive
oxygen antioxidants
species H2O
Cyclic
Light Fluorescence Heat Light electron
transport
Fd
H e-
PS I
Cyt
PS II
e- e- e-
Pq
H
H 2O e-
Pc
Xanthophylls convert excess O2
light energy to heat,
reducing the rate at which H H
electrons enter the electron
transport chain.
in short supply, the electron transport chain “backs up,” greatly directly to O2 or by the transfer of an electron, forming O2. Both
increasing the probability of creating highly reactive forms of forms of O2 can cause substantial damage to the cell.
oxygen known collectively as reactive oxygen species NADP is returned to the photosynthetic electron transport
(Fig. 8.16a). These highly reactive molecules can be formed either chain by the Calvin cycle’s use of NADPH. Thus, any factor that
by the transfer of absorbed light energy from antenna chlorophyll causes the rate of NADPH use to fall behind the rate of light-driven
168 SECTION 8.4 C H A L L E N G E S TO P H OTO S Y N T H E T I C E F F I C I E N C Y
electron transport can potentially lead to damage. Such an molecules are brightly colored, like the red pigments found
imbalance is likely to occur, for example, in the middle of the day in algae that live on snow shown in Fig. 8.1c. The presence of
when light intensity is highest. Could the cell right the balance antioxidant compounds is one of the many reasons that eating
by supplying NADP1 more quickly? Photosynthetic cells could green, leafy vegetables is good for your health.
speed up the resupply of NADP1 by synthesizing more Calvin A second line of defense is to prevent reactive oxygen species
cycle enzymes. This strategy, however, would be energetically from forming in the first place. Xanthophylls are yellow-orange
expensive. When light levels are low, such as in the morning and pigments that slow the formation of reactive oxygen species by
late afternoon, Calvin cycle enzymes would sit idle. An alternative reducing excess light energy. These pigments accept absorbed light
strategy of reducing the amount of chlorophyll in the leaf runs energy directly from chlorophyll and then convert this energy to
into similar problems. Thus, excess light energy is an everyday heat (Fig. 8.16b). Photosynthetic organisms that live in extreme
event for photosynthetic cells, rather than something that occurs environments often appear brown or yellow because they contain
only in extreme environments. high levels of xanthophyll pigments, as seen in Figs. 8.1a and
The rate at which the Calvin cycle can make use of NADPH 8.1b. Plants that lack xanthophylls grow poorly when exposed to
is also influenced by a number of factors that are independent of moderate light levels and die in full sunlight.
light intensity. For example, cold temperatures cause the enzymes Converting absorbed light energy into heat is beneficial at high
of the Calvin cycle to function more slowly, but they have little light levels, but at low light levels it would decrease the production
impact on the absorption of light energy. On a cold, sunny day, of carbohydrates. Therefore, this capability is switched on only
more light energy is absorbed than can be used by the Calvin cycle. when the photosynthetic electron transport chain is working at
Photosynthetic organisms employ two major lines of defense high capacity.
to avoid the stresses that occur when the Calvin cycle cannot
keep up with light harvesting (Fig. 8.16b). First among these Photorespiration leads to a net loss of energy
are chemicals that detoxify reactive oxygen species. Ascorbate and carbon.
(vitamin C), b-(beta-)carotene, and other antioxidants are able A second challenge to photosynthetic efficiency is the fact that
to neutralize reactive oxygen species. These compounds exist in rubisco can use both CO2 and O2 as substrates. If O2 instead of
high concentration in chloroplasts. Some of these antioxidant CO2 diffuses into the active site of rubisco, the reaction can
FIG. 8.17 Photorespiration. Carbon and energy are lost when rubisco acts as an oxygenase in photorespiration.
NADPH
Oxygenation 3-Phosphoglycerate Reduction
O2 input: (3-PGA)
Rubisco can NADP+
function as an O2 2-Phosphoglycolate
oxygenase.
Regeneration
ADP ATP
+
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 169
still proceed, although O2 is added to RuBP in place of CO2. An catalytic rate means that photosynthetic cells must produce huge
enzyme that adds O2 to another molecule is called an oxygenase. amounts of this enzyme; as much as 50% of the total protein
Recall that rubisco is shorthand for RuBP carboxylase oxygenase, within a leaf is rubisco, and it is estimated to be the most abundant
reflecting rubisco’s ability to catalyze two different reactions. protein on Earth. At the same time, because O2 is approximately
When rubisco adds O2 instead of CO2 to RuBP, the result is 500 times more abundant in the atmosphere than CO2, as much as
one molecule with three carbon atoms (3-PGA) and one molecule one-quarter of the reduced carbon formed in photosynthesis can
with only two carbon atoms (2-phosphoglycolate). The production be lost through photorespiration.
of 2-phosphoglycolate creates a serious problem because this
j Quick Check 6 Why does rubisco have such a low catalytic rate
molecule cannot be used by the Calvin cycle either to produce
(that is, why is it so slow)?
triose phosphate or to regenerate RuBP.
A metabolic pathway to recycle 2-phosphoglycolate is
Photosynthesis captures just a small percentage of
present in photosynthetic cells. A portion of the carbon atoms
incoming solar energy.
in 2-phosphoglycolate are converted into 3-PGA, which can
Typically, only 1% to 2% of the sun’s energy that lands on a leaf
reenter the Calvin cycle. However, this pathway is not able to
ends up in carbohydrates. Does this mean that photosynthesis
return all of the carbon atoms in 2-phosphoglycolate to the
is incredibly wasteful? Or is this process, the product of billions
Calvin cycle; some are released as CO2. Because the overall effect
of years of evolution, surprisingly efficient? This is not an idle
is the consumption of O2 and release of CO2 in the presence of
question. Photosynthesis is relevant to solving several pressing
light, this process is referred to as photorespiration (Fig. 8.17).
global issues: the effects of rising CO2 concentrations on Earth’s
However, whereas respiration produces ATP, photorespiration
climate, the search for a renewable, carbon-neutral fuel to power
consumes ATP. In photorespiration, ATP drives the reactions that
our transportation sector, and the agricultural demands of our
recycle 2-phosphoglycolate into 3-PGA. Thus, photorespiration
skyrocketing human population.
represents a net energy drain on two accounts: First, it results in
Photosynthetic efficiency is typically calculated relative to
the oxidation and loss, in the form of CO2, of carbon atoms that
the total energy output of the sun (Fig. 8.18). However, only
had previously been incorporated and reduced by the Calvin cycle,
visible light has the appropriate energy levels to raise the energy
and second, it consumes ATP.
state of electrons in chlorophyll. Most of the sun’s output
j Quick Check 5 In what ways is photorespiration similar to cellular
respiration (Chapter 7) and in what ways does it differ?
(~60%) is not absorbed by chlorophyll and thus cannot be used in produced chemical variants of these UV-absorbing molecules.
photosynthesis. In addition, leaves are not perfect at absorbing One or more of these variant compounds might have been capable
visible light—about 8% is either reflected or passes through the of using sunlight to meet the energy needs of the cell—perhaps
leaf. Finally, even under optimal conditions, not all of the light by transferring electrons to another molecule as a present-day
energy absorbed by chlorophyll can be transferred to the reaction reaction center does.
center and instead is given off as heat (also ~8%). As we have seen, The earliest reaction centers may have used light energy to
when light levels are high, excess light is actively converted into drive the movement of electrons from an electron donor outside
heat by xanthophyll pigments. the cell in the surrounding medium to an electron-acceptor
The photosynthetic electron transport chain therefore molecule within the cell. In this way, energy from sunlight could
captures at most about 24% of the sun’s usable energy arriving have been used to synthesize carbohydrates. The first electron
at the surface of a leaf (100% – 60% – 8% – 8% 5 24%). While donor could have been a soluble inorganic ion like reduced iron,
this number may appear low, it is on a par with the efficiency of Fe21, which is thought to have been abundant in the early ocean.
high-performance photovoltaic cells in solar panels, which convert Alternatively, the first forms of light-driven electron transport
sunlight into electricity. This comparison is even more impressive may have been cyclic and thus not required an electron donor.
when you consider that photosynthetic organisms must build and In either configuration, light-driven electron transport could
maintain all their biochemical machinery. However, energy is lost have been coupled to the net movement of protons across the
at a later step as well. The incorporation of CO2 into carbohydrates membrane, allowing for the synthesis of ATP.
results in considerable loss in free energy, equivalent to ~20% of Similarly, it is unlikely that these first photosynthetic
the total incoming solar radiation. Some of this loss in free energy organisms employed chlorophyll as a means of absorbing sunlight
is due to photorespiration. for the simple reason that the biosynthetic pathway for chlorophyll
In total, therefore, the maximum energy conversion efficiency is complex, consisting of at least 17 enzymatic steps. Yet some of
of photosynthesis is calculated to be around 4% (24% – 20%). the intermediate compounds leading to chlorophyll are themselves
Efficiencies achieved by real plants growing in nature, however, capable of absorbing light. Perhaps each of these now-intermediate
are typically much lower, on the order of 1% to 2%. In Chapter 29, compounds was, at one time, a functional end product used as a
we explore the many factors that can constrain the photosynthetic pigment by an early photosynthetic organism. The biosynthetic
output of land plants, and see how some plants have evolved pathway may have gained steps as chemical variants, produced by
ways to minimize losses in productivity due to drought and random mutations, were selected because they were more efficient
photorespiration. or able to absorb new portions of the visible spectrum. Selection
would have eventually resulted in the chlorophyll pigments that
are used by photosynthetic organisms today.
8.5 THE EVOLUTION OF
PHOTOSYNTHESIS The ability to use water as an electron donor in
photosynthesis evolved in cyanobacteria.
The evolution of photosynthesis had a profound impact on the The most ancient forms of photosynthesis have only a single
history of life on Earth. Not only did photosynthesis provide photosystem in their photosynthetic electron transport chains.
organisms with a new source of energy, but it also released However, as we have seen, a single photosystem cannot capture
oxygen into the atmosphere. As discussed in the previous chapter, enough energy from sunlight both to pull electrons from water
evolution often works in a stepwise fashion, building on what and also raise their energy level enough that they can be used
is already present. Here we consider hypotheses for how the to reduce CO2. Thus, photosynthetic organisms with a single
photosynthetic pathways that are the dominant entry point for photosystem must use more easily oxidized compounds, such
energy into the biosphere today may have evolved. as H2S, as electron donors. These organisms can exist only in
environments where the electron-donor molecules are abundant.
Because these organisms do not use water as an electron donor,
? CASE 1 THE FIRST CELL: LIFE’S ORIGINS
they do not produce O2 during photosynthesis.
How did early cells use sunlight to meet their energy A major event in the history of life was the evolution of
requirements? photosynthetic electron transport chains that use water as an
Sunlight is valuable as a source of energy, but it can also cause electron donor. The first organisms to accomplish this feat were
damage. This is particularly true of ultraviolet wavelengths, the cyanobacteria. These photosynthetic bacteria incorporated
which can damage DNA and other macromolecules. Thus, the two different photosystems into a single photosynthetic electron
earliest interactions with sunlight may have been the evolution transport chain, one to pull electrons from water molecules and
of UV-absorbing compounds that could shield cells from the one to raise the energy level of the electrons so that they can be
sun’s damaging rays. Over time, random mutations could have used to reduce CO2.
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 171
Photosynthesis
Energy captured from sunlight is stored in carbohydrates.
Photosynthesis requires light energy, CO2, and H2O, and produces carbohydrates and Carbon dioxide is reduced by NADPH and, using the energy
O2. The photosynthetic electron transport chain uses energy from sunlight to drive the provided by ATP, is incorporated into a carbohydrate molecule
movement of electrons from water to NADP⫹ and to produce ATP. in the Calvin cycle.
NADPH NADPH
Stroma
ATP ATP
Light Light NADP+ ADP NADP+
ADP
H⫹ PS I e-
PS II Cyt e-
CO2
e- e- e- Carbohydrate
ATP
e- synthase
ATP
Lumen ADP
ADP ATP
ATP ADP
Outputs:
O2 H⫹
172
Aerobic respiration
Energy released from the oxidation of carbohydrates is used to make ATP.
Aerobic respiration requires The citric acid cycle The energy released as electrons are passed down the electron transport chain
carbohydrates and O2 and produces completes the oxidation of generates a proton gradient that powers ATP production by ATP synthase.
CO2, H2O, and ATP. Glycolysis splits organic molecules.
glucose into two molecules of
pyruvate and begins the oxidation of H⫹ H2O
organic molecules. FADH2
e-
e- e-
Acetyl-
Carbohydrate Pyruvate e-
CoA e-
ATP
Complex I Complex II
synthase
ATP CO2 ATP
CO2
Intermembrane Complex III Complex IV
space
NADH Complex I
Acetyl-
Carbohydrate Pyruvate
CoA
III IV e-
FADH2 Complex II
173
174 CO R E CO N C E P T S S U M M A RY
Antenna chlorophyll molecules transfer absorbed light The maximum theoretical efficiency of photosynthesis is
energy to the reaction center. page 162 approximately 4% of total incident solar energy. page 170
CHAPTER 8 P H OTO S Y N T H E S I S : U S I N G S U N L I G H T TO B U I L D C A R B O H Y D R AT E S 175
8.5 The evolution of photosynthesis had a profound 5. Contrast what happens when antenna chlorophylls
impact on life on Earth. absorb light energy with what happens when the reaction
center absorbs light energy. Why are antenna chlorophylls
The ability to use water as an electron donor in
so important in photosynthesis?
photosynthesis evolved in cyanobacteria. page 170
6. Explain why using water as an electron donor
Cyanobacteria evolved two photosystems either by the
requires a photosynthetic electron transport chain with
transfer of genetic material, or by gene duplication and
two photosystems.
divergence. page 171
7. Show in a diagram how energy from sunlight is used
Photosynthesis in eukaryotes likely evolved by
to produce ATP.
endosymbiosis. page 171
8. List the products of linear electron transport and
All of the oxygen in Earth’s atmosphere results from
cyclic electron transport, and describe the role of cyclic
photosynthesis by organisms containing two photosystems.
electron transport.
page 171
9. Describe two strategies that plants use to limit the
formation and effects of reactive oxygen species.
Self-Assessment 10. Explain the trade-off that rubisco faces in terms of
1. Write the overall photosynthetic reaction and identify selectivity and enzymatic speed.
which molecules are oxidized and which molecules are
11. Estimate the overall efficiency of photosynthesis and
reduced.
describe where in the pathway energy is dissipated.
2. Compare the overall reactions of photosynthesis and
12. List three major steps that are hypothesized to have
cellular respiration.
occurred in the evolutionary history of photosynthesis.
3. Name the major inputs and outputs of the Calvin
cycle.
Log in to to check your answers to the Self-
4. Describe the three major steps in the Calvin cycle Assessment questions, and to access additional learning tools.
and the role of the key enzyme rubisco.
CHAPTER 1 LIFE 176
CASE 2
Cancer
When Good Cells Go Bad
Imagine a simple vaccine that could prevent about aren’t fought off by the immune system can permanently
500,000 cases of cancer worldwide every year. You’d integrate their own eight-gene DNA sequence into the
think such a discovery would be hailed as a miracle. Not host cell’s DNA.
quite. A vaccine to prevent cervical cancer, which affects Once integrated into the DNA of human epithelial
about half a million women and kills as many as 275,000 cells, two viral genes, E6 and E7, are expressed and
annually, has been available since 2006. However, in produce two proteins. These viral proteins inhibit
the United States, this vaccine (and others) has stirred the products of key tumor suppressor genes. Tumor
controversy. suppressor genes code for proteins called tumor
Cancer is uncontrolled cell division. Cell division is suppressors that keep cell division in check by slowing
a normal process that occurs during development of a down cell division, repairing DNA replication errors,
multicellular organism and subsequently as part of the or instructing defective cells to die. When tumor
maintenance and repair of adult tissues. It is carefully suppressors are prevented from doing these jobs, cancer
regulated so that it occurs only at the right time and place. can result.
But sometimes, this careful regulation can be disrupted. HPV strikes in two ways. The viral E6 protein inhibits
When the normal checks on cell division become derailed, a protein called p53, an important tumor suppressor that,
cancer can result. among other functions, prevents cell division in healthy
Most cancers are caused cells when there is DNA damage. However, when bound
When the normal by inherited or acquired by E6, p53 becomes essentially inactive. Meanwhile,
mutations, but some are the viral E7 protein inhibits a protein called Rb, which
checks on cell division caused by a virus. In fact, normally blocks transcription factors that promote cell
become derailed, nearly all cases of cervical division. Without Rb and p53 to put the brakes on cell
cancer are caused by a virus division, cervical cells divide uncontrollably.
cancer can result. called human papillomavirus As they grow and multiply, the abnormal cells push
(HPV). There are hundreds through the basal lamina, a thin layer that separates the
of strains of HPV. Some of these strains cause minor epithelial cells lining the cervix from the connective
problems such as common warts and plantar warts. tissue beneath. Untreated, invasive cancer can spread
Other strains are sexually transmitted. Some can cause to other organs. Once cancer travels beyond its primary
genital warts but aren’t associated with cancer. However, location, the situation is grim. Most cancers cannot be
a handful of “high-risk” HPV strains are strongly tied to cured after they have spread.
cancer of the cervix. More than 99% of cervical cancer The U.S. Food and Drug Administration (FDA) has
cases are believed to arise from HPV infections. approved two vaccines for HPV, both of which protect
HPV infects epithelial cells, a type of cell that lines against the high-risk strains responsible for cervical
the body cavities and covers the outer surface of the body. cancer. Medical groups such as the American Academy
Once inside a cell, the virus hijacks the cellular machinery of Pediatrics and government organizations such as
to produce new viruses. The high-risk strains of HPV that the Centers for Disease Control and Prevention (CDC)
infect the cervix go one step further: Those viruses that recommend vaccinating girls at age 11 or 12, before
176
Human papillomavirus (HPV) and cervical cancer.
Certain strains of HPV can infect epithelial cells of the cervix
and lead to cancer, which can spread to the rest of the body.
Epithelium
Basal lamina
they become sexually active. In addition, recent CDC However, there are critics of these recommendations
guidelines also recommend vaccinating boys because and mandates. Some say the government shouldn’t be
they can transmit the virus to women when they become making medical decisions. Others argue that the use of
sexually active. On the basis of these recommendations, the vaccine condones sexual activity among young girls
many states are considering legislation that would require and boys. Still others have expressed concern over the
middle-school girls to receive the vaccine. vaccine’s safety.
177
Studies have found the HPV vaccine to be safe, a At the Mayo Clinic in Rochester, Minnesota,
conclusion backed by a 2010 report from the Institute of researchers are working to design vaccines to prevent
Medicine, an independent nonprofit organization that breast and ovarian cancers from recurring in women who
advises the U.S government on issues of health. In spite have been treated for these diseases. The researchers
of these findings, the HPV vaccine has not been widely have zeroed in on proteins on the surface of cancerous
accepted. The CDC found that by 2010, a full 5 years cells. Cells communicate with one another by releasing
after the vaccine was introduced, only 32% of teenage signaling molecules that are picked up by receptor
girls had been fully vaccinated. In 2013, the percentage molecules on another cell’s surface, much the way a radio
increased to 38%, but remained low. antenna picks up a signal. Cellular communication is
Proponents of HPV vaccination say those numbers critical for a functioning organism. Sometimes, though,
should cause concern. HPV is common: A 2007 study the signaling process goes awry.
found that nearly 27% of American women ages 14–59 The Mayo Clinic team is focusing on two cell-surface
were infected with the virus. Among 20- to 24-year- receptors that, when malfunctioning, lead to cancer.
olds, the infection rate was nearly 45%. Certainly, not One, Her2/neu, promotes the growth of aggressive
everyone who contracts HPV will develop cancer. Most breast cancer cells. The other, folate receptor a (alpha)
people manage to clear the virus from their bodies protein, is frequently overexpressed in breast and
within 2 years of infection. But in some cases, the virus ovarian tumors. The researchers hope to train patients’
hangs on and cancer results. immune systems to generate antibodies that recognize
Because cancer is often difficult to treat, especially these proteins and then destroy the cancerous cells. The
in its later stages, many researchers focus on early approach successfully prevented tumors in mice. Now the
detection or prevention. Early detection of cervical researchers are testing the vaccines in humans.
cancer can be accomplished by routine Pap smears, in Even if these new therapies are successful, cancer
which cells from the cervix are collected and observed researchers have much more work to do. Cancer is not
under a microscope. As we have seen, cervical cancer is one disease but many, and most of them are caused by a
also an obvious target for prevention since it is caused complex interplay of genetic and environmental factors.
by a virus that can be averted with a conventional Any number of things can go wrong as cells communicate,
vaccine. However, most cancers are not caused by grow, and divide. But as researchers learn more about the
viruses, and developing vaccines to prevent those cellular processes involved, they can step in to prevent
cancers is a trickier proposition—but researchers are or treat cancer. As the HPV vaccine shows, there is
pushing ahead. significant progress to be made.
? CASE 2 QUESTIONS
Special sections in Chapters 9–11 discuss the following questions related to Case 2.
178
CHAPTER 9
Cell Signaling
Core Concepts
9.1 Cells communicate primarily by
sending and receiving chemical
signals.
9.2 Cells can communicate over
long and short distances.
9.3 Signaling molecules bind to
and activate cell-surface and
intracellular receptors.
9.4 G protein-coupled receptors
are a large, conserved family
of receptors that often lead to
short-term responses.
9.5 Receptor kinases are
widespread and often lead to
long-term responses.
Quest/Science Source.
179
180 SECTION 9.1 P R I N C I P L E S O F C E L L CO M M U N I C AT I O N
change in the receptor. As a result, some receptors bind to and environment. Eventually, when the density of bacteria is low, the
activate other proteins located inside the cell. Other receptors are initiating signal falls below a critical threshold and gene expression
themselves enzymes, and binding of the signal changes the shape is turned back off.
and activity of the enzyme. Still other receptors are channels that This example is relatively simple. Remarkably, however, other
open or close in response to binding a signaling molecule. more complex signaling pathways in a wide range of organisms
Once activated, the receptor often triggers a series of involve the same four elements and steps, and in many cases involve
downstream events in a process called signal transduction. During similar signaling molecules, receptors, and signal transduction
signal transduction, one molecule activates the next molecule, systems that have been evolutionarily conserved over long periods
which activates the next, and so on. In this way, signal transduction of time.
can be thought of as a chain reaction or cascade of biochemical
events set off by the binding and activation of the receptor. An
important aspect of signal transduction is that the signal is often 9.2 CELL SIGNALING OVER LONG
amplified at each step in the pathway. As a result, a low signal AND SHORT DISTANCES
concentration can have a large effect on the responding cell.
Next, there is a cellular response, which can take different In prokaryotes and unicellular eukaryotes, cell communication
forms depending on the nature of the signal and the type of occurs between individual organisms. In complex multicellular
responding cell. For example, signaling pathways can activate eukaryotes, cell signaling involves communication between cells
enzymes involved in metabolic pathways, or turn on genes that within the same organism. The same principles apply in both
cause the cell to divide, change shape, or signal other cells. instances, but there are important differences. In multicellular
The last step is termination, in which the cellular response organisms, the distance between communicating cells varies
is stopped. The response can be terminated at any point along the considerably (Fig. 9.4). When the two cells are far apart, the
signaling pathway. Termination protects the cell from overreacting signaling molecule is transported by the circulatory system. When
to existing signals and therefore helps the cell to have an appropriate they are close, the signaling molecule simply moves by diffusion.
level of response. It also allows the cell to respond to new signals. In addition, many cells in multicellular organisms are physically
In the case of pneumococcal cells, the peptide binds to and attached to one another; in this case, the signaling molecule
activates a receptor on the cell surface. When enough receptors is not released from the signaling cell at all. In this section, we
are bound by the signaling molecule, the message is relayed by explore communication over long and short distances, as well as
signal transduction pathways to the nucleoid. There, genes are communication between cells that are physically associated with
turned on that express proteins involved in DNA uptake from the one another.
FIG. 9.4 Signaling distances. Cell communication can be classified according to the distance between the signaling and responding cells.
a. Endocrine signaling
Signaling
molecule
c. Autocrine signaling
Endocrine signaling acts over long distances. type of signaling molecule that causes the responding cell to grow,
Signaling molecules released by a cell may have to travel great divide, or differentiate. One of the first growth factors discovered
distances to reach receptor cells in the body. In this case, they was found by scientists who were attempting to understand how
are often carried in the circulatory system. Signaling by means of to maintain cultures of cells in the laboratory. For decades, medical
molecules that travel through the bloodstream is called endocrine research has worked with cells maintained in culture. Initially,
signaling (Fig. 9.4a; Chapter 38). these cultured cells had limited use because they failed to divide
Adrenaline (section 9.1) provides a good example of endocrine outside the body unless they were supplied with unidentified
signaling. Adrenaline, which is produced in the adrenal glands, factors from mammalian blood serum. In 1974, American
is carried by the bloodstream to target cells that are far from the scientists Nancy Kohler and Allan Lipton discovered that one of
signaling cells. Other examples of endocrine signaling involve these factors is secreted by platelets (Fig. 9.5). Consequently,
the mammalian steroid hormones estradiol (an estrogen) and the growth factor was named “platelet-derived growth factor,”
testosterone (an androgen). These hormones travel from the ovaries or PDGF. We now know of scores of molecules secreted by cells
and the testes, respectively (although there are other minor sources that function as growth factors, and in most cases their effects are
of these hormones), through the bloodstream, to target cells in confined to neighboring cells.
various tissues throughout the body. The increased amount of Growth factors secreted by cells in an embryo work over
estrogen in girls during puberty causes the development of breast short distances to influence the kind of cells their neighbors will
tissue and the beginning of menstrual cycles. The increased amount become. In this way, they help shape the structure of the adult’s
of testosterone in boys during puberty causes the growth of muscle tissues, organs, and limbs. For example, in developing vertebrates,
cells, deepening of the voice, and growth of facial hair (Chapter 42). paracrine signaling by the growth factor Sonic Hedgehog (yes,
it’s named after a video game character) ensures that the motor
Signaling can occur over short distances. neurons in your spinal cord are located properly, that the bones of
Signaling can also occur between two cells that are close to each your vertebral column form correctly, and that your thumb and
other (Fig. 9.4b). When cells are close to each other, they do not pinky fingers are on the correct sides of your hands.
require a circulatory system to deliver the signaling molecule. A specialized form of short-range signaling is the
Instead, the signaling molecule can simply move by diffusion communication between neurons (nerve cells), or between
between the two cells. This form of signaling is called paracrine neurons and muscle cells (Chapters 35 and 37). Neurotransmitters
signaling. In this case, signaling molecules travel distances of are a type of signaling molecule released from a neuron. After
about 20 cell diameters, or a few hundred micrometers. release, they diffuse across a small space, called a synapse, between
In paracrine signaling, the signal is usually a small, water- the signaling cell and the responding cell. If the adjacent cell is a
soluble molecule such as a growth factor. A growth factor is a neuron, it often responds by transmitting a nerve impulse further
HOW DO WE KNOW?
FIG. 9.5 component of blood, but it is collected from blood that has not
clotted. American biologists Nancy Kohler and Allan Lipton were
Where do growth factors interested in identifying the source of the factor in blood serum
that allows cells to survive in culture.
come from? HYPOTHESIS Since Kohler and Lipton knew that clotting
depends on the release of substances from platelets, they
hypothesized that a growth-promoting factor was introduced into
BACKGROUND Cells can be grown outside the body in culture.
the blood by platelets during clotting.
However, they survive and grow well only under certain conditions.
Researchers hypothesized that there are substances that are EXPERIMENT 1 The investigators first confirmed earlier
required for cells to grow in culture, but the identity and source of observations using cells that are easily grown in culture called
these substances were for a long time unknown. A key insight came fibroblasts, which they obtained from mice. They cultured two
from the observation that chicken cells grow much better if they are sets of fibroblasts in small plastic dishes. To one of the cultures
cultured in the presence of blood serum rather than blood plasma. they added serum; to the other culture they added plasma. Then
Blood serum is the liquid component of blood that is collected they monitored the rate of cell division in both culture dishes
after blood has been allowed to clot. Blood plasma is also the liquid over time.
(continued on following page)
184 SECTION 9.2 C E L L S I G N A L I N G OV E R LO N G A N D S H O RT D I S TA N C E S
HOW DO WE KNOW?
RESULTS 1 They observed that the rate of cell division in the fibroblasts EXPERIMENT 2 To see if the factor is released directly from
cultured in serum was far greater than that of the cells cultured in platelets, they prepared a solution of proteins made from purified
plasma, as expected based on earlier experiments (Fig. 9.5a). platelets, added these proteins to cultured fibroblasts, and
measured cell growth.
a.
RESULTS 2 They found that the solution of platelet proteins also
Unclotted blood Clotted blood
caused the growth of fibroblasts to increase compared to the
growth of fibroblasts in plasma (Fig. 9.5b).
Plasma Serum
b.
Fibroblast 6.0
5.5
and then releasing additional neurotransmitters. If the responding developmental decision. In addition, autocrine signaling can be
cell is a muscle cell, it often responds by contracting. used by cancer cells to promote cell division.
In some cases, signaling molecules may be released by a cell
and then bind to receptors on the very same individual cell. Such Signaling can occur by direct cell–cell contact.
cases, where signaling cell and responding cell are one and the In some cases, a cell communicates with another cell through
same, are examples of autocrine signaling (Fig. 9.4c). Autocrine direct contact, without diffusion or circulation of the signaling
signaling is especially important to multicellular organisms molecule. This form of signaling requires that the two
during the development of the embryo (Chapters 20 and 42). communicating cells be in physical contact with each other. A
For example, once a cell differentiates into a specialized cell transmembrane protein on the surface of one cell acts as the
type, autocrine signaling is sometimes used to maintain this signaling molecule, and a transmembrane protein on the surface
CHAPTER 9 CELL SIGNALING 185
of an adjacent cell acts as the receptor (Fig. 9.4d). In this case, ways, this change in receptor shape is similar to the change that
the signaling molecule is not released from the cell, but instead occurs when a substrate binds to the active site of an enzyme
remains associated with the plasma membrane of the signaling cell. (Chapter 6). The conformational change in the receptor
This form of signaling is important during embryonic ultimately triggers chemical reactions or other changes in the
development. As an example, let’s look at the development of the cytosol, and is therefore a crucial step in the reception and
central nervous system of vertebrate animals. In the brain and interpretation of communications from other cells.
spinal cord, neurons transmit information in the form of electrical
signals that travel from one part of the body to another. The Receptors for polar signaling molecules are on
neurons in the central nervous system are greatly outnumbered by the cell surface.
supporting cells, called glial cells, which nourish and insulate the The location of a particular receptor in a cell depends largely on
neurons. Both the neurons and the glial cells start out as similar whether the signaling molecule is polar or nonpolar (Fig. 9.6).
cells in the embryo, but some of these undifferentiated cells Many signaling molecules, such as the growth factors we just
become neurons and many more become glial cells. discussed, are small, polar proteins that cannot pass through the
During brain development, the amount of a transmembrane
protein called Delta dramatically increases on the surface of some
of these undifferentiated cells. These cells will become neurons.
Delta proteins on each new neuron bind to transmembrane
proteins called Notch on the surface of adjacent, undifferentiated FIG. 9.6 Cell-surface and intracellular receptors. (a) Cell-surface
cells. In this case, the signaling cell is the cell with elevated receptors interact with polar signaling molecules that
levels of Delta protein. The Delta protein in turn is the signaling cannot cross the plasma membrane. (b) Intracellular
molecule, and Notch is its receptor. Cells with activated Notch receptors interact with nonpolar signaling molecules that
receptors become glial cells and not neurons. Because one can cross the plasma membrane.
signaling cell sends this same message to all the cells it contacts,
a. Cell-surface receptor
it is easy to understand how there can be so many more glial cells
than neurons in the central nervous system. Polar Ligand-binding site
signaling
As you can see from these examples, the same fundamental molecule Activated receptor
principles are at work when signaling guides a developing embryo, Extracellular
allows neurons to communicate with other neurons or muscles, domain
triggers DNA uptake by pneumococcal cells, or allows your body Trans-
to respond to stress. All these forms of communication are based membrane
domain Polar signaling
on signals that are sent from a signaling cell to a responding
molecules
cell. These signaling molecules are the language of cellular Cytoplasmic cannot cross
communication. domain the plasma
membrane
Plasma and rely on
membrane cell-surface
9.3 CELL-SURFACE AND receptors.
INTRACELLULAR RECEPTORS
Receptors are proteins that receive and interpret information
carried by signaling molecules. Regardless of the distance between
communicating cells, a message is received by a responding cell b. Intracellular receptor
when the signaling molecule binds to a receptor protein on or in Small,
the responding cell. For this reason, the signaling molecule is often nonpolar
signaling Activated receptor
referred to as a ligand (from the Latin ligare, which means “to bind”). molecule
The signaling molecule binds to a specific part of the receptor protein Small
nonpolar
called the ligand-binding site. The bond is noncovalent and highly signaling
specific: The signaling molecule binds only to a receptor with a molecules
ligand-binding site that recognizes the molecule. can freely
pass
Almost without exception, the binding of a signaling through the
molecule to the ligand-binding site of a receptor causes a Nucleus plasma
membrane
conformational change in the receptor. We say that the DNA
and activate
conformational change “activates” the receptor because it is cytoplasmic
through this change that the receptor passes the message from receptors.
the signaling molecule to the interior of the cell. In many
186 SECTION 9.3 C E L L-S U R FAC E A N D I N T R AC E L LU L A R R E C E P TO R S
FIG. 9.7 Three types of cell-surface receptor. Receptors act like (a) a light switch. (b) G protein-coupled receptors, (c) receptor kinases, and
(d) ligand-gated ion channels can be either “off” (inactive) or “on” (active).
a. A light switch
= =
Off On
Ligand
Ions
Receptor G protein
hydrophobic core of the plasma membrane. The receptor proteins often already bound to DNA and need only to bind their steroid
for these signals are on the outside surface of the responding cell counterpart to turn on gene expression.
(Fig. 9.6a). There are many examples of steroid hormones, including sex
Receptor proteins for growth factors and other polar hormones, glucocorticoids (which raise blood glucose levels), and
ligands are transmembrane proteins with an extracellular ecdysone (involved in insect molting). However, since much of
domain, a transmembrane domain, and a cytoplasmic domain. the information received by cells is transmitted across the plasma
When a signaling molecule binds to the ligand-binding site in membrane through transmembrane receptors, we focus our
the extracellular domain, the entire molecule, including the attention here on the sequence of events that takes place when
cytoplasmic domain of the receptor, undergoes a conformational receptors on the surface of cells bind their ligands.
change, and as a result the molecule is activated. In this way, the
receptor acts as a bridge between the inside and outside of the Cell-surface receptors act like molecular
responding cell that carries the message of the hydrophilic signal switches.
across the hydrophobic core of the plasma membrane. As we saw earlier, a receptor is activated after a signaling molecule
binds to its ligand-binding site. Many receptors act as binary
Receptors for nonpolar signaling molecules are molecular switches, existing in two alternative states, either “on”
in the interior of the cell. or “off” (Fig. 9.7). In this way, receptors behave similarly to a light
Some nonpolar signaling molecules, such as the steroid hormones switch (Fig. 9.7a). When bound to their signaling molecule, the
involved in endocrine signaling, don’t need a receptor on the molecular switch is turned on. When the signaling molecule is no
cell surface in order to relay information to the interior of the longer bound, the switch is turned off.
cell. Since steroids are hydrophobic, they pass easily through the There are thousands of different receptor proteins on the
hydrophobic core of the phospholipid bilayer and into the target surface of any given cell. Most of them can be placed into one
cell. Once inside, steroid hormones bind to receptor proteins of three groups on the basis of their structures and what occurs
located in the cytosol or in the nucleus to form receptor–steroid immediately after the receptor binds its ligand. One type of cell-
complexes (Fig. 9.6b). Steroid–receptor complexes formed in the surface receptor is called a G protein-coupled receptor (Fig. 9.7b;
cytosol enter the nucleus, where they act to control the expression section 9.4). When a ligand binds to a G protein-coupled receptor,
of specific genes. Steroid receptors located in the nucleus are the receptor couples to, or associates with, a G protein, as its name
CHAPTER 9 CELL SIGNALING 187
suggests. G protein-coupled receptors are evolutionary conserved channels are closed. However, when a signaling molecule binds to
and all have a similar molecular structure (section 9.4) the extracellular portion of a ligand-gated ion channel, the channel
A second group of cell-surface receptors are themselves undergoes a conformational change that opens it and allows ions
enzymes, which are activated when the receptor binds its ligand. to flow in and out. This type of signaling is especially important
Most of these are receptor kinases (Fig. 9.7c and section 9.5). for nerve and muscle cells since their functions depend on a rapid
A kinase is an enzyme that catalyzes the transfer of a phosphate change in ion flow across the plasma membrane.
group from ATP to a substrate. To catalyze this reaction, it binds What happens after a signaling molecule binds to its receptor
both ATP and the substrate. This process is called phosphorylation and flips a molecular switch? Following receptor activation,
(Fig. 9.8). Phosphorylation is important because it affects the signaling pathways transmit the signal to targets in the interior of
activity of the substrate: When a protein is phosphorylated by the cell, the cell responds, and eventually the signal is terminated.
a kinase, it typically becomes active and is switched on. The In the next two sections, we examine the signaling pathways
addition of a phosphate group to a protein can activate it by activated by G protein-coupled receptors and receptor kinases.
altering its shape or providing a new site for other proteins to
bind. Phosphatases remove a phosphate group, a process called
dephosphorylation (Fig. 9.8). When a protein is dephosphorylated 9.4 G PROTEIN-COUPLED
by a phosphatase, it typically becomes inactive and is switched off. RECEPTORS AND SHORT-
Receptors in the third group, ion channels, alter the flow of TERM RESPONSES
ions across the plasma membrane. These channels can be opened
in different ways. Some open in response to changes in voltage G protein-coupled receptors, introduced in section 9.3, are a very
across the membrane; these are called voltage-gated ion channels large family of cell-surface molecules. They are found in virtually
and are discussed in Chapter 35. Other ion channels open when every eukaryotic organism. In humans, for example, approximately
bound by their ligand; these are called ligand-gated ion channels 800 different G protein-coupled receptors have been found. They
(Fig. 9.7d) and are discussed in Chapter 37. Recall from Chapter 5 all have two characteristics in common. First, they have a similar
that channel proteins help ions and other molecules diffuse into structure, consisting of a single polypeptide chain that has seven
and out of the cell by providing a hydrophilic pathway through the transmembrane spanning regions, with the ligand-binding site on
hydrophobic core of the plasma membrane. Most of the time, the the outside of the cell and the portion that binds to the G protein
on the inside of the cell. Second, when activated, they associate
with a G protein. In this way, they are able to transmit the signal
from the outside to the inside of the cell. These characteristics
FIG. 9.8 Phosphorylation and dephosphorylation. A kinase result from their shared evolutionary history.
transfers a posphate group from ATP to a protein, typically In spite of their similarity, different G protein-coupled
activating the protein. A phosphatase removes a phosphate receptors are able to respond to a diverse set of different signaling
group from a protein, typically deactivating the protein. molecules, including hormones, neurotransmitters, and small
molecules. In addition, their effects are quite diverse. For example,
signaling through these receptors is responsible for our senses
of sight, smell, and taste (Chapter 36). In fact, it is thought
Inactive protein that G protein-coupled receptors used for cell communication
in multicellular organisms evolved from sensory receptors in
unicellular eukaryotes.
FIG. 9.9 Activation of a G protein by a G protein-coupled FIG. 9.10 Adrenaline signaling in heart muscle. Adrenaline binds
receptor. A G protein-coupled receptor is activated when to a G protein-coupled receptor, leading to production
it binds a signaling molecule, which leads to exchange of of the second messenger cAMP and activation of protein
GDP for GTP on the G protein’s a subunit, separation of kinase A. The cell’s response is increased heart rate.
the a subunit, and downstream effects.
Activated
Activated adenylyl
Ligand Inactive target receptor cyclase
protein
Receptor G protein Activated
adenylyl cyclase
When the subunit converts ATP into
is bound to GDP,
the second
the three subunits GTP ATP
messenger cAMP,
are joined together
which in turn
GDP and the G protein is Active cAMP activates protein
inactive. G protein kinase A.
j Quick Check 2 Is the term “G protein” just a shorter name for a Signals lead to a cellular response.
G protein-coupled receptor? Cells are typically exposed to many different types of signaling
molecules. What determines the response of the cell? In part, that
Signals are often amplified in the cytosol. depends on the types of receptor present on the surface of the cell.
Because different G protein-coupled receptors have different These receptors determine which signals the cell is able to respond
effects in different cells, we will follow the steps in cell signaling to. The response of the cell also depends on the set of proteins that is
by following a specific example. Adrenaline, discussed earlier, found in it, as different cell types have different sets of intracellular
CHAPTER 9 CELL SIGNALING 189
FIG. 9.11 Amplification of G protein-coupled signaling. Signaling through G protein-coupled receptors is amplified at several places, so a small
amount of signal can produce a large response in the cell.
Adrenaline
Activated
receptor
Activated
adenylyl
cyclase
GTP ATP GTP ATP GTP ATP
cAMP cAMP
Active
Amplification subunit of cAMP
G protein
Each adenylyl cyclase enzyme
produces large amounts of the second
messenger cAMP, which activates
many molecules of protein kinase A.
Inactivated
protein
kinase A
Activated
protein
kinase A
ATP
Each protein kinase A enzyme
Amplification phosphorylates and activates
multiple protein targets.
ADP
Protein
targets
Phosphate group
proteins and signaling pathways. As a result, the same signaling resulting influx of calcium ions results in shorter intervals
molecule can have different effects in different types of cells. between muscle contractions and thus a faster heart rate. As long
In the case of the heart, activated PKA leads to the opening as adrenaline is bound to its receptor, the heart rate remains rapid.
of calcium channels that are present in heart muscle cells. The This increase in the heart rate in turn results in increased blood
190 SECTION 9.4 G P ROT E I N - CO U P L E D R E C E P TO R S A N D S H O RT-T E R M R E S P O N S E S
flow to the brain and skeletal muscles to deal with the stress that Once adrenaline leaves the receptor, the receptor reverts to
set off the signal in the first place. its inactive conformation and no longer activates G proteins
This example is typical of signaling through G protein-coupled (Fig. 9.12).
receptors. These receptors tend to activate downstream enzymes Even when a receptor is turned off, a signal will continue to be
or, in some cases, open ion channels. Because they often modify transmitted unless the other components of the signaling pathway
proteins that are already synthesized in the cell, their effects tend are also inactivated. A second place where the signal is terminated
to be rapid, short-lived, and easily reversible, as we will see next. is at the G protein itself (Fig. 9.12). G proteins can catalyze the
hydrolysis of GTP to GDP and inorganic phosphate. This means that
Signaling pathways are eventually terminated. an active, GTP-bound a subunit in the “on” position automatically
After a good scare, we eventually calm down and our heartbeat turns itself “off” by converting GTP to GDP. In fact, the a subunit
returns to normal. This change means that the signaling pathway converts GTP to GDP almost as soon as a molecule of GTP binds to
initiated by adrenaline has been terminated. How does this it. Thus, a G protein is able to activate adenylyl cyclase, and adenylyl
happen? First, most ligands, including adrenaline, do not bind cyclase is able to make cAMP, only during the very short time it
to their receptors permanently. The length of time a signaling takes the a subunit to convert GTP to GDP. Without an active
molecule remains bound to its receptor depends on how tightly receptor to generate more active G protein a subunits, transmission
the receptor holds on to it, a property called binding affinity. of the signal quickly comes to a halt.
FIG. 9.12 Termination of a G protein-coupled signal. G protein-coupled signaling is terminated at several places, allowing the cell to respond
to new signals.
Activated
adenylyl
cyclase
GTP ATP
cAMP
Protein
kinase A
Inactive Active
Active Inactive
Phosphatase
Phosphatases remove phosphate
groups from proteins, causing
them to become inactive.
CHAPTER 9 CELL SIGNALING 191
Farther down the pathway, an enzyme converts the second on the surface of cells at the site of the wound, where it triggers
messenger cAMP to AMP, which no longer activates protein cell division necessary to repair the wound.
kinase A. Phosphatases remove the phosphate groups added by The cellular responses that result from receptor kinase
PKA, inactivating PKA’s target proteins (Fig. 9.12). In fact, most activation tend to involve changes in gene expression, which in
signaling pathways are counteracted at one or more points as a turn allow cells to grow, divide, differentiate, or change shape. In
means of decreasing or terminating the response of the cell to contrast, the activation of G protein-coupled receptors typically
the signal. leads to shorter-term changes in the cell, like activating enzymes
or opening ion channels.
j Quick Check 3 Name four ways in which the adrenaline signal to Signaling through receptor kinases takes place in most
the heart is terminated. eukaryotic organisms, and the structure and function of these
receptors have been conserved as organisms have evolved over
hundreds of millions of years. A well-studied receptor kinase called
9.5 RECEPTOR KINASES AND Kit provides an example. In vertebrates, signaling through the
LONG-TERM RESPONSES Kit receptor kinase is important for the production of pigment
in skin, feathers, scales, and hair. The conserved function of this
Like the communication that takes place through G protein- receptor can be seen in individuals with mutations in the kit gene,
coupled receptors, signaling through receptor kinases causes as shown in Fig. 9.13. (By convention, the name of a protein,
cells to respond in many ways. During embryonic development, like Kit, is capitalized and in roman type. The name of the gene
receptor kinase signaling is responsible for the formation and that encodes the protein, like kit, is lower case and italicized.)
elongation of limb buds that eventually become our arms and legs. As you can see from Fig. 9.13, mammals, reptiles, birds, and fish
When we cut a finger, platelet-derived growth factor (PDGF) is with a mutation in the kit gene have a similar appearance. This
released from platelets in the blood and binds to its receptor kinase observation indicates that the function of this gene has remained
FIG. 9.13 Mutations in the Kit receptor kinase. Similar patterns of incomplete pigmentation are present in mammals, reptiles, birds, and fish
that have this mutated receptor. Sources: (clockwise) Mark Boulton/Science Source; Mark Smith/Science Source; © Phillip Colla/Oceanlight.com; Werner
Bollmann/Oxford Scientific/Getty Images.
192 SECTION 9.5 R E C E P TO R K I N A S E S A N D LO N G -T E R M R E S P O N S E S
FIG. 9.14 Receptor kinase activation and signaling. Receptor kinases bind signaling molecules, dimerize, phosphorylate each other, and activate
intracellular signal molecules.
Cytoplasmic
ATP Phosphate signaling
ADP group proteins
Inactive receptor Dimerization Active receptor Active receptor
fairly constant since the appearance of the last common ancestor when Ras is activated by a receptor kinase, it exchanges GDP for
of these groups, more than 500 million years ago. GTP. Activated GTP-bound Ras triggers the activation of a protein
kinase that is the first in a series of kinases that are activated in
Receptor kinases phosphorylate each other, activate turn, as each kinase phosphorylates the next in the series. The
intracellular signaling pathways, lead to a response, series of kinases collectively are called the mitogen-activated
and are terminated. protein kinase pathway, or MAP kinase pathway (Fig. 9.15). The
Signaling through receptor kinases follows the same basic final activated kinase in the series enters the nucleus, where it
sequence of events that we saw in signaling though G protein- phosphorylates target proteins. Some of these proteins include
coupled receptors, including receptor activation, signal transcription factors that turn on genes needed for cell division so
transduction, cellular response, and termination. Let’s consider that your cut can heal.
an example. Think about the last time you got a cut. The cut The signals received by receptor kinases are amplified as the
likely bled for a minute or two, and then the bleeding stopped. signal is passed from kinase to kinase. Each phosphorylated kinase
The signaling molecule platelet-derived growth factor (PDGF) in the series activates multiple molecules of the downstream
helps the healing process get started. When platelets in the blood kinase, and the downstream kinase in turn activates many
encounter damaged tissue, they release a number of proteins, molecules of another kinase still farther downstream. In this way,
including PDGF. PDGF is the signaling molecule that binds to a very small amount of signaling molecule (PDGF in our example)
PDGF-specific receptor kinases on the surface of cells at the site of can cause a large-scale response in the cell.
a wound. Receptor kinase signaling is terminated by the same basic
Receptor kinases have an extracellular portion that binds the mechanisms that are at work in G protein-coupled receptor
signaling molecule and an intracellular portion that is a kinase, pathways. For example, protein phosphatases inactivate
an enzyme that transfers a phosphate group from ATP to another receptor kinases and other enzymes of the MAP kinase pathway.
molecule. A single molecule of PDGF binds to the extracellular Furthermore, Ras hydrolyzes GTP to GDP, just like the G protein
portion of two receptors, causing the receptors to partner with a subunit. Shortly after Ras binds to GTP and becomes active, Ras
each other. This partnering of two similar or identical molecules is converts GTP to GDP and becomes inactive. Without an active
called dimerization. Dimerization activates the cytoplasmic kinase receptor kinase to generate more active Ras, activation of the
domains of the paired receptors, causing them to phosphorylate MAP kinase pathway stops.
each other at multiple sites on their cytoplasmic tails (Fig. 9.14).
The addition of these phosphate groups provides places on the ? CASE 2 CANCER: WHEN GOOD CELLS GO BAD
receptor where other proteins bind and become active. How do cell signaling errors lead to cancer?
One of the downstream targets of an activated receptor kinase Many cancers arise when something goes wrong with the way a
is Ras. Ras is a G protein, but in contrast to the three-subunit cell responds to a signal that leads to cell division or, in some cases,
G proteins discussed earlier, Ras consists of a single subunit, when a cell behaves as if it has received a signal for cell division
similar to the a subunit of the three-subunit G proteins. In the when in fact it hasn’t. Defects in cell signaling that lead to cancer
absence of a signal, Ras is bound to GDP and is inactive. However, can take place at just about every step in the cell signaling process.
CHAPTER 9 CELL SIGNALING 193
cells are genetically modified to express an activated G protein through Ras to the MAP kinase pathway. As we better understand
a subunit, their growth after transplantation into mice is how different signaling pathways integrate in specific cell types,
significantly inhibited. In addition, in cell culture, elevated cAMP we have a chance to alter the activity of particular pathways and
levels block cells from responding to growth factors that signal ultimately the response of the cell. •
There are four essential players in communication between Receptor kinases phosphorylate each other and activate
two cells: a signaling cell, a signaling molecule, a receptor target proteins. page 187
protein, and a responding cell. page 180
Ligand-gated ion channels open in response to a signal,
The signaling molecule binds to its receptor on the allowing the movement of ions across the plasma
responding cell, leading to receptor activation, signal membrane. page 187
transduction and amplification, a cellular response, and
eventually termination of the response. page 181 9.4 G protein-coupled receptors are a large,
conserved family of receptors that often lead to short-
9.2 Cells can communicate over long and short term responses.
distances.
G protein-coupled receptors bound to signaling molecules
Endocrine signaling takes place over long distances and associate with G proteins. page 187
often relies on the circulatory system for transport of
G proteins are active when bound to GTP and inactive
signaling molecules. page 183
when bound to GDP. page 187
Paracrine signaling takes place over short distances
Some G proteins are composed of three subunits, denoted
between neighboring cells and relies on diffusion.
a, b, and γ. When a G protein encounters an activated
page 183
receptor, the a subunit exchanges GDP for GTP, dissociates
Autocrine signaling occurs when a cell signals itself. from the b and γ subunits, and becomes active. page 188
page 184
Signal transduction cascades are amplified in the
Some forms of cell communication depend on direct contact cytosol. page 188
between two cells. page 184
Intracellular, cytosolic signals are short-lived before they
are terminated. page 189
9.3 Signaling molecules bind to and activate cell-
surface and intracellular receptors.
9.5 Receptor kinases are widespread and often lead
A signaling molecule, or ligand, binds specifically to the to long-term responses.
ligand-binding site of the receptor. Binding causes the
Ligand binding to receptor kinases causes them to dimerize.
receptor to undergo a conformational change that activates
The paired receptor kinases phosphorylate each other’s
the receptor. page 185
cytoplasmic domains, leading to activation of intracellular
Receptors for polar signaling molecules, including growth signaling pathways. page 192
factors, are located on the plasma membrane. page 186
The phosphorylated receptors bind other proteins, which in
Receptors for nonpolar signaling molecules, such as turn activate other cytosolic signaling molecules, such
steroid hormones, are located in the cytosol or in the as Ras. page 192
nucleus. page 186
When Ras is activated, the GDP to which it is bound is
There are three major types of cell-surface receptor: released and is replaced by GTP. The active, GTP-bound Ras
G protein-coupled receptors, receptor kinases, and ion binds to and activates the first in a series of kinases.
channels. All act as molecular switches. page 186 page 192
CHAPTER 9 CELL SIGNALING 195
Cancer can be caused by errors in any step of the signaling 5. Explain how signals can specifically target only some cells,
pathways involved in cell division. page 192 even if they are released into the bloodstream and come
into contact with many cells.
Mutations in receptor kinases and Ras are frequently
associated with human cancers. page 193 6. Describe three different responses of a cell-surface
receptor on binding a signaling molecule and undergoing a
Several signaling pathways can take place simultaneously
conformational change.
in a single cell, and the cellular response depends on the
integration of these pathways. page 193 7. List several responses a cell might have to a signaling
molecule.
Core Concepts
10.1 Tissues and organs are
communities of cells that
perform specific functions.
10.2 The cytoskeleton is
composed of microtubules,
microfilaments, and
intermediate filaments that
help maintain cell shape.
10.3 Cell junctions connect cells
to one another to form
tissues.
10.4 The extracellular matrix
provides structural support
and informational cues.
Science Source.
197
198 SECTION 10.1 T I S S U E S A N D O RG A N S
of proteins depends on their shape. In Chapters 7 and 8, we saw Source; c. Innerspace Imaging/Science Source; d. Biophoto Associates/
that the function of organelles like mitochondria and chloroplasts Science Source; e. Don W. Fawcett/Science Source.
FIG. 10.2 The skin. The skin is a community of cells organized into
two layers—the epidermis and dermis—that together
provide protection for the underlying tissues of the body.
Photo source: Jose Luis Pelaez Inc/Blend Images/Getty Images.
Epidermis
Basal lamina
Dermis
Epidermis
Sweat
gland
Keratinocytes Basal
lamina
Melanocyte
allow them to carry out the various processes necessary to sustain The outer layer of skin, the epidermis, serves as a water-resistant,
them. In animals, for example, four types of tissue—epithelial, protective barrier. The layer beneath the epidermis is the dermis.
connective, nervous, and muscle—combine to make up all the This layer of the skin supports the epidermis, both physically
organs of the body. Two or more tissues often combine and and by supplying it with nutrients. It also provides a cushion
function together as an organ, such as a heart or lung. surrounding the body.
Tissues and organs have distinctive shapes that reflect how they As you can see in Fig. 10.2, the epidermis is several cell layers
work and what they do. In the same way, the different cell types thick. Cells arranged in one or more layers are called epithelial
that make up these organs have distinctive shapes based on what cells and together make up a type of animal tissue called epithelial
they do in the organ. In animals, the shape of cells is determined and tissue. Epithelial tissue covers the outside of the body and
maintained by structural protein networks in the cytoplasm called lines many internal structures, such as the digestive tract and
the cytoskeleton (section 10.2). The shape and structural integrity vertebrate blood vessels. The epidermal layer of skin is primarily
of tissues and organs depend on the ability of cells to connect to one composed of epithelial cells called keratinocytes. The epidermis
another. In turn, the connection of cells to one another depends on also contains melanocytes that produce pigment that gives skin its
structures called cell junctions (section 10.3). Equally important coloration.
to a strong, properly shaped tissue or organ is the ability of cells to Keratinocytes in the epidermis are specialized to protect
adhere to a meshwork of proteins and polysaccharides outside the underlying tissues and organs. They are able to perform this
cell called the extracellular matrix (section 10.4). function in part because of their elaborate system of cytoskeletal
filaments. These filaments are often connected to the cell
The structure of skin relates to its function. junctions that hold adjacent keratinocytes together. Cell junctions
To start our investigation of the cytoskeleton, cell junctions, and also connect the bottom layer of keratinocytes to a specialized
the extracellular matrix, let’s consider a community of cells very form of extracellular matrix called the basal lamina (also called
familiar to all of us—our own skin (Fig. 10.2). The structure of the basement membrane, although it is not in fact a membrane),
mammalian skin is tied to its function. Skin has two main layers. which underlies and supports all epithelial tissues.
200 SECTION 10.2 T H E C Y TO S K E L E TO N
The second layer of skin, the dermis, is made up mostly of Microtubules and microfilaments are polymers
connective tissue, a type of tissue characterized by few cells and of protein subunits.
substantial amounts of extracellular matrix. The main type of cell Microtubules are hollow tubelike structures with the largest
in the dermis is the fibroblast, which synthesizes the extracellular diameter of the three cytoskeletal elements, about 25 nm
matrix. The dermis is strong and flexible because it is composed of (Fig. 10.3a). They are polymers of protein dimers. Each dimer is
tough protein fibers of the extracellular matrix. The dermis also made up of two slightly different tubulin proteins, called
has many blood vessels and nerve endings. ␣ (alpha) and  (beta) tubulin. One ␣ tubulin and one  tubulin
We will come back to the skin several times in this chapter combine to make a tubulin dimer and the tubulin dimers are
to show more precisely how these multiple connections among assembled to form the microtubule.
cytoskeleton, cell junctions, and the extracellular matrix make the Microtubules help maintain cell shape and the cell’s internal
skin a watertight and strong protective barrier. structure. In animal cells, microtubules radiate outward to the
cell periphery from a microtubule organizing center called the
centrosome. This spokelike arrangement of microtubules
10.2 THE CYTOSKELETON helps cells withstand compression and thereby maintain their
shape. Many organelles are tethered to microtubules, and thus
Just as the bones of vertebrate skeletons provide internal microtubules guide the arrangement of organelles in the cell.
support for the body, the protein fibers of the cytoskeleton Microfilaments are polymers of actin monomers, arranged to
provide internal support for cells (Fig. 10.3). All eukaryotic form a helix. They are the thinnest of the three cytoskeletal fibers,
cells have at least two cytoskeletal elements, microtubules about 7 nm in diameter, and are present in various locations in the
and microfilaments. Animal cells have a third element, cytoplasm (Fig. 10.3b). They are relatively short and extensively
intermediate filaments. All three of these cytoskeletal elements branched in the cell cortex, the area of the cytoplasm just beneath
are long chains, or polymers, made up of protein subunits. In the plasma membrane. At the cortex, microfilaments reinforce the
addition to providing structural support, microtubules and plasma membrane and organize proteins associated with it.
microfilaments enable the movement of substances within cells as These cortical microfilaments are also important in part
well as changes in cell shape. for maintaining the shape of a cell, such as the biconcave shape
FIG. 10.3 Three types of cytoskeletal element. (a) Microtubule; (b) microfilament; and (c) intermediate filament.
Actin
monomer
Microvilli
Centrosome
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 201
FIG. 10.4 Microfilaments in intestinal microvilli. Actin microfilaments help to maintain the structure of microvilli in the intestine. Photo source:
©1982, Rockefeller University Press. Originally published in The Journal of Cell Biology. 94:425–443.
Band of microfilaments
around the circumference Microvillus
of the cell
Plasma
membrane
Cross-linking
actin-binding
proteins
Actin
microfilaments
of red blood cells discussed earlier (see Fig. 10.1a). The shape of
absorptive epithelial cells such as those in the small intestine FIG. 10.5 Plus and minus ends of microtubules and microfilaments.
is also maintained with the help of microfilaments. In these The two ends assemble at different rates.
cells, bundles of microfilaments are found in microvilli, hairlike Microtubule
projections that extend from the surface of the cell, and longer
Microfilament
bundles of microfilaments form a band that extends around the
circumference of epithelial cells (Fig. 10.4).
FIG. 10.6 Dynamic instability. The plus ends of microtubules undergo cycles of rapid disassembly followed by slow assembly.
Centrosome
Polymer-
ization
Depolymerization
of cell movement, such as a single-celled amoeba foraging for food away from the plasma membrane toward the minus end, located
or a mammalian white blood cell chasing down foreign bacteria, at the centrosome in the interior of the cell. Movement along
depend on actin polymerization and depolymerization. It is also microtubules by kinesin and dynein is driven by conformational
required when a single cell divides in two during cytokinesis changes in the motor proteins and is powered by energy harvested
(Chapter 11). from ATP.
Microtubules make up the spindles that attach to Let’s look at an especially striking example of this system at
chromosomes during cell division. In this case, the ability of work in the specialized skin cells called melanophores present in
spindle microtubules to “explore” the space of the cell and some vertebrates. Melanophores are similar to the melanocytes
encounter chromosomes is driven by a unique property of in our own skin that produce the pigment melanin. However,
microtubules: Their plus ends undergo seemingly random cycles of rather than hand off their melanin to other cells as in humans,
rapid depolymerization followed by slower polymerization. These melanophores keep their pigment granules and move them
cycles of depolymerization and polymerization are called dynamic around the cell in response to hormones or neuronal signals. This
instability (Fig. 10.6). They allow spindle microtubules to quickly redistribution of melanin within the cell allows animals such
find and attach to chromosomes during cell division. as fish or amphibians to change color. For example, at night the
melanin granules in the skin of a zebrafish embryo are dispersed
Motor proteins associate with microtubules throughout the melanophores, making it darkly colored. As
and microfilaments to cause movement. morning comes and the day brightens, the pigment granules
A motor is a device that imparts motion. We saw that microtubules aggregate at the center of the cell around the centrosome, causing
and microfilaments have some capacity to lengthen and shorten the embryo’s color to lighten (Fig. 10.8).
by polymerization and depolymerization. However, when joined The melanin granules in the melanophores move back and
by small accessory proteins called motor proteins, microtubules forth along microtubules, transported by kinesin and dynein.
and microfilaments are capable of causing amazing movements. Kinesin moves the granules out toward the plus end of the
For example, microtubules function as tracks for transport microtubule during dispersal, and dynein moves them back toward
within the cell. Two motor proteins that associate with these the minus end during aggregation. The daytime and nighttime
microtubule tracks are kinesin and dynein. Kinesin transports camouflage provided by this color change helps prevent young,
cargo toward the plus end of microtubules, located at the developing organisms from being spotted by hungry predators
periphery of the cell (Fig. 10.7). By contrast, dynein carries its load lurking below.
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 203
FIG. 10.7 Intracellular transport. The motor protein kinesin FIG. 10.8 Color change in zebrafish embryos, driven by motor
interacts with microtubules to move vesicles in the cell. proteins kinesin and dynein. Melanin granules are
redistributed along microtubules in the melanophores of
the skin. Photo sources: (left and right) Jane Bradbury, “Small Fish, Big
Kinesin carries cargo, such as vesicles, toward the
plus ends of microtubules. Science”, PLOS Biology, 2, (5), May 2004, pg. 0569, Image courtesy of
Adam Amsterdam, Massachusetts Institute of Technology, Boston, MA;
(bottom) Courtesy Darren Logan, Wellcome Trust Sanger Institute.
Kinesin Microtubule
– +
ATP
ATP
ATP
In the dark, melanin granules are In the light, melanin granules are
dispersed outward by kinesin, aggregated toward the center by
causing the embryo to be darkly dynein, causing the embryo to be
ATP colored. lightly colored.
204 SECTION 10.2 T H E C Y TO S K E L E TO N
FIG. 10.9 Cilia and flagella in diverse cell types. Cilia and flagella, composed of microtubules, move cells or allow cells to propel substances.
Sources: (from left to right) SPL/Science Source; Eye of Science/Science Source; Andrew Syred/Science Source; Juergen Berger/Science Source.
Coordinated beating of the The cilia in these human airway These unicellular algae are Some cells of multicellular
cilia that cover the epithelial cells propel mucus propelled by two flagella. organisms, including these
paramecium moves the cell containing debris out of the lungs. sperm cells, swim by
through its environment. movement of a flagellum.
j Quick Check 1 Would a defect in dynein or in kinesin cause a We have seen that different cell types use the same tubulin
zebrafish embryo to remain darkly colored after daybreak? dimers to form microtubules and the same actin monomers
to form microfilaments. By contrast, the proteins making up
In addition to providing tracks for the transport of material
intermediate filaments differ from one cell type to another. For
within the cell, microtubules are found in cilia and flagella,
example, in epithelial cells, these protein subunits are keratins;
fiberlike organelles that propel the movement of cells or
in fibroblasts, they are vimentins; and in neurons, they are
substances surrounding the cell (Fig. 10.9). In these organelles,
neurofilaments. Some intermediate filaments, called lamins, are
microtubules associate with the motor protein dynein, which
even found inside the nucleus, where they provide support for the
causes movement. Many single-celled eukaryotic organisms that
nuclear envelope (Fig. 10.10). There are well over 100 different
live in aquatic environments propel themselves through the water
kinds of intermediate filaments.
by means of the motion of cilia (which are short) or flagella (which
Once assembled, many intermediate filaments become
are long). Some cells of multicellular organisms also have cilia or
attached to cell junctions at their cytoplasmic side, providing
flagella. For example, the sperm cells of algae, some plants, and
many animals are propelled by one or more flagella. Epithelial cells
in a number of animal tissues, such as the lining of the trachea and
the upper respiratory tract, have cilia that move substances along FIG. 10.10 Intermediate filaments in the cytoplasm and the
the surface of the cell layer. nucleus of a cell. Source: Courtesy of R. D. Goldman.
Like microtubules, microfilaments also associate with motor
proteins to produce movement. Actin microfilaments associate
with myosin to transport various types of cellular cargo, such
Intermediate filaments
as vesicles, inside of cells. Furthermore, microfilaments are composed of keratins
responsible for changes in the shape of many types of cell. One of in the cytoplasm are
the most dramatic examples of cell shape change is the shortening stained red.
FIG. 10.11 Intermediate filaments in the epidermis of the skin. Intermediate filaments bind to cell junctions called desmosomes, forming
a strong, interconnected network. Epidermolysis bullosa is a group of blistering diseases of the skin that can be caused by a defect in
intermediate filaments. Source: Helen Osler/Northscot/Rex USA.
Epidermis
Keratinocytes Basal
lamina
Melanocyte
Intermediate
filaments
Cell junction
Intermediate filaments
linked to cell junctions
in keratinocytes provide
a great deal of structural Defects in intermediate
support to the skin. filaments make the skin far less
resistant to physical stress.
strong support for the cells (Fig. 10.11). In the case of epithelial section is sometimes recommended in cases where the disease is
cells, this anchoring results in structural continuity from one cell diagnosed during pregnancy.
to another that greatly strengthens the entire epithelial tissue.
This is especially important for tissues that are regularly subject to The cytoskeleton is an ancient feature of cells.
physical stress, such as the skin and the lining of the intestine. Actin and tubulin are found in all eukaryotic cells, and their
Genetic defects that disrupt the intermediate filament structure and function have remained relatively unchanged
network can have severe consequences. For example, some throughout the course of evolution. The amino acid sequences
individuals with epidermolysis bullosa, a group of rare genetic of yeast tubulin and human tubulin are 75% identical. Similar
diseases, have defective keratin genes. Intermediate filaments comparisons of actin from amoebas and animals show that they
do not polymerize properly in these individuals, thus forming are 80% identical after close to a billion years of evolution. In
weaker connections between the layers of cells that make up the fact, a mixture of yeast and human actin monomers forms hybrid
epidermis. As a consequence, the outer layers can detach, resulting microfilaments able to function normally in the cell.
in extremely fragile skin that blisters in response to the slightest Not long ago, it was believed that cytoskeletal proteins were
trauma (Fig. 10.11). The sensitivity to physical stress is so extreme present only in eukaryotic cells. However, a number of studies
that infants with epidermolysis bullosa often suffer significant have shown that many prokaryotes also have a system of proteins
damage to the skin during childbirth. Therefore, Caesarean similar in structure to the cytoskeletal elements of eukaryotic
206 SECTION 10.3 CELL JUNCTIONS
cells and are involved in similar processes, including the separation more closely at the roles of the various types of cell junction in
of daughter cells during cell division. Interestingly, at least one tissues, as well as their interaction with the cytoskeleton.
of these prokaryotic cytoskeleton-like proteins is expressed in
the chloroplasts and mitochondria of some eukaryotic cells. The Cell adhesion molecules allow cells to attach to other
presence of this protein in these organelles lends support to the cells and to the extracellular matrix.
theory that chloroplasts and mitochondria were once independent In 1907, American embryologist H. V. Wilson discovered that if
prokaryotic cells that developed a symbiotic relationship with he pressed a live sponge through fine cloth he could break up the
another cell. This idea is called the endosymbiotic theory and it is sponge into individual cells. Then if he swirled the cells together,
discussed in Chapter 27. they would coalesce back into a group resembling a sponge. If he
The major functions of microtubules, microfilaments, and swirled the cells from sponges of two different species together, he
intermediate filaments are summarized in Table 10.1. observed that the cells sorted themselves out—that is, cells from
one species of sponge associated only with cells from that same
species (Fig. 10.12a). Fifty years later, German-born embryologist
10.3 CELL JUNCTIONS Johannes Holtfreter observed that if he took neuronal cells and
skin cells from an amphibian embryo and treated them the same
The cell is the fundamental unit of living organisms (Chapter 1). way that Wilson had treated sponge cells, the embryonic cells
Some estimates place the number of cells in an adult human being would sort themselves according to tissue type (Fig. 10.12b).
at between 50 and 75 trillion, whereas others place the number Cells are able to sort themselves because of the presence of
at well above 100 trillion. Whichever estimate is more accurate, various proteins on their surface called cell adhesion molecules
humans, as well as all complex multicellular organisms, are made that attach cells to one another or to the extracellular matrix.
up of a lot of cells! What then keeps us (or any other multicellular While a number of cell adhesion molecules are now known, the
organism) from slumping into a pile of cells? And what keeps cells cadherins (calcium-dependent adherence proteins) are especially
organized into tissues, and tissues into organs? important in the adhesion of cells to other cells. There are many
Tissues are held together and function as a unit because of cell different kinds of cadherin, and a given cadherin may bind only
junctions. Cell junctions physically connect one cell to the next to another cadherin of the same type. This property explains
and anchor cells to the extracellular matrix. Some tissues have cell Holtfreter’s observations of the cells from amphibian embryos.
junctions that perform roles other than adhesion. For example, cell E-cadherin (for “epidermal cadherin”) is present on the surface of
junctions in the outer layer of the skin and the lining of intestine embryonic epidermal cells, and N-cadherin (for “neural cadherin”)
provide a seal so that the epithelial sheet can act as a selective is present on neuronal cells. The epidermal cells adhered to one
barrier. Other cell junctions allow communication between adjacent another through E-cadherin, and the neuronal cells adhered to
cells so that they work together as a unit. In this section, we look each other through N-cadherin.
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 207
FIG. 10.12 Cell type–specific cell adhesion. Experiments showed that cells from (a) sponges and from (b) amphibian embryos are in each
case able to adhere to one another in a specific manner. Photo sources: a. (top) Borut Furlan/WaterFrame/age fotostock; (bottom) Franco Banfi/
WaterFrame/age fotostock.
a. Sponge
b. Amphibian embryo
Tissues were Individual cells from The cells from each tissue
broken up into both tissues were sorted themselves out
individual cells. mixed together. and adhered to form new
tissue.
Epidermal
cells
Neural plate Neural
cells cells
Cross
section
Early
epidermal
cells
Outside
Cadherins are transmembrane proteins (Chapter 5). The proteins, and their cytoplasmic domain is linked to microfilaments
extracellular domain of a cadherin molecule binds to the or intermediate filaments (Fig. 10.13b). Also like the cadherins,
extracellular domain of a cadherin of the same type on an integrins are of many different types, each binding to a specific
adjacent cell. The cytoplasmic portion of the protein is extracellular matrix protein. Integrins are present on the
linked to the cytoskeleton, including microfilaments and surface of virtually every animal cell. In addition to their role
intermediate filaments (Fig. 10.13a). This arrangement provides in adhesion, integrins also act as receptors that communicate
structural continuity from the cytoskeleton of one cell to information about the extracellular matrix to the interior of the
the cytoskeleton of another, increasing the strength of tissues cell (section 10.4)
and organs.
As well as being stably connected to other cells, cells also Anchoring junctions connect adjacent cells and are
attach to proteins of the extracellular matrix. Cell adhesion reinforced by the cytoskeleton.
molecules that enable cells to adhere to the extracellular matrix Cadherins and integrins are often organized into cell junctions,
are called integrins. Like cadherins, integrins are transmembrane complex structures in the plasma membrane that allow cells to
208 SECTION 10.3 CELL JUNCTIONS
adhere to one another. These anchoring cell junctions are of two Tight junctions prevent the movement of substances
types: adherens junctions and desmosomes (Fig. 10.14). through the space between cells.
In our earlier discussion of microfilaments (section 10.2), we Epithelial cells form sheets or boundaries that line tissues and
saw that a long bundle of actin microfilaments forms a band that organs, including the digestive tract, respiratory tract, and outer
extends around the circumference of epithelial cells, such as the layer of the skin. Like any effective boundary, a layer of epithelial
epithelial cells that line the intestine. This band of actin is attached cells must limit or control the passage of material across it.
to the plasma membrane by cadherins in a beltlike structure called Adherens junctions and desmosomes provide strong adhesion
an adherens junction (Fig. 10.14). The cadherins in the adherens between cells, but they do not prevent materials from passing
junction of one cell attach to the cadherins in the adherens freely through the spaces between the cells. This function is
junctions of adjacent cells. This arrangement establishes a physical provided by a different type of cell junction. In vertebrates, these
connection among the actin cytoskeletons of all cells present in an are called tight junctions (Fig. 10.14). Tight junctions establish
epithelial layer of cells. a seal between cells so that the only way a substance can travel
Like adherens junctions, desmosomes are cell junctions that from one side of a sheet of epithelial cells to the other is by
allow cells to adhere to one another. However, unlike adherens moving through the cells by means of one of the cellular transport
junctions that form a belt around the circumference of cells, mechanisms discussed in Chapter 5.
desmosomes are buttonlike points of adhesion (Fig. 10.14). A tight junction is a band of interconnected strands of integral
Cadherins are at work here, too, strengthening the connection membrane proteins, particularly proteins called claudins and
between cells in a manner similar to adherens junctions. occludins. Like adherens junctions, tight junctions encircle the
Cadherins in the desmosome of one cell bind to cadherins in epithelial cell. The proteins forming the tight junction in one cell
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 209
FIG. 10.14 Cell junctions. Cell junctions connect cells to other cells or to the basal lamina and are reinforced by the cytoskeleton.
Tight junction
Cell 1
membrane
Cell 2
membrane
Extracellular
space
Tight
junction
protein
Adherens junction
Cadherin
proteins
Microfilaments
Desmosome
Intermediate
filaments
Cadherin
proteins
Gap junction
Gap junction
channel
Molecule
passing
from one cell
to another
Hemidesmosome
Epithelial
Intermediate
cells
filaments
Cell 1
Integrin
Cell 2 Basal lamina Basal
lamina
Connective
tissue Connective
tissue
210 SECTION 10.4 T H E E X T R AC E L L U L A R M AT R I X
Anchoring
Adherens junction Cadherins Microfilaments Cell–cell adhesion
Desmosome Cadherins Intermediate filaments Cell–cell adhesion
Hemidesmosome Integrins Intermediate filaments Cell–extracellular matrix adhesion
Barrier
Tight junction Claudins, occludins Epithelial boundary
Communicating
Gap junction Connexins Communication between animal cells
Plasmodesma Cell membrane Communication between plant cells
bind to the proteins forming the tight junctions in adjacent cells. Plasmodesmata (the singular form is plasmodesma) are
Also like adherens junctions, tight junctions connect to actin passages through the cell walls of adjacent plant cells. They are
microfilaments. similar to gap junctions in that they allow cells to exchange ions
Cells that have tight junctions have two sides because the tight and small molecules directly, but the similarity ends there. In
junction divides the plasma membrane into two distinct regions plasmodesmata, the plasma membranes of the two connected cells
(Fig. 10.14). The portion of the plasma membrane in contact with are actually continuous. The size of the opening is considerably
the lumen, or the inside of any tubelike structure like the gut, is larger than that of gap junctions, large enough for cells to transfer
called the apical membrane. The apical membrane defines the “top” RNA molecules and proteins, an ability that is especially important
side of the cell. The rest of the plasma membrane is the basolateral during embryonic development. Plasmodesmata allow plant cells
membrane, which defines the bottom (“baso”) and sides (“lateral”) to send signals to one another despite being enclosed within rigid
of the cell. These two regions of the plasma membrane are of cell walls.
different composition because the tight junction prevents lipids and From this discussion, we see that cell junctions interact to
proteins in the membrane on one side of the junction from diffusing create stable communities of cells in the form of tissues and
to the other side. As a result, the apical and basolateral membranes organs. These cell junctions are important for the functions of
of a cell are likely to have different integral membrane proteins, tissues, allowing cells to adhere to each other and the extracellular
which causes them to be functionally different as well. In the small matrix, act as a barrier, and communicate rapidly. The types and
intestine, for example, glucose is transported from the lumen into functions of the cell junctions are summarized in Table 10.2.
intestinal epithelial cells by transport proteins on the apical side of
the cells, and is transported out of the cells into the circulation by j Quick Check 3 Which type(s) of cell junction prevent(s)
facilitated diffusion through a different type of glucose transporter substances from moving through the space between cells? Which
restricted to the basolateral sides of the cells (Chapter 40). type(s) of cell junction attach(es) cells to one another?
are many different forms of extracellular matrix, which differ middle lamella is synthesized first, during the late stages of cell
in the amount, type, and organization of the proteins and division. It is composed of a gluelike complex carbohydrate, and
polysaccharides that make them up. In both plants and animals, it is the main mechanism by which plant cells adhere to one
the extracellular matrix not only contributes structural support another. The primary cell wall is formed next and consists mainly
but also provides informational cues that determine the activity of of cellulose, but it also contains a number of other molecules,
the cells that are in contact with it. including pectin. The primary cell wall is laid down while the cells
are still growing. It is assembled by enzymes on the surface of the
The extracellular matrix of plants is the cell wall. cell and remains thin and flexible. Once cell growth has stopped,
The paper we write on, the cotton fibers in the clothes we wear, the secondary cell wall is constructed in many, but not all, plant
the wood in the chairs we sit on are, in fact, the extracellular cells. It also is made largely of cellulose but in addition contains
matrix of plants. In plants, the extracellular matrix forms the a substance called lignin. Lignin hardens the cell wall and makes
cell wall, and the main component of the plant cell wall is the it water resistant. In woody plants, the cell wall can be up to 25%
polysaccharide cellulose (Chapters 2 and 5). Its presence in the cell lignin. The rigid secondary cell wall permits woody plants to grow
wall of every plant makes cellulose the most widespread organic to tremendous heights. Giant sequoia trees grow to more than
macromolecule on Earth. 300 feet and are supported entirely by the lignin-reinforced
The plant cell wall represents possibly one of the most cellulose fibers of the interconnected cell walls.
complex examples of an extracellular matrix. It is certainly one of As a plant cell grows, additional cell wall components must be
the most diverse in the functions it performs. Cell walls maintain synthesized to expand the area of the wall. Unlike the extracellular
the shape and turgor pressure of plant cells and act as a barrier matrix components that are secreted by animal cells, the cellulose
that prevents foreign materials and pathogens from reaching the polymer is assembled outside the cell, on the extracellular surface
plasma membrane. In many plants, cell walls collectively serve as a of the plasma membrane. Both the glucose monomers that form
skeletal support structure for the entire plant. the polymer and the enzymes that attach them are delivered to
The plant cell wall is composed of as many as three layers: the the cell surface by arrays of microtubules. Here is yet another
outermost middle lamella, the primary cell wall, and the secondary example of how the cytoskeleton plays an indispensable role in
cell wall, located closest to the plasma membrane (Fig. 10.15). The regulating the shape of a cell.
FIG. 10.15 The three layers of the plant cell wall: middle lamella, primary cell wall, and secondary cell wall. The major component of the plant
cell wall is cellulose, a polymer of glucose. Photo source: Biophoto Associates/Science Source.
Primary cell wall
Plasma
Lignin membrane
Middle lamella
Primary cell
wall
Secondary cell
wall
Plasma
membrane
212 SECTION 10.4 T H E E X T R AC E L LU L A R M AT R I X
Fibroblast
cell
FIG. 10.17 Collagen. Type I collagen molecules are organized in a
Fibroblast
nucleus triple helix and grouped into bundles called fibrils, which
in turn are grouped into bundles called fibers. This type
Gel-like
matrix of arrangement, seen in fibers and steel cables, imparts
tremendous strength. Photo sources: (top to bottom) Tom Grundy/
Alamy; Egon Bömsch/imageBROKER/age fotostock; Eye of Science/
The extracellular matrix is abundant in Science Source.
connective tissues of animals.
The extracellular matrix of animals, like
that of plants, is a mixture of proteins and
polysaccharides secreted by cells. The animal
extracellular matrix is composed of large
fibrous proteins, including collagen, elastin, Collagen
and laminin, which impart tremendous tensile molecules
(triple helices)
strength. These fibrous proteins are embedded
in a gel-like polysaccharide matrix. The matrix
is negatively charged, attracting positively
charged ions and water molecules that provide
Collagen
protection against compression and other fibrils
physical stress. Collagen
Collagen molecules are
The extracellular matrix can be found in bundled like steel
fiber
abundance in animal connective tissue (Fig. wires in a cable.
10.16). Connective tissue structurally integrates
and supports various parts of the body and,
in this way, is necessary for multicellularity.
All animals express similar connective tissue
proteins, highlighting their importance and
evolutionarily conserved function. Connective
tissue underlies all epithelial tissues, as we have
seen (section 10.1). For example, the dermis of
the skin is connective tissue. It provides support
and nutrients to the overlying epidermis.
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 213
much stronger than if it were a single fiber of the same diameter. for a cell to metastasize, it must enter and leave the bloodstream
A collagen molecule consists of three polypeptides wound around through capillaries or other vessels. Since all blood vessels,
one another in a triple helix. A bundle of collagen molecules forms including capillaries, have a basal lamina, a metastatic tumor cell
a fibril, and the fibrils are assembled into fibers (Fig. 10.17). Once needs to cross a basal lamina at least twice—once on the way into
multiple collagen fibers are assembled into a ligament or tendon, the bloodstream and again on the way out (Fig. 10.19). Since cells
the final structure is incredibly strong. attach to basal lamina proteins by means of integrins, many studies
The basal lamina is a specialized layer of extracellular have compared the integrins in metastatic and non-metastatic cells
matrix that is present beneath all epithelial tissues, including in the search for potential targets for treatment.
the lining of the digestive tract, epidermis of the skin, and
endothelial cells that line the blood vessels of vertebrates
(Fig. 10.18). The role of the basal lamina is to provide a structural
foundation for these epithelial tissues. The basal lamina is made FIG. 10.19 Metastatic cancer cells. Some cancer cells spread from
of several proteins, including a special type of collagen. The triple- the original site of cancer formation to the bloodstream
helical structure of collagen provides flexible support to and then to distant organs of the body.
the epithelial sheet.
Tumor within normal tissue
FIG. 10.18 The basal lamina. The basal lamina, found beneath
epithelial tissue, is a specialized form of extracellular
matrix. Photo source: ISM/Phototake. Metastatic cancer
cells form new
tumors at distant
sites in the body.
Epithelial
tissue
Extracellular
matrix proteins
in basal lamina
Integrins
Metastatic
cancer cell
Basal
lamina Some metastatic
cancer cells cross
the basal lamina by
means of specific
Connective types of integrins.
tissue
214 SECTION 10.4 T H E E X T R AC E L LU L A R M AT R I X
FIG. 10.22
1.00
expression? 0.40
0.20
BACKGROUND The adhesion of cells to the extracellular
matrix is required for cell division, DNA synthesis, and proper 48 72 96 120 144 166
cell shape. Research by Iranian-American cell biologist Mina Time (h)
Bissell and colleagues indicated that a cell’s interaction with
extracellular matrix proteins influences gene expression. Bissell
100
discovered that mammary cells synthesize and secrete high levels
of the milk protein b-casein when grown in a three-dimensional
(µg/ml medium/24 h)
80
Albumin secretion
collagen matrix but not in a two-dimensional collagen matrix.
American cell biologist Joan Caron followed up these studies 60
using liver cells (hepatocytes).
40
HYPOTHESIS Caron hypothesized that a specific protein in the
extracellular matrix is necessary for the expression of the protein 20
albumin from hepatocytes grown in culture. Albumin is a major
product of hepatocytes. 48 72 96 120 144 166
EXPERIMENT Caron cultured hepatocytes on a thin layer of Time (h)
type I collagen, which does not induce albumin synthesis. Next,
she added a mixture of several different extracellular matrix 1.00 72 h after plating
proteins to the culture and looked for changes in albumin gene 120 h after plating
expression and protein secretion into the media. She then
Relative level of albumin mRNA
0.80
tested individual extracellular matrix proteins from the mixture
to see which one was responsible for the increase in albumin
gene expression. 0.60
215
216 CO R E CO N C E P T S S U M M A RY
A tissue is a collection of cells that work together to perform Adherens junctions form a belt around the circumference
a specific function. page 198 of a cell. They are composed of cell adhesion molecules
called cadherins and connect to microfilaments. page 208
Two or more tissues often work together to form an
organ. page 199 Desmosomes are button-like points of adhesion between
cells. They are composed of cadherins and connect to
Cytoskeletal elements determine the shape of the
intermediate filaments. page 208
cell. page 199
Cell junctions connect cells to one another and to Hemidesmosomes are composed of cell adhesion
the extracellular matrix, a meshwork of proteins and molecules called integrins and connect cells to the
polysaccharides outside the cell. page 199 extracellular matrix and intermediate filaments.
page 208
10.2 The cytoskeleton is composed of microtubules, Tight junctions prevent the passage of substances through
microfilaments, and intermediate filaments that help the space between cells and divide the plasma membrane
maintain cell shape. into apical and basolateral regions. page 208
All eukaryotic cells have microtubules and microfilaments. Gap junctions (in animals) and plasmodesmata (in
Animal cells also have intermediate filaments. page 200 plants) allow cells to communicate rapidly with one
Microtubules are hollow polymers of tubulin dimers, and another. page 210
microfilaments are helical polymers of actin monomers.
Both microtubules and microfilaments provide structural 10.4 The extracellular matrix provides structural
support to the cell. page 200 support and informational cues.
Microtubules and microfilaments are dynamic structures The extracellular matrix is an insoluble meshwork of
and can assemble and disassemble rapidly. page 201 proteins and polysaccharides secreted by the cells it
surrounds. It provides structural support to cells, tissues,
Microtubules go through rounds of assembly and rapid and organs. page 210
disassembly called dynamic instability. page 202
In plants, the extracellular matrix is found in the cell
Microtubules associate with the motor proteins dynein and wall, and the main component of the plant cell wall is the
kinesin to transport substances in the cell. page 202 polysaccharide cellulose. page 211
Microfilaments associate with the motor protein myosin to In animals, the extracellular matrix is found in abundance
transport vesicles in the cell and to cause cell shape changes, in connective tissue. page 212
such as muscle contraction. page 204
Collagen is the primary component of connective tissues
Intermediate filaments are polymers of proteins that differ in animals and is exceptionally strong. page 212
depending on cell type. They provide stable structural
support for many types of cells. page 204 A specialized extracellular matrix called the basal lamina is
present under all epithelial cell layers. page 213
Some prokaryotic cells have protein polymer-like elements
that function similarly to microtubules and microfilaments. In addition to providing structural support for cells, the
page 205 extracellular matrix can influence cell shape and gene
expression. page 214
10.3 Cell junctions connect cells to one another to
form tissues.
Self-Assessment
Cell junctions anchor cells to each other and to the
extracellular matrix, allow sheets of cells to act as a barrier, 1. Name three types of cytoskeletal element, the subunits
and permit communication between cells in tissues. they are composed of, their relative sizes, and the major
page 206 functions of each type.
CHAPTER 10 C E L L A N D T I S S U E A RC H I T E C T U R E : C Y TO S K E L E TO N , C E L L J U N C T I O N S , A N D E X T R AC E L L U L A R M AT R I X 217
2. Explain how the dynamic nature of microtubules and 6. Predict the effects of interfering with the function of
microfilaments is important for their functions. cadherins and integrins.
3. Describe the functions of the three major motor 7. Name two places where the extracellular matrix can
proteins and state which cytoskeletal element each be found in plants and animals.
interacts with.
8. Describe two effects that the extracellular matrix can
4. Describe three major types and functions of cell have on the cells that synthesize it.
junctions.
Log in to to check your answers to the Self-
5. Identify the cytoskeletal element that interacts with Assessment questions, and to access additional learning tools.
adherens junctions, desmosomes, and hemidesmosomes.
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CHAPTER 11
Cell Division
Variations, Regulation,
and Cancer
Core Concepts
11.1 During cell division, a single
parental cell divides into two
daughter cells.
11.2 Mitotic cell division is the basis
of asexual reproduction in
unicellular eukaryotes and the
process by which cells divide in
multicellular eukaryotes.
11.3 Meiotic cell division is essential
for sexual reproduction, the
production of offspring that
combine genetic material from
two parents.
11.4 The cell cycle is regulated so
that cell division occurs only at
appropriate times and places.
11.5 Cancer is uncontrolled cell
division that results from
mutations in genes that control
cell division.
Dr. Torsten Wittmann/Science Source.
219
220 SECTION 11.1 CELL DIVISION
Cells come from preexisting cells. This is one of the fundamental genetic material (DNA) present in the single parent cell. Second,
principles of biology and a key component of the cell theory, which the parent cell must be large enough to divide in two and still
was introduced in Chapter 1. Cell division is the process by which contribute sufficient cytoplasmic components such as proteins,
cells make more cells. Multicellular organisms begin life as a single lipids, and other macromolecules to each daughter cell. Satisfying
cell, and then cell division produces the millions, billions, or in the these requirements means that key cellular components must
case of humans, trillions of cells that make up the fully developed be duplicated before cell division takes place. This duplication of
organism. Even after a multicellular organism has achieved its adult material is achieved in a series of steps that constitutes the life cycle
size, cell division continues. In plants, cell division is essential for of every cell. When you think of a life cycle, you might think of
continued growth. In many animals, cell division replaces worn-out various stages beginning with birth and ending with death. In the
blood cells, skin cells, and cells that line much of the digestive tract. case of a single cell, the life cycle begins and ends with cell division.
If you fall and scrape your knee, the cells at the site of the wound In this section, we explore the different mechanisms by which
begin dividing to replace the damaged cells and heal the scrape. prokaryotic and eukaryotic cells divide. Prokaryotic cells divide
Cell division is also important in reproduction. In bacteria, for by binary fission. When eukaryotic cells divide, they first divide
example, a new generation is produced when the parent cell divides the nucleus by mitosis, and then divide the cytoplasm into two
and forms two daughter cells. The parent cell first makes identical daughter cells by cytokinesis. As we discuss, it is likely that
copies of its genetic material so that each of the two daughter mitosis evolved from binary fission.
cells has the same genetic material as the parent cell. The type of
reproduction that occurs when offspring receive genetic material Prokaryotic cells reproduce by binary fission.
from a single parent is called asexual reproduction. Because DNA The majority of prokaryotic cells, namely bacteria and archaeons,
replication is not completely error free, the daughter cells may carry divide by binary fission. In this form of cell division, a cell
small genetic differences or mutations compared to the parent cell. replicates its DNA, increases in size, and divides into two daughter
By contrast, sexual reproduction results in offspring that cells. Each daughter cell receives one copy of the replicated
receive genetic material from two parents. Half the genetic parental DNA. The molecular mechanisms that drive binary fission
material is supplied by the female parent and is present in the have been studied most extensively in bacteria. The process of
egg and the other half is supplied by the male parent and is binary fission is similar in archaeons, as well as in chloroplasts and
contributed by the male’s sperm. Eggs and sperm are specialized mitochondria, organelles within plant, fungal, and animal cells
cells called gametes. A female gamete and a male gamete merge that evolved from free-living prokaryotic cells (Chapters 5 and 27).
during fertilization to form a new organism (Chapter 42). If the Let’s consider the process of binary fission in the intestinal
egg and the sperm each contain the complete genetic material bacterium Escherichia coli (Fig. 11.1). The circular genome of E. coli
from a parent, what prevents the offspring from having twice as is attached by proteins to the inside of the plasma membrane. DNA
many chromosomes as each parent? A unique feature of gametes replication is initiated at a specific location on the circular DNA
is that they contain half the number of chromosomes as the molecule, called the origin of replication, and proceeds in opposite
other cells in the parent organism. So when fertilization occurs, directions around the circle. The result is two DNA molecules,
the combination of genetic material from the egg and the sperm each of which is attached to the plasma membrane at a different
results in a new organism with the same number of chromosomes site. The two attachment sites are initially close together. The cell
as the parents. The production of gametes comes about by a form then elongates and, as it does so, the two DNA attachment sites
of cell division that results in daughter cells with half the number move apart. When the cell is about twice its original size and the
of chromosomes as the parent cell. As we will see, the products of DNA molecules are well separated, a constriction forms at the
this cell division are not genetically identical to the parent. midpoint of the cell. Eventually, new membrane and cell wall are
What determines when cells divide and, importantly, when synthesized at the site of the constriction, dividing the single cell
they should not? And what determines which cells divide? To into two. The result is two daughter cells, each having the same
answer these questions, we must understand the process of cell genetic material as the parent cell.
division and how it is controlled. This discussion will lay the Like most cellular processes, binary fission requires the
groundwork for exploring how cancer results from a loss of control coordination of many components in both time and space. Recent
of cell division. research has identified several genes whose products play a key
role in bacterial cell division. One of these genes, called FtsZ, has
been especially well studied. Many copies of the protein it encodes
11.1 CELL DIVISION assemble and form a ring at the site of constriction where the new
cell wall forms between the two daughter cells. FtsZ is present in
Cell division is the process by which a single cell becomes two the genomes of diverse bacteria and archaeons, suggesting that it
daughter cells. While this process may seem simple, successful plays a fundamental role in prokaryotic cell division. Interestingly,
cell division must satisfy several important requirements. First, it appears to be evolutionarily related to tubulin, which you will
the two daughter cells must each receive the full complement of recall from Chapter 10 makes up the dynamic microtubules found
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 221
6 Continued synthesis
FIG. 11.2 The cell cycle. The eukaryotic cell cycle consists of
completes the constriction M phase (mitosis and cytokinesis) and interphase.
and separates the daughter
cells. G0 phase
(cells that are
not actively
dividing)
M phase
in eukaryotic cells that are important in intracellular transport, (mitosis and
cell movement, and cell division. cytokinesis)
consists of two different events: (1) mitosis, the separation of the of preparations for DNA synthesis (Fig. 11.2). Liver cells remain in
chromosomes into two nuclei, and (2) cytokinesis, the division of G0 for as much as a year. Other cells such as nerve cells and those
the cell itself into two separate cells. Usually, these two processes that form the lens of the eye enter G0 permanently; these cells
go hand in hand, with cytokinesis typically beginning even before are nondividing. Thus, many brain cells lost to disease or damage
mitosis is complete. In most mammalian cells, M phase lasts about cannot be replaced. Although cells in G0 have exited the cell
an hour. cycle, they are active in other ways—in particular, cells in G0 still
The second stage of the cell cycle, called interphase, is the perform their specialized functions. For example, liver cells in G0
time between two successive M phases (Fig. 11.2). For many still carry out metabolism and detoxification.
years, it was thought that the relatively long period of interphase
is uneventful. Today, we know that during this stage the cell
makes many preparations for division. These preparations include 11.2 MITOTIC CELL DIVISION
replication of the DNA in the nucleus so that each daughter cell
receives a copy of the genome, and an increase in cell size so that Mitotic cell division (mitosis followed by cytokinesis) is the normal
each daughter cell receives sufficient amounts of cytoplasmic and mode of asexual reproduction in unicellular eukaryotes, and it is
membrane components to allow it to survive on its own. the means by which an organism’s cells, tissues, and organs develop
Interphase can be divided into three phases, as shown in and are maintained in multicellular eukaryotes. During mitosis
Fig. 11.2. Among the many preparations that the cell must make and cytokinesis, the parental cell’s DNA is divided and passed on to
during interphase, one particularly important task is the replication two daughter cells. This process is continuous, but is divided into
of the entire DNA content of the nucleus. Since replication discrete steps marked by dramatic changes in the cytoskeleton and
involves the synthesis of DNA, this stage is called S phase (“S” for in the packaging and movement of the chromosomes.
“synthesis”).
In most cells, S phase does not immediately precede or The DNA of eukaryotic cells is organized as
follow mitosis but is separated from it by two gap phases: chromosomes.
G1 phase between the end of M phase and the start of S phase, and One of the key challenges faced by a dividing eukaryotic cell is
G2 phase between the end of S phase and the start of M phase. ensuring that both daughter cells receive an equal and complete
Many essential processes occur during both “gap” phases, despite set of chromosomes. The length of DNA contained in the nucleus
the name. For example, during the G1 phase, specific regulatory of an average eukaryotic cell is on the order of 1 to 2 m, well
proteins are made and activated. Once active, the regulatory beyond the diameter of a cell. The DNA therefore needs to be
proteins, many of which are kinases, then promote the activity condensed to fit into the nucleus, and then further condensed
of enzymes that synthesize DNA. In the G2 phase, both the during cell division so that it does not become tangled as it
size and protein content of the cell increase in preparation for segregates into daughter cells.
division. Thus, G1 is a time of preparation for S-phase DNA synthesis, In eukaryotic cells, DNA is organized with histones and other
and G2 is a time of preparation for M-phase mitosis and cytokinesis. proteins into chromatin, which can be looped and packaged to form
How long does a cell take to pass through the cell cycle? the structures we know as chromosomes (Chapters 3 and 13). One
That depends on the type of cell and the organism’s stage of of the earliest events in mitosis is the condensing of chromosomes
development. Actively dividing cells in some human tissues such from long, thin, threadlike structures typical of interphase to short,
as the intestine and skin require frequent replenishing. It usually dense forms that are identifiable under the microscope during
takes cells in these tissues about 12 hours to complete the cell M phase.
cycle. Most other actively dividing cells in your body take about Every species is characterized by a specific number of
24 hours to complete the cycle. A unicellular eukaryote like yeast chromosomes, and each chromosome contains a single molecule
can complete an entire cell cycle in just 90 minutes. Champions of DNA carrying a specific set of genes. When chromosomes
in the race through the cell cycle are the embryonic cells of some condense and become visible during mitosis, they adopt
frog species. Early cell divisions divide the cytoplasm of the large characteristic shapes and sizes that allow each chromosome to be
frog egg cell into many smaller cells and so no growth period is identified by its appearance in the microscope. The portrait formed
needed between cell divisions. Consequently, there are virtually by the number and shapes of chromosomes representative of a
no G1 and G2 phases, and as little as 30 minutes pass between species is called its karyotype. Most of the cells in the human
cell divisions. body, with the exception of the gametes, contain 46 chromosomes
Not all the cells in your body are actively dividing since not all (Fig. 11.3). In contrast, cells from horses have 64 chromosomes,
tissues require the rapid replenishing of cells. Instead, many cells and cells from corn have 20.
pause in the cell cycle somewhere between M phase and S phase In a normal human karyotype, the 46 chromosomes can be
for periods ranging from days to more than a year. This period is arranged into 23 pairs, 22 pairs of homologous chromosomes
called the G0 phase and is distinguished from G1 by the absence numbered 1 to 22 from the longest to the shortest chromosome
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 223
FIG. 11.3 A human karyotype. This karyotype shows 22 pairs FIG. 11.4 Homologous chromosomes and sister chromatids. Sister
of chromosomes plus 2 sex chromosomes, or chromatids result from the duplication of chromosomes.
46 chromosomes in total. Source: ISM/Phototake. They are held together at the centromere.
Homologous
chromosomes Homologous Homologous
chromosomes chromosomes
1 2 3 4 5 S phase
consists of overlapping microtubules that guide vesicles containing chromosomes by half. During meiosis II, sister chromatids
cell wall components to the middle of the cell. During late separate, as in mitosis.
anaphase and telophase, these vesicles fuse to form a new cell wall, Meiosis I begins with prophase I, illustrated in Fig. 11.8. The
called the cell plate, in the middle of the dividing cell. Once this beginning of prophase I marks the earliest visible manifestation
developing cell wall is large enough, it fuses with the original cell
wall at the perimeter of the cell. Cytokinesis is then complete and
the plant cell has divided into two daughter cells.
FIG. 11.8 Prophase I of meiosis. Chromosomes condense and
j Quick Check 3 What would be the consequence if a cell homologous chromosomes pair.
underwent mitosis but not cytokinesis?
Centrosome
1 Chromosomes Nuclear
first become visible envelope
11.3 MEIOTIC CELL DIVISION as thin threads. DNA
replication is already Chromosomes
complete.
As we discussed, mitotic cell division is important in the
development of a multicellular organism and in the maintenance
and repair of tissues and organs. Mitotic cell division is also the
basis of asexual reproduction in unicellular eukaryotes. We now
turn to the basis of sexual reproduction. In sexual reproduction, Microtubule
gametes fuse during fertilization to form a new organism. A new
organism produced by sexual reproduction has the same number
2 Homologous Pair of
chromosomes continue homologous
of chromosomes as its parents because the egg and sperm each to condense and chromosomes
contain half the number of chromosomes as each diploid parent. undergo synapsis
(gene-for-gene pairing).
Gametes are produced by meiotic cell division, a form of cell
division that includes two rounds of nuclear division. By producing
haploid gametes, meiotic cell division makes sexual reproduction
possible. Bivalent
There are several major differences between meiotic cell
division and mitotic cell division. First, meiotic cell division results 3 When synapsis is Paternal homolog
in four daughter cells instead of two. Second, each of the four complete, each pair of
homologous chromo-
daughter cells contains half the number of chromosomes as the somes forms a bivalent. Maternal homolog
parent cell. (The word “meiosis” is from the Greek for “diminish” Each chromosome
or “lessen.”) Third, the four daughter cells are each genetically consists of two sister
chromatids. Non-sister chromatids
unique. In other words, they are genetically different from each
other and from the parental cell. Sister chromatids
In multicellular animals, the cells produced by meiosis are the
haploid eggs and sperm that fuse in sexual reproduction. In other
organisms, such as fungi, the products are spores, and in some
unicellular eukaryotes, the products are new organisms. In this
4 The chromosomes
continue to shorten
section, we consider the steps by which meiosis occurs, its role in and thicken and the
sexual reproduction, and how it likely evolved. chiasmata between
non-sister chromatids
become apparent.
Pairing of homologous chromosomes is unique
to meiosis.
Like mitotic cell division, meiotic cell division follows one round
of DNA synthesis, but, unlike mitotic cell division, meiotic cell
division consists of two successive cell divisions. The two cell
divisions are called meiosis I and meiosis II, and they occur one
after the other. Each cell division results in two cells, so that by 5 The nuclear envelope
the end of meiotic cell division a single parent cell has produced begins to break down.
four daughter cells. During meiosis I, homologous chromosomes
separate from each other, reducing the total number of
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 227
of chromosome condensation. The chromosomes first appear of a crossover, the physical breakage and reunion between non-
as long, thin threads present throughout the nucleus. By sister chromatids.
this time, DNA replication has already taken place, so each Through the process of crossing over, homologous
chromosome has become two sister chromatids held together at chromosomes of maternal origin and paternal origin exchange DNA
the centromere. segments. The positions of these exchanges along the chromosome
What happens next is an event of enormous importance, and are essentially random, and therefore each chromosome that
it is unique to meiosis. The homologous chromosomes pair with emerges from meiosis is unique, containing some DNA segments
each other, coming together to lie side by side, gene for gene, in from the maternal chromosome and others from the paternal
a process known as synapsis. Even the X and Y chromosomes chromosome. The process is very precise: Usually, no nucleotides
pair, but only at the tip where their DNA sequences are nearly are gained or lost as homologous chromosomes exchange material.
identical. Because one of each pair of homologs is maternal Occasionally, the exchange is imprecise and portions of the
in origin and the other is paternal in origin, chromosome chromatids may be gained or lost, resulting in loss or duplication
pairing provides an opportunity for the maternal and paternal of material. Note the results of crossing over as shown in Fig. 11.9:
chromosomes to exchange genetic information, as described in The recombinant chromatids are those that carry partly paternal
the next section. and partly maternal segments. In this way, crossing over increases
Because each homologous chromosome is a pair of sister genetic diversity.
chromatids attached to a single centromere, a pair of synapsed The number of chiasmata that are formed during meiosis
chromosomes creates a four-stranded structure: two pairs of depends on the species. In humans, the usual range is 50–60
sister chromatids aligned along their length. The whole unit chiasmata per meiosis. Most bivalents have at least one chiasma.
is called a bivalent, and the chromatids attached to different Even the X and Y chromosomes are joined by a chiasma in
centromeres are called non-sister chromatids (Fig. 11.8). the small region where they are paired. In addition to their
Non-sister chromatids result from the replication of homologous role in exchanging genetic material, the chiasmata also play a
chromosomes (one is maternal and the other is paternal in mechanical role in meiosis by holding the bivalents together while
origin), so they have the same set of genes in the same order, they become properly oriented in the center of the cell during
but are not genetically identical. By contrast, sister chromatids metaphase, the stage we turn to next.
result from replication of a single chromosome, so are genetically
identical. The first meiotic division brings about the reduction in
chromosome number.
j Quick Check 4 In a human cell at the end of prophase I, how
At the end of prophase I, the chromosomes are fully condensed
many chromatids, centromeres, and bivalents are present?
and have formed chiasmata, the nuclear envelope has begun to
disappear, and the meiotic spindle is forming. We are now ready
Crossing over between DNA molecules results in
to move through the remaining stages of meiosis I, which are
exchange of genetic material.
illustrated in Fig. 11.10.
Within the bivalents are cross-like structures, each called a
In prometaphase I, the nuclear envelope breaks down and
chiasma (from the Greek meaning a “cross piece”; the plural is
the meiotic spindles attach to kinetochores on chromosomes.
“chiasmata”) (Fig. 11.9). Each chiasma is a visible manifestation
In metaphase I, the bivalents move so that they come to lie on
an imaginary plane cutting transversely across the spindle. Each
bivalent lines up so that its two centromeres lie on opposite
sides of this plane, pointing toward opposite poles of the cell.
FIG. 11.9 Chiasmata. Crossing over at chiasmata between non- Importantly, the orientation of these bivalents is random
sister chromatids results in recombinant chromatids. with respect to each other. For some, the maternal homolog is
Homologous Recombinant attached to the spindle radiating from one pole and the paternal
chromosomes Bivalent chromatids homolog is attached to the spindle originating from the other
pole. For others, the orientation is reversed. As a result, when the
homologous chromosomes separate from each other in the next
Paternal
homolog
step, a complete set of chromosomes moves toward each pole, and
that chromosome set is a random mix of maternal and paternal
Maternal
homolog homologs. The random alignment of chromosomes on the spindle
in metaphase I further increases genetic diversity in the products
of meiosis.
Non-sister Sister Chiasma At the beginning of anaphase I, the two homologous
chromatids chromatids chromosomes of each bivalent separate as they are pulled in
228 SECTION 11.3 M E I OT I C C E L L D I V I S I O N
FIG. 11.11 Meiosis II. Meiosis II is the equational division: The number of chromosomes stays the same.
1 Prophase II:
Cells from meiosis I
The nuclear
envelope breaks
down and the
chromosomes
condense.
2 Prometaphase II:
Spindles attach to
kinetochores on
chromosomes.
3 Metaphase II:
Chromosomes align
in center of cell.
4 Anaphase II:
Sister chromatids
separate.
5 Telophase II
and cytokinesis:
The nuclear
envelope
re-forms and
the cytoplasm
divides.
230 SECTION 11.3 M E I OT I C C E L L D I V I S I O N
MEIOSIS I
Metaphase I
Anaphase I
Telophase I and
Cytokinesis
MITOSIS MEIOSIS II
Prophase Prophase II
(Duplicated
chromosomes)
Metaphase Metaphase II
Anaphase Anaphase II
MITOSIS MEIOSIS
Chromosome complement of
daughter cell compared with parent cell Same Half
A comparison of mitosis and meiosis gives us hints about how the functional egg cell, and the other meiotic products receive only
meiosis might have evolved (Fig. 11.12 and Table 11.1). During small amounts of cytoplasm. These smaller cells are called polar
meiosis I, maternal and paternal homologs separate from each bodies. In male mammals (Fig. 11.13b), the cytoplasm divides
other, whereas during meiosis II, sister chromatids separate from about equally in both meiotic divisions, and each of the resulting
each other, similar to mitosis. The similarity of meiosis II and meiotic products goes on to form a functional sperm. During the
mitosis suggests that meiosis likely evolved from mitosis. Mitosis development of the sperm, most of the cytoplasm is eliminated, and
occurs in all eukaryotes and was certainly present in the common what is left is essentially a nucleus in the sperm head equipped with
ancestor of all living eukaryotes. Meiosis is present in most, but a long whiplike flagellum to help propel it toward the egg.
not all, eukaryotes. Because the steps of meiosis are the same in
all eukaryotes, meiosis is thought to have evolved in the common Meiosis is the basis of sexual reproduction.
ancestor of all eukaryotes and has been subsequently lost in Sexual reproduction involves two processes: meiotic cell division
some groups. and fertilization. Meiotic cell division, as we just saw, produces
cells with half the number of chromosomes present in the
Division of the cytoplasm often differs between parent cell. In multicellular animals, the products of meiotic cell
the sexes. division are gametes: An egg cell is a gamete and a sperm cell
In multicellular organisms, division of the cytoplasm in meiotic cell is a gamete. Each gamete is haploid, containing a single set of
division differs between the sexes. In female mammals chromosomes. In humans, meiosis takes place in the ovaries of
(Fig. 11.13a), the cytoplasm is divided very unequally in both the female and the testes of the male, and each resulting gamete
meiotic divisions. Most of the cytoplasm is retained in one meiotic contains 23 chromosomes, including one each of the 22 numbered
product, a very large cell called the oocyte, which can develop into chromosomes plus either an X or a Y chromosome.
232 SECTION 11.3 M E I OT I C C E L L D I V I S I O N
FIG. 11.13 Cytoplasmic division in females and in males. (a) In females, cytoplasmic division results in one oocyte and three polar bodies;
(b) in males, it results in four sperm cells.
a. Female b. Male
DNA replication
Polar bodies
During fertilization, these gametes fuse to form a single cell chromosomes), and from fertilization (different gametes are
called a zygote. The zygote is diploid, having two complete sets combined to produce a new, unique individual). The increase in
of chromosomes, one from each parent. Therefore, fertilization genetic diversity made possible by sexual reproduction allows
restores the original chromosome number. organisms to evolve and adapt more quickly to their environment
As we discuss further in Chapters 16 and 42, sexual than is possible with asexual reproduction.
reproduction plays a key role in increasing genetic diversity. In the life cycle of multicellular animals like humans, then, the
Genetic diversity results from meiotic cell division (the cells that diploid organism produces single-celled haploid gametes that fuse
are produced are each genetically different from one another as a to make a diploid zygote. In this case, the only haploid cells in the
result of crossing over and the random segregation of homologous life cycle are the gametes, and the products of meiotic cell division
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 233
do not undergo mitotic cell division but instead fuse to become a of animal embryos revealed two interesting patterns. First, as the
diploid zygote. However, there are a number of life cycles in other cells undergo this rapid series of divisions, several proteins appear
organisms that differ in the timing of meiotic cell division and and disappear in a cyclical fashion. Researchers interpreted this
fertilization, discussed more fully in Chapter 27. Some organisms, observation to mean that these proteins might play a role in
like most fungi, are haploid. These haploid cells can fuse to the control of the progression through the cell cycle. Second,
produce a diploid zygote, but this cell immediately undergoes several enzymes become active and inactive in cycles. These
meiotic cell division to produce haploid cells, so that the only enzymes are kinases, proteins that phosphorylate other proteins
diploid cell in the life cycle is the zygote (Chapter 34). Other (Chapter 9). The timing of kinase activity is delayed slightly
organisms, like plants, have both multicellular haploid and diploid relative to the appearance of the cyclical proteins.
phases (Chapter 30). In this case, meiotic cell division produces These and many other observations led to the following view
haploid spores that divide by mitotic cell division to produce a of cell cycle control: Proteins are synthesized that activate the
multicellular haploid phase; subsequently, haploid cells fuse to kinases. These regulatory proteins are called cyclins because their
form a diploid zygote that also divides by mitotic cell division to levels rise and fall with each turn of the cell cycle. Once activated
produce a multicellular diploid phase. by cyclins, the kinases phosphorylate target proteins involved
in promoting cell division (Fig. 11.14). These kinases, cyclin-
dependent kinases, or CDKs, are always present within the cell
11.4 REGULATION OF THE CELL CYCLE but are active only when bound to the appropriate cyclin. It is the
kinase activity of the cyclin–CDK complexes that triggers the
Both mitotic and meiotic cell division must occur only at certain
times and places. Mitotic cell division, for example, occurs during
growth of a multicellular organism, wound healing, or in the
maintenance of actively dividing tissues such as the skin or lining FIG. 11.14 Cyclins and cyclin-dependent kinases (CDKs). Cyclins
of the intestine. Similarly, meiotic cell division occurs only at and CDKs control progression through the cell cycle.
certain times during development. Even for unicellular organisms,
cell division must be regulated so that it takes place only when
Cyclin 1 Cyclins bind to and
conditions are favorable—for example, when enough nutrients activate cyclin-
are present in the environment. Thus, a cell may have to receive a dependent kinases to
control progression
signal before it will divide. In Chapter 9, we saw how cells respond through the cell cycle.
to signals. Growth factors, for example, bind to cell-surface receptors
and activate intracellular signaling pathways that lead to cell division.
Even when a cell receives a signal to divide, it does not divide
until it is ready. Has all of the DNA been replicated during S phase?
Has the cell grown to a size sufficient to support division into Cyclin-dependent Cyclin-CDK
kinase (CDK)
viable daughter cells? If these and other preparations have not been complex
accomplished, the cell halts its progression through the cell cycle.
So, cells have regulatory mechanisms that initiate cell
division, as well as mechanisms for spotting faulty or incomplete
preparations and arresting cell division. When these mechanisms
fail—for example, dividing in the absence of a signal or when
the cell is not ready—the result is uncontrolled cell division, a
hallmark of cancer. In this section, we consider how cells control
their passage through the cell cycle. Our focus is on control of
mitotic cell division. However, many of the same factors also Target
regulate meiotic cell division, a reminder of the close evolutionary protein
connection between these two forms of cell division. Cyclin
degrades 2 Cyclin-CDK
complexes
Protein phosphorylation controls passage through phosphorylate
the cell cycle. target proteins
P that promote
Early animal embryos, such as those of frogs and sea urchins, are cell division.
useful models for studying cell cycle control because they are
large and undergo many rapid mitotic cell divisions following
fertilization. During these rapid cell divisions, mitosis and S phase Phosphorylated
alternate with virtually no G1 and G2 phases in between. Studies target protein
234 SECTION 11.4 R E G U L AT I O N O F T H E C E L L C YC L E
required cell cycle events. Therefore, the cyclical change in cyclin– These cell cycle proteins, including cyclins and CDKs, are widely
CDK activity depends on the cyclical levels of the cyclins. Cyclins conserved across eukaryotes, reflecting their fundamental role in
in turn may be synthesized in response to signaling pathways that controlling cell cycle progression, and have been extensively studied
promote cell division. in yeast, sea urchins, mice, and humans (Fig. 11.15).
HOW DO WE KNOW?
FIG. 11.15
Level of protein increases
50
Cyclin level
BACKGROUND The cell
cycle is characterized by
cyclical changes in many 25
components of the cell:
Chromosomes condense
and decondense, the
mitotic spindle forms and 0 1 2
breaks down, the nuclear Source: SeaPics.com. Time (hours)
envelope breaks down and Interphase – Mitosis – Interphase – Mitosis – Interphase
re-forms. How these regular and cyclical changes are controlled
is the subject of active research. First, clues came from studies in
yeast in which mutations in certain genes blocked progression
through the cell cycle, suggesting that these genes encode proteins
that play a role in cell cycle progression. Additional clues came Source: Biology Pics/Science Source.
from studies in embryos of the sea urchin Arbacia punctulata.
These embryos are large and divide rapidly by mitosis, making
CONCLUSION Hunt and colleagues called this new protein
them a good model system for the study of the control of cell
“cyclin.” Although they did not know its function, its fluctuating
division. In the early 1980s, it was known that inhibition of protein
level suggested it might play a role in the control of the cell cycle.
synthesis blocks key steps of cell division in sea urchins. It was also
However, more work was needed to figure out if cyclins actually
known that an enzyme called MPF, or M-phase promotion factor,
cause progression through the cell cycle or whether their levels
is important for the transition from G2 to M phase.
oscillate in response to progression through the cell cycle.
EXPERIMENT To better understand events in the cell cycle,
FOLLOW-UP WORK Hunt and colleagues found a similar
English biochemist Tim Hunt and colleagues measured protein
rise and fall in the levels of certain proteins in the sea urchin
levels in sea urchin embryos as they divide rapidly by mitosis. He
Lytechinus pictus and surf clam Spisula solidissima. MPF was
added radioactive methionine (an amino acid) to eggs, which
found to consist of a cyclin protein and a cyclin-dependent
became incorporated into any newly synthesized proteins. The
kinase that play a key role in the G2–M transition. In other
eggs were then fertilized and allowed to develop. Samples of the
words, cyclins do in fact control progression through the cell
rapidly dividing embryos were taken every 10 minutes and run on
cycle by their interactions with cyclin-dependent kinases. Hunt
a gel to visualize the levels of different proteins.
shared the Nobel Prize in Physiology or Medicine in 2001 for
RESULTS Most protein bands became darker as cell division his work on cyclins.
proceeded, indicating more and more protein synthesis. However,
SOURCE T. Evans et al. 1983. “Cyclin: A Protein Specified by Maternal
the level of one protein band oscillated, increasing in intensity and mRNA in Sea Urchin Eggs That Is Destroyed at Each Cleavage Division.”
then decreasing with each cell cycle, as shown in the graph. Cell 33:389–396.
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 235
Gene G2
turned
Nucleus DNA ON G1
damage
P
P
S
p53 P
P
P
–
p53
Inhibiting the cell
Cytoplasm cycle gives the cell
time to repair the
p53 is a protein DNA damage activates protein Phosphorylated p53 acts as a damaged DNA.
found in the nucleus. kinases that phosphorylate p53. transcription factor that turns on
genes that inhibit the cell cycle.
HOW DO WE KNOW?
chickens. He made an extract of the tumor, filtered it to remove all contrary to his hypothesis, that a small agent—a virus or
the cells, and injected the extract into a healthy chicken to see if it chemical—is capable of causing cancer. Later experiments
could induce cancer. confirmed that the cause of the cancer is a virus. This result was
surprising, controversial, and dismissed at the time. A second
HYPOTHESIS Experiments in other organisms, such as mice, rats, cancer-causing virus was not found until the 1930s. Although
and dogs, showed that an extract free of cells from a tumor does most cancers are not caused by viruses, work with cancer-
not cause cancer. Therefore, Rous hypothesized that a cell-free causing viruses helped to identify cellular genes that, when
extract of the chicken sarcoma would not induce cancer in healthy mutant, can lead to cancer. In 1966, Rous shared the Nobel Prize
chickens. in Physiology or Medicine for his discovery.
EXPERIMENT Rous took a sample of the sarcoma from a chicken,
SOURCES Rous, P. 1910. “A Transmissable Avian Neoplasm (Sarcoma of the
ground it up, suspended it in solution, and centrifuged it to Common Fowl).” J. Exp. Med. 12:696–705; Rous, P. 1911. “Transmission of a
remove the debris. In one experiment, he injected this extract malignant new growth by means of a cell-free filtrate.” JAMA 56:198.
The chicken
A sample of sarcoma is The tumor is ground The extract is injected develops a tumor at
obtained from a chicken. up, suspended, and into a healthy chicken. the site of injection.
centrifuged to create
an extract.
237
238 SECTION 11.5 W H AT G E N E S A R E I N VO LV E D I N C A N C E R ?
others led to the discovery of the first virus known to cause cancer promotes cell division by binding to and dimerizing a receptor
in animals, named the Rous sarcoma virus. kinase in the membrane of the target cell. Dimerization of the
Viruses are assemblages of protein surrounding a core of receptor leads to the activation of several signaling pathways
either RNA or DNA. They multiply by infecting cells and using and the promotion of cell division. In one type of leukemia (a
the biochemical machinery of their host to synthesize proteins cancer of blood cells), a mutation in the gene that encodes the
encoded in their genome and to make more copies of themselves. PDGF receptor results in an altered receptor that is missing
Viruses typically carry only a handful of genes, making it relatively the extracellular portion needed to bind the growth factor. The
easy to identify which of those genes is involved in cancer. The mutant receptor dimerizes on its own, independent of PDGF
investigation of cancer-causing viruses therefore provided major binding, and is therefore always turned on. The overactive PDGF
insights into our understanding of cancer. receptor activates too many target proteins over too long a time
As discussed in Chapter 9, growth factors activate several period, leading to uncontrolled proliferation of blood cells.
types of proteins inside the cell that promote cell division. The
gene from the Rous sarcoma virus that promotes uncontrolled Tumor suppressors block specific steps in the
cell division encodes an overactive protein kinase similar to the development of cancer.
kinases in the cell that function as signaling proteins. This viral Up to this point, we have considered what happens when
gene is named v-src, for viral-src (pronounced “sarc” and short for mechanisms that promote cell division are inappropriately
“sarcoma,” the type of cancer it causes). activated. Now let’s consider what happens when mechanisms
The v-src gene is one of several examples of an oncogene, that usually prevent cell cycle progression are removed.
or cancer-causing gene, found in viruses. A real surprise was the Earlier, we discussed cell cycle checkpoints that halt the cell
discovery that the v-src oncogene is found not just in the Rous cycle until the cell is ready to divide. One of these checkpoints
sarcoma virus. It is an altered version of a gene normally found depends on the p53 protein, which normally arrests cell division in
in the host animal cell, known as c-src (cellular-src). The c-src gene response to DNA damage. When the p53 protein is mutated or its
plays a role in the normal control of cell division during embryonic function is inhibited, the cell can divide before the DNA damage is
development. repaired. The result is that cells continue to divide in the presence
of damaged DNA, leading to the accumulation of mutations that
Proto-oncogenes are genes that when mutated may promote cell division. The p53 protein is mutated in many types
cause cancer. of human cancer, highlighting its critical role in regulating the
The discovery that the v-src oncogene has a normal counterpart cell cycle.
in the host cell was an important step toward determining the The p53 protein is one example of a tumor suppressor.
cellular genes that participate in cell growth and division. These Tumor suppressors are proteins whose normal activities inhibit
normal cellular genes are called proto-oncogenes. They are cell division. Some tumor suppressors participate in cell cycle
involved in cell division, but do not themselves cause cancer. Only checkpoints, as is the case for p53. Other tumor suppressors
when they are mutated do they have the potential to cause cancer. repress the expression of genes that promote cell division, while
Today, we know of scores of proto-oncogenes, most of which were still others trigger cell death.
identified through the study of cancer-causing viruses in chickens, Tumor suppressors act in opposition to proto-oncogenes.
mice, and cats. Therefore, whether a cell divides or not depends on the activities
Oncogenes also play a major role in human cancers. Most of both proto-oncogenes and tumor suppressors: Proto-oncogenes
human cancers are not caused by viruses. Instead, human proto- must be turned on and tumor suppressors must be turned
oncogenes can be mutated into cancer-causing oncogenes by off. Given the importance of controlling cell division, it is not
environmental agents such as chemical pollutants. For example, surprising that cells have two counterbalancing systems that must
organic chemicals called aromatic amines present in cigarette be in agreement before cell division takes place.
smoke can enter cells and damage DNA, resulting in mutations
j Quick Check 8 How do oncogenes differ from tumor suppressor
that can convert a proto-oncogene into an oncogene.
genes?
What types of functions are performed by the products of
proto-oncogenes? Nearly every protein that performs a key step in
a signaling cascade that promotes cell division can be the product Most cancers require the accumulation of multiple
of a proto-oncogene. These include growth factors, cell-surface mutations.
receptors, G proteins, and protein kinases. Each of these can be Most human cancers require more than the overactivation of
mutated to become oncogenes. one oncogene or the inactivation of a single tumor suppressor.
Let’s consider an example of a proto-oncogene. In Chapter 9, Given the multitude of different tumor suppressor proteins that
we discussed platelet-derived growth factor, or PDGF. This protein are produced in the cell, it is likely that one will compensate for
CHAPTER 11 C E L L D I V I S I O N : VA R I AT I O N S , R E G U L AT I O N , A N D C A N C E R 239
Metastatic
cancer
Metastasis
at a new site
V I S UA L S Y N T H E S I S Cellular Communities
FIG. 11.21 Integrating concepts from Chapters 9–11
4 Anaphase: Sister
chromatids (individual
1 Prophase: Chromosomes
chromosomes when the
centromere splits)
condense. Centrosomes
separate and travel to
radiate microtubules and
opposite poles.
migrate to opposite poles.
5 Telophase and
cytokinesis: Nuclear
envelope re-forms,
chromosomes
M phase condense, and the
G0 phase cytoplasm divides.
(mitosis and (cells that are
cytokinesis) not actively
dividing)
G2 phase
(Gap 2)
G1 phase
(Gap 1)
Interphase
S phase
(DNA synthesis)
Epidermis
Dermis
240
Cell signaling
Cells communicate with each other and respond to
their environment using signaling molecules that
bind to receptors, leading to responses inside the cell.
Termination
Cell adhesion
Tissues are communities of cells that are held together
and communicate by various types of cellular junctions.
Other junctions connect cells with protein networks
in the extracellular environment.
Response
Signal
transduction
and
amplification
Receptor
Tight junction activation
Adherens
junction
Hemidesmosome
Desmosome Signaling
molecules
Gap junction
Basal lamina
11.2 Mitotic cell division is the basis of asexual Genetic diversity is generated by crossing over and random
reproduction in unicellular eukaryotes and the process alignment and subsequent segregation of maternal and
by which cells divide in multicellular eukaryotes. paternal homologs on the metaphase plate in meiosis I.
page 227
DNA in a eukaryotic cell is packaged as linear chromosomes.
page 222 Meiosis II is similar to mitosis, in which chromosomes
align on the metaphase plate, centromeres split, and sister
Humans have 46 chromosomes: 22 pairs of homologous chromatids separate from each other. page 228
chromosomes and 1 pair of sex chromosomes. Each parent
contributes one complete set of 23 chromosomes at The similarity of meiosis II and mitosis suggests that
fertilization. page 222 meiosis evolved from mitosis. page 231
During S phase, chromosomes replicate, resulting in The division of the cytoplasm differs between the
the formation of sister chromatids held together at the sexes: Male meiotic cell division produces four functional
centromere. page 223 sperm cells, whereas female meiotic cell division produces
a single functional egg cell and three polar bodies.
Mitosis involves five steps following DNA replication: page 231
(1) prophase—the chromosomes condense and become
visible under the light microscope; (2) prometaphase—
11.4 The cell cycle is regulated so that cell division
the spindles attach to the centromeres; (3) metaphase—
occurs only at appropriate times and places.
the chromosomes line up in the middle of the cell;
(4) anaphase—the centromeres split and the chromosomes Cells have regulatory mechanisms for promoting and
move to opposite poles; and (5) telophase—the nuclear preventing cell division. page 233
envelope re-forms and chromosomes decondense. page 223
Levels of proteins called cyclins increase and decrease
Mitosis is followed by cytokinesis, in which one cell divides during the cell cycle. page 233
into two. In animals, a contractile ring of actin pinches the
cell in two. In plants, a new cell wall, called the cell plate, is Cyclins form complexes with cyclin-dependent kinases
synthesized between the daughter cells. page 225 (CDKs), activating the CDKs to phosphorylate target
proteins involved in cell division. page 233
11.3 Meiotic cell division is essential for sexual These complexes are activated by signals that promote cell
reproduction, the production of offspring that combine division. page 234
genetic material from two parents.
Different cyclin–CDK complexes control progression
Sexual reproduction involves meiosis and fertilization, both of through the cell cycle at key steps, including G1 /S phase,
which are important in increasing genetic diversity. page 226 S phase, and M phase. page 235
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The cell also has checkpoints that halt progression through Self-Assessment
the cell cycle if something is not right. page 235
1. Compare and contrast the ways in which prokaryotic cells
The p53 protein is an example of a checkpoint protein; it and eukaryotic cells divide.
prevents cell division in the presence of DNA damage.
page 235 2. Describe three situations in which mitotic cell
division occurs.
11.5 Cancer is uncontrolled cell division that results 3. Name the five steps of mitosis, and draw the
from mutations in genes that control cell division. structure and position of the chromosomes at each step.
Cancer results when mechanisms that promote cell division 4. Describe how chromosomes behave in meiosis. State when
are inappropriately activated or the normal checks on cell chromosomes are duplicated (forming sister chromatids)
division are lost. page 236 and when they are not duplicated.
Cancers can be caused by certain viruses carrying oncogenes 5. Compare and contrast mitotic cell division and
that promote uncontrolled cell division. page 238 meiotic cell division in terms of number of products,
number of cell divisions, and the processes unique to each.
Viral oncogenes have cellular counterparts called proto-
oncogenes that play normal roles in cell growth and division 6. Name two ways in which meiotic cell division creates
and that, when mutated, can cause cancer. page 238 genetic diversity, and explain how each occurs.
Oncogenes and proto-oncogenes often encode proteins 7. Explain how cytokinesis differs between animal and
involved in signaling pathways that promote cell division. plant cells.
page 238 8. Describe the roles of cyclins and cyclin-dependent
Tumor suppressors encode proteins, such as p53, that block kinases in the cell cycle.
cell division and inhibit cancers. page 238 9. Give three examples of checkpoints that the cell
monitors before proceeding through the cell cycle.
Cancers usually result from several mutations in proto-
oncogenes and tumor suppressor genes that have 10. Describe what an oncogene, a proto-oncogene, and a
accumulated over time within the same cell. page 238 tumor suppressor gene do.
CASE 3
You, from A to T
Your Personal Genome
As an American Studies painstaking work, scientists published the first draft of the
major at Georgetown complete human genome. The human genome consists of
University, Claudia the DNA in one complete set of 23 chromosomes. It contains
Gilmore had plenty about 3 billion base pairs, the structural units of DNA. In
of experience taking the years that followed, much attention has been placed on
exams. But at the age understanding the genetic differences between individuals.
of 21, she faced an In reality, there isn’t one single human genome.
altogether different Everyone on Earth (with the exception of identical twins)
kind of test—and no has his or her own unique genetic sequence. Your personal
amount of studying genome, consisting of two sets of chromosomes, is the
could have prepared blueprint that codes for your hair color, the length of
Answers in the genetic her for the result. your nose, and your susceptibility to certain diseases. On
sequence. Claudia Gilmore Gilmore had average, any two human genomes are 99.9% identical,
found that her genome contains decided to be tested meaning that they differ at about 3 million base pairs.
a mutation that can lead to breast for a mutation in a Oftentimes, those differences have no impact on
cancer. Source: Photo by Dominic gene known as BRCA1. health. In some cases, however, a particular genetic
Gutierrez, courtesy Claudia Gilmore. Specific mutations in signature is associated with disease. Sometimes a gene
the BRCA1 and BRCA2 mutation makes a given illness inevitable. Certain
genes are associated with an increased risk of breast and mutations in a gene called HTT, for instance, always result
ovarian cancers. in Huntington’s disease, a degenerative brain condition that
Gilmore’s grandmother had battled breast cancer and usually appears in middle age.
later died from ovarian cancer. Before her death, she had The link between mutations and disease isn’t always so
tested positive for the BRCA1 mutation. Her son, Gilmore’s clear-cut, however. Most genetic diseases are complex in
father, was tested origin, and it may take multiple genetic mutations, as well
Mutations that increase and discovered he as other non-genetic factors, for the disease to develop.
the risk of developing a had inherited the Mutations that increase the risk of developing a particular
mutation. After disease are called genetic risk factors.
particular disease are talking with a Certain mutations in the BRCA1 and BRCA2 genes are
called genetic risk factors. genetic counselor to known genetic risk factors for breast and ovarian cancers,
help her understand for instance. But not everyone with these mutations devel-
the implications of the test, Gilmore gave a sample of her ops cancer. According to the National Cancer Institute,
own blood and crossed her fingers. about 60% of women with a harmful BRCA1 mutation will
“I had a fifty-fifty chance of inheriting the mutation. I develop breast cancer in her lifetime, compared with about
knew there was a great possibility it would be a part of my 12% of women in the general population. And 15% to 40%
future,” she says. “But I was 21, I was healthy. A part of me of women with a BRCA1 mutation will be diagnosed with
also thought this could never really happen to me.” ovarian cancer, compared with just 1.4% of women without
Unfortunately, it could. Two weeks after her blood was that genetic change.
drawn, she learned that she, too, carried the mutated gene. The BRCA1 mutations are just some of the thousands of
Genetic testing is becoming increasingly common— harmful genetic changes that geneticists have identified so
in some cases, even routine. In 2003, after 13 years of far. Other common mutations have been shown to elevate
244
The BRCA1 and BRCA2 What does your genome say about you? Researchers have identified genes that, when
genes are associated mutated, contribute to disease, as well as differences that help reveal who you are and
BRCA2 with an increased risk
of breast and ovarian where you come from. Sources: (left to right) Willatt/Science Source; ISM/Phototake; ISM/Phototake.
gene
cancer.
Chromosome 13
A mutation in the HTT
gene on chromosome
BRCA1 3 causes Huntington’s
gene HTT disease.
gene The particular pattern
Chromosome 17 of mutations inherited
on the Y chromosome
can reveal a person’s
ancestry.
Chromosome 3
Distinct
pattern
of SNPs
Y chromosome
one’s risk of developing heart disease, diabetes, various the shape of your fingernails to the shade of your skin—
cancers, and numerous other common illnesses. Often, that don’t affect your health but make you the person you
these mutations involve changes to just a single base are. Some DTC testing services aim to tell customers about
pair of DNA. These common single-letter mutations are their history by screening genes to identify variations that
known as single nucleotide polymorphisms, or SNPs. are more common in certain geographical regions or among
Genome sequencing technology has improved members of certain ethnic groups. One such company offers
significantly over the last decade, making it easier and genetic tests to African-Americans to determine in what part
less expensive to scan an individual’s DNA for potentially of the African continent their ancestors originated.
harmful SNPs. A number of companies now offer genetic Other popular DTC tests inspect DNA samples for
tests directly to the public. Unlike tests such as the SNPs associated with certain diseases and physical traits—
BRCA1 blood test that Gilmore was given, these direct-to- everything from Parkinson’s disease and age-related macular
consumer (DTC) tests are offered to customers without degeneration to earwax type and propensity for baldness.
any involvement of a medical professional, at a cost of a Advocates of the tests say the technology puts the power
few hundred dollars. of genetic information in the hands of consumers. Critics, on
Some of these tests aren’t related to health at all. Your the other hand, argue that the information provided by DTC
personal genome contains many unique features—from tests isn’t always very meaningful. The presence of some SNPs
245
246 SECTION 11.1 P
might raise the risk of a rare disease by just 2% or 3%, for author Angelina Jolie, who recounted her experience
example. In many cases, the precise link between mutation in the New York Times, writing, “Once I knew that
and disease is still being sorted out. Also, without input from this [BRCA1 mutation] was my reality, I decided to be
a genetic counselor or medical professional, consumers may proactive and to minimize the risk as much I could. I
not know how to interpret the information revealed by the made a decision to have a preventive double mastectomy.
tests. The American Medical Association has recommended I started with the breasts, as my risk of breast cancer
that a doctor always be involved when any genetic testing is is higher than my risk of ovarian cancer, and the
performed. surgery is more complex. . . . I am writing about it now
Moreover, knowing your genetic risk factors isn’t the because I hope that other women can benefit from my
whole story. When it comes to your health and well-being, experience.” 1
the environment also plays a significant role. Someone For now, it’s still too costly to sequence every
might override a genetic predisposition for skin cancer by individual’s entire genome. But each year, many more
using sunscreen faithfully every day. On the other hand, a genetic tests hit the market. Already, doctors are
person might have a relatively low genetic risk for type 2 beginning to design medical treatments based on a
diabetes, but still boost the odds of developing the disease patient’s personal genome. People with a certain genetic
by eating a poor diet and getting little physical exercise. profile, for example, are less likely than others to benefit
Claudia Gilmore is especially careful to exercise from statins, medications prescribed to lower cholesterol.
regularly and eat a healthy diet. Still, she can only control Doctors are also choosing which cancer drugs to prescribe
her environment to a degree. She knew that, given her based on the unique genetic signatures of patients and
genetic status, her risk of breast cancer remained high. their tumors.
She made the extraordinary decision to eliminate that risk We’ve only just entered the era of personal genomics.
by undergoing a mastectomy at the age of 23. It wasn’t While there’s much left to decipher, it’s clear that each
an easy decision, she says, but she feels privileged to have of our individual genomes contains a wealth of biological
been able to take proactive steps to protect her health. “I’ll information. And, as Gilmore says, “I’ve always been
be a ‘previvor’ instead of a survivor,” she says. taught that knowledge is power.”
Two years later the same medical choice was made 1
Angelina Jolie, “My Medical Choice,” New York Times, A25, May 14,
by the American actress, film director, screenwriter, and 2013.
?C A S E 3 Q U E S T I O N S
Special sections in Chapters 12–20 discuss the following questions related to Case 3.
1. What new technologies are being developed to sequence your personal genome? See page 264.
2. Why sequence your personal genome? See page 274.
3. What can your personal genome tell you about your genetic risk factors? See page 294.
4. How can genetic risk factors be detected? See page 317.
5. How do genetic tests identify disease risk factors? See page 342.
6. How can the Y chromosome be used to trace ancestry? See page 358.
7. How can mitochondrial DNA be used to trace ancestry? See page 360.
8. Can personalized medicine lead to effective treatments of common diseases? See page 375.
9. How do lifestyle choices affect expression of your personal genome? See page 386.
10. Can cells with your personal genome be reprogrammed for new therapies? See page 403.
246
CHAPTER 12
DNA Replication
and Manipulation
Core Concepts
12.1 In DNA replication, a single
parental molecule of DNA
produces two daughter
molecules.
12.2 The replication of linear
chromosomal DNA requires
mechanisms that ensure
efficient and complete
replication.
12.3 Techniques for manipulating
DNA follow from the basics
of DNA structure and
replication.
12.4 Genetic engineering allows
researchers to alter DNA
sequences.
Dr. Gopal Murti/Science Source.
247
248 SECTION 12.1 D N A R E P L I C AT I O N
One of the overarching themes of biology discussed in Chapter 1 is the template strand determines the order of the complementary
that the functional unit of life is the cell, a theme that rests in turn bases added to the daughter strand. For example, the sequence
on the fundamental concept that all cells come from preexisting 5�-ATGC-3� in the template strand specifies the sequence 3�-TACG-5�
cells. In Chapter 11, we considered the mechanics of cell division in the daughter strand because A pairs with T and G pairs with C.
and how it is regulated. Prokaryotic cells multiply by binary fission, (The designations 3� and 5� convey the antiparallel orientation of
whereas eukaryotic cells multiply by mitosis and cytokinesis. These the strands.)
processes ensure that cellular reproduction results in daughter A key prediction of the model shown in Fig. 12.1 is
cells that are like the parental cell. In other words, in cell division, semiconservative replication. That is, after replication, each
like begets like. The molecular basis for the resemblance between new DNA duplex consists of one strand that was originally part
parental cells and daughter cells is that a double-stranded DNA of the parental duplex and one newly synthesized strand. An
molecule in the parental cell duplicates and gives rise to two alternative model is conservative replication, which proposes that
double-stranded daughter DNA molecules that are identical to each the original DNA duplex remains intact and the daughter DNA
other except for rare mutations that may have taken place. duplex is completely new. Which model is correct? If there were
The process of duplicating a DNA molecule is called DNA a way to distinguish newly synthesized daughter DNA strands
replication, and it occurs in virtually the same way in all (“new strands”) from previously synthesized parental strands
organisms, reflecting its evolution very early in life’s history. The (“old strands”), the products of replication could be observed and
process is conceptually simple—the parental strands separate and the mode of replication determined.
new complementary partner strands are made—but the molecular American molecular biologists Matthew S. Meselson and
details are more complicated. Once scientists understood the Franklin W. Stahl carried out an experiment to determine how
molecular mechanisms of DNA replication, they could devise DNA replicates. This experiment, described in Fig. 12.2, has been
improved methods for manipulating and studying DNA. An called “the most beautiful experiment in biology” because it so
understanding of DNA replication is therefore fundamental not elegantly demonstrated the scientific method (Chapter 1) of
only to understanding how cells and organisms produce offspring hypothesis, prediction, and experimental test. They distinguished
like themselves, but also to understanding some of the key “old” from “new” DNA strands by labeling them with
experimental techniques in modern biology. nonradioactive isotopes of nitrogen that have different densities:
the normal form of nitrogen, 14N, and a heavier form with an extra
neutron, denoted 15N.
12.1 DNA REPLICATION Meselson and Stahl found that DNA in fact replicates
semiconservatively (Fig. 12.2). This finding also predicted the
You may recall from Chapter 3 that double-stranded DNA consists results when cells are allowed to undergo two rounds of replication
of a pair of deoxyribonucleotide polymers wound around each in a medium containing only light 14N nitrogen. The heavy strand
other in antiparallel helical coils in such a way that a purine and light strand each serve as templates for a new light daughter
base (A or G) in one strand is paired with a pyrimidine base (T strand. The result is that half of the DNA molecules will have one
or C, respectively) in the other strand. To say that the strands
are antiparallel means that they run in opposite directions: One
strand runs in the 5�-to-3� direction and the other runs in the
3�-to-5� direction. These key elements of DNA structure are the FIG. 12.1 DNA replication. During DNA replication, each
only essential pieces of information needed to understand the parental strand serves as a template for the synthesis of a
mechanism of DNA replication. complementary daughter strand.
5’
FIG.12.2
249
250 SECTION 12.1 D N A R E P L I C AT I O N
heavy old strand and one light new strand and an intermediate
density, and half of the DNA molecules will have one light old FIG. 12.4 DNA synthesis by nucleotide addition to the 3� end of a
strand and one light new strand and a low density. This is precisely growing DNA strand.
what they observed (Fig. 12.2). Template Daughter
3’
j Quick Check 1 Suppose Meselson and Stahl had done their
OH
experiment the other way around, starting with cells fully labeled 5’
with 14N light DNA and then transferring them to medium Direction of
T A P
containing only 15N heavy DNA. What density of DNA molecule P chain growth
would you predict after one and two rounds of replication?
G C P
P
Important as it was in demonstrating semiconservative 1 Incoming
replication in bacteria, the Meselson–Stahl experiment left A T P nucleotides are
P accepted if they
open the possibility that DNA replication in eukaryotes might correctly base pair
be different. It was only some years after the Meselson–Stahl C
OH with the template.
P
experiment that methods for labeling DNA with fluorescent 3’
nucleotides were developed. These methods allowed researchers
T G
to visualize entire strands of eukaryotic DNA and follow each P 2 The 3’ OH of the
strand through replication. Fig. 12.3 shows a human chromosome P P P growing strand
with unlabeled DNA that subsequently underwent two rounds of P G attacks the high-
energy phosphate
replication in medium containing a fluorescent nucleotide. The 5’ OH bond of the
chromosome was photographed at metaphase of the second round incoming nucleotide
P P to initiate the
of mitosis, after chromosome duplication but before the separation
synthesis reaction.
of the chromatids into the daughter cells. Notice that one chromatid Pyrophosphate
contains hybrid DNA with one labeled strand and one unlabeled
strand, which fluoresces faintly (light); the other chromatid
contains two strands of labeled DNA, which fluoresces strongly implies that both daughter strands should grow in length by the
(dark). This result is conceptually the same as what was seen by addition of nucleotides near the site where the parental strands
Meselson and Stahl after two rounds of replication and exactly as separate, a site called the replication fork. As more and more
predicted by the semiconservative replication model. The result also parental DNA is unwound and the replication fork moves forward
demonstrates that each eukaryotic chromosome contains a single (to the left in Fig. 12.1), both new strands would also grow in the
DNA molecule that runs continuously all along its length. direction of replication fork movement. But it turns out that this
scenario is impossible.
New DNA strands grow by the addition of nucleotides We have seen that the two DNA strands in a double helix run in
to the 3’ end. an antiparallel fashion: One of the template strands (the bottom one
Although replication is semiconservative, this model alone does in Fig. 12.1) has a left-to-right 5�-to-3� orientation, whereas the other
not tell us the details of replication. For example, the model template strand (the top one in Fig. 12.1) has a left-to-right 3�-to-5�
orientation. Therefore, the new daughter strands also have opposite
orientations, so that near the replication fork the daughter strand in
FIG. 12.3 Eukaryotic DNA replication. Further evidence that DNA the bottom duplex terminates in a 3� hydroxyl, whereas that in the
replication is semiconservative came from observing top duplex terminates in a 5� phosphate. There’s the rub: The strand
the uptake of fluorescent nucleotides into chromosomal that terminates in the 5� phosphate cannot grow in the direction of
DNA. Source: Daniel Hartl. the replication fork because new DNA strands can grow only by the
addition of successive nucleotides to the 3�end. That is, DNA always
Half-labeled Fully labeled
After two rounds of DNA
grows in the 5�-to-3� direction.
replication in a labeled DNA polymerization occurs only in the 5�-to-3� direction
medium, one daughter because of the chemistry of nucleic acid synthesis, discussed in
molecule is half-labeled,
and the other is fully labeled Chapter 3. The building blocks of DNA (Chapter 2) are nucleotides,
(compare with Figure 12.2). each consisting of a deoxyribose sugar with three phosphate
groups attached to the 5� carbon, a nitrogenous base (A, T, G, or
C) attached to the 1� carbon, and a free hydroxyl (–OH) group
attached to the 3� carbon. DNA polymerization occurs when the
CHAPTER 12 D N A R E P L I C AT I O N A N D M A N I P U L AT I O N 251
3� hydroxyl at the growing end of the polynucleotide chain attacks polymerase enzymes, each specialized for a particular situation.
the triphosphate group at the 5� end of an incoming nucleotide But all DNA polymerases share the same basic function in that
(Fig. 12.4). Each of these incoming nucleotides is a nucleotide they synthesize a new DNA strand from an existing template.
triphosphate (three phosphate groups attached to the 5� carbon Most, but not all, also correct mistakes in replication, as we will
of the deoxyribose). As the incoming nucleotide triphosphate is see. DNA polymerases have many practical applications in the
added to the growing DNA strand, one of the nucleotide’s high- laboratory, which we will discuss later in this chapter.
energy phosphate bonds is broken to release the outermost two
phosphates (called pyrophosphate), and immediately the high- In replicating DNA, one daughter strand is synthesized
energy phosphate bond in the pyrophosphate is cleaved to drive continuously and the other in a series of short pieces.
the polymerization reaction forward and make it irreversible. Because a new DNA strand can be elongated only at the 3� end, the
The polymerization reaction is catalyzed by DNA polymerase, two daughter strands are synthesized in quite different ways
an enzyme that is a critical component of a large protein complex (Fig. 12.5). The daughter strand shown at the bottom of Fig. 12.5 has
that carries out DNA replication. DNA polymerases exist in all its 3� end pointed toward the replication fork, so that as the parental
organisms and are highly conserved, meaning that they vary double helix unwinds, nucleotides can be added onto the 3� end and
little from one species to another because they carry out an this daughter strand can be synthesized as one long, continuous
essential function. A cell typically contains several different DNA polymer. This daughter strand is called the leading strand.
FIG. 12.5 Leading and lagging strand synthesis. In DNA replication, because the template strand is made of two antiparallel strands, one daughter
strand (the leading strand) is synthesized continuously and the other (the lagging strand) is synthesized in smaller pieces.
Newly
synthesized
Template DNA
strands 5’
3’
Unwinding of the
3’ 5’ DNA duplex results
3’ RNA primer
5’ in a replication fork.
Unwinding 5’
3’
5’ Replication always
3’ occurs in the 5’ to
5’ 3’ direction. The
3’ daughter strand
Elongation
5’ 3’ on top elongates
from left to right,
5’ that on the bottom
3’ from right to left.
5’ Replication of the
3’ top strand is
3’ 5’ discontinuous
3’ 5’
3’ (fragmented),
5’
whereas that of the
5’ bottom strand is
3’ continuous.
Lagging strand
5’ Primers are
Discontinuous
3’ removed and
DNA synthesis
replaced with DNA,
3’ 5’ Primer replacement and the fragments
5’ 3’ and ligation of the discontinuous
(lagging) strand are
Leading strand 5’ ligated where they
Continuous 3’ meet.
DNA synthesis
252 SECTION 12.1 D N A R E P L I C AT I O N
FIG. 12.7 The replication fork. (a) Many proteins play different roles in replication, including separating and stabilizing the strands of the double
helix. (b) In the cell, proteins involved in replication come together to form a complex that replicates both strands at the same pace.
a.
3’
DNA polymerase
Lagging
strand
Helicase unwinds the
parental DNA strands. 5’
Topoisomerase II relieves
the stress of unwinding.
5’
b.
5’
5’
Lagging
strand
3’
3’
5’
3’
Leading
strand
While Figure 12.7a makes it clear how synthesis of the leading complexes for each strand stay in contact with each other, with the
strand and the lagging strand take place, it does not show how lagging strand’s polymerase releasing and retrieving the lagging
synthesis of these strands occurs at the same time and rate. To strand for the synthesis of each new RNA primer. The positioning
help ensure that both strands of the double helix are replicated at of the polymerases is such that both the leading strand and the
nearly the same rate, synthesis of the leading and lagging strands lagging strand pass through in the same direction, which requires
is coordinated as shown in Fig. 12.7b. The DNA polymerase that the lagging strand be looped around as shown in Fig. 12.7b. In
254 SECTION 12.2 R E P L I C AT I O N S O F C H RO M O S O M E S
FIG. 12.12 Telomerase. Telomerase prevents successive shortening of linear chromosomes. 12.3 ISOLATION,
IDENTIFICATION,
Ends of template AND SEQUENCING
Lagging strand
DNA strands OF DNA FRAGMENTS
Leading strand
Watson and Crick’s discovery of the
The terminal part of the structure of DNA and knowledge of the
telomere in the template mechanism of replication allowed biologists
DNA strand remains
unreplicated.
not only to understand some of life’s
Template strand central processes, but also to create tools
3’
to study how life works. Biologists often
GGGA T T GGGA T T GGGA T T GGGA T T GGG
T AACCC TAACCC TAACCC need to isolate, identify, and determine
5’ the nucleotide sequence of particular DNA
Lagging strand fragments. Such procedures can determine
whether a genetic risk factor for diabetes
has been inherited, blood at a crime scene
matches that of a suspect, a variety of rice
Telomerase
G A or wheat carries a genetic factor for insect
G G
T
3’ resistance, or two species of organisms are
The telomerase enzyme T
GGGA T T GGGA T T GGGA T T GGGA T T GGG closely related. Many of the experimental
contains an RNA template CCCUAACCC T AACCC TAACCC TAACCC procedures for the isolation, identification,
that allows the shortened
3’ end of the template 5’ 3’ 5’ and sequencing of DNA are based on
strand to be restored by knowledge of DNA structure and physical
the addition of more RNA template
telomere repeats. properties of DNA. Others make use of the
principles of DNA replication.
Telomere repeats In this section, we discuss how particular
3’ fragments of double-stranded DNA can be
GGGA T TGGGA T T GGGA T T GGGA T T GGGA T T GGGA T T GGG produced, how DNA fragments of different
CCCUAACCC T AACCC TAACCC TAACCC sizes can be physically separated, and how
5’ 3’ 5’
the nucleotide sequence of a piece of DNA
can be determined.
FIG. 12.13 The polymerase chain reaction (PCR). PCR results in amplification of the DNA sequence flanked by the two primers.
Cycle 1 product:
2 copies
Cycle 2 product:
4 copies
4 After n cycles of
amplification there
are 2n copies of the Cycle n product:
target sequence. 2n copies
When n = 30, there are
230 109 copies.
CHAPTER 12 D N A R E P L I C AT I O N A N D M A N I P U L AT I O N 259
amplify and detect small quantities of nucleic acids, such as HIV After sufficient time to allow new DNA synthesis, the solution
in blood-bank supplies, or to study DNA samples as minuscule is heated again, and the cycle of denaturation, annealing, and
as those left by a smoker’s lips on a cigarette butt dropped at the extension is repeated over and over, as indicated in Fig. 12.13b,
scene of a crime. The starting sample can be as small as a single usually for 25–35 cycles. In each cycle, the number of copies of
molecule of DNA. the targeted fragment is doubled. The first round of PCR amplifies
The principles of PCR are illustrated in Fig. 12.13. Because the the targeted region into 2 copies, the next into 4, the next into
PCR reaction is essentially a DNA synthesis reaction, it requires 8, then 16, 32, 64, 128, 256, 512, 1024, and so forth. By the third
the same basic components used by the cell to replicate its DNA. round of amplification, the process begins to produce molecules
In this case, the procedure takes place in a small plastic tube that are only as long as the region of the template duplex flanked
containing a solution that includes four essential components: by the sequences complementary to the primers. After several
more rounds of replication the majority of molecules are of this
1. Template DNA. At least one molecule of double-stranded
type. The doubling in the number of amplified fragments in each
DNA containing the region to be amplified serves as the
cycle justifies the term “chain reaction.”
template for amplification.
Although PCR is elegant in its simplicity, the DNA polymerase
2. DNA polymerase. The enzyme DNA polymerase is used to enzymes from many species (including humans) irreversibly lose
replicate the DNA. both structure and function at the high temperature required to
separate the DNA strands. At each cycle, you would have to open
3. All four deoxynucleoside triphosphates. Deoxynucleoside
the tube and add fresh DNA polymerase. This is possible, and
triphosphates with the bases A, T, G, or C are needed as
in fact it was how PCR was done when the technique was first
building blocks for the synthesis of new DNA strands.
developed, but the procedure is time consuming and tedious. To
4. Two primers. Two short sequences of single-stranded DNA solve this problem, we now use DNA polymerase enzymes that
are required for the DNA polymerase to start synthesis. are heat-stable, such as those from the bacterial species Thermus
Enough primer is added so that the number of primer DNA aquaticus, which lives at the near–boiling point of water in
molecules is much greater than the number of template natural hot springs, including those at Yellowstone National Park.
DNA molecules. This polymerase, called Taq polymerase, remains active at high
temperatures. Once the reaction mixtures are set up, the entire
The primer sequences are oligonucleotides (oligos is the procedure is carried out in a fully automated machine. The time
Greek word for “few”) produced by chemical synthesis and are of each cycle, temperatures, number of cycles, and other variables
typically 20–30 nucleotides long. Their base sequences are chosen can all be programmed. The fact that DNA polymerase from a
to be complementary to the ends of the region of DNA to be bacterium that lives in hot springs can be used to amplify DNA
amplified. In other words, the primers flank the specific region of from any organism reminds us again of the conserved function and
DNA to be amplified. The 3� end of each primer must be oriented evolution early in the history of life of this enzyme.
toward the region to be amplified so that, when DNA polymerase
extends the primer, it creates a new DNA strand complementary Electrophoresis separates DNA fragments by size.
to the targeted region. Because the 3� ends of the primers both PCR amplification does not always work as you might expect.
point toward the targeted region, one of the primers pairs with Sometimes the primers have the wrong sequence and so fail to
one strand of the template DNA and the other pairs with the other anneal properly; sometimes they anneal to multiple sites and
strand of the template DNA. several different fragments are amplified. To determine whether
PCR creates new DNA fragments in a cycle of three or not PCR has yielded the expected product, a researcher must
steps, as shown in Fig. 12.13a. The first step, denaturation, determine the size of the amplified DNA molecules. Usually,
involves heating the solution in a plastic tube to a temperature the researcher knows what the size of the correctly amplified
just short of boiling so that the individual DNA strands of the fragment should be, making it possible to compare the expected
template separate (or “denature”) as a result of the breaking of size to the actual size.
hydrogen bonds between the complementary bases. The second One way to determine the actual size of a DNA fragment
step, annealing, begins as the solution is cooled. Because of is by gel electrophoresis (Fig. 12.14), a procedure in which
the great excess of primer molecules, the two primers bind (or DNA samples are inserted into slots or wells near the edge of a
“anneal”) to their complementary sequence on the DNA (rather rectangular slab of porous material resembling solidified agar
than two strands of the template duplex coming back together). (the “gel”), which is composed of a tangle of polymers that
In the final step, extension, the solution is heated to the make it difficult for large molecules to pass through. The gel is
optimal temperature for DNA polymerase and the polymerase then inserted into an apparatus and immersed in a solution that
elongates (or “extends”) each primer with the deoxynucleoside allows an electric current to be passed through it (Fig. 12.14a).
triphosphates. Since fragments of double-stranded DNA are negatively charged
260 SECTION 12.3 I S O L AT I O N , I D E N T I F I C AT I O N , A N D S E Q U E N C I N G O F D N A F R AG M E N T S
FIG. 12.16 A Southern blot. Photo source: Reproduced with permission from Da’dara, A.A., Walter, R. D. 1998 Biochem J., 336(Pt 3): 545–550. © The Biochemical Society.
Labeled Sealable
Filter paper probe plastic bag
Gel
1 A 2 The resulting 3 After electrophoresis, 4 After 5 The filter paper is placed 6 To visualize the
restriction fragments are the DNA fragments in blotting, the into a plastic bag containing positions of the bands
enzyme is separated by size by the gel are denatured filter paper is a solution with the where the probe
added to a gel electrophoresis. and then transferred removed. single-stranded, labeled hybridized, the filter
solution (blotted) onto filter probe, and the probe sticks paper is exposed to
containing paper. to complementary fragments X-ray film, and either
the DNA of by hybridization. (The bands light or radioactive
interest. are not visible at this stage.) emissions darken the
film over each band.
sequences affects the temperature at which they renature: Very (Fig. 12.16) after its inventor, the British molecular biologist
closely related sequences renature at a higher temperature than Edwin M. Southern.
less closely related sequences. Evolutionary biologists have used In a Southern blot, single-stranded DNA molecules that
this principle to estimate the proportion of perfectly matched have resolved into bands on a gel are transferred to a filter paper,
bases present in the DNA of different species, which is used as such that they are on the same spot on the paper as they were
a measure of how closely those species are related. In general, on the gel. The filter paper is washed with a solution containing
the more closely two species are related, the more
similar their DNA sequences. Knowledge of species
relatedness is important in many applications,
FIG. 12.17 (a) A deoxynucleotide and (b) a dideoxynucleotide. Incorporation
including conservation, identifying endangered
of a dideoxynucleotide prevents strand elongation.
species, and tracing the evolutionary history of
organisms. a. b.
Renaturation makes it possible to use a small O O
DNA fragment as a probe. This fragment is usually -O P O -O P O
attached to a light-emitting or radioactive chemical
O O
that serves as a label. The probe can be used to
O O
determine whether or not a sample of double- 5’ CH2 OH 5’ CH2 OH
stranded DNA molecules contains sequences that 4’ 1’ 4’ 1’
H H H H H H H H
are complementary to it. Any DNA fragment can 3’ 2’ 3’ 2’
be used as a probe, and a probe can be obtained in O H H H
any number of ways, such as by chemical isolation -O P O
of a DNA fragment, amplification by PCR, or A dideoxynucleotide lacks the 3’ hydroxyl
O group, and it cannot be elongated because
synthesizing a nucleic acid from free nucleotides.
O there is no hydroxyl group to attack an
Let’s say you are interested in determining the 5’ CH2 OH incoming nucleotide triphosphate.
number of copies of a particular DNA sequence in 4’ 1’
H H H H
a genome or determining whether a given gene in 3’ 2’
human genomic DNA is intact. Recall that human H
and other genomic DNA cut with a restriction HO
enzyme yield a large number of DNA fragments that
look like a smear following gel electrophoresis. A normal deoxynucleotide has
A labeled probe can be used to determine the a hydroxyl (–OH) group on the
3’ carbon, allowing this end to
size and number of a DNA sequence of interest in be elongated.
a gel. The method is known as a Southern blot
CHAPTER 12 D N A R E P L I C AT I O N A N D M A N I P U L AT I O N 263
be produced whose sizes correspond to the positions of the Cs, and approach passes individual DNA molecules through a pore in a
likewise for dideoxy-T and dideoxy-G. charged membrane; as each nucleotide passes through the pore it
Each of the four dideoxynucleotides is chemically labeled with is identified by means of the tiny difference in charge that occurs.
a different fluorescent dye, as indicated by the different colors These miniaturized and automated devices carry out what is often
of A, C, T, and G in Fig. 12.18b, and so all four terminators can be called massively parallel sequencing, which can determine the
present in a single reaction and still be distinguished. After DNA sequence of hundreds of millions of base pairs in a few hours.
synthesis is complete, the daughter strands are separated by size The goal of technology development was captured in the
with gel electrophoresis. The smallest daughter molecules migrate catchphrase “the $1000 genome,” a largely symbolic target
most quickly and therefore are the first to reach the bottom indicating a reduction in sequencing cost from about $1 million
of the gel, followed by the others in order of increasing size. A per megabase to less than $1 per megabase. For all practical
fluorescence detector at the bottom of the gel “reads” the colors purposes, the $1000-genome target has been achieved, but $1000
of the fragments as they exit the gel. What the scientist sees is a is still too costly to make genome sequencing a routine diagnostic
trace (or graph) of the fluorescence intensities, such as the one procedure. The technologies are still evolving and the costs
shown in Fig. 12.18c. The differently colored peaks, from left to decreasing, and so it is a fair bet that in the coming years your own
right, represent the order of fluorescently tagged DNA fragments personal genome can be sequenced quickly and cheaply.
emerging from the gel. Thus, a trace showing peaks colored green-
purple-red-green-purple-purple-blue-green-blue-red corresponds
to a daughter strand having the sequence 5�-ACTACCGAGT-3� 12.4 GENETIC ENGINEERING
(Fig. 12.18c). In the Sanger sequencing method, each sequencing
reaction can determine the sequence of about 1000 nucleotides in Along with methods to manipulate DNA fragments came the
the template DNA molecule. capability of isolating genes from one species and introducing
them into another. This type of genetic engineering is called
j Quick Check 3 You have determined that the newly synthesized
recombinant DNA technology because it literally recombines
strand of DNA in your sequencing reaction has the sequence
DNA molecules from two (or more) different sources into a single
5�-ACTACCGAGT-3�. What is the sequence of the template strand?
molecule. Recombinant DNA technology involves cutting DNA
by restriction enzymes, isolating them by gel electrophoresis,
? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME and ligating them with enzymes used in DNA replication. This
What new technologies are being developed to technology is possible because the DNA of all organisms is the
sequence your personal genome? same, differing only in sequence but not in chemical or physical
One of the high points of modern biology has been the structure. When DNA fragments from different sources are
determination of the complete nucleotide sequence of the DNA in combined into a single molecule and incorporated into a cell, they
a large number of species, including ours. The human genome and are replicated and transcribed just like any other DNA molecule.
many others were sequenced by Sanger sequencing. This technique Recombinant DNA technology can combine DNA from
works well and is still the gold standard for accuracy, but it takes any two sources, including different species. DNA from one
time and is expensive for large genomes like the human genome. species of bacteria can be combined with another, or a human
There have been many improvements in Sanger sequencing since it gene can be combined with bacterial DNA, or the DNA from
was first described, including the use of four-color fluorescent dyes a plant and a fungus can be combined into a single molecule.
to label the DNA fragments, capillary electrophoresis to separate the These new sequences may be unlike any found in nature, raising
fragments, photocells to read the fluorescent signals automatically questions about their possible effects on human health and the
as the products run off the gel, and highly efficient enzymes. environment.
Together, these methods have increased the speed and decreased This section discusses one of the basic methods for producing
the cost of DNA sequencing considerably. recombinant DNA, some of the important applications of
However, being able to sequence everyone’s genome, including recombinant DNA technology such as genetically modified
yours, will require new technologies to bring down the cost organisms, and a new method that can be used to change the DNA
further and to increase the speed of sequencing. The first human sequence of any organism into any other desired sequence.
genome sequence, completed in 2003 at a cost of approximately
$2.7 billion, stimulated great interest in large-scale sequencing Recombinant DNA combines DNA molecules from two
and the development of devices that increased scale and decreased or more sources.
cost. As in the development of computer hardware, emphasis was The first application of recombinant DNA technology was the
on making the sequencing devices smaller while increasing their introduction of foreign DNA fragments into the cells of bacteria
capacity through automation. in the early 1970s. The method is simple and straightforward, and
Modern methods of sequencing include the use of fluorescent remains one of the mainstays of modern molecular research. It
nucleotides or light-detection devices that reveal the identity of can be used to generate a large quantity of a protein for study or
each base as it is added to the growing end of a DNA strand. Another therapeutic use.
CHAPTER 12 D N A R E P L I C AT I O N A N D M A N I P U L AT I O N 265
CT
G
G
cleavage site, so digestion of the vector with EcoRI opens the G CTT A A
C
TA
T
+ T
circle with a single cut that also has four-nucleotide 5� overhangs. A ATT C G A
A
A
Note that the overhangs on the donor fragment and the vector
are complementary, allowing the ends of the donor fragment
to renature with the ends of the opened vector when the two
The resulting
molecules are mixed. Once this renaturation has taken place, the fragments are mixed
ends of the donor fragment and the vector are covalently joined by together and joined
DNA ligase. The joining of the donor DNA to the vector creates the by DNA ligase. The
genomic and vector Recombinant DNA
recombinant DNA molecule. fragments have
The next step in the procedure is transformation, in which complementary
ends.
the recombinant DNA is mixed with bacteria that have been DNA
chemically coaxed into a physiological state in which they take ligase
up DNA from outside the cell. Having taken up the recombinant
DNA, the bacterial cells are transferred into growth medium,
The recombinant
where they multiply. Since the vector part of the recombinant DNA molecule is
DNA molecule contains all the DNA sequences needed for its Bacterial DNA introduced into
replication and partition into the daughter cells, the recombinant a bacterial cell
by means of
DNA multiplies as the bacterial cell multiplies. If the recombinant transformation.
DNA functions inside the bacterial cell, then new genetic
characteristics may be expressed by the bacteria. For example,
the recombinant DNA may allow the bacterial cells to produce a
human protein, such as insulin or growth hormone.
Recombinant DNA is the basis of genetically modified and many others have been engineered to resist insect pests, and
organisms. other engineered products are rice with a high content of vitamin
Applications of recombinant DNA have gone far beyond genetically A, tomatoes with delayed fruit softening, potatoes with waxy
engineered bacteria. Using methods that are conceptually similar to starch, and sugarcane with increased sugar content. To model
those described for bacteria but differing in many details, scientists disease, researchers have used recombinant DNA to produce
have been able to produce varieties of genetically engineered organisms such as laboratory mice that have been engineered to
viruses and bacteria, laboratory organisms, agricultural crops, and develop heart disease and diabetes. By studying these organisms,
domesticated animals (Fig. 12.20). Examples include sheep that researchers can better understand human diseases and begin to
produce a human protein in their milk used to treat emphysema, find new treatments for them.
chickens that produce eggs containing human antibodies to Genetically engineered organisms are known as transgenic
help fight harmful bacteria, and salmon with increased growth organisms or genetically modified organisms (GMOs).
hormone for rapid growth. Plants such as corn, canola, cotton, Transgenic laboratory organisms are indispensable in the study
FIG. 12.20 Genetically modified organisms (GMOs). Organisms can be genetically modified so that (a) wheat resists weed-killing herbicides,
(b) soybeans resist insects and have improved oil quality, (c) sheep produce more healthy fats, (d) chickens are unable to spread bird
flu, (e) salmon have faster growth, and (f) pigs digest plant phosphorus more efficiently. Sources: a. Adam Hart-Davis/Science Source; b. Steve
Percival/Science Source; c. meirion matthias/Shutterstock; d. John Daniels/Ardea; e. AquaBounty Technologies; f. Carla Gottgens/Bloomberg via Getty Images.
a b c
e
CHAPTER 12 D N A R E P L I C AT I O N A N D M A N I P U L AT I O N 267
FIG. 12.21 DNA editing. In this example, CRISPR RNA and its associated protein are used to cleave target DNA, and double-stranded template
DNA is used in DNA repair to alter its sequence.
a. CRISPR b. c. d. e.
RNA Target Editing
DNA template
DNA
Hairpin
Edited
target
Exonuclease DNA
Cleavage
Region CRISPR
complementary associated
to target DNA protein
(Cas9)
CRISPR RNA CRISPR RNA guides An exonuclease The editing The result is an
combines with Cas9 to the target widens gap in template is used edited DNA with
the Cas9 protein. DNA and the the target DNA. to repair the gap altered sequence.
target is cleaved. in the target DNA.
of gene function and regulation and to identify genetic risk One of the newest and most exciting ways to edit DNA
factors for disease. In crop plants and domesticated animals, goes by the acronym CRISPR (clustered regularly interspaced
GMOs promise enhanced resistance to disease, faster growth and short palindromic repeats), and it was discovered in an
higher yields, more efficient utilization of fertilizer or nutrients, unexpected way. Researchers noted that about half of all species
and improved taste and quality. But there are concerns about of bacteria and most species of Archaea contain small segments
unexpected effects on human health or the environment, the of DNA of about 20–50 base pairs derived from plasmids or
increasing power and influence of agribusiness conglomerates, viruses, but their function was at first a mystery. Later, it was
and ethical objections to tampering with the genetic makeup of discovered that they play a role in bacterial defense. When a
animals and plants. Nevertheless, more than 250 million acres of bacterium is infected by a virus for the first time, it makes a copy
GMO crops are grown annually in more than 20 countries. The of part of the viral genome and incorporates it into its genome.
majority of this acreage is in the United States and South America. On subsequent infection by the same virus, the DNA copy of
Resistance to the use of GMOs in Europe remains strong and vocal. the viral genome is transcribed to RNA that combines with a
protein that has a DNA-cleaving function. The RNA serves as
DNA editing can be used to alter gene sequences a guide to identify target DNA in the virus by complementary
almost at will. base pairing, and the protein cleaves the target DNA. In this way,
Recombinant DNA technology combines existing DNA from two bacteria “remember” and defend themselves from past infections.
or more different sources. Its usefulness in research, medicine, The phrase “clustered regularly interspaced short palindromic
and agriculture, however, is limited by the fact that it can make repeats” describes the organization of the viral DNA segments in
use only of existing DNA sequences. Therefore, scientists have the bacterial genome.
also developed many different techniques to alter the nucleotide In modern genetic engineering, the CRISPR mechanism is
sequence of almost any gene in a deliberate, targeted fashion. put to practical use to alter the nucleotide sequence of almost any
In essence, these techniques allow researchers to “rewrite” the gene in any kind of cell. One method is outlined in Fig. 12.21. The
nucleotide sequence so that specific mutations can be introduced first step is to transform a cell with a plasmid containing sequences
into genes to better understand their function, or mutant versions that code for a CRISPR RNA as well as the CRISPR-associated
of genes can be corrected to restore normal function. Collectively, protein Cas9. The RNA contains a region that can form a hairpin-
these techniques are known as DNA editing. shaped structure, as well as a region engineered to have bases
268 CO R E CO N C E P T S S U M M A RY
complementary to any DNA molecule in the cell to be altered, with the complementary ends of the editing template, and DNA
known as the target DNA (Fig. 12.21a). When the RNA undergoes synthesis elongates the target DNA strands and closes the gap
base pairing with the target DNA, Cas9 cleaves the target DNA (Fig. 12.21d). The result is that the target DNA is restored, but its
(Fig. 12.21b). Exonucleases in the cell then expand the gap (Fig. sequence has been altered according to the sequence present in
12.21c). The gap can be repaired using another DNA molecule that the editing template (Fig. 12.21e).
serves as a template for editing the target DNA (Fig. 12.21d). This DNA editing by CRISPR is technically straightforward and
editing template DNA is introduced to the cell by a plasmid and highly efficient. The method has generated great interest because
contains a sequence of interest to replace the degraded sequence of its potential to correct genetic disorders of the blood, immune
of the target DNA, flanked by sequences complementary to the system, or other tissues and organs in which only a subset of cells
target. The strands of the gapped target DNA undergo base pairing with restored function can alleviate symptoms. •
12.4 Genetic engineering allows researchers to alter DNA strands and how this affects the direction of DNA
DNA Sequences. synthesis.
A recombinant DNA molecule can be made by cutting DNA 3. List the differences and similarities in the way the two
from two organisms with the same restriction enzyme and daughter strands of DNA are synthesized at a replication
then using DNA ligase to join them. page 264 fork.
Recombinant DNA is the basis for genetically modified 4. Explain why replicating the tips of linear chromosomes
organisms (GMOs), which offer both potential benefits is problematic and how the cell overcomes this challenge.
and risks. page 266
5. Describe what PCR does. Name and explain its three
Almost any DNA sequence in an organism can be altered steps and give at least two uses for the PCR technique.
by means of a form of DNA editing called CRISPR, which
6. Explain how the properties of DNA determine how
uses modified forms of molecules found in bacteria and
it moves through a gel, is cut by restriction enzymes, and
archaeons that can cleave double-stranded DNA at a
hybridizes to other DNA strands.
specific site. page 267
7. Describe how DNA molecules are sequenced.
Genomes
Core Concepts
13.1 A genome is the genetic
material of a cell, organism,
organelle, or virus, and its
sequence is the order of
bases along the DNA or
(in some viruses) RNA.
13.2 Researchers annotate
genome sequences to
identify genes and other
functional elements.
13.3 The number of genes in a
genome and the size of a
genome do not correlate
well with the complexity of
an organism.
13.4 The orderly packaging
of DNA allows it to carry
out its functions and fit inside
the cell.
13.5 Viruses have diverse
genomes, but all require a
host cell to replicate.
SSPL/Getty Images.
271
272 SECTION 13.1 GENOME SEQUENCING
HOW DO WE KNOW?
In Chapter 12, we saw how small pieces of DNA are isolated,
identified, and sequenced. This technology has advanced to the point FIG.13.1
where the complete genome sequences for thousands of species have
been determined, including those of humans and our closest primate How are whole genomes
relatives, as well as dozens of other mammals. The term genome
refers to the genetic material of a specified organism, cell, nucleus, sequenced?
organelle, or virus. Some genomes, like that of HIV, are small,
whereas others, like the human genome, are large. Technically, the
BACKGROUND DNA sequencing technologies can only
human genome refers to the DNA in the chromosomes present in
a sperm or egg. However, the term is often used informally to mean determine the sequence of DNA fragments far smaller than the
all of the genetic material in an organism. So your personal genome genome itself. How can the sequences of these small fragments
consists of the DNA in two sets of chromosomes, one inherited from be used to determine the sequence of an entire genome? In the
each parent, plus a much smaller mitochondrial genome inherited early years of genome sequencing, many researchers thought
from your mother. The human genome sequence is so long that that it would be necessary to know first where in the genome
printing it in the size of the type used in this book would require each fragment originated before sequencing it. A group at Celera
1.5 million pages. As we will see, however, the human genome is far Genomics reasoned that if so many fragments were sequenced
from the largest among organisms. that the ends of one would almost always overlap with those of
The sequence of a genome is merely a long string of A’s, T’s, G’s, others, then a computer program with sufficient power might be
and C’s, which represent the order of bases present in successive able to assemble the short sequences to reveal the sequence of
nucleotides along the DNA molecules in the genome. But a genome the entire genome.
sequence, on its own, is not very useful to scientists. Additional HYPOTHESIS A genome sequence can be determined by
research is required to understand what proteins and other sequencing small, randomly generated DNA fragments and
molecules are encoded in the genome sequence, and to learn when assembling them into a complete sequence by matching regions of
these molecules are produced during an organism’s lifetime and overlap between the fragments.
what they do.
EXPERIMENT Hundreds of millions of short sequences from
In this chapter, we discuss how the sequence of a genome is
determined and analyzed to reveal its key biological features, such the genome of the fruit fly, Drosophila melanogaster, were
as the protein-coding genes. We also examine what other kinds of sequenced. Fig. 13.1a shows examples of overlapping fragments,
DNA sequences are present in genomes and how these sequences are using a sentence from Watson and Crick’s original paper on the
organized, with special emphasis on the human genome. Finally, we chemical structure of DNA as an analogy.
explore the diversity of genome types present in viruses.
RESULTS The computer program the group had written to assemble the fragments worked. The researchers were able to sequence the
entire Drosophila genome by piecing together the fragments according to their overlaps. In the sentence analogy, the fragments (Fig.
13.1a) can be assembled into the complete sentence (Fig. 13.1b) by matching the overlaps between the fragments.
a.
1 “It has not escaped our no
2 specific pairing we have post The sequences of DNA fragments are
analogous to sentence fragments.
3 suggests a plausible copying m
4 d our notice that the specifi
5 ve postulated immediately suggests
6 pying mechanism for the genetic material.”
b.
1 4 2 5 3 6
The sentence fragments can be assembled in the
“It has not escaped our no
correct order according to their overlaps and
d our notice that the specifi
the original complete sentence reconstructed.
specific pairing we have post
ve postulated immediately suggests
suggests a plausible copying m
pying mechanism for the genetic material.”
CONCLUSION The hypothesis was supported: Celera Genomics could determine the entire genomic sequence of an organism by sequencing
small, random fragments and piecing them together at their overlapping ends.
FOLLOW-UP WORK Today, the computer assembly method is routinely used to determine genome sequences. This method is also used to
infer the genome sequences of hundreds of bacterial species simultaneously—for example, in bacterial communities sampled from seawater or
from the human gut.
SOURCE Adams, M. D., et al. 2000. “The Genome Sequence of Drosophila melanogaster.” Science 287:2185–2195.
data obtained from a small DNA fragment is only a minuscule is called shotgun sequencing because the sequenced fragments
fraction of the length of the DNA molecules in most genomes, do not originate from a particular gene or region but from sites
each run of an automated sequencing machine yields hundreds scattered randomly across the chromosome.
of millions of these short sequences from random locations
j Quick Check 1 DNA sequencing technology has been around
throughout the genome. To sequence a whole genome, researchers
since the late 1970s. Why did sequencing whole genomes
typically sequence such a large number of random DNA fragments
present a challenge?
that, on average, any particular small region of the genome is
sequenced 10–50 times. This redundancy is necessary to minimize
both the number of errors present in the final genome sequence Sequences that are repeated complicate sequence
and the number and size of gaps where the genome sequence is assembly.
incomplete. Sequence assembly is not quite as straightforward as Fig. 13.1
When the sequences of a sufficient number of short stretches suggests. Real sequences are composed of the nucleotides A, T,
of the genome have been obtained, the next step is sequence G, and C, and any given short sequence could come from either
assembly: The short sequences are put together in the correct strand of the double-stranded DNA molecule. Therefore, the
order to generate the long, continuous sequence of nucleotides in overlaps between fragments must be long enough both to ensure
the DNA molecule present in each chromosome. that the assembly is correct and to determine from which strand
Assembly is accomplished by complex computer programs, of DNA the short sequence originated.
but the principle is simple. The short sequences are assembled Some features of genomes present additional challenges to
according to their overlaps, as illustrated in Fig. 13.1, which uses sequence assembly, and the limitations of the computer programs
a sentence to represent the nucleotide sequence. This approach for handling such features require hands-on assembly. Chief
273
274 SECTION 13.1 GENOME SEQUENCING
among these complicating features is the problem of repeated of this kind are troublesome for sequencing machines because
sequences known collectively as repetitive DNA. any single-stranded fragment consisting of alternating AT can fold
There are a variety of types of repeated sequence in eukaryotic back upon itself to form a double-stranded structure in which A is
genomes, and some are shown in Fig. 13.2. The repeated sequence paired with T. Such structures are more stable than the unfolded
may be several thousand nucleotides long and present in multiple single-stranded structures and are not easily sequenced. It is
identical or nearly identical copies. These long repeated sequences quite easy to see that the sequence 5�-AAAAAATTTTTT-3� can
may be dispersed throughout the genome (Fig. 13.2a), or they may fold back itself to form a hairpin because the 5�-AAAAAA-3� is
be tandem, meaning that they are next to each other (Fig. 13.2b). complementary to the 3�- TTTTTT-5�. Any sequence that contains
The difficulty with long repeated sequences is that they internal complementarity can form a foldback loop, including the
typically are much longer than the short fragments sequenced by sequence 5�-…ATATATAT…-3� in Fig. 13.2c.
automated sequencing. As a result, the repeat may not be detected
j Quick Check 2 Let’s say that a stretch of repeated AT is
at all. And if the repeat is detected, there is no easy way of knowing
successfully sequenced. From what you know of the difficulties of
the number of copies of the repeat, that is, whether the DNA
sequencing long repeated sequences, what other problems might
molecule includes two, three, four, or any number of copies of the
you encounter in assembling these fragments?
repeat. Sometimes, researchers can use the ends of repeats, where
the fragments overlap with an adjacent, nonrepeating sequence, as
a guide to the position and number of repeats. ? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME
To illustrate the assembly problems caused by repeated Why sequence your personal genome?
sequences, let’s consider an analogy. In Shakespeare’s play Hamlet, The goal of the Human Genome Project, which began in 1990, was
the word “Hamlet” occurs about 500 times scattered throughout to sequence the human genome as well as the genomes of certain
the text, like a dispersed repeat (Fig. 13.2a). If you chose short key organisms used as models in genetic research. The model
sequences of letters from the play at random and found the organisms chosen are the mainstays of laboratory biology—a
sequence “Hamlet” or “amlet” or “Haml,” you would have no way species each of bacteria, yeast, nematode worm, fruit fly, and
of knowing which of the 500 “Hamlets” these letters came from. mouse. By 2003, the genome sequences of these model organisms
Only if you found sequences that contained “Hamlet” overlapping had been completed, as well as that of the human genome. By
with adjacent unique text could you identify their origin. A similar then, the cost of sequencing had become so low and the sequence
problem occurs in the case of tandem repeats. output so high that many more genomes were sequenced than
In another type of repeat the repeating sequence is short, even originally planned. Genome sequencing is even cheaper today, and
as short as two nucleotides, such as AT, repeated over and over soon you can choose to have your personal genome sequenced.
again in a stretch of DNA (Fig. 13.2c). Short repeating sequences Why sequence more genomes? And if the human genome is
sequenced, why sequence yours? As we saw in Case 3: You, from A
to T, there is really no such thing as the human genome, any more
than there is the fruit fly genome or the mouse genome. With the
FIG. 13.2 Principal types of sequence repeats found in
exception of identical twins, every person’s genome is unique,
eukaryotic genomes. Repeats often pose problems in
the product of a fusion of a unique egg with a unique sperm.
DNA sequencing. (Repeats are not drawn to scale.)
The sequence that is called “the human genome” is actually a
a.
composite of sequences from different individuals. This sequence
Dispersed repeats is nevertheless useful because most of us share the same genes
and regulatory regions, organized the same way on chromosomes.
Detailed knowledge of your own personal genome can be valuable.
Our individual DNA sequences differ at millions of nucleotide sites
from one person to the next. Some of these differences account
b.
Tandem repeats in part for the physical differences we see among us; others have
the potential to predict susceptibility to disease and response to
medication. For Claudia Gilmore, knowledge of the sequence of
her BRCA1 gene had a significant impact on her life.
Determining these differences is a step toward personalized
c.
medicine, in which an individual’s genome sequence, by revealing
Simple-sequence repeats
his or her disease susceptibilities and drug sensitivities, allows
treatments to be tailored to that individual. There may come
a time, perhaps within your lifetime, when personal genome
sequencing becomes part of routine medical testing. Information
… A T A T A T A T A T A T A T A T A T A T A T A T A T A T A T A T AT …
about a patient’s genome will bring benefits but also raises ethical
… TATATATATATATATATATATATATATATATATA… concerns and poses risks to confidentiality and insurability.
CHAPTER 13 GENOMES 275
13.2 GENOME ANNOTATION FIG. 13.3 Genome annotation. Given the DNA sequence of a
genome, researchers can pinpoint locations of various
A goal of biology is to identify all the macromolecules in biological types of sequence.
systems and understand their individual functions and the ways
in which they interact. This research has practical applications:
Increased understanding of the molecular and cellular basis of Noncoding RNA
Single-copy gene
disease, for example, can lead to improved diagnosis and treatment. Dispersed repeat
The value of genome sequencing in identifying Tandem repeat
Simple-sequence repeat
macromolecules is that the genome sequence contains, in coded
form, the nucleotide sequence of all RNA molecules transcribed Double-stranded DNA
from the DNA as well as the amino acid sequence of all proteins.
There is a catch, however. A genome sequence is merely an
extremely long list of A’s, T’s, G’s, and C’s that represent the
order in which nucleotides occur along the DNA in one strand
of the double helix. (Because of complementarity, knowing the
sequence of one strand specifies the other.) The catch is that
in multicellular organisms, not all the DNA is transcribed into
RNA, and not all the RNA that is transcribed is translated into
protein. Therefore, genome sequencing is just the first step in
understanding the function of any particular DNA sequence.
Following genome sequencing, the next step is to identify the
locations and functions of the various types of sequence present
in the genome. that control transcription, the intron–exon boundaries in the
gene, and any known or predicted alternative forms in which
Genome annotation identifies various types the introns and exons are spliced (Chapter 3). Each single-copy
of sequence. gene is given a unique name and its protein product identified.
Genomes contain many different types of sequence, among Note in Fig. 13.3 that single-copy genes can differ in size from
them protein-coding genes. Protein-coding genes are themselves one gene to the next. The annotations in Fig. 13.3 also specify the
composed of different regions, including regulatory elements that locations of sequences that encode RNAs that are not translated
specify when and where an RNA transcript is produced, noncoding into proteins, as well as various types of repeated sequence. Most
introns that are removed from the RNA transcript during RNA genomes also contain some genes that are present in multiple
processing (Chapter 3), and protein-coding exons that contain copies that originate from gene duplication; however these are
the codons that specify the amino acid sequence of a polypeptide usually identifiable in the same way as single-copy genes because
chain (Chapter 4). Genomes also contain coding sequences for the copies often differ enough in sequence that they can be
RNAs that are not translated into protein (noncoding RNAs), distinguished.
such as ribosomal RNA, transfer RNA, and other types of small Small genomes such as that of HIV and other viruses can
RNA molecule (Chapter 3). Finally, while much of the DNA in the be annotated by hand, but for large genomes like the human
genomes of multicellular organisms is transcribed at least in some genome, computers are essential. In the human genome, some
cell types, the functions of a large portion of these transcripts in protein-coding genes extend for more than a million nucleotides.
metabolism, physiology, development, or behavior are unknown. Roughly speaking, if the sequence of the approximately 3 billion
Genome annotation is the process by which researchers nucleotides in a human egg or sperm was printed in normal-sized
identify the various types of sequence present in genomes. type like this, the length of the ribbon would stretch 4000 miles
Genome annotation is essentially an exercise in adding (6440 kilometers), about the distance from Fairbanks, Alaska,
commentary to a genome sequence that identifies which types to Miami, Florida. By contrast, for the approximately 10,000
of sequence are present and where they are located. It can be nucleotides in the HIV genome, the ribbon would extend a mere
thought of as a form of pattern recognition, where the patterns are 70 feet (21 meters).
regularities in sequence that are characteristic of protein-coding Genome annotation is an ongoing process because, as
genes or other types of sequence. macromolecules and their functions and interactions become
An example of genome annotation is shown in Fig. 13.3. better understood, the annotations to the genome must be
Genes present in one copy per genome are indicated in orange. updated. A sequence that is annotated as nonfunctional today
Most single-copy genes are protein-coding genes. In some may be found to have a function tomorrow. For this reason, the
computer programs that analyze genomes, the annotation of annotation of certain genomes—including the human genome—
a single-copy gene also specifies any nearby regulatory regions will certainly continue to change.
276 SECTION 13.2 G E N O M E A N N OTAT I O N
Genome annotation includes searching for sequence by itself is enough to annotate the DNA segment as potentially
motifs. protein coding. The qualifier “potentially” is necessary because
Because genome annotation is essentially pattern recognition, it ORFs identified in a DNA sequence do not necessarily code for
begins with the identification of patterns called sequence motifs, protein. For this reason they are often called putative ORFs. A
telltale sequences of nucleotides that indicate what types of function region containing a putative ORF may exist merely by chance (even
(or absence of function) may be encoded in a particular region of a random sequence of nucleotides will contain ORFs averaging
the genome (Fig. 13.4). Sequence motifs can be found in the DNA 21 codons in length); or a putative ORF may not be transcribed; or if
itself or in the RNA sequence inferred from the DNA sequence. Once a putative ORF is transcribed, it might be in a noncoding RNA or an
identified, sequence motifs are typically confirmed by experimental intron of a protein-coding RNA. In the next section, we discuss how
methods. One sequence motif we have already encountered in the analysis of messenger RNA sequences can determine whether a
Chapter 3 is a promoter, a sequence where RNA polymerase and putative ORF is an actual ORF in DNA coding for protein.
associated proteins bind to the DNA to initiate transcription. Fig. 13.4b shows another type of sequence motif, this one
Another example of a sequence motif is an open reading also present in a hypothetical RNA transcript inferred from the
frame (ORF) (Fig. 13.4a). The motif for an open reading frame is DNA sequence. The nucleotide sequence at one end of the RNA
a long string of nucleotides that, if transcribed and processed into is complementary to that at the other end, so the single-stranded
messenger RNA, would result in a set of codons for amino acids molecule is able to fold back on itself and undergo base pairing
that does not contain a stop codon. The presence of an ORF motif to form a hairpin-shaped structure. Such hairpin structures
are characteristic of certain types of RNA that function in
gene regulation (Chapter 19). The DNA from which this RNA is
FIG. 13.4 Some common sequence motifs useful in genome transcribed has complementary sequences on either end as well.
annotation. (a) An open reading frame; (b) a noncoding Some sequence motifs are detected directly in the double-
RNA molecule; (c) transcription factor binding sites. stranded DNA. Fig. 13.4c shows two copies of a short sequence
that is a known binding site for DNA-binding proteins called
transcription factors (Chapter 3), which initiate transcription.
a.
RNA from a protein-coding region Transcription factor binding sites are often present in multiple
contains an open reading frame
consisting of triplets of nucleotides
copies and in either strand of the DNA. Sometimes they are
that can specify amino acids. located near the region of a gene where transcription is initiated
because the transcription factor helps determine when the gene
5’ 3’
will be transcribed. However, they can also be located far upstream
A U G G C C C G A U A C C U G G C A A A U G A U
of the gene, downstream of the gene, or in introns, and so their
identification is difficult.
MET ALA ARG TYR LEU ALA ASN ASP
Comparison of genomic DNA with messenger RNA
reveals the intron–exon structure of genes.
b.
In annotating an entire genome, researchers typically make use of
Regions of some RNA molecules, such as information outside the genome sequence itself. This information
those in transfer RNA, form hairpin may include sequences of messenger RNA molecules that are
structures in which the molecule folds
back on itself. isolated from various tissues or various stages of development of
AG UC the organism. Recall from Chapter 3 that messenger RNA (mRNA)
5’ A A
C molecules undergo processing and are therefore usually simpler than
UG U U A A C G C G A U G A C A U G G
U the DNA sequences from which they are transcribed—for example,
A C A A U U G C G C U A C U G U A G A
C C
introns are removed and exons are spliced together. The resulting
3’ A
AU mature mRNA therefore contains a long sequence of codons
AC
uninterrupted by a stop codon—in other words, an ORF. The ORF in
an mRNA is the region that is actually translated into protein.
c. One aspect of genome annotation is the determination of
DNA sequences that bind transcription which portions of the genome sequence correspond to sequences
factors are often short sequences present in in mRNA transcripts. An example is shown in Fig. 13.5, which
multiple copies near a protein-coding gene.
compares the DNA and mRNA for the beta (b) chain of hemoglobin,
the oxygen-carrying protein in red blood cells. Note that the
genomic DNA contains some sequences present in the mRNA,
5’ 3’
which correspond to exons, and some sequences that are not
A A T G T A C T A C A T T G A A T G T A T G G C
T T A C A T G A T G T A A C T T A C A T A C C G present in the mRNA, which correspond to introns. Comparison
3’ 5’ of mRNA with genomic DNA therefore reveals the intron–exon
CHAPTER 13 GENOMES 277
of hosts? Sequencing and Analysis of the Human Genome” (PDF). Nature 409(6822): 860–921,
doi:10.1038/35057062, PMID 11237011.
APPROXIMATE
13.3 GENE NUMBER, GENOME SIZE, NUMBER OF PROTEIN-
AND ORGANISMAL COMPLEXITY COMMON NAME SPECIES NAME CODING GENES
with one another so that, even though there are relatively few
types of protein, they are capable of combining in many different TABLE 13.2 Genome Sizes of Several Organisms. Genome size
ways to perform different functions. We also have seen that varies tremendously among eukaryotic organisms, and there is no
a single gene may yield multiple proteins, either because of correlation between genome size and the complexity of an organism.
alternative splicing (different exons are spliced together to make Data from “Sequence Composition of the Human Genome” in International Human
different proteins) or posttranslational modification (proteins Genome Sequencing Consortium, 2001, “Initial Sequencing and Analysis of the Human
undergo biochemical changes after they have been translated). Genome” (PDF). Nature 409(6822): 860–921, doi:10.1038/35057062, PMID
13.4 ORGANIZATION
OF GENOMES
Regardless of whether an organism has a
large or a small genome, the genomes of
all organisms are large relative to the size
of the cell. For example, if the circular
genome of the intestinal bacterium
Escherichia coli were fully extended,
its length would be 200 times greater
the usual flow of genetic information from DNA into RNA (retro- than the diameter of the cell itself. The fully extended length
means “backward”). More than 40% of the human genome of DNA in human chromosome 1, our longest chromosome,
consists of various types of retrotransposons, whereas only about would be 10,000 times greater than the diameter of the average
3% of human DNA consists of DNA transposons. human cell. There is consequently a need to package an enormous
Over the course of evolutionary time, the amount of repetitive length of DNA into a form that will fit inside the cell while still
DNA in a genome can change drastically, in large part because allowing the DNA to replicate and carry out its coding functions.
The mechanism of packaging differs substantially in bacteria,
archaeons, and eukaryotes. We focus here on bacteria and
FIG. 13.10 Sequence composition of the human genome. eukaryotes, primarily because less is known about how DNA is
packaged in archaeons.
Miscellaneous category:
unrecognized, ambiguously
annotated, or nonfunctional Bacterial cells package their DNA as a nucleoid
gene duplicates Untranslated composed of many loops.
5’ ends of mRNA Bacterial genomes are circular, and the DNA double helix is
Untranslated underwound, which means that it makes fewer turns in going
3’ ends of mRNA
around the circle than would allow every base in one strand to
pair with its partner base in the other strand. Underwinding is
sa Other caused by an enzyme, topoisomerase II, that breaks the double
te
llit ding
DN es Co helix, rotates the ends to unwind the helix, and then seals the
A tr
ans break. Underwinding creates strain on the DNA molecule, which
pos
ons
is relieved by the formation of supercoils, in which the DNA
Protein- molecule coils on itself. Supercoiling allows all the base pairs to
Introns coding
genes form, even though the molecule is underwound. (You can make
(about your own supercoil by stretching and twirling the ends of a rubber
Retrotransposons 25,000) band, then relaxing the stress slightly to allow the twisted part to
form coils around itself. See Fig. 3.12.) Supercoils that result from
underwinding are called negative supercoils, and those that result
from overwinding are positive supercoils. In most organisms, DNA
is negatively supercoiled.
282 SECTION 13.4 O RG A N I Z AT I O N O F G E N O M E S
In bacteria, the supercoils of DNA form a structure with packaging. First, eukaryotic DNA is wrapped twice around a group
multiple loops called a nucleoid (Fig. 13.11). The supercoil loops of histone proteins called a nucleosome. A nucleosome is made
are bound together by proteins. In E. coli, the nucleoid has about up of eight histone proteins: two each of histones H2A, H2B,
100 loops, each containing about 50 kb of DNA. The protein H3, and H4. The histone proteins are rich in the amino acids
binding that forms the loops as well as the negative supercoiling of lysine and arginine, whose positive charges are attracted to the
the DNA compress the molecule into a compact volume. negative charges of the phosphates along the backbone of each
DNA strand.
Eukaryotic cells package their DNA as one molecule This first level of packaging of the DNA is sometimes referred
per chromosome. to as “beads on a string,” with the nucleosomes the beads and
In eukaryotic cells, DNA in the nucleus is packaged differently the DNA the string. It is also called a 10-nm fiber in reference to
from DNA in bacteria. As discussed in Chapter 3, eukaryotic DNA its diameter, which is about five times the diameter of the DNA
is linear and each DNA molecule forms a single chromosome. In double helix (Fig. 13.12). In general, these are areas of the genome
a chromosome, DNA is packaged with proteins to form a DNA- that are transcriptionally active.
protein complex called chromatin. There are several levels of The next level of packaging occurs when the chromatin is
more tightly coiled, forming a 30-nm fiber (Fig. 13.12). As the
chromosomes in the nucleus condense in preparation for cell
FIG. 13.11 Bacterial nucleoid. The circular bacterial chromosome division, each chromosome becomes progressively shorter and
twists on itself to form supercoils, which are anchored thicker as the 30-nm fiber coils onto itself to form a 300-nm coil, a
by proteins. Source. Dr. Klaus Boller/Science Source. 700-nm coiled coil, and finally a 1400-nm condensed chromosome
Nucleoid in a manner that is still not fully understood. The progressive
packaging constitutes chromosome condensation, an active,
energy-consuming process requiring the participation of several
types of proteins.
Greater detail of the structure of a fully condensed chromosome
is revealed when the histones are chemically removed (Fig. 13.13).
Without histones, the DNA spreads out in loops around a sup-
porting protein structure called the chromosome scaffold. Each
loop of relaxed DNA is 30 to 90 kb long and anchored to the scaffold
Bacterium at its base. Before removal of the histones, the loops are compact
and supercoiled. Each human chromosome contains 2000–8000
such loops, depending on its size.
In E. coli, the nucleoid Core region Protein Despite intriguing similarities between the nucleoid model
consists of about 100 in Fig. 13.11 and the chromosome scaffold model in Fig. 13.13, the
loops, each with about Supercoiled DNA
50 kb of negatively structures evolved independently and make use of different types
supercoiled DNA. of protein to bind the DNA and form the folded structure of DNA
and protein. Furthermore, the size of the eukaryotic chromosome
is vastly greater than the size of the bacterial nucleoid. To
appreciate the difference in scale, keep in mind that the volume of
a fully condensed human chromosome is five times larger than the
volume of a bacterial cell.
FIG. 13.12 Levels of chromosome condensation. DNA is wrapped around nucleosomes to form a 10-nm fiber, which can become coiled into a
30-nm fiber and higher-order structures.
6 Condensed chromatid
1400 nm in diameter
5 Coiled coil
700 nm in
diameter
3 Chromatin fiber
30 nm in diameter
Histone
proteins
Nucleosome
2 Nucleosome fiber
10 nm in diameter
1 DNA duplex
2 nm in diameter
284 SECTION 13.4 O RG A N I Z AT I O N O F G E N O M E S
FIG. 13.13 (a) A chromosome with histones and (b) a FIG. 13.14 A chromosome paint of chromosomes from a
chromosome depleted of histones, showing the human male. (a) Condensed chromosomes are
underlying scaffold. Source: Courtesy of Ulrich Laemmli. “painted” with fluorescent dyes. (b) Chromosomes
are arranged in the standard form of a karyotype.
Relaxed DNA after
DNA with histones histones removed Source: NHGRI, www.genome.gov.
Chromosome Scaffold
b
come in pairs holds up pretty well, with the exception of the 13.5 VIRUSES AND VIRAL GENOMES
sex chromosomes. Polyploids, too, are an exception, but even
in naturally occurring polyploids the number of copies of each Now we come to viral genomes—but not because they are
homologous chromosome is usually an even number, so there are particularly complex. Viral genomes are actually rather small and
pairs of homologs after all. compact with little or no repetitive DNA, and their sequences are
The occurrence of chromosomes in pairs allows eukaryotes to relatively easy to assemble, as we have seen in Fig. 13.7 for HIV.
reproduce sexually. When reproductive cells are formed during What sets viral genomes apart from those of cellular organisms
meiotic cell division, each cell receives one and only one copy of are the types of nucleic acid that make up their genomes and the
each of the pairs of homologous chromosomes (Chapter 11). When manner in which these genomes are replicated in the infected
reproductive cells from two individuals fuse to form an offspring cells. In their nucleic-acid composition and manner of replication,
cell, the chromosome number characteristic of the species is viral genomes are far more diverse than the genomes of cellular
reconstituted. organisms: All cellular organisms have genomes of double-stranded
DNA that replicate by means of the processes described in Chapter
Organelle DNA forms nucleoids that differ from 12. Not so with viruses. Furthermore, whereas biologists classify
those in bacteria. cellular organisms according to their degree of evolutionary
Most eukaryotic cells contain mitochondria, and many relatedness, they classify viruses based on their type of genome
contain chloroplasts. Each type of organelle has its own DNA, and mode of replication.
meaning that eukaryotic cells have multiple genomes. Each We mostly think of viruses as causing disease, and indeed
eukaryotic cell has a nuclear genome consisting of the DNA they do. Familiar examples include influenza (“flu”), polio, and
in the chromosomes. Cells with mitochondria also have a HIV. In some cases, they cause cancer (Case 2: Cancer). In fact, the
mitochondrial genome, and those with chloroplasts also have a term “virus” comes from the Latin for “poison.” But viruses play
chloroplast genome. other roles as well. Some viruses transfer genetic material from
Because the genome organization and mechanisms of protein one cell to another. This process is called horizontal gene transfer
synthesis in these organelles resemble those of bacteria, most to distinguish it from parent-to-offspring (vertical) gene transfer.
biologists subscribe to the theory that the organelles originated Horizontal gene transfer has played a major role in the evolution
as free-living bacterial cells that were engulfed by primitive of bacterial and archaeal genomes, as well as in the origin and
eukaryotic cells billions of years ago (Chapter 27). In Chapters 7 spread of antibiotic-resistance genes (Chapter 26). Molecular
and 8, we saw that the likely ancestor of mitochondria resembled biologists have learned to make use of this ability of viruses to
a group of today’s non-photosynthetic bacteria (a group that deliver genes into cells.
includes E. coli), and the likely ancestor of chloroplasts resembled In this section, we focus on viral diversity with an emphasis
today’s photosynthetic cyanobacteria. In both cases, the DNA on viral genomes. Thousands of viruses have been described in
286 SECTION 13.5 V I RU S E S A N D V I R A L G E N O M E S
detail, and probably millions more have yet to be discovered. It has and partially single-stranded, or single-stranded RNA or DNA with
been estimated that life on Earth is host to 1031 virus particles— a positive (1) or negative (2) sense. The sense of a nucleic acid
ten hundred thousand million more virus particles than grains molecule is positive if its sequence is the same as the sequence of
of sand! Most of these viruses infect bacteria, archaeons, and the mRNA that is used for protein synthesis, and negative if it is
unicellular eukaryotes, and they are they are especially abundant the complementary sequence. For example, a (1)RNA strand
in the ocean (1011 viruses per liter). Viruses are small, consisting has the same nucleotide sequence as the mRNA, whereas a (2)
of little more than a genome in a package, and they can reproduce RNA strand has the complementary sequence. Similarly, a (1)
only by hijacking host-cell functions, but as a group they have had DNA strand has the same sequence as the mRNA, and a (2)DNA
amazing evolutionary success. strand has the complementary sequence (except that U in RNA
is replaced with T in DNA). Because mRNA is synthesized from
Viruses can be classified by their genomes. a DNA template, it is the (2)DNA strand that is used for mRNA
The genomes of viruses are diverse. Some genomes are composed synthesis (Chapter 3).
of RNA and others of DNA. Some are single stranded, others are Two groups synthesize mRNA by the enzyme reverse
double stranded, and still others have both single- and double- transcriptase, and therefore are placed into their own groups
stranded regions. Some are circular and others are made up of a (VI and VII). Reverse transcriptase is an RNA-dependent DNA
single piece or multiple linear pieces of DNA (called linear and polymerase that uses a single-stranded RNA as a template to
segmented genomes, respectively). synthesize a DNA strand that is complementary in sequence to
Unlike forms of cellular life, there is no evidence that all the RNA (Fig. 13.16). The reverse transcriptase then displaces
viruses share a single common ancestor. Different types of the RNA template and replicates the DNA strand to produce a
virus may have evolved independently more than once. Since double-stranded DNA molecule that can be incorporated into
classification of viruses based on evolutionary relatedness is not the host genome. In synthesizing DNA from an RNA template,
possible, other criteria are necessary. One of the most useful the enzyme reverses the usual flow of genetic information from
classifications is the type of nucleic acid the virus contains DNA to RNA. This capability is so unusual and was so unexpected
and how the messenger RNA, which produces viral proteins, is that many molecular biologists at first doubted whether such
synthesized. The classification is called the Baltimore system after an enzyme could exist. Finally the enzyme was purified and its
David Baltimore, who devised it. properties verified, for which its discoverers, Howard Temin and
According to the Baltimore system, there are seven major David Baltimore, were awarded the Nobel Prize in Physiology or
groups of viruses, designated I–VII, as shown in Fig. 13.16. These Medicine in 1975, shared with Renato Dulbecco.
groups are largely based on whether their nucleic acid is double- As we saw earlier, genome size varies greatly among different
stranded DNA, double-stranded RNA, partially double-stranded viruses. RNA viral genomes tend to be smaller than DNA viral
FIG. 13.16 The Baltimore system of virus classification. This system classifies viruses by type of nucleic acid and the way mRNA is produced.
FIG. 13.18 Virus structures. Viruses come in a variety of shapes, including (a) the head-and-tail structure of a bacteriophage, (b) the helical
shape of tobacco mosaic virus, and (c) the icosahedral shape of adenovirus. Sources: a. Dept. of Microbiology, Biozentrum/Getty Images; b. Biology
Pics/Science Source; c. BSIP/Science Source.
a b c
Core Concepts Summary Eukaryotic cells package their DNA into linear
chromosomes. page 282
13.1 A genome is the genetic material of a cell,
DNA in eukaryotes is wound around groups of histone
organism, organelle, or virus, and its sequence is the
proteins called nucleosomes to form a 10-nm fiber, which
order of bases along the DNA or (in some viruses)
in turn coils to form higher-order structures, such as the
RNA.
30-nm fiber. page 282
The sequence of an organism’s genome can be determined by
Diploid organisms have two copies of each chromosome,
breaking up the genome into small fragments, sequencing
called homologous chromosomes. page 284
these fragments, and then putting the sequences together at
their overlaps. page 272 Humans have 23 pairs of chromosomes, including the X
and Y sex-chromosome pair. Females are XX and males
Sequences that are repeated in the genome can make
are XY. page 284
sequence assembly difficult. page 273
The genomes of mitochondria and chloroplasts are
13.2 Researchers annotate genome sequences to organized into nucleoids that resemble, but are distinct
identify genes and other functional elements. from, those of bacteria. page 285
The annotated HIV genome shows it is a retrovirus, and it Viruses are capable of molecular self-assembly under the
contains the genes gag, pol, and env. page 277 appropriate conditions. page 288
6. What are some reasons why, in multicellular eukaryotes, 10. Describe the steps necessary to synthesize mRNA from
genome size is not necessarily related to number of each of the following: double-stranded DNA, single-
protein-coding genes or organismal complexity? stranded (1)DNA, single-stranded (2)DNA, single-
stranded (1)RNA, and single-stranded (2)RNA.
7. Compare and contrast the mechanisms by which bacterial
cells and eukaryotic cells package their DNA.
8. Draw a nucleosome, indicating the positions of DNA and Log in to to check your answers to the Self-
proteins. Assessment questions, and to access additional learning tools.
Mutation and
DNA Repair
Core Concepts
14.1 Mutations are very rare for
any given nucleotide and
occur randomly without
regard to the needs of an
organism.
14.2 Small-scale mutations
include point mutations,
insertions and deletions,
and movement of
transposable elements.
14.3 Chromosomal mutations
involve large regions of one
or more chromosomes.
14.4 DNA can be damaged by
mutagens, but most DNA
damage is repaired.
291
292 SECTION 14.1 T H E R AT E A N D N AT U R E O F M U TAT I O N S
amounts of genetic variation, that is, different nucleotides at the “Rates of Spontaneous Mutation,” Genetics 148:1667–1686.
same site in the genome. The reference human genome sequence 10–3
is actually a composite of several genomes, displaying the most
RNA viruses
common nucleotide at most sites. 10–4 and retroviruses
Variation among different individuals’ genomes arise from
round of replication
10–6
cell division, mitotic cell division, or binary fission). The process
by which mutations occur is fundamental in biology because 10–7
mutation is the ultimate source of genetic variation. Genetic
DNA viruses
variation accounts in part for the physical differences we see
10–8
among individuals, such as differences in hair color, eye color, and
height. And, on a much larger scale, genetic variation results in the
10–9 Bacteria
diversity of organisms on this planet, from bacteria to blue whales. Fruit fly
Mouse
There are many different types of mutation, from small Yeast Nematode
10–10
changes affecting a single base to larger alterations, such as the
Bread mold Human
duplication or deletion of a segment of a chromosome. In this
10–11
chapter, we examine some of the basic principles of mutation: 104 105 106 107 108 109 1010
the different types of mutation, how and when they occur, and Genome size (base pairs)
how they are repaired. In Chapter 15, we look at common types
of mutation, or genetic variation, present in populations, and, in
Chapters 16 and 17, at how this variation is inherited from one
generation to the next. of one nucleotide pair for a different nucleotide pair. Nucleotide-
substitution mutations are nevertheless relatively rare, and their
rate of occurrence differs among organisms. Fig. 14.1 compares
14.1 THE RATE AND NATURE the rates of newly arising mutations in a given base pair in a single
OF MUTATIONS round of replication in viruses and several types of organisms.
Most of these mutations are due to errors in replication. As seen in
Mutations result from mistakes in DNA replication or from the graph, the mutation rates for different organisms range across
unrepaired damage to DNA. The damage may be caused by reactive almost eight orders of magnitude.
molecules produced in the normal course of metabolism, by The highest rates of mutation per nucleotide per replication
chemicals in the environment, or by radiation of various types, are found among RNA viruses and retroviruses, including HIV.
including X-rays and ultraviolet light. Most genomes also contain Lower rates occur in DNA viruses, and even lower rates in
DNA sequences that can “jump” from one position to another in unicellular organisms such as bacteria and yeast. The rates of
the genome, and their insertion into or near genes is a source of mutation per nucleotide per DNA replication are nearly the same
mutation. Yet another source of mutation is incorrectly repaired for all multicellular animals, including mice and humans.
chromosome breaks caused by reactive chemicals or radiation. Mutation rates vary over a large range for a number of
Most mutations are spontaneous, occurring by chance reasons. RNA viruses and retroviruses have a relatively high rate
in the absence of any assignable cause. They occur randomly, of mutation because RNA is a less stable molecule than DNA,
unconnected to an organism’s needs—it makes no difference but more importantly because the replication of these genomes
whether or not a given mutation would benefit the organism. lacks a proofreading function. For the other genomes, the rate of
Whether a favorable mutation does or does not occur is purely mutation per nucleotide per DNA replication reflects differences
a matter of chance. This key principle, that mutations are in fidelity of replication and the efficiency of proofreading and
spontaneous and random, is the focus of this section. other mechanisms of DNA repair.
For the cellular organisms plotted in Fig. 14.1, the average
For individual nucleotides, mutation is a rare event. mutation rate is about 10210, which means that, on average,
We’ll see later in this chapter that there are several different types only 1 nucleotide in every 10 billion is mistakenly substituted
of mutation, but the most common mutation is the substitution for another.
CHAPTER 14 M U TAT I O N A N D D N A R E PA I R 293
But averaging conceals many details. First, certain nucleotides per replication (Fig. 14.1), humans also have the largest rate of
are especially prone to mutation and can exhibit rates of mutation mutation per genome per generation (Fig. 14.2). This seeming
that are greater than the average by a factor of 10 or more. Sites paradox arises because humans have a large genome and undergo
in the genome that are especially mutable are called hotspots. many cell divisions per generation.
Second, in some multicellular organisms, the rates of mutation In humans, the average number of newly arising nucleotide-
differ between the sexes. In humans, for example, the rate of substitution mutations per genome in one generation is about
mutation is substantially greater in males than in females. Finally, 30, or about 60 per diploid zygote. However, about 80% of the
the rates for the multicellular animals plotted in Fig. 14.1 depend newly arising mutations in a zygote come from the father. This
on the type of cell: A distinction must be made between mutations is because, in a human male at age 30, the diploid germ cells
that occur in germ cells (haploid gametes and the diploid cells have gone through about 400 cycles of DNA replication and cell
that give rise to them) and mutations that occur in somatic cells division before meiosis takes place, as compared with about
(the other cells of the body). In mammals, the rate of mutation 30 cycles in females. Moreover, while the number of newly arising
per nucleotide per replication is greater in somatic cells than in mutations from the mother remains approximately constant
germ cells. with mother’s age, the number of newly arising mutations from
the father increases with age. Sperm from men of age 40 contain
Across the genome as a whole, mutation is common. about twice as many newly arising mutations as sperm from men
We can also look at mutation rate at another level of scale. of age 20.
Instead of considering the rate per nucleotide per replication, Such a large number of new mutations as occurs in the
we can examine the rate of mutation across an entire genome human genome in one generation would be intolerable in
in one generation. While it is clear from Fig. 14.1 that the rate of organisms with a high density of protein-coding genes, such as
mutation per nucleotide per replication in most multicellular bacteria or fungi. It is tolerable in humans and other mammals
organisms is low, the rate of mutation per genome per generation only because more than 90% of the nucleotides in the genome
depends on the size of the genome and the number of cell seem free to vary without deleterious consequences for the
divisions per generation. Taking into account genome size and organism, and a mere 2.5% of the genome code for protein
cell divisions per generation, the rate of new mutations across the (Chapter 13). The vast majority of newly arising mutations
whole genome per generation is shown in Fig. 14.2. Note that, therefore occur in noncoding DNA and are likely neutral or very
while humans have the smallest rate of mutation per nucleotide nearly neutral in their effects. It is these mutations, accumulated
through many generations and shuffled by recombination and
independent assortment (Chapter 11), that account for the
genetic diversity of most populations and the genetic uniqueness
FIG. 14.2 Rate of mutation per genome per generation. Data of each individual.
from: J. W. Drake, B. Charlesworth, D.Charlesworth, J. F. Crow, 1998,
“Rates of Spontaneous Mutation,” Genetics 148:1667–1686. Only germ-line mutations are transmitted to progeny.
100 Which is more important—the rate of mutation per nucleotide
per replication or the rate per genome per generation? That
Rate of mutation per genome per generation
a polyp. Another chance mutation in the same cell line, which now
carries mutations in both the APC and Ras genes, could lead to
malignant cancer. Normally, the occurrence of multiple mutations
in a single cell lineage is rare, but in people exposed to chemicals
that cause mutations or who carry mutations in DNA repair
processes, multiple mutations in a single cell lineage are more
likely to occur and so the risk of cancer is increased.
own particular sequence of mutations, although mutations in alcohol. While we may not be able to do much about the genetic
some genes are implicated in several different types of cancer. An risk factors for any of these conditions, knowing that we have
example is the p53 gene, the nonmutant product of which detects them may make us more careful about the lifestyle choices that
DNA damage and slows the cell cycle to allow time for DNA repair we make.
(Chapter 11). Mutations in p53 are one step in the mutational
Mutations are random with regard to an
progression of many different types of cancer, including colon
organism’s needs.
cancer and breast cancer.
How do mutations arise? Consider the following example: If
In most individuals with cancer, all the sequential mutations
an antibiotic is added to a liquid culture of bacterial cells that
that cause the cancer are spontaneous mutations that take place
are growing and dividing, most of the cells are killed, but a few
in somatic cells. They are not transmitted through the germ line,
survivors continue to grow and divide. These survivors are found
and so there is little or no increased risk of cancer in the offspring.
to contain mutations that confer resistance to the antibiotic.
In some families, however, there is a germ-line mutation in one
This simple observation raises a profound question. Does this
of the genes implicated in cancer that is transmitted from parents
experiment reveal the presence of individual bacteria with
to their children. In any child who inherits the mutation, all
mutations that had arisen spontaneously and were already
cells in the body contain the defective gene, and hence the cells
present? Or do the antibiotic-resistant mutants arise in response
already have taken one of the mutational steps that lead to cancer.
to the presence of the antibiotic?
The effect of such a germ-line mutation is therefore to reduce
These alternative hypotheses have deep implications for
the number of additional mutations that would otherwise be
all of biology because they suggest two very different ways in
necessary to produce cancer cells.
which mutations might arise. The first suggests that mutations
Any mutation that increases the risk of disease in an
occur without regard to the needs of an organism. According
individual is known as a genetic risk factor for that disease.
to this hypothesis, the presence of the antibiotic in the
For colon cancer, the major genetic risk factors are mutations
experiment with bacterial cells does not direct or induce
in APC, Ras, and p53. For breast cancer, the major genetic risk
antibiotic resistance in the cells, but instead allows the small
factors are mutations in the BRCA1 and BRCA2 genes (Case 3:
number of preexisting antibiotic-resistant mutants to flourish.
You, from A to T). A risk factor does not cause the disease, but it
The second hypothesis suggests that there is some sort of
makes the disease more likely to occur. For the genes implicated
feedback between the needs of an organism and the process of
in colon cancer, each is a risk factor because when it is mutated,
mutation, and the environment directs specific mutations that
fewer additional mutations are needed to bring about tumor
are beneficial to the organism.
growth.
To distinguish between these two hypotheses, Joshua and
The DNA sequence of each of our personal genomes can reveal
Esther Lederberg in 1952 carried out a now-famous experiment,
the genetic risk factors that each of us carries, not only for cancer
described in Fig. 14.5. Bacterial cells were grown and formed
but for many other diseases as well. Not all genetic risk factors are
colonies on agar plates in the absence of antibiotic. Then, using
known for all diseases, and a great deal of current research aims
replica plating, a technique they invented, the Lederbergs
to identify new ones. But many genetic risk factors are already
transferred these colonies to new plates containing antibiotic.
known for a large number of common diseases, including high
Only bacteria that were resistant to the antibiotic grew on the
blood pressure, diabetes, inflammatory bowel disease, age-related
new plates. Because replica plating preserved the arrangement of
macular degeneration, Alzheimer’s disease, and many forms of
the colonies, the Lederbergs were able to go back to the original
cancer. Therefore, your personal genome can be of great value in
plate and identify the colony that produced the antibiotic-resistant
identifying diseases for which you carry risk factors, as was the
colony on the replica plate. From that original colony, they were
case for Claudia Gilmore (Case 3: You, from A to T).
then able to isolate a pure culture of antibiotic-resistant bacteria.
Our personal genomes can identify only genetic risk
Replica plating allowed the Lederbergs to isolate a pure culture
factors, however. In many cases, disease risk is substantially
of antibiotic-resistant bacteria, even though the original bacteria
increased by environmental risk factors as well, especially
never were exposed to antibiotic. This result supported the first
lifestyle choices. While there are genetic risk factors for lung
hypothesis: Mutations occur randomly, and without regard to
cancer, for example, the single biggest environmental risk factor
the needs of the organisms. The role of the environment is not
is smoking tobacco. For skin cancer, the greatest environmental
to create specific mutations, but instead to select for them. The
risk factor is exposure to the damaging ultraviolet rays in sunlight
principle the Lederbergs demonstrated is true of all organisms so
or in the sunlamps used in tanning beds. For heart disease, it is
far examined.
smoking, lack of physical activity, and obesity. For diabetes, it
is an unhealthy diet. j Quick Check 1 If mutations occur at random with respect to an
For breast cancer, the environmental risk factors include organism’s needs, how does a species become more adapted to its
certain forms of hormone therapy, lack of physical activity, and environment over time?
HOW DO WE KNOW?
FIG. 14.5
Do mutations occur randomly, METHOD To distinguish between these two hypotheses, Joshua
and Esther Lederberg developed replica plating. In this technique,
or are they directed by the bacteria are grown on agar plates, where they form colonies
(Fig. 14.5a). The cells in any one colony result from the division of
environment? a single original cell, and thus they constitute a group of cells that
are genetically identical except for rare mutations that occur in the
course of growth and division. Then a disk of sterilized velvet is
BACKGROUND Researchers have long observed that beneficial pressed onto the plate. Cells from each colony stick to the velvet
mutations tend to persist in environments where they are useful—in disk (in mirror image, but the relative positions of the colonies are
the presence of antibiotic, bacterial populations become antibiotic preserved). The disk is then pressed onto the surface of a fresh
resistant; in the presence of insecticides, insect populations become plate, transferring to the new plate a few cells that originate from
insecticide resistant. each colony on the first agar plate, in their initial positions.
HYPOTHESIS These observations lead to two hypotheses about EXPERIMENT First, the Lederbergs grew bacterial colonies on
how a mutation, such as one that confers antibiotic resistance medium without antibiotic, called a nonselective medium because
on bacteria, might arise. The first suggests that mutations occur all cells are able to grow and form colonies on it. Then, by replica
randomly in bacterial populations and over time become more plating, they transferred some cells from each colony to a plate
common in the population in the presence of antibiotic (which containing antibiotic, so only antibiotic-resistant cells could multiply
destroys those bacteria without the mutation). In other words, they and form colonies. (Medium containing antibiotic is a selective
occur randomly with respect to the needs of an organism. The second medium because it “selects” for a particular attribute or element, in
hypothesis suggests that the environment, in this case the application this case antibiotic-resistant cells.) Because replica plating preserves
of antibiotic, induces or directs antibiotic resistance. the arrangement of the colonies, the location of an antibiotic-
a. resistant colony on the selective medium reveals the location of
its parental colony on the nonselective plate (Fig. 14.5b). Finally,
the Lederbergs were able to go back to the parental colony and
demonstrate that it was a pure culture of antibiotic-resistant bacteria
by plating cultures of this colony on selective medium (Fig. 14.5c).
296
CHAPTER 14 M U TAT I O N A N D D N A R E PA I R 297
14.2 SMALL-SCALE MUTATIONS FIG. 14.6 A point mutation. A point mutation is a change in a
single nucleotide.
At the molecular level, a mutation is a change in the nucleotide
sequence of a genome. Such changes can be small, affecting one A G is erroneously
incorporated into the
or a few bases, or large, affecting entire chromosomes. We begin
daughter strand
by considering the origin and effects of small-scale changes to the opposite the T and is
DNA sequence. While mutation provides the raw material that not corrected by the
proofreading function. G T C T A A T
allows evolution to take place, it can play this role only because of C A G A T T A
an important feature of living systems: Once a mutation has taken
place in a gene, the mutant genome is replicated as faithfully as the
nonmutant genome. G T C T A A T Second round of
C A G G T T A DNA replication
Transcription
FIG. 14.9 Effect of a single amino acid deletion in CFTR, the mRNA
cystic fibrosis transmembrane conductance regulator. C C U C G A GG A G A A GU C UG C C
Translation
a. Nonmutant CFTR b. Mutant CFTR
PRO ARG GLY GLU VAL CYS Protein
A T C T T T GG T A T T GG T
T A G A A A C C A T A A C C A DNA An insertion or deletion that is not an exact
multiple of three nucleotides changes the
reading frame of translation. Such a mutation
Transcribed
Transcription is called a frameshift mutation.
strand
mRNA
A U C UUUGGU AUUGGU
Translation The result is unintelligible. Similarly, an insertion of a single
nucleotide causes a one-nucleotide shift in the reading frame
ILE PHE GLY ILE GLY Protein
of the mRNA, and it changes all codons following the site of
Missing amino acid (PHE) insertion. For this reason, such mutations are called frameshift
In the most common mutant mutations.
proteins, three nucleotides Fig. 14.10 shows the consequences of a frameshift mutation in
are deleted in the CFTR the b-globin gene. The normal sequence in Fig. 14.10a corresponds
gene, resulting in a missing
amino acid at position 508. to amino acids 5–10. The frameshift mutation in Fig. 14.10b is
Chloride ions caused by the insertion of a C–G base pair. The mRNA transcript
of the DNA therefore also has a single-base insertion. When this
mRNA is translated, the one-nucleotide shift in the reading frame
CFTR results in an amino acid sequence that has no resemblance to
transporter
the original protein. All amino acids downstream of the site of
insertion are changed, resulting in loss of protein function.
Some mutations are due to the insertion of a all organisms contain several types of transposable element, each
transposable element. present in multiple copies per genome.
An important source of new mutations in many organisms is the Transposable elements were discovered by American geneticist
insertion of movable DNA sequences into or near a gene. Such Barbara McClintock in the 1940s (Fig. 14.11). She studied corn
movable DNA sequences are called transposable elements or (maize) because genetic changes that affect pigment formation
transposons. As we saw in Chapter 13, the genomes of virtually can be observed directly in the kernels. The normal color of
HOW DO WE KNOW?
FIG. 14.11
What causes sectoring in corn mutant yellow kernels reverted to normal purple, resulting in purple
sectors in an otherwise yellow kernel. From this observation, she
kernels? inferred that the Ds element had jumped out of the anthocyanin
gene, restoring its function. She also demonstrated that restoration
of the original purple color was associated with mutations
BACKGROUND In the late 1940s, Barbara McClintock discovered elsewhere in the genome. From this observation, she inferred that
what are now called transposable elements, DNA sequences that the Ds element had integrated elsewhere in the genome, where it
can move from one position to any other in the genome. She studied disrupted the function of another gene.
corn (Zea mays). Wild-type corn has purple kernels, resulting
CONCLUSION McClintock’s conclusion is illustrated in Fig.
from expression of purple anthocyanin pigment (Fig. 14.11a). A
14.11c: Transposable elements can be excised from their original
mutant with yellow kernels results from lack of purple anthocyanin
position in the genome and inserted into another position.
pigment. McClintock noticed that streaks of purple pigmentation
could be seen in many yellow kernels (Fig. 14.11b). This observation c.
indicated that the mutation causing yellow color was unstable and Transposition
that the gene could revert to the normal purple color. Transposable
element
Transposable
a b
elements can disrupt
the normal function
of a gene.
Transposable
element excised When a transposable
element is removed,
the function of the
Photo sources: a. photo_journey/Shutterstock; b. Rob Martienssen, Cold Spring Harbor original gene (dark
Laboratory. blue) can be restored.
HYPOTHESIS McClintock hypothesized that the yellow mutant FOLLOW-UP WORK McClintock won the Nobel Prize in
color resulted from a transposable element, which she called Physiology or Medicine in 1983. Later experiments showed
Dissociator (Ds), jumping into a site near or in the anthocyanin gene that Ds is a transposable element that lacks a functional gene for
and disrupting its function. She attributed the purple streaks to cell transposase, the protein needed for the element to move, and
lineages in which the transposable element had jumped out again, Ac is a transposable element that encodes transposase. Presence
restoring the anthocyanin gene. of Ac produces active transposase that allows Ds to move. Much
additional work showed that there are many different types
EXPERIMENT AND RESULTS By a series of genetic crosses,
of transposable element and that they are ubiquitous among
McClintock showed that the genetic instability of Ds was due
organisms.
to something on another chromosome that she called Activator
(Ac). She set up crosses in which she could track the Ac-bearing SOURCE McClintock, B. 1950. “The Origin and Behavior of Mutable Loci in
chromosome. She observed that in the presence of Ac, cells in Maize.” Proceedings of the National Academy of Sciences of the USA. 36:344–355.
CHAPTER 14 M U TAT I O N A N D D N A R E PA I R 301
maize kernels is purple. Each kernel consists of many cells, and pasted at various sites in the genome, potentially disrupting the
if no mutations affecting pigmentation occur in a kernel, it will function of many different genes.
be uniformly purple. The kernel pigments are synthesized by
several different enzymes in a metabolic pathway, and any of
these enzymes can be rendered nonfunctional by mutations in 14.3 CHROMOSOMAL MUTATIONS
their genes, including the insertion of transposable elements.
Since McClintock’s work, we have learned that most transposable Whereas most mutations involve only one or a few nucleotides,
elements are segments of DNA a thousand or more base pairs long. some affect larger regions extending over hundreds of thousands
When such a large piece of DNA inserts into a gene, it can interfere or millions of nucleotides and have effects on chromosome
with transcription, cause errors in RNA processing, or disrupt the structure that are often large enough to be visible through an
open reading frame. The result in the case of maize is that the cell ordinary optical microscope. Double-stranded breaks in DNA that
is unable to produce pigment, and so the kernels will be yellow. are incorrectly repaired can lead to chromosomal mutations. The
Among mutants affecting kernel pigmentation, McClintock breaks may result from interactions between DNA and reactive
observed certain mutants that resulted in kernels that were molecules produced in metabolism or from reactive chemicals in
mostly yellow but speckled with purple. She suspected that these the environment or by radiation (especially X-rays). Chromosomal
particular mutants might result from a transposable element mutations can also arise from errors in DNA replication,
jumping into and out of a gene. Each colored sector consists of particularly in sequences that are tandemly repeated along the
a lineage of daughter cells from a single ancestral cell in which DNA (Chapter 13).
pigment synthesis had been restored. McClintock realized that, Chromosomal mutations can delete or duplicate regions of a
just as the inability of the kernel cells to produce pigment was chromosome containing several or many genes, and the resulting
caused by a transposable element jumping into a gene, restoration change in gene copy number also changes the amount of the
of that ability could be caused by the transposable element products of these genes in the cell. Chromosomal mutations
jumping out again. Her hypothesis that transposable elements are can also alter the linear order of genes along a chromosome or
responsible for the pigment mutations was confirmed when she interchange the arms of nonhomologous chromosomes. While
found that in cells where pigment had been restored, mutations these types of chromosomal mutations do not change gene copy
affecting other genes had also occurred. She deduced that these number, they do affect chromosome pairing and segregation in
other mutations were due to a transposable element jumping out meiosis. These effects distinguish chromosome abnormalities
of a pigment gene and into a different gene in the same cell. from nucleotide substitutions, small-scale deletions and
The movement, or transposition, of transposable elements duplications, transpositions, and other submicroscopic mutations.
occurs by different mechanisms according to the type of transposon In this section, we briefly consider the major types of chromosome
(Chapter 13). McClintock’s original discovery was of a DNA abnormalities in more detail.
transposon that transposes by a cut-and-paste mechanism in which
the transposon is cleaved from its original location in the genome Duplications and deletions result in gain or loss
by a specific enzyme (transposase) and inserted into a different of DNA.
position. Removal of the transposon from its original position and Among the most common chromosomal abnormalities are those
repair of the cleavage leads to restoration of gene function, which in which a segment of the chromosome is either present in two
in McClintock’s experiment was the ability to produce purple copies or is missing altogether (Fig. 14.12). A chromosome in
pigment. Unstable mutations due to DNA transposons can occur in which a region is present twice instead of once is said to contain a
almost any organism, including the Japanese morning glory, whose duplication (Fig. 14.12a). Although large duplications that include
sectored flowers are shown in Fig. 14.3. hundreds or thousands of genes are usually harmful and quickly
Not all transposons undergo transposition by a cut-and- eliminated from the population, small duplications including only
paste mechanism. As discussed in Chapter 13, retrotransposons
undergo transposition by an RNA intermediate, and when these
types of transposable elements move, the retrotransposon FIG. 14.12 Duplication and deletion. (a) In a duplication, a
used as a template for transcription stays behind in its original segment of chromosome is repeated. (b) In a deletion,
location. This mode of transposition might be called a copy-and- a segment of chromosome is missing.
paste mechanism. It is mediated by two enzymes. One is reverse
transcriptase (Chapter 13), which produces a double-stranded DNA Normal chromosome
copy of the retrotransposon from its RNA transcript, much in the
same way that reverse transcriptase produces double-stranded
DNA from viral RNA genomes. The other enzyme is an integrase,
which cuts genomic DNA and inserts the retrotransposon at the a. Duplication b. Deletion
cut site. By this mechanism, a retrotransposon can be copied and
302 SECTION 14.3 C H RO M O S O M A L M U TAT I O N S
FIG. 14.13 Origin of the b-globin gene family. The b-globin gene family evolved through several episodes of duplication and divergence.
Data from: Y. A. Trusov and P. H. Dear, 1996, “A Molecular Clock Based on the Expansion of Gene Families,” Nucleic Acids Research 24(6):995–999.
DNA on chromosome 11
G A
-globin -globin -globin -globin -globin
(embryo) (fetus) (fetus) (adult) (adult)
20 MY
40 MY
Time (in millions of years)
100 MY
Gene for Gene for
prenatal -globin adult -globin
Duplication
event
200 MY
Original single copy
of globin gene
one or a few genes can be maintained over many generations.
Usually, duplication of a region of the genome is less harmful than New genes can be created by duplication and
divergence. The resulting genes usually remain
deletion of the same region. similar in function, forming a gene family.
An example of a deletion, in which a region of the
chromosome is missing, is shown in Fig. 14.12b. A deletion can
result from an error in replication or from the joining of breaks
in a chromosome that occur on either side of the deleted region. It is worth emphasizing that one rarely observes deletions
Even though a deletion may eliminate a gene that is essential or duplications that include the centromere, the site associated
for survival, the deletion can persist in the population because with attachment of the spindle fibers that move the chromosome
chromosomes usually occur in homologous pairs. If one member during cell division (Chapter 11). The reason is that an abnormal
of a homologous pair has a deletion of an essential gene but the chromosome without a centromere, or one with two centromeres,
gene is present in the other member of the pair, that one copy is usually lost within a few cell divisions because it cannot be
of the gene is often sufficient for survival and reproduction. In directed properly into the daughter cells during cell division.
these cases, the deletion can be transmitted from generation to
generation and persist harmlessly, as long as the chromosome is Gene families arise from gene duplication and
present along with a normal chromosome. evolutionary divergence.
But some deletions decrease the chance of survival or Small duplications play an important role in the origin of new
reproduction of an organism even when the homologous genes in the course of evolution. In most cases, when a gene is
chromosome is normal. In general, the larger the deletion, the duplicated, one of the copies is free to change without causing
smaller the chance of survival. In the fruit fly Drosophila, individuals harm to the organism because the other copy continues to carry
with deletions of more than 100–150 genes rarely survive even out the normal function of the gene. Occasionally, a mutation in
when the homologous chromosome is normal. The interpretation of the “extra” copy of the gene may result in a beneficial effect on
the reduced survival is that organisms are sensitive to the dosage, survival or reproduction, and gradually a new gene is formed from
or number of copies, of each gene. Normal embryonic development the duplicate. These new genes usually have a function similar to
requires that genes be present in a particular dosage. Although small that of the original gene.
deviations from normal gene dosage can be tolerated, as indicated This process of creating new genes from duplicates of old ones
by the survival of individuals containing small duplications or is known as duplication and divergence. The term divergence
deletions, the cumulative effects of large deviations from normal refers to the slow accumulation of differences between duplicate
gene dosage are incompatible with life. It is usually not the total copies of a gene that occurs on an evolutionary time scale.
number of copies of each gene that matters, but rather the number Multiple rounds of duplication and divergence can give rise to a
of copies of each gene relative to other genes. This explains why group of genes with related functions known as a gene family.
some plant populations can include polyploids with multiple The largest gene family in the human genome has about 400 genes
complete sets of chromosomes (Chapter 13), but in the same species and encodes for proteins that detect odors. These proteins are
large duplications and deletions are lethal. structurally very similar, but differ in the region that binds small
CHAPTER 14 M U TAT I O N A N D D N A R E PA I R 303
FIG. 14.16 Major types of DNA damage. Most types of DNA damage can be repaired by specialized enzymes.
The presence of a mutagen can increase the probability of j Quick Check 3 Earlier, we described the Lederbergs’
mutation by a factor of 100 or more. experiment, which demonstrated that mutations are not directed
Some of the most important types of DNA damage induced by the environment. But mutagens, which are environmental, can
by mutagens are illustrated in Fig. 14.16, which shows a highly lead to mutations. What’s the difference?
damaged DNA molecule. Some types of damage affect the
structure of the DNA double helix. These include breaks in the Most DNA damage is corrected by specialized
sugar–phosphate backbone, one of the main mutagenic effects repair enzymes.
of X-rays. Breaks can occur in just one strand of the DNA or Cells contain many specialized DNA-repair enzymes that correct
both. Ultraviolet light can cause cross-links between adjacent specific kinds of damage, and in this section we examine a few
pyrimidine bases, especially thymine, resulting in the formation examples. Perhaps the simplest is the repair of breaks in the sugar–
of thymine dimers. Covalent bonding between adjacent thymines phosphate backbone, which are sealed by DNA ligase, an enzyme
in a DNA strand causes the double helix to become pinched, both that can repair the break by using the energy in ATP to join the
the major groove and the minor groove become wider, and the 3� hydroxyl of one end to the 5� phosphate of the other end. Most
T–A base pairing is weakened. organisms have multiple different types of DNA ligase, some of
Yet another type of structural damage is loss of a base from which participate in DNA replication (Chapter 12) and others in
one of the deoxyribose sugars, resulting in a gap in one strand DNA repair. One type of ligase seals single-stranded breaks in
where no base is present. Spontaneous loss of a purine base is one DNA, and a different type seals double-stranded breaks. Double-
of the most common types of DNA damage, occurring at the rate stranded breaks often result in chromosomal rearrangements
of about 13,000 purines lost per human cell per day. Most of these because they are less likely to be repaired than single-stranded
mutations result from the interaction between DNA and normal breaks. In addition to their importance in DNA replication and
metabolic by-products. The rate increases with age, and it can also repair, ligases are an important tool in research in molecular
be increased by exposure to oxidizing agents such as household biology because they allow DNA molecules from different sources
bleach or hydrogen peroxide. to be joined to produce recombinant DNA (Chapter 12).
Other types of damage affect the bases themselves. Bases that As we saw earlier in this chapter, mispairing of bases during
are chemically damaged tend to mispair. Some bases are damaged DNA replication leads to the incorporation of incorrect nucleotides
spontaneously when reaction with a water molecule replaces and potentially to nucleotide substitutions. About 99% of the
an amino group (2NH2) with an atom of oxygen (5O), which mispaired bases are corrected immediately by the proofreading
interferes with the base’s ability to form hydrogen bonds with a function of DNA polymerase, in which the mispaired nucleotide
complement. Some naturally occurring molecules mimic bases and is removed immediately after incorporation and replaced by the
can be incorporated into DNA and cause nucleotide substitutions. correct nucleotide (Chapter 12).
Caffeine mimics a purine base, for example (although to be Even after proofreading by DNA polymerase, the proportion of
mutagenic, the amount of caffeine required is far more than any mismatched nucleotides in replicated DNA is about 1026, which is
normal person could possibly consume). at least 1000 times greater than the actual frequency of errors in
Chemicals that are highly reactive tend to be mutagenic, often cellular organisms (see Fig. 14.1). What accounts for the difference
because they add bulky side groups to the bases that hinder proper is a second-chance mechanism for catching mismatches that is
base pairing. The main environmental source of such chemicals is known as postreplication mismatch repair (Fig. 14.17).
tobacco smoke. Other chemicals can perturb the DNA replication In the bacterium E. coli, postreplication mismatch repair
complex and cause the insertion or deletion of one or occasionally begins when a protein known as MutS binds to the site of a
several nucleotides. mismatch (Fig. 14.17a) and brings two other proteins (MutL
CHAPTER 14 M U TAT I O N A N D D N A R E PA I R 305
C C
G T An exonuclease removes
successive nucleotides, including FIG. 14.18 Base excision repair. In base excision repair, an
the one with the mismatched base.
C
Corrected mismatch
b.
DNA replication. Cells have evolved many other systems that Uracil replaced
repair different types of DNA damage that can occur even in with cytosine
306 CO R E CO N C E P T S S U M M A RY
d.
Damage repaired
gene, it can result in a change in the amino acid sequence Many specialized DNA repair enzymes can correct DNA
(nonsynonymous mutation), no change in the amino acid damage. page 304
sequence (synonymous mutation), or the introduction of a
DNA ligase seals breaks in DNA and is an important tool
stop codon (nonsense mutation). page 297
for molecular biologists. page 304
Small insertions or deletions in DNA add or remove one
Postreplication mismatch repair provides a backup
base or a few contiguous bases. Their effect depends on
mechanism for mistakes not caught by the proofreading
where in the genome they occur and on their size. An
function of DNA polymerase. page 304
insertion or deletion of a single nucleotide in a protein-
coding gene results in a frameshift mutation, in which all Base excision repair corrects individual nucleotides
the codons downstream of the insertion or deletion are and involves several DNA repair enzymes working
changed. page 298 together. page 305
Transposable elements are DNA sequences that can jump Nucleotide excision repair functions similarly to
from one place in a genome to another. They can affect the postreplication mismatch repair but excises longer
expression of a gene if they insert into or near a gene. stretches of damaged nucleotides. page 306
page 300
14.4 DNA can be damaged by mutagens, but most 7. Explain how a gene family, such as the odorant receptor
DNA damage is repaired. gene family, is thought to have evolved.
Some types of damage alter the structure of DNA, such as 8. What is a mutagen? Name two common mutagens and
single-stranded or double-stranded breaks, cross-linked their effects on DNA.
thymine dimers, or missing bases. page 304
9. Describe a DNA repair mechanism.
Other types of DNA damage, such as changes in the side
groups that form hydrogen bonds or the addition of side
Log in to to check your answers to the Self-
groups that interfere with base pairing, affect the bases Assessment questions, and to access additional learning tools.
themselves. page 304
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CHAPTER 15
Genetic
Variation
Core Concepts
15.1 Genetic variation describes
common genetic differences
(polymorphisms) among the
individuals in a population at
any given time.
15.2 Human genetic variation can
be detected by DNA typing,
which can uniquely identify
each individual.
15.3 Two common types of
genetic variation are single-
nucleotide polymorphisms
(SNPs) and copy-number
variation (CNV).
15.4 Chromosomal variants can
also occur but are usually
harmful.
309
310 SECTION 15.1 G E N OT Y P E A N D P H E N OT Y P E
In the last chapter, we saw how errors in DNA arise and what one difference per thousand nucleotides across the genome. In
common types of error occur. What is the fate of all these mistakes? other words, we differ from one person to the next in a very large
Most, as we have seen, are corrected by DNA repair mechanisms. number but very small fraction of nucleotides.
In this case, the DNA sequence is not changed. Some errors escape Mutations, as we have seen, are the ultimate source of
these repair mechanisms and are replicated as faithfully as the differences among genotypes. If we consider any present-day
original DNA sequence. If such mutations occur in somatic (body) population of organisms, we find that some mutations are very
cells, they can be passed on in the individual’s cells through mitotic common. Geneticists use the term polymorphism to refer to any
cell divisions, but they will not be passed on to progeny. If they genetic difference among individuals that is sufficiently common
occur in the germ line, they can be passed on to progeny. Over that it would almost certainly be present in a group of
time, through evolution (Chapters 1 and 21), the proportion of 50 randomly chosen individuals. For example, if many people have
individuals in a population carrying these mutations may increase an A–T pair at a particular site in the genome, but many others
or decrease. Therefore, if we look at any present-day population have a G–C pair at the same site, this difference is a polymorphism.
of organisms, such as the human population, we will find that Of course, the polymorphism is the result of a mutation. All
it harbors lots of genetic differences, all of which result from individuals once had the same genotype at this site, but a mutation
mutations that occurred sometime in the past. Genetic variation occurred at this site sometime in the past, and is now commonly
refers to genetic differences that exist among individuals in a found in the population.
population at a particular point in time. Phenotype is an individual’s observable characteristics
In the human population, you can observe the effects of or traits, such as height, weight, eye color, and so forth. The
common genetic differences by looking at the people around you. phenotype may be visible, as in these characteristics, or may
They differ in height, weight, facial features, skin color, eye color, be seen in the development, physiology, or behavior of a cell or
hair color, hair texture, and in many other ways. These traits differ organism. For example, color blindness and lactose intolerance
in part because of genetic variation, and in part because of the are phenotypes. The phenotype results in part from the genotype:
environment. Weight is affected by diet, for example, and skin A genotype with a mutated gene for an enzyme that would
color by exposure to sunlight. normally metabolize lactose can lead to the phenotype of lactose
In this chapter, we consider examples of major types of DNA intolerance. However, the environment also commonly plays
variation and chromosomal variation in populations today and an important role, so it is most accurate to say that a phenotype
examine their consequences for the organism. We also describe results from an interaction between the genotype and the
key molecular techniques that allow genetic variation to be environment. These genotype–environment interactions are
studied directly in DNA molecules. The emphasis here is primarily, discussed in Chapter 18.
but not exclusively, on human populations.
The effect of a genotype often depends on several
factors.
15.1 GENOTYPE AND PHENOTYPE Let’s examine how genotype influences phenotype with an
example of a genetic polymorphism that we introduced in the
We tend to think of mutations as something negative or harmful; previous chapter. Fig. 15.1 shows genetic variation in the gene for
the term “mutant” ordinarily connotes something abnormal. But b-(beta-)globin, one of the subunits of hemoglobin that carries
because mutations result in genetic variation among individuals oxygen in red blood cells. Three forms of the b-globin gene are
and organisms, we are all mutants, different from one another shown in the figure: A, S, and C. These three forms of the gene are
genetically because of mutations, that is, differences in our DNA. relatively common in certain African populations. The different
Whereas some mutations are harmful, some have no effect on an forms of any gene are called alleles, and they correspond to
organism, and some indeed are beneficial. Without mutations, different DNA sequences (polymorphisms) in the genes. In this
evolution would not be possible. Mutations generate the occasional case, the most common allele is the A allele, which has a GAG
favorable variants that allow organisms to evolve and become codon in the position indicated. This codon translates to glutamic
adapted to their environment over time (Chapter 21). acid (Glu) in the resulting polypeptide.
The allele denoted “S” in Fig. 15.1 is associated with sickle-cell
Genotype is the genetic makeup of a cell or organism; anemia (Chapter 14). In this allele, the GAG codon of the A allele
phenotype is its observed characteristics. is instead a GTG codon, with the result that the glutamic acid in
The genetic makeup of a cell or organism constitutes its the protein is replaced with valine (Val). The third allele in Fig. 15.1
genotype. A population with a gene pool that has many variants is the C allele. It has a variation in the same codon as the S allele,
in many different genes will consist of organisms with numerous but in this case the change is from GAG to AAG, with the result
different genotypes. For example, any two human genomes that glutamic acid is replaced by lysine (Lys). Although in each case
are likely to differ at about 3 million nucleotide sites, or about only one amino acid of the b-globin protein is affected, this change
CHAPTER 15 G E N E T I C VA R I AT I O N 311
FIG. 15.2 A harmful mutation. (a) The enzyme alpha-1 antitrypsin (α1AT) normally inhibits the activity of elastase, which breaks down elastin in
the lung. (b) Cigarette smoke inhibits α1AT activity and increases the risk of emphysema. (c) A mutation in α1AT called PiZ is harmful
because it reduces α1AT activity and also leads to increased risk of emphysema.
a. Normal
α1AT gene α1AT Inhibited
The α1AT gene encodes elastase Normal lung elasticity
an enzyme that inhibits is maintained by a
the function of elastase, balance between
an enzyme that breaks elastin production and
Expression of
down elastin in the lung. destruction.
α1AT enzyme
b. Smoking
α1AT gene Active
Cigarette smoking Emphysema results
reduces the activity of elastase
from too much
α1AT, decreasing breakdown in the lung,
inhibition of elastase which can result from
and leading to increased Expression of
cigarette smoking…
elastin breakdown. α1AT enzyme
c. Mutant
eventual death. Onset of the disease usually occurs in middle age, PiZ allele, and about 1 in 3000 is homozygous PiZ/PiZ. Individuals
and the lifespan of affected individuals is shortened by 10 to 30 with the homozygous genotype produce α1AT with reduced
years depending on the effect of treatment. activity and hence have reduced elastase inhibition, leading
About 80% of all cases of emphysema are associated with to severe emphysema and death in more than 70% of affected
cigarette smoking, which affects the action of the enzyme alpha-1 individuals (Fig. 15.2c). Smoking markedly increases both the
antitrypsin (α1AT). The main function of α1AT is to inhibit severity of the disease and the rapidity of its progression in PiZ/PiZ
another enzyme, known as elastase, which breaks down the individuals. The life expectancy of PiZ/PiZ nonsmokers is 65 years,
connective-tissue protein elastin in lungs (Fig. 15.2). The elasticity whereas that of PiZ/PiZ smokers is only 40 years.
of the lung, which allows normal breathing, requires a balance The combination of homozygous PiZ and smoking is an
between the production and the breakdown of elastin. Too-rapid example of a genotype-by-environment interaction, in which
breakdown by elastase is normally prevented by the inhibition of a phenotype is the result of an interplay between genes and the
elastase by α1AT (Fig. 15.2a). Cigarette smoke reduces the activity environment. In this case, a particular combination of genetic and
of α1AT, resulting in excessive destruction of elastin, loss of lung environmental risk factors is much worse than either risk factor
elasticity, and emphysema (Fig. 15.2b). acting alone. Chapter 18 includes a more detailed discussion of
While most cases of emphysema are due to smoking, in some genotype-by-environment interactions.
individuals genetics plays a role. An individual’s chance of getting
emphysema is significantly increased by inheriting a mutation in Not all genetic differences are harmful.
the gene that encodes α1AT. Among the many different alleles of Some mutations have no effect on the organism, or have
this gene, a defective allele denoted PiZ is particularly common effects that are not associated with differences in survival or
in populations of European descent. Among Caucasians in the reproduction. Such mutations are considered neutral. Many
United States, about 1 person in 30 is heterozygous for the mutations have neutral effects on organisms because they occur
CHAPTER 15 G E N E T I C VA R I AT I O N 313
in noncoding DNA. Neutral mutations are therefore especially should still eat your vegetables! But if you find broccoli and its
likely to occur in organisms with large genomes and abundant relatives somewhat bitter, you may well be a taster.
noncoding DNA (Chapter 13).
A few genetic differences are beneficial.
j Quick Check 2 Given what you read about the human genome
While many mutations are neutral, or nearly so, and many
in Chapter 13, would you predict that most mutations in humans
others are harmful, some mutations are beneficial. In human
are harmful, beneficial, or neutral?
populations, beneficial mutations are often discovered through
Sometimes common, seemingly harmless genetic variations their effects in protecting against infectious disease. The most
occur in coding sequences. One example in human populations is widely known example is probably the sickle-cell allele in the gene
the taster phenotype associated with perception of a bitter taste encoding the β chain of hemoglobin, which when heterozygous
from certain chemicals, including phenylthiocarbamide (PTC). The protects against malaria (see Fig. 15.1). In this section, we consider
taster polymorphism was discovered in 1931 when a commercial another example: This one protects against AIDS, which is caused
chemist seeking a new artificial sweetener accidentally released by the human immunodeficiency virus (HIV).
a cloud of fine crystalline PTC and heard his colleague working By means of its surface glycoprotein (a product of the env
nearby complain about its bitter taste. The chemist himself tasted region in the annotated HIV genome shown in Fig. 13.7), HIV
nothing. He began testing his own and other families, and set the combines with a cell-surface receptor called CD4 to gain entry
stage for future genetic studies. into immune cells called T cells. Interaction with CD4 alone,
The minimal concentration for PTC tasting varies among however, does not enable the virus to infect the T cell. The HIV
individuals, but being able to taste a concentration of 0.5 millimolar surface glycoprotein must also interact with another receptor on
or less is often taken as the cutoff between the taster and nontaster the T cell, which is denoted CCR5, in the early stages of infection
phentoypes. In a sample from Utah, the frequency of nontasters is (Fig. 15.3). The normal function of CCR5 is to bind certain small
about 30%. This is typical for people of European descent, but the secreted proteins that promote tissue inflammation in response to
frequency of nontasters differs among populations, from as low as infection. But because CCR5 is also an HIV receptor, cells lacking
3% in West Africa to as high as 40% in India. CCR5 are more difficult to invade.
The ability or inability to taste PTC is due largely, but not A beneficial effect of a particular mutation in the CCR5 gene
exclusively, to alleles of a single gene called TAS2R38 that encodes a was discovered in studies focusing on HIV patients whose infection
taste receptor in the tongue. Nonhuman primates are homozygous had not progressed to full-blown AIDS after 10 years or more. The
for an allele of this gene known as the PAV allele, so called because protective allele is denoted the Δ32 allele because the mutation is
the protein it encodes has the amino acids proline (P), alanine (A), a 32-base-pair deletion in the coding sequence of the CCR5 gene
and valine (V) at specific positions. Humans also have the PAV allele, (Fig. 15.4). Because 32 is not a multiple of 3, the reading frame
and PAV/PAV homozygous genotypes are almost all tasters. for translation is shifted at the site of the deletion, and instead of
The most common allele associated with the nontaster the normal amino acid sequence Ser–Gln–Tyr–Gln–Phe · · ·, the
phenotype is AVI, in which the amino acids in the taste receptor mutant sequence is Ile–Lys–Asp –Ser–His · · · . Not only is the amino
are alanine ( A), valine (V), and isoleucine (I) instead of proline,
alanine, and valine. About 80% of homozygous AVI/AVI genotypes
are nontasters. One copy of the PAV allele is usually sufficient FIG. 15.3 HIV infection of T cells. HIV gains entry into a T cell by
for the taster phenotype; about 98% of PAV/AVI heterozygous interacting with a CD4 protein and a CCR5 receptor on
genotypes are tasters. the surface of T cells.
The factors contributing to the taster phenotype are more HIV surface
complex than a genotype at a single gene, however. The AVI/AVI HIV glycoprotein
genotype tips the balance toward the nontaster phenotype, but
not completely. Other genes and the environment also play a role.
Why is this strange variation present in the human
population? One hypothesis is that an aversion to compounds that
For HIV to invade
contain a thiourea group (N–C⫽S), as PTC does, may discourage a T cell, it must
eating certain plants that produce poisonous defense compounds. interact with a
CD4 receptor
One class of such compounds is the glycosinolates, which are and a CCR5
present in many wild plants and some cultivated vegetables, co-receptor.
including broccoli, watercress, turnip, and horseradish. Sure
CD4 surface protein CCR5 co-receptor
enough, PAV/PAV tasters rate such vegetables as significantly more
bitter than AVI/AVI nontasters, whereas PAV/AVI heterozygous Extracellular
fluid
genotypes are intermediate in their perception of bitterness.
We hasten to add, however, that the low level of glycosinolates
Cytoplasm CD4+ T cell
in broccoli and other cultivated vegetables is nontoxic, so you
314 SECTION 15.2 G E N E T I C VA R I AT I O N A N D I N D I V I D UA L U N I Q U E N E S S
FIG. 15.4 A beneficial mutation in the human population. Mutant CCR5 has a 32-nucleotide deletion that results in defective CCR5 protein and
therefore slows the progression of HIV to AIDS.
HIS PHE PRO TYR SER GLN TYR GLN PHE TRP LYS ASN PHE GLN THR LEU LYS ILE VAL ILE
acid sequence different from the nonmutant form, the ribosome important effects on phenotypes, most of the genetic variation
encounters a stop codon a mere 26 amino acids farther along in populations is neutral or has no obvious effects. Much of the
and translation terminates. The mutant protein is 215, not 352, neutral variation consists of differences in noncoding DNA.
amino acids long. The CCR5 protein produced by the ∆32 allele is Nonetheless, this variation can be revealed by direct studies of
completely inactive. DNA that employ many of the techniques for DNA manipulation
The effect of the ∆32 allele is pronounced. In individuals with described in Chapter 12.
the homozygous ∆32/∆32 genotype, HIV progression to AIDS
is rarely observed. There is some protection even in individuals Areas of the genome with variable numbers of tandem
with heterozygous ∆32 genotypes, where progression to AIDS is repeats are useful in DNA typing.
delayed by an average of about 2 years after infection by HIV. At many locations in the human genome, short (10–50 base-pair)
Much has been written about the evolutionary history of the sequences are repeated in multiple tandem copies. At each location
∆32 allele. It is found almost exclusively in European populations, the number of copies of the repeat may differ from chromosome to
where the frequency of heterozygous genotypes ranges from chromosome. This kind of variation, in which chromosomes have
10% to 25%. The narrow geographical distribution was originally different numbers of a repeated sequence at a particular location,
interpreted to mean that the allele was selected over time because is called a variable number tandem repeat, or VNTR. There are
it provided protection against some other infectious agent that about 30,000 different VNTR locations in the human genome.
also interacted with the CCR5 protein. Just as an individual has two copies of each gene, possibly with
Beneficial mutations not only provide protection against two different alleles, so each individual has two copies of each of
disease. Many beneficial mutations permit organisms to become these VNTRs, with copies differing in the number of repeats being
better adapted to their environment. For example, certain birds, analogous to different alleles of a gene. Each VNTR typically has
such as Rüppell’s vulture, commonly fly at altitudes of 20,000 many alleles differing in copy number, so that, except for identical
feet and sometimes much higher. This feat is possible because of twins, an individual’s genotype for 6–8 VNTR locations is usually
mutations in the structure of hemoglobin that allow hemoglobin sufficient to identify the individual uniquely. Differences among
to bind oxygen with high affinity, even at the low pressure of individuals, such as VNTRs, are the basis of DNA typing, in which
oxygen high in the atmosphere. These mutations were selected the analysis of a small quantity of DNA can be as reliable for
and passed on generation after generation, making the birds well identifying individuals as fingerprints. This is why DNA typing is
adapted to flying at high altitudes. often called DNA fingerprinting.
Any of several methods can be used to DNA fingerprint
someone on the basis of that individual’s VNTRs. Amplification by
15.2 GENETIC VARIATION AND the polymerase chain reaction (PCR, Chapter 12) is a convenient
INDIVIDUAL UNIQUENESS and reliable technique because each VNTR in the genome is flanked
by a unique sequence that can be used to design PCR primers that
While examples like sickle-cell anemia, emphysema, and HIV will amplify one and only one VNTR. Although the number of
susceptibility show that genetic variation in some genes has alleles of a particular VNTR can be very large, an example with only
CHAPTER 15 G E N E T I C VA R I AT I O N 315
FIG. 15.5 Variable number tandem repeats (VNTRs). (a) The number of short, repeated sequences at a given site in a human chromosome can
vary. (b) These differences can be visualized using PCR followed by gel electrophoresis.
a. b.
Evidence (blood or
Allele A1 other tissue from
Position a crime scene)
of PCR Genotype
primers
A1 A2 A3 A4 A5 A1 A1 A1 A1 A2 A2 A2 A3 A3 A4
Allele A2
A1 A2 A3 A4 A5 A2 A3 A4 A5 A3 A4 A5 A4 A5 A5 E
A5
Allele A3 A4
A3
Allele A4 A2
A1
Allele A5
Each of the different genotypes yields
a unique pattern of bands in the gel.
AGTAGTAGTAGTAGT
five alleles is shown in Fig. 15.5, where the repeated sequence is very likely that the samples come from the same individual (or from
shown in green between the flanking unique sequences. identical twins). On the other hand, if any of the polymorphisms
No matter how many alleles exist in the population as a whole, fails to match band for band, then it is almost certain that the
any one diploid individual can have only two alleles, which are samples come from different individuals (barring such technical
present at the same positions in the homologous chromosomes mishaps as samples whose DNA is contaminated, degraded, or
inherited from the mother and father. With five alleles there are mislabeled).
5 possible homozygous genotypes and 10 possible heterozygous One of the advantages of DNA typing is that a large amount
genotypes. These can be visualized after PCR by separating the of DNA is not needed. Even minuscule amounts of DNA can
resulting molecules by size by gel electrophoresis (Chapter 12). be typed, so tiny spots of blood, semen, or saliva are sufficient
The pattern of bands expected from the DNA in each genotype samples. A cotton swab wiped across the inside of your cheek will
formed from the alleles in Fig. 15.5a is shown in Fig. 15.5b. Note contain enough DNA for typing; so will a discarded paper cup or a
that each genotype yields a distinct pattern of bands, and so these cigarette butt. One enterprising researcher in England used PCR
patterns can be used to identify the genotype of any individual for to type the dog feces on his lawn and matched it to the DNA from
a particular region of DNA. hair he obtained from neighborhood dogs, much to the chagrin of
With as few as 10 equally frequent alleles, the likelihood that the guilty dog’s owner.
any two individuals would have the same genotype at a particular
location by chance alone is about 1 in 50, and with 20 equally j Quick Check 3 In typing DNA from a sample found at a crime
frequent alleles the likelihood decreases to about 1 in 200. These scene, how can a DNA mismatch prove that a suspect is not the
numbers suggest why DNA typing can yield a genetic fingerprint source of that sample, whereas a DNA match does not necessarily
that can uniquely match DNA samples. prove that a suspect is the source?
The lane labeled “E” at the far right in Fig. 15.5b shows the
DNA bands for this same polymorphism from biological material Some polymorphisms add or remove restriction sites
collected at the scene of a crime. In this case, the bands in lane E in the DNA.
imply that the source of the evidence is an individual of genotype Restriction enzymes, which cleave double-stranded DNA at
A2 /A4 because this is the only genotype with bands with vertical specific sequences known as restriction sites, typically four or six
positions in the gel that exactly match those of the evidence sample. nucleotides long, were among the first tools used to study genetic
A single polymorphism of the type shown in Fig. 15.5 is not enough variation in DNA. These enzymes are useful in DNA fingerprinting
to establish for sure that two pieces of DNA come from the same because DNA from different individuals can differ in the distance
person, but because the human genome has polymorphic sites between adjacent restriction sites or in the presence or absence
scattered throughout, many polymorphisms can be examined. If six of a particular restriction site at some location in the genome.
or eight of these polymorphisms match between two samples, it is This kind of polymorphism, in which differences in restriction
316 SECTION 15.3 G E N O M E W I D E S T U D I E S O F G E N E T I C VA R I AT I O N
sites result in different lengths of restriction fragments, is called a Just as with VNTRs, any individual can carry at most two
restriction fragment length polymorphism, or RFLP. different alleles of a restriction fragment length polymorphism.
Fig. 15.6 shows an example. Here, a restriction enzyme cleaves As seen in the RFLP in Fig. 15.6b, DNA from homozygous AA
DNA near the sequence GAGGAG. The three sites shown are in and individuals yields only the short and medium fragments, and that
flanking the b-globin gene from the sickle-cell example we explored from homozygous SS individuals yields only the long fragment.
earlier in the chapter. However, in the S allele (see Figure 15.1), the DNA from heterozygous AS individuals yields all three fragments.
restriction site in the middle includes a GAG that is mutated to GTG, Therefore, each of the three genotypes AA, AS, and SS yields a
making the sequence unrecognizable to the restriction enzyme. As unique pattern of bands, allowing each of the possible genotypes
a result, the DNA of the S allele is cleaved at only two sites, whereas to be identified.
the DNA of the A allele is cleaved at all three. How many restriction fragment length polymorphisms
These differences can be visualized by gel electrophoresis are there in the human genome? As in the case of VNTRs, the
(Chapter 12), in which DNA is isolated from different individuals, human genome has many restriction sites, so there are numerous
cut with restriction enzymes, and separated by size on a gel. RFLPs in the human population, making it another type of
In this case, we use a restriction enzyme that recognizes the polymorphism that can be used in DNA typing.
GAGGAG sequence. The A allele produces two fragments: a short
fragment that moves rapidly through the gel and ends up near the j Quick Check 4 When a segment of DNA containing either a
bottom, and a longer fragment that ends up near the middle. The VNTR or an RFLP is analyzed, the result is fragments of DNA of
fragment produced by the S allele is even longer because there is different lengths. How, then, are VNTRs and RFLPs different?
no restriction site in the middle. This fragment ends up forming a
band near the top of the gel.
15.3 GENOMEWIDE STUDIES
OF GENETIC VARIATION
FIG. 15.6 Restriction fragment length polymorphism (RFLP) VNTRs and RFLPs are forms of genetic variation that are still
between the A and S alleles of the b-globin gene. widely used in DNA fingerprinting. But large-scale and relatively
inexpensive DNA sequencing methods are now also used to
a.
GAGGAG GTGG AG identify and study genetic variation. These methods have revealed
two types of genetic variation that are very common in the human
Allele A Allele S genome: variation of individual nucleotides and variation in copy
number of regions of DNA that can include one or more genes. In
A restriction enzyme
this section, we focus on these two types of genetic variation.
Position of cleaves both DNA
restriction samples at all of the sites
site Single-nucleotide polymorphisms (SNPs) are single-
it recognizes, producing
fragments of different base changes in the genome.
lengths. Following One of the most common types of genetic variation is a
electrophoresis, the gels difference in a nucleotide at a specific site. A single-nucleotide
show the position of the
fragments to which the polymorphism (SNP) is a site in the genome where either of two
probe hybridizes. different nucleotide pairs can occur and where each nucleotide
b.
Genotype AA Genotype SS Genotype AS
FIG. 15.7 Single-nucleotide polymorphisms (SNPs). A SNP in the ? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME
region neighboring OCA2 is strongly associated with blue How can genetic risk factors be detected?
eyes. Sources: (left) Amos Morgan/Getty Images; (right) Stockbroker SNPs result from point mutations, the most frequent type of
xtra/age fotostock. mutation, which occurred in the past and then spread through
the population. A point mutation is the substitution of one base
C–G allele T–A allele
G T pair for another in double-stranded DNA (Chapter 14). Each of
Site of single- us is genetically unique partly because of the abundance of SNPs
C nucleotide A
polymorphism in the human genome. There are approximately 3 million SNPs
(SNP) that distinguish any one human genome from any other. SNPs are
abundant in the genomes of most species, and while many have no
effect on the organism, some are thought to be the main source
of evolutionary innovation and others are major contributors
to inherited disease. Practically speaking, SNPs are important
because they can be used to detect the presence of a genetic risk
factor for a disease before the onset of the disease. For example,
the ability to detect the b-globin SNPs shown in Fig. 15.1 allows
prenatal identification of the b-globin genotype of a fetus.
While there is great interest in developing ultrafast DNA
sequencing machines that can determine anyone’s personal
genome quickly at relatively low cost, 99.9% of the nucleotides
pair is common enough in the population to be present in a
between any two genomes are identical. An alternative is to focus
random sample of 50 diploid individuals. The differences among
on genotyping just SNPs. As many as one million SNPs at different
the hemoglobin alleles are SNPs. The A, S, and C alleles differ from
positions in the genome can be genotyped simultaneously, and the
one another at just one nucleotide site (see Fig. 15.1).
genotyping can be carried out on thousands or tens of thousands
Eye color is also associated with a SNP. The blue eye phenotype
of individuals. Such massive genotyping allows any SNP associated
results from reduced expression of a gene called OCA2, which
with a disease to be identified, which is especially important for
encodes a membrane protein involved in the transport of small
complex diseases affected by many different genetic risk factors
molecules, including the amino acid tyrosine, which is a precursor
(Chapter 18).
of the melanin pigment associated with the brown eye phenotype.
What does it mean to say that a given SNP is associated with
Although more than a dozen alleles of OCA2 are known that have
a disease? It means that individuals carrying one of the alleles of
an amino acid replacement in the protein, none of these results in
that SNP are more likely to develop the disease than those carrying
blue eyes.
the other allele. The increased risk depends on the disease and
The SNP implicated in blue eyes is a site that is a C–G base
can differ from one SNP to the next. Sickle-cell anemia affords an
pair in one allele. The other common allele has a T–A at this
example at one extreme of the spectrum of effects. In this case,
position, which is not associated with blue eyes (Fig. 15.7). In one
the T–A base pair in the S allele of the b-globin gene is the SNP
study, the homozygous C–G genotype was found in 94% of 183
that results in the amino acid replacement of glutamic acid with
individuals with blue eyes and in only 2% of 176 individuals with
valine in the protein. Because SS individuals always have sickle-cell
brown eyes. This strong association is quite unexpected because
anemia, it would be fair to say that homozygous S “causes” sickle-
the SNP associated with blue eyes is in an intron of a neighboring
cell anemia.
gene, and is therefore noncoding. The proposed mechanism for
But except for inherited diseases that result from single mutant
the association is that the C–G allele makes the adjacent OCA2
genes, which are usually rare, the vast majority of SNPs implicated
gene less accessible to transcription factors, thereby reducing
in disease increase the risk only moderately as compared with
the amount of the transporter protein and consequently the
individuals lacking the risk factor. We then say that the SNP is
production of melanin in the iris. The proposed mechanism may be
“associated” with the disease since the SNP alone does not cause
right or wrong; this example emphasizes that scientists have much
the disease but only increases the risk. For heart disease, diabetes,
to learn about the possible phenotypic effects of noncoding DNA.
and some other diseases, many SNPS at different places in the
The C–G versus T –A SNP is typical of most SNPs in that only
genome, as well as environmental risk factors, can be associated
two of the four possible base pairs (G–C and A–T in addition to
with the disease. Usually, genetic and environmental risk factors
C–G and T–A) are present in the population at any appreciable
act cumulatively: the more you have, the greater the risk.
frequency.
As emphasized in the case of Claudia Gilmore’s genome,
j Quick Check 5 What’s the difference between a point mutation certain SNPs in the BRCA1 and BRCA2 genes are associated with
and a SNP? an increased risk of breast and ovarian cancers. Women who carry
318 SECTION 15.4 G E N E T I C VA R I AT I O N I N C H RO M O S O M E S
In certain high-risk populations, however, such as Ashkenazi Jews, F. A. Villanea, J. L. Mountain, R. Misra, N. P. Carter, C. Lee, and A. C.
only a few mutations predominate, and the SNPs associated with Stone, 2007, “Diet and the Evolution of Human Amylase Copy Number
these mutations can be detected easily and efficiently. Variation,” Nature Genetics 39:1256–1260.
0.70
Copy-number variation constitutes a significant High-starch diet
proportion of genetic variation. 0.60 Low-starch diet In societies with low-starch
Proportion of chromosomes
diets the average AMY1 copy
In addition to SNPs, another very common form of genetic
number per chromosome 1
variation present in the modern human population is copy- 0.50
is about 2.5, whereas in
number variation (CNV), or differences among individuals in those with high-starch diets
0.40 it is about 3.5.
the number of copies of a region of the genome. In contrast to
the short repeats characteristic of VNTRs, the regions involved in 0.30
CNVs are large and may include one or more genes. An example
is shown in Fig. 15.8. In this case, a region of the genome that is 0.20
normally present in only one copy per chromosome (Fig. 15.8a) 0.10
may in some chromosomes be duplicated (Fig. 15.8b) or deleted
(Fig. 15.8c). The multiple copies of the CNV region are usually 0.00
1 2 3 4 5 6 7
adjacent to one another along the chromosome.
Number of copies of AMY1 in chromosome 1
One of the surprises that emerged from sequencing the human
genome was that CNV is quite common in the human population.
Any two individuals’ genomes differ in copy number at about five
different regions, each with an average length of 200 kb to 300 kb. groups of people: societies with a long history of a high-starch
Across the genome as a whole, about 10% to 15% of the genome is diet, and societies with a long history of a low-starch diet. There
subject to copy-number variation. is a clear tendency for chromosomes from the latter group to
Some CNVs occur in noncoding regions, but others consist have fewer copies of AMY1 than those from the former group. On
of genes that are present in multiple tandem copies along the average, a chromosome 1 from the low-starch group has a copy
chromosome. An example is the human gene AMY1 for the salivary number of about 2.5, whereas one from the high-starch group has
gland enzyme amylase, which aids in the digestion of starch. This an average of about 3.5. Because each individual has two copies of
gene is located in chromosome 1, and the AMY1 copy number chromosome 1, this difference means that the average individual
differs from one chromosome 1 to the next. Fig. 15.9 shows the in the low-starch group has about 5 copies of AMY1, whereas the
distribution of AMY1 copy number along chromosome 1 in two average individual in the high-starch group has about 7 copies. A
plausible hypothesis is that extra copies were selected in groups
with a high-starch diet because of the advantage extra copies
conferred in digesting starch.
FIG. 15.8 Copy-number variation in a region of a chromosome.
a.
One copy of region 15.4 GENETIC VARIATION IN
CHROMOSOMES
Copy-number variation usually involves only one or a small
b.
number of genes, and the size of the duplicated or deleted region
Two copies of region
(duplication) is physically so small that the differences are undetectable
with conventional microscopy. In the human genome, some
common variants involve large regions of the chromosome and
c. In copy-number variation,
are big enough to be visible through a microscope. Most of these
No copies the size of the duplicated or variations involve regions of the genome with an extremely low
(deletion) deleted region can include density of genes, such as regions around the centromere or on the
one or more complete genes.
long arm of the Y chromosome.
CHAPTER 15 G E N E T I C VA R I AT I O N 319
X chromosomes ( XX), and males have one X and one Y chromosome absence of detectable phenotypic effects in 47, XXX females has a
( XY). The presence of the Y chromosome, not the number of completely different explanation that has to do with the manner
X chromosomes, leads to male development. The female karyotype in which the activity of genes in the X chromosome is regulated.
47, XXX (47 chromosomes, including three X chromosomes) and In the cells of female mammals, all X chromosomes except one are
the male karyotype 47, XYY (47 chromosomes, including one X and inactivated and gene expression is largely repressed. (This process,
two Y chromosomes) are found among healthy females and males. called X-inactivation, is discussed in Chapter 20.) Because of
These persons are in the normal range of physical development and X-inactivation, a 47, XXX female has one active X chromosome per
mental capability, and usually their extra sex chromosome remains cell, the same number as in a 46, XX female.
undiscovered until their chromosomes are examined for some
other reason. j Quick Check 6 A male baby is born with the sex-chromosome
The reason that 47, XYY males show no detectable phenotypic constitution XYY. Both parents have normal sex chromosomes
effects is the unusual nature of the Y chromosome. The Y contains (XY in the father, XX in the mother). In which meiotic division of
only a few functional genes other than the gene that stimulates which parent did the nondisjunction take place that produced the
the embryo to take the male developmental pathway. The XYY baby?
321
322 SECTION 15.4 G E N E T I C VA R I AT I O N I N C H RO M O S O M E S
not occur. Although the mental abilities of affected females are 0 500 1000 1500 2000 2500 3000 3500
very nearly normal, they have specific defects in spatial abilities Number of fetuses per
and arithmetical skills. 100,000 recognized pregnancies
CHAPTER 15 G E N E T I C VA R I AT I O N 323
FIG. 15.15 Formation of polyploid organisms. (a) A triploid organism can result from failure of division in meiosis. (b) A tetraploid organism can
result from failure of cell division in mitosis.
No cell
division Triploid Tetraploid
fertilized zygote
egg
Mitosis
Metaphase I Metaphase II
Diploid
gametes
Meiosis
chromosomes, the dosage of genes in these chromosomes is Altogether, about 15% of all recognized pregnancies terminate
unbalanced relative to the rest of the genome, and the embryos with spontaneous abortion of the fetus, and roughly half of these
usually fail to complete development. At some time during are due to major chromosomal abnormalities. This number tells
pregnancy—in some cases very early, in other cases relatively only part of the story because embryos with a missing autosome
late—the chromosomally abnormal embryo or fetus undergoes are not found among spontaneously aborted fetuses. These must
spontaneous abortion. occur at least as frequently as those with an extra autosome
The relative proportions of some of the major chromosomal because both are created by the same event of nondisjunction (see
abnormalities in spontaneous abortion are shown in Fig. 15.14. Fig. 15.12). The explanation seems to be that in fertilized eggs with
The bars in red represent recognized pregnancies that terminate in a missing autosome the abortion occurs shortly after fertilization,
spontaneous abortion, and those in blue represent those in which
the fetus develops to term and is born alive. Note the large number
and most cases are not recognized. •
of autosomal trisomies, none of which (with the exception of
trisomies 13, 18, and 21) permits live births. Even among these,
about 75% of fetuses with trisomy 21 undergo spontaneous FIG. 15.16 (a) A balanced and (b) an unbalanced translocation.
abortion, and the proportions are even greater for trisomies 13 and
18. The 45, X karyotype also very infrequently results in live birth. a. Balanced b. Unbalanced
A surprisingly large number of fetuses that undergo translocation translocation
A variable number tandem repeat (VNTR) results from 2. Describe the relationship between a genotype and a
differences in the number of small-sequence repeats in a phenotype: Does the same genotype always result in
given area of the genome. page 314 the same phenotype? Must individuals with the same
phenotype have the same genotype?
DNA typing (DNA fingerprinting) analyzes genetic
polymorphisms at multiple genes with multiple alleles. 3. With regard to mutations, what is meant by the terms
Because there are so many possible genotypes in the “harmful,” “beneficial,” and “neutral”? Why it is
population, this procedure can uniquely identify an sometimes an oversimplification to consider a mutation as
individual with high probability. page 315 either harmful, beneficial, or neutral?
A restriction fragment length polymorphism (RFLP) 4. Describe two types of genetic polymorphism that are
results from small changes in the DNA sequence between useful in DNA typing.
chromosomes, such as point mutations, that create or
5. Define the term “SNP” and explain why researchers are
destroy restriction sites. page 316
interested in detecting SNPs.
15.3 Two common types of genetic polymorphism 6. Diagram how nondisjunction in meiosis I or II can result
are single-nucleotide polymorphisms (SNPs) and in extra or missing chromosomes in reproductive cells
copy-number variation (CNV). (gametes).
An SNP is a common difference in a single nucleotide. The 7. Describe the consequences of an extra copy of
DNA in any two human genomes differs at about 3 million chromosome 21 (Down syndrome).
SNPs. Most SNPs are not associated with any detectable
effect on phenotype. page 316
Log in to to check your answers to the Self-
CNV is a difference in the number of copies of a particular Assessment questions, and to access additional learning tools.
DNA sequence among chromosomes. page 318
CHAPTER 16
Mendelian
Inheritance
Core Concepts
16.1 Early theories of heredity
incorrectly assumed the
inheritance of acquired
characteristics and blending of
parental traits in the offspring.
16.2 The study of modern
transmission genetics began
with Gregor Mendel, who
used the garden pea as his
experimental organism and
studied traits with contrasting
characteristics.
16.3 Mendel’s first key discovery
was the principle of
segregation, which states
that members of a gene pair
separate equally into gametes.
16.4 Mendel’s second key
finding was the principle of
independent assortment,
which states that different
gene pairs segregate
independently of one another.
16.5 The patterns of inheritance
that Mendel observed in peas
can also be seen in humans.
Koichi Saito/A.collection/Getty Images.
325
326 SECTION 16.1 E A R LY T H E O R I E S O F I N H E R I TA N C E
Except for identical twins, each of us has his or her own personal this theory is that any trait, or characteristic, of an individual
genome, a unique human genome differing from all that have can be transmitted from parent to offspring. Even traits that
existed before and from all that will come after. Genetic variation are acquired during the lifetime of an individual, such as muscle
from one person to the next leads in part to our individuality, from strength or bodily injury, were thought to be heritable because
differences in appearance to differences in the ways our bodies of the substance supposedly passed from each body part to the
work. Examples of genetic variation in the human population reproductive organs.
range from harmless curiosities like the genetic difference in taste The theory that acquired characteristics can be inherited
receptors that determine whether or not you taste broccoli as being was invoked to explain such traits as the webbed feet of ducks,
unpleasantly bitter, to mutant forms of genes resulting in serious which were thought to result from many successive generations
diseases like sickle-cell anemia or emphysema. in which adult ducks stretched the skin between their toes
This chapter focuses on how that genetic variation is inherited. while swimming and passed this trait to offspring. A few
Transmission genetics deals with the manner in which genetic decades later, however, Aristotle (384–322 BCE) emphasized
differences among individuals are passed from generation to several observations that the theory of inheritance of acquired
generation. We are all aware of the effects of genetics. We know characteristics cannot account for:
that children resemble their parents and that there are sometimes
• Traits such as hair color can be inherited, but it is difficult to
uncanny similarities among even distant relatives. But some
see how hair—a nonliving tissue—could send substances to
patterns are more difficult to discern. Traits such as eye color, nose
the reproductive organs.
shape, or risk for a particular disease may be passed down faithfully
generation after generation, but sometimes they are not, and • Traits that are not yet present in an individual can be
sometimes they appear and disappear in seemingly random ways. transmitted to the offspring. For example, a father and his
As a modern science, transmission genetics began with the pea- adult son can both be bald, even though the son was born
breeding experiments carried out by the monk Gregor Mendel in before the father became bald.
the 1860s. However, even before then, people understood enough
• Parts of the body that are lost as a result of surgery or
about inheritance that they were able to select crops and livestock
accident are not missing in the offspring.
with particular characteristics.
From these and other observations, Aristotle concluded that
the process of heredity transmits only the potential for producing
16.1 EARLY THEORIES traits present in the parents, and not the traits themselves.
OF INHERITANCE Nevertheless, Hippocrates’ theory influenced biology until
well into the 1800s. It was incorporated into an early theory of
Thousands of years before Mendel, many societies carried out evolution proposed by the French biologist Jean-Baptiste Lamarck
practical plant and animal breeding. The ancient practices were around 1800. Charles Darwin, however, developed an alternative
based on experience rather than on a full understanding of the theory—the theory of evolution by natural selection (Chapter 21).
rules of genetic transmission, but they were nevertheless highly While traits acquired during the lifetime of a parent are not
successful. In Mesoamerica, for example, Native Americans chose transmitted to the offspring, parental misfortune or misbehavior
corn (maize) plants for cultivation that had the biggest ears and can nevertheless result in impaired fetal development and in some
softest kernels. Over many generations, their cultivated corn came cases permanent damage. For example, maternal malnutrition, drug
to have less and less physical resemblance to its wild ancestral addiction, alcoholism, infectious disease, and other conditions can
species. Similarly, people in the Eurasian steppes selected their severely affect the fetus, but these effects are due to disruption of
horses for a docile temperament suitable for riding or for hitching fetal development and not to changes in the genome.
to carts or sleds. Practical breeding of this kind provided the crops
and livestock from which most of our modern domesticated Belief in blending inheritance discouraged studies of
animals and plants derive. hereditary transmission.
Darwin subscribed to the now-discredited model of blending
Early theories of heredity predicted the transmission inheritance, in which traits in the offspring resemble the average
of acquired characteristics. of those in the parents. For example, this model predicts that the
The first written speculations about mechanisms of heredity offspring of plants with blue flowers and those with red flowers
were made by the ancient Greeks. Hippocrates (460–377 BCE), will have purple flowers. While traits of offspring are sometimes
considered the founder of Western medicine, proposed that each the average of those of the parents (think of certain cases of
part of the body in a sexually mature adult produces a substance human height), the idea of blending inheritance—which implies
that collects in the reproductive organs and that determines the blending of the genetic material—as a general rule presents
the inherited characteristics of the offspring. An implication of problems. For example, it cannot explain the reappearance of a
CHAPTER 16 M E N D E L I A N I N H E R I TA N C E 327
seed suppliers. His experimental approach was similar to that of seven physical features expressed in contrasting fashion among
a few botanists of the eighteenth and nineteenth centuries who the strains: seed color, seed shape, pod color, pod shape, flower
studied the results of hybridization, or interbreeding between color, flower position, and plant height.
two different varieties or species of an organism. Where Mendel The expression of each trait in each of the original strains
differed from his predecessors was in paying close attention that Mendel obtained was true breeding, which means that the
to a small number of easily classified traits with contrasting physical appearance of the offspring in each successive generation
characteristics. For example, where one strain of peas had yellow is identical to the previous one. For example, plants of the strain
seeds, another had green seeds; and where one had round seeds, with yellow seeds produced only yellow seeds, and those of the
another had wrinkled seeds (Fig. 16.3). Altogether Mendel studied strain with green seeds produced only green seeds. Likewise,
plants of the strain with round seeds produced only round seeds,
and those of the strain with wrinkled seeds produced only
wrinkled seeds.
FIG. 16.3 Contrasting traits. Mendel focused on seven contrasting The objective of Mendel’s experiments was simple. By
traits. means of crosses between the true-breeding strains and crosses
among their progeny, Mendel hoped to determine whether
Dominant Recessive
there are statistical patterns in the occurrence of the contrasting
a. Color of seeds characteristics, such as yellow seeds or green seeds. If such
(yellow or green)
patterns could be found, he would seek to devise a hypothesis to
explain them and then use his hypothesis to predict the outcome
b. Shape of seeds of further crosses.
(round or wrinkled)
In designing his experiments, Mendel departed from other
plant hybridizers of the time in three important ways:
c. Color of pod
(green or yellow) 1. Mendel studied true-breeding strains, unlike many other
plant hybridizers, who used complex and poorly defined
d. Shape of pod material.
(smooth or indented)
2. Mendel focused on one trait, or a small number of traits,
e. Color of flower at a time, with characteristics that were easily contrasted
(purple or white) among the true-breeding strains. Other plant hybridizers
crossed strains differing in many traits and tried to follow
all the traits at once. This resulted in amazingly complex
inheritance, and no underlying patterns could be discerned.
f. Position of flowers 3. Mendel counted the progeny of his crosses, looking for
(along stem or at tip) statistical patterns in the offspring of his crosses. Others
typically noted only whether offspring with a particular
characteristic were present or absent, but did not keep
track of and count all the progeny of a particular cross.
cells in the ovule at the base of the flower. And finally, a cloth
bag must be tied around the female flower to prevent stray FIG. 16.5 The first-generation hybrid (F1). A cross between two
pollen from entering. No wonder Mendel complained that his of Mendel’s true-breeding plants (the parental, or P1,
eyes hurt! generation) yielded first-generation hybrids displaying
For each of the seven pairs of contrasting traits, true-breeding the dominant trait.
strains differing in the trait were crossed. Fig. 16.5 illustrates a
typical result, in this case for a cross between a plant producing
yellow seeds and a plant producing green seeds. In these kinds of
crosses, the parental generation is referred to as the P1 generation,
Plant grown from Plant grown from
and the first offspring, or filial, generation is referred to as the true-breeding strain true-breeding strain
F1 generation. In the cross of P1 yellow × P1 green, Mendel observed with yellow seeds with green seeds
that all the F1 progeny had yellow seeds. This result was shown to be
independent of the seed color, yellow or green, of the pollen donor
because both of the crosses shown below yielded progeny plants
True-breeding
with yellow seeds: strains that are
crossed constitute
Pollen from strain Ovules from strain Offspring the P1 or parental
generation.
with yellow seeds with green seeds seeds yellow
P1 generation
Pollen from strain Ovules from strain Offspring
F1 generation
with green seeds with yellow seeds seeds yellow
Genes come in pairs that segregate in the formation 2. Each reproductive cell, or gamete, contains only one allele
of reproductive cells. of each gene. In this case, a gamete can contain the A allele
The explanation for the 3 : 1 ratio in the F2 and Mendel’s or the a allele, but not both.
observations in general can be summarized with reference to
3. In the formation of gametes, the two members of a gene
Fig. 16.7:
pair segregate (or separate) equally into gametes so that
1. Except for cells involved in reproduction, each cell of a half the gametes get one allele and half get the other allele.
pea plant contains two alleles of each gene. In each true- This separation of alleles into different gametes defines
breeding strain constituting the P1 generation, the two the principle of segregation. In the case of homozygous
alleles are identical. In Fig. 16.7, we designate the allele plants (such as AA or aa), all the gametes from an individual
associated with yellow seeds as A and that associated with are the same. That is, the homozygous AA strain with
green seeds as a. The genotype of the true-breeding strain yellow seeds produces gametes containing the A allele,
with yellow seeds can therefore be written as AA, and that and the homozygous aa strain with green seeds produces
of the true-breeding strain with green seeds as aa. The AA gametes containing the a allele.
CHAPTER 16 M E N D E L I A N I N H E R I TA N C E 331
yields yellow seeds (Fig. 16.8b). In other words, the testcross gives
TABLE 16.2 Genetic Ratios from Self-Fertilization of Plants different results depending on whether the parent is heterozygous
Showing the Dominant Phenotype ( Aa) or homozygous (AA).
Note that in a testcross the phenotypes of the progeny reveal
HOMOZYGOUS HETERO-
TRAIT DOMINANT ZYGOUS RATIO
the alleles present in the gametes from the tested parent. A
testcross with an Aa individual yields ½ Aa (yellow seeds) and
Yellow seeds 166 353 0.94:2 ½ aa (green seeds) since the Aa parent produces ½ A-bearing and
Round seeds 193 372 1.04:2 ½ a-bearing gametes. A testcross with an AA individual yields only
Green pods 40 60 1.33:2
Smooth pods 29 71 0.82:2 Aa (yellow seeds) since the AA parent produces only A-bearing
Purple flowers 36 64 1.13:2 gametes. These results are a direct demonstration of the principle
Flowers along stem 33 67 0.99:2 of segregation since the ratio of the phenotypes of progeny
Tall plants 28 72 0.78:2 reflect the equal segregation of alleles into gametes. Some of
Mendel’s testcross data indicating 1 : 1 segregation in heterozygous
genotypes are shown in Table 16.3.
The second prediction from the Punnett square in Fig. 16.7
is more complex. It has to do with the seeds in the F2 generation Segregation of alleles reflects the separation of
that show the dominant yellow phenotype. Note that although chromosomes in meiosis.
these seeds have the same phenotype, they have two different The principles of transmission genetics have a physical basis in
genotypes ( AA and Aa). Among just the yellow seeds, ⅓ should the process of meiosis (Chapter 11). During meiosis I, maternal
have the genotype AA and ⅔ should have the genotype Aa, for and paternal chromosomes (homologous chromosomes) align on
a ratio of 1 AA : 2 Aa. (The proportions are ⅓ : ⅔ because we the metaphase plate. Then, during anaphase I, the homologous
are considering only the seeds that are yellow.) Plants with the chromosomes separate, and each chromosome goes to a different
AA and Aa genotypes can be distinguished by the types of seed pole. Because gene pairs are carried on homologous chromosomes,
they produce when self-fertilized. The AA plants produce only the segregation of alleles observed by Mendel corresponds to the
seeds with the dominant yellow phenotype (that is, they are separation of chromosomes that takes place in anaphase I.
true breeding), whereas the Aa plants yield dominant yellow Fig. 16.9 illustrates the separation of a pair of homologous
and recessive green seeds in the ratio 3 : 1. Mendel did such chromosomes in anaphase I. In the configuration shown, the
experiments, and the prediction turned out to be correct. His data copies of the A allele (dark blue) separate from the copies of the
confirming the 1 : 2 ratio of AA : Aa among F2 individuals with the a allele (light blue) in anaphase I. The separation of chromosomes
dominant phenotype are shown in Table 16.2. is the physical basis of the segregation of alleles.
TABLE 16.3 Phenotype of Progeny from Testcrosses of FIG. 16.10 Incomplete dominance for flower color in
Heterozygotes snapdragons. In incomplete dominance, an
intermediate phenotype is seen.
DOMINANT RECESSIVE
TRAIT TRAIT TRAIT RATIO
CRCW CWCW
¼ ¼
FIG. 16.9 Segregation of alleles of a single gene. Homologous
F2 generation
chromosomes separate during meiosis, leading to
segregation of alleles.
The principles of transmission genetics are statistical
Resulting
Segregation reflects the separation
gametes
and are stated in terms of probabilities.
of homologous chromosomes
during anaphase I of meiosis. The element of chance in fertilization implies that the genotype
A of any particular progeny cannot be determined in advance.
However, one can deduce the likelihood, or probability, that a
specified genotype will occur. The probability of occurrence of a
Copies of A allele
A A genotype must always lie between 0 and 1; a probability of 0 means
in replicated
A Meiosis II that the genotype cannot occur, and a probability of 1 means
chromosome
that the occurrence of the genotype is certain. For example, in
a the cross Aa × AA, no offspring can have the genotype aa, so
a Copies of a allele in this mating the probability of aa is 0. Similarly, in the mating
a in replicated
homologous AA × aa, all offspring must have the genotype Aa, so in this mating
chromosome a the probability of Aa is 1.
In many cases, the probability of a particular genotype is
Anaphase I neither 0 nor 1, but some intermediate value. For one gene, the
334 SECTION 16.3 S E G R E G AT I O N : M E N D E L’ S K E Y D I S COV E RY
probabilities for a single individual can be deduced from the one nearest the stem is green and the others yellow. Here,
parental genotypes in the mating and the principle of segregation. the word “and” is a simple indicator that the multiplication
For example, the probability of producing a homozygous recessive rule should be used. Because each seed results from an
individual from the cross Aa × Aa is ¼ (see Fig. 16.7), and that independent fertilization, this probability is given by the
from the cross Aa × aa is ½ (see Fig. 16.8a). product of the probability that the seed nearest the stem is
The genotype and phenotype probabilities for a single aa and the probability that each of the other seeds is either
individual can also be inferred from observed data because the AA or Aa, and hence the probability is ¼ × ¾ × ¾ × ¾ =
overall proportions of two (or more) genotypes among a large 27/256, as shown for the top pod in Fig. 16.11.
number of observations approximates the probability of each of
the genotypes for a single observation. For example, in Mendel’s The addition and multiplication rules are very powerful when
F2 data (see Table 16.1), the overall ratio of dominant : recessive is used in combination. Consider the following question: In the
2.98 : 1, or very nearly 3 : 1. This result implies that the probability mating Aa × Aa, what is the probability that, among four seeds in
that an individual F2 plant has the homozygous recessive a pod, exactly one is green? We have already seen in Fig. 16.11 that
phenotype is very close to ¼, which is the value inferred from the the multiplication rule gives the probability of the seed nearest the
principle of segregation. stem being green as 27/256. As illustrated in Fig. 16.11, there are only
Sometimes it becomes necessary to combine the probabilities four possible ways in which exactly one seed can be green, each of
of two or more possible outcomes of a cross, as in determining the which has a probability of 27/256, and these outcomes are mutually
probability of a genotype occurring based on the probabilities of the exclusive. Therefore, by the addition rule, the probability of there
gametes occurring. In such cases either of two rules are helpful: being exactly one green and three yellow seeds in a pod, occurring
in any order, is given by 27/256 + 27/256 + 27/256 + 27/256 =
1. Addition rule. This principle applies when the possible 108/256, or approximately 42%.
outcomes being considered cannot occur simultaneously.
For example, suppose that a single offspring is chosen at j Quick Check 4 What is the probability that any two peas are
random from the progeny of the mating Aa × Aa, and we green and two are yellow in a pea pod with exactly four seeds?
wish to know the probability that the offspring is either AA
or Aa. The key words here are “either” and “or.” Each of these Mendelian segregation preserves genetic variation.
outcomes is possible, but both cannot occur simultaneously As noted earlier, Darwin was befuddled because blending
in a single individual; the outcomes are mutually exclusive. inheritance would make genetic variation disappear so rapidly that
When the possibilities are mutually exclusive, the addition evolution by means of natural selection could not occur. Although
rule states that the probability of either event occurring is
given by the sum of their individual probabilities. In this
example, the chosen offspring could either have genotype AA FIG. 16.11 Application of the multiplication and addition rules.
(with probability ¼, according to Fig. 16.7), or the offspring
could have genotype Aa (with probability ½). Therefore,
the probability that the chosen individual has either the AA Probability that the seed closest
to the stem is green and the
or the Aa genotype is given by ¼ + ½ = ¾ (see Fig. 16.7). (¼) (¾) (¾) (¾) = 27/256 others are yellow is determined
Alternatively, the ¾ could be interpreted to mean that, by the multiplication rule.
among a large number of offspring from the mating
Aa × Aa, the proportion exhibiting the dominant phenotype
will be very close to ¾. This interpretation is verified by the (¾) (¼) (¾) (¾) = 27/256
data in Table 16.1.
The ratio of these phenotypes is 9.9 : 3.3 : 3.1 : 1.0, which Mendel FIG. 16.14
realized is close to 9 : 3 : 3 : 1. The latter ratio is that expected if the A
and a alleles for seed color undergo segregation and form gametes
independently of the B and b alleles for seed shape. How did Mendel
How are single-gene traits
come to expect a 9 : 3 : 3 : 1 ratio of phenotypes? For seed color alone
we expect a ratio of ¾ yellow : ¼ green, and for seed shape alone we
inherited?
expect a ratio of ¾ round : ¼ wrinkled. If the traits are independent, BACKGROUND Gregor Mendel’s experiments, carried out in the
then we can use the multiplication rule to predict the outcomes for years 1856–1863, are among the most important in all of biology.
both traits:
EXPERIMENTS Mendel set out to improve upon previous research
yellow round (¾) × (¾) = 9/16
in heredity. He writes that “among all the numerous experiments
green round (¼) × (¾) = 3/16
made, not one has been carried out to such an extent and in such
yellow wrinkled (¾) × (¼) = 3/16
a way as to make it possible to determine the number of different
green wrinkled (¼) × (¼) = 1/16
forms under which the offspring of the hybrids appear, or to arrange
these forms with certainty according to their separate generations, or
Note that 9/16 : 3/16 : 3/16 : 1/16 is equivalent to 9 : 3 : 3 : 1.
definitely to ascertain their statistical relations.” By studying simple
The underlying reason for the 9 : 3 : 3 : 1 ratio of phenotypes
traits across several generations of crosses, Mendel observed how
in the F2 generation is that the alleles for yellow versus green
these traits were inherited.
and those for round versus wrinkled are assorted into gametes
independently of each other. In other words, the hereditary RESULTS Mendel concluded that the “statistical relations” were
transmission of either gene has no effect on the hereditary very clear. Crosses between plants that were hybrids of a single trait
transmission of the other. A Punnett square depicting independent displayed two phenotypes in a ratio of 3:1. Crosses between plants
assortment is shown in Fig. 16.13. The A and a alleles segregate that were hybrids of two traits displayed four different phenotypes in
equally into gametes as ½ A : ½ a, and likewise the B and b a ratio of 9:3:3:1.
alleles segregate equally into gametes as ½ B : ½ b. The result of
HYPOTHESIS From observing these ratios among several different
independent assortment is that the four possible gametic types are
traits, Mendel made two key hypotheses about the inheritance of
produced in equal proportions:
traits, now called Mendel’s laws:
¼ AA Bb AA bb Aa Bb Aa bb
1/16 1/16 1/16 1/16
aB
¼ Aa BB Aa Bb aa BB aa Bb
1/16 1/16 1/16 1/16
AB gametes (½) × (½) = ¼
Ab gametes (½) × (½) = ¼
ab
¼ aB gametes (½) × (½) = ¼
Aa Bb Aa bb aa Bb aa bb
1/16 1/16 1/16 1/16
ab gametes (½) × (½) = ¼
There are 9 possible genotypes and 4 possible As the Punnett square in Fig. 16.13 shows, random union of
phenotypes. The ratio of phenotypes is 9:3:3:1.
these gametic types produces the expected ratio of 9 yellow round,
CHAPTER 16 M E N D E L I A N I N H E R I TA N C E 337
2. The principle of independent assortment states that the two 2. The principle of independent assortment: Although the
copies of each gene segregate into gametes independently of the Punnett square for two pairs of alleles has 16 squares, there are
two copies of another gene. only 9 genotypes, and the hypothesis of independent assortment
predicts that these genotypes should appear in the ratio of
Hypothesis: Independent assortment
1 AA BB : 2 AA Bb : 1 AA bb : 2 Aa BB; 4 Aa Bb : 2 Aa bb : 1 aa BB :
AB Ab aB ab
¼ ¼ ¼ ¼ 2 aa Bb : 1 aa bb. As before, Mendel tested this hypothesis by
self-fertilization of plants grown from the F2 seeds, classifying
AB any that bred true for either trait as homozygous and any that
¼ AA BB AA Bb Aa BB Aa Bb
1/16 1/16 1/16 1/16
segregated to yield both dominant and recessive phenotypes as
heterozygous. In the experimental test, once again the observed
Ab
¼ AA Bb AA bb Aa Bb Aa bb numbers fit the expected values within the margins that would be
1/16 1/16 1/16 1/16
expected by chance.
aB
¼ Aa BB Aa Bb aa BB aa Bb Experimental test
1/16 1/16 1/16 1/16
ab AA BB AA Bb AA bb
¼ Aa Bb Aa bb aa Bb aa bb
1/16 1/16 1/16 1/16
Observed 38 60 28
Expected 33 66 33
ANALYSIS Mendel found support for his two hypotheses in the
statistical analysis of the results of his meticulous crosses.
Aa BB Aa Bb Aa bb
1. The principle of segregation: A prediction of the hypothesis of
Observed 65 138 68
segregation is that, among seeds with the dominant phenotype,
Expected 66 132 66
the ratio of homozygous to heterozygous genotypes should be
1: 2. Mendel tested this prediction in several ways, one of which
was simply to allow plants grown from F2 seeds to self-fertilize. aa BB aa Bb aa bb
Any that were true breeding for the dominant phenotype he
classified as homozygous, and any that segregated to yield both Observed 35 67 30
Expected 33 66 33
dominant and recessive phenotypes he classified as heterozygous.
In the experimental test, the observed numbers fit the expected
values within the margins that would be expected by chance. FOLLOW-UP WORK Mendel’s work was ignored during his
lifetime, and its importance was not recognized until 1900,
Experimental test
16 years after his death. The rediscovery marks the beginning of
the modern science of genetics.
3 green round, 3 yellow wrinkled, and 1 green wrinkled. Fig. 16.14 of homologous chromosomes align randomly on the metaphase
summarizes how Mendel’s experiments led him to formulate his plate in meiosis I. For some pairs of chromosomes, the maternal
two laws. chromosome goes toward one pole during anaphase I, and the
paternal chromosome goes to the other pole, but for other pairs, just
Independent assortment reflects the random the opposite occurs. Because the alignment is random, gene pairs on
alignment of chromosomes in meiosis. different chromosomes assort independently of one another.
Independent assortment of genes on different chromosomes results Fig. 16.15 illustrates two possible alignments that are equally
from the mechanics of meiosis (Chapter 11), in which different pairs likely. In one alignment, the B allele (dark red) goes to the same
337
338 SECTION 16.4 I N D E P E N D E N T A S S O RT M E N T
FIG. 16.15 Independent assortment of genes in different FIG. 16.16 Epistasis, the interaction of genes affecting the
chromosomes. Chromosomes are sorted into daughter same trait. Epistasis can modify the 9 : 3 : 3 : 1 ratio of
cells randomly during meiosis, resulting in independent phenotypes, in this example to 13 : 3.
assortment of genes.
The White Leghorn is white The White Wyandotte is
because the inhibitor allele white because the pigment
Independent assortment of genes in different chromosomes reflects I blocks expression of the allele c does not produce
the fact that nonhomologous chromosomes can orient in either of two pigment allele C. pigment.
ways that are equally likely.
A A b
ⴛ
B
A B A b P1 generation
CC I I cc i i
a b a B
a B
a b
ⴛ
F1 generation
Anaphase I Anaphase I
Cc I i Cc I i
CI Ci cI ci
Resulting gametes Resulting gametes ¼ ¼ ¼ ¼
A A A A CI
¼
B B b b CC I I CC I i Cc I I Cc Ii
a a a a
Ci
¼
b b B B CC Ii CC ii Cc Ii Cc ii
cI
¼
Cc II Cc Ii cc II cc Ii
pole as the A allele (dark blue), and, in the other alignment, the
ci
b allele (light red) goes in the same direction as the A allele. The first ¼
type of alignment results in a 1 : 1 ratio of AB : ab gametes, and the Cc Ii Cc ii cc Ii cc ii
second type of alignment results in a 1 : 1 ratio of Ab : aB gametes.
Because the two orientations are equally likely, the overall ratio Genotypes of the form C– ii have colored
feathers, whereas all other genotypes have
of AB : ab : Ab : aB from a large number of cells undergoing meiosis white feathers. The result is an F2 ratio of
is expected to be 1 : 1 : 1 : 1. This is the principle of independent white : colored of 13:3, which is a modified
assortment for genes located in different chromosomes. form of the expected 9:3:3:1.
FIG. 16.18 Pedigree of a trait caused by a dominant allele. This pedigree shows the inheritance of shortened fingers associated with a form of
brachydactyly (inset). Photo source: Stefan Mundlos.
Recessive traits skip generations. in Fig. 16.19. For a recessive trait that is sufficiently rare,
Recessive inheritance shows a pedigree pattern very different from virtually all affected individuals have unaffected parents.
that of dominant inheritance. The pedigree shown in Fig. 16.19
4. Affected individuals often result from mating between
pertains to albinism, in which the amount of melanin pigment
relatives, typically first cousins.
in the skin, hair, and eyes is reduced. In most populations, the
frequency of albinism is about 1 in 36,000, but it has a much
Recessive inheritance has these characteristics because
higher frequency—about 1 in 200—among the Hopi and several
recessive alleles can be transmitted from generation to generation
other Native American tribes of the Southwest. (It is not unusual
without manifesting the recessive phenotype. In order for an
for genetic diseases to have elevated frequencies among isolated
affected individual to occur, the recessive allele must be inherited
populations.) This type of albinism is due to a mutation in the gene
from both parents. Mating between relatives often allows rare
OCA2, which encodes a membrane transporter protein thought
recessive alleles to become homozygous because an ancestor
to be important in transport of the amino acid tyrosine, which is
that is shared between the relatives may carry the gene ( Aa). The
used in the synthesis of the melanin pigment responsible for skin,
recessive allele in the common ancestor can be transmitted to both
hair, and eye color.
parents, making them each a carrier of the allele as well. If both
As noted in Chapter 15, another type of mutation affecting
parents are unaffected carriers of the allele, they both have the
expression of this same gene is associated with blue eyes. As shown
genotype Aa, and therefore ¼ of their offspring are expected to be
in Fig. 16.19, double lines represent matings between relatives, and
homozygous aa and affected.
in both cases shown here the mating is between first cousins.
These are the principal pedigree characteristics of recessive
traits: Many genes have multiple alleles.
The examples discussed so far in this chapter involve genes
1. The trait may skip one or more generations. with only two alleles, such as A for yellow seeds and a for green
seeds. Similarly, as noted in Chapter 15, most single-nucleotide
2. Affected individuals are equally likely to be females or
polymorphisms (SNPs) have only two alleles, differing only in
males.
which particular base pair is present at a particular position in
3. Affected individuals may have unaffected parents, as in the genomic DNA. On the other hand, because a gene consists of a
offspring of the second mating in the second generation sequence of nucleotides, any nucleotide or set of nucleotides in
CHAPTER 16 M E N D E L I A N I N H E R I TA N C E 341
In this case, tobacco smoking is an environmental factor that BRCA2 for breast cancer can have frequent mammograms, and those
increases the severity of the disease. with the TCF7L2 risk factor for type 2 diabetes can decrease their
Incomplete penetrance and variable expressivity both provide risk by lifestyle choices that include weight control and exercise.
examples where a given genotype does not always produce the While there are many potential benefits to genetic testing,
same phenotype, since the expression of genes is often influenced there are also some perils. One major concern is maintaining the
by other genes, the environment, or a combination of the two. privacy of those who choose to be tested. With medical records
? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME increasingly going online, who will have access to your test results,
and how will this information be used? Could your test results be
How do genetic tests identify disease risk factors? used to deny you health or life insurance because you have a higher
Your personal genome, as well as that of every human being, than average risk of some medical condition? Or could an employer
contains a unique combination of alleles of thousands of different who got hold of your genetic test results decide to reassign you
genes. Most of these have no detectable effects on health or to another job, or even eliminate your position because of your
longevity, but many are risk factors for genetic diseases. Molecular genetic predispositions? There are some safeguards designed to
studies have discovered particular alleles of genes associated with a protect you from such discrimination. The Genetic Information
large number of such conditions, and the presence of these alleles Nondiscrimination Act (GINA) was signed into law in 2008 and
can be tested. More than a thousand genetic tests have already forbids the use of genetic information in decisions concerning
been deployed, and many more are actively being developed. employment and health insurance. The protection provided by
A genetic test is a method of identifying the genotype of an GINA will, it is hoped, allow for the responsible and productive use
individual. The tests may be carried out on entire populations or of genetic information.
restricted to high-risk individuals. There is also increasing concern about the reliability and
The benefits of genetic testing can be appreciated by an accuracy of genetic tests, especially direct-to-consumer (DTC)
example. Screening of newborns for phenylketonuria identifies genetic tests. DTC tests can be purchased directly without the
babies with high blood levels of phenylalanine. In the absence of intervention of medical professionals. Since the consumer sends a
treatment, 95% of such newborns will progress to moderate or biological sample and DTC tests are carried out by the provider, the
severe mental retardation, whereas virtually all those placed on a tests are not regarded as medical devices and so are unregulated.
special diet with a controlled amount of phenylalanine will have One problem is that some DTC tests are based on flimsy and
mental function within the normal range. For recessive conditions unconfirmed evidence connecting a gene with a disease. Another
like phenylketonuria, tests can be carried out on people with is that the link between genotype and risk may be exaggerated
affected relatives to identify the heterozygous genotypes. Testing for marketing purposes. Yet another is lack of information
can also identify genetic risk factors for disease, and carriers can on quality control in the DTC laboratories. Finally, consumer
take additional precautions. For example, individuals with a1AT misinterpretation may regard genotype as destiny, at one extreme
deficiency can prolong and improve the quality of their lives by descending into depression and despair, and at the other using a
not smoking tobacco, women with genetic risk factors BRCA1 and low-risk genotype to justify an unhealthy lifestyle. •
Mendel explained this result by hypothesizing that there orientation of different chromosomes on the meiotic
is a hereditary factor for each trait (now called a gene); that spindle. page 337
each pea plant carries two copies of the gene for each trait;
In some cases, genes interact with each other, modifying the
and that one of two different forms of the gene (alleles) is
expected ratios in crosses. Epistasis is a gene interaction in
dominant to the other one. page 329
which one gene affects the expression of another. page 338
6. Describe an instance in which you would use a 9. Construct a human pedigree for a dominant and a
testcross, and why. recessive trait and explain the patterns of inheritance.
7. Define the multiplication and addition rules, and 10. Discuss the benefits and risks of genetic testing and
explain how these rules can help you predict the outcome personal genomics.
of a cross between parents with known genotypes.
8. What are some reasons why a single trait might not Log in to to check your answers to the Self-
Assessment questions, and to access additional learning tools.
show a 3 : 1 ratio of phenotypes in the F2 generation of a
cross between true-breeding strains, and why a pair of
traits might not show a 9 : 3 : 3 : 1 ratio of phenotypes in the
F2 generation of a cross between true-breeding strains?
CHAPTER 17
Inheritance of Sex
Chromosomes,
Linked Genes,
and Organelles
Core Concepts
17.1 Many organisms have
a distinctive pair of
chromosomes, often called
the X and Y chromosomes,
that differ between the sexes
and show different patterns
of inheritance in pedigrees
from other chromosomes.
17.2 X-linked genes, which show
a crisscross inheritance
pattern, provided the first
evidence that genes are
present in chromosomes.
17.3 In genetic linkage, two
genes are sufficiently
close together in the same
chromosome that the
particular combination
of alleles present in the
chromosome tends to remain
together in inheritance.
17.4 Most Y-linked genes are
passed from father to son.
17.5 Mitochondria and chloroplast
DNA follow their own
inheritance pattern.
SSPL/Getty Images.
345
346 SECTION 17.1 T H E X A N D Y S E X C H RO M O S O M E S
Mendel’s principles of segregation and independent assortment Reciprocal crosses do not produce the same types and numbers
are the foundation of transmission genetics (Chapter 16). For traits of progeny. In one type of cross, when a color-blind man mates
such as pea color and seed shape that are encoded by single genes with a woman who is not color blind, all of the sons and daughters
and display simple dominance, these principles predict simple have normal color vision. However, in the reciprocal cross, when a
phenotypic ratios in the progeny from self-crosses of heterozygous color-blind woman mates with a man who is not color blind, all of
genotypes. The principle of segregation also defines the inheritance the daughters have normal color vision but all of the sons are color
patterns expected in human pedigrees for traits due to recessive blind. For the X and Y sex chromosomes, reciprocal crosses are not
or dominant mutations, as we saw in the case of albinism and equivalent.
brachydactyly.
However, we also saw in Chapter 16 that not all crosses are as In many animals, sex is genetically determined
simple as those for Mendel’s pea plants. For example, the and associated with chromosomal differences.
3 : 1 phenotypic ratio in progeny of self-crosses of heterozygotes is Most chromosomes come in pairs that match in shape and size.
1 : 2 : 1 in the case of alleles that show incomplete dominance. The The members of each pair are known as homologous chromosomes
9 : 3 : 3 : 1 ratio of phenotypes observed for two genes that show because they have the same genes along their length (Chapter 11).
independent assortment can be altered by epistasis, producing One member of each pair of homologous chromosomes is
ratios such as 12 : 3 : 1 or 13 : 3. None of these is an exception to inherited from the mother and the other from the father.
Mendel’s laws since his laws reflect chromosome movement In many animal species, however, the sex of an individual is
during meiosis (Chapter 11). Instead, they reflect how genes are determined by a distinctive pair of unmatched chromosomes
expressed or how different genes interact to produce a phenotype. known as the sex chromosomes, which are usually designated
This chapter highlights additional patterns of inheritance as the X chromosome and the Y chromosome (Chapter 13).
that Mendel did not observe owing to his choice of experimental Chromosomes other than the sex chromosomes are known as
organism and the traits he studied. None of these patterns autosomes.
undermines or invalidates his insight that alternative alleles of a In humans, a normal female has two copies of the
gene can have different effects on the expression of a phenotype. X chromosome (a sex-chromosome constitution denoted XX), and
Nor do they contradict later discoveries that genes in the nucleus a normal male has one X chromosome and one Y chromosome
are present in homologous chromosomes that pair and segregate ( XY). The sizes of the human X and Y chromosomes are very
in meiosis. Since Mendel’s time, researchers have observed many different from each other (Fig. 17.1). The X chromosome DNA
inheritance patterns that seem to defy one or both of Mendel’s
laws. What such examples reveal is that the location of a gene is
as important to our predictions about the inheritance of a trait as
whether its alleles are dominant or recessive. FIG. 17.1 Human sex chromosomes. The human X and Y sex
In this chapter, we discuss how genes carried in the sex chromosomes differ in size and number of genes. Source:
chromosomes are transmitted differently in males and in females Science Photo Library/Science Source.
and how genes close to each other in the same chromosome do not
undergo independent assortment and therefore violate Mendel’s Almost none of the genes
in the X chromosome
second law. Genes located in the genomes of mitochondria and have counterparts in the
chloroplast appear to defy Mendel’s laws altogether since the Y chromosome.
organelles are inherited differently from the way chromosomes are The tips of the arms of the
X
inherited. Such unique patterns of inheritance expand the types of X and Y chromosomes
ratios and predictions we saw in Chapter 16 and draw our attention share a small region of
Y
homology (red).
to the location and organization of genes—in specific chromosomes,
relative to other genes, or outside the nucleus altogether.
17.2 INHERITANCE OF GENES IN FIG. 17.3 Morgan’s white-eyed fly. Morgan’s discovery of
THE X CHROMOSOME X-linked genes derived from his crosses of a white-eyed
male in 1910.
Genes in the X chromosome are called X-linked genes. These Parental generation
genes have a unique pattern of inheritance first discovered by
Thomas Hunt Morgan in 1910. Morgan’s pioneering studies of
genetics of the fruit fly Drosophila melanogaster helped bring
Mendelian genetics into the modern era. The discovery of X-linked X
inheritance was not only important in itself, but also provided the
first experimental evidence that chromosomes contain genes. Red-eyed White-eyed
female male
X-linked inheritance was discovered through studies
of male fruit flies with white eyes.
Morgan’s discovery of X-linked genes began when he noticed a F1 generation
white-eyed male in a bottle of fruit flies in which all the others
had normal, or wild-type, red eyes. (The most common phenotype
in a population is often called the wild type.) This was the first All of the progeny have
X red eyes.
mutant he discovered, and finding it was a lucky break. As we saw
in Chapter 16, most mutations are recessive, which means that
when they occur their effect on the organism (the phenotype) is Red-eyed Red-eyed
female male
not observed because of the presence of the nonmutant gene in
the homologous chromosome. Recall that the nonmutant form of
a recessive mutant gene is dominant, and that the different forms F2 generation
of the gene are alleles.
Morgan’s initial crosses are outlined in Fig. 17.3. In the first White eyes reappear in
the next generation,
generation, he crossed the mutant white-eyed male with a wild- but only in males. All
type red-eyed female. All of the progeny (F1) fruit flies had red eyes, of the females have
red eyes, and among
as you would expect from a cross with any recessive mutation. the males, the ratio of
Morgan then carried out matings between brothers and sisters Red-eyed Red-eyed White-eyed red:white eyes is 1:1.
among the F1 generation, and he found that the phenotype of female male male
white eyes reappeared among the progeny. This result, too, was
1:1
expected. However, there was a surprise: Morgan observed that the
white-eye phenotype was associated with the sex of the fly. In the F2
allele of this gene, the recessive mutation will be reflected in the
generation, all the white-eyed fruit flies were male, and the white-
male’s phenotype—in this case, white eyes.
eyed males appeared along with red-eyed males in a ratio of 1 : 1. No
The Punnett square in Fig. 17.4a explains why all the
females with white eyes were observed; all the females had red eyes.
offspring had red eyes when Morgan crossed the white-eyed
male with a red-eyed female in the parental generation. During
Genes in the X chromosome exhibit a “crisscross”
meiosis in the male, the mutant X chromosome segregates from
inheritance pattern.
the Y chromosome, and each type of sperm, X or Y, combines with
When Morgan did his crosses with the white-eyed male, the
a normal X-bearing egg. The result is that the female progeny are
X chromosome had only recently been discovered by microscopic
heterozygous. They have only one copy of the mutant allele, and
examination of the chromosomes in male and female
because the mutant allele is recessive, the heterozygous females
grasshoppers. Morgan was the first to understand that the pattern
do not express the mutant white-eye trait. The male progeny are
of inheritance of the X chromosome would be different from
also red-eyed because they receive their X chromosome from their
that of the autosomes, and he proposed the hypothesis that the
wild-type red-eyed mother.
white-eyed phenotype was due to a mutation in a gene in the
The Punnett square in Fig. 17.4a illustrates two important
X chromosome. This hypothesis could explain the pattern of
principles governing the inheritance of X-linked genes:
inheritance shown in Fig. 17.3.
The key features of X-linked inheritance are shown in Fig. 17.4. 1. The phenotypes of the XX offspring indicate that a male
In Drosophila, as in humans, females are XX and males are XY. transmits his X chromosome only to his daughters. In this
Fig. 17.4a shows an XY male in which the X chromosome contains case, the X chromosome transmitted by the male carries
a recessive mutation. Because the Y chromosome does not carry an the white-eye mutation.
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 349
a. b.
X X
In this case,
white eyes
appear in both
sexes in the
ratio red:white
of 1:1.
Red-eyed Red-eyed White-eyed Red-eyed White-eyed Red-eyed White-eyed
female male male female female male male
w+w+ or w+w– w+Y w–Y w+w– w–w– w+Y w–Y
they receive their X chromosome from their mother. The female X chromosome. However, it was one of Morgan’s students who
offspring from this cross receive one of their X chromosomes showed experimentally that the white-eye mutation was actually
from their father, and hence they are heterozygous, w1w2. When a physical part of the X chromosome. Today, it seems obvious that
the male and female progeny are mated together, their offspring genes are in chromosomes because we know that genes consist
consist of all red-eyed females (half of which are heterozygous) and of DNA and that DNA in the nucleus is found in chromosomes.
a 1 : 1 ratio of red-eyed to white-eyed males, exactly as Morgan had But in 1916, when Calvin B. Bridges, who had joined Morgan’s
observed. laboratory as a freshman, was working on his PhD research under
The hypothesis of X-linkage not only explained the original Morgan’s direction, neither the chemical nature of the gene nor
data, but it also predicted the results of other crosses. One the chemical composition of chromosomes was known.
important test is outlined in Fig. 17.5b. Here, the parental cross In one set of experiments, Bridges crossed mutant white-eyed
is the same as that in Fig. 17.5a, but instead of mating the females with wild-type red-eyed males (Fig. 17.6). Usually, the
F1 females to their brothers, they are mated to white-eyed males. progeny consisted of red-eyed females and white-eyed males (Fig.
The prediction is that there should be a 1 : 1 ratio of red-eyed to 17.6a). This is the result expected when the X chromosomes in the
white-eyed females as well as a 1 : 1 ratio of red-eyed to white-eyed mother separate normally at anaphase I in meiosis because all the
males. Again, these were the results observed. By the results of daughters receive a w1-bearing X chromosome from their father and
these crosses and others, Morgan demonstrated that the pattern all the sons receive a w2-bearing X chromosome from their mother.
of inheritance of the white-eye mutation parallels the pattern of But Bridges noted a few rare exceptions among the progeny.
inheritance of the X chromosome. He saw that about 1 offspring in 2000 from the cross was
“exceptional”—either a female with white eyes or a male with red
X-linkage provided the first experimental evidence eyes. The exceptional females were fertile, and the exceptional
that genes are in chromosomes. males were sterile. To explain these exceptional progeny, Bridges
Morgan’s original experiments indicated that the white-eye proposed the hypothesis diagrammed in Fig. 17.6b: The X chromo-
mutation showed a pattern of inheritance like that expected of the somes in a female occasionally fail to separate in anaphase I in
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 351
Rare XO males
receive their X Genes in the X chromosome show characteristic
In a cross with
white-eyed females,
chromosome patterns in human pedigrees.
from their
nondisjunction of the father.
The features of X-linked inheritance can be seen in human
X chromosome pedigrees for traits due to an X-linked recessive mutation.
results in XXY female
progeny with white These are illustrated in Fig. 17.7 for red–green color blindness, a
eyes and XO male White-eyed Red-eyed condition that affects about 1 in 20 males. An individual with red–
progeny with red female male
w+
green color blindness will have difficulty seeing the number in the
eyes. w–w–Y
colored dots in Fig. 17.7.
352 SECTION 17.2 I N H E R I TA N C E O F G E N E S I N T H E X C H RO M O S O M E
Unaffected male
Unaffected female
Affected male
Proven carrier female
Possible carrier female
Albert Victoria
Edward VII
George VI Alexis
GERMANY RUSSIA
Elizabeth II Philip
Juan
Carlos
BRITAIN
George Charlotte
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 353
wild-type females that are heterozygous for both genes, and progeny consists of w1cv2 and w2cv1 combinations of alleles.
phenotypically wild-type males. When these are crossed with each These are called recombinants, and they result from a crossover,
other, the female F2 progeny do not tell us anything because they the physical exchange of parts of homologous chromosomes,
are all wild type; each female receives the w1cv1 X chromosome which takes place in prophase I of meiosis (Chapter 11).
from her father and therefore has red eyes and normal crossveins. Crossing over is a key process in meiosis (Chapter 11). Most
In the male F2 progeny, however, the situation is different: Each chromosomes have one or more crossovers that form between
male progeny receives its X chromosome from the mother and its the homologous chromosomes as they pair and undergo meiosis.
Y chromosome from the father, and so the phenotype of each male Human females average about 2.75 crossovers per chromosome
immediately reveals the genetic constitution of the X chromosome pair, and human males average about 2.50 crossovers per
that the male inherited from the mother. chromosome pair. As noted earlier for the X and Y chromosomes,
As shown in Fig. 17.9, the male F2 progeny consist of four types: crossovers between homologous chromosomes are important
mechanically because they help hold the homologs together so
Genotype of F2 Progeny Number of Fruit Flies they can align properly at metaphase I and segregate to opposite
w1cv1/Y (red eyes, normal crossveins) 357 poles at anaphase I.
w2cv2/Y (white eyes, missing crossveins) 341 Fig. 17.10 shows how recombinant chromosomes arise from
crossing over between genes, using the hypothetical genes A and
w1cv2/Y (red eyes, missing crossveins) 52 B. In a cell undergoing meiosis in which a crossover takes place
w cv /Y (white eyes, normal crossveins)
2 1
45 between the genes, the allele combinations are broken up in the
chromatids involved in the exchange, and the resulting gametes
Although all four possible classes of maternal gametes are are AB, Ab, aB, and ab (Fig. 17.10a).
observed in the male progeny, they do not appear in the ratio Note that crossing over does not result only in recombinant
1 : 1 : 1 : 1 expected when gametes contain two independently chromosomes. Fig. 17.10a shows that, even when a crossover
assorting genes (Chapter 16). The lack of independent assortment occurs in the interval between the genes, two of the resulting
means that the genes show linkage. chromosomes contain the nonrecombinant configuration of
The male progeny fall into two groups. One group, alleles. These nonrecombinant configurations occur because
represented by larger numbers of progeny, derives from maternal crossing over occurs at the four-strand stage of meiosis (when
gametes containing either w1cv1 or w2cv2. These are called each homologous chromosome is a pair of sister chromatids),
nonrecombinants because the alleles are present in the same but only two of the four strands (one sister chromatid from each
combination as that in the parent. The other group of male homologous chromosome) are included in any crossover.
FIG. 17.10 Linkage and recombination. (a) Crossing over between genes results in recombination between the alleles of the genes. (b) When
crossing over occurs outside the interval between genes, there is no recombination between the alleles of the genes.
a.
b.
A B A B A B
a b a b
A B
Nonrecombinant
a b for A and B genes
A B A B
a b a b a b
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 355
Fig. 17.10b shows a second way in which nonrecombinant In the example with the genes w and cv, the total number of
chromosomes originate. When two genes are close together in a chromosomes observed among the progeny is 357 1 341 1 52 1
chromosome, a crossover may not occur in the interval between 45 5 795, and the number of recombinant chromosomes is
the genes but at some other location along the chromosome. 52 1 45 5 97. The frequency of recombination between w and cv
In this example, the crossover occurs in the region between is therefore 97/ 795 5 0.122, or 12.2%, and this serves as a measure
gene A and the centromere, and therefore the combination of of the genetic distance between the genes. In studies of genetic
alleles A and B remains intact in one pair of chromatids and the linkage, the distance between genes is not measured directly by
combination of alleles a and b remains intact in the homologous physical distance between them, but rather by the frequency of
chromatids. The resulting gametes are equally likely to have either recombination.
AB or ab, both of which are nonrecombinant. The frequency of recombination between any two genes
Nonrecombinant chromosomes can also be the result of two on the same chromosome ranges from 0% (when crossing over
crossover events occurring between two genes, in which the between the genes never takes place) to 50% (when the genes
effects of the first crossover (creating recombinants) is reversed by are so far apart that a crossover between the genes almost
a second crossover (re-creating nonrecombinants). always takes place). Genes that are linked have a recombination
frequency somewhere between 0% and 50%. The maximum
The frequency of recombination is a measure of the frequency of recombination is 50% because, when nonsister
genetic distance between linked genes. chromatids involved in crossovers are chosen at random, any new
When two genes are on separate chromosomes, a ratio of 1 : 1 : 1 : 1 crossover has two equally likely consequences: It can either change
is expected for the nonrecombinant (parental) and recombinant a previously recombinant chromatid into a nonrecombinant
(nonparental) gametic types, as described by the principle of chromatid, or change a previously nonrecombinant chromatid
independent assortment (Chapter 16). For two genes present in into a recombinant chromatid. The result is that however many
the same chromosome, we can consider two extreme situations. crossovers there may be (as long as there is at least one), the
If they are located very far apart from each other, one or more maximum frequency of recombination remains 50%. A frequency
crossovers will almost certainly occur between them, and there of recombination of 50% yields the same ratio of gametic types
will be a 1 : 1 : 1 : 1 ratio of nonrecombinant and recombinant as observed with independent assortment, which means that
gametes (as shown for the case of a single crossover in Fig. 17.10a). genes that are far enough apart in the same chromosome show
At the other extreme, if two genes are so close together that independent assortment.
crossing over never takes place between them, we would expect
j Quick Check 2 Why is the upper limit of recombination
only nonrecombinant chromosomes (Fig. 17.10b).
50% rather than 100%?
What happens in between these extremes? In these cases,
in some cells undergoing meiosis, no crossover takes place Recombination plays an important role in creating new
between the genes, in which case all the resulting chromosomes combinations of alleles in each generation and in ensuring
are nonrecombinant (Fig. 17.10b); and in other cells undergoing the genetic uniqueness of each individual. If there were no
meiosis, a crossover occurs between the genes, in which case half recombination (that is, if all the alleles in each chromosome
the resulting chromosomes are nonrecombinant and half are were completely linked), any individual human would be able
recombinant (Fig. 17.20a). Since the meioses with no crossover to produce only 223 5 8.4 million types of reproductive cells.
between the genes result only in nonrecombinant chromosomes While this is a large number, the average number of sperm per
and those with a crossover result in half nonrecombinant and half ejaculate is much larger—approximately 350 million. Because
recombinant chromosomes, the nonrecombinant chromosomes recombination does occur, and because the crossovers resulting in
in the offspring will be more numerous than the recombinant recombination can occur at any of thousands of different positions
chromosomes. in the genome, each of the 350 million sperm is virtually certain
The actual frequency of recombinants depends on the distance to carry a different combination of alleles.
between the genes. The distance between the genes is important
because whether or not a crossover occurs between the genes Genetic mapping assigns a location to each gene along
is a matter of chance, and the closer the genes are along the a chromosome.
chromosome, the less likely it is that a crossover will take place in With the exception of a few regions, such as the area near the
the interval between them. Because the formation of recombinant centromere, the likelihood of a crossover occurring somewhere
chromosomes requires at least one crossover between the between two points on a chromosome is approximately
genes, genes that are close together (more tightly linked) show proportional to the length of the interval between the points.
less recombination than genes that are far apart. In fact, the Therefore, the frequency of recombination can be used as a
proportion of recombinant chromosomes observed among measure of the physical distance between genes. These distances
the total, which is called the frequency of recombination, are used in the construction of a genetic map, which is a diagram
is a measure of genetic distance between the genes along the showing the relative position of genes along a chromosome.
chromosome. The maps are drawn using a scale in which one unit of distance
HOW DO WE KNOW?
FIG. 17.11
Can recombination be used EXPERIMENT Taking this idea a step further, Sturtevant reasoned
that if one knew the frequency of recombination between genes
to construct a genetic map of a and b, between b and c, and between a and c, then one should be
able to deduce the order of genes along the chromosome. He also
a chromosome? predicted that, if the order of genes were known to be a–b–c, then
if the genes were close enough, the frequency of recombination
between a and c should equal the sum of the frequencies between
BACKGROUND In 1910, Thomas Hunt Morgan discovered a and b and that between b and c.
X-linkage by studying the white-eye mutation in Drosophila. RESULTS Sturtevant studied the frequencies of recombination
Soon other X-linked mutations were found. Alfred H. Sturtevant, between many pairs of genes along the X chromosome, including
Morgan’s student, decided to test whether mutant genes in the same some of those shown in the illustration shown here.
X chromosome were inherited together, that is, linked. He found
that genes in the X chromosome were linked, but not completely, CONCLUSION The results confirmed Sturtevant’s hypothesis
and that different pairs of genes showed great differences in their and showed that genes could be arranged in the form of a genetic
linkage. Some genes showed almost no recombination, whereas map, depicting their linear order along the chromosome, with the
others underwent so much recombination that they showed distance between any pair of genes proportional to the frequency
independent assortment. of recombination between them. Across sufficiently short regions,
the frequencies of recombination are additive.
HYPHOTHESIS Sturtevant hypothesized that recombination was
due to crossing over between the genes, and that genes farther FOLLOW-UP WORK Genetic mapping remains a cornerstone of
apart in the chromosome would show more recombination. genetic analysis, showing which chromosome contains a mutant
gene and where along the chromosome the gene is located. The
w, white rb, ruby
(white eyes) (ruby eye color) method helped to identify the genes responsible for many single-
y, yellow ec, echinus cv, crossveinless gene inherited disorders, including Huntington’s disease, cystic
(yellow body) (large eyes) (missing wing vein)
fibrosis, and muscular dystrophy.
1.5 4.0 2.0 6.2 SOURCE Sturtevant, A. H. 1913. “The Linear Arrangement of Six Sex-Linked Factors
in Drosophila, as Shown by Their Mode of Association.” Journal of Experimental Zoology
14:43–59.
The distance between adjacent Across sufficiently short
genes is given in map units, distances, the map units are
which is equal to the frequency additive. Thus, the expected
of recombination when frequency of recombination
expressed as a percentage. between w and cv is
4.0 + 2.0 + 6.2 = 12.2%.
(called a map unit) is the distance between genes resulting in 1% However, for two genes that are farther apart than about
recombination. Thus, in a Drosophila genetic map containing the 15 map units, the observed recombination frequency is somewhat
genes w and cv, the distance between the genes is 12.2 map units. smaller than the sum of the map distances between the genes.
Genetic maps are built up step by step as new genes are The reason is that, with greater distances, two or more crossovers
discovered that are genetically linked, as shown in Fig. 17.11. between the genes may occur in the same chromosome, and
Across distances that are less than about 15 map units, the map thus an exchange produced by one crossover may be reversed by
distances are approximately additive, which means that the another crossover farther along the way.
distances between adjacent genes can be added to get the distance
j Quick Check 3 For two genes that show independent
between the genes at the ends. For example, in Fig. 17.11, there are
assortment, what is the frequency of recombination?
two genes between w and cv. The map distance between w and the
next gene, ec, is 4.0, the distance between ec and the next gene, rb,
is 2.0, and the distance between rb and cv is 6.2. The map distance Genetic risk factors for disease can be localized by
between w and cv is therefore 4.0 1 2.0 1 6.2 5 12.2 map units, genetic mapping.
and hence the expected frequency of recombination between The discovery of abundant genetic variation in DNA sequences
these genes is 12.2%, which is the value observed. in human populations, such as single-nucleotide polymorphisms
356
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 357
(Chapter 15), made it possible to study genetic linkage in the of the chromosomes that carry the nonmutant allele show the
human genome. At first, the focus was on finding mutations that A–T nucleotide pair. The two chromosomes in which the mutant
cause disease, such as the mutation that causes cystic fibrosis and nonmutant genes are associated with the other SNPs can be
(Chapter 14). The method was to study large families extending attributed to recombination.
over three or more generations in which the disease was present The association in Fig. 17.12a may be contrasted with the
and then to identify the genotypes of each of the individuals pattern in Fig. 17.12b, in which there is no association. In this case,
for thousands of genetic markers (previously discovered DNA each of the alleles of the disease gene is equally likely to carry
polymorphisms) throughout the genome. The goal was to find either form of the SNP. The failure to find an association means
genetic markers that showed a statistical association with the that the SNP is not closely linked to the disease gene, and may in
disease gene, which would indicate genetic linkage and reveal the fact be in a different chromosome. In actual studies, an association
approximate location of the disease gene along the chromosome. is almost never observed, but the lucky find of an association helps
Fig. 17.12 illustrates the underlying concept. It assumes identify the location of the disease gene in the genetic map. Using
100 chromosomes observed among different individuals in a such association methods, hundreds of important disease genes
pedigree, of which 50 carry a mutant allele of a gene and have been located by genetic mapping. Once the location of the
50 carry a nonmutant allele. These chromosomes are tested disease gene is known, the identity and normal function of the
for a marker of known location, in this case a single-nucleotide gene can be determined.
polymorphism (SNP) in which one of the nucleotide pairs in the
DNA is a G–C base pair in some chromosomes and A–T in others.
In Fig. 17.12a, there is clearly an association between the disease 17.4 INHERITANCE OF GENES IN
gene and the SNP. Almost all of the chromosomes that carry the THE Y CHROMOSOME
mutant allele show the G–C nucleotide pair, whereas almost all
Like the X chromosome, the Y chromosome exhibits a particular
pattern of inheritance because of its association with the male
sex. In humans and other mammals, all embryos initially develop
FIG. 17.12 Genetic mapping. SNPs associated with a mutant gene immature internal sexual structures of both females and males.
show where that gene is located in the genetic map. SRY, a gene in the Y chromosome, encodes a protein that is the
trigger for male development. (“SRY” stands for “sex-determining
a. Association b. No association region in the Y chromosome.”) In the presence of SRY, male
Disease Percent Disease Percent structures complete their development and female structures
gene SNP observed gene SNP observed
degenerate. In the absence of SRY, male embryonic structures
G G degenerate and female structures complete their development.
49 25
C C The SRY gene is therefore the male-determining gene in humans
and other mammals. Because they are linked to SRY, most genes
A A in the Y chromosome show a distinctive pattern of inheritance in
1 25 pedigrees, different from the patterns of autosomal genes Mendel
T T
observed in his pea plants, in that they are transmitted only from
Normal
Mendelian father to son.
G G ratios
1 25
C C Y-linked genes are transmitted from father to son
to grandson.
A A Genes that are present in the unique region of the Y chromosome
49 25
T T (the part that cannot cross over with the X) are known as
Y-linked genes, of which there are not many. As well as the
SRY male-determining gene, they include a number of genes in
In an analysis of 100 In this case, there is no which mutations are associated with impaired fertility and low
chromosomes, most association between a
show an association disease gene and a SNP, sperm count.
between a mutant so the location of the The pedigree characteristics of Y-linked inheritance are
allele of a gene and a disease gene in relation
G–C SNP, suggesting to this specific SNP striking (Fig. 17.13):
that the mutant allele cannot be determined.
is located near the SNP. 1. Only males are affected with the trait.
2. Females never inherit or transmit the trait, regardless of
Mutant how many affected male relatives they have.
Nonmutant
3. All sons of affected males are also affected.
358 SECTION 17.4 I N H E R I TA N C E O F G E N E S I N T H E Y C H RO M O S O M E
pair with another chromosome and does not undergo crossing over.
Because of this complete linkage, each hereditary lineage of The first G TGC TACG C T Each unique
occurrence of combination
Y chromosomes is separate from every other lineage. As mutations
each red letter of nucleotides
occur along the Y chromosome, they are completely linked to any represents a represents a
past mutations that may be present and also completely linked new mutation different Y
GA G C TACG C T
at that site. chromosome
to any future mutations that may take place. The mutations
Time
haplotype.
therefore accumulate, and this allows the evolutionary history of a
set of sequences to be reconstructed.
GA G TTACG C T
Fig. 17.14 shows an evolutionary tree based on the G AGC TACGCA
accumulation of mutations at a set of nucleotide sites along
the Y chromosome. Each unique combination of nucleotides
GA G TC ACG C T
constitutes a Y-chromosome haplotype, or haploid genotype. GA GC TACGAA
In the figure, the most ancient Y chromosomes are at the top, GAG C TAA GCA
and the accumulation of new mutations as the generations
GA G TCGCG C T
proceed results in the successive creation of new haplotypes. Each GAT TC ACG C T GA GC TAATCA
CHAPTER 17 I N H E R I TA N C E O F S E X C H RO M O S O M E S , L I N K E D G E N E S , A N D O RG A N E L L E S 359
Sex chromosomes and linked genes are not the only genes that are In most organisms, either maternal inheritance or paternal
inherited in ways that are unlike the patterns of inheritance that inheritance predominates, but sometimes there is variation
Mendel observed in peas. Genes in mitochondria and chloroplasts from one offspring to the next. For example, transmission of the
also show distinct inheritance patterns. Mitochondria and chloroplasts ranges from strictly paternal in the giant redwood
chloroplasts are ancient organelles of eukaryotic cells originally Sequoia, to strictly maternal in the sunflower Helianthus, to either
acquired by the engulfing of prokaryotic cells (Chapter 5). maternal or paternal (or less frequently biparental) in the fern
Mitochondria generate ATP that cells use for their chemical energy. Scolopendrium, to mostly maternal but sometimes paternal or
Chloroplasts are found only in plant cells and eukaryotic algae. biparental in the snapdragon Antirrhinum.
360 SECTION 17.5 I N H E R I TA N C E O F M I TO C H O N D R I A L A N D C H LO RO P L A S T D N A
There is likewise great diversity among organisms in the 1. Both males and females can show the trait.
inheritance of mitochondrial DNA. Most animals show maternal
2. All offspring from an affected female show the trait.
transmission of the mitochondria, as would be expected from their
large, cytoplasm-rich eggs and the small, cytoplasm-poor sperm. 3. Males do not transmit the trait to their offspring.
Among other organisms, there is again much variation, including
maternal transmission of mitochondria in flowering plants and The pedigree in Fig. 17.16 follows a mitochondrial disease
paternal transmission in the green alga Chlamydomonas. known as MERRF syndrome (the acronym stands for “myoclonic
epilepsy with ragged red fibers”). As its name suggests, the
Maternal inheritance is characteristic of mitochondrial syndrome is characterized by epilepsy, a neurological disease
diseases. characterized by seizures, as well as by the accumulation
In humans and other mammals, mitochondria normally of abnormal mitochondria in muscle fibers. This extremely
show strictly maternal inheritance—the mitochondria in the rare disease is associated with a single point mutation in a
offspring cells derive from those in the mother. Fig. 17.16 shows mitochondrial gene involved in protein synthesis that affects
the characteristic pedigree patterns of a trait encoded by a oxidative phosphorylation (Chapter 7).
mitochondrial genome transmitted through maternal inheritance: More than 40 different diseases show these pedigree
characteristics. They all result from mutations in the
mitochondrial DNA, but the tissues and organs affected as well as
FIG. 17.16 Maternal inheritance. Human mitochondrial DNA is
the severity differ from one to the next. All of the mutations affect
transmitted from a mother to all of her offspring. Source:
energy production in one way or another. In some cases, disease
Courtesy of Dr. Kurenai Tanji, Columbia University Medical Center,
results directly from lack of adequate amounts of ATP, in other
New York, NY.
cases from intermediates in energy production that are toxic to
the cell or that damage the mitochondrial DNA.
Because mitochondrial DNA does not undergo 5. Describe how recombination frequency can be
recombination and is maternally inherited, it can be used to used to build a genetic map.
trace human ancestry and migration. page 360
6. Describe the pattern of inheritance expected from
a Y-linked gene in a human pedigree.
363
364 SECTION 18.1 H E R E D I T Y A N D E N V I RO N M E N T
Biologists initially had a hard time accepting the principles of single-gene traits, Mendel was able to infer underlying mechanisms
Mendelian inheritance because they seem so at odds with everyday of inheritance based on physical factors we now call genes. By
observations. Common and easily observed traits like height, contrast, complex traits, such as human height, are influenced
weight, hair color, and skin color give no evidence of segregation by multiple genes as well as by the environment. As a result,
in pedigrees, and simple phenotypic ratios like 3 : 1 or 9 : 3 : 3 : 1 are their inheritance patterns are more difficult to follow and simple
not observed for them. The lack of these characteristic ratios raised phenotypic ratios are not observed.
serious doubt whether Mendel’s principles are valid for common In many ways, complex traits are more important than single-
traits. Some biologists concluded that they apply only to seemingly gene Mendelian traits. One reason is their prevalence—complex
trivial traits like round and wrinkled seeds in peas. traits are found in all organisms and include most of the traits we
At about the time that Mendel was studying inheritance in can see around us. By contrast, there are relatively few examples
garden peas, the biologist Francis Galton, a friend and cousin of of common single-gene traits. Complex traits are also important in
Charles Darwin, was studying common traits including human human health and disease. In the most common disorders—among
height. From studies of height and other common traits in parents them heart disease, diabetes, and cancer—single-gene Mendelian
and their offspring, Galton discovered general principles in the inheritance is seldom found. It is therefore important to understand
inheritance of such traits. For example, parents who are tall tend the inheritance of complex traits and common disorders, which
to have offspring who are taller than average but not as tall as are the subjects of this chapter. We begin by describing some of the
themselves. Galton’s principles for the inheritance of common features of complex traits, and then show how these principles are
traits did not invoke genes, segregation, independent assortment, not only compatible with, but are in fact predicted by, Mendelian
or other features of Mendelian inheritance, but they did describe inheritance. Finally, we describe how modern molecular genetics
Galton’s observations. Not only were genes—what Mendel called and genomics have allowed the identification of genes affecting
“hereditary factors”—thought to be unnecessary in Galton’s theory complex traits.
of inheritance, but also many biologists thought that Galton’s
theories and Mendel’s were incompatible.
This, it turned out, was not the case. The traits that Mendel 18.1 HEREDITY AND ENVIRONMENT
studied are now called single-gene traits because each one is
determined by variation at a single gene and the traits for the Complex traits are important not only in humans, but also in
most part are not influenced by the environment. By focusing on agricultural plants and animals. We will examine human height
in some detail because it has been widely
studied, but equally well known complex
FIG. 18.1 Examples of complex traits.(a) Human height, (b) egg number, (c) milk traits are number of eggs laid by hens,
production, and (d) grain yield. Sources: a. Randy Faris/Corbis; b. muratart/Shutterstock; milk production in dairy cows, and yield
c. smereka/Shutterstock; d. Radius Images/Getty Images. per acre of grain (Fig. 18.1).
Many common human diseases,
a b including high blood pressure, obesity,
diabetes, and depression, are complex
traits (Fig. 18.2). High blood pressure,
for example, affects about one-third of
the U.S. population, and obesity another
third. Type 2 diabetes affects around
8% of the U.S. population, and an
estimated 15% will suffer at least one
episode of severe depression in the
course of a lifetime. Taken together,
c d
about 200 million Americans—two-thirds
of the entire population—suffer from
one or more of these common disorders.
None of these traits shows single-gene
Mendelian inheritance.
In many complex traits, the phenotype
of an individual is determined by
measurement: Human height is measured
in inches, milk yield by the gallon, grain
yield by the bushel, egg production by
CHAPTER 18 T H E G E N E T I C A N D E N V I RO N M E N TA L B A S I S O F CO M P L E X T R A I T S 365
FIG. 18.2 Examples of human diseases that are complex traits. (a) High blood pressure, (b) obesity, (c) diabetes, and (d) depression. Sources:
a. Burwell and Burwell Photography/iStockPhoto; b. Ocean/Corbis; c. Junophoto/Getty Images; d. Imago/ZUMApress.com.
a b c d
the number of eggs, blood pressure by millimeters of mercury, may seem, there are always minor differences from one area to
and blood sugar by millimoles per liter. Because the phenotype the next, and these differences can result in variation in complex
of complex traits such as these is measured along a continuum traits. In the example in Fig. 18.3, the plants in the foreground
with only small intervals between similar individuals, complex are shorter than the others because that corner of the field has
traits like these are often called quantitative traits. By contrast, poorer drainage, and the plants growing there have to compete for
single-gene traits often appear in one of two or more different nutrients with the grass growing nearby.
phenotypes, such as round versus wrinkled seeds, or green versus
yellow seeds.
Aa Bb Cc Aa Bb Cc is as shown in the Punnett square. The bar to differences in the environment. For other traits, the variation
graph below the Punnett square shows the seed-color phenotypes is due mainly to genetic differences. In the case of human height,
and their relative proportions, from which Nilsson-Ehle inferred roughly 80% of the variation among individuals of the same sex is
three genes with independent assortment. The distribution of due to genetic differences, and the remaining 20% to differences in
seed-color phenotypes is approximated by a bell-shaped curve their environment, primarily differences in nutrition during their
known as a normal distribution. The phenotypes of many years of growth.
complex traits, including human height, conform to the normal
distribution. Nilsson-Ehle’s seed-color case is exceptional in Genetic and environmental effects can interact in
that virtually all complex traits are affected by many more unpredictable ways.
genes than three (in the case of human height, hundreds, as One of the features of complex traits is that genetic and
discussed below). environmental effects may interact, often in unpredictable ways.
When differences in phenotype due to the environment Consider the example shown in Fig. 18.5. In this experiment,
can be ignored, the genetic variation affecting complex traits two strains of corn were each grown in a series of soils in which
can be detected more easily. And when studying inbred lines, the amount of nitrogen had been enriched by the growth of
differences in phenotype due to genotype can be ignored legumes. The yield of strain 1 varies little across these different
because all individuals have the same genotype, and the effects environments. The yield of strain 2, however, increases
of environment can be observed. In most cases, however, both dramatically with soil nitrogen. Each of the lines is known as a
genetic variation and environmental variation among individuals norm of reaction, which for any genotype graphically depicts
are present, and it is difficult to quantify how much variation in how the environment (shown on the x-axis) affects phenotype
phenotype is due to genes and how much is due to environment. (shown on the y-axis) across a range of environments. Note that in
It’s important to point out that complex traits are not really one case in Fig. 18.5, the environment has little to no effect on the
more “complex” than any other biological trait. The term is used phenotype (the norm of reaction is nearly flat), but in the other it
merely to imply that both genetic factors and environmental has a very noticeable effect. In cases like strain 2, it is impossible
factors contribute to variation in phenotype among individuals. to predict the phenotype of a given genotype without knowing
Just as there are environmental factors that affect complex what the environmental conditions are and how the phenotype
traits such as height, so there are genetic factors that affect changes in response to variation in the environment.
height. Similarly, just as an environmental risk factor increases Such variation in the effects of the environment on different
the likelihood of a common disease, so does a genetic risk factor genotypes is known as genotype-by-environment interaction.
predispose an individual to the condition. For example, the This type of interaction is important because it implies that the
human gene ApoE encodes a protein that helps transport fat and effect of a genotype cannot be specified without knowing the
cholesterol. Certain alleles of ApoE are associated with high levels environment, and the other way around. A further implication is
of cholesterol, and one particular allele is a genetic risk factor for that there may be no genotype that is the “best” across a broad
Alzheimer’s disease, the most common serious form of age-related
loss of cognitive ability. Lifestyle environmental factors such as
diet, physical exercise, and mental stimulation are also thought to
play a role in the risk of Alzheimer’s disease. FIG. 18.5 Genotype-by-environment interaction for grain yield
in corn. The effect of soil nitrogen on grain yield is
The relative importance of genes and environment can minimal in strain 1, but dramatic in strain 2. Data courtesy
of J. W. Dudley.
be determined by differences among individuals.
For any one individual, it is impossible to specify the relative roles
of genes and environment in the expression of a complex trait. For 5000 Corn strain 1
Corn strain 2
example, in an individual 66 inches tall it would be meaningless
Grain yield (kg/hectare)
A
FIG. 18.7 Galton’s data showing distribution of height of
offspring of (a) the tallest parents and (b) the shortest
parents. Data from F. Galton, 1888, “Co-Relations and Their
Measurement, Chiefly from Anthropometric Data,” Proceedings of the
B
Royal Society, London 45:135–145, reprinted in K. Pearson, 1920,
“Notes on the History of Correlation,” Biometrika 13:25– 45.
a.
Population Offspring Parental
mean mean mean
When parents are
above average
2.0 height, on average
their offspring are
shorter than the
parents, but taller
Number of offspring
1.0
crosses yielded simple ratios such as 3 : 1 or 1 : 1, which could be greater than the mean height of the whole population of the study
interpreted in terms of segregation of dominant and recessive (68.25 inches) but less than that of the parents. The bar graph in
alleles. Fig. 18.7b is the distribution of height of progeny of the shortest
By contrast, Galton studied variation in such traits as parents, who averaged 66 inches. In this case, the mean height of
height in humans. Humans are obviously not true breeding the progeny is 67 inches, which is less than the mean height of the
and have few offspring. Galton had one big advantage, though: population but greater than that of the parents. Note, however,
Whereas most simple Mendelian traits are relatively uncommon, that some of the offspring of tall parents are taller than their
Galton’s traits are readily observed in everyday life. What did parents, and likewise some of the offspring of short parents are
Galton discover? shorter than their parents. It is only on average that the height of
the offspring is less extreme than that of the parents.
For complex traits, offspring resemble parents but Galton’s results can be plotted on a graph, represented as the
show regression toward the mean. blue data points in Fig. 18.8, in which the average height of each
Galton’s observations are as important in understanding complex pair of parents (called the midparent value) is compared with that
traits as Mendel’s are in understanding single-gene traits. He of their child. For convenience in visualization, midparent heights
studied many complex traits, including human height, strength, are grouped into categories, and the mean of each group is plotted
and various other physical characteristics, including number of along the x-axis. For each group of parents, the height of the
fingerprint ridges. The discovery he regarded as fundamental offspring is also averaged and plotted along the y-axis.
resulted from his data on adult height of parents and their progeny Galton regarded this observation as his most important
(Fig. 18.7). Galton noted that each category of parent (tall or discovery, publishing his results in 1886. Today, we call it regression
short) produced a range of progeny forming a distribution with its toward the mean. The offspring exhibit an average phenotype that
own mean. is closer to the population mean than the phenotype of the parents.
The bar graph in Fig. 18.7a shows the distribution of height In other words, when the average height of the parents is smaller
among the progeny of the tallest parents, whose average height is than the population mean, then the average height of the offspring
72 inches. The mean height of the offspring is 71 inches, which is is greater than that of the parents (but smaller than the population
mean). Likewise, when the average
height of the parents is greater than
the population mean, then the average
FIG. 18.8 Regression toward the mean. Galton’s data on the average adult height of
height of the offspring is smaller than
parents and that of their offspring show that offspring mean height (blue line) falls
that of the parents (but greater than the
between the parental mean (dashed red line) and the population mean (dashed
population mean).
black line).
Regression toward the mean is
This line is expected when observed for two reasons. The first is that
all variation is due to
74 genotype. The offspring during meiotic cell division (Chapter 11),
mean equals the parental segregation and recombination break
0
1. mean. up combinations of genes that result in
=
e
l op extreme phenotypes, such as very tall or
S Galton’s result shows what
72 very short, that are present in the parents.
happens when variation is
0.6 due to genotype and
Mean height of offspring (inches)
Heritability is the proportion of the total variation due among individuals, and specifically to the proportion of
to genetic differences among individuals. the variation among individuals in a population due to differences
How much of the difference in height among individuals is due in genotype.
to genetic differences, and how much is due to environmental Hence, a heritability of 100% does not imply that the
differences? The slope of the line that relates the average phenotype environment cannot affect a trait. As emphasized earlier, the
of parents to the average phenotype of their offspring (in the case environment is always important, just as oxygen is important
of Galton’s data, the blue line in Fig. 18.8) can answer this question to life. What a heritability of 100% means is that variation in the
because it provides a measure of the heritability of the trait. The environment does not contribute to differences among individuals
heritability of a trait in a population of organisms is the proportion in a specific population. For example, if genetically different
of the total variation in the trait that is due to genetic differences strains of chrysanthemums are grown in a greenhouse and
among individuals. For a complex trait, the heritability determines subject to identical environmental conditions, then differences
how closely the mean of the progeny resembles that of the parents. in flowering time have to be due to genetic differences, and the
In Galton’s data, the slope of the line is 0.6 and therefore the heritability of the trait would be 100%. Similarly, a heritability
heritability of height in this population is 60%. of 0% does not imply that genotype cannot affect the trait. A
The red dashed line in Fig. 18.8 presumes a hypothetical ideal heritability of 0% merely means that differences in genotype do
trait in which variation is determined completely by genetic not contribute to the variation in the trait among individuals
differences among individuals and the heritability is 100%. When in a specific population. If genetically identical strains of
heritability is 100%, the slope of the line representing the trait chrysanthemums are grown in different environments, then
is 1. As we do with most complex traits, such as Nilsson-Ehle’s differences in flowering time must be due to the environment, and
wheat seed color, we assume that each of a large number of genes heritability would be 0%.
contributing to the trait has two alleles, one that contributes Heritability therefore is not an intrinsic property of a trait. For
to the trait and one that does not, and the genes undergo chrysanthemum flowering time, the heritability in one case was
independent assortment. The number of alleles in the genotype 100% and in the second 0%. Heritability applies only to the trait in
contributing to the trait determines the phenotype in any a particular population across the range of environments that exist
individual for that trait. (The genetic model is like that shown in at a specific time. Similarly, the heritability depicted by the slope
Fig. 18.4 but with many more genes.) In this ideal case in which of the blue line in Fig. 18.8 applies only to the population studied
heritability is 100%, the average phenotype of the offspring from (205 pairs of British parents and their 930 adult offspring, in the
any pair of parents will equal the average phenotype of the parents late nineteenth century) and may be larger or smaller in different
themselves. In the real world, the ideal is rarely encountered, populations at different times. In particular, the magnitude of the
and deviations from the red line result from complications heritability cannot specify how much of the difference in average
such as dominance, genetic linkage, and epistasis (non-additive phenotype between two populations is due to genotype and how
contributions of the alleles of different genes). much due to environment.
The black dashed line in Fig. 18.8 represents the opposite If the heritability of a trait can change depending on the
extreme, a hypothetical ideal trait in which variation is population and the conditions being studied, why is it useful?
determined completely by differences in the environment Heritability is important in evolution, particularly in studies of
among individuals and the heritability is 0%. When heritability artificial selection, a type of selective breeding in which only
is 0%, the line representing the trait has a slope of 0. As long as certain chosen individuals are allowed to reproduce (Chapter 21).
environmental effects are not transmitted from one generation Practiced over many generations, artificial selection can result in
to the next, the average phenotype of the offspring will be equal considerable changes in morphology or behavior or almost any
to the average of the population as a whole, no matter what the trait that is selected. The large differences among breeds of pigeons
phenotypes of the parents. Although environmental effects are and other domesticated animals prompted Charles Darwin to
usually not transmitted in plant and animal populations, human point to artificial selection as an example of what natural selection
populations are exceptional in showing cultural transmission of could achieve. Heritability is important because this quantity
some environmental effects. For example, the average wealth of determines how rapidly a population can be changed by artificial
the offspring of rich parents is greater than that of the offspring of selection. A trait with a high heritability responds rapidly to
poor parents, and this difference is obviously due to transmission selection, whereas a trait with a low heritability responds slowly
of the parents’ money, not their genes. or not at all.
The term “heritability” is often misinterpreted. The
problem is that, in non-scientific contexts, the word means “the j Quick Check 2 Many people are surprised to learn that,
capability of being inherited or being passed by inheritance.” This while each individual’s fingerprints are unique, the total
definition suggests that heritability has something to do with number of fingerprint ridges is highly heritable, about 90%
the inheritance of a trait. But “heritability” as used for complex heritability in many populations. What does high heritability
traits means no such thing. It refers only to the variation in a trait of this trait mean?
CHAPTER 18 T H E G E N E T I C A N D E N V I RO N M E N TA L B A S I S O F CO M P L E X T R A I T S 371
In this example, the 336 twin pairs who do not show the trait
provide no information. The concordance is based only on the first
two types of twin pairs, among which in 36 pairs both members
show the trait and in 40 pairs only one shows the trait. In this
372 SECTION 18.3 T WIN STUDIES
case the concordance among identical twins is 36/(36 1 40) 5 (which we now know to include diet and exercise) are also
47%. Among fraternal twins, by contrast, the concordance for important in the risk of adult-onset diabetes.
adult-onset diabetes is only 10%. The difference in concordance Table 18.1 shows identical and fraternal twin concordance
between identical and fraternal twins (47% for identical twins rates for a number of other disorders. Just as with diabetes, the
versus 10% for fraternal twins) implies that differences in the risk marked difference in concordance rates between identical and
of adult-onset diabetes have an important genetic component. fraternal twins for high blood pressure, asthma, rheumatoid
Furthermore, the observation that the concordance for identical arthritis, and epilepsy suggests that all these disorders have an
twins is much less than 100% implies that environmental factors important genetic component. In addition, the fact that the
HOW DO WE KNOW?
FIG. 18.10
For some traits the Some traits show
50
me
on
ia
sa
le)
ity
le)
de
de
en
tis
rvo
ma
tiv
si
idea in 1924. In Galton’s time, it was not even known that there are
ro
or
or
(m
es
hr
Au
rac
nd
ne
dis
dis
(fe
pr
op
sm
genetically two kinds of twins.
sy
e
ia
de
sm
nic
ing
hiz
yp
oli
lim
te
al
oli
/h
Pa
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ad
oh
et
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oh
EXPERIMENT The rationale of a twin study is to compare identical
Re
ur
Alc
cit
Cli
To
Alc
efi
fraternal twins differ more from each other than identical twins
differ from each other measures the effects of genotype. Some CONCLUSION The examples shown here indicate very large
twin studies focus on twins reared apart in order to compensate for differences in the importance of genotype versus environment
shared environmental influences that may be stronger for identical among complex traits. These results are typical of most complex
twins than for fraternal twins. traits.
RESULTS The bar graph shows the results of typical twin studies FOLLOW-UP WORK Twin studies must be interpreted in light of
for various traits. The concordance between twins is the fraction of other studies comparing complex traits among individuals with
twin pairs in which both twins show the trait among all those pairs various degrees of genetic relatedness. On the whole, twin studies
in which at least one twin shows the trait. Roughly speaking, the of complex traits have yielded results that are consistent with other
difference in the concordance between identical twins and fraternal available evidence.
twins is a measure of the relative importance of genotype. In the
data shown here, for example, autism and clinical depression both SOURCES Rende, R. D., R. Plomin, and S. G. Vandenberg. 1990. “Who Discovered the
Twin Method?” Behavior Genetics 20:277–285; McGue, M., and T. J. Bouchard, Jr. 1998.
show strong genetic influences, whereas female alcoholism shows “Genetic and Environmental Influences on Human Behavioral Differences.” Annual Review
almost no genetic influence. of Neuroscience 21:1–24.
CHAPTER 18 T H E G E N E T I C A N D E N V I RO N M E N TA L B A S I S O F CO M P L E X T R A I T S 373
Trisomy
13, 18, 21
18.4 COMPLEX TRAITS IN (7157) Metabolic
HEALTH AND DISEASE disorders
(3104)
Much evidence beyond twin studies implies an important role for
particular alleles as risk factors for diabetes, high blood pressure, Cleft palate and
other deformities Congenital defects
asthma, rheumatoid arthritis, epilepsy, schizophrenia, clinical of the mouth of the skeleton
depression, autism, and many other conditions. These are all and palate and muscles
complex traits, affected by genotype, environment, and genotype- (7012) (6001)
by-environment interactions. Congenital defects
Even the most common birth defects are affected by multiple of the heart and
blood vessels
genetic risk factors. The most common birth anomalies and (6754)
the numbers of affected babies born in the United States each
374 SECTION 18.4 CO M P L E X T R A I T S I N H E A LT H A N D D I S E A S E
only a major goal of much current research in human genetics, Circulation Research 96:27– 42.
Core Concepts Summary 18.4 Many common diseases and birth defects are
affected by multiple genetic and environmental risk
18.1 Complex traits are those influenced both by the factors.
action of many genes and by environmental factors. Complex traits are often influenced by many genes with
Complex traits that are measured on a continuous scale, like multiple, interacting, and unequal, effects. page 374
human height, are called quantitative traits. page 364 Hundreds of genes affect human height. page 374
It is usually difficult to assess the relative roles of genes Personalized medicine tailors treatment to an individual’s
and the environment (“nature” versus “nurture”) in genetic makeup. page 375
the production of a given trait in an individual, but it is
reasonable to consider the relative roles of genetic and
environmental variation in accounting for differences among Self-Assessment
individuals for a given trait. page 365
1. Explain why some complex traits are also called quantitative
The relative importance of genes and environment in causing traits, and give at least one example.
differences in phenotype among individuals differs among
traits. For some traits (like height), genetic differences are 2. Name several factors that influence variation in
the more important source of variation, whereas for others complex traits.
(such as cancer), environmental differences can be the more 3. Explain why it does not make sense to try to separate
important. page 366 the effects of genes (“nature”) and the environment
Genetic and environmental factors can interact in (“nurture”) in a single individual, while it does make sense
unpredictable ways, resulting in genotype-by-environment to separate genetic and environmental effects on differences
interactions. page 367 among individuals.
Genetic and
Epigenetic
Regulation
Core Concepts
19.1 The regulation of gene
expression in eukaryotes
takes place at many levels,
including DNA packaging in
chromosomes, transcription,
and RNA processing.
19.2 After an mRNA is transcribed
and exported to the
cytoplasm in eukaryotes,
gene expression can be
regulated at the level of
mRNA stability, translation,
and posttranslational
modification of proteins.
19.3 Transcriptional regulation
is illustrated in bacteria by
the control of the production
of proteins needed for the
utilization of lactose, and in
viruses by the control of the
lytic and lysogenic pathways.
Lawrence Berkeley National Laboratory/Science Source.
377
378 SECTION 19.1 C H RO M AT I N TO M E S S E N G E R R N A I N E U K A RYOT E S
FIG. 19.1 Levels of gene regulation. FIG. 19.2 Histone modifications. Typical modifications of the amino
acid lysine observed in the histone tails of nucleosomes
a. Chromatin
include addition of a methyl group (Me), addition of three
methyl groups (Me3), and acetylation (Ac).
Nucleosomes Nucleosome
DNA
b. Transcription
RNA Histone
transcript
Histone tail
of amino acids
c. RNA processing
Exon Intron
O
CH3
CH3 CH3 C CH3
CH3
mRNA AAAAA
Lysine Monomethyl Trimethyl Acetyl
(Me) lysine (Me3) lysine (Ac) lysine
FIG. 19.3 Methylation states of CpG islands in or near the promoter of a gene.
N O
CpG island Undermethylation of the CpG
H island allows transcription.
Normal cytosine
silenced, so only the allele inherited from the father is expressed. gene dosage increases the level of expression because each copy of
For other imprinted genes, the allele of the gene inherited from the gene is regulated independently of other copies. For example,
the father is imprinted and therefore silenced, so only the allele as we saw in Chapter 15, the presence of an extra copy of most
inherited from the mother is expressed. The imprinting persists in human chromosomes results in spontaneous abortion because of
somatic cells through the lifetime of the individual but is reset in the increase in the expression of the genes in that chromosome.
its germ line according to the individual’s sex. XX females have twice as many X chromosomes as XY males.
Some of the genes that are imprinted affect the growth rate of For genes located in the X chromosome, the dosage of genes is
the embryo. For example, in matings between lions and tigers that twice as great in females as it is in males. However, the level
take place in captivity, the offspring of a male tiger with a female of expression of X-linked genes is about the same in both sexes.
lion (a “tigon”) is about the same size as its parents, whereas the These observations imply that the regulation of genes in the
offspring of a male lion and a female tiger (a “liger”) is a giant cat— X chromosome is different in females and in males. This
the largest of any big cat that exists. Much of the size difference differential regulation is called dosage compensation.
between a liger and a tigon is thought to result from whether Different species have evolved different mechanisms of
genes for rapid embryonic growth that are subject to imprinting dosage compensation. In the fruit fly Drosophila, males double
are inherited from the mother or the father. the transcription of the single X chromosome to achieve equal
expression compared to the two X chromosomes in females.
Gene expression can be regulated at the level of In the nematode worm Caenorhabditis, transcription of both
an entire chromosome. X chromosomes in females is decreased to one-half the level of
A striking example of an epigenetic form of gene regulation is the the single X chromosome in males. In mammals, including
manner in which mammals equalize the expression of X-linked humans, dosage compensation occurs through the inactivation
genes in XX females and XY males. For most genes, there is a direct of one X chromosome in each cell in females. This process,
relation between the number of copies of the gene (the gene known as X-inactivation, was first proposed by Mary F. Lyon in
dosage) and the level of expression of the gene. An increase in the early 1960s.
CHAPTER 19 G E N E T I C A N D E P I G E N E T I C R E G U L AT I O N 381
FIG. 19.4 X-inactivation in female mammals. X-inactivation equalizes the expression of most genes in the X chromosome between XX females
and XY males. Source: b. Eyal Nahmias/Alamy.
a. b.
Maternal X
chromosome Paternal X
chromosome
Fertilized egg
Early
divisions
Early
divisions
Random X-inactivation in
the embryo occurs at about
the time of implantation in
Inactivated X the uterine wall.
chromosome
splicing, but it does not encode a protein. Xist RNA is therefore Transcriptional regulation in eukaryotic cells requires the
an example of a noncoding RNA (Chapter 3). Instead of being coordinated action of many proteins that interact with one
translated, the processed Xist RNA coats the XIC region, and as it another and with DNA sequences near the gene. Let’s first review
accumulates, the coating spreads outward from the XIC until the the basic process of transcription in eukaryotes (Chapter 3). First,
entire chromosome is coated with Xist RNA. The presence of Xist an important group of proteins called general transcription
RNA along the chromosome recruits factors that promote DNA factors are recruited to the gene’s promoter, which is the region
methylation, histone modification, and other changes associated of a gene where transcription is initiated. The transcription
with transcriptional repression. factors are brought there by one of the proteins that bind to a
The Xist gene is both necessary and sufficient for short sequence in the promoter called the TATA box, which is
X-inactivation: If it is deleted, X-inactivation does not occur; usually situated 25–30 nucleotides upstream of the nucleotide
if it is inserted into another chromosome, it inactivates that site where transcription begins. Once bound to the promoter,
chromosome. Using recombinant DNA techniques of the sort the transcription factors recruit the components of the RNA
described in Chapter 12, researchers were able to insert Xist polymerase complex, the enzyme complex that synthesizes the
into one of the three copies of chromosome 21 present in cells RNA transcript complementary to the template strand of DNA.
taken from a patient with Down syndrome. Remarkably, Xist in Where in the many steps of transcription initiation does
its new location in chromosome 21 produced an RNA transcript regulation occur? The first point at which transcription can be
that coated that copy of chromosome 21 and repressed most regulated is in the recruitment of the general transcription factors
transcription of its genes! Whether all genes in chromosome 21 are and components of the RNA polymerase complex (Fig. 19.6).
repressed, and whether they are as fully repressed as those in the Recruitment of these elements is controlled by proteins called
inactive X chromosome, are questions still being investigated, but regulatory transcription factors. Transcription does not occur if
this finding raises clear (but still speculative) ideas about how Xist the regulatory transcription factors do not recruit the components
might be used as a potential treatment for Down syndrome and of the transcription complex to the gene. Some regulatory
various other chromosomal disorders. transcription factors recruit chromatin remodeling proteins that
allow physical access to a gene. Other regulatory transcription
Transcription is a key control point in gene expression. factor have two binding sites, one of which binds with a particular
While access to DNA and appropriate histone modifications DNA sequence in or near a gene known as an enhancer (Fig. 19.6)
are necessary for transcription, they are not sufficient. The and the other of which recruits one or more general transcription
molecular machinery that actually carries out transcription is factors to the promoter region. The general transcription factors
also required once the template DNA is made accessible through then recruit the RNA polymerase complex, and transcription can
chromatin remodeling and histone modification. The mechanisms begin (Chapter 3).
that regulate whether or not transcription occurs are known Hundreds of different regulatory transcription factors control
collectively as transcriptional regulation (see Fig. 19.1b). the transcription of thousands of genes. Some bind with enhancers
and stimulate transcription; others bind
with DNA sequences known as silencers
FIG. 19.6 Protein–DNA and protein–protein interactions in the eukaryotic transcription and repress transcription. Enhancers and
complex. silencers are often in or near the genes
they regulate, but in some cases they
1 Regulatory transcription Enhancer 5’ may be many thousands of nucleotides
factors bind with a DNA sequence 3’
distant from the genes. A typical
sequence called an enhancer.
General
3 The general transcription gene may be regulated by multiple
factors recruit the components enhancers and silencers of different
transcription
DNA factors of the RNA polymerase complex, types, each with one or more regulatory
and transcription takes place.
transcription factors that can bind with
it. Transcription takes place only when
Regulatory Components of the proper combination of regulatory
transcription RNA polymerase
factor complex
transcription factors is present in
5’ the same cell, as shown in Fig. 19.6.
3’ Since transcription of a gene with
Direction of
multiple silencers and enhancers
2 Binding of regulatory TATA box transcription
transcription factors depends on the presence of a particular
recruits the general combination of regulatory transcription
transcription factors to Promoter of gene
factors, this type of regulation is called
the promoter of the gene.
combinatorial control.
CHAPTER 19 G E N E T I C A N D E P I G E N E T I C R E G U L AT I O N 383
digestive enzyme trypsin must be kept inactive until secreted out multiple levels, and because there is much feedback and signaling
of the cell. If they were not, their activity would kill the cell. These back and forth between nucleus and cytoplasm. It is because of
types of protein are often controlled by being translated in inactive these feedback and signaling mechanisms that the effects of
forms that are made active by modification after secretion. lifestyle choices can be propagated up the regulatory hierarchy.
Folding and acquiring stability are key control points for For example, it has been shown that dietary intake of fats and
some proteins (Chapter 4). While many proteins fold properly cholesterol affects not only the activity of enzymes directly
as they come off the ribosome, others require help from other involved in the metabolism of fats and cholesterol, but also the
proteins, called chaperones, which act as folding facilitators. levels of transcription of the genes encoding these enzymes by
Correct folding is important because improperly folded proteins affecting the activity of their regulatory transcription factors.
may form aggregates that are destructive to cell function. Similarly, lifestyles that combine balanced diets with exercise
Many diseases are associated with protein aggregates, including and stress relief have been shown to increase transcription of
Alzheimer’s disease, Huntington’s disease, and the human genes whose products prevent cellular dysfunction and decrease
counterpart of mad cow disease. transcription of genes whose products promote disease.
Posttranslational modification also helps regulate protein So far, we have been talking primarily about complex traits
activity. Many proteins are modified by the addition of one or of the type discussed in Chapter 18, which are affected by
more sugar molecules to the side chains of some amino acids. This multiple genes and by multiple environmental factors as well
modification can alter the protein’s folding and stability, or target as by genotype-by-environment interaction. For example, there
the molecule to particular cellular compartments. Reversible are both genetic and environmental risk factors for breast and
addition of a phosphate group to the side groups of amino acids ovarian cancers, as we have seen. Simple Mendelian traits caused
such as serine, threonine, or tyrosine is a key regulator of protein by mutations in single genes, such as cystic fibrosis and alpha-1
activity (Chapter 9). Introduction of the negatively charged antitrypsin (a-1AT) deficiency (Chapter 17), are less responsive
phosphate group alters the conformation of the protein, in some to lifestyle choices. But even in these cases, lifestyle matters. For
cases switching it from an inactive state to an active state and example, people with a-1AT deficiency should not smoke tobacco
in other cases the reverse. Because the function of a protein and should avoid environments with low air quality.
molecule results from its shape and charge (Chapter 4), a change
in protein conformation affects protein function.
Marking proteins for enzymatic destruction by the addition of 19.3 TRANSCRIPTIONAL REGULATION
chemical groups after translation is also important in controlling IN PROKARYOTES
their activity. For example, we have seen how the destruction of
successive waves of cyclin proteins helps move the cell through its The central message of Fig. 19.1 is that the regulation of gene
division cycle (Chapter 11). expression occurs through a hierarchy of regulatory mechanisms
acting at different levels (and usually at multiple levels) from
DNA to protein. Gene regulation in prokaryotes is simpler
? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME than gene regulation in eukaryotes since DNA is not packaged
How do lifestyle choices affect expression of your into nucleosomes, mRNA is not processed, and transcription
personal genome? and translation are not separated by a nuclear envelope. In
If you examine Fig. 19.1 as a whole and consider the DNA sequence prokaryotes, expression of a protein-coding gene entails
shown as your personal genome, the situation looks pretty grim. transcription of the gene into messenger RNA and translation
You might be led to believe that genes dictate everything, and that of the messenger RNA into protein. Each of these levels of gene
biology is destiny. But if you focus on the lower levels of regulation expression is subject to regulation.
in Fig. 19.1, a different picture emerges. The picture is different Because gene regulation in prokaryotes is simpler than gene
because much of the regulation that occurs after transcription regulation in eukaryotes, prokaryotes have served as model
(regulation of mRNA stability, regulation of translation, organisms for our understanding of how genes are turned on
posttranslational modifications) is determined by the physiological and off. In this section, we consider in more detail how gene
state of your cells, which in turn is strongly influenced by your expression is regulated at the level of transcription in bacteria
lifestyle choices. For example, your cells can synthesize 12 of the and in viruses that infect bacteria. We focus on two well-studied
amino acids in proteins, but if any of these is present in sufficient systems: (1) the regulation of genes in the intestinal bacterium
amounts in your diet, it is absorbed during digestion and not Escherichia coli that allows proteins needed to utilize the sugar
synthesized. The amino acid you ingest blocks the synthetic lactose to be produced only when lactose is present in the
pathway through feedback effects. environment and only when it is the best nutrient available,
The effect of an intervention—genetic or environmental—at and (2) the regulation of genes in a virus that infects E. coli that
any given level can affect regulatory processes at both higher and controls whether the virus integrates its DNA into the bacterial
lower levels. This cascade of regulatory effects in both directions host or lyses (breaks open) the cell. In both cases, specific genes
can occur because the expression of any gene is regulated at are turned on and off in response to environmental conditions.
CHAPTER 19 G E N E T I C A N D E P I G E N E T I C R E G U L AT I O N 387
FIG. 19.18 Lactose operon regulatory mutants. Jacob and Monod found two classes of constitutive mutants, (a) one that affects the repressor
and (c) one that affects the operator. In cells containing both a mutant and a nonmutant lactose operon, (b) those with the repressor
mutant become regulated, and (d) those with the operator mutant remained constitutive.
a. b.
Repressor
lacl mutant promoter
protein
lacl lacP lacO lacZ lacY
Constitutive Regulated
expression expression
c. d.
lacOc mutant
Constitutive Regulated
expression expression
FIG. 19.19 The CRP–cAMP complex, a positive regulator of the lactose operon. (a) In the absence of large amounts of glucose, cAMP levels
are high and the CRP–cAMP complex binds to a site near the promoter, where it activates transcription. (b) In the presence of large
amounts of glucose, cAMP levels are low and the CRP–cAMP complex does not bind, so transcription is not induced to high levels,
even in the presence of lactose.
CRP
Operator
CRP–cAMP
(lacO)
complex
Promoter
(lacP)
Lactose Repressor
Glucose
of viruses known as bacteriophages (“bacteriophage” literally recombination is reversed, freeing the phage DNA and initiating
means “bacteria-eater,” and is often shortened to just “phage”). the lytic pathway.
Among bacteriophages is a type that can undergo one of two fates At the molecular level, the choice between the lytic and
when infecting a cell. The best known example is bacteriophage lysogenic pathways is determined by the positive and negative
λ (lambda), which infects cells of E. coli. The possible results of regulatory effects of a small number of bacteriophage proteins
λ infection are illustrated in Fig. 19.20. produced soon after infection. Which pathway results depends
Upon infection, the linear DNA of the phage genome is on the outcome of a competition between the production of a
injected into the bacterial cell, and almost immediately the ends protein known as cro and that of another protein known as cI. If
of the molecule join to form a circle. In normal cells growing in the production of cro predominates, the lytic pathway results; if cI
nutrient medium, the usual outcome of infection is the lytic predominates, the lysogenic pathway takes place.
pathway, shown on the left in Fig. 19.20. In the lytic pathway, the Fig. 19.21 shows the small region of the bacteriophage DNA
virus hijacks the cellular machinery to replicate the viral genome in which the key interactions take place. Almost immediately
and produce viral proteins. After about an hour, the infected cell after infection and circularization of the bacteriophage
undergoes lysis and bursts open to release a hundred or more DNA, transcription takes place from the promoters PL and PR.
progeny phage capable of infecting other bacterial cells. Transcription of genes controlled by the PR promoter results in
The alternative to the lytic pathway is lysogeny, shown on a transcript encoding the proteins cro and cII. The cro protein
the right in Fig. 19.20. In lysogeny, the bacteriophage DNA and the represses transcription of a gene controlled by another promoter PM,
bacterial DNA undergo a process of recombination at a specific site which encodes the protein cI. In normal cells growing in nutrient
in both molecules, which results in a bacterial DNA molecule that medium, proteases present in the bacterial cell degrade cII and
now includes the bacteriophage DNA. Lysogeny often takes place prevent its accumulation. With cro protein preventing cI expression
in cells growing in poor conditions. The relative sizes of the DNA and cII protein unable to accumulate, transcription of bacteriophage
molecules in Fig. 19.20 are not to scale. In reality, the length of the genes in the lytic pathway takes place, including those genes needed
bacteriophage DNA is only about 1% of that of the bacterial DNA. for bacteriophage DNA replication, those encoding proteins in the
When the bacteriophage DNA is integrated by lysogeny, the only bacteriophage head and tail, and, finally, those needed for lysis.
bacteriophage gene transcribed and translated is one that represses Alternatively, in bacterial cells growing in poor conditions,
the transcription of other phage genes, preventing entry into the reduced protease activity allows cII protein to accumulate. When
lytic pathway. The bacteriophage DNA is replicated along with the cII protein reaches a high enough level, it stimulates transcription
bacterial DNA and transmitted to the bacterial progeny when the from the promoter PE . The transcript from PE includes the coding
cell divides. Under stress, such as exposure to ultraviolet light, sequence for cI protein, and the cI protein has three functions:
CHAPTER 19 G E N E T I C A N D E P I G E N E T I C R E G U L AT I O N 393
FIG. 19.21 Transcriptional regulation of cI and cro genes, which determine the lytic versus lysogenic pathway.
cII Reduced
protease
Transcription activity allows
takes place cII to
from accumulate,
promoters PL PL OL cl PM PE PL OL cl PM PE stimulating
and PR, transcription
leading to PR OR cro cII PR OR cro cII from promoter
the synthesis Lysogenic PE and the
of proteins pathway synthesis of cl
cro and cII. protein.
Lytic
pathway
cro cl cl cl protein
cro protein binds with OL
inhibits PM, and OR,
preventing cl preventing
expression. transcription
PL OL cl PM PE PL OL cl PM PE from PL and
Proteases
degrade PR OR cro cII PR OR cro cII expression of
excess cII cro and cII. cl
protein. protein also
increases its
Proteases degrade own
cII protein production by
cII cl
stimulating PM.
V I S UA L S Y N T H E S I S Virus: A Genome in Need of a Cell
FIG. 19.22 Integrating concepts from Chapters 11, 13, and 19
Diversity
Viruses come in many different shapes and viral genomes include a diverse array of types and structures of
nucleic acids.
Mature
assembled
viruses are
released.
Fragmented
bacterial DNA
Replicated viral
components
Lysis
Mature
Bacterial λ phage
cell
Circular DNA
Lysogeny
Viral DNA
integrated
into bacterial
DNA
Transcriptional regulation
When bacterial cells are grown in favorable conditions, bacterial proteases degrade a key
viral protein and genes are transcribed that lead to the bursting of the bacterial cell (lysis).
When bacterial cells are grown in poor conditions, the viral protein accumulates and genes
are transcribed that allow the viral genome to remain integrated in host genome (lysogeny).
394
Replication cycle
Viruses are not considered 1 Attachment: HIV attaches to
living organisms because proteins on the surface of the cell and
they cannot replicate on fuses with the plasma membrane.
their own and absolutely
require a cell to complete
their replication cycle.
Human immunodeficiency
virus (HIV)
gp120
Viral RNA
2 Entry:
Co-receptor The virus
enters the
Viral Reverse cytoplasm.
DNA transcriptase
CD4
Host range
A given virus can only infect some
organisms and types of cell, determined
by specific interactions of viral proteins
with cell-surface host proteins.
Host
DNA
4 Self-assembly:
The viral components
assemble on their
own inside of the cell.
395
396 SELF-ASSESSMENT
Small regulatory RNAs, especially microRNA (miRNA) and In infection of E. coli cells by bacteriophage λ, predominance
small interfering RNA (siRNA), affect gene expression through of cro protein results in the lytic pathway, whereas
their effects on translation or mRNA stability. page 384 predominance of the cI protein results in the lysogenic
pathway. page 392
Translational regulation controls the rate, timing, and
location of protein synthesis. page 384
Translational regulation is determined by many features of an Self-Assessment
mRNA molecule, including the 5� and 3� UTR, the cap, and the
1. Distinguish between gene expression and gene regulation.
poly(A) tail. page 385
2. Explain what is meant by different “levels” of gene
Posttranslational modification comes into play after a protein
regulation and give some examples.
is synthesized, and includes chemical modification of side
groups of amino acids, affecting the structure and activity of a 3. Give two examples of how DNA bases and chromatin
protein. page 385 can be modified to regulate gene expression, and explain
CHAPTER 19 G E N E T I C A N D E P I G E N E T I C R E G U L AT I O N 397
why these kinds of modifications result in increased or how expression is controlled in the presence and in the
decreased gene expression. absence of lactose.
4. Explain how X-inactivation in female mammals results in 8. Describe the role of the CRP–cAMP complex in positive
patchy coat color in calico cats. regulation of the lactose operon in E. coli.
5. Explain how one protein-coding gene can code for more 9. Describe what is meant by lysis and lysogeny, and explain
than one polypeptide chain. how gene regulation controls these two pathways.
6. Name and describe three ways in which gene expression Log in to to check your answers to the Self-
can be influenced after mRNA is processed and leaves the Assessment questions, and to access additional learning tools.
nucleus.
Genes and
Development
Core Concepts
20.1 In the development
of humans and other
animals, stem cells become
progressively more
restricted in their possible
pathways of cellular
differentiation.
20.2 The genetic control of
development is a hierarchy
in which genes are activated
in groups that in turn
regulate the next set of
genes.
20.3 Many proteins that play key
roles in development are
evolutionarily conserved
but can have dramatically
different effects in different
organisms.
20.4 Combinatorial control
is a developmental
strategy in which cellular
differentiation depends on
the particular combination
of transcription factors
present in a cell.
20.5 Ligand–receptor
interactions activate signal
transduction pathways that
converge on transcription
factors and genes that
determine cell fate.
Perrennou Nuridsany/Science Source.
399
400 SECTION 20.1 G E N E T I C P RO G R A M S O F D E V E LO P M E N T
Altogether, the human body contains about 200 different types the genetic program of development—that is, the genetic
of cell, all of which derive from a single cell, the zygote. Some instructions that lead a single fertilized egg to become a complex
cells derived from the zygote become muscle cells, others nerve multicellular organism.
cells, still others connective tissue. Almost all of these cells have
exactly the same genome: They differ not in their content of The fertilized egg is a totipotent cell.
genes, but instead in the groups of genes that are expressed or In all sexually reproducing organisms, the fertilized egg is
repressed. In other words, these cell types differ as a result of gene special because of its developmental potential. The fertilized
regulation, discussed in the previous chapter. egg is said to be totipotent, which means that it can give rise
Gene regulation is especially important in multicellular to a complete organism. In mammals, the egg also forms the
organisms because it underlies development, the process in membranes that surround and support the developing embryo
which a fertilized egg undergoes multiple rounds of cell division (Chapter 42).
to become an embryo with specialized tissues and organs. During After fertilization, the fertilized egg, or zygote, undergoes
development, cells undergo changes in gene expression as genes successive mitotic cell divisions as it moves along a fallopian tube.
are turned on and off at specific times and places. Gene regulation One cell becomes two, two become four, four become eight, eight
causes cells to become progressively more specialized, a process become sixteen, and so on, with all the cells contained within
known as differentiation. the egg’s outer membrane (Fig. 20.1). Within 4 –5 days after
In this chapter, we focus on the general principles by
which genes control development. We will see that, as cells
differentiate along one pathway, they progressively lose their FIG. 20.1 Early development of a human embryo. The zygote is a
ability to differentiate along other pathways. Yet gene expression totipotent cell because its daughter cells can develop into
can sometimes be reprogrammed to reopen pathways of any cell type and eventually into a complete organism.
differentiation that had previously been shut off, a process
Four-cell stage
that has important implications for therapeutic replacement of
diseased or damaged tissue. From a broader perspective, the study Two-cell stage
of evolutionary changes in developmental processes constitute Morula
fertilization, the zygote has turned into a ball of cells called the j Quick Check 1 From what you know about embryonic
morula and has traveled from the site of fertilization in one of development, do you think that a cell from the inner cell mass or
the fallopian tubes to the uterus. one from the ectoderm has more developmental potential?
These early cell divisions are different from the mitotic cell
Why do differentiating cells increasingly lose their
divisions that occur later in life because the cells do not grow
developmental potential? One hypothesis focuses on gene
between divisions; they merely replicate their chromosomes
regulation. When cells become committed to a particular
and divide again. The result is that the cytoplasm of the egg is
developmental pathway, genes no longer needed are turned off
partitioned into smaller and smaller packages, with the new
(that is, repressed) and are difficult to turn on again. Another
cells all bunched together inside the membrane that covers the
hypothesis is genome reduction: As cells become differentiated,
developing embryo.
they delete the DNA for genes they no longer need.
Cell division continues in the morula until there are a few
These hypotheses can be distinguished by an experiment
thousand cells. The cells then begin to move relative to one
in which differentiated cells are reprogrammed to mimic
another, pushing against and expanding the membrane that
earlier states. If loss of developmental potential is due to gene
encloses them and rearranging themselves to form a hollow
regulation, then differentiated cells could be reprogrammed to
sphere called a blastocyst (Fig. 20.1). In one region of the inner
become pluripotent or multipotent. If loss of developmental
wall of the blastocyst, there is a group of cells known as the
potential is due to genome reduction, then differentiated
inner cell mass, from which the body of the embryo develops.
cells could not be reprogrammed to become pluripotent or
The wall of the blastocyst forms several membranes that envelop
multipotent.
and support the developing embryo. Once the blastocyst forms,
British developmental biologist John Gurdon carried out
it implants in the uterine wall.
such experiments in the early 1960s (Fig. 20.2). Gurdon used
Once implanted in the uterine wall, the multiplying
a procedure called nuclear transfer, in which a hollow glass
cells of the inner cell mass reorganize to form a gastrula, in
needle is used to insert the nucleus of a cell into the cytoplasm
which the blastula becomes organized into three germ layers
of an egg whose own nucleus has been destroyed or removed.
(Fig. 20.1). Germ layers are sheets of cells that include the
Previous nuclear transfer experiments had been carried
ectoderm, mesoderm, and endoderm and that differentiate
out in the leopard frog, Rana pipiens. Whereas nuclei from
further into specialized cells. Those formed from the ectoderm
pluripotent or multipotent cells could often be reprogrammed
include the outer layer of the skin and nerve cells in the brain;
to develop into normal tadpoles, attempts with nuclei from fully
cells from the mesoderm include cells that make up the inner
differentiated cells failed.
layer of the skin, muscle cells, and red blood cells; and cells
Gurdon tried the experiments in a different organism, the
formed from the endoderm include cells of the lining of the
clawed toad Xenopus laevis, and demonstrated that nuclei from
digestive tract and lung, as well as liver cells and pancreas cells
fully differentiated intestinal cells could be reprogrammed
(Chapter 42).
to support normal development of the tadpole (Fig. 20.2).
Only 10 of 726 experiments succeeded, but this was sufficient
Cellular differentiation increasingly restricts to show that intestinal cell nuclei still contained a complete
alternative fates. Xenopus genome. In other words, his findings supported the first
At each successive stage in development in which the cells hypothesis—all of the same genes are present in intestinal cells
differentiate, they lose the potential to develop into any kind of as in early embryonic cells, but some of the genes are turned off,
cell. The fertilized egg is totipotent because it can differentiate or repressed, during development.
into both the inner cell mass and supporting membranes, and Fig. 20.3 summarizes the results of many nuclear transfer
eventually into an entire organism. The cells of the inner cell experiments carried out in mammals and amphibians. The
mass, called embryonic stem cells, are pluripotent because percentage of reprogramming experiments that fail increases
they can give rise to any of the three germ layers, and therefore as cells differentiate. The best chance of success is to use
to any cell of the body. However, pluripotent cells cannot on pluripotent nuclei from cells in the blastocyst (or its amphibian
their own give rise to an entire organism, as a totipotent cell equivalent, the blastula). However, even some experiments
can. Cells further along in differentiation are multipotent; using nuclei from fully differentiated cells have been successful.
these cells can form a limited number of types of specialized When nuclear transfer succeeds, the result is a clone—an
cell. Cells of the germ layers are multipotent because they can individual that carries an exact copy of the nuclear genome of
give rise only to the cell types specified for each germ layer another individual. In this case, the new individual shares the
in Figure 20.1. Totipotent, pluripotent, and multipotent cells same genome as that of the individual from which the donor
are all stem cells, cells that are capable of differentiating into nucleus was obtained. (The mitochondrial DNA is not from the
different cell types. nuclear donor, but from the donor of the egg cytoplasm.) The
HOW DO WE KNOW?
FIG. 20.2
1 The nucleus of an
differentiate into
any cell type? Xenopus laevis
tadpole 10 experiments:
Development to tadpole
BACKGROUND During differentiation, cells
2 The nucleus from an stage occurred.
become progressively more specialized and intestinal cell of a tadpole is
restricted in their fates. Early studies left the injected into the egg cell.
mechanisms of differentiation unclear.
HYPOTHESIS One hypothesis is that differentiation occurs as a the cytoplasm of the unfertilized egg are able to support complete
result of changes in gene expression. A second hypothesis is that development of a normal animal. This result allows us to reject the
differentiation occurs as a result of genome reduction, in which genes hypothesis that differentiation occurs by the loss of genes. The first
that are not needed are deleted. hypothesis—that cells become differentiated as a result of changes in
gene expression—was supported. But, because of the small number of
EXPERIMENT John Gurdon carried out experiments in the amphibian successes in reprogramming, additional experiments were needed to
Xenopus laevis to test these hypotheses. He transferred nuclei from validate the conclusions.
differentiated cells into unfertilized eggs whose nuclei had been
inactivated with ultraviolet light. If differentiation is due to changes FOLLOW-UP WORK Gurdon’s work was controversial. Some critics
in gene expression, then the differentiated nucleus should be able to argued that the successful experiments resulted from a small number of
reprogram itself in the egg cytoplasm and differentiate again into all undifferentiated cells present in intestinal epithelium. Others accepted
the cells of a tadpole. If differentiation is accompanied by loss of genes, the conclusion but expressed misgivings about possible applications to
then differentiation is irreversible and development will not proceed. humans. Later experiments that succeeded in cloning mammals from
fully differentiated cells confirmed the original conclusion.
RESULTS The experiment was carried out 726 times. In 716 cases,
development did not occur; in 10, development proceeded normally. SOURCE Gurdon, J. B. 1962. “The Developmental Capacity of Nuclei Taken from Intestinal
Epithelium Cells of Feeding Tadpoles.” Journal of Embryology & Experimental Morphology
CONCLUSION Although the experiment succeeded in only 10 of 10:622–640.
first mammalian clone was a lamb called Dolly (Fig. 20.4a), born in
Cells that are further along
in differentiation are more 1996. She was produced from the transfer of the nucleus of a cell in
difficult to reprogram. the mammary gland of a sheep to an egg cell with no nucleus, and
50 was the only successful birth among 277 nuclear transfers. Successful
cloning in sheep soon led to cloning in cattle, pigs, and goats.
Percentage of nuclear transplant
Amphibian Mammal The first household pet to be cloned was a kitten named
40
experiments that succeed
CopyCat (Fig. 20.4b), born in 2001 and derived from the nucleus of
a differentiated ovarian cell. CopyCat was the only success among
30 Blastocyst 87 attempts. As shown in Fig. 20.4b, the cat from which the donor
nucleus was obtained was a calico, but CopyCat herself was not,
20
10
402
CHAPTER 20 G E N E S A N D D E V E LO P M E N T 403
FIG. 20.4 Celebrity clones and their genetic mothers. (a) Dolly; (b) CopyCat. Sources: a. AP Photo/John Chadwick; b. AP Photo/Pat Sullivan.
a b
even though the two cats are clones of each other. The reason for because obtaining embryonic stem cells requires the destruction
their different appearance has to do with X-inactivation, discussed of human blastocysts—that is, early-stage embryos. A major
in Chapter 19. Recall that the mottled orange and black calico breakthrough occurred in 2006 when Japanese scientists
pattern results from random inactivation of one of the two X demonstrated that adult cells can be reprogrammed by activation
chromosomes during development. The lack of a calico pattern of just a handful of genes, most of them encoding transcription
in CopyCat implies that the X chromosomes in the transferred factors or chromatin proteins. The reprogrammed cells were
nucleus did not “reset” as they do in normal embryos. Instead, the pluripotent and were therefore called induced pluripotent stem
inactive X in the donor nucleus remained inactive in all the cells in cells (iPS cells).
the clone. Hence, while CopyCat and her mother share the same The success rate was only about one iPS cell per thousand,
nuclear genome, the genes were not expressed in the same way and the genetic engineering technique required the use of viruses
because of irreversible epigenetic regulation in the donor nucleus. that can sometimes cause cancer. Nevertheless, the result was
regarded as spectacular. Other researchers soon found other genes
j Quick Check 2 X-inactivation can result in two clones of a
that could be used to reprogram adult cells into pluripotent or
cell that differ in the genes they express. Can you think of other
multipotent stem cells, and still other investigators developed
reasons why two genetically identical individuals might look
virus-free methods for delivering the genes. In recent years,
different from each other?
researchers have even discovered small organic molecules that can
reprogram adult cells.
This kind of reprogramming opens the door to personalized
? CASE 3 YOU, FROM A TO T: YOUR PERSONAL GENOME stem cell therapies. The goal is to create stem cells derived from
Can cells with your personal genome be the adult cells of the individual patient. Since these cells contain
reprogrammed for new therapies? the patient’s own genome, problems with tissue rejection are
Stem cells play a prominent role in regenerative medicine, minimized or eliminated (Chapter 43). There remains much
which aims to use the natural processes of cell growth and to learn before therapeutic use of induced stem cells becomes
development to replace diseased or damaged tissues. Stem cells are routine. Researchers will face challenges such as increasing the
already used in bone marrow transplantation and may someday efficiency of reprogramming, verifying that reprogramming
be used to treat Parkinson’s disease, Alzheimer’s disease, heart is complete, making sure that the reprogrammed cells are not
failure, certain types of diabetes, severe burns and wounds, and prone to cancer, and demonstrating that the reprogrammed cells
spinal cord injury. differentiate as they should. Nevertheless, researchers hope that
At first, it seemed as though the use of embryonic stem cells someday soon your own cells containing your personal genome
gave the greatest promise for regenerative medicine because of could be reprogrammed to restore cells or organs damaged by
their pluripotency. This approach proved ethically controversial disease or accident.
404 CHAPTER 20.2 H I E R A RC H I C A L CO N T RO L O F D E V E LO P M E N T
the egg and sperm nuclei fuse (Fig. 20.5a). Unlike in mammalian
20.2 HIERARCHICAL CONTROL development, the early nuclear divisions in the Drosophila embryo
OF DEVELOPMENT occur without cell division, and therefore the embryo consists of a
single cell with many nuclei in the center (Fig. 20.5b). When there
During development of a complex multicellular organism, are roughly 5000 nuclei, they migrate to the periphery (Fig. 20.5c),
many genes are activated and repressed at different times, thus where each nucleus becomes enclosed in its own cell membrane,
restricting cell fates. One of the key principles of development and together they form the cellular blastoderm (Fig. 20.5d).
is that genes expressed early in an organism’s development Then begins the process of gastrulation, in which the cells of
control the activation of other groups of genes that act later in the blastoderm migrate inward, creating layers of cells within the
development. Gene regulation during development is therefore embryo. As in humans and most other animals (section 20.1 and
hierarchical in the sense that genes expressed at each stage in the Chapter 42), gastrulation forms the three germ layers (ectoderm,
process control the expression of genes that act later. mesoderm, and endoderm) that differentiate into different types
of cell. A Drosophila embryo during gastrulation is shown in Fig.
Drosophila development proceeds through egg, larval, 20.5e. At this stage, the embryo already shows an organization
and adult stages. into discrete parts or segments, the formation of which is known
The fruit fly Drosophila melanogaster has played a prominent role as segmentation. There are three cephalic segments, C1–C3 (the
in our understanding of the genetic control of early development, term “cephalic” refers to the head); three thoracic segments, T1–T3
and in particular the hierarchical control of development. (the thorax is the middle region of an insect); and eight abdominal
Researchers have isolated and analyzed a large number of segments (A1–A8). Each of these segments has a different fate in
mutant genes that lead to a variety of defects at different stages development.
in development. These studies have revealed many of the key About one day after fertilization, the embryo hatches from
genes and processes in development, which are the focus of the the egg as a larva (Fig. 20.5f). Over the next eight days, the larva
following sections. grows and replaces its rigid outer shell, or cuticle, twice (Fig. 20.5g
The major events in Drosophila development are illustrated in and 20.5h). After a week of further growth, the cuticle forms a
Fig. 20.5. DNA replication and nuclear division begin soon after casing—called the pupa (Fig. 20.5i)—in which the larva undergoes
FIG. 20.5 Life cycle of the fruit fly Drosophila melanogaster. The life cycle begins with (a) a fertilized egg, followed by (b –e) a developing
embryo, (f–h) larval stages, (i) pupa, and (j) adult.
15–80 minutes
h.
5 days
c.
g.
2.5–3.5 hours
1 day
7.5–9.5 hours
f.
d. Cellular blastoderm
FIG. 20.8 Caudal and Hunchback gradients in the developing embryo. (a) mRNA levels of hunchback and caudal are uniform across the
embryo. (b) Hunchback and Caudal protein levels are localized to the anterior and posterior ends of the embryo, respectively, because
Bicoid and Nanos control the translation of hunchback and caudal mRNA.
a.
bicoid
nanos
The gradient of hunchback The gradient of
bicoid mRNA caudal nanos mRNA
peaks near the peaks near the
anterior end of posterior end
the oocyte. of the oocyte.
0
Anterior Posterior
Position in oocyte
b.
Relative protein abundance
Bicoid
1
Nanos
Hunchback
Caudal
Nanos protein
Bicoid protein represses
represses translation of
translation of hunchback
caudal mRNA. mRNA.
0
Anterior Posterior
Position in 2.5-hour embryo
The anterior–posterior axis set up by the gradients of Bicoid genes of the embryo needed for the development of posterior
and Nanos proteins is reinforced by gradients of two transcription structures like genitalia. In this way, maternal genes expressed
factors called Caudal and Hunchback (Fig. 20.8). Like the mRNAs early in development influence the expression of genes of the
for Bicoid and Nanos, the mRNAs for Caudal and Hunchback are embryo that are important in later development. Because the
transcribed from the mother’s genome and transported into the products of the bicoid and nanos mRNA are the ones initially
egg. As shown in Fig. 20.8a, the mRNAs for caudal and hunchback responsible for organizing the anterior and posterior ends of the
are spread uniformly in the cytoplasm of the fertilized egg. embryo, respectively, mothers that are mutant for bicoid have
However, the mRNAs are not translated uniformly in the egg. larvae that lack anterior structures, and mothers that are mutant
Bicoid protein represses translation of caudal, and Nanos protein for nanos have larvae that lack posterior structures.
represses translation of hunchback (Fig. 20.8b). Caudal protein
j Quick Check 3 Would development happen normally if the
is therefore concentrated at the posterior end and Hunchback
mother has normal bicoid function, but the embryo does not? Why
protein is concentrated at the anterior end. The expression of
or why not?
Caudal and Hunchback illustrates gene regulation at the level
of translation, discussed in Chapter 19. Bicoid protein is also a
transcription factor that promotes transcription of the hunchback Development proceeds by progressive regionalization
gene from zygotic nuclei, which reinforces the localization of and specification.
Hunchback protein at the anterior end. Nusslein-Volhard and Wieschaus also discovered mutants of the
The Hunchback and Caudal gradients set the stage for the embryo’s developmental genes. They discovered three classes of
subsequent steps in development. The Hunchback transcription such mutants, and their analysis showed that genes in the embryo
factor targets genes of the embryo needed for the development controlling its development are turned on in groups, and that
of anterior structures like eyes and antennae, and Caudal targets each successive group acts to refine and narrow the pattern of
CHAPTER 20 G E N E S A N D D E V E LO P M E N T 407
FIG. 20.9 Normal gap-gene expression pattern and mutant FIG. 20.10 Normal pair-rule gene expression pattern and mutant
phenotype. Source: James Langeland, Steve Paddock and Sean phenotype. Source: James Langeland, Steve Paddock and Sean
Carroll, HHMI, University of Wisconsin–Madison. Carroll, HHMI, University of Wisconsin–Madison.
differentiation generated by previous groups. This, too, is a general of pair-rule genes (Fig. 20.10). Pair-rule genes receive their
principle of development in many multicellular organisms. name because larvae with these mutations lack alternate body
The anterior–posterior gradient set up by the maternal-effect segments. The example in Fig. 20.10 is hairy, whose mutants lack
genes is first narrowed by genes called gap genes (Fig. 20.9), each the odd-numbered thoracic segments and the even-numbered
of which is expressed in a broad region of the embryo. The name abdominal segments. The pair-rule genes help to establish the
“gap gene” derives from the phenotype of mutant embryos, which uniqueness of each of seven broad stripes across the anterior–
are missing groups of adjoining segments, leaving a gap in the posterior axis.
pattern of segments. Fig. 20.9 shows the expression pattern of the The pair-rule genes in turn help to regulate the next level in
gap gene Krüppel, which is expressed in the middle region of the the segmentation hierarchy, which consists of segment-polarity
embryo. Mutants of Krüppel lack some thoracic and abdominal genes (Fig. 20.11). The segment-polarity genes refine the 7-striped
segments when they reach the larval stage. Krüppel is expressed pattern still further into a 14-striped pattern. Each of the
in the pattern shown in Fig. 20.9 because it is under the control 14 stripes has distinct anterior and posterior ends determined by
of the transcription factor Hunchback, which in this embryo the segment-polarity genes. Embryos with mutations in segment-
is stained in green. High concentrations of Hunchback repress polarity genes lose this anterior–posterior differentiation, with
Krüppel transcription entirely, and low concentrations fail to the result that the anterior and the posterior halves of each
induce Krüppel transcription. Because Hunchback is present segment are mirror images. The example in Fig. 20.11 is engrailed,
in an anterior–posterior gradient (see Fig. 20.8), the pattern of which eliminates the posterior pattern element in each stripe and
Hunchback expression means that Krüppel is transcribed only in replaces it with a mirror image of the anterior pattern element.
the middle region of the embryo where Hunchback is present but
not too abundant. j Quick Check 4 Would the pattern of segment-polarity
The gap genes encode transcription factors that control genes gene expression be normal if one or more gap genes were not
in the next level of the regulatory hierarchy, which consists expressed properly? Why or why not?
408 CHAPTER 20.2 H I E R A RC H I C A L CO N T RO L O F D E V E LO P M E N T
FIG. 20.11 Normal segment-polarity gene expression pattern FIG. 20.12 Homeotic genes and segment identity. (a) Normal
and mutant phenotype. Source: James Langeland, Steve antennae are transformed into legs in an Antennapedia
Paddock and Sean Carroll, HHMI, University of Wisconsin–Madison. mutant. (b) Normal structures in the third thoracic
segment are transformed into wings in a Bithorax
mutant. Sources: a. (left and right) F. Rudolf Turner, Ph.D., Indiana
Anterior Posterior
University; b. (left) Thomas Deerinck, NCMIR/Science Source;
(right) David Scharf/Science Source.
Nonmutant larva
The green segments
depend on the
function of the gene.
C1 T1 T2 T3
A1 A2 A3 A4 A5 A6 A7 A8
C2
C3 Mutant segment-
polarity gene results
Mutant larva in loss of half of each
segment and
replacement by
mirror image of
C1 T1 T2 T3
A1 A2 A3 A4 A5 A6 A7 A8 remaining half.
C2 b. Bithorax
C3
FIG. 20.13 Tissues controlled by homeotic genes. Homeotic FIG. 20.14 Organization of the Hox gene clusters in Drosophila
genes specify the fate of clumps of tissue in the and the body parts that they affect. The order of
Drosophila larva. genes along the chromosome corresponds to their
positions along the anterior–posterior axis in the
developing embryo.
Mouth parts
The Drosophila Hox genes are found in two clusters called
Antenna the Antennapedia complex and the Bithorax complex.
Eye
Leg Antennapedia complex Bithorax complex
Wing
Haltere
lab pb Dfd Scr Antp Ubx AbdA AbdB
Genitalia
The Drosophila genome contains eight Hox genes comprising Because the amino acid sequences of the homeodomains
two distinct clusters, the Antennapedia complex and the of Hox gene products are very similar from one organism to the
Bithorax complex (Fig. 20.14). The genes are arranged along next, Hox gene clusters have been identified in a wide variety of
the chromosome in the same order as their products function animals with bilateral symmetry (organisms in which both sides
in anterior–posterior segments along the embryo. In addition, of the midline are mirror images), from insects to mammals.
the timing of their expression corresponds to their order along Comparison of the number and types of Hox genes in different
the chromosome and location of expression, with genes that are species supports the hypothesis that the ancestral Hox gene
expressed closer to the anterior end turned on earlier than genes cluster had an organization very similar to what we now see
that are expressed closer to the posterior end. The correlation in most organisms with Hox gene clusters. In its evolutionary
among linear order along the chromosome, anterior–posterior history, the vertebrate genome underwent two whole-genome
position in the embryo, and timing of expression is observed in duplications; hence, vertebrates have four copies of the Hox gene
Hox clusters in almost all organisms studied. cluster (Fig. 20.15).
FIG. 20.15 Organization and content of Hox gene clusters in the mouse and the regions of the embryo in which they are expressed.
a.
Inferred Hox gene organization in Gene duplications The mammalian genome contains four
unidentified common ancestor copies of Hox gene clusters. The genes figure
prominently in the regional differentiation of
parts of the brain and vertebral column.
b.
HoxA
a-1 a-2 a-3 a-4 a-5 a-6 a-7 a-9 a-10 a-11 a-13
HoxB
b-1 b-2 b-3 b-4 b-5 b-6 b-7 b-8 b-9
HoxC
c-4 c-5 c-6 c-8 c-9 c-10 c-11 c-12 c-13
HoxD
d-1 d-3 d-4 d-8 d-9 d-10 d-11 d-12 d-13
Gene deletions Anterior
Posterior
410 CHAPTER 20.3 E VO L U T I O N A RY CO N S E RVAT I O N O F K E Y T R A N S C R I P T I O N FAC TO R S I N D E V E LO P M E N T
spinal cord, and vertebral column (Fig. 20.15). As in Drosophila, fotostock; d. Andrey Armyagov/iStockphoto; e. Julian Brooks/age
the genes in each cluster are expressed according to their linear fotostock; f. Walter Geiersperger/age footstock.
order along the chromosome, which coincides with the linear a. Planarian b. Jellyfish
order of regions the genes affect in the embryo. Each gene helps
to specify the identity of the region in which it is expressed. Many
of the genes in the mammalian Hox clusters have redundant or
overlapping functions so that learning exactly what each gene
does continues to be a research challenge. The evolutionary and
developmental study of Hox gene conservation and expression is a
good example of recent evo-devo research.
in diverse eyes argues that it may have been present in the Gehring/Science Source.
common ancestor of all animals with eyes and has been retained a b c
over time.
Another argument against multiple independent origins
of eyes came from studies of eye development. Researchers
identified eyeless, a gene in the fruit fly Drosophila. As its name
implies, the phenotype of eyeless mutants is abnormal eye
development (Fig. 20.17a). When the protein product of the
eyeless gene was identified, it was found to be a transcription factor
called Pax6. Mutant forms of a Pax6 gene were already known to Normal antenna Antennal eye Antennal eye
cause small eyes in the mouse (Fig. 20.17b) and aniridia (absence induced by induced by mouse
of the iris) in humans. Drosophila Pax6 gene Pax6 gene
compound eye, and electrical recordings demonstrated that in the history of life as a transcription factor able to bind to and
some of these antennal eyes were functional (Fig. 20.18b). The regulate genes involved in early eye development. Over time,
researchers also created other gain-of-function mutations that led different genes in different organisms acquired new Pax6-binding
to eyes on the legs, wings, and other tissues, which the New York cis-regulatory elements by mutation, and if these were beneficial
Times publicized in an article headlined “With New Fly, Science they persisted. The downstream genes that are targets of Pax6
Outdoes Hollywood.” therefore are different in different organisms, but they share two
Gehring and his group then went one step further. They features—they are regulated by Pax6 and they are involved in eye
took the Pax6 gene from mice and expressed it in fruit flies to development. So, the early steps are conserved, but the later ones
see whether the mouse Pax6 gene is similar enough to the fruit are not.
fly version of the gene that it could induce eye development in The Pax6 gene and the Hox genes reveal an important principle
the fruit fly. Specifically, they created transgenic fruit flies that in evo-devo, which is that master regulatory genes that control
expressed the Pax6 gene from mice in the fruit fly antenna. The development are often evolutionarily conserved, whereas the
mouse gene induced a miniature eye in the fly (Fig. 20.18c). downstream genes that they regulate may not be. Downstream
Note, however, that the Pax6 gene from mice induced the genes can evolve new functions, or genes not originally controlled
development of a compound eye of Drosophila, not the single- by the master regulator may evolve to come under its influence,
lens eye of mouse. or genes formerly controlled by the master regulator may evolve
The ability of mouse Pax6 to make an eye in fruit flies suggests to be unresponsive. In this way, a conserved master regulatory
that mouse and fruit fly Pax6 are not only similar in DNA and mechanism may result in distinct developmental outcomes in
amino acid sequence, but also similar in function, and indeed act different organisms. In the case of Pax6, for example, the master
as a master switch that can turn on a developmental program regulatory mechanism for eye development evolved early and is
leading to the formation of an eye. But these observations lead to shared among a wide range of animals, even though the eyes that
another question: Why did the mouse Pax6 gene produce fruit fly are produced are quite diverse.
eyes instead of mouse eyes?
The answer is that the fruit fly genome does not include the
genes needed to make mouse eyes. Mouse Pax6 protein induces 20.4 COMBINATORIAL CONTROL
fly eyes because of the downstream genes affected by Pax6, IN DEVELOPMENT
those that function later in the process of eye development.
Transcription factors like Pax6 interact with their target genes by Most cis-regulatory elements are located near one or more binding
binding with short DNA sequences adjacent to the gene, usually sites for transcription factors, some of which are activators of
at the 5� end, called cis-regulatory elements. These regulatory transcription and others repressors of transcription. The rate
elements are located in the promoter and help determine whether of transcription of any gene in any type of cell is therefore
the adjacent DNA is transcribed. When bound to cis-regulatory determined by the combination of transcription factors that are
elements, some transcription factors act as repressors that prevent present in the cell and by the relative balance of activators and
transcription of the target gene, and others serve as activators repressors. Regulation of gene transcription according to the mix
by recruiting the transcriptional machinery to the target gene of transcription factors in the cell is known as combinatorial
(Chapter 19). A transcription factor can even repress some of its control. Combinatorial control of transcription is another general
target genes and activate others. principle often seen in all multicellular organisms at many stages
In the fruit fly, Pax6 binds to cis-regulatory elements in of development. Here, we discuss flower development as an
many genes, turning some genes on and others off. The products example of this general principle.
of these downstream genes in turn affect the expression of
further downstream genes. The total number of genes that are Floral differentiation is a model for plant development.
downstream of Pax6 and that are needed for eye development is The plant Arabidopsis thaliana, a weed commonly called mouse-ear
estimated at about 2000. Most are not direct targets of cress, is a model organism for developmental studies and presents
Pax6 but are activated indirectly through other transcription a clear case of combinatorial control. As in all plants, Arabidopsis
factors downstream of Pax6. When mouse Pax6 is expressed in has regions of undifferentiated cells, called meristems, where
fruit flies, it is similar enough in sequence to activate the genes growth can take place (Chapter 31). Meristem cells are similar
involved in fruit fly eye development, so it makes sense that to stem cells in animals. They are the growing points where
mouse Pax6 leads to the development of a fruit fly eye, not a shoots, roots, and flowers are formed. Floral meristems consist of
mouse eye. multipotent cells that can differentiate into different structures in
One scenario of how Pax6 became a master switch for eye the flower. In floral meristems of Arabidopsis, the flowers develop
development in a wide range of organisms, but produces a from a pattern of four concentric circles of cells, or whorls, each of
diversity of eyes in these organisms, is that Pax6 evolved early which differentiates into a distinct type of floral structure.
CHAPTER 20 G E N E S A N D D E V E LO P M E N T 413
FIG. 20.20 Phenotypes of the normal flower and floral mutants of Arabidopsis. Source: Courtesy of John Bowman.
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
The combination of A, B, and C activities j Quick Check 6 Predict the phenotype of a flower in which
in each whorl determines which floral APETALA-2 (activity A) and AGAMOUS (activity C) are expressed
organs develop from that whorl.
normally, but APETALA-3 and PISTILLATA (activity B) are
C Whorl 4 Carpel expressed in all four whorls.
Tail
Vulva
20.5 CELL SIGNALING IN The vulva is an
DEVELOPMENT opening into
the body cavity
Eggs through which
As we have seen in the discussion of stem cells, differentiated cells fertilized eggs
are laid.
can be reprogrammed by the action of only a few key genes or
small organic molecules. In some cases, the processes that push
differentiation in a forward direction are also quite simple. An
important example is signal transduction, in which an extracellular
molecule acts as a signal to activate a membrane protein that in
Head
turn activates molecules inside the cell that control differentiation
(Chapter 9). The signaling molecule is called the ligand and the
membrane protein that it activates is called the receptor. The
following example shows how a simple ligand–receptor pair can
have profound effects not only on the differentiation of the cell that
carries the receptor, but also on its neighbors.
AC
EGF ligand
Induction
Lateral
inhibition
1 An epidermal growth
factor (EGF) ligand binds EGF ligand
with its receptor on the
cell surface.
EGF receptor EGF receptor
Notch
receptor –
–
2 Stimulation of the EGF
receptor initiates a chain Notch Signal
of protein activation in ligand transduction
the cytoplasm (signal +
transduction).
Notch
receptor
Type 1 Type 2
genes genes
3 Activated proteins enter the nucleus and result in: 4 Stimulation of the Notch receptor results in:
• Type 1 differentiation genes turned ON, • Type 2 differentiation genes turned ON,
• Gene for Notch ligand turned ON, • EGF receptor gene turned OFF.
• Notch receptor gene turned OFF.
Fig. 20.24a), which secretes a protein called epidermal growth not only of the cell itself but also of its neighbors? Fig. 20.25
factor (EGF) that binds to and activates a transmembrane EGF shows the mechanisms in simplified form. On the left is the
receptor (Chapter 9). The progenitor cell closest to the anchor cell progenitor cell nearest the anchor cell, which receives the
receives the most amount of signal, and upon activation of its EGF strongest EGF signal. Activation of the EGF receptor by the ligand
receptor the progenitor cell carries out three functions: initiates a process of signal transduction in the cytoplasm, in
which the signal is transmitted from one protein to the next by
• It activates the genes for differentiation into a type 1 cell
means of proteins at each stage phosphorylating several others,
(Fig. 20.24a).
which amplifies the signal at each stage (Chapter 9). The result
• It prevents the adjacent cells from differentiating as type 1 of signal transduction is that a set of transcription factors is
(a process called lateral inhibition). activated.
In the nucleus, the transcription factors activate transcription
• It induces the adjacent cells to differentiate as type 2 cells.
of genes for type 1 differentiation. The transcription factors also
activate transcription of genes that prevent type 1 differentiation
Developmental signals are amplified and expanded. in neighboring cells, including the genes that produce another
How can a single ligand–receptor pair cause so many changes in type of protein ligand, called Notch. The Notch ligand is a
gene expression that it determines the pathway of differentiation transmembrane protein that activates Notch receptors in the
CHAPTER 20 G E N E S A N D D E V E LO P M E N T 417
neighboring cells. Activation of the Notch receptor in these cells differentiation and repair of multiple types of cells in the skin;
activates a signal transduction cascade in these cells, which results it is present in all body fluids and helps regulate rapid metabolic
in transcription of the genes for type 2 differentiation. The cascade responses to changing conditions. Human Notch ligands are
started by the binding of Notch also activates transcription of involved in development of the nervous and immune systems as
other genes whose products inhibit the EGF receptor. Inhibiting well as heart, pancreas, and bone. Abnormalities in EGF or Notch
the EGF receptor in type 2 cells prevents EGF from eliciting a type signaling are associated with many different types of cancer.
1 response in the type 2 cell. In addition, at the same time that the Therefore, just as we saw in our discussion of eye and flower
type 1 cell produces the Notch ligand, it produces proteins that development, the molecular players involved in development are
inhibit its own Notch receptors, and this prevents Notch from often evolutionarily conserved across a wide range of organisms.
initiating a type 2 response in the type 1 cell. This is true even of genes that we typically associate with disease,
While vulva development in nematodes is a fairly simple such as BRCA1 and BRCA2 and their link with cancer. These
example of the importance of ligand–receptor signaling in genes not only play a role in cell cycle control in the adult, but
development, EGF and Notch ligands and their receptors are also in early development in many organisms. In fact, although
found in virtually all animals. They are among dozens of ligand– heterozygous mutations in these genes predispose individuals to
receptor pairs that have evolved as signaling mechanisms to breast and ovarian cancers in humans, homozygous mutations are
regulate processes in cellular metabolism and development. lethal in early embryonic stages. In Fig. 20.26, we focus on the
Humans have several distinct but related gene families of EGF BRCA1 gene to summarize key concepts about DNA replication,
and Notch ligands and receptors. Human EGF is important in cell mutation, genetic variation, inheritance, gene regulation, and
survival, proliferation, and differentiation. EGF functions in the development. •
V I S UA L S Y N T H E S I S Genetic Variation and Inheritance
FIG. 20.26 Integrating concepts from Chapters 12–20
Genetic variation:
BRCA1 Genetics Everyone carries two copies of the
The BRCA1 gene on chromosome 17 encodes a protein that repairs double-stranded BRCA1 gene on chromosome 17. Some
breaks in DNA that result from DNA replication or environmental agents. The BRCA1 individuals have an allele of the gene
that increases the risk of breast and
gene is present in all cells, but is expressed, or turned on, in rapidly dividing cells,
ovarian cancer. In some populations,
including breast and ovarian cells. If BRCA1 does not function properly because of such as Ashkenazi Jews, the frequency
a mutation, damaged DNA is not repaired, which in turn increases the risk for of specific mutations in the gene is high.
certain kinds of cancers, particularly breast and ovarian cancers in women.
Healthy Chromosome 17
cell
Wild type allele
Mutant BRCA1
Mutation:
This individual inherits one mutation in the BRCA1
and is heterozygous. In one cell or a few of her
cells, a new mutation is acquired in the normal Susan Ben Sarah
BRCA1 gene, and these cells go on to be
cancerous.
418
? ? ? ?
Ruth
½ ½
Unaffected male
Unaffected female
Affected male
Affected female
Photo sources: (left to right) Michael Poehlman/Getty Images; Digital
Vision/Getty Images, Fabrice Lerouge/age fotostock, Piotr Marcinsk/
Dreamstime.com.
419
420 SELF-ASSESSMENT
Core Concepts Summary light perception are evolutionarily conserved suggests that
the ability to perceive light may have evolved once, early in
the evolution of animals. page 410
20.1 In the development of humans and other animals,
stem cells become progressively more restricted in their The Pax6 transcription factor is a master regulator of eye
possible pathways of cellular differentiation. development. Loss-of-function mutations in Pax6 result in
abnormalities in eye development, whereas gain-of-function
The fertilized egg can give rise to a complete organism.
mutations result in eye development in tissues in which eyes
page 400
do not normally form. page 410
At each successive stage in development, cells lose
developmental potential as they differentiate. page 401 20.4 Combinatorial control is a developmental
strategy in which cellular differentiation depends on the
Embryonic stem cells can give rise to any of the three germ
particular combination of transcription factors present in
layers, those further along in differentiation can form only
a cell.
a limited number of specialized cell types, and those still
further along can form only one cell type. page 401 By analyzing mutants that affect flower development in the
plant Arabidopsis, researchers were able to determine the
Stem cells play a prominent role in regenerative medicine, in
genes involved in normal flower development. page 412
which stem cells—in some cases reprogrammed cells from the
patient’s own body—are used to replace diseased or damaged The ABC model of flower development invokes three activities
tissues. page 403 (A, B, and C) present in circular regions (whorls) of the
developing flower, with the specific combination of factors
20.2 The genetic control of development is a hierarchy determining the developmental pathway in each whorl.
in which genes are activated in groups that in turn page 413
regulate the next set of genes.
20.5 Ligand–receptor interactions activate signal
Hierarchical gene control can be seen in fruit fly (Drosophila)
transduction pathways that converge on transcription
development. page 404
factors and genes that determine cell fate.
The oocyte of a fruit fly is highly polarized, with gradients of
Cell signaling involves a ligand, an extracellular molecule
maternal mRNA that set up anterior–posterior and dorsal–
that acts as a signal to activate a membrane receptor protein,
ventral axes. page 405
which in turn activates molecules inside the cell. page 415
These gradients in turn affect the expression of segmentation
Activation of a receptor sets off a pathway of signal
genes in the zygote, including the gap, pair-rule, and segment-
transduction, in which a series of proteins in the cytoplasm
polarity genes, which define specific regions in the developing
become sequentially activated. page 416
embryo. page 407
Because signal transduction can amplify and expand a
The segmentation genes direct the expression of homeotic
developmental signal, a single ligand–receptor pair can cause
genes, key transcription factors that specify the identity of
major changes in gene expression and ultimately determine
each segment of the fly and that are conserved in animal
the pathway of differentiation. page 416
development. page 408
An example of signal transduction in development is
20.3 Many proteins that play key roles in development differentiation of the nematode vulva, which is determined by
are evolutionarily conserved but can have dramatically means of an EGF ligand and receptor. page 416
different effects in different organisms.
Many proteins important in development are similar in Self-Assessment
sequence from one organism to the next. Such proteins are said
to be evolutionarily conserved. page 410 1. Distinguish among totipotent, pluripotent, and multipotent
stem cells, and give an example of where you would find each
The downstream targets of homeotic genes are different
type of cell.
in different animals, allowing homeotic genes to
activate different developmental pathways in different 2. Explain how an individual’s own cells might be used in
organisms. page 410 stem cell therapy.
Although animals exhibit an enormous diversity in eye 3. Draw a diagram to illustrate how a concentration
morphology, the observation that the proteins involved in gradient of a transcription factor along the anterior–posterior
CHAPTER 20 G E N E S A N D D E V E LO P M E N T 421
axis of a Drosophila embryo can create a region in the middle in 6. Define combinatorial control in the context of the ABC
which transcription of a target gene takes place without being model of floral development.
transcribed in either the anterior or posterior region.
7. Diagram a pathway of signal transduction including a
4. Expression of a homeotic gene in the wrong tissue in ligand, receptor, and ultimately a transcription factor that
Drosophila results in the development of an inappropriate activates a gene that inhibits the receptor.
body part from that tissue. Explain why this happens and
how it shows that homeotic genes are positive regulators of
developmental pathways. Log in to to check your answers to the Self-
Assessment questions, and to access additional learning tools.
5. Explain why master regulatory genes tend to be more
strongly conserved in evolution than are the downstream
genes they regulate.
CASE 4
Malaria
Coevolution of Humans and a Parasite
1 As it feeds, the mosquito injects
Plasmodium parasites along with its
saliva into the host. The parasites
migrate through the bloodstream
to the host’s liver.
Most people would say the world has more than enough
mosquitoes, but in 2010 scientists at the University
of Arizona conjured up a new variety. The high-tech life cycle. The human part of the cycle begins with a single
bloodsuckers were genetically engineered to resist bite from an infected mosquito. As the insect draws blood,
Plasmodium, the single-celled eukaryote that causes it releases Plasmodium-laden saliva into the bloodstream.
malaria. Once inside their human host, the Plasmodium parasites
Normally, the parasite grows in the mosquito’s gut invade the liver cells. There they undergo cell division for
and is spread to humans by the insect’s bite. By altering a several days, their numbers increasing. Eventually, the
single gene in the mosquito’s genome, the researchers had parasites infect red blood cells, where they continue to
made the insects immune grow and multiply. The mature parasites burst from the
As humans have to the malaria parasite. red blood cells at regular intervals, triggering malaria’s
The accomplishment is a telltale cycle of fever and chills.
tried a succession of noteworthy advance, the Some of the freed Plasmodium parasites go on to infect
weapons to defeat latest in a long line of efforts new red blood cells; others divide to form gametocytes,
to stop Plasmodium in its precursor cells to male and female gametes, which
P. falciparum, the tracks. travel through the victim’s blood vessels. When another
parasite has evolved, Malaria is one of the most mosquito bites the infected individual, it takes up the
devastating diseases on the gametocytes with its blood meal. Inside the insect, the
thwarting their planet. The World Health parasite completes its life cycle. The gametocytes fuse
efforts. Organization estimates that to form zygotes. Those zygotes bore into the mosquito’s
500 million people contract stomach, where they form cells called oocysts that give
malaria annually, primarily in tropical regions. The disease rise to a new generation of parasites. When the infected
is thought to claim about a million lives each year. Of mosquito sets out to feed, the cycle begins again.
those deaths, 85% to 90% occur in sub-Saharan Africa, The battle between malaria and humankind has raged
mostly among children under 5. through the ages. Scientists have recovered Plasmodium
Five species of Plasmodium can cause malaria in DNA from the bodies of 3500-year-old Egyptian
humans. One of them, P. falciparum, is particularly mummies—evidence that those ancient humans were
dangerous, accounting for the vast majority of malaria infected with the malaria parasite. The close connection
fatalities. Over thousands of years, this parasite and its between humans, mosquitoes, and the malaria parasite
human host have played a deadly game of tug-of-war. almost certainly extends back much further.
As humans have tried a succession of weapons to defeat In fact, people who hail from regions where malaria
P. falciparum, the parasite has evolved, thwarting their is endemic are more likely than others to have certain
efforts. And in turn, the tiny organism has helped to shape genetic signatures that offer some degree of protection
human evolution. from the parasite. That indicates that Plasmodium has
Plasmodium is a wily and complicated parasite, been exerting evolutionary pressure on humankind for
requiring both humans and mosquitoes to complete its quite some time.
422
Meanwhile, we’ve done our best to fight back. For Just as bacteria develop resistance to antibiotics,
centuries, humans fought the infection with quinine, Plasmodium evolves resistance to the antiparasitic drugs
a chemical found in the bark of the South American designed to fight it. In poor, rural areas where malaria is
cinchona tree. In the 1940s, scientists developed a more prevalent, people often can’t follow the recommended
sophisticated drug based on the cinchona compound. protocols for antimalarial treatment. Sick individuals
That drug, chloroquine, was effective, inexpensive, easy may be able to afford only a few pills rather than the full
to administer, and caused few side effects. As a result, recommended dose. The strength and quality of those
it was widely used, and in the late 1950s, P. falciparum pills may be questionable, and the drugs are often taken
began showing signs of resistance to chloroquine. Within without oversight from a medical professional.
20 years, resistance had spread to Africa, and today most Unfortunately, inadequate use of the drugs fuels
strains of P. falciparum have evolved resistance to the resistance. When the pills are altered or the course of
once-potent medication. treatment is abbreviated, not all Plasmodium parasites are
Liver
Liver
Malaria
cell
parasite
6 This mosquito then
leaves and infects
2 5 Gametocytes combine
another human host,
beginning the cycle
Plasmodium incubates in
to form zygotes in the again.
liver cells, maturing into a
mosquito gut. These
form that can invade red
mature into oocysts, and
blood cells.
spread thousands of
parasites through the
mosquito.
Blood vessel
3 The parasite
continues to grow and
multiply by mitosis, 4 Some parasites
bursting from red blood develop into male and
cells to infect other red female gametocytes, Gamete
blood cells. which infect another
mosquito when it takes
Red blood a blood meal from the Zygote
cells host.
Malaria Malaria
parasites parasites
Mature Oocyst
gametocytes
423
wiped out. Those that survive in the presence of the drug Plasmodium itself. The genetically engineered insects
are likely to evolve resistance to the drug. Because the created by the team in Arizona are a promising step in that
resistant parasites have a survival advantage, the genes for direction.
drug resistance spread quickly through the population. The Arizona researchers set out to alter a cellular
Since chloroquine resistance emerged, pharmaceutical signaling gene that plays a role in the mosquito’s life cycle.
researchers have developed a variety of new medications Mosquitoes normally live 2 to 3 weeks, and Plasmodium
to prevent or treat malaria. Most, however, are far too takes about 2 weeks to mature in the mosquito’s gut.
expensive for people in the poverty-stricken regions The researchers hoped to create mosquitoes that would
where malaria is rampant. And just as was the case die prematurely, before the parasite is mature. The
with chloroquine, almost as quickly as new drugs are genetic modification worked as planned. The engineered
developed, Plasmodium begins evolving resistance. mosquitoes’ life-spans were shortened by 18% to 20%. The
One of the weapons more recently added to the genetic tweak also had a surprising side effect. The altered
drug arsenal is artemisinin, a compound derived from gene completely blocked the development of Plasmodium
the Chinese wormwood tree. It has turned out to be an in the mosquitoes’ guts. The engineered mosquitoes are
effective and relatively inexpensive way to treat malaria incapable of spreading malaria to humans, regardless of
infections. However, pockets of artemisinin resistance how long they live.
have already been uncovered in Southeast Asia. Public While the finding was a laboratory success, it will be
health workers now recommend that artemisinin be much harder to translate the results to the real world.
given in combination with other drugs. Treating infected To create malaria-free mosquitoes in the wild, scientists
patients with multiple drugs is more likely to wipe out would have to release the genetically modified mosquitoes
Plasmodium in their bodies, reducing the chances that and hope that their altered gene spreads through the wild
more drug-resistant strains will emerge. mosquito population. But that gene would be passed on
Given the challenges of developing practical drugs to only if it gave the insects a distinct evolutionary advantage.
prevent or treat malaria, some scientists have turned their The engineered mosquitoes may be malaria free, but so far
attention to other approaches. One goal is to produce a they have no advantage over their wild counterparts.
malaria vaccine. The parasite’s complex life cycle makes It’s clear that slashing malaria rates will not be an
that a complicated endeavor, though. Several vaccines are easy task. Despite decades of research, insecticide-treated
now in various stages of testing, and some show promise. bed nets are still the best method for preventing the
But researchers expect it will be years before a safe, disease. For millennia, the malaria parasite has managed to
effective vaccine for malaria could be available. withstand our efforts to squelch it, yet science continues
Other researchers are focusing their efforts on to push the boundaries. Who will emerge the victor? Stay
the mosquitoes that carry the parasite, rather than on tuned.
?CASE 4 QUESTIONS
Special sections in Chapters 21–24 discuss the following questions related to Case 4.
1. What genetic differences make some individuals more and some less susceptible
to malaria? See page 434.
2. How did malaria come to infect humans? See page 455.
3. What human genes are under selection for resistance to malaria? See page 501.
424
CHAPTER 21
Evolution
How Genotypes and
Phenotypes Change
over Time
Core Concepts
21.1 Genetic variation refers
to differences in DNA
sequences.
21.2 Patterns of genetic variation
can be described by allele
frequencies.
21.3 Evolution is a change in
the frequency of alleles or
genotypes over time.
21.4 Natural selection leads to
adaptations, which enhance
the fit between an organism
and its environment.
21.5 Migration, mutation,
genetic drift, and non-
random mating are non-
adaptive mechanisms of
evolution.
21.6 Molecular evolution is a
change in DNA or amino
acid sequences over time.
Roc Canals Photography/Getty Images.
425
426 SECTION 21.1 G E N E T I C VA R I AT I O N
Variation is a fact of nature. A walk down any street reveals how color in butterflies. As we saw in Chapter 18, two factors contribute
variable our species is: Skin color and hair color, for example, vary to phenotype: an individual’s genotype, which is the set of alleles
from person to person. Until the publication in 1859 of Charles possessed by the individual, and the environment in which the
Darwin’s On the Origin of Species, scientists tended to view all individual lives. We can take the environment out of the equation
the variation we see in humans and other species as biologically by looking directly at genotypic differences through sequencing
unimportant. According to the traditional view, not only were DNA regions in multiple individuals. We now explore genetic
species individually created in their modern forms by a divine variation directly, in terms of differences at the DNA sequence level.
Creator, but, because the Creator had a specific design in mind
for each species, they were fixed and unchanging. Departures or Population genetics is the study of patterns of genetic
variations from this divinely ordained type were therefore ignored. variation.
Since Darwin, however, we have appreciated that a species Remarkably, in spite of a high degree of phenotypic variation,
does not conform to a type. Rather, a species consists of a range humans actually rank low in terms of overall genetic variation
of variants. In our own species, people may be tall, short, dark- compared with other species. Any two randomly selected humans
haired, fair-haired, and so on. Furthermore, variation is an essential differ from each other on average by one DNA base per thousand
ingredient of Darwin’s theory because the mechanism he proposed (the two genomes are 99.9% identical), while two fruit flies differ
for evolution, natural selection, depends on the differential by ten bases per thousand (the two genomes are 99% identical).
success—in terms of surviving and reproducing—of variants. Even one of the most seemingly uniform species on the planet,
Darwin changed how we view variation. Before Darwin, variation the Adélie penguins seen in Fig. 21.1, is two to three times more
was irrelevant, something to be ignored; after Darwin, it was genetically variable than we are.
recognized as the key to the evolutionary process. As we discuss in Chapter 22, a species consists of individuals
that can exchange genetic material through interbreeding. From
a genetic perspective, a species is therefore a group of individuals
21.1 GENETIC VARIATION capable, through reproduction, of sharing alleles with one another.
Individuals represent different combinations of alleles drawn from
Variation is a major feature of the natural world. We humans the species’ gene pool, that is, from all the alleles present in all
are particularly good at noticing phenotypic variation among individuals in the species. The human gene pool includes alleles
individuals of our own species. As we discussed in Chapter 16, a that cause differences in skin color, hair type, eye color, and so
phenotype is an observable trait, such as human height or wing on. Each one of us has a different set of those alleles—alleles that
cause brown hair and brown
eyes, for example, or black hair
and blue eyes—drawn from that
FIG. 21.1 Genetic diversity in Adélie penguins. Adélie penguins are uniform in appearance but are gene pool.
actually more genetically diverse than humans. Source: Tim Davis/Corbis. Population genetics is the
study of genetic variation in
natural populations, which
are interbreeding groups of
organisms of the same species
living in the same geographical
area. What factors determine
the amount of variation in a
population and in a species?
Why are humans genetically
less variable than penguins?
What factors affect the
distribution of particular
variations? Population genetics
addresses detailed questions
about patterns of variation.
And small differences, given
enough time, can lead to the
major differences we see among
organisms today.
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 427
Mutation and recombination are the two sources of Advantageous mutations, as we will see, can increase in frequency
genetic variation. in a population until eventually they are carried by every member
Genetic variation has two sources: Mutation generates new of a species. These mutations are the ones that result in a species
variation, and recombination followed by segregation of that is adapted to its environment—better able to survive and
homologous chromosomes during meiotic cell division shuffles reproduce in that environment.
mutations to create new combinations. In both cases, new alleles
are formed, as shown in Fig. 21.2.
As we saw in Chapter 14, mutations can be somatic, occurring 21.2 MEASURING GENETIC VARIATION
in the body’s tissues, or germline, occurring in the reproductive
cells and therefore passed on to the next generation. From an Mutations, whether deleterious, neutral, or advantageous, are
evolutionary viewpoint, we are primarily interested in germ-line sources of genetic variation. The goal of population genetics is to
mutations. A somatic mutation affects only the cells descended make inferences about the evolutionary process from patterns of
from the one cell in which the mutation originally arose, and thus genetic variation in nature. The raw information for this comes
affects only that one individual. However, a germ-line mutation from the rates of occurrence of alleles in populations, or allele
appears in every cell of an individual derived from the fertilization frequencies.
involving the mutation-bearing gamete, and thus appears in its
descendants. To understand patterns of genetic variation, we
Mutations can also be classified by their effects on an require information about allele frequencies.
organism (Chapter 15). Mutations occur randomly throughout The allele frequency of an allele x is simply the number of x’s
the genome, and, because most of the genome consists of present in the population divided by the total number of alleles.
noncoding DNA, most mutations are neutral, having little or no Consider, for example, pea color in Mendel’s pea plants. In Chapter
effect on the organism. Most mutations that do occur in protein- 16, we discussed how pea color (yellow or green) results from
coding regions of the genome, however, have a deleterious, or variation at a single gene. Two alleles of this gene are the dominant
harmful, effect on an organism. Rarely, a mutation occurs that A (yellow) allele and the recessive a (green) allele. AA homozygotes
has a beneficial effect. Mutations like these are advantageous if and Aa heterozygotes produce yellow peas, and aa homozygotes
they improve their carriers’ chances of survival or reproduction. produce green peas. Imagine that in a population every pea plant
produces green peas, meaning that only one allele, a, is present:
The allele frequency of a is 100%, and the allele frequency of A is
0%. When a population exhibits only one allele at a particular gene,
we say that the population is fixed for that allele.
FIG. 21.2 Mutation and recombination. The formation of new Now consider another population of 100 pea plants with
alleles occurs by mutation and recombination. genotype frequencies of 50% aa, 25% Aa, and 25% AA. A genotype
frequency is the proportion in a population of each genotype at a
Allele 1
Generation 1 particular gene or set of genes. These genotype frequencies give
T T T T us 50 green-pea pea plants (aa), 25 yellow-pea heterozygotes
Mutation No mutation (Aa), and 25 yellow-pea homozygotes (AA). What is the allele
frequency of a in this population? Each of the 50 aa homozygotes
Allele 2 Allele 1 has two a alleles and each of the 25 heterozygotes has one a allele.
Generation 2
C T T T T T T T Of course, there are no a alleles in AA homozygotes. The total
number of a alleles is thus (2 50) 1 25 5 125. To determine
No mutation Mutation No mutation
the allele frequency of a, we divide the number of a alleles by the
Allele 2 Allele 3 Allele 1 total number of alleles in the population, 200 (because each pea
Generation 3 plant is diploid, meaning that it has two alleles): 125/200 5 62.5%.
C T T T C T G T T T T T
Because we are dealing with only two alleles in this example, the
allele frequency of A is 100% 2 62.5% 5 37.5%
Recombination Thus, the allele frequencies of A and a provide a measure
C T G T shuffles mutations
Recombination to produce new
of genetic variation at one gene in a given population. In this
T T T T sequences. example, we were given the genotype frequencies, and from this
information we determined the allele frequencies. But how are
genotype and allele frequencies measured? We consider three
Allele 4 ways to measure genotype and allele frequencies in populations:
Generation 4
T T G T observable traits, gel electrophoresis, and DNA sequencing.
428 CHAPTER 21.2 M E A S U R I N G G E N E T I C VA R I AT I O N
PHENOTYPE GENOTYPE
A AA or AO
B BB or BO
move from one end of the gel to the other is determined by their
AB AB
charge and their size.
O OO
Early studies of protein electrophoresis focused on enzymes
that catalyze reactions that can be induced to produce a dye when
Other instances in which phenotypic variation can be the substrate for the enzyme is added. If we add the substrate, we
readily correlated with genotype include certain markings in can see the locations of the proteins in the gel. The bands in the
invertebrates. For example, the coloring of the two-spot ladybug gel provide a visual picture of genetic variation in the population,
Adalia bipunctata is controlled by a single gene (Fig. 21.3). revealing what alleles are present and what their frequencies are.
However, the genetic basis of most traits is not so simple. Fig. 21.4 shows this sort of experiment.
Single-gene variation became much easier to detect in the
1960s with the application of gel electrophoresis. In Chapter DNA sequencing is the gold standard for measuring
12, we saw how gel electrophoresis separates segments of DNA genetic variation.
according to their size. Before DNA technologies were developed, Protein gel electrophoresis was a leap forward in our ability
the same basic process was applied to proteins to separate to detect genetic variation, but this technique had significant
them according to their electrical charge and their size. In gel limitations. Researchers could study only enzymes because
electrophoresis, the proteins being studied migrate through a gel they needed to be able to stain specifically for enzyme activity
when an electrical charge is applied. The rate at which the proteins and could detect only mutations that resulted in amino acid
HOW DO WE KNOW?
FIG. 21.4 RESULTS The Adh gene has two common alleles, distinguished by a
single amino acid difference that changes the charge of the protein.
How is genetic variation One allele, Fast (F ), accordingly runs faster than the other, Slow
(S). Four individuals are S homozygotes; two are F homozygotes;
measured? and two are FS heterozygotes. Note that the heterozygotes do not
stain as strongly on the gel because each band has half the intensity
of the single band in the homozygote. We can measure the allele
BACKGROUND The introduction of protein gel electrophoresis in frequencies simply by counting the alleles. Each homozygote has two
1966 gave researchers the opportunity to identify differences in of the same allele, and each heterozygote has one of each.
amino acid sequence in proteins both among individuals and, in the
The gel is stained with a biochemical agent
case of heterozygotes, within individuals. Proteins with different
that produces color in the presence of Adh
amino acid sequences run at different rates through a gel in an enzyme.
electric field. Often, a single amino acid difference is enough to
affect the mobility of a protein in a gel.
Each well of the gel is loaded with a sample Number of F in the population 2 (number of F homozygotes)
from one individual, and an electric current
is passed through the gel. The proteins in
(number of heterozygotes) 4 2 6
each sample migrate toward the positive 6 3
electrode according to their charge and size. Frequency of F 16 = 8
SOURCE Lewontin, R. C., and J. L. Hubby. 1966. “A Molecular Approach to the Study of Genic
Heterozygosity in Natural Populations. II. Amount of Variation and Degree of Heterozygosity in
⫹ Natural Populations of Drosophila pseudoobscura.” Genetics 54:595–609.
429
430 CHAPTER 21.3 E VO L U T I O N A N D T H E H A R DY – W E I N B E RG E Q U I L I B R I U M
substitutions that changed a protein’s mobility in the gel. Only genotype frequencies to change. Regardless of which mechanisms
with DNA sequencing did researchers finally have an unambiguous are involved, any change in allele frequencies, genotype
means of detecting all genetic variation in a stretch of DNA, frequencies, or both constitutes evolution.
whether in a coding region or not. The variations studied by
modern population geneticists are differences in DNA sequence, The Hardy–Weinberg equilibrium describes situations
such as a T rather than a G at a specified nucleotide position in a in which allele and genotype frequencies do not
particular gene. change.
Calculating allele frequencies, then, simply involves collecting Allele and genotype frequencies change over time only if specific
a population sample and counting the number of occurrences of forces act on the population. This principle was demonstrated
a given mutation. We can look even closer at the example of the independently in 1908 by the English mathematician G. H. Hardy
Drosophila Adh gene from Fig. 21.4 to focus not on the amino acid and the German physician Wilhelm Weinberg, and has become
difference between the Fast and Slow phenotypes, but on the A known as the Hardy–Weinberg equilibrium. In essence, the
or G nucleotide difference corresponding to the two phenotypes. Hardy–Weinberg equilibrium describes the situation in which
If we sequence the Adh gene from 50 individual flies, we will evolution does not occur. In the absence of evolutionary forces
then have 100 gene sequences from these diploid individuals. We (such as natural selection), allele and genotype frequencies do
find 70 sequences have an A and 30 have a G at the position in not change.
question. Therefore, the allele frequency of A is 70/100 5 0.7 and To determine whether or not evolutionary forces are at work,
the allele frequency of G is 0.3. In general, in a sample of n diploid we need to determine whether or not a population is in Hardy–
individuals, the allele frequency is the number of occurrences of Weinberg equilibrium. The Hardy–Weinberg equilibrium specifies
that allele divided by twice the number of individuals. the relationship between allele frequencies and genotype
frequencies when a number of key conditions are met. In these cases,
j Quick Check 2 Data on genetic variation in populations have
we can conclude that evolutionary forces are not acting on the gene
become ever more precise over time, from phenotypes that are
in the population we are studying. In many ways, then, the Hardy–
determined by a single gene to gel electrophoresis that looks at
Weinberg equilibrium is most interesting when we find instances in
variation among genes that encode for enzymes, to analysis of
which allele or genotype frequencies depart from expectations. This
the DNA sequence. Has this increase in precision resulted in the
finding implies that one or more of the conditions are not met and
uncovering of more genetic variation or less?
that evolutionary mechanisms are at work.
A population that is in Hardy–Weinberg equilibrium meets
these conditions:
21.3 EVOLUTION AND THE HARDY–
WEINBERG EQUILIBRIUM 1. There can be no differences in the survival and
reproductive success of individuals. Let’s examine what
Determining allele frequencies gives us information about genetic happens when this condition is not met. Given two alleles, A
variation. Following and measuring change in that variation over and a, consider what occurs when a, a recessive mutation, is
time is key to understanding the genetic basis of evolution. lethal. All aa individuals die. Therefore, in every generation,
there is a selective elimination of a alleles, meaning that the
Evolution is a change in allele or genotype frequency frequency of a will gradually decline (and the frequency of A
over time. correspondingly increase) over the generations. As we discuss
At the genetic level, evolution is simply a change in the frequency below, we call this differential success of alleles selection.
of an allele or a genotype from one generation to the next. For
2. Populations must not be added to or subtracted from by
example, if there are 200 copies of an allele that causes blue eye
migration. Again, let’s see what happens when this condition
color in a population in generation 1 and there are 300 copies
is not met. Consider a second population adjacent to the one
of that allele in a population of the same size in generation 2,
we used in the preceding example in which all the alleles are
evolution has occurred. In principle, evolution may occur without
A and all individuals have the genotype AA. Then there is a
allele frequencies changing. For instance, even if, in our fruit
sudden influx of individuals from the first population into the
fly example, the A/G allele frequencies stay the same from one
second. The frequency of A in the second population changes
generation to the next, the frequencies of the different genotypes
in proportion to the number of immigrants.
(that is, of AA, AG, and GG) may change. This would be evolution
without allele frequency change. 3. There can be no mutation. If A alleles mutate into a alleles
Evolution is therefore a change in the genetic makeup of a (or other alleles, if the gene has multiple alleles), and vice
population over time. Note an important and often misunderstood versa, then again we see changes in the allele frequencies over
aspect of this definition: Populations evolve, not individuals. the generations. In general, because mutation is so rare, it
Note, too, that this definition does not specify a mechanism for has a very small effect on changing allele frequencies on the
this change. As we will see, many mechanisms can cause allele or timescales studied by population geneticists.
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 431
4. The population must be sufficiently large to prevent we know the frequency of the two alleles, one with A and the
sampling errors. Small samples are likely to be more other with G in the Adh gene. What are the genotype frequencies?
misleading than large ones. Campus-wide, a college’s That is, how many AA homozygotes, AG heterozygotes, and GG
homozygotes do we see? The Hardy–Weinberg equilibrium predicts
sex ratio may be close to 50 : 50, but in a small class of
the expected genotype frequencies from allele frequencies.
8 individuals it is not improbable that we would have 6
women and 2 men (a 75 : 25 ratio). Sample size, in the The logic is simple. Random mating is the equivalent of putting
all the population’s gametes into a single pot and drawing out pairs
form of population size, also affects the Hardy–Weinberg
of them at random to form a zygote, which is the same principle
equilibrium such that it technically holds only for infinitely
we saw in action in the discussion of independent assortment in
large populations. A change in the frequency of an allele
Chapter 16. We therefore put in our 70 A alleles and 30 G alleles
due to the random effects of limited population size is
called genetic drift. and pick pairs at random. What is the probability of picking an AA
homozygote (that is, what is the probability of picking an A allele
5. Individuals must mate at random. For the Hardy–
followed by another A allele)? The probability of picking an A allele
Weinberg equilibrium to hold, mate choice must be made
is its frequency in the population, so the probability of picking
without regard to genotype. For example, an AA homozygote
the first A is 0.7. What is the probability of picking the second A?
when offered a choice of mate from among AA, Aa, or aa
Also 0.7. What then is the probability of picking an A followed by
individuals should choose at random. In contrast, non-
another A? It is the product of the two probabilities: 0.7 0.7 5
random mating occurs when individuals do not mate
0.49. Thus, the frequency of an AA genotype is 0.49. We take the
randomly. For example, AA homozygotes might preferentially
same approach to determine the genotype frequency for the GG
mate with other AA homozygotes. Non-random mating
genotype: Its frequency is 0.3 0.3, or 0.09.
affects genotype frequencies from generation to generation,
What about the frequency of the heterozygote, AG? This is
but does not affect allele frequencies.
the probability of drawing G followed by A, or A followed by G.
There are thus two separate ways in which we can generate the
The Hardy–Weinberg equilibrium relates allele heterozygote. Its frequency is therefore (0.7 0.3) 1 (0.3 0.7)
frequencies and genotype frequencies. 5 0.42.
Now that we have established the conditions required for a As seen in the Punnett square on the left in Fig. 21.5, we can
population to be in Hardy–Weinberg equilibrium, let us explore generalize these calculations algebraically by substituting letters for
the idea in detail. In the Drosophila example we looked at earlier, the numbers we have computed to derive the relation defined by
the Hardy–Weinberg equilibrium.
If the allele frequency of one allele,
A, is p, and the other, G, is q, then
p 1 q 5 1 (because there are no other
FIG. 21.5 Hardy–Weinberg relation. The Hardy–Weinberg relation predicts genotype alleles at this site).
frequencies from allele frequencies, and vice versa.
Genotypes AA AG GG
Eggs Frequencies p2 2pq q2
A a Allele
p q Allele frequency Genotype Genotype
frequency frequency In the graph on the right hand side
AA Aa
A p
(p2) (pq) of aa is q2. of AA is p2. of Fig 21.5, we have replaced the p’s
Sperm
probability of frequency
having both an 0.6 are AA and, accordingly, the blue line
of Aa is 2pq.
a sperm 0.5
(probability q) representing the frequency of AA
0.4
and an a egg in the population is at 1, and the red
(also q): q2. 0.3
line representing the frequency of aa
0.2
0.1 and the purple line representing the
If Hardy–Weinberg conditions are met, This simple
we can compute the frequencies of the relationship
frequency of Aa are both at 0. When
p (A) 0 0.2 0.4 0.6 0.8 1.0 no A alleles are present, all individuals
three possible genotypes: allows us to q (a) 1.0 0.8 0.6 0.4 0.2 0
translate have genotype aa, and the red line is at
Genotypes: AA Aa aa between allele Allele frequency
frequencies 1 and the others at 0.
Genotype and genotype Each line on the graph represents Not only does the Hardy–
frequencies: p2 2pq q2 frequencies. one of the three genotypes.
Weinberg relation predict genotype
432 CHAPTER 21.4 N AT U R A L S E L E C T I O N
frequency from allele frequencies, but it works in reverse, too: deleterious and eliminated by natural selection have no long-term
Genotype frequencies predict allele frequencies. evolutionary impact; ones that are beneficial, however, can result
The graph in Fig. 21.5 also shows how allele and genotype in adaptation to the environment over time.
frequencies are related. We can use the graph to determine
allele frequencies for given genotype frequencies and genotype Natural selection brings about adaptations.
frequencies for given allele frequencies. For example, if the The adaptations we see in the natural world—the exquisite fit of
population we are examining has a 0.5 frequency of heterozygotes, organisms to their environment—were typically taken by pre-
Aa, the purple line in the graph indicates that both p and q are 0.5. Darwinian biologists as evidence of a divine Creator’s existence.
If we know that p 5 0.5 (and therefore q 5 0.5), we can look at the Each species, they argued, was so well adapted—the desert plant
lines to infer that the frequency of heterozygotes is 0.5 and the so physiologically adept at coping with minimal levels of rainfall
frequency of both homozygotes, AA and aa, is the same, 0.25. and the fast-swimming fish so hydrodynamically streamlined—
We can do this mathematically as well. Knowing the genotype that it must have been designed by a Creator.
frequency of AA, for example, permits us to calculate allele With the publication of On the Origin of Species in 1859, Darwin,
frequencies: if, as in our Adh example, p2 is 0.49 (that is, 49% of pictured in Fig. 21.6, overturned the biological convention of his
the population has genotype AA), then p, the allele frequency of A, day on two fronts. First, he showed that species are not unchanging;
is 5 0.7. Because p 1 q 5 1, then q, the allele frequency of a, they have evolved over time. Second, he suggested a mechanism,
is 1 2 0.7 5 0.3. natural selection, that brings about adaptation. Natural selection
Note that these relationships hold only if the Hardy–Weinberg was a brilliant solution to the central problem of biology: how
conditions are met. If not, then allele frequencies can be organisms come to fit so well in their environments. From where
determined only from genotype frequencies, as described earlier in does the woodpecker get its powerful chisel of a bill? And the
section 21.2. hummingbird its long delicate bill for probing the nectar stores
day-to-day processes operating over vast timescales. Darwin Sometimes, however, natural selection is inefficient in getting rid
applied this worldview to biology. He recognized that small of a deleterious allele. Consider a recessive lethal mutation, b (that
changes, like subtle shifts in the frequencies of alleles, could add is, one that is lethal only as a homozygote, bb, and has no effect as
up to major changes given long enough time periods. What might a heterozygote, Bb). When it first arises, all the other alleles in the
seem to us to be a trivial change over the short term can, over the population are B, which means that the first b allele that appears
long term, result in substantial differences among populations. in the population must be paired with a B allele, resulting in a
Bb heterozygote. Because natural selection does not act against
The Modern Synthesis combines Mendelian genetics heterozygotes in this case, the b allele may increase in frequency
and Darwinian evolution. by chance alone (we discuss below how this happens). Only when
Darwinian evolution involves the change over time of the two b alleles come together to form a bb homozygote does natural
genetic composition of populations and is thus a genetic theory. selection act to rid the population of the allele. Natural selection
Although Mendel published his genetic studies of pea plants in that decreases the frequency of a deleterious allele is called
1866, not long after The Origin, Darwin never saw them, so a key negative selection.
component of the theory was missing. The rediscovery of Mendel’s Many human genetic diseases show this pattern: The
work in 1900 unexpectedly provoked a major controversy among deleterious allele is rare and recessive. Because it is rare,
evolutionary biologists. Some argued that Mendel’s discoveries homozygotes for it are formed only infrequently. Remember that
did not apply to most genetic variation because the traits studied the expected frequency of homozygotes in a population under
by Mendel were discrete, meaning that they had clear alternative the Hardy–Weinberg equilibrium is the square of the frequency
states, such as either yellow or green color in peas. Most of the of the allele in the population. Therefore, if the allele frequency
variation we see in natural populations, in contrast, is continuous, is 0.01, we expect 0.01 0.01, or 1 in every 10,000 individuals, to
meaning that variation occurs across a spectrum (Chapter 18). be homozygous for it. Thus, the genetic disease occurs rarely, and
Human height, for example, does not come in discrete classes. the allele remains in the population because it is recessive and not
People are not either 5 feet tall or 6 feet tall and of no height in expressed as a heterozygote.
between. Instead, they may be any height within a certain range.
How could the factors that controlled Mendel’s discrete traits ? CASE 4 MALARIA: CO-EVOLUTION OF HUMANS AND
account for the continuous variation seen in natural populations? A PARASITE
This question was answered by the English theoretician Ronald What genetic differences have made some individuals
Fisher, who realized that, instead of a single gene contributing more and some less susceptible to malaria?
to a trait like human height, there could be several genes that In addition to allowing alleles to be either eliminated or fixed,
contribute to the trait. He argued that extending Mendel’s theory natural selection can also maintain an allele at some intermediate
to include multiple genes per trait could account for patterns of frequency between 0% and 100%. This form of natural selection is
continuous variation that we see all around us. called balancing selection, and it acts to maintain two or more
Fisher’s insight formed the basis of a synthesis between alleles in a population. A simple case is members of a species that
Darwin’s theory of natural selection and Mendelian genetics face different conditions depending upon where they live. One
that was forged during the middle part of the twentieth century. allele might be favored by natural selection in a dry area, but a
The product of this Modern Synthesis is our current theory different one favored in a wet area. Taking the species as a whole,
of evolution. these alleles are maintained by natural selection at intermediate
frequencies.
Natural selection increases the frequency of Another example of balancing selection occurs when
advantageous mutations and decreases the frequency the heterozygote’s fitness is higher than that of either of the
of deleterious mutations. homozygotes, resulting in selection that ensures that both alleles
Natural selection increases the frequency of advantageous alleles, remain in the population at intermediate frequencies. This form
resulting in adaptation. In some cases, it can promote the fixation of balancing selection is called heterozygote advantage, and it
of advantageous alleles, meaning the allele has a frequency of 1. is exemplified by human populations in Africa, where malaria has
To start with, a new advantageous allele will exist as a single been a long-standing disease. Because the malaria parasite spends
copy in a single individual (that is, as a heterozygote), but, under part of its life cycle in human red blood cells, mutations in the
the influence of natural selection, the advantageous allele can hemoglobin molecule that affect the structure of the red blood
eventually replace all the other alleles in the population. Natural cells have a negative impact on the parasite and can reduce the
selection that increases the frequency of a favorable allele is called severity of malarial attacks.
positive selection. Two alleles of the gene for one of the subunits of hemoglobin
As we have seen, most mutations to functional genes are are A and S (Chapter 15). The A allele codes for normal hemoglobin,
deleterious. In extreme cases, they are lethal to the individuals resulting in fully functional, round red blood cells. The S allele
carrying them and are thus eliminated from the population. encodes a polypeptide that differs from the A allele’s product in
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 435
Number of finches
30
natural selection operated in favor of the heterozygote, still carry
25
the S allele, even though the allele is no longer useful to them in
20
their malaria-free environment. If natural selection were to run its
15
course among African-Americans, the S allele would gradually be
eliminated. However, this is a slow process, and many more people 10
70
50
birthweight who die
15 30
finches on the Galápagos Islands (Fig. 21.9). A severe drought in
given birthweight
had higher survival rates than birds with smaller bills. Because bill A third mode of selection, known as disruptive selection,
size is genetically determined, the drought resulted in directional operates in favor of extremes and against intermediate forms.
selection for increased bill size. Apple maggot flies of North America, Rhagotletis pomonella,
Artificial selection, which has been practiced by humans provide an example (Fig. 21.11). The larvae of these flies feed on
since at least the dawn of agriculture, is a form of directional the fruit of hawthorn trees. However, with the introduction
selection. Artificial selection is analogous to natural selection, of apples from Europe about 150 years ago, these flies have
but the competitive element is removed. Successful genotypes become pests of apples. Apple trees flower and produce fruit
are selected by the breeder, not through competition. Because it earlier every summer than hawthorns, so disruptive selection
can be carefully controlled by the breeder, artificial selection is has resulted in the production of two genetically distinct groups
astonishingly efficient at generating genetic change. Practiced of flies, one specializing on apple trees and the other on hawthorn
over many generations, artificial selection can create a population trees. Disruptive selection acts against intermediates between
in which the selected phenotype is far removed from that of the the two groups, which miss the peaks of both the apple and
starting population. Fig. 21.10 shows the result of long-continued hawthorn seasons. We explore this mechanism, which can lead to
artificial selection for the oil content in kernels of corn. the evolution of new species, in more detail in the next chapter.
HOW DO WE KNOW?
FIG. 21.10 23
22 Selection for high oil content
of corn, this experiment has become one of the longest-running higher than
12
biological experiments in history. the starting
11 point.
HYPOTHESIS Researchers hypothesized that there is a limit to the 10
9
extent to which a population can respond to continued directional
8
selection. 7
EXPERIMENT Corn was artificially selected for either high oil 6
5
content or low oil content: Every generation, researchers bred
4
together just the plants that produced corn with the highest oil 3
content, and did the same for the plants that produced corn with 2
the lowest oil content. Every generation, kernels showed a range of 1
oil levels, but only the 12 kernels with the highest or the lowest oil
0 10 20 30 40 50 60 70 80 90 100
content were used for the next generation. Oil content
RESULTS In the line selected for high oil content, the percentage
of oil more than quadrupled, from about 5% to more than 20%. FOLLOW-UP WORK Genetic analysis of the selected lines
In the line selected for low oil content, the oil content fell so indicates that the differences in oil content are due to the effects of
close to zero that it could no longer be measured accurately, and at least 50 genes.
the selection was terminated. Both selected lines are completely
SOURCE Moose, S. P., J. W. Dudley, and T. R. Rocheford. 2004. “Maize Selection Passes
outside the range of any phenotype observed at the beginning of the Century Mark: A Unique Resource for 21st Century Genomics.” Trends in Plant
the experiment. Science 9:358–364.
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 437
FIG. 21.11 Disruptive selection. Disruptive selection has produced two genetically distinct populations of apple maggot fly, each one
coordinated with fruiting times of two different species of tree. Sources: (photo) Rob Oakleaf (National Science Foundation); Data from Filchak et al.
2000 Nature 407:739– 42.
June 15
July 1
July 15
Aug. 1
Aug. 15
Sept. 1
Sept. 15
Oct. 1
Oct’ 15
Date (1991)
Sexual selection increases an individual’s reproductive selection is indeed acting to reduce the showiness and size of the
success. peacock’s tail, but another form of selection, sexual selection, is
Initially, Darwin was puzzled by features of organisms that acting in the opposite direction. Sexual selection promotes traits
seemed to reduce an individual’s chances of survival. In a letter that increase an individual’s access to reproductive opportunities.
a few months after the publication of The Origin, he wrote, “The Darwin recognized that this could occur in two different ways
sight of a feather in a peacock’s tail, whenever I gaze at it, makes (Fig. 21.12). In one form of sexual selection, members of one sex
me sick!” The tail is metabolically expensive to produce; it is an (usually the males) compete with one another for access to the
advertisement to potential predators; and it is an encumbrance in other sex (usually the females). This form is called intrasexual
any attempt to escape a predator. How could such a feature evolve selection since it focuses on interactions between individuals of
under natural selection? one sex. Because competition typically occurs among males, it is
In his 1871 book, The Descent of Man, and Selection in Relation in males that we see physical traits such as large size and horns and
to Sex, Darwin introduced a solution to this problem. Natural other elaborate weaponry, as well as fighting ability. Larger, more
FIG. 21.12 Sexual selection. (a) Intrasexual selection often involves competition between males, as in this battle between two male elk.
(b) Intersexual selection often involves bright colors and displays by males to attract females, as shown by this male and female
Japanese Red-crowned Crane. Source: (a) Kelly Funk/All Canada Photos/Corbis; (b) Steven Kaufman/Getty Images.
a b
438 CHAPTER 21.5 M I G R AT I O N , M U TAT I O N , G E N E T I C D R I F T , A N D N O N - R A N D O M M AT I N G
powerful males tend to win more fights, hold larger territories, and worse than merely non-adaptive—it may be maladaptive, in that
have access to more females. it causes a decrease in a population’s average fitness. Fair-skinned
Darwin also recognized a second form of sexual selection. people arriving in an equatorial region, for example, are at risk of
Here, males (typically) do not fight with one another, but instead sunburn and skin cancer.
compete for the attention of the female with bright colors
or advertisement displays. In this case, females choose their Mutation increases genetic variation.
mates. This form of selection is called intersexual selection As we saw earlier in this chapter, mutation is a rare event. This
since it focuses on interactions between females and males. means that it is generally not important as an evolutionary
The peacock’s tail is thought to be the product of intersexual mechanism that leads allele frequencies to change. However, as we
selection: Its evolution has been driven by a female preference have also seen, it is the source of new alleles and the raw material
for ever-showier tails. In the absence of sexual selection, natural on which the other forces act. Without mutation, there would be
selection would act to minimize the size of the peacock’s tail. no genetic variation and no evolution.
Presumably, the peacocks’ tails we see are a compromise, a
trade-off between the conflicting demands of reproduction and Genetic drift has a large effect in small populations.
survival. Genetic drift is the random change in allele frequencies from
generation to generation. By “random,” we mean that frequencies
j Quick Check 4 Sexual selection tends to cause bigger size, more
can either go up or down simply by chance. An extreme case is a
elaborate weaponry, or brighter colors in males. Is this an example
population bottleneck, which occurs when an originally large
of stabilizing, directional, or disruptive selection?
population falls to just a few individuals.
Consider a rare allele, A, with a frequency of 1/1000. Habitat
destruction then reduces the population to just one pair of
21.5 MIGRATION, MUTATION, individuals, one of which is carrying A. The frequency of A in this
GENETIC DRIFT, AND NON- new population is 1/4 because each individual has two alleles,
RANDOM MATING giving a total of four alleles. In other words, the bottleneck
resulted in a dramatic change in allele frequencies. It also caused
Selection is evolution’s major driving force, enriching each new a loss of genetic variation as much of the variation present in the
generation for the mutations that best fit organisms to their original population was not present in the surviving pair. That
environments. However, as we have seen, it is not the only is, the surviving pair carries only a few of the alleles that were
evolutionary mechanism. There are other mechanisms that present in their original population. A population of Galápagos
can cause allele and genotype frequencies to change. These are tortoises that has very low levels of genetic diversity probably
migration, mutation, genetic drift, and non-random mating. went through just such a bottleneck about 100,000 years ago
Like natural selection, these mechanisms can cause allele when a volcanic eruption eliminated most of the tortoises’ habitat.
frequencies to change. Unlike natural selection, they do not lead Genetic drift also occurs when a few individuals start a new
to adaptations. population, in what is called a founder event. Such events
occur, for example, when a small number of individuals arrive
Migration reduces genetic variation between on an island and colonize it. Once again, relative to the parent
populations. population, allele frequencies are changed and genetic variation
Migration is the movement of individuals from one population is lost.
to another, resulting in gene flow, the movement of alleles Earlier, we considered the fate of beneficial and harmful
from one population to another. It is relatively simple to see mutations under the influence of natural selection. What about
how movements of individuals and alleles can lead to changes neutral mutations? Natural selection, by definition, does not
in allele frequencies. Consider two isolated island populations govern the fate of neutral mutations. Consider a neutral mutation,
of rabbits, one white and the other black. Now imagine that the m, which occurs in a noncoding region of DNA and therefore has
isolation breaks down—a bridge is built between the islands— no effect on fitness. At first, it is in just a single heterozygous
and migration occurs. Over time, black alleles enter the white individual. What happens if that individual fails to reproduce
population and vice versa, and the allele frequencies of the two (for reasons unrelated to m)? In this case, m is lost from the
populations gradually become the same. population, but not by natural selection (which does not select
The consequence of migration is therefore the homogenizing against m). Alternatively, the m-bearing individual might by
of populations, making them more similar to each other and chance leave many offspring (again for reasons unrelated to m), in
reducing genetic differences between them. Because populations which case the frequency of m increases. In principle, it is possible
are often adapted to their particular local conditions (think of over a long period of time for m to become fixed in the population.
dark-skinned humans in regions of high sunlight versus fair- At the end of the process, every member of the population is
skinned humans in regions of low sunlight), migration may be homozygous mm.
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 439
Allele frequency
(Fig. 21.13). If m arises in a very small population, its frequency 0.8 A computer can model how the
will change rapidly, as shown in Figs. 21.13a and 21.13b. Imagine m frequency of a given allele might
0.6 randomly change over time
arising in a population of just six individuals (or three pairs).
because of genetic drift. In this
Its initial frequency is 1 in 12, or about 8% (there are a total of 0.4
simulation, the allele drifts from
12 alleles because each individual is diploid). If, by chance, one pair 0.2 a frequency of 0.5 to fixation.
fails to breed and the other two (including the one who is an Mm 0
heterozygote) each produce three offspring, and all three of the 20 40 60 80 100
Mm individual’s offspring happen to inherit the m allele, then the
frequency of m will increase to 3 in 12 (25%) in a single generation. b. Population size = 4
In effect, genetic drift is equivalent to a sampling error. In a small 1
Allele frequency
sample, extreme departures from the expected outcome are 0.8 Each line represents a different
common. simulation of the effect of drift
0.6 on a population of 4 individuals.
On the other hand, if the population is large, as in Figs. 21.13c
All simulations result in fixation
and 21.13d, then changes in allele frequency from generation 0.4
or extinction of the allele in
to generation are much smaller, typically less than 1%. A large 0.2 relatively few generations.
population is analogous to a large sample size, in which we tend 0
not to see large departures from expectation. Toss a coin 1000 20 40 60 80 100
times, and you will end up with approximately 500 heads. Toss a
coin 5 times, and you might well end up with zero heads. In other c. Population size = 40
words, in a small sample of coin tosses, we are much more likely to 1
Allele frequency
them (0.5 0.5), or (0.5)4 5 0.0625. Needless to say, 0.0625 is a Mutations will occur in one population that will not have arisen in
considerably higher probability than 0.000001. the other population, and vice versa.
If b is a deleterious recessive mutation, it may contribute to A mutation in either population has one of three fates: It
inbreeding depression in the child, a reduction in the child’s goes to fixation (either through genetic drift or through positive
fitness caused by homozygosity of deleterious recessive mutations. selection); it is maintained at intermediate frequencies (by
Inbreeding depression is a major problem in conservation biology, balancing selection); or it is eliminated (either through natural
especially when endangered species are bred in captivity in selection or genetic drift). Different mutations will be fixed in
programs starting with a just a small number of individuals. each population. When we come back thousands of generations
later and sequence the DNA of our original identical individuals’
descendants, we will find that many differences have accumulated.
21.6 MOLECULAR EVOLUTION The populations have diverged genetically. What we are seeing is
evidence of molecular evolution.
How do DNA sequence differences arise among species? Imagine Species are the biological equivalents of islands because
starting with two pairs of identical twins, one pair male and the they, too, are isolated. They are genetically isolated because, by
other female. Now we place one member of each pair together definition, members of one species cannot exchange genetic
on either side of a mountain range (Fig. 21.14). Let’s assume material with members of another (Chapter 22). The amount of
the mountain range completely isolates each couple. What, in time that two species have been isolated from each other is the
genetic terms, will happen over time? The original pairs will time since their most recent common ancestor. Thus, humans and
found populations on each side of the mountain range. The chimpanzees, whose most recent common ancestor lived about
genetic starting point, in each case, is exactly the same, but, over 6–7 million years ago, have been isolated from each other for about
time, differences will accumulate between the two populations. 6–7 million years. Mutations arose and were fixed in the human
lineage over that period; mutations, usually different ones, also
arose and were fixed in the chimpanzee lineage over the same
period. The result is the genetic difference between humans and
FIG. 21.14 Genetic divergence in isolated populations. chimpanzees.
FIG. 21.15 The molecular clock. Different genes evolve at different rates because of differences in the intensity of negative selection.
After Fig. 20-3, p. 733, in A. J. F. Griffiths, S. R. Wessler, S. B. Carroll, and J. Doebley, 2012, Introduction to Genetic Analysis, 10th ed., New York: W. H. Freeman.
Vertebrates
Mammals
Mammals
Lamprey
Reptiles
Reptiles
Reptiles
Insects
Birds
Carp
Separation of
Fish
ancestors of plants
and animals
200
180
Number of amino acid substitutions per 100 residues
160
s
eptide
in
140 lob
og
p
m
He
Fibrino
120
100
80
60
ec
hrom
Cytoc
40
20
Histone gene
0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400
Millions of years since divergence
Since vertebrates and insects diverged 600 million years ago,
the amino acid sequences of cytochrome c have acquired 30
differences. Amino acid sequences of hemoglobin have acquired
many more differences in the same time period.
the rates of molecular clocks vary from gene to gene, clock data histone mutation over 2 billion years of evolution. The histone
should be interpreted cautiously. These rate differences can be molecular clock is breathtakingly slow.
attributed largely to differences in intensity of negative selection Other proteins are less subject to such rigorous negative
(which results in the elimination of harmful mutations) among selection. Occasional mutations may therefore become
different genes. The slowest molecular clock on record belongs fixed, either through drift (if they are neutral) or selection (if
to the histone genes, which encode the proteins around which beneficial). The extreme case of a fast molecular clock is that
DNA is wrapped to form chromatin (Chapters 3 and 13). These derived from a pseudogene, a gene that is no longer functional.
proteins are exceptionally similar in all organisms; only 2 amino Because all mutations in a pseudogene are by definition
acids (in a chain of about 100) distinguish plant and animal neutral—there is no function for a mutation to disrupt, so a
histones. Plants and animals last shared a common ancestor more mutation is neither deleterious nor beneficial—we expect to
than 1 billion years ago, which means, because each evolutionary see a pseudogene’s molecular clock tick at a very fast rate. In
lineage is separate, that there have been at least 2 billion years of the histone genes, virtually all mutations are selected against,
evolution since they were in genetic contact. And yet the histones constraining the rate of evolution; in pseudogenes, none is.
have hardly changed at all. Almost any amino acid change fatally Fig. 21.15 shows the varying rates of the molecular clock for
disrupts the histone protein, preventing it from carrying out its different genes.
proper function. Negative selection has thus been extremely In the next chapter, we examine how genetic divergence
effective in eliminating just about every amino acid–changing between populations can lead to the evolution of new species. •
442 CO R E CO N C E P T S S U M M A RY
21.4 Natural selection leads to adaptation, which Correlation between sequence differences among species and
enhances the fit between an organism and its time since common ancestry of those species is known as the
environment. molecular clock. page 440
CHAPTER 21 E VO LU T I O N : H O W G E N OT Y P E S A N D P H E N OT Y P E S C H A N G E OV E R T I M E 443
The rate of the molecular clock varies among genes because 6. Describe what happens to allele and genotype
some genes are more selectively constrained than others. frequencies under the Hardy–Weinberg equilibrium.
page 441
7. Name the five assumptions of the Hardy–Weinberg
equilibrium and, for each one, explain what happens in a
Species and
Speciation
Core Concepts
22.1 Reproductive isolation is
the key to the biological
species concept.
22.2 Reproductive isolation
is caused by barriers to
reproduction before or after
egg fertilization.
22.3 Speciation underlies the
diversity of life on Earth.
22.4 Speciation can occur with or
without natural selection.
Rangzen/Shutterstock.
445
446 SECTION 22.1 T H E B I O LO G I C A L S P E C I E S CO N C E P T
Antenna length
generates this breathtaking biodiversity, as it is about adaptation,
the result of natural selection. If we represent
individuals as dots
and score them for
two characteristics,
22.1 THE BIOLOGICAL we see that
individuals cluster
SPECIES CONCEPT in discrete clouds,
representing
The definition of species has been a long-standing problem in species.
Wing length
biology. Many biologists respond to the problem in the same way
that Darwin himself did. In On the Origin of Species, Darwin wrote,
“No one definition has as yet satisfied all naturalists; yet every
naturalist knows vaguely what he means when he speaks of a members of the same species is not a matter of judgment, but
species.” The difficulty of defining species has come to be called rather a reflection of their ability (or inability) to exchange
the species problem. genetic material by producing fertile offspring. Consider a new
Here is the problem in a nutshell: The species, as an advantageous mutation that appears initially in a single individual.
evolutionary unit, must by definition be fluid and capable of That individual and its offspring inheriting the mutation will have
changing, giving rise through evolution to new species. The whole a competitive advantage over other members of the population,
point of the Darwinian revolution is that species are not fixed. How, and the mutation will increase in frequency until it reaches
then, can we define something that changes over time, and, by the 100%. Migration among populations causes the mutation to
process of speciation, even gives rise to two species from one? spread further until all individuals within the species have it. The
mutation spreads within the species but, with some exceptions,
Species are reproductively isolated from other species. cannot spread beyond it.
We can plainly see biodiversity, but are what we call “species” real Therefore, a species represents a closed gene pool, with alleles
biological entities? Or was the term coined by biologists to simplify being shared among members of that species but usually not with
their description of the natural world? To test whether or not members of others. As a result, it is species that become extinct
species are real, we can examine the natural world, measure some and it is species that, through genetic divergence, give rise to new
characteristic of the different living organisms we see, and then species.
plot these measurements on a graph. Fig. 22.1 shows such a plot, The definition of “species” continues to be debated to this
graphing antenna length and wing length of three different types day. The most widely used and generally accepted definition of a
of butterfly. Note that the dots, representing individual organisms, species is known as the biological species concept (BSC). The
fall into non-overlapping clusters. Today, we can add a molecular BSC was described by the great evolutionary biologist Ernst Mayr
dimension to this kind of analysis. When we compare genomes (1904–2005) as follows:
of multiple organisms, they, too, cluster on the basis of similarity.
Each cluster is a species, and the fact that the clusters are distinct Species are groups of actually or potentially interbreeding
implies that species are biologically real. populations that are reproductively isolated from other such
The distances we see between the dots within a cluster groups.
reflect variation from one individual to the next within a species
(Chapter 21). Humans are highly variable, but overall we are more Let us look at this definition closely. At its heart is the idea
similar to one another than to our most humanlike relative, the of reproductive compatibility. Members of the same species are
chimpanzee. We form a messy cluster, but that cluster does not capable of producing offspring together, whereas members of
overlap with the chimpanzee cluster. different species are incapable of producing offspring together. In
Species, then, are real biological entities, not just a convenient other words, members of different species are reproductively
way to group organisms. Whether or not two individuals are isolated from one another.
CHAPTER 22 S P E C I E S A N D S P E C I AT I O N 447
populations comes all the way round to the more eastern of the
FIG. 22.3 Three species of Agrodiaetus butterflies. These similar- two Russian populations. Thus, though members of the two
appearing butterflies are identifiable only by differences Russian populations cannot exchange genes directly, they can
in their chromosome numbers. Source: Vladimir Lukhtanov, do so indirectly, with the genetic material passing through many
Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia. intermediate populations. This situation is more complicated
than anything predicted by the BSC. The two Russian populations
A direct view through are reproductively isolated from each other but they are not
the microscope of
genetically isolated from each other because of gene flow around
chromosomes that
have been stained so the ring.
they can be counted. We also see a complicated situation in some groups of
closely related species of plants. Despite apparently being good
morphospecies that can be distinguished by appearance alone,
many different species of willow (Salix), oak (Quercus), and
dandelion (Taraxacum) are still capable of exchanging genes
with other species in their genera through hybridization, or
interbreeding, between species. By the BSC, these different forms
should be considered one large species because they are able to
reproduce and produce fertile offspring. However, because they
maintain their distinct appearances, natural selection must work
against the hybrid offspring.
This unusual phenomenon seems to occur mainly in plants,
but, with the application of powerful comparative genomic
approaches, we are discovering that the boundaries between
closely related animal species are also not as strictly drawn as
traditionally supposed. As we will see in Chapter 24, for example,
we now know that our own species, Homo sapiens, interbred in the
past with another species, Homo neanderthalensis.
Russia
Pre-zygotic isolating factors occur before egg they fit only with the genitalia of females of the same species.
fertilization. Attempts by males of D. melanogaster to copulate with females of
Most species are reproductively isolated by pre-zygotic isolating another species of fruit fly, D. virilis, are prevented by mechanical
factors, which can take many forms. Among animals, species are incompatibility.
often behaviorally isolated, meaning that individuals mate only Both plants and animals may also be pre-zygotically isolated
with other individuals based on specific courtship rituals, songs, in time (temporal isolation). For example, closely related plant
or other behaviors. Chimpanzees may be our closest relative— species may flower at different times of the year, so there is no
and therefore the species we are most likely to confuse with our chance that the pollen of one will come into contact with the
own—but a chimpanzee of the appropriate sex, however attractive flowers of the other. Similarly, members of a nocturnal animal
to a chimpanzee of the opposite sex, fails to provoke even the species simply will not encounter members of a closely related
faintest reproductive impulse in a human. In this case, the pre- species that are active only during the day.
zygotic reproductive isolation of humans and chimpanzees is Plants and animals can also be isolated in space (geographic
behavioral. or ecological isolation). This type of isolation can be subtle. For
Behavior does not play a role in plants, but pre-zygotic factors example, the two Japanese species of ladybug beetle shown in
can still be important in their reproductive isolation. Pre-zygotic Fig. 22.5 can be found living side by side in the same field, but they
isolation in plants can take the form of incompatibility between feed on different plants. Because their life cycles are so intimately
the incoming pollen and the receiving flower, so fertilization fails associated with their host plants (adults even mate on their host
to take place. We see similar forms of isolation between members plants), these two species never breed with each other. This
of marine species, such as abalone, which simply discharge their ecological separation is what leads to their pre-zygotic isolation.
gametes into the water. In these cases, membrane-associated
proteins on the surface of sperm interact specifically with Post-zygotic isolating factors occur after egg
membrane-associated proteins on the surface of eggs of the same fertilization.
species but not with those of different species. These specific Post-zygotic isolating factors involve mechanisms that come into
interactions ensure that a sperm from one abalone species, Haliotis play after fertilization of the egg. Typically, they involve some kind
rufescens, fertilizes only an egg of its own species and not an egg of genetic incompatibility. One example, which we saw earlier
from H. corrugata, a closely related species. Incompatibilities in Fig. 22.3 and will explore later in the chapter, is the case of two
between the gametes of two different species is called gametic organisms with different numbers of chromosomes.
isolation. In some instances, the effect can be extreme. For example,
In some animals, especially insects, incompatibility arises the zygote may fail to develop after fertilization because the two
earlier in the reproductive process. The genitalia of males of the parental genomes are sufficiently different to prevent normal
fruit fly Drosophila melanogaster are configured in such a way that development. In others, the effect is less obvious. Some matings
between different species produce
perfectly viable adults, as in the case of
the horse–donkey hybrid, the mule. As we
FIG. 22.5 Ecological isolation. The ladybugs (a) Henosepilachna yasutomii and (b) H. niponica
have seen, though, all is not well with the
are reproductively isolated from each other because they feed and mate on different
mule from an evolutionary perspective.
host plants. Source: Courtesy Dr. Haruo Katakura.
The horse and donkey genomes are
a. b. different enough to cause the mule to
be infertile. As a general rule, the more
closely related—and therefore genetically
similar (Chapter 21)—a pair of species, the
less extreme the genetic incompatibility
between their genomes.
22.3 SPECIATION
Recognizing that species are groups
of individuals that are reproductively
isolated from other such groups, we
are now in a position to recast the key
question: How does speciation occur?
CHAPTER 22 S P E C I E S A N D S P E C I AT I O N 451
FIG. 22.7
Eastern Pacific Colombia SOURCE Knowlton, N., et al. 1993. “Divergence in Proteins, Mitochondrial DNA,
population Pacific Ocean and Reproductive Compatibility Across the Isthmus of Panama.” Science 260 (5114):
1629–1632.
452
CHAPTER 22 S P E C I E S A N D S P E C I AT I O N 453
place, such as an island, far from the main source population. disperse to a new location remote from the original population
The second is by vicariance, in which a geographic barrier arises and evolve separately. This may be an intentional act of dispersal,
within a single population, separating it into two or more isolated such as young mammals migrating away from where they were
populations. For example, when sea levels rose at the end of the raised, or it could be an accident brought about by, for example,
most recent ice age, new islands formed along the coastline as an unusual storm that blows migrating birds off their normal
the low-lying land around them was flooded. The populations on route. The result is a distant, isolated island population.
those new islands suddenly found themselves isolated from other “Island” in this case may refer to a true island—like Hawaii—or
populations of their species. This kind of island formation is a may simply refer to a patch of habitat on the mainland that is
vicariance event. appropriate for the species but is geographically remote from
Regardless of how the allopatric populations came about— the mainland population’s habitat area. For a species adapted to
whether through dispersal or vicariance—the outcome is the life on mountaintops, a new island might be another previously
same. The two separated populations will diverge genetically until uninhabited mountaintop. For a rain forest tree species, that
speciation occurs. new island might be a patch of lowland forest on the far side of
Often, vicariance-derived speciation is the easier to study a range of mountains that separates it from its mainland forest
because we can date the time at which the populations were population.
separated if we know when the vicariance occurred. One such The island population is classically small and often in an
event whose history is well known is the formation of the environment that is slightly different from that of the mainland
Isthmus of Panama between Central and South America, shown population. The peripatric speciation model suggests that change
in Fig. 22.7. This event took place about 3.5 million years ago. As a accumulates faster in these peripheral isolated populations than in
result, populations of marine organisms in the western Caribbean the large mainland populations, both because genetic drift is more
and eastern Pacific that had formerly been able to interbreed pronounced in smaller populations than in larger ones and because
freely were separated from each other. After a period of time, the the environment may differ between the mainland and island in a
result was the formation of many distinct species, with each one’s way that results in natural selection driving differences between
closest relative being on the other side of the isthmus. the two populations. These mechanisms cause genetic divergence
Dispersal is important in a specific kind of allopatric of the island population from the mainland one, ultimately leading
speciation known as peripatric speciation (that is, in a to speciation.
peripheral place). In this model, a few individuals from a It is possible to glimpse peripatric differentiation in action
mainland population (the central population of a species) (Fig. 22.8). Studies of a kingfisher, Tanysiptera galatea, in New
FIG. 22.8 Peripatric speciation in action among populations of New Guinea kingfishers. Sources: Data from D. J. Futuyma, 2009, Evolution, 2nd ed.,
Sunderland, MA: Sinauer Associates, Fig. 18.7, p. 484; Photo from C. H. Greenewalt/VIREO.
Australia
Mainland subspecies of Tanysiptera
galatea are similar to one another, but
island subspecies are more distinct,
suggesting faster genetic divergence
on island populations.
New Guinea
The eight
subspecies on New
Guinea and nearby
islands are marked
in different colors.
454 SECTION 22.3 S P E C I AT I O N
Cactus finch
(G. scandens)
Bud-eater
Only one finch species
Vegetarian finch evolved with adaptations
(Platyspiza crassirostris) for pulling buds off trees.
Ancestor finch
from South
America
mainland Small tree finch
(Camarhynchus parvulus)
Warbler finch
(Certhidea olivacea)
20
Number of islands
Number of finch species
15
Numbers
10
The number of species
increased as more islands
appeared, suggesting that
allopatric isolation of
5 populations on different
islands was important for
speciation in these birds.
0
5 4 3 2 1 0
Millions of years ago
CHAPTER 22 S P E C I E S A N D S P E C I AT I O N 455
Guinea and nearby islands show the process under way. There When the medium-billed immigrant finches first arrived on
are eight recognized subspecies of T. galatea, three on mainland the Galápagos, however, no such competition existed. Therefore,
New Guinea (where they exist in large populations separated by natural selection promoted the formation of new species of small-
mountain ranges) and five on nearby islands (where, because the and large-seed specialists from the original medium-seed-eating
islands are small, the populations are correspondingly small). The ancestral stock. With the elimination of the stabilizing selection
mainland subspecies are still quite similar to one another, but the that kept the medium-billed finches medium-billed on the
island subspecies are much more distinct, suggesting that genetic mainland, selection actually operated in the opposite direction,
divergence is occurring faster in the small island populations. If we favoring the large and small extremes of the bill-size spectrum
wait long enough, these subspecies will probably diverge into new because these individuals could take advantage of the abundance
species. of unused resources, small and large seeds. It is this combination
Because dating such dispersal events is tricky—newcomers of emptiness—the availability of ecological opportunity—and the
on an island tend not to leave a record of when they arrived—we potential for allopatric speciation that results in adaptive radiation.
can sometimes use vicariance information to study the timing
j Quick Check 2 Why do we see so many wonderful examples
of peripatric speciation. For instance, we know that the oldest
of adaptive radiation on mid-ocean volcanic archipelagos like the
of the Galápagos Islands were formed 4–5 million years ago by
Galápagos?
volcanic action. Sometime early in the history of the Galápagos,
individuals of a small South American finch species arrived there.
Co-speciation is speciation that occurs in response to
Conditions on the Galápagos are very different from those on the
speciation in another species.
South American continent, where the mainland population of this
As we have seen, physical separation is often a critical ingredient in
ancestral finch lived, and so the isolated island population evolved
speciation. Two populations that are not fully separated from each
to become distinct from its mainland ancestor and eventually
other—that is, there is gene flow between them—will typically
became a new species.
not diverge from each other genetically, because genetic exchange
The finches’ subsequent dispersal among the other islands
homogenizes them. This is why most speciation is allopatric.
of the Galápagos has promoted further peripatric speciation
Allopatric speciation brings to mind populations separated from
(Fig. 22.9). In the graph at the bottom of the figure, we see
each other by stretches of ocean or deserts or mountain ranges.
that the number of finch species is correlated with the number
However, separation can be just as complete even in the absence of
of islands in the archipelago. This is clear indication of the
geographic barriers.
importance of geographic separation (allopatry) in speciation: The
Consider an organism that parasitizes a single host species.
availability of islands provided opportunities for populations to
Suppose that the host undergoes speciation, producing two
become isolated from one another, allowing speciation. The result
daughter species. The original parasite population will also be split
was the evolution of 13 different species of finches, collectively
into two populations, one for each host species. Thus, the two
known today as Darwin’s finches.
new parasite populations are physically separated from each other
The Galápagos finches and their frenzy of speciation illustrate
and will diverge genetically, ultimately undergoing speciation.
the important evolutionary idea of adaptive radiation, a bout
This divergence results in a pattern of coordinated host–parasite
of unusually rapid evolutionary diversification in which natural
speciation called co-speciation, a process in which two groups of
selection accelerates the rates of both speciation and adaptation.
organisms speciate in response to each other and at the same time.
Adaptive radiation occurs when there are many ecological
Phylogenetic analysis of lineages of parasites and their hosts
opportunities available for exploitation. Consider the ancestral
that undergo co-speciation reveals trees that are similar for each
finch immigrants arriving on the Galápagos. A wealth of ecological
group. Each time a branching event—that is, speciation—has
opportunities was open and available. Until the arrival of the
occurred in one lineage, a corresponding branching event occurred
colonizing finches, there were no birds on the islands to eat the
in the other (Fig. 22.10).
plant seeds, or to eat the insects on the plants, and so on. Suppose
that the ancestral finches fed specifically on medium-sized seeds
on the South American mainland (that is, they were medium-seed ? CASE 4 MALARIA: CO-EVOLUTION OF HUMANS AND
specialists, with bills that are the right size for handling medium- A PARASITE
sized seeds). On the mainland, they were constrained to that size How did malaria come to infect humans?
of seed because any attempt to eat larger or smaller ones brought Now let’s look at a human parasite, Plasmodium falciparum, the
them into conflict with other species—a large-seed specialist and a single-celled eukaryote that causes malaria. It had been suggested
small-seed specialist—that already used these resources. In effect, that P. falciparum’s closest relative is another Plasmodium species,
stabilizing selection (Chapter 21) was operating on the mainland P. reichenowi, found in chimpanzees, our closest living relative.
to eliminate the extremes of the bill-size spectrum in the medium- Were P. falciparum and P. reichenowi the products of co-speciation?
seed specialists. When the ancestral population split millions of years ago to give
456 SECTION 22.3 S P E C I AT I O N
FIG. 22.10 Co-speciation. Parasites and their hosts often evolve together, and the result is similar phylogenies. Sources: Data from J. P. Huelsenbeck and
B. Rannala, 1997, “Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context,” Science 276:227, doi: 10.1126/science.276.5310.227;
Louse photo by Alex Popinga, courtesy of James Demastes; pocket gopher photo by Richard Ditch @ richditch.com.
rise to human and chimpanzee lineages, that population’s parasitic population A can, in principle, appear in population B as members
Plasmodium population could also have been split, ultimately of the two populations interbreed. The new mutation may indeed
yielding P. falciparum and P. reichenowi. have become fixed in population A, but a migrant from population A
Recent studies, however, have disproved this hypothesis. We to population B may introduce the mutation to population B as well.
now know that P. falciparum was introduced to humans relatively Gene flow effectively negates the genetic divergence of populations.
recently from gorillas. Why doesn’t the evolutionary history If there is gene flow, a pair of populations may change over time, but
of Plasmodium follow the classical host–parasite co-speciation they do so together. How, then, can speciation occur if gene flow
pattern? We know that this history is complex and is still being exists? The term we use to describe populations that are in the same
unraveled. However, we also know that the mosquito-borne phase geographic location is sympatric (literally, “same place”). So we
of its life cycle facilitates transfer to new hosts. Malaria parasites can rephrase the question in technical terms: How can speciation
are thus not as inextricably tied to their hosts as the pocket gopher occur sympatrically?
lice in Fig 22.10 and so their evolutionary history is
not as parallel to their hosts.
Sympatric populations—those not FIG. 22.11 Sympatric speciation by disruptive selection. Natural selection
geographically separated—may undergo eliminates individuals in the middle of the spectrum.
speciation.
Can speciation occur without complete
Small-seed specialist Large-seed specialist Natural selection
physical separation of populations? Yes, though
Number of individuals
eliminates medium-
evolutionary biologists are still exploring Natural billed birds in an
selection environment with no
how common this phenomenon is. Recall medium-sized seeds,
how separated populations inevitably diverge and favors small-billed
genetically over time (see Fig. 22.6). If a mutation birds and large-billed
birds in response to
arises in population A after it has separated from the availability of small
population B, that mutation is present only in and large seeds.
population A and may eventually become fixed
(100% frequency) in that population, either
through natural selection, if it is advantageous, or
through drift, if it is neutral. Once the mutation
is fixed in population A, it represents a genetic
Number of individuals
For speciation to occur sympatrically, natural selection must related species in the same location and argue that they must
act strongly to counteract the homogenizing effect of gene have arisen through sympatric speciation. However, there is an
flow. Consider two sympatric populations of finch-like birds, alternative explanation. One species could have arisen elsewhere
represented in the graph in Fig. 22.11. One population begins to by, for example, peripatric speciation and subsequently moved into
specialize on small seeds and the other on large seeds. If the two the environment of the other one. In other words, the speciation
populations freely interbreed, no genetic differences between the occurred in the past by allopatry, and the two species are only
two will occur and speciation will not take place. Now suppose currently sympatric because migration after speciation occurred.
that the offspring produced by the pairing of a big-seed specialist However, recent studies of plants on an isolated island have
with a small-seed specialist is an individual best adapted to eat provided strong, if not definite, evidence of sympatric speciation.
medium seeds, and there are no medium-sized seeds available in Lord Howe Island is a tiny island (about 10 km long and 2 km
the environment. Natural selection will act against the hybrids, across at its widest) about 600 km east of Australia. Two species of
which will starve to death because there are no medium-sized palm tree that are only found on the island are each other’s closest
seeds for them to eat and they are not well adapted to compete relatives. Because the island is so small, there is little chance that
with the big- or small-seed specialists. Natural selection would the two species could be geographically separated from each other,
then, in effect, eliminate the products of gene flow. So, although meaning that the species are and were sympatric, and, because of
gene flow is occurring, it does not affect the divergence of the the distance of Lord Howe from Australia (or other islands), it is
two populations because the hybrid individuals do not survive extremely likely that they evolved and speciated from a common
to reproduce. As discussed in Chapter 21, this form of natural ancestor on the island.
selection, which operates against the middle of a spectrum of This and other demonstrations show that sympatric speciation
variation, is called disruptive selection. can occur. We must recognize, however, that we do not yet know
However, it turns out to be difficult to find evidence of just how much of all speciation is sympatric and how much is
sympatric speciation in nature, though it may not be especially allopatric. Fig. 22.12 summarizes modes of speciation based on
rare in plants, as we will see. We might find two very closely geography.
Allopatric: Speciation with no gene flow between diverging populations Sympatric: Speciation with gene
flow between diverging populations
Ancestral Ancestral
population population
In peripatric Disruptive
A B A B A B speciation, selection
Population the ancestral results in two
splits either by population seeds genetically
vicariance or a small peripheral distinct sub-
by dispersal. population (e.g., populations
on an island). within the
River changes course Some individuals population.
to split population. move to new habitat.
Divergence Eventually,
Populations the sub-
occurs over
diverge populations
time, but most
genetically diverge
of the change
over time. sufficiently
accumulates
in the small to become
A B population. two distinct
A B A B species.
458 SECTION 22.3 S P E C I AT I O N
j Quick Check 3 There are hundreds of species of cichlid fish in double the number of chromosomes (that is, the hybrid inherits
Lake Victoria in Africa. Some scientists argue that they evolved a full paired set of chromosomes from each parental species)—a
sympatrically, but recent studies of the lake suggest that it total of 20. In this case, the hybrid has four genomes rather
periodically dried out, leaving a series of small ponds. Why is than the diploid number of two. We call such a double diploid
this observation relevant to evaluating the hypothesis that these a tetraploid. In general, animals cannot sustain this kind of
species arose by sympatric speciation? expansion in chromosome complement, but plants are more
likely to do so. As a result, the formation of new species through
Speciation can occur instantaneously. polyploidy—multiple chromosome sets (Chapter 13)—has been
Although speciation is typically a lengthy process, it can relatively common in plants.
occasionally occur in a single generation, making it sympatric by Polyploids may be allopolyploids, meaning that they are
definition. Typically, cases of such instantaneous speciation produced from hybridization of two different species. For
are caused by hybridization between two species in which the example, related species of Chrysanthemum appear, on the basis
offspring are reproductively isolated from both parents. of their chromosome numbers, to be allopolyploids. Alternatively,
For example, hybridization in the past between two sunflower polyploids may be autopolyploids, meaning that they are derived
species, Helianthus annuus and H. petiolaris (the ancestor of the from an unusual reproductive event between members of a single
cultivated sunflower) has apparently given rise to three new species. In this case, through an error of meiosis in one or both
sunflower species, H. anomalus, H. paradoxus, and H. deserticola parents in which homologous chromosomes fail to separate, a
(Fig. 22.13). H. petiolaris and H. annuus have probably formed gamete may be produced that is not haploid. For example, Anemone
innumerable hybrids in nature, virtually all of them inviable. rivularis, a plant in the buttercup family, has 16 chromosomes,
However, a few—the ones with a workable genetic complement— and its close relative A. quinquefolia has 32. Anemone quinquefolia
are the ones that survived to yield these three daughter species. In appears to be an autopolyploid derived from the joining of A.
this case, each one of these new species has acquired a different mix rivularis gametes with two full sets of chromosomes each.
of parental chromosomes. It is this species-specific chromosome So rampant is speciation by polyploidy in plants that it
complement that makes all three distinct and reproductively affects the pattern of chromosome numbers across all plants. In
isolated from the parent species and from one another. Fig. 22.14, we see the haploid chromosome numbers of thousands
In many cases of hybridization, chromosome numbers may of plant species plotted on a graph. Note that as the numbers
change. Two diploid parent species with 5 pairs of chromosomes, get higher, even numbers tend to predominate, suggesting
for a total of 10 chromosomes each, may produce a hybrid with that the doubling of the total number of chromosomes (a form
Helianthus anomalus
Genetic Drift
Neutral mutations increase and decrease in frequency in the population because of the random effects of generation-to-generation sampling error.
1 Different mutations arise in each population. Some (black) are deleterious and are Parent population
eliminated by selection. Some (red) are advantageous and swept to fixation (100%
frequency) by selection. Some (blue) are neutral, so their fate is governed by
genetic drift, and they ultimately drift either to extinction or fixation. Past
Change in
pigment Daughter population A
Generations
A neutral mutation that 1
briefly drifts up in frequency 2
3
before drifting to extinction 4
1.0
0.6
0.4
0.2
0.0
Change in
pigment Generations
A neutral mutation that A fixed difference
drifts to fixation occurs when the
e
Tim
Generations
Present
460
Natural Selection
Mutations that increase the fitness of individuals become more common, and those that decrease the fitness of individuals become less common over time.
A deleterious
mutation decreases
Less the fitness of the
streamlined organism.
fin shape
A neutral
A deleterious mutation mutation does not
that is eliminated by affect the fitness
natural selection of the organism.
Daughter population B
Generations Change in A beneficial
1
2 pigment mutation increases
3 A neutral mutation that the fitness of an
4
briefly drifts up in frequency organism.
before drifting to extinction
1.0
0.6
0.4
Allopatric 0.2
speciation 0.0
When two populations
are separated by a
geographic boundary, Generations
they diverge genetically
over time and
eventually become
reproductively isolated. Larger
mass
A beneficial mutation driven
to fixation by natural selection
1.0
Generations
461
462 SELF-ASSESSMENT
Core Concepts Summary Co-speciation occurs when one species undergoes speciation in
response to speciation in another. In parasites and their hosts,
co-speciation can result in host and parasite phylogenies that
22.1 Reproductive isolation is the key to the biological
have the same branching patterns. page 455
species concept.
Speciation may be sympatric, meaning that there is no
The biological species concept (BSC) states that species are
geographic separation between the diverging populations.
groups of actually or potentially interbreeding populations that
For this type of speciation to occur, natural selection for two
are reproductively isolated from other such groups.
or more different types within the population must act so
page 446
strongly that it overcomes the homogenizing effect of gene
We cannot apply the BSC to asexual or extinct organisms. flow. page 456
page 447
Ring species and hybridization further demonstrate that the 22.4 Speciation can occur with or without natural
BSC is not a comprehensive definition of species. page 448 selection.
The BSC is nevertheless especially useful because it Separated populations can diverge as a result of genetic drift,
emphasizes reproductive isolation. page 449 natural selection, or both. page 459
Natural selection may act on mutations that allow individuals
22.2 Reproductive isolation is caused by barriers to to identify and mate with individuals that are more
reproduction before or after egg fertilization. like themselves. This process is called reinforcement of
Reproductive barriers can be pre-zygotic, occurring before egg reproductive isolation. page 459
fertilization, or post-zygotic, occurring after egg fertilization.
page 449
Self-Assessment
Pre-zygotic isolation may be behavioral, gametic, temporal,
or ecological. page 450 1. Define the term “species.”
In post-zygotic isolation, mating occurs but genetic 2. Given a group of organisms, describe how you would
incompatibilities prevent the development of a viable, fertile test whether they all belong to one species or whether they
offspring. page 450 belong to two separate species.
Evolutionary
Patterns
Phylogeny and Fossils
Core Concepts
23.1 A phylogenetic tree is a
reasoned hypothesis of the
evolutionary relationships
among organisms.
23.2 A phylogenetic tree is built
on the basis of shared derived
characters.
23.3 The fossil record provides
direct evidence of evolutionary
history.
23.4 Phylogeny and fossils provide
independent and corroborating
evidence of evolution.
463
464 SECTION 23.1 R E A D I N G A P H Y LO G E N E T I C T R E E
All around us, nature displays nested patterns of similarity among again, giving rise to multiple descendant species. The result is the
species. For example, as noted in Chapter 1, humans are more pattern of nested similarities observed in nature (see Fig. 1.17).
similar to chimpanzees than either humans or chimpanzees are This history of descent with branching is called phylogeny, and is
to monkeys. Humans, chimpanzees, and monkeys, in turn, are much like the genealogy that records our own family histories.
more similar to one another than any one of them is to a mouse. The evolutionary changes inferred from patterns of
And humans, chimpanzees, monkeys, and mice are more similar to relatedness among present-day species make predictions about
one another than any of them is to a catfish. This pattern of nested the historical pattern of evolution we should see in the fossil
similarity was recognized more than 200 years ago and used by the record. For example, groups with features that we infer to have
Swedish naturalist Carolus Linnaeus to classify biological diversity. evolved earlier than others should appear earlier in time as
A century later, Charles Darwin recognized this pattern as the fossils. Paleontological research reveals that the history of life is
expected outcome of a process of “descent with modification,” or indeed laid out in the chronological order predicted on the basis
evolution. of comparative biology. How do we reconstruct the history of life
Evolution produces two distinct but related patterns, both from evolution’s two great patterns, and how do they compare?
evident in nature. First is the nested pattern of similarities found
among species on present-day Earth. The second is the historical
pattern of evolution recorded by fossils. Life, in its simplest form, 23.1 READING A PHYLOGENETIC TREE
originated more than 3.5 billion years ago. Today, an estimated
10 million species inhabit the planet. Short of inventing a time Chapter 22 introduced the concept of speciation, the set of
machine, how can we reconstruct those 3.5 billion years of processes by which physically, physiologically, or ecologically
evolutionary history in order to understand the extraordinary isolated populations diverge from one another to the point where
events that have ultimately resulted in the biological diversity we they can no longer produce fertile offspring. As illustrated in
see around us today? These two great patterns provide the answer. Fig. 23.1, speciation can be thought of as a process of branching.
Darwin recognized that the species he observed must be the Now consider what happens as this process occurs over and over
modified descendants of earlier ones. Distinct populations of an in a group through time. As species proliferate, their evolutionary
ancestral species separate and diverge through time, again and relationships to one another unfold in a treelike pattern, with
individual species at the twig tips and
their closest relatives connected to them
FIG. 23.1 The relationship between speciation and a phylogenetic tree. The phylogenetic tree, at the nearest fork in the branch, called
on the right, depicts the evolutionary relationships that result from the two successive a node. A node thus represents the
speciation events diagrammed on the left. most recent common ancestor of two
descendant species.
Present
Phylogenetic trees provide
3 species
want to tell someone about a small animal we have seen with fur,
mammary glands, and extended finger bones that permit it to fly, FIG. 23.2 A phylogeny of vertebrate animals. The branching
we can give them this long description, or we can just say we saw a order constitutes a hypothesis of evolutionary
bat, or a member of Order Chiroptera. All the rest is understood (or relationships within the group.
can be looked up in a reference). Hagfish
Phylogenetics, on the other hand, aims to discover the pattern Jawless fish
of evolutionary relatedness among groups of species or other Lampreys
groups by comparing their anatomical or molecular features, Sharks
Cartilaginous fish
and to depict these relationships as a phylogenetic tree. A and Rays
phylogenetic tree is a hypothesis about the evolutionary history,
Ray-finned fish
or phylogeny, of the species. Phylogenetic trees are hypotheses
because they represent the best model, or explanation, of the Coelacanths Bony fish
relatedness of organisms on the basis of all the existing data. As Lobe-finned
fish
with any model or hypothesis, new data may provide evidence for Lungfish
alternative relationships, leading to changes in the hypothesized
pattern of branching on the tree. Frogs
Many phylogenetic trees explore the relatedness of particular
Salamanders Amphibians
groups of individuals, populations, or species. We may, for
example, want to understand how wheat is related to other, Caecilians
non-commercial grasses, or how disease-causing populations of
Escherichia coli relate to more benign strains of the bacterium. At Lizards
and snakes
a much larger scale, universal similarities of molecular biology Tetrapods
indicate that all living organisms are descended from a single Turtles
Sauropsids
common ancestor. This insight inspires the goal of reconstructing Crocodiles
phylogenetic relationships for all species in order to understand and alligators
how biological diversity has evolved since life originated.
Birds
This universal tree is commonly referred to as the tree of life
(Chapter 1). In Part 2 of this book, we will make use of the tree of Mammals
life and many smaller-scale phylogenetic trees to understand our
planet’s biological diversity.
Fig. 23.2 shows a phylogenetic tree for vertebrate animals.
The informal name at the end of each branch represents a group of earlier. A modern lungfish, for example, is not more primitive or
organisms, many of them familiar. We sometimes find it useful to “less evolved” than an alligator, even though its group branches
refer to groups of species this way (for example, “frogs,” or “Class off the trunk of the vertebrate tree earlier than the alligator
Anura”) rather than name all the individual species or list the group does. After all, both species are the end products of the
characteristics they have in common. It is important, however, to same interval of evolution since their divergence from a common
remember that such named groups represent a number of member ancestor more than 370 million years ago.
species. If, for example, we were able to zoom in on the branch
labeled “Frogs,” we would see that it consists of many smaller The search for sister groups lies at the heart
branches, each representing a distinct species of frog, either living of phylogenetics.
or extinct. Two species, or groups of species, are considered to be closest
This tree provides information about evolutionary relatives if they share a common ancestor not shared by any other
relationships among vertebrates. For example, it proposes that the species or group. In Fig. 23.2, for example, we see that frogs are
closest living relatives of birds are crocodiles and alligators. The more closely related to salamanders than to any other group
tree also proposes that the closest relatives of all tetrapod (four- of organisms because frogs and salamanders share a common
legged) vertebrates are lungfish, which are fish with lobed limbs amphibian ancestor not shared by any other group. Similarly,
and the ability to breathe air. Phylogenetic trees are built from lungfish are more closely related to tetrapods than to any other
careful analyses of the morphological and molecular attributes group. A lungfish may look more like a fish than it does an
of the species or other groups under study. A tree is therefore a amphibian, but lungfish are more closely related to amphibians
hypothesis about the order of branching events in evolution, and it than they are to other fish because lungfish share a common
can be tested by gathering more information about anatomical and ancestor with amphibians (and other tetrapods) that was more
molecular traits. recent than their common ancestor with other fish (Fig. 23.2).
A phylogenetic tree does not in any way imply that more Groups that are more closely related to each other than either
recently evolved groups are more advanced than groups that arose of them is to any other group, like lungfish and tetrapods, are
466 SECTION 23.1 R E A D I N G A P H Y LO G E N E T I C T R E E
called sister groups. Simply put, phylogenetic hypotheses amount The resulting classification emphasizes groups that are
to determining sister-group relationships because the simplest monophyletic, meaning that all members share a single common
phylogenetic question we can ask is which two of any three species ancestor not shared with any other species or group of species.
(or other groups) are more closely related to each other than either In Fig. 23.2, the tetrapods are monophyletic because they all
is to the third. In this light, we can see that a phylogenetic tree is share a common ancestor not shared by any other taxa. Similarly,
simply a set of sister-group relationships; adding a species to the amphibians are monophyletic.
tree entails finding its sister group in the tree. In contrast, consider the group of animals traditionally
Closeness of relationship is then determined by looking to recognized as reptiles, which includes turtles, snakes, lizards,
see how recently two groups share a common ancestor. Shared crocodiles, and alligators (Fig. 23.2). The group “reptiles” excludes
ancestry is indicated by a node, or branch point, on a phylogenetic birds, although they share a common ancestor with the included
tree. Nodes can be rotated without changing the evolutionary animals. Such a group is paraphyletic. A paraphyletic group
relationships of the groups. Fig. 23.3, for example, shows four includes some, but not all, of the descendants of a common
phylogenetic trees depicting evolutionary relationships among ancestor. Early zoologists separated birds from reptiles because
birds, crocodiles and alligators, and turtles. In all four trees, they are so distinctive. However, many features of skeletal
birds are a sister group to crocodiles and alligators because birds, anatomy and DNA sequence strongly support the placement of
crocodiles, and alligators share a common ancestor not shared by birds as a sister group to the crocodiles and alligators.
turtles. The more recent a common ancestor, the more closely There is a simple way to distinguish between monophyletic
related two groups are. Evolutionary relatedness therefore is and paraphyletic groups, illustrated in Fig. 23.4. If in order to
determined by following nodes from the tips to the root of the separate a group from the rest of the phylogenetic tree you need
tree, and is not determined by the order of the tips from the top to only to make one cut, the group is monophyletic. If you need a
bottom of a page. second cut to trim away part of the separated branch, the group is
paraphyletic.
j Quick Check 1 Does either of these two phylogenetic trees indicate
Groupings that do not include the last common ancestor of all
that humans are more closely related to lizards than to mice?
members are called polyphyletic. For example, clustering bats and
birds together as flying tetrapods results in a polyphyletic group
Humans Lizards
(Fig. 23.4).
Identifying monophyletic groups is a main goal of
Mice Humans phylogenetics because monophyletic groups include all
descendants of a common ancestor and only the descendants of
that common ancestor. This means that monophyletic groups
Lizards Mice alone show the evolutionary path a given group has taken since
its origin. Omitting some members of a group, as in the case of
A monophyletic group consists of a common ancestor reptiles and other paraphyletic groups, can provide a misleading
and all its descendants. sense of evolutionary history. By using monophyletic groups in
Up to this point, we have used the word “group” to mean all taxonomic classification, we effectively convey our knowledge of
the species in some taxonomic entity under discussion. A more their evolutionary history.
technical word is taxon (plural, taxa), with taxonomy providing a
formal means of naming groups. Recently, biologists have worked j Quick Check 2 Look at Fig. 23.4. Are fish a monophyletic
to integrate evolutionary history with taxonomic classification. group?
FIG. 23.3 Sister groups. The four trees illustrate the same set of sister-group relationships.
Crocodiles
Turtles Turtles Birds
and alligators
Crocodiles = = = Crocodiles
Birds Birds
and alligators and alligators
Crocodiles
Birds Turtles Turtles
and alligators
CHAPTER 23 E VO LU T I O N A RY PAT T E R N S : P H Y LO G E N Y A N D F O S S I L S 467
FIG. 23.4 Monophyletic, paraphyletic, and polyphyletic groups. Only monophyletic groups reflect evolutionary relationships because only they
include all the descendants of a common ancestor.
Hagfish
Lampreys
Ray-finned fish
Coelacanths
Lungfish
Taxonomic classifications are FIG. 23.5 Classification. Classification reflects our understanding of phylogenetic
information storage relationships, and the taxonomic hierarchy reflects the order of branching.
and retrieval systems.
Genus 1 Species 1
The nested pattern of similarities among
species has been recognized by naturalists Species 2
Family 1
for centuries. In the vocabulary of formal Species 3
classification, closely related species are Order 1 Genus 2 Species 4
grouped into a genus (plural, genera). Species 5
Closely related genera, in turn, belong to Family 2 Genus 3
Species 6
a larger, more inclusive branch of the tree,
Genus 4 Species 7
as a family. Closely related families, in Class 1
Species 8
turn, form an order, orders form a class, Family 3
classes form a phylum (plural, phyla), Species 9
Genus 5
and phyla form a kingdom, each more Species 10
inclusive taxonomic level occupying a Order 2 Species 11
successively larger limb on the tree Genus 6 Species 12
(Fig. 23.5). Biologists today commonly Phylum I Species 13
refer to the three largest limbs of the Family 4
Species 14
entire tree of life as domains (Eukarya, or
Species 15
eukaryotes; Bacteria; and Archaea). Genus 7
The ranks of classification form a Species 16
nested hierarchy, but the boundaries of Species 17
Class 2
ranks above the species level are arbitrary
468 SECTION 23.2 B U I L D I N G A P H Y LO G E N E T I C T R E E
in that there is nothing particular about a group that makes it, for
example, a class rather than an order. A taxonomist examining the FIG. 23.6 Homology and analogy. A homology is a similarity that
17 species included in Fig. 23.5 might decide that species 3 and 4 results from shared ancestry, whereas an analogy is a
are sufficiently distinct from species 5 to warrant placing them into similarity that results from convergent evolution.
a distinct genus. The same taxonomist might then decide that the
Lizards
grouping of the two new genera together should rank as a family. and snakes
For this reason, it is not necessarily true that orders or classes of, for
Turtles
example, birds and ferns are equivalent in any meaningful way. In The amniotic egg Sauropsids
contrast, sister groups are equivalent in several ways—notably, in is a homology of Crocodiles
sauropsids and and alligators
that they diverged from a single ancestor at a single point in time.
mammals because
Therefore, if one branch is a sister group that contains 500 species it evolved once in Birds
and another has 6, the branches have experienced different rates their common
ancestor.
of speciation, extinction, or both since they diverged. In Fig 23.5, Mammals (bats)
Families 1 and 2 are sister groups, but Family 1 has five species while
Family 2 has just one. The presence of wings in birds
and bats is an analogy since wings
evolved independently in birds
and bats, and were not present in
their common ancestor.
23.2 BUILDING A PHYLOGENETIC
TREE
Up to this point, we have focused on how to interpret a Consider two examples. Mammals and birds both produce
phylogenetic tree, a diagram that depicts the evolutionary history of amniotic eggs. Amniotic eggs occur only in groups descended from
organisms. But how do we infer evolutionary history from a group the common ancestor at the node connecting the mammal and
of organisms? That is, how do we actually construct a phylogenetic sauropsid branches of the tree, and so we reason that birds and
tree? Biologists use characteristics of organisms to figure out mammals each inherited this character from a common ancestor
their relationships. Similarities among organisms are particularly in which the trait first evolved (Fig. 23.6). Characters that are
important in that similarities sometimes suggest shared ancestry. similar because of descent from a common ancestor are said to be
However, a key principle of constructing trees is that only some homologous.
similarities are actually useful. Others can in fact be misleading. Not all similarities arise in this way, however. Think of wings,
a character exhibited by both birds and bats. Much evidence
Homology is similarity by common descent. supports the view that wings in these two groups do not reflect
Phylogenetic trees are constructed by comparison of character descent from a common, winged ancestor but rather evolved
states shared among different groups of organisms. Characters independently in the two groups. Similarities due to independent
are the anatomical, physiological, or molecular features that adaptation by different species are said to be analogous. They are
make up organisms. In general, characters have several observed the result of convergent evolution.
conditions, called character states. In the simplest case, a Innumerable examples of convergent evolution less dramatic
character can be present or absent—lungs are present in than wings are known. In some, we even understand the genetic
tetrapods and lungfish, but absent in other vertebrate animals. basis of the convergence. For example, echolocation has evolved
Commonly, however, there are multiple character states. Petals in bats and in dolphins, but not in other mammals. Prestin is
are a character of flowers, for example, and each observed a protein in the hair cells of mammalian ears that is involved
arrangement—petals arranged in a helical pattern, petals arranged in hearing ultrasonic frequencies. Both bats and dolphins
in a whorl, or petals fused into a tube—can be considered a state independently evolved similar changes in their Prestin genes,
of the character of petal arrangement. All species contain some apparently convergent adaptations for echolocation. Similarly,
character states that are shared with other members of their unrelated fish that live in freezing water at the poles, Arctic
group, some that are shared with members of other groups, and and Antarctic, have evolved similar glycoproteins that act as
some that are unique. molecular “antifreeze,” preventing the formation of ice in their
Character states in different species can be similar for one of tissues.
two reasons: The character state (for example, helically arranged In principle, two characters or character states are homologous
petals) was present in the common ancestor of the two groups if they are similar because of descent from a common ancestor
and retained over time (common ancestry), or the character state with the same character or character state; they are analogous if
independently evolved in the two groups as an adaptation to they arose independently because of similar selective pressures.
similar environments (convergent evolution). In practice, to determine if characters observed in two organisms
CHAPTER 23 E VO LU T I O N A RY PAT T E R N S : P H Y LO G E N Y A N D F O S S I L S 469
are homologous or analogous, we can weigh evidence from where group of tetrapods. Phylogenetic reconstruction on the basis of
other traits place the two organisms on a phylogenetic tree, we can synapomorphies is called cladistics.
look at where on the organisms the trait occurs, and we can look
at the anatomical or genetic details of how the trait is constructed.
The simplest tree is often favored among multiple
Wings in birds and bats are similar in morphological position (both
possible trees.
are modified forelimbs) but differ in details of construction (the
To show how synapomorphies help us chart out evolutionary
bat wing is supported by long fingers), and all other traits of birds
relationships, let’s consider the simple example in Fig. 23.8. We
and bats place them at the tips of different lineages, with many
begin with four species of animals (labeled “A” through “D”) in a
nonwinged species between them and their most recent common
group we wish to study that we will call our ingroup; we believe
ancestor.
the species to be closely related to each other. For comparison, we
have a species that we believe is outside this ingroup—that is, it
j Quick Check 3 Fish and dolphins have many traits in common,
falls on a branch that splits off nearer the root of the tree—and
including a streamlined body and fins. Are these traits homologous
so is called an outgroup (labeled “OG” in Fig. 23.8). Each species
or analogous?
in the ingroup and the outgroup has a different combination of
characters, such as leg number, presence or absence of wings, and
Shared derived characters enable biologists to whether development of young to adult is direct or goes through a
reconstruct evolutionary history. pupal stage (Fig. 23.8a).
Because homologies result from shared ancestry, only We are interested in the relationships among species A–D and so
homologies, and not analogies, are useful in constructing focus on potential synapomorphies, character states shared by some
phylogenetic trees. However, it turns out that only some but not all species within the group. For example, only C and D have
homologies are useful. For example, character
states that are unique to a given species
or other monophyletic group can’t tell us FIG. 23.7 Synapomorphies, or shared derived characters. Homologies that are present in
anything about its sister group. They evolved some, but not all, members of a group help us to construct phylogenetic trees.
after the divergence of the group from its
Jawless fish
sister group and so can be used to characterize Hagfish
a group but not to relate it to other groups.
Similarly, homologies formed in the common Lampreys
Cartilaginous
ancestor of the entire group and therefore
Sharks
fish
present in all its descendants do not help to and rays
identify sister-group relationships among the Sharks,
ray-finned fish,
descendants of that common ancestor. coelacanths, Ray-finned fish
What we need to build phylogenetic lungfish, and
Bony fish
tetrapods have
Lobe-finned
trees are homologies that are shared by Coelacanths
a hinged jaw.
some, but not all, of the members of the group
fish
under consideration. These shared derived Lungfish
characters are called synapomorphies. A Coelacanths and
lungfish have lobed fins. Frogs
derived character state is an evolutionary
Amphibians
innovation (for example, the change from
Salamanders
five toes to a single toe—the hoof—in the Lungfish and
ancestor of horses and donkeys). When such a tetrapods have lungs.
Caecilians
novelty arises in the common ancestor of two
taxa, it is shared by both (thus, the hoof is a Lizards Tetrapods
Tetrapods have and snakes
synapomorphy defining horses and donkeys as walking legs.
Sauropsids
FIG. 23.8 Constructing a phylogenetic tree from shared derived traits. The strongest hypothesis of evolutionary relationships overall is the tree
with the fewest number of changes because it minimizes the total number of independent origins of character states.
a. Character states
OG OG OG
A A C
3
3 B B
3 D
C C A
D D B
This phylogeny This phylogeny requires five changes, This phylogeny requires six changes,
requires four changes. including one loss of wings. including one loss of wings and one
reversion to direct development.
OG Shrimp
A Silverfish
B Dragonfly Class
Hexapoda
Subclass (910,000
Pterygota species)
C Beetle (900,000
Holometabola
species)
(800,000
species)
D Butterfly
pupae. This character suggests that C and D are more closely related In practice, biologists examine multiple characters and choose the
to each other than either is to the other species. The alternatives are phylogenetic hypothesis that best fits all of the data.
that C and D each evolved pupae independently or that pupae were How do we determine “best fit”? Fig. 23.8b illustrates three
present in the common ancestor of A–D but were lost in A and B. different hypotheses for the relationships among the species based
How do we choose among the alternatives? Studies of the on four characters and their various character states. Each reflects
outgroup show that it does not form pupae, supporting the the sister-group relationship between C and D proposed earlier. The
hypothesis that pupal development evolved within the ingroup. leftmost tree requires exactly four character-state changes during
CHAPTER 23 E VO LU T I O N A RY PAT T E R N S : P H Y LO G E N Y A N D F O S S I L S 471
the evolution of these species: reduction of leg pairs to three in the be read as admissions of defeat, but instead as problems awaiting
group ABCD, wings in the group BCD, and pupae in group CD, plus a resolution and opportunities for future research.
change of form of the mandible, or jaw, in species D.
Now consider the middle tree in Fig. 23.8b. It groups A and B Molecular data complement comparative morphology
together, and so differs from the tree on the left in requiring either a in reconstructing phylogenetic history.
loss of wings in A, or an additional origin of wings in B, independent Trees can be built using anatomical features, but increasingly tree
of that in the common ancestor of C and D—five changes in all. construction relies on molecular data. The amino acids at particular
The tree on the right groups A and B together, and requires two positions in the primary structure of a protein can be used, as can
extra steps for a total of six steps. No tree that we can construct the nucleotides at specific positions along a strand of DNA.
from species A–D requires fewer than four evolutionary changes, so From genealogy to phylogeny, tracing mutations in DNA or
the left-hand version in Fig. 23.8b is the best available hypothesis RNA sequences has revolutionized the reconstruction of historical
of evolutionary relatedness. In fact, this is the phylogeny for a genetic connections. Whether we are tracing the paternity of the
sample of species from the largest group of animals on Earth, the children of Sally Hemings, mistress of Thomas Jefferson, identifying
Hexapoda—insects and their closest relatives (Fig. 23.8c). the origin of a recent cholera epidemic in Haiti, or placing baleen
In general, trees with fewer character changes are whales near the hippopotamus family in a phylogenetic tree of
preferred to ones that require more because they provide the mammals, molecular data are a rich source of phylogenetic insight.
simplest explanation of the data. This approach is an example There is nothing about molecular data that provides a better
of parsimony, that is, choosing the simpler of two or more record of history than does anatomical data; molecular data simply
hypotheses to account for a given set of observations. When we provide more details because there are more characters that can
use parsimony in phylogenetic reconstruction, we make the vary among the species. A sequence of DNA with hundreds or
implicit assumption that evolutionary change is typically rare. thousands of nucleotides can represent that many characters, as
Over time, most features of organisms stay the same—we have the opposed to the tens of characters usually visible in morphological
same number of ears as our ancestors, the same number of fingers, studies. Indeed, for microbes and viruses there is very little
and so on. Thus, biologists commonly prefer the phylogenetic tree morphology available, so molecular information is critical for
requiring the fewest evolutionary steps. phylogenetic reconstruction. Once a gene or other stretch of DNA
In systematics, parsimony suggests counting character changes or RNA is identified that seems likely (based on previous studies
on a phylogenetic tree to find the simplest tree for the data (the of other species) to vary among the species to be studied,
one with the fewest number of changes). Each change corresponds sequences are obtained and aligned to identify homologous
to a mutation (or mutations) in an ancestral species, and the more nucleotide sites. Analyses of this kind commonly involve
changes or steps we propose, the more independent mutations we comparisons of sequences of about 1000 nucleotides from
must also hypothesize. one or more genes. Increasingly, though, the availability of
Note also that it isn’t necessary to make decisions in advance whole-genome sequences is changing the way we do molecular
about which characters are homologies and which are analogies. We phylogenetics. Rather than comparing the sequences of a few
can construct all possible trees and then choose the one requiring genes, we compare the sequences of entire genomes.
the fewest evolutionary changes. This is a simple matter for the The process of using molecular data is conceptually similar
example in Fig. 23.8 because four species can be arranged into only to the process described earlier for morphological data. Through
15 possible different trees. As the number of groups increases, comparison to an outgroup, we can identify derived and ancestral
however, the number of possible trees connecting them increases molecular characters (whether DNA nucleotides or amino
as well, and dramatically so. There are 105 trees for 5 groups and acids in proteins) and generate the phylogeny on the basis of
945 trees for 6 groups, and there are nearly 2 million possible trees synapomorphies as before.
for 10. For 50 groups the possibilities balloon to 3 1076! Clearly, An alternative method of reconstruction is based on overall
computers are required to sort through all the possibilities. similarity rather than synapomorphies. Here, the premise is
As is true for all hypotheses, phylogenetic hypotheses can be simple: The descendants of a recent common ancestor will have
supported strongly or weakly. Biologists use statistical methods had relatively little time to evolve differences, whereas the
to evaluate a given phylogenetic hypothesis. Available character descendants of an ancient common ancestor have had a lot of time
data may not strongly favor any hypothesis. When support for a to evolve differences. Thus, the extent of similarity (or distance)
specific branching pattern is weak, biologists commonly depict the indicates how recently two groups shared a common ancestor.
relationships as unresolved and show multiple groups diverging Underpinning this approach is the assumption that the rate
from one node, rather than just two. Such branching patterns are of evolution is constant. (Otherwise, a pair of taxa with a recent
not meant to suggest that multiple species diverged simultaneously, common ancestor could be more different than expected because of
but rather to indicate that we lack the data to choose unequivocally an unusually fast rate of evolution.) This rate-constancy assumption
among several different hypotheses of relationship. In Part 2, we is less likely to be violated when we are using molecular data than
show unresolved branches in a number of groups. These shouldn’t when we are using morphological data. Recall from Chapter 21
472 SECTION 23.2 B U I L D I N G A P H Y LO G E N E T I C T R E E
FIG. 23.9 Phylogenetic trees of DNA sequences based on (a) synapomorphies and (b) overall similarity.
Nucleotide position OG C B A
8
1 2 3 4 5 6 7 8 9 6
Synapomorphic T C 7 G A
OG A C C T C C G T G C T
reconstruction 9 5 C T Synapomorphy
A T A G G T C A T G G A groups A + B
Taxon 1 A T
B T A G G T T G T G 2 C A
Synapomorphy
C T A G G C C G C A 3 C G groups A, B, + C
The tree shown here is 4 T G
In our experiment, 1000 base pairs of the the most parsimonious
same gene have been sequenced for our four one, meaning that it The nucleotide changes marked on the
species. What is shown are the character incorporates a minimal tree may not be useful in identifying sister
states for each species for the nine nucleotide number of evolutionary groups (for example, 8 T C is a change
sites that vary among the sequences. changes. that is unique to species C) or they may
be synapomorphies, shared between
descendant taxa (for example, the C T
change at 5 pairs species B and A).
Distance
reconstruction
DNA changes: There are 2
differences between A + B
so we assume 1 per branch.
OG 6 6 6 -
OG C B A 3 We add The total distance between two
3 2 1 1 the OG. taxa is the sum of the differences
1 along all the branches that
1 connect the taxa.
Counting up the number of sequence
differences between individuals gives us a
distance matrix. The number of differences
between any one taxon and the others can
be read across any row or down any column.
that the molecular clock is based on the observation of constant than 100 billion observations (mostly nucleotides) collected
accumulation of genetic divergence through time. Fig. 23.9 shows under more than 430,000 taxonomic names. A growing internet
a simple DNA sequence dataset that we can analyze either on the resource is the Encyclopedia of Life, which is gathering additional
basis of synapomorphies (Fig. 23.9a) or on the basis of distance (Fig. biological information about species, including ecology, geographic
23.9b). Note that both give the same result in this case. distributions, photographs, and sounds in pages for individual
Molecular data are often combined with morphological data, species that are easy to navigate. Another web resource, the Tree of
and each can also serve as an independent assessment of the Life, provides information on phylogenetic trees for many groups of
other. Not surprisingly, results from analyses of each kind of data organisms.
are commonly compatible, at least for plants and animals rich in
morphological characters. Phylogenetic trees can help solve practical problems.
The single largest library of taxonomic information is The sequence of changes on a tree from its root to its tips
GenBank, the National Institutes of Health’s genetic data storage documents evolutionary changes that have accumulated through
facility. As of this writing, GenBank gives users access to more time. Trees suggest which groups are older than others, and which
H
4 7O
3W DT O
SEC I O NW
2 2 .E
1 K
THNE O W
BIO LO?
G I C A L S P E C I E S CO N C E P T
FIG. 23.10
HYPOTHESIS It was hypothesized that the patients acquired HIV during dental procedures carried out by the infected dentist.
these patients, D and F, had acquired their HIV infections from other Patient G-1
sources. Patient G-2
CONCLUSION HIV phylogeny makes it highly likely that the dentist LP02-1
infected several of his patients. The details of how the patients were LP03-1
infected remain unknown, but rigidly observed safety practices make it LP02-2
unlikely that such a tragedy could occur again. Patient D-1
traits came first and which followed later. Proper phylogenetic Phylogenetics solved a famous case in which an HIV-positive
placement thus reveals a great deal about evolutionary history, dentist in Florida was accused of infecting his patients (Fig. 23.10).
and it can have practical consequences as well. For example, HIV nucleotide sequences evolve so rapidly that biologists can
oomycetes, microorganisms responsible for potato blight and build phylogenetic trees that trace the spread of specific strains
other important diseases of food crops, were long thought to be from one individual to the next. Phylogenetic study of HIV present
fungi because they look like some fungal species. The discovery, in samples from several infected patients, the dentist, and other
using molecular characters, that oomycetes belong to a very individuals provided evidence that the dentist had, indeed, infected
different group of eukaryotic organisms, has opened up new his patients.
possibilities for understanding and controlling these plant Similarly, phylogenetic studies of influenza virus strains
pathogens. Similarly, in 2006, researchers used DNA sequences to show their origins and subsequent movements among geographic
identify the Malaysian parent population of a species of butterfly regions and individual patients. Today, there is a growing effort to
called lime swallowtails that had become an invasive species in use specific DNA sequences as a kind of fingerprint or barcode for
the Dominican Republic, pinpointing the source populations from tracking biological material. Such information could quickly identify
which natural enemies of this pest can be sought. samples of shipments of meat as being from endangered species, or
473
474 SECTION 23.3 T H E F O S S I L R E CO R D
track newly emerging pests. The Consortium for the Barcode of Life The evolutionary relationship between birds and crocodiles
has already accumulated species-specific DNA barcodes for more highlights a second kind of information provided by fossils. Not
than 100,000 species. Phylogenetic evidence provides a powerful only do fossils record past life, they also provide our only record of
tool for evolutionary analysis and is useful across timescales ranging extinct species. The phylogeny in Fig. 23.7 contains a great deal of
from months to the entire history of life, from the rise of epidemics information, but it is silent about dinosaurs. Fossils demonstrate
to the origins of metabolic diversity. that dinosaurs once roamed Earth, and details of skeletal structure
place birds among the dinosaurs in the vertebrate tree. Indeed,
some remarkable fossils from China show that the dinosaurs most
23.3 THE FOSSIL RECORD closely related to birds had feathers (Fig. 23.11).
A third, and also unique, contribution of fossils is that they
Phylogenies based on living organisms provide hypotheses place evolutionary events in the context of Earth’s dynamic
about evolutionary history. Branches toward the root of the environmental history. Again, dinosaurs illustrate the point. As
tree occurred earlier than those near the tips, and characters discussed in Chapter 1, geologic evidence from several continents
change and accumulate along the path from the root to the suggests that a large meteorite triggered drastic changes in the
tips. Fossils provide direct documentation of ancient life, and global environment 66 million years ago, leading to the extinction
so, in combination, fossils and phylogenies provide strong of dinosaurs (other than birds). In fact, at five times in the past,
complementary insights into evolutionary history. large environmental disturbances sharply decreased Earth’s
biological diversity. These events, called mass extinctions, have
Fossils provide unique information. played a major role in shaping the course of evolution.
Fossils can and do provide evidence for phylogenetic hypotheses,
showing, for example, that groups that branch early in phylogenies Fossils provide a selective record of past life.
appear early in the geologic record. But the fossil record does more Fossils are the remains of once-living organisms, preserved
than this. First, fossils enable us to calibrate phylogenies in terms through time in sedimentary rocks. If we wish to use fossils to
of time. It is one thing to infer that mammals diverged from the complement phylogenies based on modern organisms, we must
common ancestor of birds, crocodiles, turtles, and lizards and snakes understand how fossils form and how the processes of formation
before crocodiles and birds diverged from a common ancestor (see govern what is and is not preserved.
Fig. 23.7), but another matter to state that birds and crocodiles For all its merits, the fossil record should not be thought of as
diverged from each other about 220 million years ago, whereas a complete dictionary of everything that ever walked, crawled, or
the group represented today by mammals branched from other swam across our planet’s surface. Fossilization requires burial, as
vertebrates about 100 million years earlier. As we saw in Chapter 21, when a clam dies on the seafloor and is quickly covered by sand,
estimates of divergence time can be made using molecular sequence or a leaf falls to the forest floor and ensuing floods cover it in mud.
data, but all such estimates must be calibrated using fossils. Through time, accumulating sediments harden into sedimentary
FIG. 23.11 Microraptor gui, a remarkable fossil discovered in approximately 125-million-year-old rocks from China. The structure of its
skeleton identifies M. gui as a dinosaur, yet it had feathers on its arms, tail, and legs. Source: Nature/Xing Xu/Getty Images.
CHAPTER 23 E VO LU T I O N A RY PAT T E R N S : P H Y LO G E N Y A N D F O S S I L S 475
Fossils record the evolution of life on Earth. They eventually possible with the discovery of radioactive decay. In Chapter 2, we
mapped out the geologic timescale, the series of time divisions discussed isotopes, variants of an element that differ from one
that mark Earth’s long history (Fig. 23.16). another in the number of neutrons they contain. Many isotopes
The layers of fossils in sedimentary rocks can tell us that are unstable and spontaneously break down to form other, more
some rocks are older than others, but they cannot by themselves stable isotopes. In the laboratory, scientists can measure how fast
provide an absolute age. Calibration of the timescale became unstable isotopes decay. Then, by measuring the amounts of the
FIG. 23.16 The geologic timescale, showing major events in the history of life on
Earth. Sources: (top, left to right) Scott Orr/iStockphoto; Hans Steur, The Netherlands;
T. Daeschler/VIREO; Reconstruction artwork: Mark A. Klingler/Carnegie Museum
of Natural History, from the cover of Science, 25 MAY 2001 VOL 292, ISSUE 5521,
Reprinted with permission from AAAS; dimair/Shutterstock; DEA/G. Cigolini/Getty
Images; (bottom, left to right) Eye of Science/Science Source; Andrew Knoll, Harvard
University; Antonio Guillén, Proyecto Agua, Spain; Andrew Knoll, Harvard University.
First land
Marine animals vertebrates
diversify. First land First mammals
plant fossils
Homo sapiens
Carboniferous
Quaternary
Paleogene
Neogene
Silurian
Period
Cambrian Ordovician Devonian Permian Triassic Jurassic Cretaceous
Eon Era
Paleozoic Mesozoic Cenozoic
Phanerozoic
541 485 443 419 359 299 252 201 145 66 23 2.5 Present
Millions of years ago
Eon
Major diversification
Formation First First eukaryotic of eukaryotic
of Earth evidence of life First evidence microfossils microorganisms First animal fossils
of an oxygen-rich
environment
478 SECTION 23.3 T H E F O S S I L R E CO R D
Neutron Nitrogen-14 Carbon-14 Proton can measure the amount of 14C in an archaeological sample
and, by comparing it to the amount of 14C in a sample of known
age—annual rings in trees, for example, or yearly growth of coral
14C that ends up in skeletons—determine the age of the sample.
CO2 carbon dioxide can Because its half-life is so short (by geological standards),
be incorporated in
plants through
14
C is useful only in dating materials younger than 50,000 to
photosynthesis.14C 60,000 years. Beyond that, there is too little 14C left to measure
is next incorporated
accurately. Older geological materials are commonly dated
into animals when
they eat the plants. using the radioactive decay of uranium (U) to lead (Pb): 238U,
incorporated in trace amounts into the minerals of volcanic
rocks, breaks down to 206Pb with a half-life of 4.47 billion
years; 235U decays to 207Pb with a half-life of 704 million years.
After the plant or Calibration of the geologic timescale is based mostly on the ages
animal dies and
is buried, its 14C
of volcanic ash interbedded with sedimentary rocks that contain
decays to the key fossils, as well as volcanic rocks that intrude into (and so are
more stable 14N. younger than) layers of rock containing fossils. In turn, the ages
of fossils provide calibration points for phylogenies.
Half of the 14C in
a fossil turns to The sedimentary rocks that contain fossils also preserve,
14N in 5730 encrypted in their physical features and chemical composition,
years. In another
information about the environment in which they formed.
5730 years, half
of the remaining Sandstone beds, for example, may have rippled surfaces, like
14C decays to
the ripples produced by currents that we see today in the sand
14N, and so on.
of a seashore or lake margin. Pyrite (FeS2), or fool’s gold, forms
+ + when H2S generated by anaerobic bacteria reacts with iron. As
+ + + ++
+ e-
+
+
+ + + + these conditions generally occur where oxygen is absent, pyrite
enrichment in ancient sedimentary rocks can signal oxygen
Carbon-14 Nitrogen-14 Electron
depletion.
100
Percent carbon-14 remaining
FIG. 23.18 Pangaea, 290 million years ago. Plate tectonics has shaped and reshaped Earth’s geography through time. The white area near the
South Pole is glacial ice. Source: © Ron Blakey and Colorado Plateau Geosystems, Inc.
just 20,000 years ago, 2 km of glacial ice stood where Boston lies its braincase, and, especially, its winglike forearms—are distinctly
today. Sedimentary rocks record the changing state of Earth’s birdlike. Spectacularly, the fossils preserve evidence of feathers.
surface over billions of years and show that life and environment Archaeopteryx clearly suggests a close relationship between birds
have changed together through time, each influencing the other. and dinosaurs, and phylogenetic reconstructions that include
information from fossils show that many of the characters
Fossils can contain unique combinations of characters. found today in birds accumulated through time in their dinosaur
Phylogenies hypothesize impressive morphological and ancestors. As noted earlier, even feathers first evolved in dinosaurs
physiological shifts through time—amphibians from fish, for (Fig. 23.19).
example, or land plants from green algae. Do fossils capture a Tiktaalik roseae and other skeletons in rocks deposited 375 to
record of these transitions as they took place? 362 million years ago record an earlier but equally fundamental
Let’s begin with an example introduced earlier in this chapter. transition: the colonization of land by vertebrates. Phylogenies
Phylogenies based on living organisms generally place birds as the show that all land vertebrates, from amphibians to mammals, are
sister group to crocodiles and alligators, but birds and crocodiles descended from fish. As seen in Fig. 23.20, Tiktaalik had fins, gills,
are decidedly different from each other in structure—birds and scales like other fish of its day, but its skull was flattened,
have wings, feathers, toothless bills, and a number of other more like that of a crocodile than a fish, and it had a functional
skeletal features distinct from those of crocodiles. In 1861, just neck and ribs that could support its body—features today found
two years after publication of On the Origin of Species, German only in tetrapods. Along with other fossils, Tiktaalik captures
quarry workers discovered a remarkable fossil that remains key moments in the evolutionary transition from water to land,
paleontology’s most famous example of a transitional form. confirming the predictions of phylogeny.
Archaeopteryx lithographica, now known from 11 specimens
splayed for all time in fine-grained limestone, lived 150 million j Quick Check 4 You have just found a novel vertebrate skeleton
years ago. Its skeleton shares many characters with dromaeosaurs, in 200-million-year-old rocks. How would you integrate this new
a group of small, agile dinosaurs, but several features—its pelvis, fossil species into the phylogenetic tree depicted in Fig. 23.7?
480 SECTION 23.3 T H E F O S S I L R E CO R D
FIG. 23.19 Dinosaurs and birds. A number of dinosaur fossils link birds phylogenetically to their closest living relatives, the crocodiles. The
fossil at the bottom is Archaeopteryx. Data from C. Zimmer, 2009, The Tangled Bank, Greenwood Village, CO: Roberts and Company; (photo) Jason Edwards/
Getty Images.
Crocodiles
Ornithischian
dinosaurs
Eoraptor
Coelophysoids
Allosaurids
Four digits
in hands Compsognathids
Archaeopteryx
Long arms
Living birds
Toothless beak, fused wing
digits, short feathered tail
s
De rian n
og ne
Pa eou
Or rian
Ca ian
u ia
e
23.4 COMPARING EVOLUTION’S
Ne ge
en
i
Sil vic
sic
on
Ju sic
n
c
mb
leo
eta
vo
do
ras
rb
as
Pe
Cr
2500
Number of animal genera
550
500
450
400
350
300
250
200
containing all vertebrate animals, which include fish. This
arrangement predicts that the earliest fossil fish should be older Millions of years ago
than the earliest fossil mammals, the earliest fossil mammals older
than the earliest primates, and the earliest primates older than
the earliest humans. This is precisely what the fossil record shows years ago, the earliest tetrapod vertebrates about 360 million
(Fig. 23.22). years ago, the earliest mammals 210 million years ago, the earliest
The agreement between fossils and phylogenies can be seen primates perhaps 55 million years ago, the earliest fossils of our
again and again when we examine different branches of the tree of own species a mere 200,000 years ago. Similarly, if we focus on
life or, for that matter, the tree as a whole. All phylogenies indicate photosynthetic organisms, we find a record of photosynthetic
that microorganisms diverged early in evolutionary history, and bacteria beginning at least 3500 million years ago, algae
mammals, flowering plants, and other large complex organisms 1200 million years ago, simple land plants 470 million years ago,
diverged more recently. The tree’s shape implies that diversity has seed plants 370 million years ago, flowering plants about
accumulated through time, beginning with simple organisms and 140 million years ago, and the earliest grasses 70 million years ago.
later adding complex macroscopic forms. In Part 2, we explore the evolutionary history of life in some
The geologic record shows the same pattern. For nearly detail. Here, it is sufficient to draw the key general conclusion: The
3 billion years of Earth history, microorganisms dominate the fact that comparative biology and fossils, two complementary but
fossil record, with the earliest animals appearing about independent approaches to reconstructing the evolutionary past,
600 million years ago, the earliest vertebrate animals 520 million yield the same history is powerful evidence of evolution. •
Core Concepts Summary Sister groups are more closely related to one another than they
are to any other group. page 465
23.1 A phylogenetic tree is a reasoned hypothesis of the A node is a branching point on a tree, and it can be rotated
evolutionary relationships among organisms. without changing evolutionary relationships. page 466
The nested pattern of similarities seen among organisms is a A monophyletic group includes all the descendants of a common
result of descent with modification and can be represented as a ancestor, and it is considered a natural grouping of organisms
phylogenetic tree. page 465 based on shared ancestry. page 466
The order of branches on a phylogenetic tree indicates the A paraphyletic group includes some, but not all, of the
sequence of events in time. page 465 descendants of a common ancestor. page 466
484 SELF-ASSESSMENT
A polyphyletic group includes organisms from distinct groups The extinction at the end of the Cretaceous Period 66 million
based on shared characters, but it does not include a common years ago led to the extinction of the dinosaurs (other than
ancestor. page 466 birds). page 481
Organisms are classified into domain, kingdom, phylum, The extinction at the end of the Permian Period 252 million
class, order, family, genus, and species. page 467 years ago is the largest documented mass extinction in the
history of Earth. page 481
23.2 A phylogenetic tree is built on the basis of shared
derived characters. 23.4 Phylogeny and fossils provide independent and
corroborating evidence of evolution.
Characters, or traits, existing in different states are used to
build phylogenetic trees. page 468 Phylogeny makes use of living organisms, and the fossil record
supplies a record of species that no longer exist, absolute dates,
Homologies are similarities based on shared ancestry,
and environmental context. page 482
while analogies are similarities based on independent
adaptations. page 468 Data from phylogeny and fossils are often in agreement,
providing strong evidence for evolution. page 482
Homologies can be ancestral, unique to a particular group, or
present in some, but not all, of the descendants of a common
ancestor (shared derived characters). page 468
Self-Assessment
Only shared derived characters, or synapomorphies, are
1. Draw a phylogenetic tree of three groups of organisms and
useful in constructing a phylogenetic tree. page 469
explain how a nested pattern of similarity can be seen in the
Molecular data provide a wealth of characters that tree and how it might arise.
complement other types of information in building 2. Distinguish among monophyletic, paraphyletic, and
phylogenetic trees. page 471 polyphyletic groups, and give an example of each.
Phylogenetic trees can be used to understand evolutionary 3. List the levels of classification, from the least inclusive
relationships of organisms and solve practical problems, such (species) to the most inclusive (domain).
as how viruses evolve over time. page 473
4. Define “homology” and “analogy” and describe two traits
that are homologous and two that are analogous.
23.3 The fossil record provides direct evidence of
evolutionary history. 5. Name a type of homology that is useful in building
phylogenetic trees and explain why this kind of homology, and
Fossils are the remains of organisms preserved in sedimentary
not others, is useful.
rocks. page 474
6. Describe three ways that an organism can leave a record
The fossil record is imperfect because fossilization requires in sedimentary rocks and explain why this means that there
burial in sediment, sediments accumulate episodically and are gaps in the fossil record.
discontinuously, and fossils typically preserve only the hard
7. Explain how the fossil record can be used to determine
parts of organisms. page 474
both the relative and the absolute timescales of past events.
Radioactive decay of certain isotopes of elements provides a
8. Describe the significance of Archeopteryx and Tiktaalik.
means of dating rocks. page 477
9. Describe how mass extinctions have shaped the
Archaeopteryx and Tiktaalik are two fossil organisms that ecological landscape.
document, respectively, the bird–dinosaur transition and
the fish–tetrapod transition. page 479
Log in to to check your answers to the Self-
The history of life is characterized by five mass extinctions Assessment questions, and to access additional learning tools.
that changed the course of evolution. page 481
CHAPTER 24
Human Origins
and Evolution
Core Concepts
24.1 Anatomical, molecular, and
fossil evidence shows that the
human lineage branches off the
great apes tree.
24.2 Phylogenetic analysis of
mitochondrial DNA and the Y
chromosome shows that our
species arose in Africa.
24.3 During the 5–7 million
years since the most recent
common ancestor of humans
and chimpanzees, our
lineage acquired a number of
distinctive features.
24.4 Human history has had an
important impact on patterns
of genetic variation in our
species.
24.5 Culture is a potent force for
change in modern humans.
Brad Wilson/ Getty Images.
485
486 SECTION 24.1 T H E G R E AT A P E S
Charles Darwin carefully avoided discussing the evolution of our molecular analysis, and through the fossil record. In this section,
own species in On the Origin of Species. Instead, he wrote only we use data from all three sources as we apply the standard
that he saw “open fields for far more important researches,” and methods of phylogenetic reconstruction (Chapter 23) to figure
that “[l]ight will be thrown on the origin of man and his history.” out the evolutionary relationships between humans and other
Darwin, an instinctively cautious man, realized that the ideas mammals.
presented in On the Origin of Species were controversial enough
without his adding humans to the mix. He presented his ideas on Comparative anatomy shows that the human lineage
human evolution to the public only when he published The Descent branches off the great apes tree.
of Man 12 years later, in 1871. There are about 400 species of primates, which include
As it turned out, Darwin’s delicate sidestepping of human prosimians (lemurs, bushbabies), monkeys, and apes (Fig. 24.1).
origins had little effect. The initial print run of The Origin sold out All primates share a number of general features that distinguish
on the day of publication, and the public was perfectly capable them from other mammals: nails rather than claws together
of reading between the lines. The Victorians found themselves with a versatile thumb allow objects to be manipulated more
wrestling with the book’s revolutionary message: that humans are dexterously, and eyes on the front of the face instead of the side
a species of ape. allow stereoscopic (three-dimensional) vision.
Darwin’s conclusions remain controversial to this day among Prosimians are thought to represent a separate primate group
the general public, but they are not controversial among scientists. from the one that gave rise to humans. Lemurs, which today
The evidence that humans are descended from a line of apes whose are confined to the island of Madagascar, are thus only distantly
modern-day representatives include gorillas and chimpanzees is related to humans. Monkeys underwent independent bouts of
compelling. We know now that about 5–7 million years ago the evolutionary change in the Americas and in Africa and Eurasia, so
family tree of the great apes split, one branch ultimately giving the family tree is split along geographic lines into New World and
rise to chimpanzees and the other to our species. It is those Old World monkeys. Though both groups have evolved similar
5–7 million years that hold the key to our humanity. It was over habits, there are basic distinctions. There are differences between
this period—brief by evolutionary standards—that the attributes the teeth of the two groups, and in New World monkeys the
that make our species so remarkable arose. This chapter discusses nostrils tend to be widely spaced, whereas in Old World species
what happened over those 5–7 million years and how we came to they are closer together.
be the way we are. One line of Old World monkeys gave rise to the apes, which
lack a tail and show more sophisticated behaviors than other
monkeys. The apes are split into two groups, the lesser and the
24.1 THE GREAT APES great apes (Fig. 24.2). Lesser apes include the fourteen species
of gibbon, all of which are found in Southeast Asia. The great
We can approach the question of our place in the tree of life in apes include orangutans, gorillas, chimpanzees, and humans.
three different ways: through comparative anatomy, through Taxonomists classify all the descendants of a specified common
FIG. 24.1 The primate family tree. This tree shows the evolutionary relationships of prosimians, monkeys, and apes. Sources: (left to right) George
Holton/Science Source; Penelope Dearman/Getty Images; Daily Mail/Rex/Alamy; Patrick Shyu/Getty Images; Yellow Dog Productions/Getty Images.
Prosimians: Bushbabies and lemurs New World monkeys Old World monkeys Apes
Tail loss
Opposable thumb
Eyes located at front
of face enable better
depth perception.
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 487
FIG. 24.2 The family tree of the lesser and great apes. The apes consist of two major groups, the lesser apes and great apes. The great apes
group includes humans. Sources: (left to right) Zoonar/K. Jorgensen/age fotostock; S Sailer/A Sailer/age fotostock; J & C Sohns/age fotostock; Michael Dick/
Animals Animals–Earth Scenes; FLPA/Jurgen & Christi/age fotostock; Yellow Dog Productions/Getty Images.
Delayed puberty
Earlobes
Lesser apes
Great apes
ancestor as belonging to a monophyletic group (Chapter 23). Just how closely are humans and chimpanzees related?
Thus, humans, blue whales, and hedgehogs are all mammals To answer this question, we need to know the timing of the
because all three are descended from the first mammal, the evolutionary split that led to chimpanzees along one fork and to
original common ancestor of all mammals. Because human humans along the other. As we saw in Chapter 21, DNA sequence
ancestry can be traced to the common ancestor of orangutans, differences accumulate between isolated populations or species,
gorillas, and chimpanzees, humans, too, are a member of the and they do so at a more or less constant rate. As a result, the
monophyletic great ape group. extent of sequence difference between two species is a good
indication of the amount of time they have been separate, that is,
Molecular analysis reveals that the human lineage the amount of time since their last common ancestor.
split from the chimpanzee lineage about 5–7 million The first thorough comparison of DNA molecules between
years ago. humans and chimpanzees was carried out before the advent of
Which great ape is most closely related to humans? That is, which DNA sequencing methods by Mary-Claire King and Allan Wilson
is our sister group? Traditional approaches of reconstructing at the University of California at Berkeley (Fig. 24.3). One of
evolutionary history by comparing anatomical features failed to their methods of measuring molecular differences between
determine which of two candidates, gorillas or chimpanzees, is species relied on DNA–DNA hybridization (Chapter 12). Two
the sister group to humans. It was only with the introduction complementary strands of DNA in a double helix can be separated
of molecular methods of assessing evolutionary relationships— by heating the sample. If the two strands are not perfectly
through the comparison of DNA and amino acid sequences from the complementary, as is the case if there is a base-pair mismatch (for
different species—that we had the answer. Our closest relative is example, a G paired with a T rather than with a C), less heat is
the chimpanzee (Fig. 24.2), or, more accurately, the chimpanzees, required to separate the strands.
plural, because there are two closely related chimpanzee species, King and Wilson used this observation to examine the
the smaller of which is often called the bonobo. differences between a human strand and the corresponding
H
4 8O
8W DT O
SEC I O NW
2 2 .E
1 K
THNE O W
BIO LO?
G I C A L S P E C I E S CO N C E P T
488
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 489
FIG. 24.6 Hominin lineages. Three main lineages, Ardipithecus, Australopithecus, and Homo existed at various and sometimes overlapping times
in history. The Homo lineage led to modern humans, Homo sapiens. Sources: Data from R. G. Klein, 2009, The Human Career, Chicago: University of
Chicago Press, p. 244; Homo floresiensis skull from R. D. Martin, A. M. MacLarnon, J. L. Phillips, L. Dussubieux, P. R. Williams and W. B. Dobyns, 2006, Comment on
“The Brain of LB1, Homo floresiensis,” Science 312:999.
garhi Paranthropus
Australopithecus
africanus aethiopicus
p
3
Kenyanthropus Lucy Ardi and
platyops Australopithecus Lucy are
afarensis especially
complete
fossils.
4
Australopithecus
anamensis
Ardi
Ardipithecus
ramidus
5
Ardipithecus
kadabba
Sahelanthropus
tchadensis
6
Orrorin Fossil material
tugenensis
Inferred relationships
among forms
7
Remarkably, there were many different hominin species living The earliest hominin fossils found in Asia are about 2 million years
in Africa at the same time. Fig. 24.6 shows the main hominin old, indicating that at least one group of hominins ventured out of
species and the longevity of each in the fossil record, along with Africa then. The individuals that first left Africa were members of a
suggested evolutionary relationships among the species. Note that species that is sometimes called Homo ergaster and sometimes Homo
all hominins have a common ancestor, but not all of these groups erectus. The confusion stems from the controversies that surround the
lead to modern humans, producing instead other branches of the naming of fossil species. Some researchers contend that H. ergaster
hominin tree that ultimately went extinct. is merely an early form of H. erectus. Here, we designate this first
A number of trends can be seen when we look over the entire hominin Homo ergaster and a later descendant species H. erectus (see
record. Body size increased. Most striking is the increase in size Fig. 24.6). The naming details, however, are relatively unimportant.
of the cranium and therefore, by inference, of the brain, as shown What matters is that some hominins first colonized areas beyond
in Fig. 24.7. Africa about 2 million years ago.
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 491
this event was unclear. Can all modern humans, Homo sapiens,
FIG. 24.7 Increase in brain size (as inferred from fossil cranium date their ancestry to early hominins in Africa that migrated
volume) over 3 million years. Data from T. Deacon, “The out and spread around the world about 2 million years ago? Or
Human Brain,” pp. 115–123, in J. Jones, R. Martin, and D. Pilbeam did the groups that left Africa ultimately go extinct, so that
(eds.), 1992, The Cambridge Encyclopedia of Human Evolution, modern humans evolved from a group of hominins in Africa that
Cambridge, England: Cambridge University Press. migrated out much more recently? Molecular studies helped to
answer this question.
Some of the increase in brain size is due to
increase in body size, but brain size increased
in hominins much faster than body size. Studies of mitochondrial DNA reveal that modern
humans evolved in Africa relatively recently.
Homo sapiens
2000 For a long time, it was argued that modern humans derive
from the Homo ergaster (or H. erectus) populations that spread
Homo erectus
Estimated brain volume (mL)
around the world starting from around the time of the early
1500
Homo habilis emigration from Africa 2 million years ago. This idea is called the
multiregional hypothesis of human origins because it implies
Australopithecus that different Homo ergaster populations throughout Africa
1000
and Eurasia evolved in parallel, with some limited gene flow
among them, each producing modern H. sapiens populations. In
Each point
500 denotes a short, racial differences among humans would have evolved over
measured 2 million years in different geographic locations.
individual.
This idea was overturned in 1987 by another study from
0
3 2 1 0 Allan Wilson’s laboratory, which instead suggested that
Millions of years ago modern humans arose much more recently from Homo ergaster
descendants that remained in Africa (sometimes called Homo
heidelbergensis; see Fig 24.6), and are all descended from an
Another hominin species was Homo neanderthalensis, whose African common ancestor dating from around 200,000 years
fossils appear in Europe and the Middle East. Neanderthals ago. This newer idea is the out-of-Africa hypothesis of human
represent a second hominin exodus from Africa dating from origins.
around 600,000 years ago. Thicker boned than us, and with flatter To test these two hypotheses about human origins, Rebecca
heads that contained brains about the same size as, or slightly Cann, a student in Allan Wilson’s laboratory, analyzed DNA
larger than, ours, Neanderthals disappeared around 30,000 sequences to reconstruct the human family tree. Specifically,
years ago. As we will see, genetic analysis suggests that this she studied sequences of a segment of mitochondrial DNA from
group likely interbred with our own group, Homo sapiens, so this people living around the world (Fig. 24.8).
disappearance was perhaps not as complete as the fossil record Mitochondrial DNA (mtDNA) is a small circle of DNA,
suggests. about 17,000 base pairs long, found in every mitochondrion
Another hominin species became extinct only about (Chapter 17). Cann chose to study mtDNA for several reasons.
12,000 years ago. This was H. floresiensis, known popularly as Although a typical cell contains a single nucleus with just two
the Hobbit. H. floresiensis is peculiar. Limited to the Indonesian copies of nuclear DNA, each cell has many mitochondria, each
island of Flores, adults were only just over 3 feet tall. Some have carrying multiple copies of mtDNA, making mtDNA much
suggested that H. floresiensis is not a genuinely distinct species, more abundant than nuclear DNA and therefore easier to
but, rather, is an aberrant H. sapiens. Plenty of morphological extract. More important, however, is its mode of inheritance.
evidence, however, suggests that H. floresiensis is a distinct All your mtDNA is inherited from your mother in the egg she
species derived from an archaic Homo species, probably H. erectus. produces because sperm do not contribute mitochondria to
Mammals often evolve small body size on islands because of the the zygote. This means that there is no opportunity for genetic
limited availability of food. recombination between different mtDNA molecules, so the
only way in which sequence variation can arise is through
mutation. In nuclear DNA, by contrast, differences between
24.2 AFRICAN ORIGINS two sequences can be introduced through both mutation
and recombination. Recombination obscures genealogical
From the wealth of fossil evidence, it’s clear that modern relationships because it mixes segments of DNA with different
humans first evolved in Africa. But for a while the timing of evolutionary histories.
HOW DO WE KNOW?
FIG. 24.8
HYPOTHESIS The multiregional hypothesis of human origins suggests that our most recent common ancestor was living at the time
Homo ergaster populations first left Africa, about 2 million years ago.
METHOD Rebecca Cann compared mitochondrial DNA (mtDNA) sequences from 147 people from around the world. This approach
required a substantial amount of mtDNA from each individual, which she acquired by collecting placentas from women after
childbirth. Instead of sequencing the mtDNA, Cann inferred differences among sequences by digesting the mtDNA with different
restriction enzymes, each of which cuts DNA at a specific sequence (Chapter 12). If the sequence is present, the enzyme cuts. If any
base in the recognition site of the restriction enzyme has changed in an individual, the enzyme does not cut. The resulting fragments
were then separated by gel electrophoresis. By using 12 different enzymes, Cann was able to assay a reasonable proportion of all the
mtDNA sequence variation present in the sample.
Here, we see a sample dataset for four people and a chimpanzee. There are seven varying restriction sites:
mtDNA (Japan)
mtDNA (Chimpanzee)
ANALYSIS The data were converted into a family tree by using shared derived characters, described in Chapter 23. By mapping
the pattern of changes in this way, the phylogenetic relationships of the mtDNA sequences can be reconstructed. For example, the
derived “cut” state at restriction site 1 shared by the East African, Japanese, and Native American sequences implies that the three
groups had a common ancestor in which the mutation that created the new restriction site occurred.
Mitochondrial DNA sequences offered Cann a clear advantage. time—are African. All non-Africans are branches off the African
With sequence information from the mtDNA of 147 people from tree. The implication is that Homo sapiens evolved in Africa and
around the world, Cann reconstructed the human family tree only afterward did populations migrate out of Africa and become
(Fig. 24.8). The tree contained two major surprises. First, the two established elsewhere. This finding contradicted the expectations
deepest branches—the ones that come off the tree earliest in of the multiregional theory, which predicted that Homo sapiens
492
Chimpanzee S. Africa E. Africa Japan Native American
1 2 345 67 1 2 345 67 1 2 34 5 67 1 2 345 67 1 2 345 67
Loss of Gain of
6 7
Loss of
3 Gain of
5 Both Japanese and Native
Gain of American sequences share
2 the gain of restriction site
Gain of 5, implying that the site
1 gain occurred in their
common ancestor.
Loss of
4 Most recent common
ancestor of the four human
sequences analyzed.
Ancestral
The chimpanzee is the 1 2 345 67
phylogenetic outlier
because its common
ancestor with the rest
of the group is the
oldest node on the RESULTS AND CONCLUSION A simplified version of Cann’s phylogenetic tree based on mtDNA is
tree. We can thus treat
it as an outgroup and shown below. Modern humans arose relatively recently in Africa, and their most common ancestor lived
assume that its about 200,000 years ago. The multiregional hypothesis is rejected. Also, the data revealed that all non-
sequence represents Africans derive from within the African family tree, implying that H. sapiens left Africa relatively recently.
the ancestral state.
The Cann study gave rise to the out-of-Africa theory of human origins.
Present
Chimpanzee African Non-African African
The common
ancestor of all
living humans
Past
FOLLOW-UP WORK This study set the stage for an explosion in genetic studies of human prehistory
that used the same approach of comparing sequences in order to identify migration patterns. Today, with
molecular tools vastly more powerful than those available to Cann, studies of the distribution of genetic
variation are giving us a detailed pattern, even on relatively local scales, of demographic events.
SOURCE Cann, R. L., M. Stoneking, and A. C. Wilson. 1987. “Mitochondrial DNA and Human Evolution.” Nature 325:31–36.
evolved independently in different locations throughout the occur in mtDNA, Cann was able to estimate the time back to the
Old World. common ancestor of all modern humans as about 200,000 years.
Second, the tree is remarkably shallow. That is, even the Subsequent analyses have somewhat refined this estimate, but the
most distantly related modern humans have a relatively recent key message has not changed: The data contradict the multiregional
common ancestor. By calibrating the rate at which mutations hypothesis, which predicted a number closer to 2 million years.
493
494 SECTION 24.2 AFRICAN ORIGINS
FIG. 24.10 Evidence for and against early interbreeding between 24.3 DISTINCT FEATURES
Neanderthals and early humans. (a) Studies using only OF OUR SPECIES
mtDNA did not support the idea of interbreeding, but
(b) later studies using whole genomes did. Many extraordinary changes in anatomy and behavior occurred
in the 5–7 million years since our lineage split from the lineage
a. mtDNA phylogeny for Neanderthals and modern humans that gave rise to the chimpanzees. Fossils tell us a great deal about
Homo sapiens those changes, especially when high-quality material such as Lucy
or Ardi is available, but in general this is an area in which fossils
Chimpanzee Neanderthal African Non-African African
are hard to come by and there is a lot of speculation. Speculation
Because is especially common when we try to explain the reasons behind
Neanderthal
mtDNA does not the evolution of a particular trait. Why, for example, did language
fall within the evolve? It is easy enough to think of a scenario in which natural
human family tree
(red), we initially selection favors some ability to communicate—maybe language
believed that arose to facilitate group hunting. There are plenty of plausible
Neanderthals and ideas on the subject, but, in most cases, no evidence, so it is
our ancestors did
not interbreed. impossible to distinguish among competing hypotheses. We can,
b. however, be confident that the events that produced language
occurred in Africa, and, through paleontological studies of past
environments, we can conclude that humans evolved in an
Asia environment similar in many ways to today’s East African savanna.
that natural selection acted in favor of. What are the selective
FIG. 24.12 A juvenile and an adult orangutan. Humans look more factors? Here are some possibilities:
like juvenile orangutans than like adult orangutans,
suggesting that humans may be neotenous great apes. • Tool use. Bipedalism permitted the evolution of manual
Sources: (top to bottom) McPHOTO/W. Layer/age fotostock; Russell
dexterity, which in turn requires a complex nervous
Watkins/Shutterstock.
organization if hands are to be useful.
FIG. 24.13 Brain size plotted against body size for different
species. Humans have large brains for their body size.
Data from Fig. 2.4, p. 44, in H. J. Jerison, 1973, Evolution of the Brain
and Intelligence, New York: Academic Press.
10,000 Elephant
5000 Blue
Human
Whale
1000 Chimpanzee
500 Australopithecus Male gorilla
Baboon Lion
100 Sting ray Tiger shark
Brain weight (g)
50 Ostrich
Wolf
Crow
10
are large even for our body size (Fig. 24.13). It is our large 5 Opossum Ostriches are the
brains that have allowed our species’ success, extraordinary Vampire bat most divergent
1 Rat
species below the
technological achievements, and at times destructive dominion 0.50 Mole line (with
over the planet. disproportionately
0.10 small brains).
What factors acted as selective pressure for the evolution 0.05 Goldfish
of the large human brain? Again, speculation is common, but
0.01
because a large brain is metabolically expensive to produce and to 0.001 0.01 0.1 1 10 100 1000 10,000 100,000
maintain, we can conclude that the brain has adaptive features Body weight (kg)
498 SECTION 24.4 H U M A N G E N E T I C VA R I AT I O N
3 billion base pairs, so 0.1% variation means that 3 million bp Middle East (Fig. 24.15). The first phase of colonization took our
differ between any two people chosen at random. Many of those ancestors through Asia and into Australia by about 50,000 years
differences are in noncoding DNA, but some fall in regions of ago. Archaeological evidence indicates that it was not until about
DNA that encode proteins and therefore influence the phenotype. 15,000 years ago that the first modern humans crossed from
When those mutations are reshuffled by recombination, we get Siberia to North America to populate the New World.
the vast array of genetic combinations present in the human Genetic analyses also indicate that other colonizations
population. were even later. Despite its closeness to the African mainland,
the first humans arrived in Madagascar only about 2000 years
The prehistory of our species has had an impact on the ago, and the colonists came from Southeast Asia, not Africa.
distribution of genetic variation. Madagascar populations to this day bear the genetic imprint of
The reasons for our species’ relative lack of genetic variation this surprising Asian input. The Pacific Islands were among the last
compared to other species lie in prehistory, and factors affecting habitable places on Earth to be colonized during the Polynesians’
the geographical distribution of that variation also lie in the past. extraordinary seaborne odyssey from Samoa, which began about
Studies of the human family tree initiated by Rebecca Cann’s 2000 years ago. Hawaii was colonized about 1500 years ago, and
original mtDNA analysis are giving a detailed picture of how our New Zealand only 1000 years ago.
ancestors colonized the planet and how that process affected By evolutionary standards, the beginning of the spread
the distribution of genetic variation across populations today. of modern humans out of Africa about 60,000 years ago is
Detailed analyses of different populations, often using mtDNA very recent. There has therefore been relatively little time for
or Y chromosomes, allow us to reconstruct the history of human differences to accumulate among regional populations, and most
population movements. of the variation in human populations today arose in ancestral
As we have seen, Homo sapiens arose in Africa. Genetic populations before any humans left Africa. When we compare
analyses indicate that perhaps 60,000 years ago, populations levels of variation in a contemporary African population with
started to venture out through the Horn of Africa and into the that in a non-African population, like Europeans or Asians, we
FIG. 24.15 Human migratory routes. Tracking the spread of mitochondrial DNA mutations around the globe allows us to reconstruct the
colonization history of our species. Data from Fig. 6.18, p. 149, in D. J. Futuyma, 2009, Evolution, 2nd ed., Sunderland, MA: Sinauer Associates.
Migratory route 1
(60,000–45,000 years ago)
Migratory route 2
(30,000–20,000 years ago)
Migratory route 3
(15,000?–10,000 years ago)
Migratory route 4
After Homo sapiens evolved in Africa, (<10,000 years ago)
groups moved out, beginning the
colonization of the rest of the planet.
500 SECTION 24.4 H U M A N G E N E T I C VA R I AT I O N
find there is more variation in the African population. This is variants, for example, are subject to genetic drift, and, given the
because the individuals that left Africa 60,000 years ago to found stepwise global colonization history of our species, it is likely that
populations in the Middle East and beyond were a relatively small founder events have played a role as well.
sample of the total amount of genetic variation then present in Selection, too, has been important. It is apparent, for example,
the human population. Non-African populations therefore began that the genetic variants affecting traits we can easily see are an
with less genetic variation, and that initial lower variation is especially prominent feature of the 7% of human genetic variation
reflected in their genetic profiles today. that occurs between so-called races. If we look at other genetic
variants, ones that don’t affect traits that we can see, there is little
The recent spread of modern humans means that there or no racial pattern. An African is as likely to have a particular
are few genetic differences between groups. base-pair mutation in a randomly chosen gene as a European. So
Because the out-of-Africa migration was so recent, the genetic why are visible traits so markedly different among races and other
differences we see among geographical groups—sometimes called traits are not? Given the short amount of time (by evolutionary
races—are minor. This fact is highly counterintuitive. We see standards) since all Homo sapiens were in Africa, it is likely that the
many superficial differences between an African and a Caucasian, differences we see between groups are the product of selection.
such as skin color, facial form, and hair type, and assume that these People with dark skin tend to originate from areas in lower
superficial differences must reflect extensive genetic differences. latitudes with high levels of solar radiation, and people with light
This assumption made sense when the standard theory about the skin tend to originate from areas in higher latitudes with low levels
origin of modern humans was the multiregional one. If European of solar radiation. It is likely that natural selection is responsible
and African populations really had been geographically isolated for the physical differences between these populations. Assuming
from each other for as long as 2 million years, then we would that the ancestors of non-African populations were relatively
expect significant genetic differences among populations. dark-skinned, what selective factors can account for the loss of
We expect isolated populations to diverge genetically over pigmentation?
time as different mutations occur and are fixed in each population. A likely factor is an essential vitamin, vitamin D, which is
The longer two populations have been isolated from each other, particularly important in childhood because it is needed for the
the more genetic differences between them we expect to see production of bone. A deficiency of vitamin D can result in the
(Chapter 21). Isolation lasting 2 million years implies that the skeletal malformation known as rickets. The body can synthesize
differences are extensive, but isolation of just 60,000 years vitamin D, but the process requires ultraviolet radiation. Heavily
suggests they are relatively few. Patterns of genetic variation pigmented skin limits the entry of UV radiation into cells and
among different human populations support the hypothesis that so limits the production of vitamin D. This does not present a
human populations dispersed as recently as 60,000 years ago. difficulty in parts of the world where there is plenty of sunlight,
What we see when we look at genetic markers—variable A’s, T’s, but it can be problematic in regions of low sunlight. Presumably,
G’s, and C’s in human DNA—is that there is indeed very little natural selection favored lighter skin in the ancestors of Eurasian
genetic differentiation by what is sometimes called race. populations because lighter skin promoted the production of
In short, there’s a disconnect: Different groups may look the vitamin.
very different, but, from a genetic perspective, they’re not very Some aspects of body shape and size may also have been
different at all. Any two humans may differ from each other by, influenced by natural selection. In hot climates, where dissipating
on average, only 3 million base pairs, and statistical analyses have body heat is a priority, a tall and skinny body form has evolved.
shown that approximately 85% of that genetic variation occurs Exemplified by East African Masai, this body type maximizes the
within a population (for example, the Yoruba in West Africa); 8% ratio of surface area to volume and thus aids heat loss. In colder
occurs between populations within races (for example, between climates, by contrast, selection has favored a more robust, stockier
Yoruba and Kikuyu, another African group); and the remaining 7% body form, as exemplified by the Inuit, who have a low ratio
occurs between races. The characteristics we use when we assess of surface area to volume that promotes the retention of heat
an individual’s ethnicity, such as skin color, eye type, and hair (Fig. 24.16). In these two cases, these are plausible explanations
form, are encoded by genetic variants that lie in that 7%. If Earth of body form. We should bear in mind, however, that simple one-
were threatened with destruction and only one population— size-fits-all explanations of human difference are almost always
Yoruba, for example—survived, 85% of the total amount of too simplistic. Our species is complex and diverse and often defies
human genetic variation that exists today would still be present in generalizations.
that population. Attempts have been made to identify the adaptive value
of visual differences between races, such as facial features. It’s
Some human differences have likely arisen by natural possible that natural selection played a role in the evolution of
selection. these differences, but an alternative explanation, one originally
Patterns of genetic variation in human populations are shaped suggested by Charles Darwin, is more compelling: sexual selection
by the set of evolutionary forces discussed in Chapter 21. Neutral (Chapters 21 and 45).
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 501
FIG. 24.16 Evolutionary responses of body shape to climate. (a) A heat-adapted Masai in Kenya and (b) a cold-adapted Inuit in Greenland.
Sources: a. Ryan Heffernan/Aurora/Getty Images; b. B&C Alexander/ArcticPhoto.
a b
As we have seen, there is an apparent mismatch between the Homozygotes for the allele encoding normal hemoglobin are also
extent of difference among groups in visible characters, such as at a disadvantage because they are entirely unprotected from the
facial features, and the overall level of genetic difference between parasite.
human groups. Sexual selection can account for this mismatch The S allele is beneficial only in the presence of malaria. If
because it operates solely on characteristics that can readily be there is no malaria in an area, the S allele is disadvantageous, so
seen—think of the peacock’s tail. As we learn more about the natural selection presumably acted rapidly to eliminate it in the
genetic underpinnings of the traits in question, we will be able to ancestors of Europeans when they arrived in malaria-free regions.
investigate directly the factors responsible for the differences we The continued high frequency of the S allele in Africans, some
see among groups. Mediterranean populations, and in populations descended recently
from Africans (such as African-Americans) is, however, a reflection
? CASE 4 MALARIA: CO-EVOLUTION OF HUMANS AND of the response of natural selection to a regional disease.
A PARASITE The hemoglobin genes are not the only genes that are
What human genes are under selection for resistance under selection for resistance to malaria. Glucose-6-phosphate
to malaria? dehydrogenase (G6PD), a gene involved in glucose metabolism,
We see evidence of regional genetic variation in response to is one of several other genes implicated. People who are
local challenges, especially those posed by disease. Malaria, heterozygotes for a mutation in the G6PD gene—and therefore
for example, is largely limited to warm climates because it is have a G6PD enzyme deficiency—can develop severe anemia
transmitted by a species of mosquito that can survive only in when they eat certain foods (most notably fava beans; hence,
these regions. Historically, the disease has been devastating the condition is called favism). People who are heterozygotes
in Africa and the Mediterranean. As we saw in Chapter 21, the for a mutation in the G6PD gene, however, also have increased
sickle allele of hemoglobin, S, has evolved to be present at high resistance to malaria, apparently because they are better at
frequencies in these regions because in heterozygotes it confers clearing infected red blood cells from their bloodstream. In areas
some protection against the disease. But in homozygotes, the S where malaria is common, the advantage of malaria resistance
allele is highly detrimental because it causes sickle-cell anemia. offsets the disadvantage of favism.
502 SECTION 24.5 C U LT U R E , L A N G UAG E , A N D CO N S C I O U S N E S S
Detailed evolutionary analysis of mutations in G6PD shows extraordinarily inhospitable parts of the planet, like the Arctic
that favism has arisen multiple times, each time selectively (Fig. 24.17). The capacity to innovate coupled with the ability to
favored because of its role in the body’s response to the malaria transmit culture is the key to the success of humans.
parasite. As expected, favism, like sickle-cell anemia, is mainly a Culture, of course, changes over time. In many ways, cultural
feature of populations in malarial areas or of populations whose change is responsible for our species’ extraordinary achievements.
evolutionary roots lie in these areas. Genetic evolution is slow because it involves mutation followed
by changes in allele frequencies that take place over many
generations. Cultural change, on the other hand, can occur much
24.5 CULTURE, LANGUAGE, more rapidly. Ten years ago, nobody had heard of smartphones,
AND CONSCIOUSNESS but today, millions of people own them. Or think of the speed at
which a change in clothing style—a shift from flared to straight-
The most remarkable outcome of the evolutionary process leg jeans, for example—spreads through a population. Today’s
described in this chapter is the human brain. This allows us to do human population as a whole is genetically almost identical to the
extraordinary things, like appreciate Bach’s music, read books, population when your grandparents were young. But think of the
and build skyscrapers. But does this wonderful brain make us cultural changes that have occurred in the 50 years or so between
qualitatively different from other organisms? Does it in some way your grandparents’ youth and your own.
take us out of nature? Traditionally, the answer to these questions Despite this clear contrast between biological evolution
would have been a resounding yes. However, research into the and cultural change, we should not necessarily think of the two
capabilities of other species is questioning this conclusion: The processes as independent of each other. Sometimes cultural
human brain is certainly remarkable, but, in essence, what we can change drives biological evolution.
do is merely an extension of what other animals can do. A good example of the interaction between cultural change
and biological evolution is the evolution of lactose tolerance in
Culture changes rapidly. populations for which domesticated animals became an important
Culture is generally defined as a body of learned behavior that is source of dairy product. Most humans are lactose intolerant.
socially transmitted among individuals and passed down from Lactose, a sugar, is a major component of mammalian milk,
one generation to the next. Culture has permitted us in part to including human breast milk. We have an enzyme, lactase, that
transcend our biological limits. To take a simple example, clothing breaks down lactose in the gut, but, typically, the enzyme is
and ingeniously constructed shelters have enabled us to live in produced only in the first years of life, when we are breast-feeding.
Once a child is weaned, lactase production
is turned off. Lactase, however, is clearly a
useful enzyme to have if there is a major
FIG. 24.17 The power of culture. Inventions (such as clothing) have allowed our species to dairy component to your diet.
expand its geographic range. Source: B&C Alexander/ArcticPhoto. Archaeological and genetic analyses
indicate that cattle were domesticated
probably three separate times in the past
10,000 years, in three separate places: in
the Middle East, in East Africa, and in the
Indus Valley. In at least two of these cases,
there has been subsequent human biological
evolution in favor of lactose tolerance, that
is, continued lactase production throughout
life. Analysis of the gene region involved in
switching lactase production on and off has
revealed mutations in European lactose-
tolerant people that are different from those
in African lactose-tolerant people, implying
independent, convergent evolution of this
trait in the two populations. Furthermore, we
see evidence that these changes have evolved
very recently, implying that they arose as
a response to the domestication of cattle.
Here, we see the interaction between cultural
change and biological evolution. Biological
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 503
FIG. 24.18 Nonhuman culture. (a) English blue tits steal cream from a milk bottle on the doorstep. (b) Adult meerkats teach their young how to
handle their prey. (c) Chimpanzees in different populations have devised different ways of using tools to hunt insects. Sources: a. Colin F.
Sargent; b. Dr. Alex Thornton, University of Exeter; c. FLPA/Peter Davey/age fotostock.
a b c
evolution of continued lactase production has resulted from the transmission all benefit from another extraordinary human
change in a cultural practice, namely cattle domestication. attribute, language.
FIG. 24.19 Dr. Susan Savage Rumbaugh with Panbanisha, a female bonobo who learned to
communicate using sign language. Chimpanzees and bonobos are able to learn and
use sign language to express words and simple sentences. Source: Anna Clopet/CORBIS.
of the animal rights movement, particularly in reference to the considerable trouble to bend a hook into the straight wire. She
treatment of animals in factory farms, this question is of more succeeded in getting the food. It is difficult to deny that the crow
than academic interest. We now have many examples of animal thought about the problem and was able to solve it, perhaps in the
thinking from a range of species, including, not surprisingly, same way as we would. Definitions of consciousness are contested,
chimpanzees and gorillas. but, as with language and culture, it seems clear that other species
Perhaps more remarkable are the examples that come from are capable of some form of conscious thought.
animal species that are not closely related to us. In experiments The evolutionary biologist Theodosius Dobzhansky once
carried out by Alex Kacelnik in Oxford, England, a pair of New said, “All species are unique, but humans are uniquest.” Our
Caledonian Crows was presented with two pieces of wire, one “uniquest” status is not derived from having attributes absent in
straight and the other hooked, and offered a food reward that other species, but from the extent to which those attributes are
could be obtained only by using the hooked wire. One member of developed in us. Human language, culture, and consciousness are
the pair, the male, disregarded the experiment and flew off with extraordinary products of our extraordinary brains. Nevertheless,
the hooked wire. The female, however, having discovered that she as Darwin taught us and as we should never forget, we are fully a
could not get the food reward with the straight wire, went to some part of the natural world.•
Core Concepts Summary The great apes include orangutans, gorillas, chimpanzees, and
humans. page 487
24.1 Anatomical, molecular, and fossil evidence shows Analysis of sequence differences between humans and our
that the human lineage branches off the great apes tree. closest relatives, chimpanzees, indicate that our lineage split
from chimpanzees 5–7 million years ago. page 487
Anatomical features indicate that primates are a
monophyletic group that includes prosimians, monkeys, and Lucy, an unusually complete specimen of Australopithecus
apes. The apes in turn include the lesser and great apes. afarensis, demonstrates that our ancestors were bipedal by
page 486 about 3.2 million years ago. page 489
CHAPTER 24 H U M A N O R I G I N S A N D E VO L U T I O N 505
Hominin fossils occur only in Africa until about 2 million years Humans have very little genetic variation, with only about
ago, when Homo ergaster migrated out of Africa to colonize the 1 in every 1000 base pairs varying among individuals.
Old World. page 490 page 499
24.3 During the 5–7 million years since the most recent
common ancestor of humans and chimpanzees, our Self-Assessment
lineage acquired a number of distinctive features.
1. Describe the evidence suggesting that chimpanzees are the
The development of bipedalism involved a wholesale closest living relatives of humans.
restructuring of anatomy. page 495
2. Explain the out-of-Africa theory of human origins and
Neoteny is the process in which the timing of development how studies of mitochondrial DNA and the Y chromosome
is altered over evolution so that a sexually mature organism support it.
retains the physical characteristics of the juvenile form;
3. List four anatomical differences between chimpanzees
humans are neotenous, exhibiting many traits as adults that
and humans, and explain how these changes facilitated
chimpanzees exhibit as juveniles. page 496
walking upright.
There are many possible selective factors that explain the
4. Given the high genetic similarity of humans and
evolution of our large brain, including tool use, social living,
chimpanzees, how can we account for the differences we see
and language. page 497
between the two species?
FOXP2, a transcription factor involved in brain development,
5. Describe three possible selective factors underlying the
may be important in language, as mutations in the gene that
evolution of large brains in our ancestors.
encodes FOXP2 are implicated in speech pathologies.
page 498 6. Explain how differences among different human
populations arose by natural and sexual selection.
24.4 Human history has had an important impact on 7. Provide arguments for and against the idea that culture,
patterns of genetic variation in our species. language, and consciousness are uniquely human.
Because our ancestors left Africa very recently in
evolutionary terms, there has been little chance for genetic Log in to to check your answers to the Self-
differences to accumulate among geographically separated Assessment questions, and to access additional learning tools.
populations. page 499
Gallery Stock.
PA RT 2
FROM
ORGANISMS
TO THE
ENVIRONMENT
” From so simple a beginning
endless forms most beautiful
and most wonderful have been,
and are being, evolved.”
— CHARLES DARWIN
CHAPTER 25
Cycling Carbon
Core Concepts
25.1 Photosynthesis and respiration
are the key biochemical
pathways for the biological, or
short-term, carbon cycle.
25.2 Physical processes govern the
long-term carbon cycle.
25.3 The carbon cycle can help
us understand ecological
interactions and the evolution
of biological diversity.
509
510 SECTION 25.1 T H E S H O RT-T E R M C A R B O N C YC L E
Let’s imagine that we could tag a carbon atom at its moment of properties of environments. And it provides a basis for assessing the
origin and then follow its odyssey through time and space. Formed role that humans play in our environmental present and future.
in a nuclear blast furnace deep within an ancient star and then
ejected into space as the star died, our atom was eventually swept
up with other materials to form the Earth, a small planet orbiting 25.1 THE SHORT-TERM
the newer star we now call the sun. Volcanoes introduced our CARBON CYCLE
carbon atom into the early atmosphere as carbon dioxide (CO2),
and slowly, over millions of years, this CO2 reacted chemically with In 1958, American chemist Charles David Keeling began a novel
rocks, transferring the carbon to limestone that accumulated on program to monitor the atmosphere. At the time he began
the sea floor. Here, our atom sat for many millions of years, until his study, scientists had only a vague notion of how carbon
earthquakes, erosion, or other geologic activities returned it to dioxide (CO2) behaves in air. Many thought that CO2 might
the atmosphere as, once again, CO2. Slowly but surely, geologic vary unpredictably from time to time, and from place to place.
processes on the early Earth cycled carbon from atmosphere to Keeling decided to find out if in fact it did. From five towers
rocks, and back again. set high on Mauna Loa in Hawaii, 3400 m above sea level, he
Sometime between 4 and 3.5 billion years ago, our carbon sampled the atmosphere every hour and measured its composition
atom began to cycle more rapidly—much more rapidly—as the with an infrared gas analyzer. Within the first few years of his
carbon cycle gained new players. Photosynthetic microorganisms project, a pattern of seasonal oscillation became apparent: CO2
converted CO2 into organic molecules, and respiring concentration in the air reached its annual high point in spring
microorganisms returned CO2 to the environment, completing and then declined by about 6 parts per million (ppm, by volume)
a rapid biological carbon cycle. To this day, the biological carbon to a minimum in early fall (Fig. 25.1). Such regular variation was
cycle endlessly propels our atomic wayfarer from atmosphere and unexpected: What could be causing it?
oceans to cells and back again, while the slow burial of organic Perhaps the pattern was local. Airplane traffic to Hawaii peaked
matter and limestone in sedimentary rocks continues to bring in winter, and maybe that was affecting the air around Mauna
carbon atoms to the solid Earth, returning it to the atmosphere Loa. As measurements continued through a number of years,
only slowly, on geologic timescales. however, the pattern persisted, even as trends in air traffic changed.
In Part 1, we explored the molecular and cellular basis Moreover, monitoring stations in many other parts of the globe gave
of life, culminating in a discussion of how genetic variation similar results. Knowing that the Mauna Loa measurements are
and natural selection shape evolution. Part 2 examines the representative of the atmosphere as a whole allows us to appreciate
products of evolution as it has played out through Earth history: what an annual variation of 6 ppm really means. With calendar-
our emerging sense of the immense biological diversity of Bacteria like regularity, approximately 47 billion metric tons of CO2 were
and Archaea; the myriad microscopic eukaryotes found in oceans, entering and leaving the atmosphere annually—that’s 13 billion
lakes and soils; and the millions of plant, fungal, and animal species metric tons of the element carbon (the rest of the mass is oxygen).
that define our biological landscape. As we will see, function To explain such a pattern, we must consider processes that affect
and diversity underpin the ecological interactions that shape the planet as a whole.
communities, ecosystems, and biomes across our planet. A second pattern is evident in Fig. 25.1. Summertime
We begin with an introduction to the carbon cycle, the removal of CO2 from the atmosphere does not quite balance
intricately linked network of biological and physical processes winter increase, with the result that the amount of CO2 in the
that shuttles carbon among rocks, soil, oceans, air, and organisms. atmosphere on any given date is greater than it was a year earlier.
Why start here? Because the carbon cycle provides a fundamental Atmospheric CO2 levels have therefore increased steadily through
organizing principle for understanding life on Earth. Indeed, it the period of monitoring. For example, mean annual CO2 levels,
lies at the heart of everything else we discuss in Part 2. The about 315 ppm in 1958, reached 404 ppm by late April 2015. This
chemistry of life is, to a first approximation, the chemistry of is an increase of more than 25%, and there is no indication that the
carbon. How organisms move carbon from one species to another, rise will slow or stop any time soon.
and between organisms and their surrounding environment, What causes atmospheric CO2 to vary through the year and
underpins both the efficient functioning of ecosystems and over a timescale of decades? To answer this question, we need to
their persistence over an immense span of time. In no small part, ask what processes introduce CO2 into the atmosphere and what
biological diversity can be understood in terms of the varied processes remove it. Carbon dioxide is added to the atmosphere
ways that organisms obtain the carbon needed for growth and by (1) geologic inputs, mainly from volcanoes and mid-ocean
reproduction. Much of ecology, in turn, concerns the ways that ridges; (2) biological inputs, especially respiration; and (3) human
organisms interact to cycle carbon and transfer the energy stored activities, including deforestation and the burning of fossil fuels.
in organic molecules. The carbon cycle focuses our attention on the Processes that remove CO2 from the atmosphere include
ways that physical and biological processes together determine the (1) geologic removal, especially by chemical weathering in which
CHAPTER 25 C YC L I N G C A R B O N 511
CO2 concentration
CO2 concentrations decreasing rapidly—it is rising. Moreover, the geologic record
regularly cycle up
and down over the indicates that photosynthesis has fueled ecosystems for billions of
course of a year. years without causing CO2 depletion.
What processes return CO2 to the atmosphere, balancing
photosynthetic removal? In Chapter 7, we discussed aerobic
respiration. Humans and many other organisms gain both the
Jan Apr Jul Oct Jan energy and carbon needed for growth from organic molecules
Month (that is, by consuming food). As explained in Chapter 7, aerobic
respiration uses oxygen to oxidize organic molecules to CO2,
400 converting chemical energy in the organic compounds to ATP for
use in cellular processes. Aerobic respiration can be summarized
390
by this chemical equation:
380
CO2 concentration (ppm)
Photosynthesis and respiration are key processes in FIG. 25.2 The short-term carbon cycle. The complementary
short-term carbon cycling. metabolic processes of photosynthesis and respiration
To grow, all organisms require both carbon and energy. As we drive the short-term cycling of carbon through the
saw in Chapter 8, photosynthetic organisms use energy from the biosphere.
sun to form ATP and NADPH, which reduce CO2 to carbohydrates.
As photosynthesis pulls CO2 out of the atmosphere (or water, for Photosynthesis Photosynthesis uses sunlight to
aquatic organisms), the carbon is transferred to carbohydrates, reduce CO2 to carbohydrates,
while oxidizing water to O2.
and oxygen is given off as a by-product. The overall chemical 6CO2 + 6H2O C6H12O6 + 6O2 Respiration runs the same
reaction is shown here: reaction in reverse. Together,
Respiration the processes form a cycle.
6CO2 1 6H2O → C6H12O6 1 6O2
512 SECTION 25.1 T H E S H O RT-T E R M C A R B O N C YC L E
HOW DO WE KNOW?
FIG. 25.3
290
270
1000 1200 1400 1600 1800 2000
Ice core drilled from a Viewed under the Year
glacier in Antarctica microscope, glacial ice Measurements of air samples in glacial ice from
contains small bubbles the Law Dome, Antarctica, show that atmospheric
that trap samples of air. CO2 varied little between 1000 and 1800.
Photo sources: (left) Courtesy of Ted Scambos & Rob
Bauer, National Snow and Ice Data Center, University
of Colorado, Boulder, (right) Courtesy Vin Morgan.
CONCLUSIONS Before the Industrial Revolution, atmospheric CO2 levels had varied little over 1000 years, generally falling between
270 and 280 ppm. From this, scientists have concluded that current changes in atmospheric CO2 are unusual on the timescale of the
past millennium.
SOURCE Etheridge, D. M., et al. 1996. “Natural and Anthropogenic Changes in Atmospheric CO2 over the Last 1000 Years from Air in Antarctic Ice and Firn.” Journal of
Geophysical Research 101:4115–4128.
The regular oscillation of CO2 reflects the a narrow band around the equator, photosynthesis is seasonal,
seasonality of photosynthesis in the Northern with higher rates in the summer and lower rates in the winter.
Hemisphere. Respiration, in contrast, remains more or less constant through
Now that we have identified the major processes in the short- the year.
term (days to decades) carbon cycle, we can examine what Even cursory examination of the Earth shows that land
makes atmospheric CO2 level oscillate seasonally. Except in is distributed asymmetrically, with more land—and hence
512
CHAPTER 25 C YC L I N G C A R B O N 513
more plants—in the Northern Hemisphere than in the Carbon isotopes show that much of the CO2 added
Southern Hemisphere. For this reason, global atmospheric to air over the past half century comes from burning
CO2 declines through the northern summer, when the ratio fossil fuels.
of photosynthesis to respiration is highest, and then increases We can test the hypothesis that human activities have
through fall and winter, when the ratio is reversed. The result is contributed to the increases in atmospheric CO2 measured at
the seasonal oscillation of atmospheric CO2 levels documented Mauna Loa and in ice cores by making careful measurements of
by Keeling. a chemical detail: the isotopic composition of atmospheric CO2.
In Chapter 2, we saw that many elements have several isotopes,
Human activities play an important role in the atoms of the element that vary in atomic mass because they
modern carbon cycle. have different numbers of neutrons. Carbon has three isotopes:
Now let us ask about the second major pattern evident in the 12
C (with six neutrons, about 99% of all carbon atoms); 13C (with
Keeling curve. Although CO2 levels oscillate on an annual basis, seven neutrons, most of the remaining 1%); and the rare 14C (with
the overall pattern is one of sustained increase. During the eight neutrons, about one part per trillion of atmospheric carbon).
1960s, the observed increase was less than 1 ppm each year. In More than 40 years ago, the Austrian-born chemist Hans
the first decade of the new millennium, it has been closer to Suess began to measure the relative abundances of the three
2 ppm. The current level of atmospheric CO2 is more than 25% isotopes of carbon in atmospheric CO2, a program that continues
higher than it was 50 years ago. Why has CO2 input into the today. He observed that the proportion of 13C in atmospheric
atmosphere outstripped removal for the past half century? CO2 has declined as the total amount of CO2 has increased
Should we consider this pattern unusual? (Fig. 25.4). This subtle change in isotopic composition has
Answering the second question helps us to address the first. occurred because the CO2 being added to the atmosphere has
Conclusions about whether it is unusual for atmospheric CO2 to less 13C than the CO2 already in the air.
increase 25% in 50 years can be answered only if we can compare How does this result influence the hypotheses we
the Keeling curve with longer records of atmospheric CO2 levels. developed to account for increasing atmospheric CO2 levels?
Before Keeling, no one systematically collected air samples. In photosynthesis, CO2 containing the lighter isotope 12C
Fortunately, however, nature did it for us. is incorporated into biomolecules preferentially over CO2
When glacial ice forms, it traps tiny bubbles of air. Each year, containing 13C, and for this reason organic matter generated by
snowfall gives rise to a new layer of ice, and as layers accumulate photosynthesis (and the organic matter of organisms that eat
through time their bubbles preserve a history of the atmosphere. photosynthetic organisms) differs in its proportions of 13C and
The graph in Fig. 25.3 shows the amount of CO2 in air bubbles 12
C from CO2 from volcanic gases and inorganic carbon dissolved
trapped in Antarctic ice that has accumulated over the past in the oceans. Volcanic and dissolved marine carbon do not have
1000 years. Ice samples show that CO2 levels actually began to the right ratio of 13C to 12C to explain the isotopic change observed
increase slowly in the 1800s, the time of major transformations in the atmosphere over time. In contrast, organic matter in
in mining, manufacturing, and transportation we call the living organisms has just the right ratio of 13C to 12C to account
Industrial Revolution. Before that, however, atmospheric CO2 for Suess’s measurements. Therefore, processes that cause a net
levels had varied little since the Middle Ages, staying at 270–280 conversion of organic matter to CO2, for example by burning,
ppm for centuries on end. On a 1000-year timescale, then, big must be adding CO2 to the atmosphere.
changes in CO2 abundance happened only once, in the last 200 Here’s where the other isotope of carbon, 14C, comes in.
years. Atmospheric CO2 inputs and outputs were approximately Measurements also show that the sources of added CO2 are
in balance until the Industrial Revolution. depleted in 14C relative to the CO2 already in the air. Modern
Fig. 25.3 shows that there is a correlation between the organic matter contains too much 14C to account for the
increasing CO2 content of the atmosphere and human activities. observed pattern, but ancient organic matter—the coal,
A correlation simply indicates that two events or processes occur petroleum, and natural gas burned as fossil fuels—is isotopically
together. Can we actually demonstrate that humans have played just right. Chemical analyses, therefore, support the hypothesis
a role in recent atmospheric change? By itself, correlation does that human activities cycle carbon in amounts high enough to
not establish causation, a relationship in which one event leads affect the chemical composition of the atmosphere.
to another. We might propose instead that recent CO2 increase That atmospheric CO2 is increasing is not a hypothesis;
reflects natural processes and only matches the period of it is a measurement. That the burning of fossil fuels plays
industrialization by coincidence. an important role in this increase is also unambiguously
documented by chemical analyses. Current debate focuses not
j Quick Check 1 How does the graph in Fig. 25.3 suggest that on these observations, but instead on the more difficult problem
human activities have influenced CO2 levels in the atmosphere? of understanding how increasing CO2 will affect climate. We
What might be a plausible alternative hypothesis? discuss this debate in Chapter 49. For now, however, we can use
514 SECTION 25.1 T H E S H O RT-T E R M C A R B O N C YC L E
HOW DO WE KNOW?
FIG. 25.4
360 –6.2 80
14C relative to a standard (1000)
(1000, relative to a standard ratio)
350 –6.4
320 –6.8
Ratio of 13C to 12C
330 –7.0
60
310 –7.2
The total amount of
300 atmospheric CO2 has –7.4
increased. 50
Amount of
290 –7.6
280 –7.8
40
1700 1750 1800 1850 1900 1950 2000 2002 2004 2006 2008 2010
Year Year
DISCUSSION The ratio of 13C to 12C in CO2 added to the CONCLUSION Fossil fuel burning by industrialized societies has
atmosphere over the past 200 years is lower than that in CO2 that been, and continues to be, a principal source of CO2 buildup in
was already in the air more than 200 years ago. The ratio of Earth’s atmosphere.
13
C to 12C in CO2 emitted by volcanoes is too high to account for the
SOURCES Revelle, R., and H. E. Suess. 1957. “Carbon dioxide exchange between
data, as is the ratio in CO2 released from the oceans. In contrast, atmosphere and ocean and the question of an increase of atmospheric CO2
organic matter formed by photosynthesis has just the right ratio during the past decades.” Tellus 9:18–27; Turnbull, J. C., et al. 2007. “A new
high precision 14CO2 time series for North American continental air.” Journal of
of 13C to 12C to account for Suess’s measurements. By itself, the Geophysical Research: Atmospheres 112, no. D11. Article Number: D11310. doi:
changing abundance of 13C in the air could reflect the conversion 10.1029/2006JD008184.
514
CHAPTER 25 C YC L I N G C A R B O N 515
CO2 Sources
Civil War, human
8 Fossil fuel burning generation of CO2 years, CO2 levels in air have changed even more dramatically.
Deforestation (tropics) came mostly from These longer-term changes mean that we must consider additional
of C per year)
6 Deforestation the clearing of contributions to the carbon cycle: physical processes, including
(outside the tropics) forests for agricul-
ture. Today, about volcanism and climate change. Indeed, the complete carbon
4
80% of annual cycle links Earth’s physical and biological processes, providing a
human additions are
2
due to burning of foundation for understanding the interconnected histories of life
fossil fuels. and environment through our planet’s long history.
CO2 Sinks
CO2 (in billion metric tons
FIG. 25.8 Geological processes that drive the long-term carbon cycle. Numbers are estimates for annual fluxes of carbon, in gigatons.
Source: Data from J. Gaillardet and A. Galy, 2008, “Himalaya—Carbon Sink or Source?” Science 320:1728, doi:10.1126/science.1159279.
Oxidation of coal,
oil, and ancient
organic matter
0.05
Organic
Silicate burial on land
weathering 0.2
0.14 Carbonate
weathering
0.29
Oceanic crust
weathering
0.02
Subduction
Sedimentation 0.083
of carbonate Burial of organic
shells and skeletons matter in sediments
0.22 0.2 Subduction carries CaCO3 and organic
matter down to the mantle, providing
a source of carbon for volcanoes that
will return CO2 to the atmosphere.
Weathering of ancient
rocks effectively removes
The amount of organic matter
CO2 from the atmosphere
buried in sediments effectively
and deposits it in the
reflects the excess of photosynthesis
oceans as CaCO3.
over respiration. Only a small
proportion of this buried organic
matter will become coal or oil.
appreciably for 1000 years or more. Longer-term records, shows that atmospheric CO2 has oscillated between 285 ppm and
however, show that the CO2 levels in air can change substantially 180 ppm for at least 400,000 years. On long timescales, therefore,
through time. the natural variations in the carbon cycle can be large.
At Vostok, high on the Antarctic ice sheet, glacial ice records The bottom graph in Fig. 25.9 shows an estimate of surface
more than 400,000 years of environmental history (Fig. 25.9). temperature obtained by chemical analysis of oxygen isotopes
As shown in the top graph of Fig. 25.9, the youngest samples show in ice from the same glacier and how it differed from the average
about 285 ppm CO2 in the atmosphere, consistent with direct temperature in 1950. Over the last 400,000 years, Antarctic
measurements of air, including the first years of the Keeling curve. temperature has oscillated between peaks of a few degrees warmer
Notice, however, that 20,000 years ago, CO2 levels were much than today and temperatures as much as 6°C to 8ºC colder than
lower—about 180 ppm. In fact, the Vostok ice core in its entirety the present. Interestingly, the temperature and CO2 curves closely
CHAPTER 25 C YC L I N G C A R B O N 519
FIG. 25.9 Atmospheric CO2 content for the past 400,000 years. These measurements were recorded from air bubbles trapped in glacial ice
at Vostok, Antarctica. Source: Data from P. Rekacewicz, “Temperature and CO2 Concentration in the Atmosphere over the Past 400,000 Years,” from Vital Climate
Graphics, UNEP/GRID–Arendal Maps & Graphics Library, JPG file, 2005, http://www.grida.no/publications/vg/climate/page/3057.aspx. Based on J. R. Petit et al.,
1999, “Climate and Atmospheric History of the Past 420,000 Years from the Vostok Ice Core, Antarctica,” Nature 399:429–436.
Interglacial Glacial
300
CO2 concentration (ppm)
280
260
240
220
200
180
For the past 400,000 years,
160 temperatures have followed
+4 a pattern similar to that of
CO2 levels.
Temperature change
relative to 1950 (C)
+2
0
2
4
6
8
10
400,000 350,000 300,000 250,000 200,000 150,000 100,000 50,000 Present
Years before present
parallel each other. As discussed more fully in Chapter 49, CO2 is The two curves correlate closely with one further
known to be an effective greenhouse gas, meaning that it allows phenomenon, the periodic growth and decay of continental ice
incoming solar radiation to reach Earth’s surface but traps heat sheets. Large glaciers expanded in the Northern and Southern
that is re-emitted from land and sea. Higher concentrations of hemispheres a few million years ago, ushering in an ice age. Today,
CO2 result in warmer temperatures. Therefore, it is not surprising we live in an interglacial interval, when climate is relatively mild,
that climate and atmospheric CO2 levels show the parallel history but 20,000 years ago thick sheets of ice extended far enough away
documented in the figure. from the poles to cover the present site of Boston (Fig. 25.10).
The repeated climatic shifts recorded in ice cores reflect periodic For the past 30 million years or so, atmospheric CO2 levels have
variations in the amount and distribution of solar radiation on probably not exceeded those recorded today at Mauna Loa by much
Earth’s surface, which are caused by oscillating changes in Earth’s (Fig. 25.11). Before that, however, higher levels of CO2—perhaps
orbit around the sun. four to six times the 1958 level—characterized the Mesozoic Era
The temperature and CO2 increases recorded by Vostok ice (252 to 66 million years ago), a generally warm interval commonly
between 20,000 and 10,000 years ago coincide with the last great known as the age of dinosaurs. Levels more like those of today
retreat of continental ice sheets. What processes might explain existed earlier, during much of the late Paleozoic Era (350–252
how atmospheric CO2 could increase by 100 ppm in just a few million years ago), another time of extensive glaciation. And
thousand years, as glaciers began to retreat? Can the short-term before that, about 500 million years ago, early in the Paleozoic Era,
carbon cycle processes of photosynthesis and respiration account atmospheric CO2 may have reached values as high as 15 to 20 times
for this much carbon? Certainly, the amount of forests on Earth’s the present-day level.
surface has varied through the past 500,000 years as ice sheets On timescales of millions of years, atmospheric CO2 and,
grew and decayed, but forests expand as glaciers shrink, so changes hence, climate, are determined in large part by geologic processes:
in forests cannot account for a pattern of increasing atmospheric changes in the rate of organic carbon burial in sediments,
CO2 with the retreat of glaciers. Volcanism and weathering also continental weathering of rocks uplifted into mountains, and
fail to account for the observed pattern. There is no evidence that volcanic gas release. All these processes reflect the action of
volcanic activity has waxed and waned in a pattern that could Earth’s great physical engine: plate tectonics. Seafloor formation
explain observed CO2 variations. And rates of weathering, which and destruction together influence rates of volcanic gas release,
remove CO2 from the atmosphere, should increase as temperature and mountain formation strongly influences rates of weathering
rises, but CO2 levels have actually increased. Something else must and, therefore, the fluxes of sediments that bury organic carbon
be going on. beneath the seafloor.
Scientists continue to debate why atmospheric CO2 oscillates
in parallel with glacial expansion and retreat, but, increasingly,
proposed mechanisms suggest interactions involving the ocean FIG. 25.11 Atmospheric CO2 content for the past 541 million
and its large reservoir of inorganic carbon. For example, it has years. Models and indirect estimates from geological
been hypothesized that during glacial advances, the circulation measurements suggest that CO2 levels have varied
of carbon-rich deep-ocean waters back to the sea surface slows, substantially through Earth’s history. Data from Fig 3.4
causing more inorganic carbon to accumulate in the deep sea. With in K. Wallmann and G. Aloisi, 2012, “The Global Carbon Cycle:
glacial retreat, the oceans circulate more vigorously, returning Geological Processes,” in Fundamentals of Geobiology, A. H. Knoll,
CO2 to the surface and then to the atmosphere. Whatever the D. E. Canfield, and K. O. Konhauser (eds.), Chichester, England:
explanation, the historical record of the past 400,000 years shows Wiley-Blackwell, pp. 20–35.
that climate can and does change without any input from humans,
something we must take into account when considering our Paleozoic Mesozoic Cenozoic
climatic future (Chapter 49). 8000
Estimates of atmospheric CO2
Uncertainty
Atmospheric CO2 (ppm)
fossil leaves: Experiments show that stomata, the small pores on Millions of years ago
leaf surfaces (Chapter 29), decrease in density as atmospheric
CO2 levels increase. The chemistry of ancient soils is also thought The dark blue line Atmospheric CO2 The light blue shading
shows the best levels are thought around the dark blue line
to reflect atmospheric history. Such indirect observations and estimate for CO2 to have been high indicates that actual
analyses come with a large degree of uncertainty, but most Earth through time. before about 350 levels have a 95% chance
scientists accept at least the broad pattern of atmospheric history million years ago. of falling within the
shading.
shown in Fig. 25.11.
CHAPTER 25 C YC L I N G C A R B O N 521
25.3 THE CARBON FIG. 25.12 A food web. Food webs trace the cycling of carbon through communities.
CYCLE: ECOLOGY,
BIODIVERSITY,
AND EVOLUTION
So far, we have outlined the biological and Secondary
physical pathways that cycle carbon through consumers obtain
Wastes and dead
Earth’s surface environments. How can their carbon by
organisms
eating primary
the carbon cycle provide a framework for consumers.
understanding basic features of ecology,
biodiversity, and evolution?
respiration of fungi, bacteria, and other decomposers that break and maintain diversity by performing comparable metabolic
down dead tissues. The cycle has come full circle. functions in different habitats (Chapter 48). In the forests of
The transfer of carbon from one organism to another is called New England, the tree species that thrive in wet regions differ
a food chain. Because most heterotrophs within a community can from those found on well-drained hillsides. And seasonally dry
consume or be consumed by a number of other species, biologists woodlands in southern California support yet another set of plant
often prefer to speak of food webs, a term that provides a better species. In general, plants of varying size, shape, and physiology
sense of the complexity of biological interactions within the inhabit physically and biologically distinct environments, and the
carbon cycle (Fig. 25.12). Food webs define the interactions among same is true of photosynthetic organisms in lakes and oceans.
organisms in ponds, forests, and many other habitats; we discuss Thus, the immense diversity of photosynthetic organisms
them in detail in Chapter 47. For now, the main point is that food found today does not reflect evolutionary variations in the
webs track the passage of carbon atoms through the biological biochemistry of photosynthesis (although some of that occurs;
carbon cycle. Put another way, the carbon cycle underpins the see Chapter 29) so much as it does structural and physiological
ecological structure of biological communities. adaptations. These adaptations allow the effective gathering of
The complementary metabolic processes of photosynthesis light, nutrients, and—critical to life on land—water, in widely
and respiration cycle carbon through forest and pond varying local environments. Natural selection, acting on local
communities. Furthermore, as we discuss in the next chapter, populations, links the diversity of photosynthetic organisms to the
complementary metabolic processes also cycle nitrogen, sulfur, carbon cycle.
and other elements required for life. By continually recycling If half a million species function as primary producers,
materials, biogeochemical cycles, which involve both biological an estimated 10 million species help to cycle carbon through
and physical processes, sustain life over long intervals. In their respiration. These include the plants, algae, and bacteria that
absence, life could hardly have persisted for 4 billion years. generate carbohydrates by photosynthesis, as well as animals,
fungi, and microorganisms that obtain both carbon and energy
Biological diversity reflects the many ways that from organic compounds in photosynthetic organisms or the
organisms participate in the carbon cycle. consumers that eat them. These organisms are essential to the
Among the most remarkable features of life is its astonishing completion of the short-term carbon cycle, returning carbon
diversity. Biological diversity, or biodiversity, is the product of atoms to the environment as CO2.
evolution, but it is shaped and sustained by ecological interactions Heterotrophic bacteria, amoebas, and humans may use
among organisms and between organisms and the physical essentially the same biochemical pathway to respire organic
environment. molecules, but they differ markedly in how they feed and,
To begin, an estimated 500,000 species of photosynthetic therefore, in what they can eat. Bacteria (and also fungi) absorb
organisms fuel the carbon cycle in all but a few deep-sea and molecules from their environment, but amoebas and many
subterranean environments. In terms of carbon and energy other eukaryotic microorganisms can capture and ingest cells—
metabolism, all these species do pretty much the same thing. Why, they are capable of predation. Animals capture prey, as well,
then, is there such a diversity of photosynthetic organisms? Why but commonly feed on organisms far too large for an amoeba
don’t just a few species dominate the world’s photosynthesis? to eat. As photosynthetic organisms have adapted structurally
The example of the pond and forest helps to make the basis and physiologically to local environments across the globe,
of photosynthetic diversity clear. In the forest community, the consumers have adapted by means of locomotion, mouth and
leaves of several different tree species form a photosynthetic limb specialization, perception, and behavior to obtain their
canopy above the forest floor. Below, shrubs grow, making use of food. So, as you read about bacteria, amoebas, and insects in the
light not absorbed by the leaves above them. And below the shrubs chapters that follow, think about how each operates within the
are grasses, herbs, ferns, and mosses that can grow in the reduced carbon cycle and so contributes to the operation of Earth’s diverse
light levels of the forest floor. In the nearby pond, a few species ecosystems.
of aquatic plants line the water’s edge, but beyond that algae and
photosynthetic bacteria dominate photosynthesis, with some The carbon cycle weaves together biological evolution
species anchored to the pond bottom and others floating in the and environmental change through Earth history.
water column. The world did not always support the biological diversity we see
Locally, then, the different photosynthetic species that today. Indeed, 2 billion years ago, the carbon cycle included mostly
transfer carbon atoms from CO2 to organic molecules subdivide photosynthetic bacteria and microbial heterotrophs because
the forest on the basis of light, water, and nutrient availability—a there were no plants or animals (Fig. 25.13). Subsequently, algae
pattern complicated by grazing and environmental disturbances gained an ecological foothold as nutrients such as nitrate became
such as fire and landslides (Chapter 47). On a larger scale, climate more widely available, and single-celled eukaryotic heterotrophs
and topography vary tremendously from one region to another, expanded their reach by gathering food in ways not possible for
and these features, as well, help to explain how plants can build bacteria, ingesting cells and other types of particulate food. With
CHAPTER 25 C YC L I N G C A R B O N 523
they cycle oxygen (and water) as well. For this reason, the history
(% of modern level)
100
of atmospheric oxygen is closely tied to the workings of the carbon
cycle through time. When oxygen production by photosynthesis 1210
and oxygen consumption by respiration are in balance, oxygen
levels do not change. However, when some of the organic carbon
generated by photosynthesis is buried in sediments, thereby
,,1023
avoiding being returned to the environment through respiration,
4 3 2 1 0
some of the O2 also generated by primary producers can accumulate
Age (billions of years ago)
in the atmosphere and oceans. In other words, because sedimentary Animals
organic matter burial can break the tight coupling depicted in
Oxygen levels did not increase to
Fig. 25.2, it can facilitate an increase in O2 through time. The levels that humans could breathe
geologic history of oxygen shown in Fig. 25.14 results from the until about 580 million years ago,
interactions through time between the carbon (and sulfur) cycle coinciding with the first appearance
of animals in the fossil record.
with plate tectonics. Our oxygen-rich world is the result.
524 SELF-ASSESSMENT
Core Concepts Summary Over time spans of hundreds of millions of years, movements
of Earth’s plates become major influences on the carbon cycle.
page 520
25.1 Photosynthesis and respiration are the key
biochemical pathways of the biological, or short-term,
carbon cycle. 25.3 The carbon cycle can help us understand ecological
interactions and the evolution of biological diversity.
Keeling’s program to monitor CO2 levels in the atmosphere
revealed two patterns: (1) CO2 levels oscillate on a yearly basis, Photosynthetic and other autotrophic organisms are primary
and (2) CO2 levels have increased steadily to the present day producers, converting CO2 into organic molecules. page 521
since measurements began. page 510 Heterotrophic organisms that eat primary producers are called
The first pattern (seasonal oscillation) can be explained by the primary consumers. page 521
global imbalance between photosynthesis and respiration in
Heterotrophs that prey on grazers are called secondary
the summer and in the winter months. page 512
consumers. page 521
The second pattern (steady increase) can be extended further
Interacting networks of species, linked by predator–prey
back in time by measuring the composition of air trapped in
interactions, are called food webs, and they are an important
gas bubbles within polar ice. These measurements indicate
feature of the carbon cycle. page 522
that CO2 levels in the atmosphere remained steady for more
than a thousand years, but then started to increase in the Primary producers are well adapted to obtaining sunlight,
mid-1800s, the time of the Industrial Revolution. page 513 water, and nutrients in different environments. page 522
The ratio of different isotopes of carbon in the atmosphere Primary and secondary consumers are adapted to obtaining
indicates that most of the carbon added to the atmosphere in different sources and sizes of food. page 522
recent decades comes from human activities, particularly the
The evolution of life on Earth can be considered a long history
burning of fossil fuels. page 513
during which organisms have evolved different ways of
25.2 Physical processes govern the long-term obtaining energy and carbon from their environment.
page 523
carbon cycle.
The interactions between biological and geologic processes
Physical processes, which act at slower rates and over longer
at work in the carbon cycle are also responsible for Earth’s
timescales, are the major drivers of the long-term carbon cycle.
oxygen-rich atmosphere and oceans. page 523
page 515
Physical processes that remove CO2 from the atmosphere 3. Draw and explain the curve representing changing
include the weathering of rocks, and those that add CO2 to the atmospheric levels of CO2 over the past 150 years.
atmosphere include volcanoes and the oxidation of ancient 4. Describe one way by which the source of the modern
organic matter in sedimentary rocks. page 516 increase in CO2 in the atmosphere can be determined.
The short- and long-term carbon cycles are linked by the slow 5. How do geologic processes participate in the long-term
leakage of organic matter from biological communities to carbon cycle?
sediments accumulating on the seafloor. page 516
6. Draw and explain the curve representing changing
Over the last 400,000 years, CO2 levels in the atmosphere have
atmospheric levels of CO2 over the last 400,000 years.
gone through periodic shifts that coincide with repeated cycles
of glaciation. page 518
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been as much as 15 to 20 times higher than present-day levels.
page 520
525 SECTION 12.1 P
CASE 5
Nostril
Hair
Oral cavity
Esophagus
Skin Stomach
H. pylori (+)
Stomach
H. pylori (–)
Colon
Urogenital
tract
Actinobacteria
Firmicutes
Proteobacteria
Bacteroidetes
Cyanobacteria
Fusobacteria
chambers) contains microbes that break down the cellulose in converting material containing cellulose, such as
in plant material. Without them, cattle wouldn’t be able switchgrass, into biofuels.
to extract adequate nutrition from the grass they graze. As researchers look for more sustainable replacements
Those microbes are the particular focus of scientists at for fossil fuels, many have pinned their hopes on biofuels.
the Department of Energy (DOE), who are interested But the enzymes currently used commercially to break
526
The bobtail squid and its luminescent bacteria. This squid contains specialized
organs that harbor light-emitting bacteria. Source: Gary Bell/OceanwideImages.com.
down cellulose aren’t efficient or cost effective enough light from the surface as a way to camouflage themselves
to produce biofuels on an industrial scale. That’s where from would-be predators below.
the cows come in. DOE scientists recently analyzed In many cases, animals and their bacterial symbionts
the microbial genes present in the cow rumen. They are so intimately connected that it’s hard to separate one
discovered nearly 28,000 genes for proteins that metabolize from the other. Many human gut bacteria are poorly studied
carbohydrates, and at least 50 new proteins. The hope is that because scientists haven’t been able to grow them outside
some of these newly discovered proteins will help break the body. But some species have taken their intimate
down cellulose in ways that will produce biofuels more bacterial partnership a step further.
efficiently and cheaply. Aphids are small insects that feed on plant sap. They
Mammals such as cows and humans are hardly the rely on the bacterium Buchnera aphidicola to synthesize
only organisms that have symbiotic relationships with certain amino acids for them that aren’t available from
bacteria. All living animals have their own microbiomes. their plant-based diet. The partnership between aphids
Even tiny single-celled eukaryotes can harbor still-tinier and Buchnera dates back as far as 250 million to 150
bacterial guests. million years ago. Over time, the organisms have become
Symbiotic bacteria provide a variety of benefits to completely dependent on one another for survival. The
their hosts. Consider the bobtail squid, Euprymna scolopes, Buchnera bacteria actually live inside the aphid’s cells. In
which possesses a specialized organ to house bacteria. The some ways, the bacteria resemble organelles rather than
bacteria, Vibrio fischeri, are luminescent—that is, capable independent organisms. Intracellular symbionts may not
of generating light. The squid use their Vibrio-filled light be so unusual. In fact, mitochondria and chloroplasts—
organs like spotlights, projecting light downward to match key organelles of eukaryotic cells—are thought to have
527
originated from symbiotic bacteria. Over time, the Clearly, there are many good reasons to learn more
progenitor bacteria became so intertwined with their host about our bacterial comrades. From evolution to energy to
cells that they developed into an integral part of the cells human health, our microbiomes hold great promise—and
themselves. Studying simple sap-sucking aphids, it turns great mystery. We’ve evolved hand in hand with these
out, may offer insights into the evolutionary history of all bacteria for millions of years. Let’s hope it takes less time to
eukaryotic cells. uncover their secrets.
? CASE 5 QUESTIONS
Special sections in Chapters 26 and 27 discuss the following questions related to Case 5.
528
CHAPTER 26
Bacteria
and Archaea
Core Concepts
26.1 The tree of life has three main
branches, called domains:
Eukarya, Bacteria, and
Archaea.
26.2 Bacteria and Archaea are
notable for their metabolic
diversity.
26.3 In addition to their key roles
in the carbon cycle, Bacteria
and Archaea are critical to the
biological cycling of sulfur and
nitrogen.
26.4 The extent of bacterial
diversity was recognized when
sequencing technologies could
be applied to non-culturable
bacteria.
26.5 The diversity of Archaea has
only recently been recognized.
26.6 The earliest forms of life
on Earth were Bacteria and
Archaea.
Steve Gschmeissner/SPL/Getty Images.
529
530 SECTION 26.1 T W O P RO K A RYOT I C D O M A I N S
In Chapter 25, we discussed how the cycling of carbon by plants membrane-bounded nuclei, no energy-producing organelles, no
and animals is linked to their production and consumption of sex. This point of view turns out to be more than a little misleading.
oxygen. But can carbon cycle through the deep waters of the Bacteria are the diverse and remarkably successful products of
Black Sea, within black muds beneath swamps and marshlands, nearly 4 billion years of evolution. Today, bacterial cells outnumber
or in other habitats where oxygen is limited or absent? Can eukaryotic cells by several orders of magnitude. Even in your own
biological communities even survive without oxygen? The body, bacteria outnumber human cells 10 to 1.
answer, emphatically, is yes. Indeed, life existed on Earth for more Fig. 26.1 illustrates the bacterial cell, which was briefly
than a billion years before oxygen-rich habitats first appeared on introduced in Chapter 5. The cell’s DNA is present in a single
our planet. circular chromosome, in contrast to the multiple linear
The seemingly alien oxygen-poor environments on today’s chromosomes characteristic of eukaryotic cells. Many bacteria
Earth are populated by organisms that neither produce nor carry additional DNA in the form of plasmids, small circles
consume oxygen, yet are able to cycle carbon. The organisms of DNA that replicate independently of the cell’s circular
responsible for this expanded cycle share one fundamental feature: chromosome. In general, plasmid DNA is not essential for the
They have prokaryotic cell organization. Prokaryotes, which cell’s survival, but it may contain genes that have adaptive value
include bacteria and archaeons, lack a nucleus (Chapter 5). They under specific environmental conditions. No nuclear membrane
inhabit the full range of environments present on Earth, including separates DNA from the surrounding cytoplasm, and so transcribed
those rich in oxygen, but their presence in habitats where plants mRNA is immediately translated into proteins by ribosomes.
and animals cannot live suggests that some of these organisms Bacteria lack the membrane-bounded organelles found in
have biological features quite unlike those of our familiar world. eukaryotic cells. Instead, cell processes such as metabolism are
We’ll look at the carbon cycle again later in this chapter, but first carried out by proteins that float freely in the cytoplasm or are
we discuss Bacteria and Archaea, the prokaryotic domains of embedded in the plasma membrane. A few bacteria, notably the
microscopic organisms so critical to the cycling of carbon and photosynthetic bacteria, contain internal membranes similar
other elements essential to life. We examine their diversity and to those found in chloroplasts and mitochondria. The light
how they have evolved through time. reactions of photosynthetic bacteria take place in association with
membranes distributed within the cytoplasm.
Structural support is provided by a cell wall made of
peptidoglycan, a complex polymer of sugars and amino acids.
26.1 TWO PROKARYOTIC DOMAINS
Some bacteria have thick walls made up of multiple peptidoglycan
Chapter 5 outlined the two distinct ways that cells are organized layers, while others have thin walls surrounded by an outer layer
internally. Eukaryotic cells, which include the cells that make up of lipids. For many years, it was believed that bacteria lacked the
our bodies, have a membrane-bounded nucleus and organelles that cytoskeletal framework that organizes cytoplasm in eukaryotic
form separate compartments for distinct cell functions. Prokaryotic cells. However, careful studies now show that bacteria do have
cells have a simpler organization. No membrane surrounds the an internal scaffolding of proteins that plays an important role in
cell’s DNA, and there is little in the way of cell compartments. determining the shape, polarity, and other spatial properties of
Prokaryotic cell organization is an ancestral character for life as a bacterial cells (Chapter 10).
whole—that is, it is a feature that was present in the last common
ancestor of all organisms alive today. The group defined traditionally Diffusion limits cell size in bacteria.
as the prokaryotes, however, is paraphyletic in that it excludes some Most bacterial cells are tiny: The smallest are only 200–300
descendants of the last common ancestor of all living organisms, nanometers (nm) in diameter, and relatively few are more than
namely eukaryotes (Chapter 23). 1–2 micrometers (µm) long. Why are bacteria so small? The
Bacteria and Archaea are the two domains characterized by answer has to do with diffusion, a critical process introduced in
prokaryotic cell structure. These organisms are present almost Chapter 5. If you could watch the movement of any particular
everywhere on Earth. What they lack in complexity of cell molecule in air or water, you would see that its motion is random,
structure, these tiny cells more than make up for in their dazzling sometimes in one direction and sometimes in another. On
metabolic diversity. As will become clear over the course of this average, however, more molecules move from a region with a
chapter, Bacteria and Archaea underpin the efficient operation of higher concentration of the molecule to a region with a lower
ecosystems on our planet. concentration of the molecule than move in the other direction.
Net movement stops only when the two regions achieve equal
The bacterial cell is small but powerful. concentration, but diffusion continues. Photosynthetic bacteria
Because of their small size and deceptively simple cell organization, gain the carbon dioxide they need by the diffusion of CO2 from the
bacteria were long dismissed as primitive organisms, distinguished environment into the cell, and that is also how respiring bacteria
mostly by the eukaryotic features they lack: They have no take in small organic molecules and oxygen.
CHAPTER 26 B AC T E R I A A N D A RC H A E A 531
FIG. 26.1 A bacterial cell. The cells of Bacteria (and Archaea) do not have a membrane-bounded nucleus or other organelles.
Chromosomal DNA
The DNA of bacteria is
contained in a circular Cytoplasm
chromosome, folded
into many loops.
Plasmid DNA
Cell wall
Plasma membrane
Flagellum
Diffusion explains why bacterial cells tend to be small. A that of Escherichia coli (Fig. 26.3). But, in one sense, T. namibiensis
small cell has more surface area in proportion to its volume, and cheats: 98% of its volume is taken up by a large vacuole, so the
the interior parts of a small cell are closer to the surrounding metabolically active cytoplasm is restricted to a thin film around the
environment than those of a larger cell. As a consequence, slowly cell’s periphery. Thus, the distance through which nutrients move
diffusing molecules do not have to travel far to reach every part by diffusion is only a few micrometers, as in many other bacteria.
of a small cell’s interior. The surface area of a spherical cell—the Some bacteria are multicellular, forming simple filaments or
area available for taking up molecules from the environment— sheets of cells. More unusual are myxobacteria, which aggregate to
increases as the square of the radius. However, the cell’s volume— form multicellular reproductive structures that are composed of
the amount of cytoplasm that is supported by diffusion—increases several distinct cell types (see Fig. 26.2e).
as the cube of the radius. Therefore, as cell size increases, it
becomes harder to supply the cell with the materials needed for Horizontal gene transfer promotes genetic diversity
growth. For this reason, most bacterial cells are tiny spheres, rods, in bacteria.
spirals, or filaments—small enough for molecules to diffuse into Bacterial genomes are generally smaller than the genomes of
cell interiors (Fig. 26.2). eukaryotes, in part because bacteria lack the large stretches
A few exceptional bacteria exceed 100 µm in maximum of noncoding DNA characteristic of eukaryotic chromosomes
dimension. For example, Thiomargarita namibiensis, a bacterium (Chapter 13). The streamlining of the bacterial genome confers
that lives in oxygen-poor sediments off the coast of southwestern certain benefits. For example, bacteria can reproduce rapidly when
Africa, has a total volume about 100,000,000 times larger than nutrients required for growth are available in the local environment.
532 SECTION 26.1 T W O P RO K A RYOT I C D O M A I N S
FIG. 26.2 Cell shape and size in Bacteria and Archaea. Sources: a. Eye of Science/Science Source; b. Scimat/Getty Images; c. Courtesy Mike Dyall-Smith;
d. David Scharf/Science Source; e. © ANIMA RES.
2 μm 2 μm 2 μm
2 μm 30 μm
second cell, the pilus contracts, drawing the two a. DNA transfer by conjugation
cells close together. A pore-like opening develops
where the two cells are in close contact, providing a
migration route for the direct cell-to-cell transfer of
DNA. This process, called conjugation, commonly
transfers plasmids from one cell to another, spreading
novel genes throughout a population. Genes that
confer resistance to antibiotics are a well-studied
example of horizontal gene transfer by conjugation.
Genes can also be transferred from one cell to
another without any direct bridge between cells.
DNA released to the environment by cell breakdown
can be taken up by other cells, a process called
transformation (Fig. 26.4b). Transformation was In conjugation, DNA
revealed when experiments showed that harmless (usually a plasmid)
from a donor cell is
strains of the bacteria causing pneumonia could transferred to an
be transformed into virulent strains by exposure adjacent recipient cell.
to media containing dead cells of disease-causing First, a pilus tethers
Pilus the donor to the
strains (Chapter 3). Scientists reasoned that the recipient and brings
transformation occurred because some substance the cells together.
was being taken up by the living bacteria. The
“transforming substance” was later shown to be DNA. Donor Recipient
Today, biologists commonly use transformation in the
laboratory to introduce genes into cells. Once the cells are
closely aligned, the
Viruses provide a third mechanism of horizontal
DNA passes
gene transfer. Recall from Chapter 19 that viruses in through a small
bacterial cells sometimes integrate their DNA into the opening formed
between the cells.
host bacterial DNA. This viral DNA persists within the
cells as they grow and divide. Before the virus leaves
the cell to infect others, the viral DNA removes itself Donor Recipient
from the bacterial genome and is packaged in a protein
b. DNA transfer by transformation
capsule to produce the complete virus particle. This
excision is not always precise, and sometimes genetic
material from the bacterial host is incorporated into In transformation,
the virus. Viruses released from their host cell go on to DNA released into
the environment by
infect others, bringing host-derived genes with them. dead cells is taken
Horizontal gene transfer by means of viruses is called up by a recipient
transduction (Fig. 26.4c). It is common in nature and cell.
f
fO
H no
f li
no
nd ratio
tab oph
tab hic
sm
sm
2S
tio
tio
me rotr
tra
tra
ne
to
te
2 a
Au
He
Co
Pe
Pe
O
Depth beneath surface (mm)
FIG. 26.10 The sulfur cycle. Plants take up sulfur as sulfate ions for
incorporation into proteins and other compounds, and
Oxidized and reduced molecules react readily with each fungi release sulfur during decomposition. However,
other and so are rarely present in the same environment. For the major role in cycling sulfur through the biosphere
this reason, chemoautotrophs tend to live along the interface is played by microbes that oxidize or reduce sulfur
between an environment where oxygen is present and one in compounds to gain energy or carbon.
which oxygen is absent. Chemoautotrophic prokaryotes therefore
thrive where reduced gases from Earth’s interior meet oxygen- SO42–
rich seawater.
j Quick Check 4 How could the biological carbon cycle have Assimilation
Primary producers
worked on the primitive Earth, where oxygen gas was essentially
Energy metabolism
absent from the atmosphere and oceans? Photosynthetic bacteria
Energy metabolism
Anaerobic respiration by Organic S Chemoautotrophic
bacteria and archaeons in proteins bacteria
Chemoautotrophic
26.3 OTHER BIOGEOCHEMICAL archaeons
Decomposition
CYCLES Fungi
Bacteria
Let’s think further about prokaryotic metabolism. We saw that
some photosynthetic and chemosynthetic bacteria oxidize
reduced sulfur compounds like H2S to sulfate (SO422), whereas H2S
CHAPTER 26 B AC T E R I A A N D A RC H A E A 539
much the same thing in lakes, rivers, and oceans. Why don’t
primary producers take up H2S directly? There are two answers FIG. 26.11 The nitrogen cycle. Unique bacterial and archaeal
to this question. First, H2S is rapidly oxidized in the presence of metabolisms include nitrogen fixation, nitrification and
oxygen and so does not occur in environments where oxygenic denitrification, as well as anammox.
photosynthesis is common. Second, H2S is generally toxic to Nitrogen gas
eukaryotic organisms, so plants and algae do not thrive where it is N2
abundant. (The H2S produced within eukaryotic cells has a short
lifetime and is restricted to intracellular sites distant from those
that are vulnerable to its toxic effects.)
We’ve now seen half the sulfur cycle, the conversion of
sulfate to H2S within cells. How did sulfate molecules get
Denitrification
into the soil in the first place? After death, fungi and bacteria Organic N in
proteins, etc. Nitrogen
decompose cells, returning carbon, sulfur, and other compounds Assimilation fixation
to the environment. Reduced sulfur compounds released from
decomposing cells are oxidized by bacteria and archaeons, Nitrate
Anammox
NO3
completing the cycle. These microbes are chemoautotrophs that Decomposition Bacteria
obtain energy by oxidizing H2S or photosynthesizers that use H2S and
Archaea
as the electron donor. In addition to being taken up by plants, the Nitrification
Assimilation
sulfate produced by these processes is consumed by heterotrophic
Nitrite NO2
bacteria living in oxygen-free environments found in soil,
sediments, and occasionally in lakes and seawater. Sulfate rather
than oxygen is used as the final electron acceptor in respiration Nitrification
and is reduced to H2S. In fact, most of the sulfur cycled biologically
is used to drive energy metabolism in oxygen-poor environments, Ammonia
NH3
not to build proteins.
Note that eukaryotes use neither H2S for photo- (or chemo-)
synthesis nor sulfate in respiration. Thus, the biological sulfur
cycle is completed by bacteria and archaeons alone. nodules that harbor nitrogen-fixing bacteria (Fig. 26.12). That is,
plants like soybean have entered into an intimate partnership with
The nitrogen cycle is also driven by bacteria nitrogen-fixing bacteria to obtain the biologically useful forms of
and archaeons. nitrogen needed for growth (Chapter 29).
The model provided by the sulfur cycle can be extended to other
biologically important elements. Nitrogen is the fourth most
abundant element in the human body, contributing 4% by weight
FIG. 26.12 Roots of a soybean plant. The nodules contain bacteria
as a component of proteins, nucleic acids, and other compounds.
capable of reducing nitrogen gas to ammonia. Source:
As is true of sulfur, primary producers incorporate inorganic forms
Scimat/Getty Images.
of nitrogen into biomolecules, and we get the nitrogen we need
from our food. As we’ll see, however, there is a twist.
Let’s examine the biological nitrogen cycle (Fig. 26.11).
Carbon is a minor component of the atmosphere and sulfur only a
trace constituent, but the air we breathe consists mostly (78%) of
nitrogen gas (N2). Indeed, most of the nitrogen at Earth’s surface
resides in the atmosphere. Although nitrogen is plentiful, the
nitrogen available to primary producers in many environments
is limited. The reason is that plants cannot make use of nitrogen
gas and neither can algae. Only certain bacteria and archaeons
can reduce N2 to ammonia (NH3), a form of nitrogen that can be
incorporated into biomolecules.
The process of converting N2 into a biologically useful form
such as ammonia is called nitrogen fixation, and it is one of the
most important reactions ever evolved by organisms. Farmers
plant soybeans to regenerate nitrogen nutrients in soils, but it is
not the soybean that fixes nitrogen. Rather, soybean roots have
540 SECTION 26.4 T H E D I V E R S I T Y O F B AC T E R I A
FIG. 26.13
om ia
cu ari AR ob + lb
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06 eria n
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- op bgr ia)
R1 udo ob ia)
ns cte ra
eo ei )
eo opl p II
)
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on rin teo dete
ria
ib lad
d
to
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fu r cla
r
ou
SA bac ank
te
te
o
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ro s la
the rRNA sequences were amplified by PCR, separated by gel
a
ltu ne 11 ac
ac
as e A ba
p
rb
e
r
( rou
c su
t
electrophoresis, and sequenced, thus providing a library of tags that
te
te
y
(F
h
a
h
g
ro
ul
ub
-P
-P
document bacterial diversity
R4
1s
(
ot
pi
S
Pr
R1
a
24
6
16
en
/
R8
SA
R3
SA
d
METHOD 2 In another set of experiments, scientists collected
SA
(G
re
Un M
02
ro
samples of seawater from the Sargasso Sea, and from these they
te
R2
Al
SA
amplified whole genomes—more than a billion nucleotides’ worth.
They used small-subunit rRNA and other genes to characterize Relative abundance of different bacterial groups in samples from the Sargasso
species richness, and also characterized a large assortment of Sea, based on percent representation of small subunit rRNA sequences. Note the
abundance of SAR11, only recently characterized.
additional sequence data to understand genetic and physiological
diversity.
RESULTS Both surveys found that the bacterial diversity of marine 25,000
environments is much higher than had been thought. The barcode
survey (method 1) found as many as 20,000 distinct types of
20,000
Number of sequence tags
541
542 SECTION 26.4 T H E D I V E R S I T Y O F B AC T E R I A
but only occasionally do we suffer from maladies such as staph unicellular rods and spheroidal cells, as well as multicellular balls
infection, toxic shock syndrome, or food poisoning induced by and filaments (Fig. 26.16). Some filamentous cyanobacteria can
staphylococcal bacteria. even form several different cell types, including specialized cells for
In contrast to these pathogens, gram-positive bacteria called nitrogen fixation and resting cells that provide protection when the
streptomycetes have proved invaluable to medicine because local environment does not favor growth.
of a remarkable property. More than half of the species in this In contrast to the monophyly of cyanobacteria, molecular
group secrete compounds that kill other bacteria and fungi. sequence comparisons show that anoxygenic photosynthesis is
Streptomycetes have provided us with tetracycline, streptomycin, distributed widely on the bacterial tree (see Fig. 26.15). Think of the
erythromycin, and numerous other antibiotics that combat purple layer beneath the surface of many microbial mats (see
infectious disease. Fig. 26.7). The vivid color comes from the light-sensitive
pigments of the aptly named purple bacteria, found within the
Photosynthesis is widely distributed on the bacterial Proteobacteria. Purple bacteria are capable of photoautotrophic
tree. growth using bacteriochlorophyll and a single photosystem. Most,
Molecular studies confirm that all bacteria capable of oxygenic however, show evidence of metabolic diversity and can grow
photosynthesis form a single branch of the bacterial tree: the heterotrophically in the absence of light or appropriate electron
cyanobacteria. Cyanobacteria can be found in environments that donors. A green layer lies beneath the surface of other microbial
range from deserts to the open ocean. Their diverse species include mats, its color caused by light reflected by the pigments of another
group of photosynthetic bacteria, called
green sulfur bacteria because they
commonly gain electrons from hydrogen
sulfide and deposit elemental sulfur
FIG. 26.16 Diversity of form among cyanobacteria. Sources: a. Dr. Ralf Wagner; b. blickwinkel/Alamy;
on their walls. Unlike most groups of
c. Hecker/Sauer/age fotostock; d. Jason Oyadomari.
photosynthetic bacteria, the green sulfur
b. Chroococcus, larger cells bound into a colony by bacteria are intolerant of oxygen gas.
a common extracellular envelope made of Oddly, a species of green sulfur bacteria
a. Aphanothece, small single cells polysaccharides
has been found in hydrothermal rift vents
2 km beneath the surface of the ocean.
Light doesn’t penetrate to these depths,
so if these organisms harvest light, it must
come from incandescent lava as it erupts
on the bottom of the ocean.
Light-harvesting bacteria occur
on several other branches of the
bacterial tree—the photoheterotrophic
heliobacteria, for example, and the
green nonsulfur bacteria often found
in freshwater hot springs. Despite a
10 µm 10 µm century of research, our knowledge of
photosynthesis within the bacterial
tree remains incomplete, as illustrated
d. Anabaena, strings of undifferentiated cells at
either end of the filament, flanking two by the discovery in 2007 of unique
elongated resting cells, and in the middle, light-harvesting bacteria in Yellowstone
c. Oscillatoria, filaments with no cell differentiation a heterocyst specialized for nitrogen fixation National Park. Genomic surveys of hot
springs turned up evidence of a previously
unknown bacteriochlorophyll-containing
microorganism, and gene sequencing
established that this organism belongs
to the phylum Acidobacteria. There is no
evidence for carbon fixation, however,
suggesting that the Yellowstone bacterium
is a photoheterotroph. To date, these
unusual microorganisms have not been
50 µm 20 µm grown in pure culture, so they remain
difficult to study.
CHAPTER 26 B AC T E R I A A N D A RC H A E A 545
30
20
10
10
90
80
70
60
50
40
Crenarchaeota Optimum growth temperature (C)
Methane producer
Salt tolerant
Acid tolerant
Korarchaeota
Thaumarchaeota
FIG. 26.19
a. b.
0.6 1.50 x 10
Thaumarchaeota
Euryarchaeota 0.5 1.25 x 10
Bacteria NO2 concentration
NH4 concentration
Concentration (mM)
0.2
Depth (m)
5.00 x 10
0.0 0.00
2 4 6 8 10 12 14 16 18 20 22 24
Time (d)
1000 Growth of a marine thaumarchaeote in a medium containing ammonium
chloride and bicarbonate as the only sources of energy and carbon,
respectively. As cell number increased, ammonia (the ammonium ion NH41)
was increasingly converted to nitrite (NO22), supporting the hypothesis that
5000
these cells are ammonia-oxidizing chemoautotrophs.
0
20 40 60 80
Percentage of cells belonging
to domain SOURCES Karner, M. B., E. F. DeLong, and D. M. Karl. 2001. “Archaeal
Dominance in the Mesopelagic Zone of the Pacific Ocean.” Nature 409:507–510
Surveys of cell abundance through a depth profile of the Pacific Ocean show (The figure has been modified to reflect more recent nomenclature.); Könneke, K.,
that bacteria dominate cell numbers near the surface, but thaumarchaeotes et al. 2005. “Isolation of an Autotrophic Ammonia-Oxidizing Marine Archaeon.”
make up about 40% of all cells in deeper waters. Nature 437:543–546.
547
548 SECTION 26.6 T H E E VO L U T I O N A RY H I S TO RY O F P RO K A RYOT E S
? CASE 5 THE HUMAN MICROBIOME: DIVERSITY WITHIN A fertilized human egg has no bacteria attached to it, so our
microscopic passengers arrive by colonization—by infection, if
How do intestinal bacteria influence human health? you will. Research on children from Europe and rural Africa clearly
It has been estimated that the bacteria (and, to a much lesser shows the importance of diet in establishing our gut microbiota
extent, archaeons) in and on your body outnumber your own (Fig. 26.24). The African children, raised on a diet low in fat and
cells by as much as 10 to 1. Estimates of the number of microbial animal protein but rich in plant matter, have gut microbiotas
species that inhabit our bodies vary, but about 750 types have been
identified in the mouth alone, and the list remains incomplete
(Fig. 26.23). An equal number resides in the colon, and still more
live on the skin and elsewhere. Some are transients, entering FIG. 26.24 Diet and the intestinal microbiota. Studies of
and leaving the body within a few bacterial generations. Others gut bacteria in children from (a) rural Africa and
are specifically adapted for life within humans, forming complex (b) Western Europe show markedly different
communities of interacting species. communities. Source: Data from C. De Filippo, D. Cavalieri,
At present, much research is focused on the bacteria within M. Di Paola, M. Ramazzotti, J. B. Poullet, S. Massart, S. Collini,
our intestinal tracts. We commonly think of gut bacteria as G. Pieraccini, and P. Lionetti, 2010, “Impact of Diet in Shaping
harmful, but this perception arises from only a small—albeit Gut Microbiota Revealed by a Comparative Study in Children from
devastating—subset of our microbial guests. Illnesses known to be Europe and Rural Africa,” Proceedings of the National Academy of
caused by bacteria within our bodies include cholera, dysentery, Sciences USA 107(33):14693, doi:10.1073/pnas.1005963107.
and tuberculosis. Once the leading causes of death in New York a.
and London, they remain major killers in Africa. Other diseases,
not previously thought to be of microbial origin, are now known
Others
to be caused by bacteria—ulcers, for example, and stomach 15%
cancer, both mediated by the acid-tolerant bacterium Helicobacter Subdoligranulum 4%
pylori. More often than not, however, intestinal bacteria have a Prevotella
Faecalibacterium 4% 53%
beneficial effect. They help to break down food in our digestive
system and secrete vitamins and other biomolecules into the colon Acetitomaculum 4%
Xylanibacter
for absorption into our tissues. Molecular signals from bacteria 20%
guide the proper development of cells that line the interior of our
intestines.
Blood 1% Others
22% Bacteroides
Urogenital 23%
tract 9%
Subdoligranulum
9%
Airways GI tract
29% Faecalibacterium
14% Roseburia 5%
25%
Acetitomaculum 12%
Skin
21% Bacteroidetes European children have
Mouth
26% Firmicutes intestinal bacteria
enriched in members of
the phylum Firmicutes.
CHAPTER 26 B AC T E R I A A N D A RC H A E A 551
enriched in species of the phylum Bacteroidetes that are known inflammatory bowel disease, a disabling inflammation of the colon,
to help digest cellulose. European children raised on a typical increases in humans who have been treated with antibiotics.
Western diet rich in sugar and animal fat lack these bacteria, To understand the relationships between the human
harboring instead diverse members of the phylum Firmicutes. We microbiome and human health, we need to know what constitutes
do not understand the full ramifications of these differences, but a healthy gut biota, and this means studying the metabolism,
active research suggests that they may help to explain the relative ecology, and population genetics of the bacteria in our bodies. We
prominence in Western societies of allergies and other disorders need to know which bacteria have evolved to take advantage of
involving the immune system. the environments provided by the human digestive system, and
We also influence our gut biota by ingesting antibiotics. which are “just passing through.” Future visits to the doctor may
Although prescribed for the control of pathogens, most antibiotics include routine genetic fingerprinting of our bacterial biota, as
kill a wide range of bacteria and so can change the balance of our well as treatments designed to keep our microbiome—and, so,
intestinal microbiota. Clinical studies show that the incidence of ourselves—healthy. •
Core Concepts Summary organic molecules and the production of ATP in limited
quantities. page 536
26.1 The tree of life has three main branches, called Some photosynthetic bacteria are photoheterotrophs, obtaining
domains: Eukarya, Bacteria, and Archaea. energy from sunlight but using preformed organic compounds
rather than CO2 as a source of carbon. page 537
Prokaryotic cells are cells that lack a nucleus; they include
Bacteria and Archaea. page 530 Chemoautotrophy, in which chemical energy is used to convert
CO2 to organic molecules, is unique to Bacteria and Archaea.
Bacteria are small and lack membrane-bounded organelles.
page 537
page 530
The bacterial genome is circular. Some bacteria also carry 26.3 In addition to their key roles in the carbon cycle,
smaller circles of DNA called plasmids. page 530 Bacteria and Archaea are critical to the biological cycling
Diffusion limits size in bacterial cells. page 530
of sulfur and nitrogen.
Bacteria can obtain DNA by horizontal gene transfer from Plants and algae can take up sulfur and incorporate it into
organisms that may be distantly related. page 532 proteins, but bacteria and archaeons dominate the sulfur cycle
by means of oxidation and reduction reactions that are linked to
Like Bacteria, Archaea lack a nucleus, but form a second
the carbon cycle. page 538
prokaryotic domain distinct from Bacteria. page 534
Some bacteria and archaeons can reduce nitrogen gas to
Some archaeons are extremophiles, living in extreme
ammonia in a process called nitrogen fixation. page 539
environments characterized by low pH, high salt, or high
temperatures, but others live in less extreme environments like The nitrogen cycle also involves oxidation and reduction
the upper ocean or soil. page 534 reactions by Bacteria and Archaea that are linked to the
carbon cycle. page 540
26.2 Bacteria and Archaea are notable for their
metabolic diversity. 26.4 The extent of bacterial diversity was recognized
when sequencing technologies could be applied to non-
Bacteria are capable of oxygenic photosynthesis, using water
culturable bacteria.
as a source of electrons and producing oxygen as a by-product,
and of anoxygenic photosynthesis, using electron donors other Traditionally, bacterial groups were recognized by morphology,
than water, such as H2S, H2, and Fe21. page 535 physiology, and the ability to take up specific stains in culture.
Some bacteria and archaeons are capable of anaerobic page 540
respiration, in which NO32, SO422, Mn41, and Fe31 serve as the Direct sequencing of ribosomal RNA genes from organisms in
electron acceptor instead of oxygen gas. page 535 soil and seawater samples revealed new groups of bacteria.
Many bacteria and archaeons obtain energy from page 540
fermentation, which involves the partial oxidation of
552 SELF-ASSESSMENT
Proteobacteria are the most diverse group of bacteria and are The early atmosphere and ocean contained little or no free
involved in many of the biogeochemical processes that are linked oxygen. page 548
to the carbon cycle. page 543
Oxygen began to accumulate in the atmosphere and oceans
Gram-positive bacteria include important disease-causing strains about 2.4 billion years ago as a result of the success of
as well as species that are principal sources of antibiotics. cyanobacteria utilizing oxygenic photosynthesis. page 549
page 543
Prokaryotic metabolisms were not only essential in the early
Photosynthetic bacteria are not limited to a single branch of the history of Earth, but are also vital today, as many forms of life
bacterial tree. page 544 depend on biogeochemical cycles and metabolisms unique to
Bacteria and Archaea. page 549
26.5 The diversity of Archaea has only recently been Most animals, including humans, live in intimate association
recognized. with bacteria, which in turn affect health. page 550
Archaeons tend to thrive where energy available for growth is
limited. page 545
Self-Assessment
Archaea are commonly divided into three major groups, the
1. Name and describe the three domains of life.
Crenarchaeota, Thaumarchaeota, and Euryarchaeota.
page 545 2. Describe shared and contrasting features of bacterial and
archaeal cells.
Archaeons at the base of the Crenarchaeota and Euryarchaeota
are hyperthermophiles, meaning that they grow at high 3. Explain how prokaryotic cells obtain nutrients and how this
temperatures. page 545 process puts constraints on their size.
A number of archaeons grow in highly acidic waters, such as 4. Describe how surface area and volume change with size.
those associated with acid mine drainage. page 546
5. Explain how photosynthesis can occur without the
Some archaeons (but no bacteria or eukaryotes) generate production of oxygen, and how respiration can occur without
methane as a by-product of their energy metabolism, requiring oxygen.
contributing in important ways to the carbon cycle. page 546
6. Describe the roles of bacteria and archaeons in the sulfur
Haloarchaea are archaeons that can live only in extremely salty and nitrogen cycles.
environments. page 546 7. Explain how horizontal gene transfer complicates our
Thaumarchaeotes are among the most abundant cells in the understanding of evolutionary relationships among bacteria
oceans. page 546 and archaeons.
Eukaryotic Cells
Origins and Diversity
Core Concepts
27.1 Eukaryotic cells are defined
by the presence of a nucleus,
but features like a dynamic
cytoskeleton and membrane
system explain their success in
diversifying.
27.2 The endosymbiotic hypothesis
proposes that the chloroplasts
and mitochondria of eukaryotic
cells were originally free-living
bacteria.
27.3 Eukaryotes were formerly
divided into four kingdoms, but
are now divided into at least
seven superkingdoms.
27.4 The fossil record extends our
understanding of eukaryotic
diversity by providing
perspectives on the timing
and environmental context of
eukaryotic evolution.
Lebendkulturen.de/Shutterstock.
553
554 SECTION 27.1 T H E E U K A RYOT I C C E L L : A R E V I E W
FIG. 27.2 Phagocytosis. The flexibility of the eukaryotic cytoskeleton and membrane system enables eukaryotic cells to engulf food particles,
including other cells. This sequence shows an amoeba engulfing a yeast cell. Note how the cell membrane (green) folds inward locally
to form a vesicle around the red food particle. Source: V. Mercanti, S. J. Charette, N. Bennett, J. J. Ryckewaert, F. Letourneur, and P. Cosson, 2006, “Selective
Membrane Exclusion in Phagocytic and Macropinocytic Cups,” Journal of Cell Science 119:4079– 4067.
Intracellular vesicles and the molecules they carry are foodstuffs, including other animals and plants. In consequence,
transported through the cytoplasm by means of molecular motors eukaryotes can exploit sources of food not readily available to
associated with the cytoskeleton (Chapter 10). In this way, both bacterial heterotrophs, which feed on individual molecules. This
nutrients and signaling molecules move through the cell at speeds ability opens up a great new ecological possibility—predation—
much greater than diffusion allows. A major consequence is that increasing the complexity of interactions among organisms.
eukaryotic cells can be much larger than most bacteria. The structural flexibility of eukaryotic cells also allows
The cytoskeleton and membrane system are flexible in another photosynthetic eukaryotes to interact with their environment
way: A change in the expression of a few genes can change their in ways that photosynthetic bacteria cannot. Unicellular algae
shape and organization. This makes possible yet another hallmark (which are eukaryotes) can move effectively through surface
of eukaryotic evolution—complex multicellularity (Chapter 28). waters vertically as well as horizontally and therefore can seek
In complex multicellular organisms, patterns of gene expression and exploit local patches of nutrients. Diatoms, discussed shortly,
can modify the cytoskeleton and membranes of individual cells, go one step further. Large internal vacuoles allow them to store
enabling them to function in different ways. nutrients for later use when nutrient levels in the environment
may become low. Plants have evolved multicellular bodies with
In eukaryotic cells, energy metabolism is localized in many different cell types, allowing them to capture sunlight many
mitochondria and chloroplasts. meters above the ground. That ability gives plants a tremendous
Relative to prokaryotic organisms, eukaryotes are fairly limited in advantage on land, as long as their leaves can obtain water and
the ways they obtain carbon and energy. Moreover, the metabolic nutrients from the soil in which the plants are rooted.
processes that power eukaryotic cells take place only in specific
organelles—aerobic respiration in the mitochondrion (Chapter 7) The organization of the eukaryotic genome also helps
and photosynthesis in the chloroplast (Chapter 8). Only limited explain eukaryotic diversity.
anaerobic processing of food molecules takes place within the Bacteria and Archaea absorb available nutrients quickly, and both
cytoplasm. rapid deployment of metabolic proteins and rapid reproduction
As noted above, many eukaryotic cells engulf food particles are key to the exploitation of patchily distributed nutrients.
and package them inside a vesicle, which is then transported As the majority of a prokaryote’s DNA is arrayed in a single
into the cytoplasm. Within the cytoplasm, enzymes break circular chromosome, speed of replication allows for speed of
down the particles into molecules that can be processed by the reproduction. As a result, selection favors those strains of Bacteria
mitochondria. Many single-celled eukaryotes feed on bacteria and Archaea that retain only the genetic material vital to the
or other eukaryotic cells, and animals, in turn, ingest larger organism.
556 SECTION 27.1 T H E E U K A RYOT I C C E L L : A R E V I E W
Eukaryotes have multiple linear chromosomes and can bdelloid rotifers. The genetic diversity of these organisms is
begin replication from many sites on each one. Eukaryotes are actually high, maintained by high rates of horizontal gene transfer.
thus able to replicate multiple strands of DNA simultaneously Meiotic cell division results in cells with one set of
and rapidly (Chapter 12). This ability relieves the evolutionary chromosomes. Such cells are haploid. Sexual fusion brings two
pressure for streamlining, allowing eukaryotic genomes to build haploid (1n) cells together to produce a diploid (2n) cell that has
up large amounts of DNA that do not code for proteins. Most of two sets of chromosomes. The life cycle of sexually reproducing
this additional DNA was originally considered to have no function eukaryotes, then, necessarily alternates between haploid and
and, indeed, was called “junk DNA.” That view, however, has been diploid states.
modified in recent years, as the complete genome has come to Many single-celled eukaryotes normally exist in the haploid
be better understood (Chapter 13). Eukaryotic genomes appear stage and reproduce asexually by mitotic cell division (Fig. 27.3a).
to contain truly junky DNA, but at least some of the DNA that The green alga Chlamydomonas is one such organism. Under
does not code for proteins functions in gene regulation (Chapter the right conditions, however—typically, starvation or other
19). This regulatory DNA gives eukaryotes the fine control of environmental stress—two cells fuse, forming a diploid cell, or
gene expression required for both multicellular development and zygote. The zygote formed by these single-celled eukaryotes
complex life cycles, two major features of eukaryotic diversity. commonly functions as a resting cell. It covers itself with a
At this point, it can be seen that the evolutionary success of protective wall and then lies dormant until environmental
eukaryotes rests on a combination of features. The innovations conditions improve. In time, further signals from the environment
of dynamic cytoskeletal and membrane systems gave eukaryotes induce meiotic cell division, resulting in four genetically distinct
the structure required for larger cells with complex shapes and haploid cells that emerge from their protective coating to
the ability to ingest other cells. Thus, early unicellular eukaryotes complete the life cycle.
did not gain a foothold in microbial ecosystems by outcompeting As shown in Fig. 27.3b, some single-celled eukaryotes
bacteria and archaeons. Instead, they succeeded by evolving normally exist as diploid cells. An example is provided by the
novel functions. Along with the capacity to remodel cell shape, diatoms, single-celled eukaryotes commonly found in lakes, soils,
eukaryotes evolved complex patterns of gene regulation, which in and the oceans. Diatom cells are mostly diploid and reproduce
turn enabled unicellular eukaryotes to evolve complex life cycles asexually by mitotic cell division to make more diploid cells.
and multicellular eukaryotes to generate multiple, interacting cell Because their mineralized skeletons constrain growth, diatoms
types during growth and development. These abilities opened up become smaller with each asexual division. Once a critical size
still more possibilities for novel functions, which we explore in is reached, meiotic cell division is triggered, producing haploid
this and later chapters. gametes that fuse to regenerate the diploid state as a round, thick-
walled cell. This cell eventually germinates to form an actively
j Quick Check 1 How did the evolutionary expansion of
growing, skeletonized cell. In diatoms, then, short-lived gametes
eukaryotic organisms change the way carbon is cycled through
constitute the only haploid phase of the life cycle.
biological communities?
The two life cycles just introduced, of Chlamydomonas and
diatoms, are similar in many ways. In both, haploid cells fuse to
Sex promotes genetic diversity in eukaryotes and gives form diploid cells, and diploid cells undergo meiotic cell division to
rise to distinctive life cycles. generate haploid cells. Both life cycles also commonly include cells
In Chapter 26, we saw how Bacteria and Archaea generate genetic capable of persisting in a protected form when the environment
diversity by horizontal gene transfer. Horizontal gene transfer becomes stressful. Why some single-celled eukaryotes usually
has been documented in eukaryotic species, but it is relatively occur as haploid cells and others usually occur as diploid cells
uncommon. How then do eukaryotes generate and maintain remains unknown—a good question for continuing research.
genetic diversity within populations? The answer is sex. Sexual reproduction has never been observed in some
Sexual reproduction involves meiosis and the formation eukaryotes, but most species appear to be capable of sex, even
of gametes, and the subsequent fusion of gametes during if they reproduce asexually most of the time. Variations on
fertilization (Chapters 11 and 42). Sex promotes genetic variation the eukaryotic life cycle can be complex, especially in parasitic
in two simple ways. First, meiotic cell division results in microorganisms that have multiple animal hosts. All, however,
gametes or spores that are genetically unique. Each gamete has a have the same fundamental components as the two life cycles
combination of alleles different from the other gametes and from described here.
the parental cell as a result of recombination and independent In the following chapters, we discuss multicellular organisms in
assortment. Second, in fertilization, new combinations of genes detail. Here we note only that animals, plants, and other complex
are brought together by the fusion of gametes. Interestingly, a few multicellular organisms have life cycles with the same features as
eukaryotic groups have lost the capacity for sexual reproduction. those just discussed. The big difference is that in animals, the zygote
The best-studied of these eukaryotes are tiny animals called divides many times to form a multicellular diploid body before a
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 557
FIG. 27.3 Eukaryotic life cycles. (a and b) The life cycles of single-celled eukaryotes differ in the proportion of time spent as haploid (1n) versus
diploid (2n) cells. (c) The life cycles of animals have many mitotic divisions between formation of the zygote and meiosis. (d) Vascular
plants have two multicellular phases.
a. Unicellular eukaryote with prominent haploid phase b. Unicellular eukaryote with prominent diploid phase
1n 1n
Fusion Fusion
Asexual Asexual
reproduction Sexual Sexual
1n 2n 1n 2n reproduction
by mitosis cycle cycle
by mitosis
Meiosis Meiosis
1n 1n
1n 1n
1n 1n
1n Sperm 1n
1n
1n 1n 1n multi- Fusion Zygote
Reproductive 2n
2n multi- cellular body
cell Meiosis 1n
cellular body 2n 1n Growth
Gamete by mitosis
Egg Fusion (egg/sperm)
Zygote 2n
Spore
Growth by mitosis Growth 2n multi-
by mitosis 1n cellular body
2n
1n Meiosis Reproductive
cell
1n
small subset of cells within the body undergoes meiotic cell division 1n
symbiotic cyanobacteria that through time became permanently became clear that the chloroplasts in red and green algae (and in
incorporated into their hosts. Such a symbiosis, in which one land plants) are separated from the cytoplasm that surrounds them
partner lives within the other, is called an endosymbiosis. by two membranes. This is expected if a cyanobacterial cell had been
Merezkhovsky’s hypothesis of chloroplast origin by endosymbiosis engulfed by a eukaryotic cell. The inner membrane corresponds
was difficult to test with the tools available in the early twentieth to the cell membrane of the cyanobacterium, and the outer one is
century, and his idea was dismissed, more neglected than part of the engulfing cell’s membrane system, as shown in Fig. 27.2.
disproved, by most biologists. In addition, the biochemistry of photosynthesis was found to be
In 1967, American biologist Lynn Margulis resurrected the essentially the same in cyanobacteria and chloroplasts. Both use
endosymbiotic hypothesis, supporting her arguments with new two linked photosystems, a common mechanism for extracting
types of data made possible by the then-emerging techniques electrons from water, and the same reactions to reduce carbon
of cell and molecular biology (Fig. 27.4). Transmission electron dioxide (CO2) into organic matter (Chapter 8).
microscopy showed that structural similarities between chloroplasts Such observations kindled renewed interest in the
and cyanobacteria extend to the submicrometer level, for example endosymbiotic hypothesis, but the decisive tests were made
in the organization of the photosynthetic membranes. It also possible by another, and unexpected, discovery. It turns out
HOW DO WE KNOW?
FIG. 27.4
SOURCE Giovannoni, S. J., et al. 1988. “Evolutionary Relationships Among Cyanobacteria and
Green Chloroplasts.” Journal of Bacteriology 170:3584–3592. Photos (top to bottom): Dr. Kari
Lounatmaa/Science Source; Biology Pics/Getty Images; Dr. Jeremy Burgess/Science Source.
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 559
FIG. 27.6 Transmission electron microscope images comparing mitochondria within the aerobic protist Euplotes (left) and Nyctotherus, a
close relative that lives in anoxic environments (right). The organelle in Nyctotherus is halfway between a normal mitochondrion and
a hydrogenosome, supporting the view that these two organelles are descended from a common ancestor. Source: Reprinted by permission
from Macmillan Publishers Ltd: B. Boxma, et al., 2005, “An Anaerobic Mitochondrion That Produces Hydrogen,” Nature 434:74–79. Copyright 2005.
1µm 1µm
Normal mitochondrion in Euplotes Altered mitochondrion in Nyctotherus produces ATP and generates hydrogen.
The small dark body in lower right is an endosymbiotic archaeon.
? CASE 5 THE HUMAN MICROBIOME: DIVERSITY WITHIN recently revealed a previously known archaeon whose genome
How did the eukaryotic cell originate? encodes actin-like proteins and other molecules fundamental
If mitochondria originated as proteobacteria and chloroplasts to cell organization, vesicle trafficking and phagocytosis in
are descended from cyanobacteria, where does the rest of the eukaryotes. Gene sequence comparisons, in fact, place these
eukaryotic cell come from? Analysis of the nuclear genome alone novel archaeons as the closest relatives of eukaryotes. An
provides no clear picture because genes of bacterial, archaeal, archaeal component of the eukaryotic cell seems assured, but
and purely eukaryotic origin are all present. As discussed, many some biologists argue that no eukaryotic cell existed before
nuclear genes originated with the mitochondria and chloroplasts there were mitochondria. Instead, they propose that the
acquired from specific bacteria. However, genes from other eukaryotic cell as a whole began as a symbiotic association
groups of bacteria also reside in the eukaryotic nucleus, between a proteobacterium and an archaeon (Fig. 27.7). The
recording multiple episodes of horizontal gene transfer through proteobacterium became the mitochondrion and provided many
evolutionary history. In contrast, some genes are present only in genes to the nuclear genome. The archaeon provided other
eukaryotes and apparently evolved after the domain originated. genes, including those used to transcribe DNA and translate it
Still others, including the genes that govern DNA transcription into proteins.
and translation, are clearly related to the genes of Archaea. Biologists continue to debate these alternatives. Both
Two starkly different hypotheses have been proposed to hypotheses explain the hybrid nature of the eukaryotic genome,
explain this mix of genes. Some biologists believe that the but neither fully explains the origins and evolution of the
host for mitochondrion-producing endosymbiosis was itself a nucleus, linear chromosomes, the eukaryotic cytoskeleton, or
true eukaryotic cell. This cell had a nucleus, cytoskeleton, and a cytoplasm subdivided by ever-changing membranes. There is
endomembrane system, but only limited ability to derive energy no consensus on the question of eukaryotic origins—it is one
from organic molecules (Fig. 27.7). In this view, nuclear genes of biology’s deepest unanswered questions, awaiting novel
in Eukarya resemble those of Archaea because the primordial observations by a new generation of biologists. Once a dynamic
eukaryotic host cell was closely related to Archaea. cytoskeleton became coupled to a flexible membrane system,
In striking support of this hypothesis, microbiological however, the evolutionary possibilities of eukaryotic form were
exploration of hydrothermal vents beneath the Arctic ocean established.
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 561
FIG. 27.7 Two hypotheses for the origin of the eukaryotic cell. Both hypotheses lead to the evolution of a mitochondrion-bearing protist.
Hypothesis 1 Hypothesis 2
Eukaryotic cells evolved from an ancestral archaeon Eukaryotic cells evolved from a symbiosis
and only later incorporated the proteobacterial cell between an archaeon and a proteobacterium.
that became a mitochondrion. The proteobacterium became a mitochondrion.
DNA Ancestral
archaeon
Cytoplasm
Plasma
membrane Archaeon
Proteobacterium
Infolding
of plasma
membrane
True eukaryotic
cell with nucleus,
cytoplasm, and
endomembrane
system
Engulfing
of facultatively
aerobic
proteobacterium
Infolding of
plasma membrane
to produce true
eukaryote
Mitochondria Mitochondria
In the oceans, many single-celled eukaryotes harbor substance. Scientists hypothesize that the bacteria benefit from
symbiotic bacteria. this association as well because they get a free ride through the
The evolution of the eukaryotic cell is marked by intimate sediments, enabling these chemoautotrophs to maximize growth
associations between formerly free-living organisms. An by remaining near the boundary between waters that contain
unexpected symbiosis was recently discovered in the Santa Barbara oxygen and those rich in sulfide.
Basin, a local depression in the seafloor off the coast of southern The diversity of these eukaryotic–bacterial symbioses is
California. Sediments accumulating in this basin contain little remarkable—and poorly studied. What has been learned to
oxygen but large amounts of hydrogen sulfide (H2S) generated by date, however, shows that single-celled eukaryotes have evolved
anaerobic bacteria within the sediments. We might predict that numerous symbiotic relationships with chemoautotrophic
eukaryotic cells would be uncommon in these sediments. Not bacteria, associations that feed and protect the eukaryotes,
only is oxygen scarce, but also sulfide actively inhibits respiration enabling them to colonize habitats where most eukaryotes cannot
in mitochondria. It came as a surprise, then, that samples of live. Clearly, then, the types of symbioses that led to mitochondria
sediment from the Santa Barbara Basin contain large populations and chloroplasts on the early Earth were not rare events, but basic
of single-celled eukaryotes. associations between cells that continue to evolve today.
Some of these cells have hydrogenosomes, mitochondria
altered by evolution to generate energy where oxygen is absent.
Others, however, appear to thrive by supporting populations of 27.3 EUKARYOTIC DIVERSITY
symbiotic bacteria on or within their cells. In one case, rod-shaped
bacteria cover the surface of their eukaryotic host (Fig. 27.8). Historically, Domain Eukarya was divided into four kingdoms:
Research has shown that the bacteria metabolize sulfide in the plants, animals, fungi, and protists. Plants, animals, and fungi
local environment, thereby protecting their host from this toxic received special consideration for the obvious reason that
they include large and relatively easily studied species. All
remaining eukaryotes were grouped together as protists, which
were defined as organisms having a nucleus but lacking other
FIG. 27.8 Scanning electron microscope image of bacterial cells features specific to plants, animals, or fungi. The term “protist”
on the surface of a single-celled eukaryote found in is frowned on by some biologists because it doesn’t refer to a
oxygen-depleted sediments in the Santa Barbara Basin, monophyletic grouping of species—that is, an ancestral form
off the coast of California. The bacteria are hypothesized and all its descendants. Nonetheless, as an informal term that
to metabolize the H2S in this environment, thereby draws attention to a group of organisms sharing particular
protecting the eukaryote that they enclose. Source: Reprinted characteristics, “protist” usefully describes the diverse world of
by permission from Macmillan Publishers Ltd: V. P. Edgcomb, S. A. microscopic eukaryotes and seaweeds.
Breglia, N. Yubuki, D. Beaudoin, D. J. Patterson, B. S. Leander, and Two other terms scorned by some biologists but embraced by
J. M. Bernhard, 2011, “Identity of Epibiotic Bacteria on Symbiontid ecologists are “algae” and “protozoa.” Algae are photosynthetic
Euglenozoans in O2-Depleted Marine Sediments: Evidence for Symbiont protists. They may be microscopic single-celled organisms or the
and Host Co-evolution,” The ISME Journal 5:231–243. Copyright 2010. highly visible, multicelled organisms we call seaweed. Protozoa
Courtesy of Naoji Yubuki. are heterotrophic protists. These are almost exclusively single-
celled organisms. “Algae” and “protozoa” in fact are simple and
2 µm useful terms that have little phylogenetic meaning but which
convey a great deal of information about the structure and
function of these organisms.
Protist cells exhibit remarkable diversity. Some have cell
walls, while others do not. Some make skeletons of silica (SiO2)
or calcium carbonate (CaCO3), and others are naked or live within
tests, or “houses,” constructed exclusively of organic molecules.
Some are photosynthetic, while others are heterotrophic. Some
move by beating flagella, and others, like Amoeba, can extend
fingers of cytoplasm, called pseudopodia, to move and capture
food. Most are aerobic, but there are anaerobic protists as well.
Surprisingly, most of these distinctive features have evolved
multiple times and so do not define phylogenetically coherent
groups. As a result, our understanding of evolutionary pattern in
Eukarya had to wait for the molecular age.
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 563
Fig. 27.9 shows a phylogenetic tree of eukaryotes as biologists seem to wander from position to position from one phylogenetic
currently understand it. As in the case of Bacteria, it is easier analysis to the next, sometimes moving together, sometimes
to identify major groups of Eukarya than to establish their separately. Whether the well-resolved superkingdoms constitute
evolutionary relationships to one another. Molecular sequence the only major limbs on the eukaryotic tree is less certain. Many
comparisons consistently recognize seven major groups, called microscopic protists remain unstudied, and we may yet be
superkingdoms, noted in the figure. Animals fall within one surprised by what they show.
of these superkingdoms, the Opisthokonta, whereas plants fall In the following sections, we introduce the major features
within another, the Archaeplastida. Most, but not all, of the of eukaryotic diversity. The species numbers we present indicate
divisions into these major eukaryotic branches are strongly only the taxonomic diversity that is known to us; most protistan
supported by data from genes and genomes. A few groups, notably species remain unknown. Many biologists estimate that only
the cryptophytes, haptophytes, and centrohelid heliozoans, about 1 in 10 protist species has been described so far. As this
is also the case for animals and fungi (but arguably not for land
plants because they are all visible to the naked eye), the relative
FIG. 27.9 The eukaryotic tree of life showing major groups. numbers of species within different superkingdoms may reflect
Branches with photosynthetic species (shown in green) something like the actual distribution of biodiversity among
are distributed widely. Additional branches, including eukaryotes.
animals, foraminiferans, radiolarians, and ciliates, contain
Our own group, the opisthokonts, is the most diverse
species that harbor photosynthetic symbionts. Dashed
eukaryotic superkingdom.
lines indicate a high degree of uncertainty.
Over the past 250 years, biologists have described about
Animals 1.8 million species. Of these, 75% or so fall within the
Choanoflagellates Opisthokonts Opisthokonta (Fig. 27.10), a group that encompasses animals,
fungi, and some protists. The name for this superkingdom is
Fungi
derived from Greek words meaning “posterior pole,” calling
Dictyostelid slime molds
attention to the fact that cell movement within this group is
Plasmodial slime molds propelled by a single flagellum attached to the posterior end of the
Entamoebas Amoebozoans cell. Not all cells in this superkingdom move around. In humans,
Flabellinea for example, the flagellum is limited to sperm. Opisthokonts are
Tubulinea heterotrophic, although some species harbor photosynthetic
symbionts. Animals are the most diverse and conspicuous
Glaucocystophytes
opisthokonts. More than 1.3 million animal species, mostly insects
Red algae Archaeplastids
and their relatives, have been described. Fungi are also diverse,
Green algae (land plants) with more than 75,000 described species, including the visually
Diatoms arresting mushrooms (Fig. 27.10a). Here, however, we focus on
Brown algae Stramenopiles opisthokont protists, somewhat poorly known microorganisms
that hold clues to the origins of complex multicellularity in this
Oomycetes
superkingdom (Chapter 28).
Dinoflagellates It isn’t easy to find morphological characters that unite all
Apicomplexans Alveolates opisthokonts. One reason is that animals and fungi have diverged
Ciliates so strikingly from what must have been the ancestral condition
Cercozoans of the group. However, as molecular sequence comparisons began
to reshape our understanding of eukaryotic phylogeny, it soon
Foraminifera Rhizarians
became clear that fungi and animals are closely related.
Radiolaria
Even more closely related to the animals are the
Cryptophytes choanoflagellates, a group of mostly unicellular protists
Haptophytes characterized by a ring of microvilli, fingerlike projections that
Centrohelid heliozoans form a collar around the cell’s single flagellum (Fig. 27.10b). About
150 choanoflagellate species have been described from marine
Euglenids
and freshwater environments, where they prey on bacteria. As
Trypanosomes
Excavates early as 1841, the close similarity between choanoflagellates
Diplomonads and the collared feeding cells of sponges suggested that these
Parabasalids minute organisms might be our closest protistan relatives. This
564 SECTION 27.3 E U K A RYOT I C D I V E R S I T Y
FIG. 27.10 Opisthokonts. This superkingdom includes animals and fungi, as well as several protistan groups, including choanoflagellates, the
closest protistan relatives of animals. Photo source: Nicole King, Steve Paddock, and Sean Carroll, HHMI, University of Wisconsin.
a. b. Choanoflagellates
Opisthokonts Most diverse groups
Stramenopiles
Alveolates
Rhizarians
Excavates Animals
10 µm
Choanoflagellates
Filastereans
Ichthyosporids
Nucleariids
Microsporidians Cell Microvilli Flagellum
body
Fungi
view gained widespread popularity with the discovery in 1880 of mitochondria, no Golgi apparatus, and no flagella. Furthermore,
Proterospongia haeckeli, a choanoflagellate that lives in colonies of they have a highly reduced metabolism and among the smallest
cells joined by adhesive proteins. genomes of any known eukaryote. The cellular simplicity of
Molecular sequence comparisons now confirm the close microsporidians does not mean that they are early-evolved
relationship between animals and choanoflagellates. For example, organisms, however. Molecular sequencing studies show that
the complete genome of the choanoflagellate Monosiga brevicollis microsporidians are the descendants of more complex organisms.
shows that a number of signaling molecules known to play a Their simplicity is an adaptation for life as an intracellular parasite.
role in animal development are present in our choanoflagellate It is now widely accepted that microsporidians are closely related
relatives, although their function in these single-celled organisms to the fungi.
remains largely unknown. More generally, many genes once Other protistan opisthokonts have been identified in recent
thought to be unique to animals have now been identified years. These are mostly bacteria-eating unicells or parasites of
in choanoflagellates and other unicellular opisthokonts, aquatic animals, but like the choanoflagellates described earlier,
underscoring the deep evolutionary roots of animal biology. their biology is beginning to illuminate the evolutionary path to
Microsporidia form another group of single-celled complex multicellularity in animals and fungi.
opisthokonts. Microsporidia are parasites that live inside animal
cells. Only their spores survive in the external environment, Amoebozoans include slime molds that produce
where they await the opportunity to infect a host and complete multicellular structures.
their life cycle. Microsporidia infect all animal phyla, so the Previously in this chapter, we learned one thing about amoebas:
approximately 1000 known species probably represent only the they move and feed by extending cytoplasmic fingers called
tip of the iceberg. More than a dozen species have been isolated pseudopodia. As its name implies, the superkingdom Amoebozoa
from human intestinal tissues. Microsporidia infections can be (Fig. 27.11a) is a group of eukaryotes with amoeba-like cells
particularly devastating in AIDS patients. (illustrated by Amoeba proteus in Fig. 27.11b). More than 1000
Beyond their importance in human health, microsporidians amoebozoan species have been described. In some amoebozoan
have attracted the attention of biologists because of features species, large numbers of cells aggregate to form multicellular
they lack: Microsporidian cells have no aerobically respiring structures as part of their life cycle.
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 565
FIG. 27.11 Amoebozoans. This group includes protists with an amoeboid stage in their life cycle. Photo sources: b. M. I. Walker/Science Source; c. AFIP/
Science Source.
Amoebozoans
Archaeplastids
Stramenopiles
Alveolates
Rhizarians
200 µm 10 µm
Excavates
Although there are amoeba-like cells that are not members one giant cell. The plasmodia can move and so seek out and feed
of the Amoebozoa superkingdom, all members of this group have on the bacteria and small fungi commonly found on bark or
cells similar to that of Amoeba, at least at some stage of their life plant litter on the forest floor. Triggered by poorly understood
cycle. Amoebozoans play an important role in soils as predators environmental signals, plasmodia eventually differentiate to form
on other microorganisms. Some amoebozoans cause disease in stalked structures called sporangia that can be 1 to 2 mm high (Fig.
humans. For example, Entamoeba histolytica (Fig. 27.11c), an 27.12b). Within the mature sporangium, cell walls form around the
anaerobic protist that causes amoebic dysentery, is responsible for many nuclei, producing discrete cells. These cells undergo meiosis,
50,000–100,000 deaths every year. generating haploid spores that disperse into the environment.
Beyond considerations of human health, the amoebozoans Germination of these spores begins the life cycle anew.
of greatest biological interest are the slime molds. In plasmodial Cellular slime molds (Fig. 27.13) are a second type of slime
slime molds (Fig. 27.12), haploid cells fuse to form zygotes that mold. These slime molds spend most of their life cycle as solitary
subsequently undergo repeated rounds of mitosis but not cell amoeboid cells feeding on bacteria in the soil. Starvation,
division to form colorful, often lacy structures visible to the however, causes these cells to produce the chemical signal cyclic
naked eye (Fig. 27.12a). These structures, called plasmodia, are AMP (Chapter 9), which induces as many as 100,000 cells to
coenocytic, which means they contain many nuclei within aggregate into a large multicellular slug-like form (Fig. 27.13a).
FIG. 27.12 Plasmodial slime molds. (a) Plasmodia, such as this pretzel slime mold, are coenocytic structures containing many nuclei.
(b) Plasmodia generate sporangia, stalked structures that produce spores for dispersal. Sources: a. Matt Meadows/Science Source;
b. Ray Simons/Getty Images.
a b
10 mm 1 mm
566 SECTION 27.3 E U K A RYOT I C D I V E R S I T Y
FIG. 27.14 Archaeplastids. (a) Archaeplastids are a photosynthetic group descended from the protist that acquired photosynthesis from an
endosymbiotic cyanobacterium. They include the (b) glaucocystophytes, (c) red algae, and (d) green algae and their descendants,
the land plants. Photo sources: b. Jerome Pickett-Heaps/Science Source; c. Dr. D. P. Wilson/Science Source; d. D. J. Patterson.
a. b. Glaucocystophyte
Opisthokonts Most diverse groups
Alveolates
Rhizarians 2 µm
c. Red algae
Excavates
Glaucocystophytes
Red algae
Chlorophytes
100 µm
Flagellated
unicells Green
algae d. Green algae
Viridoplantae
Streptophyte
algae
Land plants 10 µm
tiny single-celled flagellates to meter-scale seaweeds (Fig. 27.15). branch, the chlorophytes, radiated mostly in the sea and includes
They all are united by two features: the presence of chlorophyll a common seaweeds seen globally along seashores (Fig. 27.15e).
and chlorophyll b in chloroplasts that have two membranes, and a Chlorophyte green algae have also played a major role in laboratory
unique attachment for flagella. studies of photosynthesis (Chlamydomonas, Fig. 27.15a) and
It is thought that green algae originated as small flagellated multicellularity (Volvox, Fig. 27.15d).
cells, and today most species that branch early on the green algal For humans, however, the more important branch of the green
tree still live as photosynthetic cells in marine or fresh waters (Fig. algal tree is the one that diversified in freshwater and, eventually,
27.15a). The larger diversity of green algae, however, is found on on land. Called streptophytes, the species on this branch show
two branches that diverged from these flagellated ancestors. One a progression of form from unicells at the base through simple
568 SECTION 27.3 E U K A RYOT I C D I V E R S I T Y
FIG. 27.15 Diversity of green algae. (a) Chlamydomonas reinhardtii, a tiny flagellated unicell widely used in laboratory research on
photosynthesis; (b) Spirogyra, a freshwater green alga with distinctive helical chloroplasts; (c) a desmid, among the most diverse
and widespread of all green algae in fresh water; (d) Volvox, a simple multicellular organism; and (e) Acetabularia, a macroscopic
(but single-celled!) green alga found in coastal marine waters in tropical climates. Sources: a. DeAgostini/Getty Images; b. Eric Grave/Phototake;
c. Gerd Guenther/Science Source; d. Frank Fox/Science Source; e. Wolfgang Poelzer/age fotostock.
a c e
FPO
50 µm
5 µm d
50 µm 50 µm 1 mm
cell clusters and filaments on intermediate branches (Figs. and these protists also play important roles in the ecology of lakes,
27.15b and 21.15c), to complex multicellular algae that form rivers, and soils.
the closest relatives of land plants (Chapter 33). As was true of The superkingdom Stramenopila (see Fig. 27.9) includes
choanoflagellates and animals, green algae display features of cell unicellular organisms and giant kelps, algae and protozoa, free-
biology and genomics that tie them unequivocally to land plants. living cells and parasites. All have an unusual flagellum that bears
two rows of stiff hairs (Fig. 27.16). Most also have a second,
j Quick Check 2 Do plants and animals have a common
smooth flagellum.
multicellular ancestor?
Despite the presence of heterotrophic species, most
stramenopiles are photosynthetic. There are about a dozen
Stramenopiles, alveolates, and rhizarians dominate groups of stramenopile algae, of which the brown algae and
eukaryotic diversity in the oceans. diatoms deserve special mention. Brown seaweeds are common
The phylogenetically related superkingdoms called the along rocky shorelines across the world, and in the Sargasso Sea,
stramenopiles, alveolates, and rhizarians may not be household huge masses of ropy brown algae (aptly named Sargassum)
names, but perhaps they should be. The surface ocean hosts three float at the surface. Easily the most impressive brown algae are
species belonging to these groups for every marine animal species, the kelps, giant seaweeds that form forests above the seafloor
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 569
FIG. 27.16 Stramenopiles. This electron micrograph of a FIG. 27.17 Kelps. These complex multicellular brown algae can
unicellular stramenopile shows a flagellum with two form “forests” tens of meters high in the ocean. Source:
rows of stiff hairs. Like this cell, most stramenopiles Mark Conlin/Alamy.
also have a second, smooth flagellum. Source: D. J.
Patterson,image used under license to MBL (micro*scope).
Hairy
flagellum
Smooth
5 µm
flagellum
a b
FIG. 27.18 Diatoms. Diatoms are the most
diverse stramenopiles, and
among the most diverse of all
protists. Their shapes, outlined
by their tiny skeletons made of
silica (SiO2), can be (a) like a
pill-box, (b) elongated, or
(c) twisted around the long
axis of the cell. Some diatom
10 µm 50 µm
species form colonies, like
those shown in (d). Sources:
c d
a. and b. Steve Gschmeissner/Science
Source; c. Andrew Syred/Science
Source; d. Biophoto Associates/Science
Source.
50 µm 100 µm
570 SECTION 27.3 E U K A RYOT I C D I V E R S I T Y
FIG. 27.20
Amoebozoans
BACKGROUND Many different branches on the eukaryotic tree include Glaucocystophytes
photosynthetic species, commonly interspersed with non-photosynthetic Red algae Archaeplastids
lineages. Did eukaryotes gain photosynthesis once, by the endosymbiotic Green algae
incorporation of a cyanobacterium, and then lose this capacity multiple Diatoms
Brown algae Stramenopiles
times? Or, is the history of photosynthetic endosymbioses more complicated,
involving multiple events of symbiont capture and transformation?
Dinoflagellates
HYPOTHESIS 1 Photosynthesis was established early in eukaryotic Alveolates
evolution and was subsequently lost in some lineages.
Chlorarachniophyte algae
HYPOTHESIS 2 Eukaryotes acquired photosynthesis multiple times by Rhizarians
repeated episodes of endosymbiosis.
Cryptophyte algae
PREDICTIONS The two hypotheses make different predictions. If
photosynthesis were acquired in a single common ancestor of all living
eukaryotes and then lost in some lineages, we would expect chloroplast Euglenids
and nuclear gene phylogenies to show the same pattern of branching.
Excavates
If photosynthesis were acquired multiple independent times, we would
expect chloroplast and nuclear phylogenies to show different patterns.
EXPERIMENT Chloroplasts have DNA, so scientists developed a RESULTS Molecular sequence comparisons show that evolutionary
phylogenetic tree based on molecular sequence comparison of chloroplast relationships among chloroplasts do not mirror those based on
genes (Fig. 27.20a). This phylogeny was then compared with a second nuclear genes. The chlorarachniophyte algae and photosynthetic
phylogeny, for all eukaryotes, based on molecular sequence comparison of euglenids (shown in green) fall in a monophyletic group with the
nuclear genes (Fig. 27.20b). green algae when chloroplast DNA is analyzed (Fig. 27.20a).
However, these groups lie far from
green algae in the phylogeny based
a. Phylogenetic relationships based on chloroplast genes Nuclear genes place brown algae
and diatoms among the on nuclear genes (Fig. 27.20b).
Brown algae
Diatoms
stramenopiles, dinoflagellates Similarly, brown algae, diatoms, most
within the alveolates, and
Most photosynthetic photosynthetic dinoflagellates, and
cryptophytes on their own poorly
dinoflagellates resolved branch. Chloroplast genes, cryptophyte algae (shown in red) form
Cryptophyte algae however, relate them to red algae. a monophyletic group with the red
These groups gained
Red algae algae in the phylogeny based on
photosynthesis by incorporating red
Red algae algal cells as endosymbionts. chloroplast DNA (Fig. 27.20a), but
Green algae analysis of nuclear genes places them in
Euglenids Nuclear genes place different groups (Fig. 27.20b).
chlorarachniophytes and euglenids
Green algae
among the rhizarians and excavates, CONCLUSION The chloroplast and
Chlorarachniophyte algae respectively, but chloroplast genes
Green algae relate them to green algae. Both nuclear phylogenies show different
Green algae groups gained photosynthesis by patterns of branching, supporting the
incorporating green algal cells as
Green algae endosymbionts.
hypothesis that photosynthesis spread
Green algae through the Eukarya by means of
Land plants Chloroplasts form a monophyletic multiple eukaryotic endosymbionts.
Glaucocystophytes grouping nested within the
cyanobacteria—a principal line of
SOURCE Hackett, J. D., et al. 2007. “Plastid
Cyanobacteria evidence supporting the
Endosymbiosis: Sources and Timing of
endosymbiotic origin of chloroplasts.
the Major Events.” In Evolution of Primary
Producers in the Sea, edited by P. G. Falkowski
For branches in black, chloroplast relationships match the phylogeny and A. H. Knoll, 109–132. Boston: Elsevier
indicated by nuclear genes—these groups diverged from the ancestor Academic Press.
in which endosymbiosis first gave rise to chloroplasts.
571
572 SECTION 27.4 T H E F O S S I L R E CO R D O F P ROT I S T S
(a)
on roup be
ils
f lif
Fir of pr (b)
of animals.
oss
nim tists
tes
n
eo
te t ca
yo
ryo ha
en
kar
g
Div uka es t
vid
st a
t
st e
sil
g e yo
vin kar
e
Old
ific
a li eu
ers
Old
to ssil
diversify since that time (Fig. 27.23). Some algal seaweeds also
lin
a b
2 µm
CHAPTER 27 E U K A RYOT I C C E L L S : O R I G I N S A N D D I V E R S I T Y 575
Core Concepts Summary 27.3 Eukaryotes were formerly divided into four
kingdoms, but are now divided into at least seven
27.1 Eukaryotic cells are defined by the presence superkingdoms.
of a nucleus, but features like a dynamic cytoskeleton The terms “protist,” “algae,” and “protozoa” are useful, but do
and membrane system explain their success in not describe monophyletic groups. page 562
diversifying.
Protists are eukaryotes that do not have features of animals,
Eukaryotic cells have a network of proteins inside the plants, and fungi; algae are photosynthetic protists; and protozoa
cell that allow them to change shape, move, and transfer are heterotrophic protists. page 562
substances in and out of the cell. page 554
The seven superkingdoms of eukaryotes are Opisthokonta,
Eukaryotic cells have dynamic membranes that facilitate
Amoebozoa, Archaeplastida, Stramenopila, Alveolata, Rhizaria,
movement and feeding. page 554
and Excavata. page 563
Eukaryotic cells compartmentalize their machinery for
energy metabolism into mitochondria and chloroplasts, Opisthokonts are the most diverse eukaryotic superkingdom.
freeing the cell to interact with the environment in novel They include animals and fungi, as well as choanoflagellates (our
ways not available to prokaryotes. page 555 closest protistan relatives). page 563
The eukaryotic genome is larger than that of prokaryotes, Amoebozoans produce multicellular structures by the
allowing new mechanisms of gene regulation. page 556 aggregation of amoeba-like cells, and include organisms that
cause human disease and those important in biological research.
Sexual reproduction promotes genetic diversity in eukaryotic
page 564
populations. page 556
The archaeplastids, which include land plants, are photo-
27.2 The endosymbiotic hypothesis proposes that the synthetic, and are divided into three major groups. page 566
chloroplasts and mitochondria of eukaryotic cells were
The related superkingdoms called the stramenopiles,
originally free-living bacteria.
alveolates, and rhizarians dominate eukaryotic diversity in the
The endosymbiotic hypothesis is based on physical, oceans. page 568
biochemical, and genetic similarities between chloroplasts
and cyanobacteria, and between mitochondria and 27.4 The fossil record extends our understanding of
proteobacteria. page 557 eukaryotic diversity by providing perspectives on the
Chloroplasts and mitochondria have their own genomes, timing and environmental context of eukaryotic evolution.
but their genomes are small relative to free-living bacteria,
Fossils in sedimentary rocks as old as 1800 million years have
to which they are closely related, mostly because of gene
unmistakable signs of eukaryotic cells, including complicated
migration to the nuclear genome. page 559
wall structures. page 573
Symbiosis between a heterotrophic host and photosynthetic
partner is common throughout the eukaryotic domain; reef- The earliest fossil eukaryotes that can be placed into one of the
forming corals are an example. page 559 present-day superkingdoms are 1100 –1200 million years old and
belong to the red algae. page 573
Photosynthesis spread through Eukarya by means of multiple
independent events involving a protozoan host and a Eukaryotic fossils diversified greatly about 800 million years ago,
eukaryotic endosymbiont. page 559 reflecting a new capacity for predation on other protists and,
perhaps, a modest increase in oxygen. page 573
Most eukaryotic cells have mitochondria, but a few do not.
Evidence suggests that cells lacking mitochondria once had Protists continue to diversify to the present. Green algae
them but lost them. page 559 and cyanobacteria dominated primary production in earlier
oceans, but, since about 200 million years ago, dinoflagellates,
The eukaryotic nuclear genome contains genes unique to
coccolithophorids, and diatoms have become the primary
Eukarya, but also genes related to Bacteria and Archaea,
photosynthetic organisms in the oceans. page 574
suggesting that the ancestor of the modern eukaryotic cell
was either a primitive eukaryote descended from archaeal Protists have evolved to take advantage of the environments
ancestors or an archaeon that engulfed a bacterium. provided by animals and plants; these protists include many that
page 560 cause disease in humans. page 574
576 SELF-ASSESSMENT
Being
Multicellular
Core Concepts
28.1 Complex multicellularity arose
several times in evolution.
28.2 In complex multicellular
organisms, bulk flow
circumvents the limitations of
diffusion.
28.3 Complex multicellularity
depends on cell adhesion,
communication, and a genetic
program for development.
28.4 Plants and animals evolved
complex multicellularity
independently of each other,
and solved similar problems
with different sets of genes.
28.5 The evolution of large
and complex multicellular
organisms, which required
abundant oxygen, is recorded
by fossils.
irawansubingarphotography/Getty Images.
577
578 SECTION 28.1 T H E P H Y LO G E N E T I C D I S T R I B U T I O N O F M U LT I C E L LU L A R O RG A N I S M S
Chapters 26 and 27 introduced the extraordinarily diverse, but eukaryotes have evolved those. Simple multicellular organisms,
largely unseen, world of microorganisms. Among the Bacteria, composed of multiple similar cells, occur widely within the
Archaea, and protists, each cell usually functions as an individual, eukaryotic tree of life, and a few of these evolved into complex
growing and reproducing, moving from one place to another, multi-cellular organisms characterized by differentiated tissues and
taking in nutrients, and both sensing and transmitting molecular organs. How are these different types of organization distributed on
signals. In contrast, complex multicellular organisms contain as the eukaryotic tree of life?
many as a trillion or more cells that work in close coordination.
In your own body, for example, different cells are specialized for Simple multicellularity is widespread among
specific functions, so that while your body as a whole can perform eukaryotes.
the broad range of tasks accomplished by microorganisms, A recent survey of eukaryotic organisms recognized 119 major
individual cells for the most part cannot. Cells lining the intestine groups within the superkingdoms discussed in Chapter 27. Of
absorb food molecules, but nutrients must then be transported these, 83 contain only single-celled organisms, predominantly
to other parts of the body. Lungs take up oxygen from inhaled cells that engulf other microorganisms or ingest small organic
air, but this, too, must be distributed to other tissues and organs. particles, photosynthetic cells that live suspended in the water
And while cells at the body’s surface sense signals from the column, or parasitic cells that live within other organisms. Each
environment, the signals affecting interior cells come mostly of the 36 remaining branches exhibits some cases of simple
from surrounding cells. multicellularity, mostly in the form of filaments, hollow balls, or
The biological gulf between microbes and complex sheets of little-differentiated cells (Fig. 28.1).
multicellular organisms is enormous, but complex multicellularity Simple multicellular eukaryotes share several properties.
has evolved a half dozen times. In the chapters that follow, we In many, cell adhesion molecules cause adjacent cells to stick
explore the structure and diversity of plants, fungi, and animals. together, but there are few specialized cell types and relatively
Here, however, we address the broader question of how complex little communication or transfer of resources between cells. Most
multicellular organisms evolved in the first place. or all of the cells in simple multicellular organisms retain a full
range of functions, including reproduction, and so the organism
usually pays only a small penalty for individual cell death.
28.1 THE PHYLOGENETIC Importantly, in simple multicellular organisms, nearly every cell
DISTRIBUTION OF is in direct contact with the external environment, at least during
MULTICELLULAR ORGANISMS phases of the life cycle when the cells must acquire nutrients.
Simple multicellularity occurs most prominently among
Most prokaryotic organisms are composed of a single cell, algae, although stalklike colonies of particle feeders have evolved
although some form simple filaments or live in colonies. A few in at least three groups of heterotrophic protists, and simple
types of bacterium, notably some cyanobacteria, differentiate filamentous fungi absorb organic molecules as sources of carbon
to form several distinct cell types. No bacteria, however, develop and energy. In addition, four eukaryotic groups have achieved
macroscopic bodies with functionally differentiated tissues. Only simple multicellularity by a different route, aggregating during
FIG. 28.1 Simple multicellularity. Cells in simple multicellular organisms show little differentiation and remain in close contact with the external
environment. Many groups of eukaryotic organisms display simple multicellularity: (a) Uroglena, a stramenopile alga found commonly
in lakes; (b) Epistylis, a stalked ciliate protozoan that lives attached to the surfaces of fish and crabs; and (c) Prasiola, a bladelike green
alga only a single cell thick, found on tree trunks and rock surfaces. Sources: a. Jason Oyadomari; b. D. J. Patterson; c. Fabio Rindi.
a b c
25 µm 50 µm 1 mm
CHAPTER 28 B E I N G M U LT I C E L L U L A R 579
FIG. 28.2 Coenocytic organization. Nuclei divide repeatedly but are not partitioned into individual cells. Two different groups of green algae
have evolved large size as coenocytic organisms: (a) Codium, found abundantly along temperate coastlines, and (b) Caulerpa, common
in shallow tropical seas and aquaria. Sources: a. Marevision/age fotostock; (b) Wolfgang Poelzer/WaterFrame/age fotostock.
a b
just one stage of the life cycle. Slime molds are the best-known do not reproduce, instead supporting the few that do. This requires
example (Chapter 27). cooperation among cells, but it creates opportunities for cells to
Six groups (two algal, three protozoan, and one fungal) include “cheat”—to use nutrients for their own proliferation rather than
species characterized by coenocytic organization. In coenocytic the growth and reproduction of the organism as a whole. Cancer
organisms, the nucleus divides multiple times, but the cell does is the most conspicuous and lethal example of non-cooperation,
not, so the nuclei are not partitioned into individual cells. The perhaps the defining disease of complex multicellular organisms.
result is a large cell—sometimes even visible to the naked eye— As we will see, complex multicellular organisms evolved
with many nuclei. The green algae Codium and Caulerpa, found from simple multicellular ancestors, but most taxonomic groups
along the shorelines of temperate and tropical seas, respectively, containing simple multicellular organisms never gave rise to
are common examples of coenocytic organisms (Fig. 28.2). complex descendants.
Coenocytic rhizarians on the deep seafloor can be 10 to 20 cm
long. There is no evidence that any coenocytic organisms evolved Complex multicellularity evolved several times.
from truly multicellular ancestors, nor have any given rise to Complex multicellular organisms are conspicuous parts of our
complex multicellular descendants. daily existence. Plants, animals, and, if you look a little more
What selection pressures favored the evolution of simple closely, mushrooms and complex seaweeds are what we notice
multicellular organisms from single-celled ancestors? One when we view a landscape or the coastal ocean (Fig. 28.3).
selective advantage is that multicellularity helps organisms avoid Complex multicellular organisms differ from one another in
getting eaten. In an illuminating experiment, single-celled green many ways, but they share three general features. They have
algae were grown in the presence of a protistan predator. Within highly developed molecular mechanisms for adhesion between
10 to 20 generations, most of the algae were living in eight-cell cells. They display specialized structures that allow cells to
colonies that were essentially invulnerable to predator attack. communicate with one another. And they display complex
Another advantage is that multicellular organisms may be able patterns of cellular and tissue differentiation, guided by
to maintain their position on a surface or in the water column networks of regulatory genes. Without these features, complex
better than their single-celled relatives. Seaweeds, for example, multicellularity would be impossible.
live anchored to the seafloor in places where light and nutrients For example, plants and animals both have differentiated
support growth. Feeding provides a third potential advantage: cells and tissues with specialized functions. Only some tissues
In colonial heterotrophs such as the stalked ciliate Epistylis (see photosynthesize or absorb organic molecules; other tissues
Fig. 28.1b), the coordinated beating of flagella assists feeding by transport food and oxygen through the body; and still others
directing currents of food-laden water toward the cells. generate the molecular signals that govern development. Only a
There are also costs associated with multicellularity, small subset of all cells contributes to reproduction. Because of
particularly for complex multicellular organisms with this functional differentiation, cell or tissue loss can be lethal for
differentiated reproductive tissues. In these organisms, most cells the entire organism.
580 SECTION 28.2 D I F F U S I O N A N D B U L K F LO W
FIG. 28.3 Complex multicellular organisms. Complex multicellularity evolved independently in (a) red algae, (b) brown algae, (c) land plants,
(d) animals, and (e) fungi (at least twice). Sources: a. Dr. Keith Wheeler/Science Source; b. Dave Fleetham/Getty Images; c. Filmfoto/Dreamstime.com;
d. Jack Milchanowski/age fotostock; e. AntiMartina/Getty Images.
a b c
d e
There is one more feature of complex multicellular organisms characterizes animals, but it also evolved at least twice in the
that is key to understanding their biology: They have a three- fungi, once in the green algal group that gave rise to land plants,
dimensional organization, so only some cells are in direct contact once in the red algae, and once in the brown algae, producing the
with the environment. Cells that are buried within tissues, giant kelps that form forests in the sea.
relatively far from the exterior of the organism, do not have direct
j Quick Check 1 How do simple multicellular organisms differ
access to nutrients or oxygen. Therefore, interior cells cannot
from complex multicellular organisms?
grow as fast as surface cells unless there is a way to transfer
resources from one part of the body to another. Similarly, interior
cells do not receive signals directly from the environment, even 28.2 DIFFUSION AND BULK FLOW
though all cells must be able to respond to environmental signals
if the organism is to grow, reproduce, and survive. Complex We already mentioned a key functional challenge of complex
multicellular organisms, therefore, require mechanisms for multicellularity: transporting food, oxygen, and molecular signals
transferring environmental signals received by cells at the body’s rapidly across large distances within the body. How does oxygen
surface to interior cells, where genes will be activated or repressed get from the air in your lungs into your bloodstream? How does
in response. Development in complex multicellular organisms can, atmospheric carbon dioxide get into leaves? How does ammonia
in fact, be defined as increasing or decreasing gene expression in get from seawater into the cells of seaweeds? The answer to all
response to molecular signals from surrounding cells (Chapter 20). three questions is the same: by diffusion. But oxygen absorbed
Complex multicellularity evolved at least six separate times in by your lungs doesn’t reach your toes by diffusion alone—it is
different eukaryotic groups (Fig. 28.4). Complex multicellularity transported actively, and in bulk, by blood pumped through your
CHAPTER 28 B E I N G M U LT I C E L L U L A R 581
FIG. 28.5 Circumventing limits imposed by diffusion. (a) Sponges can attain a large size because the many pores and canals in their bodies
ensure that all cells are in close proximity to the environment. (b) Jellyfish also have thin layers of metabolically active tissue, but their
familiar bell can be relatively thick because it is packed with metabolically inert molecules (the mesoglea, or “jelly”). Sources: a. Andrew J.
Martinez/SeaPics.com; b. D. R. Schrichte/SeaPics.com.
a b
circulation of fluids to transport oxygen and other essential nutrients and signaling molecules upward and downward through
molecules, including food and molecular signals, across distances roots, stems, and leaves.
far larger than those that could be traversed by diffusion alone. Still other complex multicellular organisms also have
Indeed, without a mechanism like bulk flow, animals could not specialized tissues to transport essential materials over long
have achieved the range of size, shape, and function familiar to us. distances at rates faster than could be accomplished by diffusion.
Bulk flow is any means by which molecules move through Fungi transport nutrients through networks of filaments that may
organisms at rates beyond those possible by diffusion across be meters long, relying on osmosis to pump materials from sites
a concentration gradient (Fig. 28.6). In humans and other of absorption to sites of metabolism (Chapter 34). The giant kelps
vertebrate animals, the active pumping of blood through blood have an internal network of tubular cells that transports molecules
vessels supplies oxygen to tissues that may be more than a meter through a body that can be tens of meters long. We will discuss
distant from the lungs (Fig. 28.6a). Most invertebrate animals lack the biology of plants, fungi, and animals in subsequent chapters.
well-defined blood vessels but circulate fluids freely throughout For now, it is important to understand the functional similarities
the body cavity. among these diverse multicellular organisms. In general, when
Bulk flow also distributes nutrients through the body, some cells within an organism are buried within tissues, far from
transporting the organic molecules required for respiration large the external environment, bulk flow is required to supply those
distances from the intestinal cells that absorb these molecules cells with molecules needed for metabolism.
from the digestive tract. (Again, the molecules are transported
j Quick Check 2 How do mechanisms for bulk flow enable
actively in the bloodstream.) Endocrine signaling molecules such
organisms to achieve large size?
as hormones (Chapters 9 and 38) also move rapidly through the
body by means of the blood and other fluids.
Complex organisms other than animals also rely on bulk
flow. A redwood tree must transport water upward from its roots 28.3 HOW TO BUILD A
to leaves that may be 100 m above the soil. If plants relied on MULTICELLULAR ORGANISM
diffusion to transport water, they would be only a few millimeters
tall. How, then, do they move water? Plants move water by bulk We have emphasized three general requirements for complex
flow through a system of specialized tissues powered by the multicellular life: Cells must stick together; they must
evaporation of water from leaf surfaces (Fig. 28.6b; Chapter 29). communicate with one another; and they must participate in a
Vascular plants also have specialized tissues for the transport of network of genetic interactions that regulates cell division and
CHAPTER 28 B E I N G M U LT I C E L L U L A R 583
FIG. 28.6 Bulk flow. (a) The circulatory system in animals and (b) the vascular system in plants allow these organisms to get around the size limits
of diffusion.
Vascular tissues
The transport water and Other vascular tissues
circulatory nutrients upward from transport sugars
system the soil to leaves, downward from
transports where photosynthesis leaves to other parts
oxygen and takes place. of the plant.
nutrients to
tissues and
carbon Water flows upwards through specialized
dioxide and tissues, while sugars are transported downward
other wastes from the leaves where they are synthesized.
away from
tissues.
differentiation. Once these are in place, the stage is set for the Cadherins and integrins do not occur in complex multicellular
evolution of specialized tissues and organs observed in plants, organisms other than animals, but all such organisms require some
animals, and other complex multicellular organisms. means of keeping their cells stuck together. How do they do it?
Plants also synthesize cell adhesion molecules that bind cells into
Complex multicellularity requires adhesion tissues, but, in this case, the molecules are polysaccharides called
between cells. pectins (pectins are what make fruit jelly jell). Molecules that
If a fertilized egg is to develop into a complex multicellular control adhesion between adjacent cells are less well known in
organism, it must divide many times, and the cells produced other complex multicellular organisms, but the general picture is
from those divisions must stick together. In addition, they must clear. Without adhesion there can be no complex multicellularity,
retain a specific spatial relationship with one another in order for and different groups of eukaryotes have evolved distinct types of
the developing organism to function. Chapter 10 introduced the molecular “glue” for this purpose.
molecular mechanisms that hold multicellular organisms together.
We begin by reviewing those mechanisms briefly before placing How did animal cell adhesion originate?
them in evolutionary context. The genome of the choanoflagellate Monosiga brevicollis
In animal development, proliferating cells commonly become provides fascinating insight into the evolution of cell adhesion
organized into sheets of cells called epithelia that line the inside molecules. Choanoflagellates, the closest protistan relatives of
and cover the outside of the body. Within epithelia, adjacent animals, are unicellular microorganisms. Therefore, it came as
cells adhere to each other by means of transmembrane proteins, a surprise that the genes of M. brevicollis code for many of the
especially cadherins, which form molecular attachments between same protein families that promote cell adhesion in animals.
cells. Epithelial cells also secrete an extracellular matrix made The choanoflagellate genome contains genes for both cadherin
of proteins and glycoproteins, and these cells attach themselves and integrin proteins. Clearly, these proteins are not supporting
to this matrix by means of other transmembrane proteins called epithelia in M. brevicollis, so what are they doing?
integrins. Cadherins, integrins, and additional transmembrane One approach to an answer came from the observation that
proteins thus provide the molecular mechanisms for adhesion in cells stick not only to one another but also to rock or sediment
animals. surfaces. Proteins that originally evolved to promote adhesion
584 SECTION 28.3 H O W TO B U I L D A M U LT I C E L LU L A R O RG A N I S M
of individual cells to sand grains or a rock surface may have been deeper into eukaryotic phylogeny—they are found in single-
modified during evolution for cell–cell adhesion. It is also possible celled protists that branch near the base of the opisthokont
that adhesion molecules were originally used in the capture of superkingdom (Chapter 27). Such a phylogenetic distribution
bacterial cells, to make prey adhere to the predator. provides strong support for the general hypothesis that cell
An intriguing clue to the role of these proteins in adhesion in animals resulted from the redeployment of protein
choanoflagellates comes from careful laboratory studies (Fig. 28.7). families that evolved to perform other functions before animals
Although choanoflagellates are unicellular, simple multicellular diverged from their closest protistan relatives.
structures can be induced in a number of species. Molecular
signals induce some choanoflagellates to form a novel multicellular Complex multicellularity requires communication
structure, and, unexpectedly, the source of these signals is a between cells.
bacterium, the preferred prey of the choanoflagellates. The function In complex multicellular organisms, it is not sufficient for cells to
of the multicellular structures in these choanoflagellates has not yet adhere to one another. They must also be able to communicate.
been determined, but these observations support the hypothesis Communication is important during development, guiding the
that they aid predation. patterns of gene expression that differentiate cells, tissues, and
To date, cadherins have been found only in choanoflagellates organs. The functional integration of cells within tissues and tissues
and animals, but proteins of the integrin complex extend even within organs also depends on the flow of information among cells.
HOW DO WE KNOW?
FIG. 28.7
a b c
FIG. 28.8 Gap junctions. Gap junctions facilitate the transport of ions and molecules between adjacent cells in animals.
Gap junctions
are intercellular
connections
made up of a
Gap ring of proteins.
junction
Plasma membrane
Intercellular space
As discussed in Chapter 9, cells communicate by molecular than sponges have gap junctions, protein channels that allow
signals. A signaling molecule (generally a protein) synthesized by ions and signaling molecules to move from one cell into another
one cell binds with a receptor protein on the surface of a second (Fig. 28.8). Gap junctions not only help cells to communicate with
cell, essentially flipping a molecular switch that activates or their neighbors, they allow targeted communication between a cell
represses gene expression in the receptor cell’s nucleus. Plants and and specific cells adjacent to it (Chapter 10).
animals both have receptors of the receptor kinase type, and these Plants, in contrast, have an intrinsic barrier to intercellular
initiate similar signaling pathways within the cell. As in the case communication: the cell wall. Careful observation of plant cell
of adhesion molecules, these signaling pathways, or components walls with the electron microscope reveals that these walls
of the pathways, have also been identified in their close protistan have tiny holes through which thin strands of cytoplasm extend
relatives. Evidently, many of the signaling pathways used for from one cell to the next (Fig. 28.9). Called plasmodesmata,
communication between cells in complex multicellular organisms these intercellular channels are lined by extensions of the cell
first evolved in single-celled eukaryotes. Again we can ask, what membrane (Chapter 10). Tubules running through these channels
function did molecular signals and receptors have in the protistan connect the endomembrane systems of the two cells. Like gap
ancestors of complex organisms? junctions, plasmodesmata permit signaling molecules to pass
All cells have transmembrane receptors that respond to signals between cells in such a way that they can be targeted to only one
from the environment. In some cases, the signal is a molecule or a few adjacent cells.
released by a food organism (such as the bacteria that induce Complex red and brown algae also have plasmodesmata,
simple multicellularity in choanoflagellates), and in some cases and complex fungi have pores between cells that enable
the cells sense nutrients, temperature, or oxygen level. Single- communication by means of cytoplasmic flow. As similar channels
celled eukaryotes also communicate with other cells within the do not occur in most other eukaryotic organisms, they appear
same species, for example to ensure that two cells can find each to represent an important step in the evolution of complex
other to fuse in sexual reproduction. Signaling between two cells multicellularity.
within an animal’s body can be seen as a variation on this more
general theme of a cell responding to other cells and the physical Complex multicellularity requires a genetic program
environment. for coordinated growth and cell differentiation.
While all eukaryotic cells have molecular mechanisms for All of the cells in your body derive from a single fertilized egg, and
communication between cells, complex multicellular organisms most of those cells contain the same genes. Yet your body contains
have distinct cellular pathways for the movement of molecules about 200 distinct cell types precisely arranged in a variety of
from one cell to another. For example, animals more complex tissues and organs. How can two cells with the same genes become
586 SECTION 28.3 H O W TO B U I L D A M U LT I C E L LU L A R O RG A N I S M
FIG. 28.9 Plasmodesmata. Plasmodesmata facilitate the movement of ions and molecules between cells in land plants and in complex red and
brown algae. Photo source: Biophoto Associates/Science Source.
Plasmodesmata Vacuole
Cell
interior
Cell wall
Plasma
membrane
Plasmodesma
Cell
interior
Cell wall
Endoplasmic
reticulum
different cell types? The answer lies in development, the system conditions. For example, if we experimentally starve dinoflagellate
of gene regulation that guides growth from zygote to adult cells, two cells undergo sexual fusion to form morphologically
(Chapter 20). and physiologically distinct resting cells protected by thick walls.
Development is the result of molecular communication That is, a nutrient shortage induces a change in gene expression
between cells. Cells have different fates depending on which that leads to the formation of resting cells. When food becomes
genes are switched off or on, and genes are switched off and on by available again, the cells undergo meiotic cell division to form new
the molecular signals that cells receive. A signal commonly alters feeding cells. Many other single-celled eukaryotes form resting
the production of proteins—inducing the reorganization of the cells in response to environmental cues, especially deprivation of
cytoskeleton, for example. As a result, a stem cell may become an nutrients or oxygen.
epithelial cell, or a muscle cell, or a neuron. This observation leads The innovation of complex multicellularity was to
to another question: What causes the same gene to be turned on in differentiate cells in space instead of time. In a three-dimensional
one cell and off in another? The ultimate answer is that two cells multicellular organism, only surface cells are in direct contact
in the same developing organism can be exposed to very different with the outside environment. Interior cells are exposed to a
environments. different physical and chemical environment because nutrients,
When we think about development as a process of oxygen, and light become less abundant with increasing depth
programmed cell division and differentiation, the link to within tissues. In effect, there is a gradient of environmental
unicellular ancestors becomes clearer. Many biological innovations signals within multicellular organisms. We might, therefore,
accompanied the evolution of complex multicellularity, but, as hypothesize that in the earliest organisms with three-dimensional
noted in Chapter 27, the differentiation of distinct cell types is not multicellularity, a nutrient or oxygen gradient triggered oxygen- or
one of them. Many unicellular organisms have life cycles in which nutrient-starved interior cells to differentiate, much as happens to
different cell types alternate in time, depending on environmental trigger the formation of resting cells in their single-celled relatives.
CHAPTER 28 B E I N G M U LT I C E L L U L A R 587
With increasing genetic control of cellular responses to signaling results of these separate evolutionary events by examining cell
gradients, the seeds of complex development were sown. adhesion, signaling, and development in plants and animals.
Green algae provide a fascinating example that links cell Both plants and animals have evolved sophisticated systems
differentiation in unicellular and multicellular organisms. that cause adjacent cells to adhere to each other and that promote
The simple multicellular organism Volvox (see Fig. 27.15) has the targeted movement of signaling molecules between cells.
two types of cells, vegetative cells that photosynthesize and Plant and animal mechanisms, however, must differ because plant
control movement of the organism, and reproductive cells. Cell cells have cell walls and animal cells do not. Likewise, plants and
differentiation in Volvox is regulated by a gene also involved in the animals have evolved similar genetic logic to govern development,
formation of distinct cell types in the life cycle of Volvox’s single- but use mostly distinct sets of genes. In both plants and animals,
celled relative Chlamydomonas, supporting the hypothesis that many proteins switch genes encoding other proteins on or off,
the spatial differentiation of cells in multicellular organisms began so that the spatial organization of multicellular organisms arises
with the redeployment of genes that regulate cell differentiation from networks of interacting genes and their protein products.
in single-celled ancestors. Ancestral plants and animals simply recruited distinct families of
Bulk flow, which transports nutrients, oxygen, and genes to populate regulatory networks.
water within complex multicellular organisms, also carries
developmental signals. Signals carried by bulk flow can travel far Cell walls shape patterns of growth and development
greater distances through the body than signals transmitted by in plants.
diffusion alone. For example, in animals the endocrine system The plant cell wall (Chapter 5), made of cellulose, provides
releases hormones directly into the bloodstream, enabling them to structural support to cells. In fact, the cell wall provides the
affect cells far from those within which they formed (Chapter 38). mechanical support that allows plants to stand erect (Chapter 29).
Thus, the sex hormones estrogen and testosterone are synthesized The presence of cell walls has largely determined the evolutionary
in reproductive organs but regulate development throughout the fate of plants. For example, because their cells cannot engulf
body, contributing to the differences between males and females. particles or absorb organic molecules, most plants gain carbon and
In this way, signals carried by bulk flow can induce the formation energy only through photosynthesis. In addition, because all plant
of distinct cell types and tissues along the path of signal transport. cells except eggs and sperm are completely surrounded by cell
The genome of the choanoflagellate Monosiga brevicollis, walls, they have no pseudopodia and no flagella (in conifers and
discussed earlier, has been a treasure trove of information on the flowering plants, even sperm have lost their flagella). This being
antiquity of signaling molecules deployed in animal development. the case, plant cells cannot move. Therefore, the plant as a whole
In addition to expressing proteins that govern cell adhesion and is constrained to obtain nutrients, evade predators, and cope with
epithelial cohesion in animals, M. brevicollis expresses a number environmental stress without moving parts.
of proteins active in animal cell differentiation. For example, The inability of plant cells to move has major consequences
signaling based on specific receptor kinases was long thought to for development. At the level of the cell, the entire program of
be restricted to animals, but it also occurs in M. brevicollis. In other growth and development involves cell division, cell expansion
cases, individual components of signaling proteins are present (commonly by developing large vacuoles in cell interiors), and cell
in the M. brevicollis genome, but not the complex multidomain differentiation. The mechanical consequence is that plant growth
proteins formed by animals. This is true, for example, of several is confined to meristems (Fig. 28.10), populations of actively
protein complexes that are important in development. Similarly, dividing cells at the tips of stems and roots (Chapter 31). The cells
molecules that play an important role in plant development are also in meristem regions are more or less permanently undifferentiated
being identified in the genomes of morphologically simple green cells that repeatedly undergo mitosis. A few millimeters from the
algae. The key point is that genome sequences interpreted in light of region of active cell division in a stem or root meristem, cells stop
eukaryotic phylogeny are now enabling biologists to piece together dividing and begin to expand. Within another few millimeters,
the patterns of gene evolution that accompanied the evolution of this activity is curtailed as well. There, individual cells respond
morphological complexity and diversity in plants and animals. to signaling molecules that induce differentiation, forming the
mature cells that will function in photosynthesis, storage, bulk
flow, or mechanical support. In general, then, plant development
28.4 VARIATIONS ON A THEME: involves site-specific cell division, followed by differentiation into
PLANTS VERSUS ANIMALS distinct cell types that govern the function of the plant as a whole.
Because cell walls render plants immobile, plants have evolved
Plants and animals are the best-known examples of complex mechanisms to transport water and nutrients from the soil to
multicellular organisms. The study of phylogenetic relationships leaves that may be tens of meters distant without the use of
makes it clear that complex multicellularity evolved any moving parts or even the expenditure of ATP. And because
independently in the two groups. In other words, they do not plants are anchored in place, they are unable to move in response
share a common ancestor that was multicellular. We can see the to unfavorable growth conditions. Instead, plants respond to
588 SECTION 28.4 VA R I AT I O N S O N A T H E M E : P L A N T S V E R S U S A N I M A L S
Zone of cell
expansion
FIG. 28.11 Gastrulation. Gastrulation is the movement of cells
during embryogenesis that in animals transforms a
blastula to a gastrula.
Zone of cell
division
Fertilized egg
Meristem
during development, animal embryos are not restricted to growth cell adhesion, modes of communication between cells, and
only from localized regions like meristems. Cell division and tissue a genetic program to guide growth and development. These
differentiation occur throughout the developing animal body. three requirements had to be acquired in a specific order. If the
Because they are not constrained by cell walls, animals can products of cell division don’t stick together, there can be no
form organs with moving parts—muscles that power active complex multicellularity. Adhesion, however, is not sufficient. It
transport of food and fluids and allow movement. Thus, animals must be followed by mechanisms for communication between
have possibilities for function that are far different from those cells. Moreover, cells must be able to send molecular messages to
of plants. If the environment offers a challenge, like drought or specific targets or regions, assisted in animals by gap junctions and
predators, animals can respond by changing their behavior—for in plants by plasmodesmata.
example, they can move to a new location (Chapter 37). With these requirements in place, natural selection would
Plants and animals, then, display contrasting patterns of favor the increase and diversification of genes that regulate growth
development and function that reflect both their independent and development, making possible more complex morphology
origins from different groups of protists and the constraints and anatomy. The biological stage was finally set for the functional
imposed by cell walls in plants. key to complex multicellularity: the differentiation of tissues and
organs that govern the bulk flow of fluids, nutrients, signaling
j Quick Check 3 How do plants and animals differ in the ways their
molecules, and oxygen through increasingly large and complex
cells adhere, communicate, and differentiate during development?
bodies. This differentiation freed organisms from the tight
constraints imposed by diffusion. When all these features are
placed onto phylogenies, they show both the predicted order of
28.5 THE EVOLUTION OF COMPLEX acquisition and the tremendous evolutionary consequences of
MULTICELLULARITY complex multicellularity (Fig. 28.12).
The differences between an amoeba and a lobster seem vast, Fossil evidence of complex multicellular organisms
but research over the past decade increasingly shows how this is first observed in rocks deposited 579–555 million
apparent gap was bridged through a series of evolutionary years ago.
innovations. Throughout this chapter, we have emphasized In Chapter 23, we noted that phylogenies based on living
that complex multicellular organisms require mechanisms for organisms make predictions about the fossil record. Characters
a.
Bulk flow
Gap junctions
Insects, mammals, and other animals
with bilateral symmetry (~10,000,000)
Animals
Jellyfish and their relatives (10,000)
Adhesion, cell
signaling
Sponges (10,000)
b.
Bulk flow
Vascular plants (350–400,000)
Land plants
Plasmodesmata Mosses and their
† relatives (20,000) FIG. 28.11 The evolution of complex
multicellularity. Phylogenetic
Simple multicellular
relationships of complex (a) animals
Adhesion, cell
signaling and (b) plants, with their close
Green algae (6000*)
evolutionary relatives, show similar
Single-celled patterns of character accumulation
and its consequences for biological
* Only species on the branch leading to land plants diversity. Estimated species
† Limited development of transport tissues in some mosses numbers are shown.
590 SECTION 28.4 T H E E VO L U T I O N O F CO M P L E X M U LT I C E L LU L A R I T Y
and groups associated with lower branches in phylogenies should animals, with distinct head and tail, top and bottom, left and
appear as earlier fossils than those associated with later branches. right, enter the record (Fig. 28.13b). At the same time, we begin
Although fossils don’t preserve molecular features, the record to see tracks and trails made by animals whose muscles enabled
supports the phylogenetic pattern shown in Fig. 28.12. them to move across and through surface sediments (Fig. 28.13c),
Single-celled protists are found in sedimentary rocks as an indirect but complementary record of increasing animal
old as 1800 million years, and a number of simple multicellular complexity. These, then, are the first known occurrences of the
forms have been discovered that are nearly as old (see Fig. 27.23). types of animal that dominate ecosystems today, both in the sea
Nonetheless, the oldest fossils that record complex multicellularity and on land. These animals must have possessed a diverse array of
are found in rocks that were deposited only 579–555 million years genes to guide development, something akin to those seen today in
ago. Fig. 28.13a shows one of the oldest known animal fossils, insects or snails.
a frondlike form preserved in 575-million-year-old rocks from Clearly, by 579–555 million years ago, the animal tree was
Newfoundland, near the eastern tip of Canada. This fossil and many beginning to branch. This, however, raises a new question: Why
others found in rocks of this age are enigmatic. There is complex did complex multicellular animals appear so much later than
morphology to be sure, but it is difficult to understand these simple multicellular organisms?
forms by comparing them to the body plans of living animals. The
Newfoundland fossils show no evidence of head or tail, no limbs, Oxygen is necessary for complex multicellular life.
and no opening that might have functioned as a mouth. They Earlier in the chapter, we discussed the key biological
appear to be very simple organisms that gained both carbon and requirements for complex multicellularity. There is a critical
oxygen by diffusion. These fossils are long and wide, but they are environmental requirement as well: the presence of oxygen.
not thick. In fact, it is likely that active metabolism occurred only There are other potential electron acceptors for respiration, like
along the surfaces of these structures. sulfate and ferric iron. However, they not only occur in much
Such animals lie near the base of the animal tree (Chapter lower abundances than oxygen, but they are not gases and so do
44), and probably would have developed under the guidance of not accumulate in air. Only the oxidation of organic molecules by
regulatory genes similar to those present in modern sponges or, O2 provides sufficient energy to support biological communities
perhaps, jellyfish. By 560–555 million years ago, more complex that include large and active predators like wolves and lions. And
FIG. 28.13 The earliest fossils of animals. (a) Among the oldest known macroscopic animal fossils is a frond-like form made up of tubular
structures, preserved in 575-million-year-old rocks from Newfoundland. (b) The oldest known animal fossil showing bilateral
symmetry is a mollusk-like form preserved in 560–555-million-year-old rocks from northern Russia. (c) The oldest tracks and
trails of mobile animals are found in rocks 560 million years old and younger. Sources: a. Guy Narbonne; b. Mikhail Fedonkin; c. Andrew Knoll,
Harvard University.
a b c
CHAPTER 28 B E I N G M U LT I C E L L U L A R 591
Complex multicellularity
Atmospheric oxygen
FIG. 28.15 Evolution of complex fungi. (a) This trunklike fossil, discovered in France, is actually a giant fungus that towered over early land
plants 375 million years ago. (b) This image shows the interior of the fungus, which consists of tubes that transported nutrients
through the large body. Sources: Carol Hotton; b. Martha E. Cook, School of Biological Sciences, Illinois State University.
a b
100 µm
organic matter, radiated by taking advantage of this resource The answer has to do with the network of genes that guide
(Fig. 28.15), evolving complex multicellularity in two distinct development. Since the 1950s, biologists have learned a remarkable
lineages (Chapter 34). amount about this genetic network and its host of interacting genes
(Chapter 20). Many of the genes involved in development are what
Regulatory genes played an important role in the we might consider middle managers: A molecular signal induces
evolution of complex multicellular organisms. the expression of a gene, and the protein product, in turn, prompts
Complex multicellular organisms account for a large proportion the expression or repression of another gene. It is the complex
of all eukaryotic species. Thus, one evolutionary consequence of interplay of these genetic switches—turning specific genes on in
complex multicellularity was an increase in biological diversity. one cell and off in another, depending on where those cells occur
Let’s compare the diversity of complex multicellular groups with in the developing body—that results in crabs with large pincers or
their simpler phylogenetic sisters. Choanoflagellates, for example, butterflies with patterned wings (Fig. 28.16).
number about 150 species; simple animals such as sponges and It makes sense that if regulatory genes guide development of
jellyfish about 20,000; and complex animals with circulatory the body in each complex multicellular species, then mutations
systems perhaps as many as 10 million. Plants and their relatives in regulatory genes may account for many of the differences we
show a comparable pattern. There are about 6000 species of green observe among different species. Our growing understanding
algae on the branch that includes land plants, but about 400,000 of how developmental genes underpin evolutionary change has
species of anatomically complex land plants capable of bulk flow. given rise to a whole new field of biology called evolutionary-
Similarly, complex fungi and red algae include more species by an developmental biology, or evo-devo for short.
order of magnitude than their simpler relatives. In evo-devo research, scientists compare the genetic programs
How did this immense diversity arise? At one level, the answer for growth and development in species found on different branches
is functional and ecological. Complex multicellular organisms of phylogenetic trees. In addition to wanting to discover the
can perform a range of functions that simpler organisms cannot, molecular mechanisms that guide development in individual species,
and so they have evolved many specific types of interaction with these scientists aim to understand the genetic differences associated
other organisms and the physical environment. Carnivory, for with differences in form and function among species. Evo-devo
example, requires both sophisticated sensory systems and jaws or is an exciting and rapidly expanding field of research because it is
limbs to locate and capture prey, but once established, carnivorous helping to illuminate the long-suspected relationship between the
animals radiated throughout the oceans and, eventually, on land. development of individuals and patterns of evolutionary relatedness
This explanation, however, prompts another question: What is among species. Continuing research promises to shed new light on
the genetic basis for the bewildering range of sizes and shapes the similarities and differences among plants, animals, and other
displayed by complex multicellular organisms? complex multicellular organisms. •
HOW DO WE KNOW?
FIG. 28.16
RESULTS The expression pattern of Distalless (on the left in CONCLUSION Regulatory genes play an important role in butterfly
each panel of the figure) in developing wings closely resembles wing coloration, and mutations in these genes can account for
the pattern of eyespots on the wing (on the right in each panel). differences in wing color patterns among species.
The two patterns match for both wild-type (top left) and mutant SOURCE Brakefield, P. M., et al. 1996. “Development, Plasticity and Evolution of
butterfly wings. Butterfly Eyespot Patterns.” Nature 384: 236–242.
Eukaryotes are unicellular or multicellular and exhibit both Bulk flow is an active process that allows multicellular
simple and complex multicellularity. page 578 organisms to nourish cells located far from the external
environment, thereby circumventing the constraints
Simple multicellularity involves the adhesion of cells
imposed by diffusion. page 582
with little cell differentiation. Complex multicellularity
involves cell adhesion, cell signaling, and differentiation and
specialization among cells. page 578 28.3 Complex multicellularity depends on cell
adhesion, communication, and a genetic program for
Complex multicellular organisms have evolved
development.
independently at least six times: in animals, vascular plants,
red algae, brown algae (the kelps), and at least twice in the Animal and plant cells are organized into tissues characterized
fungi page 580 by specific molecular attachments between cells. page 583
55
9933
594 SELF-ASSESSMENT
Choanoflagellates express some of the same proteins that The evolution of complex multicellularity observed in the
permit cell adhesion in animals, even though choanoflagellates fossil record correlates with increases in atmospheric oxygen
are unicellular. Experiments suggest that choanoflagellates use that occurred 580–560 million years ago. page 591
these proteins to capture bacteria, not for cell adhesion. Complex multicellular organisms evolved later on land, as
page 583 ancestral plants evolved the capacity to photosynthesize
Gap junctions in animals and plasmodesmata in plants allow surrounded by air rather than water. page 591
cells to communicate with each other in a targeted fashion. Evolutionary-developmental biology, or evo-devo, is a field
page 585 of research that looks at both individual development and
The cells of complex multicellular organisms are genetically evolutionary patterns in an attempt to understand the
programmed to differentiate into multiple cell types in space. developmental changes that allowed organisms to diversify and
page 586 adapt to changing environments. page 592
The cell wall of plants has led to distinct solutions to 5. Describe a key difference between multicellular plants
the problems of cell adhesion, cell communication, and and animals.
development. For example, plants grow by the activity of 6. Describe environmental changes recorded by the
meristems, populations of actively dividing cells at the tips of sedimentary rocks that contain the oldest fossils of large
stems and roots. page 587 active animals.
Animal cells do not have cell walls, allowing cell movement
that is not possible in plants. For example, during animal Log in to to check your answers to the Self-
development, cells of the embryo migrate inward to form a Assessment questions, and to access additional learning tools.
layered structure called a gastrula. page 588
Agriculture
Feeding a Growing Population
You may have noticed that while your grocery store or Cultivated bananas are vulnerable to infection in a
supermarket has several types of apple for sale, there way that wild bananas are not. The bananas that we eat
is usually only one type of banana. In fact, it’s possible are sterile; they do not produce seeds. This means they must
that every banana you have ever eaten has been the same be propagated vegetatively by replanting cuttings taken
variety. Now the popular yellow fruit may be in trouble. from parent plants. As a result, banana plantations contain
Years ago, the Western world favored a banana variety almost no genetic diversity. As Panama disease and black
known as the Gros Michel. In the first part of the twentieth sigatoka are proving, that lack of diversity can have
century, a devastating fungal infection called Panama disastrous effects.
disease wiped out Gros Michel plantations around the As sterile clones, bananas are particularly vulnerable
world. In the 1950s, banana growers turned instead to the to disease outbreaks. Other agricultural crops face similar
Cavendish, a variety that displayed some natural resistance threats. For example, a new, virulent strain of yellow wheat
to Panama disease. Half a century later, the Cavendish rust fungus emerged in the Middle East in 2010. In its first
remains the top-selling banana in supermarkets in North year, the disease wiped out as much as half of Syria’s wheat
America and beyond. crop and has since spread to several other countries in the
Yet the reign of the Cavendish may be coming to an region. Meanwhile, crop scientists have warned that Ug99,
end. For years, banana growers have battled black sigatoka, a new, virulent strain of an even more damaging fungal
a fungal infection pathogen that first surfaced in eastern Africa, could devastate
Agriculture has that can cause global wheat crops as it spreads.
losses of 50% or Wheat was one of the first crops that our ancestors
transformed our planet more of the banana cultivated when agriculture emerged 10,000 years ago. The
and our species; without yield in infected early farmers learned to choose wheat plants that were
regions. Making easiest to harvest and whose seeds germinated without
it, modern civilization matters worse, delay. Over time, wheat evolved by this process of artificial
would not be possible. Panama disease is selection. Those earliest farmers set in motion a long chain
once again posing a of genetic modifications that ultimately led to the high-yield
threat. A strain of the disease has emerged against which the wheat varieties grown today.
Cavendish plants have no resistance. The disease has spread In the wild, natural selection favored wheat whose seeds
across Asia and Australia, and experts fear it’s only a matter were protected by tough barbs and separated easily from
of time before it reaches prime banana-growing regions in the plant, allowing efficient dispersal across the landscape.
Latin America. Farmers, on the other hand, preferred wheat plants whose
For those who enjoy bananas sliced into their breakfast seeds remained attached to the plant and so were easier
cereal, the loss of bananas would be disappointing. For to harvest. But the tendency for seeds to remain attached
the millions of people in tropical countries who depend would interfere with the plant’s ability to self-seed in the
on bananas and related plantains for daily sustenance, the wild. By selecting for traits that would be disadvantageous
destruction of those crops would be much more serious. in nature, humans created a plant dependent on humans for
Agriculture has transformed our planet and our species; its survival. The codependency between domestic plants and
without it, modern civilization would not be possible. people is a hallmark of agriculture.
But as the case of the banana shows, there are challenges In addition to selecting desirable traits in their crop
to overcome if we’re to continue feeding a growing plants, early agriculturalists altered the environment to
population. be favorable for those plants. They provided water, chose
595
Domestication of wheat. Wild wheat (left) and modern domesticated wheat
(right). The seeds of wild wheat are protected by tough barbs (the long spikes), and
they fall easily from the plant, enhancing dispersal. The seeds of domesticated wheat
remain attached to the plant, making the grain easier to harvest. Sources: (left) Bob
Gibbons/FLPA/Science Source; (right) Nigel Cattlin/Science Source.
planting sites to ensure optimal sunlight, and removed contain a gene from the bacterium Bacillus thuringiensis (Bt)
nearby plants that would compete with the crops for vital that confers pest resistance.
resources such as water and nutrients. By changing the At a glance, it would seem that we’ve successfully taken
community structure and the availability of resources domesticated species under our control, and indeed, we’ve
to support growth and reproduction, humans allowed made great strides in increasing yields to feed an ever-growing
domesticated crops to thrive. population. But evolution never takes a break. Crop pests and
By the 1940s, scientists had developed industrially pathogens continue to evolve ways to evade our savviest plant
fixed nitrogenous fertilizers that significantly boosted plant breeders.
growth. They had also learned enough about genetics and The nature of modern agriculture only compounds the
DNA to begin applying that knowledge to plant breeding. problem. Most modern farms consist largely of monocultures,
These advances led to an amazingly productive period single types of crop each grown over a large area. Growing
during the 1960s and 1970s now known as the Green only a single crop at a time makes it much easier to mechanize
Revolution. During that time, plant yields ballooned. Food planting and harvesting. In a given field of corn or wheat,
production actually out-stripped population growth through therefore, the individual plants are often genetically quite
the second half of the twentieth century. similar to one another. With so little genetic variation, each
Today, we are entering a new phase of agriculture, plant is vulnerable to pathogens in exactly the same way. This
with genetic engineering being added to the traditional means that a pathogen that can overcome one plant’s natural
approaches of crossbreeding and artificial selection. defenses has the potential to wipe out the entire field.
Most of the corn and soy products now consumed in the Lately, many consumers are taking a hard look at these
United States come from plants that have been genetically problems and at the source of the food on their plates.
engineered to resist certain pests and herbicides. Some of Critics of modern agriculture argue that monocultures,
the genes employed come from different species altogether. with their heavy reliance on fungicides and pesticides,
For example, corn and cotton plants are often engineered to are unsustainable and unhealthy. Proponents of genetic
596
modification and high-tech agriculture argue that we In many parts of the world, agricultural productivity
will need every tool to meet food-production demands is limited by the availability of water or nutrients
for the expanding human population. Sometime in 2011, or both. Global climate change is predicted to cause
the human population surpassed 7 billion people. The regional droughts and flooding that may further weaken
population continues to grow, expanding at its fastest rate the global food supply. There will be no easy solutions
at any time in human history. By 2100, experts predict, as we move forward into civilization’s next phase
our planet will be home to more than 9 billion people. One of agriculture. One thing that is certain, however, is
point that both sides agree on is that unless agricultural that understanding how plants grow, reproduce, and
productivity continues to increase, more and more land protect themselves from pests will help us survive in an
will be needed to produce food. increasingly crowded world.
? CASE 6 QUESTIONS
Special sections in Chapters 29 –34 discuss the following questions related to Case 6.
1. How has nitrogen availability influenced agricultural productivity? See page 616.
2. How did scientists increase crop yields during the Green Revolution? See page 637.
3. What is the developmental basis for the shorter stems of high-yielding rice and wheat?
See page 649.
4. Can modifying plants genetically protect crops from herbivores and pathogens?
See page 683.
5. What can be done to protect the genetic diversity of crop species? See page 708.
6. How do fungi threaten global wheat production? See page 734.
597
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CHAPTER 29
Plant Structure
and Function
Moving Photosynthesis
onto Land
Core Concepts
29.1 The evolution of land plants
from aquatic ancestors
introduced a major challenge
for photosynthesis: acquiring
carbon dioxide without
drying out.
29.2 Leaves have a waxy cuticle and
stomata, both of which are
important in regulating carbon
dioxide gain and water loss.
29.3 Xylem allows vascular plants to
replace water evaporated from
leaves with water pulled from
the soil.
29.4 Phloem transports
carbohydrates to the non-
photosynthetic portions of the
plant for use in growth and
respiration.
29.5 Roots expend energy to obtain
nutrients from the soil.
Frank Krahmer/Getty Images.
599
600 SECTION 29.1 P L A N T S T RU C T U R E A N D F U N C T I O N : A N E VO LU T I O N A RY P E R S P E C T I V E
FIG. 29.4 Leaf structure. The uptake of CO2 by diffusion is accompanied by a much
larger outward diffusion of water vapor.
Cuticle
Upper
epidermis Mesophyll cells near the
upper surface of the leaf have
a columnar arrangement that
maximizes light interception.
CO2 gradient
to spread easily throughout
Lower the leaf.
epidermis
Vein
Cuticle
Guard cell
Stoma H2O
~400
400 ppm ~20,000
~20
20 000 ppm
would quickly run out of CO2 and come to a halt. But they’re not plants can sustain such high rates of water loss because they can
sealed off—the leaf’s air spaces are connected to the air surrounding access the only consistently available source of water on land: the
the leaf by pores in the epidermis. As photosynthesis lowers the soil. Water moves from the soil, through the bodies of vascular
concentration of CO2 molecules within the leaf’s air spaces relative plants, and then, as water vapor, into the atmosphere. Therefore,
to the concentration of CO2 in the outside air, the difference in the challenge of keeping photosynthetic cells hydrated is met
concentration between the inside and the outside of the leaf causes partly by the continual supply of water from the soil. As we discuss
CO2 to diffuse into the leaf, replenishing the supply of CO2 for next, it is also met by limiting the rate at which water already in
photosynthesis. leaf tissues is lost to the atmosphere.
The ability of leaves to draw in CO2 comes at a price: If CO2
j Quick Check 1 Why do plants transpire?
can diffuse into the leaf, water vapor can diffuse out (Fig. 29.4).
Furthermore, water vapor diffuses out of a leaf at a much faster
rate than CO2 diffuses inward. Molecules diffuse from regions of The cuticle restricts water loss from leaves but inhibits
higher concentration to regions of lower concentration, and the the uptake of CO2.
rate of diffusion is proportional to the difference in concentration. Epidermal cells secrete a waxy cuticle on their outer surface
On a sunny summer day, the difference in water vapor that limits water loss. Without a cuticle, the humidity within
concentration between the air spaces within a leaf and the air the internal air spaces would drop and the photosynthetic
outside can be more than 100 times greater than the difference in mesophyll cells would dry out. However, the cuticle prevents CO2
concentration of CO2. Add the fact that water is lighter than CO2, from diffusing into the leaf even as it restricts water vapor from
and so diffuses 1.6 times faster for the same concentration gradient, diffusing out of it.
and it becomes clear why, on a sunny summer day, several hundred As noted above, small pores in the epidermis allow CO2 to
water molecules are lost for every molecule of CO2 acquired for diffuse into the leaf (Fig. 29.5a). These pores are called stomata
photosynthesis. (singular, stoma). Stomata can be numerous—there can be
The loss of water vapor from leaves is referred to as hundreds per square millimeter. Yet because each one is small, less
transpiration, and the rates at which plants transpire are often than 1% to 2% of the leaf surface is actually covered by these pores.
quite high. A sunflower leaf, for example, can transpire an amount Thus, even with stomata, the epidermis is a significant barrier to
equal to its total water content in as little as 20 minutes. To put the diffusion of CO2 and water vapor.
this rate of water loss in perspective, you would have to drink The epidermis with its stomatal pores represents a
about 2 liters per minute to survive a similar rate of loss. Vascular compromise between the challenges of providing food
CHAPTER 29 P L A N T S T RU C T U R E A N D F U N C T I O N : M OV I N G P H OTO S Y N T H E S I S O N TO L A N D 603
its stomata to capture CO2 at night, when cool air limits rates of By opening stomata only at night, CAM plants greatly increase
evaporation? the amount of CO2 gain per unit of water loss. Indeed, the
In fact, a number of plants have evolved precisely this CO2 : H2O exchange ratio for CAM plants is in the range of 1 : 50,
mechanism, called crassulacean acid metabolism, or CAM, to nearly 10 times higher than that of plants that open their stomata
help balance CO2 gain and water loss (Fig. 29.6). CAM (named after during the day. However, CAM has a drawback. The carbohydrate
the Crassulaceae family of plants, which uses this pathway) provides production by CAM photosynthesis is slower because ATP is
a system for storing CO2 overnight by converting it into a form that needed to drive the uptake of organic acids into the vacuole and
will not diffuse away. The storage form of CO2 is produced by the because only so much organic acid can accumulate overnight in
activity of the enzyme PEP carboxylase, which combines a dissolved the vacuole. CAM is therefore most common in habitats such
form of CO2 (bicarbonate ion, HCO32) with a 3-carbon compound as deserts, where water conservation is crucial, and among
called phosphoenol pyruvate (PEP). The resulting product is a epiphytes, plants that grow on the branches of other plants,
4-carbon organic acid that is stored in the cell’s vacuole. without contact with the soil.
When the sun comes up the next morning, the stomata close, Because CAM uses enzymes (for example, PEP carboxylase)
conserving water. At the same time, the 4-carbon organic acids and compartments (for example, vacuoles) that exist in all plant
are retrieved from the vacuole and transferred to the chloroplasts. cells, it is not surprising that it has evolved multiple times. CAM
The 4-carbon organic acids are then decarboxylated—that is, their occurs in all four groups of vascular plants shown in Fig. 29.1. It
CO2 is released. Because the stomata are now closed, this newly is most widespread in the angiosperms, occurring in 5% to 10%
released CO2 does not escape from the leaf. Instead, it becomes of species. Vanilla orchids and Spanish moss, two well-known
incorporated into carbohydrates by the Calvin cycle. As we saw in epiphytes, as well as many cacti, are CAM plants.
Chapter 8, the Calvin cycle requires a continual supply of energy
in the form of ATP and NADPH produced by the light reactions C4 plants suppress photorespiration by concentrating
of photosynthesis and so can operate only in the light. The CO2 in bundle-sheath cells.
3-carbon PEP molecules are converted into starch and stored in the Photorespiration adds another wrinkle to the challenge of
chloroplast until the sun goes down and they are again needed to acquiring CO2 from the air. Recall from Chapter 8 that either
capture and store CO2 in the vacuole. CO2 or O2 can be a substrate for rubisco, the key enzyme in the
FIG. 29.6 CAM photosynthesis. CAM plants store CO2 at night in the vacuole; leaves can then photosynthesize during the day without opening
their stomata.
Night Day
4-carbon 4-carbon
organic acid Vacuole organic acid
ATP
ADP + Pi
HCO3–
4-carbon
4-carbon PEP
carboxylase organic acid
organic acid
PEP
Rubisco
Carbohydrates
CO2
Night, Day,
stomata stomata
open closed
H 2O Stoma
CHAPTER 29 P L A N T S T RU C T U R E A N D F U N C T I O N : M OV I N G P H OTO S Y N T H E S I S O N TO L A N D 605
FIG. 29.7 C4 photosynthesis. C4 plants suppress photorespiration by concentrating CO2 in bundle-sheath cells. Photo source: Ken Wagner/Phototake.
Bundle-sheath cell
Mesophyll cell
PEP 4-C
carboxylase
Rubisco Leaf vein
CO2 -
HCO3
CO2 Calvin cycle
PEP C4 cycle
Carbohydrates
ADP
3-C
Chloroplast ATP
Bundle-
Bundle- sheath
sheath Chloroplasts cells
cells
Cuticle
Upper
epidermis
Mesophyll
CO2 cells
Lower
Vein epidermis
Stoma Cuticle Stoma Vein
Guard cell
H2O
Calvin cycle. When CO2 is the substrate, the Calvin cycle produces use PEP carboxylase to produce 4-carbon organic acids that
carbohydrates through photosynthesis. When O2 is the substrate, subsequently supply the Calvin cycle with CO2. The Calvin cycle
there is a net loss of energy and a release of CO2, the process produces 3-carbon compounds (Chapter 8), and plants that do not
called photorespiration. (Photorespiration is similar to aerobic use 4-carbon organic acids to supply the Calvin cycle with CO2 are
respiration only in the sense that it uses O2 and releases CO2. thus referred to as C3 plants.
However, plants do not gain energy; they lose it.) Both CAM and C4 plants produce 4-carbon organic acids as
Photorespiration presents a significant challenge for land the entry point for photosynthesis. However, in CAM plants, CO2
plants for two reasons. The first is that air contains approximately capture and the Calvin cycle take place at different times; in C4
21% O2 but only 0.04% CO2. Although rubisco reacts more readily plants, they take place in different cells.
with CO2 than with O2, the sheer abundance of O2 means that C4 plants initially capture CO2 in mesophyll cells by means
rubisco uses O2 as a substrate some of the time. The second reason of PEP carboxylase, which combines a dissolved form of CO2
is that air provides much less of a thermal buffer than does water, (bicarbonate ion, HCO3⫺) with the 3-carbon compound PEP.
such that organisms on land experience higher and more variable This produces 4-carbon organic acids that diffuse through
temperatures than do organisms that live in water. Temperature plasmodesmata into the bundle sheath (Fig. 29.7), a cylinder of
has a major effect on photorespiration because the selectivity of cells that surrounds each vein. Once inside bundle-sheath cells,
rubisco for CO2 over O2 is reduced as temperatures increase. At the 4-carbon compounds are decarboxylated, releasing CO2 that
moderate leaf temperatures, O2 is the substrate instead of CO2 as is then incorporated into carbohydrates through the Calvin cycle
often as 1 time out of 4. At higher temperatures, O2 is even more (Chapter 8). The C4 cycle is completed as the 3-carbon molecules
likely to be the substrate for rubisco. generated during decarboxylation diffuse back to the chloroplasts
Some plants have evolved a way to reduce the energy and in the mesophyll cells, where ATP is used to re-form PEP.
carbon losses associated with photorespiration. These are the The significance of the C4 cycle is that it operates much faster
C4 plants, which suppress photorespiration by increasing the than the Calvin cycle because of the very low catalytic rate of
concentration of CO2 in the immediate vicinity of rubisco. C4 rubisco (Chapter 8). As a result, the concentration of CO2 within
plants take their name from the fact that they, like CAM plants, bundle-sheath cells builds up, reaching levels as much as five times
higher than in the air surrounding the leaf. The
HOW DO WE KNOW? high concentration of CO2 in bundle-sheath
cells makes it unlikely that rubisco will use O2
as a substrate. Thus, the C4 cycle functions like
FIG. 29.8
a “fuel-injection” system that increases the
efficiency of the Calvin cycle in bundle sheath
How do we know that C4 cells.
C4 plants have high rates of photosynthesis
photosynthesis suppresses because they do not suffer the losses in
energy and reduced carbon associated with
photorespiration? photorespiration (Fig. 29.8). At the same
time, C4 plants lose less water because they
BACKGROUND Studies using radioactively labeled CO2 showed can restrict diffusion through their stomata
that some species initially incorporate CO2 into 4-carbon to a greater extent than a C3 plant while still
compounds instead of the 3-carbon compounds that are the first maintaining high concentrations of CO2 in
products in the Calvin cycle. These C4 plants also have high rates bundle-sheath cells. However, C4 photosynthesis
of photosynthesis. Is this a new, more efficient photosynthetic has a greater energy requirement than
pathway? Or do C4 plants have high rates of photosynthesis because conventional (C3) photosynthesis, as ATP must
they are able to avoid the carbon and energy losses associated with be used to regenerate PEP in the C4 cycle.
photorespiration? Thus, C4 photosynthesis confers an advantage
in hot, sunny environments where rates of
HYPOTHESIS C4 plants do not exhibit photorespiration.
photorespiration and transpiration would
METHOD “Air tests,” as these experiments were first called, otherwise be high. C4 photosynthesis has evolved
compared rates of photosynthesis in normal air (21% O2) and in as many as 20 times, but is most common among
an experimental gas mixture in which the concentration of O2 is tropical grasses and plants of open habitats with
only 1%. When the concentration of O2 is low, rubisco has a low warm temperatures. C4 plants include a number
probability of using O2 (instead of CO2) as a substrate, and thus of important crops, including maize (corn),
photorespiration does not occur. sugarcane, and sorghum, as well as some of the
most noxious agricultural weeds.
RESULTS
j Quick Check 2 How does the formation of
21% O2 4-carbon organic acids increase the efficiency of
Photosynthetic rate
The rate of
1% O2 photosynthesis water use in both CAM and C4 plants?
21% 1% is different in
O2 O2 21% O2 and 1%
O2 in C3 plants,
but not in C4
plants. 29.3 THE STEM:TRANSPORT
C3 plant C4 plantt OF WATER THROUGH
XYLEM
CONCLUSION Photosynthesis in C4 plants is not affected by
differences in O4 concentration, indicating that significant On a summer day, a tree can transport many
photorespiration is not occurring in these plants. In contrast, hundreds of liters of water from the soil to its
the photosynthetic rate of the C3 plants increased in the low O4 leaves. Impressively, this feat is accomplished
environment, indicating that photorespiration depresses rates of without any moving parts. Even more remarkably,
photosynthesis in 21% O4. trees and other plants transport water without
any direct expenditure of energy. The structure of
FOLLOW-UP WORK The higher photosynthetic efficiency of
vascular plants allows them to use the evaporation
C4 photosynthesis has prompted efforts, so far unsuccessful, to
of water from leaves to pull water from the soil.
incorporate this pathway into C3 crops such as rice.
Fig. 29.9 shows the cross section of a
sunflower stem. Like a leaf, it has a surface layer
SOURCE Bjorkman, O., and J. Berry. 1973. “High-Efficiency Photosynthesis.” of epidermal cells. This layer encloses thin-
Scientific American 229:80–93. walled, undifferentiated parenchyma cells in
the interior. Notice that the stem also contains
differentiated tissues that lie in a ring near the
606
CHAPTER 29 P L A N T S T RU C T U R E A N D F U N C T I O N : M OV I N G P H OTO S Y N T H E S I S O N TO L A N D 607
outside of the stem. These are the vascular tissues, which form a
continuous pathway that extends from near the tips of the roots,
through the stem, and into the network of veins within leaves.
The outer tissue, called phloem, transports carbohydrates from
leaves to the rest of the plant body. The inner tissue, called xylem,
transports water from the roots to the leaves. b. Multicellular vessels
In addition, both the xylem and the phloem transport dissolved
nutrients and signaling molecules, such as hormones, throughout
the plant. Importantly, the xylem is the pathway by which mineral
nutrients absorbed from the soil are transported to the aboveground Pits
portions of the plant. The total concentration of solutes in the
xylem, however, is very low (typically less than 0.01%). We thus
focus on the xylem as a means for transporting water from soil to Thick,
leaves and discuss the uptake of nutrients in section 29.5. lignified
walls
FIG. 29.11
How large are the forces that allow leaves to pull water
from the soil?
BACKGROUND The idea that water is pulled through the plant by through the branch when attached to the transpiring plant with
forces generated in leaves was first suggested in 1895. However, the flow rate generated by the vacuum pump.
without a way to measure these forces, there was no way to know
RESULTS Renner found that the flow rates generated by
how large they were.
transpiring plants were two to nine times greater than the flow
HYPOTHESIS In 1912, German physiologist Otto Renner rates generated by the vacuum pump.
hypothesized that leaves are able to exert stronger suctions than
CONCLUSION A transpiring plant pulls water through a
could be generated with a vacuum pump.
branch faster than a vacuum pump. Therefore, the pulling force
EXPERIMENT Renner measured the rate at which water flowed generated by a transpiring plant must be greater than that of
from a reservoir into the cut tip of a branch of a transpiring plant. He a vacuum pump. Because vacuum pumps create suctions by
next cut off about 10 cm of the branch and attached a vacuum pump reducing the pressure in the air, the maximum suction that a
in place of the transpiring plant. He then compared the flow rate vacuum pump can generate is 1 atmosphere. Thus, the maximum
height that one can lift water using a vacuum pump is 10 m
(33 feet). The forces that pull water through plants have no
comparable limit because they are generated within the partially
To
vacuum dehydrated cell wall. This is why plants can pull water from dry
pump soils and why they can grow to more than 100 m in height.
Transpiring Vacuum
plant pump
pits into an adjacent, partially overlapping, tracheid. Water also through longer conduits because the water does not need to
enters and exits a vessel through pits. Once the water is inside the flow so often from conduit to conduit across pits, which exert a
vessel, little or nothing blocks the flow of water from one vessel significant resistance to flow. Like the flow through pipes, water
element to the next. That is because during the development of flow through xylem conduits is also greater when the conduits
a xylem vessel, the end walls of the vessel elements are digested are wider. The flow is proportional to the radius of the conduit
away, allowing water to flow along the entire length of the vessel raised to the fourth power, so doubling the radius increases flow
without having to cross any pits. At the end of a vessel, however, sixteenfold. Because vessels are both longer and wider than
the water must flow through pits if it is to enter an adjacent vessel tracheids, plants with vessels achieve greater rates of water
and thereby continue its journey from the soil to the leaves. transport. Tracheids are the type of xylem conduit found in
The rate at which water moves through xylem depends on lycophytes, ferns and horsetails, and most gymnosperms, whereas
both the number of conduits and their size. Water flows faster vessels are the principal conduit in angiosperms.
608
CHAPTER 29 P L A N T S T RU C T U R E A N D F U N C T I O N : M OV I N G P H OTO S Y N T H E S I S O N TO L A N D 609
Water is pulled through xylem by an evaporative moving water through the plant itself. To replace water lost by
pump. transpiration with water pulled from the soil, the leaves must
If you cut a plant’s roots off under water, the leaves continue to exert forces that are many times greater than the suctions that
transpire for some time. The persistence of transpiration when we can generate with a vacuum pump (Fig. 29.11). How do leaves
roots are absent demonstrates that the driving force for water exert this force?
transport is not generated in the roots, but instead comes from When stomata are open, water evaporates from the walls
the leaves. In essence, water is pulled through xylem from above of cells lining the intercellular air spaces of leaves. The partial
rather than being pushed from below. dehydration of the cell walls creates a force that pulls water toward
The forces pulling water upward through the plant are large. the sites of evaporation, much as water is drawn into a sponge.
Not only must these forces be able to lift water against gravity, This force is transmitted through the xylem, beginning in the leaf
they must also be able to pull water from the soil, which becomes veins, then down through the stem, and out through the roots to
increasingly difficult as the soil dries. In addition, they must the soil (Fig. 29.12). Water can be pulled through xylem because of
be able to overcome the physical resistance associated with the strong hydrogen bonds that form between water molecules.
FIG. 29.12 Xylem transport from roots to leaves. Water is pulled through the plant by forces generated in the leaves, preventing them from
drying out.
Mesophyll
cells
1 The evaporation
of water from leaves
Stoma causes water to flow
from the soil.
2 Hydrogen
bonds that form
Cell wall between water
molecules allow
water to be pulled
through the xylem.
Water
molecule
Xylem 3
Root The forces
hair that develop in
leaves must be
Water large enough to
flow overcome the
Soil capillary forces
particle in the soil.
610 SECTION 29.4 T H E S T E M : T R A N S P O RT O F C A R B O H Y D R AT E S T H RO U G H P H LO E M
The phloem supports not only the growth of roots, but also the
development of non-photosynthetic organs such as reproductive FIG. 29.14 Phloem structure. Phloem conduits are formed of
structures and stems. living cells. (a) Sieve tubes and associated companion
cells and (b) scanning electron microscope image
Phloem transports carbohydrates from sources showing sieve plates of squash (Cucurbita maxima).
to sinks. Photo source: Michael Knoblauch.
diameter) (Fig. 29.14). The plasma membrane of adjacent cells is Cell wall
continuous through each of these pores, so each multicellular sieve
tube can be considered a single cytoplasm-filled compartment.
Phloem transports carbohydrates as sucrose or larger
sugars. Phloem also transports amino acids, inorganic forms b.
of nitrogen, and ions including K1, which are present in much
lower concentrations. Finally, phloem transports informational
molecules such as hormones, protein signals, and even RNA.
Thus, phloem forms a multicellular highway for the movement of
raw materials and signaling molecules through the entire length
of the plant.
relative to a lower concentration of sugars in sinks. In sources, Like the xylem, the phloem is subject to risks that arise from
a high concentration of sugars in sieve tubes causes water to the way the flow is generated. The contents of damaged sieve
be drawn into the phloem by osmosis. Because the cell walls tubes can leak out, pushed by high turgor pressures in the phloem.
of the sieve tube resist being stretched outward, the turgor Damage is an ever-present danger because the sugar-rich phloem
pressure (Chapter 5) at the source end increases. At sinks, sugars is an attractive target for insects. Cell damage activates sealing
are transported out of the phloem into surrounding cells. This mechanisms that block flow through sieve plates and thus prevent
withdrawal of sugars causes water to leave the sieve tube, again phloem sap from leaking out. In some respects, these mechanisms
by osmosis, reducing turgor pressure at the sink end. It is the are comparable to the formation of blood clots in humans, except
difference in turgor pressure that drives the movement of phloem that phloem can seal itself much more rapidly, typically in less
sap from source to sink (Fig. 29.15). than a second.
In some plants, sugars are actively transported into sieve
j Quick Check 4 How is phloem able to transport carbohydrates
tubes using energy from ATP. In others, sugars diffuse passively
from the shoot to the roots, as well as from the roots to the shoot
from the sites of photosynthesis into the sieve tubes as the
(although not at the same time)?
sugar concentration builds up in photosynthesizing cells. These
mechanisms are quite effective. The pressures that develop in
sieve tubes are approximately 100 times the pressures that occur Phloem feeds both the plant and the rhizosphere.
in our own circulatory system. All the cells in a plant’s body contain mitochondria that carry out
The water that exits the phloem can remain within the sink respiration to provide a constant supply of ATP. Typically, about
or it can be carried back to the leaves in the xylem (Fig. 29.15). 50% of the carbohydrates produced by photosynthesis in one day is
The volume of water that moves through the phloem, however, is converted back to CO2 by respiration within 24 hours.
tiny compared to the amount that must be transported through Carbohydrates that are not immediately consumed in
the xylem to replace water lost by transpiration. Therefore, the respiration can be used as raw materials for growth, or they can be
number and size of xylem conduits greatly exceeds the number stored for later use. Carbohydrates stored within roots and stems as
and size of sieve tubes. starch, or in tubers (specialized storage organs such as potatoes), can
support new growth in the spring or following a period of drought.
Stored reserves can also be used to repair mechanical damage or
replace leaves consumed by insects or grazing mammals.
FIG. 29.15 Phloem transport from source to sink. Sources
What determines how carbohydrates become distributed
produce carbohydrates or supply them from storage,
within the plant? Phloem transport to reproductive organs
and sinks require carbohydrates for growth and
appears to have priority over transport to stems and developing
respiration.
leaves, and these have priority over transport to roots. In Chapter
31, we discuss the role that hormones play in controlling the
Companion
growth and development of plants and how these hormones may
cell
influence the ability of different sinks to compete successfully for
resources transported in the phloem.
Source Phloem also supplies carbohydrates to organisms outside the
(leaf cell) plant. A fraction of the carbohydrates transported to the roots spills
Sucrose out into the rhizosphere, the soil layer that surrounds actively
growing roots. This supply of carbohydrates stimulates the growth
Sieve tube of soil microbes. As a result, the density of microbial organisms
near roots is much greater than in the rest of the soil. These soil
bacteria decompose soil organic matter rich in nutrients such as
nitrogen and phosphorus. Thus, by releasing carbohydrates into the
Xylem Phloem soil, roots are thought to acquire more nutrients from the soil.
CONCENTRATION
ELEMENT IN DRY MATTER (%) FUNCTIONS
Data from Table 5.2 in Lincoln Taiz et al., Plant Physiology and Development, 6th ed., 2015, Sinauer Associates, Inc.; Table 8.1 in Emmanuel
Epstein and Arnold J. Bloom, Mineral Nutrition of Plants: Principles and Perspectives, 2nd ed., 2004, Sinauer Associates, Inc.
614 SECTION 29.5 T H E RO OT : U P TA K E O F WAT E R A N D N U T R I E N T S F RO M T H E S O I L
journey to the xylem. Energy is also required to make specific produced by photosynthesis, and the fungus provides nutrients
nutrients in the soil accessible to the root. The mitochondria of they have obtained from the soil.
root cells must, therefore, respire at high rates to provide energy Mycorrhizae are of two main types (Fig. 29.18).
needed for nutrient uptake. Their high respiration rates explain Ectomycorrhizae produce a thick sheath of fungal cells that
why plants are harmed by flooding: Waterlogged soils slow the surrounds the root tip. Some of the fungus extends into the
diffusion of oxygen, limiting respiration. interior of the root, producing a dense network of filaments that
To understand how roots acquire nutrients and why this surrounds individual root cells. Endomycorrhizae do not form
requires energy, let’s first look at how nutrients move through the structures that are visible on the outside of the root. Instead, their
soil. Nutrients move by diffusion through the films of water that networks form highly branched structures, called arbuscules,
surround individual soil particles. In addition, when transpiration which grow inside root cells.
rates are high, the flow of water through the soil helps to convey Why do fungi enhance the ability of roots to obtain nutrients
nutrients toward the root. The active uptake of nutrients by root from the soil? One reason is that fungal networks can extend more
cells, a process that requires an expenditure of energy in the form than 10 cm from the root surface, greatly increasing the absorptive
of ATP, decreases nutrient concentrations at the root surface, surface area in contact with the soil. And because fungal filaments
creating a concentration gradient that drives diffusion from are so thin, they can penetrate tiny spaces between soil particles
the bulk soil to the root. However, because diffusion transports and thus access nutrients that would otherwise be unavailable to
compounds efficiently only over short distances, each root is roots. Another reason is that fungi secrete enzymes that make soil
able to acquire nutrients only from a small volume of
soil. This limitation explains why plants produce so
many roots and so many root hairs: Both structures
increase the volume of soil from which a root can obtain FIG. 29.18 Mycorrhizae. These fungus–root associations allow plants to use
nutrients. It also explains why roots elongate more carbohydrates to help gain nutrients from the soil.
or less continuously, exploiting new regions of soil to
obtain nutrients required for growth. Ectomycorrhizae Epidermis
Nutrients vary dramatically in the ease and speed
with which they move through the soil. For example, Root cortex
nitrate (NO32) and sulfate (SO422) are extremely mobile. Endoderm
In contrast, interactions with clay minerals keep zinc Phloem
and inorganic phosphate attached to soil particles. One Xylem
way that roots gain access to highly immobile nutrients Fungal
is by releasing protons or compounds that make the soil sheath
environment close to the root more acidic. This requires
energy in the form of ATP, but the decrease in pH
weakens the attachment of immobile nutrients to soil
particles. As a result, these formerly immobile nutrients Fungal cells surround but do not
are able to move by diffusion to the root. Fungal strands
penetrate root cells. Carbon and
nutrients are exchanged through
Soil microorganisms—both fungi and bacteria— extending from
the plasma membrane.
are more adept than plants at obtaining nutrients. the root
symbiotic association with roots or as free-living bacteria in accomplished only by prokaryotes. Like nitrogen fixation by
the soil. bacteria, the Haber–Bosch process requires large inputs of
As populations grew, fields could not be left unplanted for long energy; unlike nitrogen fixation by bacteria, it occurs only at
periods. Organic fertilizers such as crop residues, manure, and high temperatures and pressures. The prospect of an essentially
even human feces recycled some of the lost nitrogen, but unless unlimited supply of nitrogen in a form that plants can make use of
they are brought in from off the farm, they cannot replace all the has proved irresistible. Today industrial fertilizers produced by the
nitrogen removed during harvest. Haber–Bosch process account for more than 99% of fertilizer use.
Crop rotation has been widely practiced throughout the history Industrial fixation of nitrogen is approximately equal to the entire
of agriculture as a means of sustaining soil fertility. Every few years, rate of natural fixation of nitrogen, which is largely due to bacteria,
a field is planted with legumes harboring nitrogen-fixing bacteria. although a small amount of nitrogen is fixed by lightning.
Typically, the legume plants are not harvested, but instead are As we discuss in Chapter 49, human use of fertilizer is
treated as “green manure” that is allowed to decay and replenish soil altering the nitrogen cycle on a massive scale, posing a threat to
nitrogen. During the eighteenth and nineteenth centuries, legume biodiversity and the stability of natural ecosystems. Yet abundant
rotation contributed to the higher crop yields needed to support nitrogen fertilizers are a cornerstone of modern agriculture. The
increasing populations. Therefore, along with the mechanization high-yielding varieties of corn, wheat, and rice introduced in the
of agriculture, nitrogen-fixing symbioses contributed to the social mid-twentieth century achieve their high levels of growth and
conditions that fueled the Industrial Revolution. grain production only when abundantly supplied with nitrogen.
By the second half of the nineteenth century, more abundant The fact that plants such as legumes (including beans, soybeans,
and more concentrated supplies of nitrogen fertilizers were alfalfa, and clover) form symbiotic relationships with nitrogen-
sought. Mining of guano and sodium nitrate mineral deposits fixing bacteria suggests a possible way around this problem. If
helped meet the demand for the nitrogen, but with time these it were possible to engineer nitrogen fixation into crops such
natural nitrogen sources were depleted. A mechanism was needed as wheat and rice, either by inducing them to form symbiotic
to obtain nitrogen fertilizer from the vast storehouse of nitrogen relationships with nitrogen-fixing bacteria or by transferring the
in the atmosphere. genes that would enable them to fix nitrogen on their own, would
German chemist Fritz Haber developed an industrial that eliminate the need for nitrogen fertilizers? The answer is
method of fixing nitrogen in the years 1908–1911, and Karl yes—but with a caveat. As we have seen, nitrogen fixation requires
Bosch subsequently adapted it for industrial production. Their a large amount of energy, diverting resources that could otherwise
method allows humans to achieve what, until then, had been be used to support growth and reproduction. •
Core Concepts Summary The waxy cuticle on the outside of the epidermis slows rates of
water loss from leaves but also slows the diffusion of CO2 into
29.1 The evolution of land plants from aquatic leaves. page 602
ancestors introduced a major challenge for Stomata are pores in the epidermis that open and close, allowing
photosynthesis: acquiring carbon dioxide without CO2 to enter into the leaf and also allowing water vapor to
drying out. diffuse out of the leaf. page 602
Early-branching groups of land plants, commonly grouped CAM plants capture CO2 at night when evaporative rates are
as bryophytes, balance CO2 gain and water loss passively, low. During the day, they close their stomata and use this stored
photosynthesizing in wet conditions and tolerating desiccation CO2 to supply the Calvin cycle, resulting in increases in the
in dry ones. page 600 exchange ratio of CO2 and H2O. page 604
Vascular plants maintain the hydration of their photo- C4 plants suppress photorespiration by concentrating CO2 in
synthetic cells with water pulled from the soil. page 600 bundle-sheath cells. The buildup of CO2 in bundle-sheath cells
results from the rapid production of C4 compounds in the
29.2 Leaves have a waxy cuticle and stomata, both of mesophyll cells, which then diffuse into the bundle-sheath cells
which are important in regulating carbon dioxide gain and release CO2 that can be used in the Calvin cycle. page 605
and water loss.
29.3 Xylem allows vascular plants to replace water
The low concentration of CO2 in the atmosphere forces plants evaporated from leaves with water pulled from the soil.
to expose their photosynthetic cells directly to the air. The
outward diffusion of water vapor leads to a massive loss of Water flows through xylem conduits from the soil to the leaves.
water. page 601 page 607
618 SELF-ASSESSMENT
Xylem is formed from cells that lose all their cell contents as Plants exchange carbohydrates with symbiotic fungi in return
they mature. page 607 for assistance obtaining nutrients from the soil. page 615
Xylem conduits have thick, lignified cell walls. Water flows Plants supply carbohydrates to symbiotic nitrogen-fixing
into xylem conduits across small thin-walled regions called bacteria in exchange for available forms of nitrogen. page 616
pits. page 607
Agricultural productivity is closely linked to nitrogen supply.
Xylem conduits are of two types: tracheids and vessels. page 616
Tracheids are unicellular xylem conduits; vessels are formed
from many cells. page 607
Plant
Reproduction
Finding Mates and Dispersing
Young
Core Concepts
30.1 Alternation of generations
evolved in plants by the
addition of a diploid
sporophyte generation that
allows plants to disperse spores
through the air.
30.2 Pollen allows the male
gametophyte to be transported
through the air, while
resources stored in seeds
support the growth and
development of the embryo.
30.3 Angiosperms (flowering
plants) attract and reward
animal pollinators, and they
provide resources for seeds
only after fertilization.
30.4 Many plants also reproduce
asexually.
JAPACK/amanaimagesRF/amanaimages/Corbis.
619
620 SECTION 30.1 A LT E R N AT I O N O F G E N E R AT I O N S
As plants moved onto land, the challenges of carrying out with the parent plant. Early-diverging groups of plants evolved the
photosynthesis in air were matched by the difficulties of capacity to disperse their offspring through the air, but they still
completing their life cycle. The algal ancestors of land plants required water for fertilization. How could these plants exist in both
relied on water currents to carry sperm to egg and to disperse water and air? They couldn’t—at least not at the same time. Instead,
their offspring. On land, the first plants were confronted with early land plants evolved a life cycle in which one generation, or
the challenge of moving gametes and offspring through air. Air is phase of the life cycle, released sperm into a moist environment
less buoyant than water, provides a poor buffer against changes and the following generation dispersed offspring through the air.
in temperature and ultraviolet radiation, and increases the risk of Thus, a pattern of alternating haploid and diploid generations,
drying out. As plants diversified on land, structures evolved that which occurs in all plants, is thought to have evolved as a means
allow gametes and offspring to survive being transported through of allowing fertilization in water while enhancing the dispersal of
air. For these structures to be useful, plant life cycles had to offspring on land.
undergo radical change. The modification of land plant life cycles
is a major theme in plant evolution. The algal sister groups of land plants have one
The gametes and offspring of many land plants are carried multicellular generation in their life cycle.
passively by the movement of the air (or in a few cases, water— Molecular sequence comparisons identify three groups of green
think coconuts). However, some plants evolved the capacity to algae as being closely related to land plants (Fig. 30.1). These close
harness animals as transport agents. In particular, the flowers relatives include Coleochaetales and Charales, two groups of green
and fruits of angiosperms influence animal behavior through algae that share a number of features with plants, including cellular
their colors, scents, and food resources. Animals attracted by the structures like plasmodesmata and developmental features like
food provided by flowers (or in a few cases, by the false promise apical growth (i.e, at the tip). Another group of green algae, the
of a mate) transport male gametes from one flower to another. microscopic Zygnematales, may also be closely related to plants,
Animals that eat fruits or inadvertently carry them attached to but this group has gone down a distinct evolutionary path and so
their fur are key agents of seed dispersal. As plants diversified on exhibits fewer plant-like features. The life cycles of all three groups,
land, coevolution with animals emerged as a second major theme however, share many features. Here we use Coleochaete and Chara to
in plant evolution. gain insights into the evolution of land plant life cycles. Coleochaete
is an inconspicuous green pincushion that grows on aquatic plants
or rocks in freshwater environments, and Chara is an erect alga
30.1 ALTERNATION OF GENERATIONS found along the margins of lakes and estuaries (Fig. 30.2).
In animals, the multicellular body consists of diploid (2n) cells.
Land plants are rooted in one place, yet must be able to disperse Coleochaete and Chara have a multicellular body as well, shown in
their offspring to minimize competition for space and resources Fig. 30.2, but it consists entirely of haploid (1n) cells. In animals,
FIG. 30.1 The phylogeny of land plants. This phylogenetic tree shows the evolutionary
trajectory of the environmental setting for fertilization and dispersal.
Fertilization Dispersal
Other green algae Water Water
Sister group of
Water Water
green algae
FIG. 30.5 Moss sporangia. (a) When spores of Polytrichum commune are mature, a cap falls off, allowing the salt shaker–like sporangium to
release the spores. (b) The sporangia of Homalothecium sericeum have a ring of teethlike projections that curl back as they dry, flinging
spores into the air. Sources: a. Keith Burdett/age footstock; b. Power and Syred/Science Source.
a b
Following dispersal, most spores germinate within a few habitats. The evolution of new structures to enhance dispersal on
days, but some can survive within the spore wall for months or land is a major theme in plant evolution.
even years. When conditions for growth are favorable, the spore
j Quick Check 1 In what ways are spores similar to gametes, and in
wall ruptures, and the haploid cell inside can then develop into a
what ways do spores and gametes differ?
multicellular and free-living gametophyte.
Dispersal enhances reproductive fitness in several Spore-dispersing vascular plants have free-living
ways. gametophytes and sporophytes.
With the evolution of the multicellular sporophyte generation, In Chapter 29, we saw that the evolution of vascular tissues
land plants were able to make many spores and disperse them allowed plants to grow tall. Xylem and phloem are present only
across large distances on land. Dispersal is one of the most in the sporophyte generation because spore dispersal is enhanced
important stages in a plant’s life cycle. To understand why, by height whereas gametophytes must remain small and
imagine what would happen if a plant’s spores (or seeds) simply close to the ground to increase the chances of fertilization. A
dropped straight down onto the ground below the parent plant. All major change in the plant life cycle is that in vascular plants
the plant’s offspring would then attempt to grow in a very small the sporophyte is the dominant generation both because the
space that might contain enough nutrients and light for only a few sporophyte is physically larger than the gametophyte and because
to establish themselves. In contrast, offspring dispersed by wind or its photosynthetic production is much higher than that of the
other means are more likely to settle in a spot where they will not gametophyte.
be forced to compete with closely related individuals for resources. The first two groups of vascular plants—the lycophytes
In addition, dispersal allows offspring to avoid pathogens and the ferns and horsetails—depend on swimming sperm for
and parasites. Viruses and bacteria travel easily from individual fertilization and disperse by spores that are released into the air
to individual in a densely packed population. An individual that (see Fig. 30.1). In these ways, their life cycle is similar to that of
settles away from the parent plant is less likely to encounter the bryophytes. However, the spore-dispersing vascular plants are
a pathogen. Finally, dispersal allows offspring to colonize new distinct from bryophytes in that both the gametophyte and the
624 SECTION 30.1 A LT E R N AT I O N O F G E N E R AT I O N S
FIG. 30.6 The life cycle of the bracken fern Pteridium aquilinum. This life cycle illustrates the alternation between a free-living gametophyte
generation that remains small and a free-living vascularized sporophyte generation that grows tall. Photo sources: (left) Biophoto Associates/
Science Source; (right) Jess Merrill/Alamy.
HAPLOID DIPLOID
(1n) (2n)
The sporophyte is
Sporophyte initially supplied
Sperm are released with nutrients by
when moisture is the gametophyte.
present. Fertilization
The egg is
retained.
Leaf
Gametophytes
Dispersal
Haploid gametophyte Haploid
spores
Sporangia are produced on
Spores are released into air. the lower surfaces of leaves.
Those that land in a suitable Meiosis
site will germinate and grow
into new gametophytes. Sporopollenin Underground stem
walls
Roots
Sporophyte
sporophyte generation are free-living, meaning that each is able to a weak link in the fern life cycle. In fact, because fern gametophytes
supply its own nourishment. tolerate drying out, they often live longer and withstand stressful
To illustrate this, let’s examine the life cycle of the bracken environmental conditions better than the much larger sporophytes.
fern Pteridium aquilinum. We begin with the largest component of As discussed in Chapter 29, desiccation tolerance is important for
the life cycle—the leafy diploid sporophyte generation (Fig. 30.6). plants that lack roots, which include both bryophytes and free-
If you examine a bracken leaf closely, you may find tiny brown living gametophytes.
packets along its lower margin. These are sporangia, and each Fern gametophytes typically produce either male or female
contains diploid cells that undergo meiosis to generate haploid gametes. The male gametes swim to the egg on a nearby
spores. The spores become covered by a thick wall containing gametophyte through a film of water. The union of a male and a
sporopollenin, making them well suited for dispersal through female gamete forms a diploid zygote, which develops in place and
the air. is supported by the gametophyte as it begins to grow. Eventually,
As the sporangia dry out, they break open and the spores are the developing sporophyte forms leaves and roots that allow it to
released. Most spores travel only short distances, but a few may become a physiologically independent, diploid plant.
end up far from their parent. Bracken ferns can be found on every Ferns release swimming sperm and thus are able to reproduce
continent except Antarctica, as well as on isolated oceanic islands, only when conditions are wet. That is true of the other spore-
testimony to the ability of spores to travel long distances. dispersing plants (lycophytes, horsetails, and bryophytes) as well.
Spores that land in a favorable location can germinate and grow What if a plant could eliminate the requirement for swimming
to form the haploid gametophyte generation. You have probably sperm? Seed plants did just that.
never seen a fern gametophyte—or never noticed one. Typically
of most ferns, the bracken gametophyte is less than 2 cm long and j Quick Check 2 In what ways is fern reproduction similar to moss
only one to a few cells thick (Fig. 30.6). The small size of the fern reproduction? In what ways is fern reproduction different from
gametophyte has led many to assume that the haploid generation is moss reproduction?
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 625
FIG. 30.7 The life cycle of the loblolly pine tree, Pinus taeda. Photo source: Charles O. Cecil/Alamy.
HAPLOID DIPLOID
Egg
(1n) Pollen is released into the air Multicellular female (2n)
and transported by wind; some gametophyte
land on ovule cones.
Before fertilization can occur, the
pollen must germinate to form a
pollen tube that grows to the
female gametophyte.
Pollination
Fertilization
Ovule
Haploid spores
Four Sporangium
cells (2n)
Pollen Seed
grain coat
Multicellular (2n)
A fertilized
male gametophyte Embryo ovule develops
Protective into a seed.
(2n)
Sporangium layers
(2n) Meiosis Female
gametophytes Female Seed dispersal
develop from gametophyte
Haploid (1n)
spores spores within
ovule cones.
Meiosis Winged
seeds
Germination
Male gametophytes
develop from spores
within pollen cones. Seeds that land in
a suitable site can
grow into new
sporophytes. Sporophyte
repeated mitoses to form a multicellular female gametophyte must germinate and the male gametophyte produce a pollen
consisting of a few thousand haploid cells, one or more of which tube that grows outward through an opening in the sporopollenin
differentiate as eggs. The female gametophyte remains attached to coat. In pines, pollination occurs as much as 15 months before
the sporophyte as part of the ovule fertilization. In fact, it is the arrival of the pollen that
Pollen cones are compact shoots with modified leaves that stimulates the development of the female gametophyte. When the
produce sporangia on their surface. Within the sporangia, many female gametes are ready to be fertilized, the male gametophyte’s
cells divide by meiosis to form haploid spores. The haploid spores pollen tube grows to the female gametophyte, attracted by chemical
then divide mitotically to form a multicellular male gametophyte signals. Two sperm, which lack flagella, travel down the pollen tube
inside the spore wall. In pine, the male gametophyte consists and one of them fuses with the egg to form a zygote. Fertilization
of only four cells at the time the pollen is shed from the parent in seed plants thus takes place without the male gametes ever being
plant. exposed to the external environment.
In pine, pollen is carried to the ovule by the wind. To reach the In seed plants, the relationship between sporophyte and
egg, however, and penetrate the tissues of the ovule, the pollen gametophyte has been reversed completely from that found in
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 627
FIG. 30.8 Life-cycle evolution in land plants. A major trend in the evolution of land plants is a decrease in the size and independence of the
gametophyte generation and a corresponding increase in the prominence of the sporophyte generation.
Gametophyte Sporophyte
Sister group Photosynthetic, persistent Physically and physiologically
of green algae dependent on gametophyte
Liverworts
50 mm
Mosses 10 cm
Multicellular
sporophyte
Hornworts
Lycophytes
50 cm
Spore-dispersing 2 cm
Ferns and vascular plants
Vascularized sporophyte horsetails
generation
Gymnosperms 50 m
Green algae Seed plants < 0.5 cm
Pollen
Bryophytes Angiosperms Physically and physiologically
and seeds Photosynthetic, persistent
dependent on sporophyte
Vascular plants
bryophytes. The gametophyte, so prominent in mosses, is important food resource for animals and are the cornerstone of
reduced to a small number of cells that depend entirely on their agricultural production. Because seeds are larger than spores,
parent sporophyte for nutrition (Fig. 30.8). however, they are not as easily dispersed by wind. As a result,
seed plants have evolved structures to enhance seed dispersal.
j Quick Check 3 How do the male and female gametophyte
For example, pine seeds have flattened extensions, referred to
generations differ in seed plants?
as “wings,” that increase the distances over which they can be
carried by a breeze. Other seed plants produce brightly colored
Seeds enhance the establishment of the next and/or fleshy structures to attract and reward animals that
sporophyte generation. may inadvertently carry seeds farther away from the parent
The union of gametes triggers the ovule to develop into a seed plant than they could disperse on their own. Many plants
that can carry the new embryo away from the parent plant. dispersed by animals develop seed coats that allow their seeds
Because seeds develop from fertilized ovules, they contain to pass unharmed through an animal’s digestive system.
tissues produced by three generations (Fig. 30.9). On the
outside is the protective seed coat, which is formed from
tissues that surround the sporangium and thus is a product
FIG. 30.9 Structure of a pine seed. A pine seed contains
of the diploid sporophyte. At the center is the embryo, which
tissues from three generations: the seed coat formed
develops from the zygote and represents the next sporophyte
from diploid sporophyte layers, the haploid female
generation. In seed plants, the embryo develops an embryonic
gametophyte, and the diploid embryo, which will grow
root at one end and an embryonic shoot with one to several
into the next sporophyte generation. Source: Jim French.
embryonic leaves at the other. In gymnosperms such as
pine trees, the embryo is surrounded by the haploid female Female
Seed coat (2n) gametophyte (1n)
gametophyte, which provides the raw materials that support
the growth of the embryo. In angiosperms, the origin of this
storage tissue differs, but it serves the same role of nourishing
the embryo.
Compared with a unicellular spore, a seed is able to store
more resources to support the growth and establishment of a Embryo (2n)
new sporophyte generation. Many seeds contain high levels of
protein and energy-rich oils (Chapter 2). As a result, seeds are an
628 SECTION 30.3 F LO W E R I N G P L A N T S
During seed maturation, most seeds lose water. And as water Seeds span over 11 orders of magnitude in size (Fig. 30.10).
content falls, the seeds’ metabolic activity drops to extremely The 100-nanogram (ng) seeds of orchids are so small (100 ng 5
low levels and the embryo ceases to grow. The combination of 0.0001 mg) that they cannot germinate successfully without
low metabolic activity and ample stored resources allows seeds to obtaining nutrients from a symbiotic fungus. At the other end of
survive for long periods, in many cases one to several years, and the spectrum are the 30-kilogram (kg) seeds of the coco-de-mer,
sometimes much longer. Some seeds exhibit dormancy, meaning a palm tree found on islands in the Indian Ocean. Large seeds,
that they can delay germination even when conditions for growth, being better provisioned, are well adapted for the deep shade
notably temperature and moisture, are favorable. Dormancy of a forest understory. However, large seeds typically disperse
prevents seeds from germinating at the wrong time, for example shorter distances and they often have little or no dormancy. In
on an uncharacteristically warm day at a time of year when the contrast, for the same investment in resources, a plant can make
seedlings would be unable to survive. It also prevents seeds from many small seeds, which can persist in the soil until the right
germinating all at once, thus spreading the risk of making the combination of conditions triggers germination. As a result, most
transition from embryo to seedling over a larger time span and weeds produce small seeds.
range of conditions.
j Quick Check 4 Name three advantages of seeds over spores in
terms of the probability that the next sporophyte generation will
become successfully established.
FIG. 30.11 Flower diversity. Shown here are (a) a lady’s-slipper orchid (Cypripedium reginae); (b) a magnolia (Magnolia grandiflora); (c) French
lavender (Lavandula stoechas); and (d) a tropical tree (Brownea grandiceps). Sources: a. Barrett & MacKay/age fotostock; b. Florida Images/Alamy;
c.. Jonathan Buckley/age fotostock; d. Tim Lamen/Getty Images.
a b
d c
produced both. Such “unisexual” flowers are often found in the whorls of floral organs (Fig. 30.12; Chapter 20). The outer whorls
approximately 20% of angiosperm species that have reverted to consist of sepals and petals, while the inner whorls are made up
wind pollination. of pollen-producing stamens and ovule-producing carpels. Let’s
Flowers are spectacularly diverse in size, color, scent, and look at the floral organs in more detail, starting with the carpels at
form, but they all have the same basic organization: concentric the center of the flower.
FIG. 30.12 Flower organization. The four whorls of organs in a flower are carpels, stamens, petals, and sepals. Photo source: Cora Niele/Getty Images.
Sepals
p
Petals
Stamens
Carpels
FIG. 30.13 Spore formation and gametophyte development in (a) carpels and (b) stamens.
a. Ovule development
Spore formation Gametophyte development
Stigma
Within each sporangium, One of the haploid
one cell undergoes spores develops into a
meiosis, forming four female gametophyte
haploid spores. that fills the sporangium.
Style
Protective Protective
layers (2n) layers (2n)
Meiosis Mitosis
Ovary
b. Pollen development
Spore formation Gametophyte development
Sporangium Sporopollenin
Filament wall
Many haploid spores Male gametophyte (1n)
Stamen Pollen
Carpels are modified leaves that have become folded over and grains at once, the fastest growing pollen tubes are the most likely
sealed along the edges to form a hollow chamber. Sporangia are to deliver sperm to an egg. In some plants, the style can be more
produced on the inner surface of this cavity (Fig. 30.13a). Within than 10 cm long—corn silks, for instance, are styles—creating the
each sporangium a single cell undergoes meiosis, forming four opportunity for competition, and thus natural selection, between
haploid spores, one of which develops into a female gametophyte. genetically distinct male gametophytes.
Recall that an ovule consists of a female gametophyte surrounded Immediately surrounding the carpels are the pollen-producing
by protective tissues and that ovules, when fertilized, develop into stamens. A stamen can have a leaflike structure bearing sporangia on
seeds. The fact that the ovules develop within the carpel is what its surface, but more commonly it consists of a filament that supports
gives rise to the name “angiosperm,” which is from Greek words a structure known as the anther, which contains several sporangia
meaning “vessel” and “seed.” In gymnosperms, the ovules are not (Fig. 30.13b). Within each sporangium, many cells undergo meiosis
enclosed, and their name, again from the Greek, literally means to form haploid spores. The male gametophyte then develops within
“naked seeds.” the spore wall, forming pollen. In most flowers, the anther splits
Each flower produces one or more carpels (typically 3 to 5, but open, exposing the pollen grains. Once exposed, the pollen can come
sometimes more than 20), but because the carpels are often fused, into contact with the body of a visiting pollinator or, in the case of a
there may be only a single structure at the center of the flower. At wind-pollinated species, be carried off by the wind. However, in some
the base is the ovary in which one to many ovules develop. The plants, for example tomato, small holes open at the top of anthers. To
ovary protects the ovules from being eaten or damaged by animals, extract the pollen, bees land on the flower and vibrate at just the right
but also makes it impossible for pollen to land directly on the frequency to shake loose the pollen inside. Orchids and milkweeds
surface of the ovule. To reach the ovules, pollen must land on the do not release individual pollen grains. Instead, they disperse their
stigma, a sticky or feathery surface at the top of the carpel(s), and pollen all together in a package with a sticky tag that attaches to a
grow down through the stalklike style. The female gametophytes visiting pollinator.
produce chemicals that guide the pollen tubes toward unfertilized The outer whorls of the flower produce neither pollen nor ovules
ovules. Because animal pollinators can deposit many pollen but instead contribute to reproductive success in other ways. Most
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 631
FIG. 30.14 Flowers providing food or other rewards for their pollinators. (a) A butterfly collecting pollen from flowers; (b) a hummingbird
visiting a flower for nectar; (c) a bat visiting Agave palmeri for nectar; and (d) flies attracted to Rhizanthes lowii with its smell of rotting
flesh. Sources: a. Sue Kennedy/Flowerphotos/ardea.com; b. Glenn Bartley/age fotostock; c. Rolf Nussbaumer/age fotostock; d. David M. Dennis/age footstock.
a b
d c
flowers have two outer whorls, of which the outermost is made the same time as the diversification of bees (Hymenoptera) and
up of sepals. Sepals, which are often green, encase and protect the butterflies (Lepidoptera). The evolution of flowers allowed animals
flower during its development. In contrast, petals are frequently to specialize on new food resources. At the same time, animal
brightly colored and distinctively shaped. Their role is to attract pollinators greatly facilitated the movement of pollen between
and orient animal pollinators. In addition to serving as visual cues, plants within the same population.
petals in many flowers produce volatile oils. These are the source of Flowers communicate their presence through both scent and
the distinctive odors, some pleasant, some decidedly not, that many color. For pollination to be reliable, however, it must be in the
flowers use to advertise their presence to pollinators. interest of the animal pollinator to move repeatedly between
flowers of the same species. Flowers earn fidelity from their
j Quick Check 5 What is the name and function of the structures in pollinators by providing rewards, frequently in the form of food
each whorl of a flower? (Fig. 30.14). Many insects consume some of the pollen itself,
while many flowers also produce nectar, a sugar-rich solution
The diversity of floral morphology is related to modes attractive to bats and birds as well as to insects.
of pollination. Some species provide rewards other than food. For example,
The evolutionary histories of the angiosperms and their animal many orchids secrete chemicals that male bees need to make
pollinators are closely intertwined. A rapid increase in angiosperm their own sexual pheromones. Other flowers provide an enclosed
diversity occurred between 100 and 65 million years ago, about and sometimes heated chamber in which insects can aggregate. But
632 SECTION 30.3 F LO W E R I N G P L A N T S
some flowers do not provide rewards at all: Instead, they “trick” FIG. 30.17 Germination and growth of pollen tubes. The pollen
their pollinators into visiting. For example, flowers that look and tubes of Arabidopsis thaliana can be seen here because
smell like rotting flesh attract flies, and orchids that look like a they have been stained with a fluorescent dye. Source:
female bee even emit similar pheromones to attract male bees Courtesy Keun Chae.
(Fig. 30.15). Male bees find these orchids irresistible and, as they
attempt to copulate with the flower, deliver and receive pollen.
Producing rewards and attractants such as nectar and petals
requires resources. Thus, while animals can provide more efficient
pollination than can the wind, the resources spent may be wasted
if nonpollinating visitors “steal” pollen or nectar. For this reason,
many flowers have mechanisms to protect their investments. For
example, tubular cardinal flowers provide rewards to hummingbirds
able to probe their depths, and snapdragons provide rewards only to
insects that are strong enough to push apart their petals.
Many plants have evolved flowers that match rewards and
attractants to the metabolic needs and sensory capabilities
of their pollinators. For example, flowers pollinated by larger
pollinators such as bats and birds produce copious amounts of
nectar. Bat-pollinated flowers tend to be large, white or cream
colored, and strongly scented, all traits appropriate to the size and
nocturnal habits of their pollinators. The flowers are positioned
among branches and leaves in such a way that they can be found
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 633
HOW DO WE KNOW?
FIG. 30.16
HYPOTHESIS The recent radiation of columbines corresponds with shifts from short-tongued pollinators (bumblebees) to ones with
increasingly longer tongues (hummingbirds, hawkmoths).
METHOD Researchers mapped changes in flower color and nectar spur length onto a phylogenetic tree of columbines. To do this, they
assigned each of 25 species examined to one of three groups based on length of nectar spur, flower color, and most common pollinator
(bumblebees, hummingbirds, or hawkmoths). The group is indicated by the color circle at the tip of each branch in the phylogenetic tree in the
figure. The researchers then did a statistical analysis that suggested the most likely pollinator type at each node representing an ancestor, also
indicated by color circles in the figure. They used this information to infer the history of pollinator shifts during the radiation of this group.
Short nectar spurs, blue petals, visited by bumble bees * indicates a likely evolutionary
shift in pollinator
Medium-length nectar spurs, red petals, visited by hummingbirds
Long nectar spurs, white or yellow petals, visited by hawkmoths
633
634 SECTION 30.3 F LO W E R I N G P L A N T S
thus preventing gametes from two different species from coming of angiosperm species are self-incompatible, meaning that
into contact. pollination by the same or a closely related individual does not
Plants do not have the elaborate courtship rituals that many lead to fertilization. Self-incompatible plants must be able to
animal species use to select an appropriate mate. Nevertheless, recognize that a gamete comes from a closely related individual.
angiosperms have a wide range of mating systems. At one Self-recognition is based on the proteins produced from self-
extreme are self-compatible species in which gametes from incompatibility genes, or S-genes. If the pollen’s proteins match
male (pollen) and female (ovules) gametophytes produced those of the carpel, the pollen either fails to germinate or
by flowers on the same plant can form viable offspring. Self- germinates but the pollen tube grows slowly and eventually stops
compatible plants can reproduce even when they are physically elongating. S-genes may have originated as a defense against
isolated from other individuals of the same species or when fungal invaders but subsequently evolved as a means of promoting
pollinators are rare. Many weedy species and the majority of crops outcrossing. Because there can be dozens of S-gene alleles in a
are self-compatible. population, only pollen transfers between closely related individuals
At the other extreme are species in which pollen must be are blocked. Apples are examples of self-incompatible plants, so
transferred between different plants. Approximately half of all apple orchards always contain a mixture of different varieties.
Egg
Each carpel Endosperm (3n)
produces one
Meiosis or more ovules.
Embryo (2n)
Carpels
Seed coat (2n)
Stamen Dispersal and
germination
Fertilized ovules
develop into seeds.
The ovary develops
into a fruit.
Sporophyte
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 635
FIG. 30.19 Double fertilization. In double fertilization one sperm fuses with the egg to form a zygote, while a second sperm fuses with the
diploid cell of the female gametophyte, leading to the formation of triploid endosperm.
Sporopollenin Seed
Female
gametophyte wall
Endosperm
Triploid (3n)
cell
Central Embryo
cell with (2n)
Diploid
2 haploid zygote Seed
nuclei Egg Sperm Nucleus controlling coat (2n)
pollen tube growth
Angiosperms delay provisioning their ovules until endosperm develops only when fertilization has occurred. In many
after fertilization. flowering plants, including corn, wheat, and rice, the mature seed
As we have seen, a major trend in the evolution of plants is the consists largely of endosperm (Fig. 30.20). The embryo itself
decreasing size and independence of the gametophyte generation is small. As the seeds germinate, the embryo draws resources
and the increasing prominence of the sporophyte generation. In from the endosperm to help it become established. It is no
angiosperms, this trend is taken even further (Fig. 30.18). The overstatement to suggest that the human population is sustained
male gametophyte has only three cells: One of these cells controls mostly by endosperm produced in the seeds of cereal crops.
the growth of the pollen tube, while the other two are male In other angiosperms, the growing embryo consumes all the
gametes or sperm. In most angiosperms, the female gametophyte endosperm before the seed leaves the parent plant. For example, a
contains only eight nuclei, arranged as six haploid cells (one of
which gives rise to the egg) plus a central cell containing two
nuclei. The female gametophyte of angiosperms is thus too small
to support the growth of the embryo, as it does in gymnosperms. FIG. 30.20 Endosperm. Endosperm develops from the triploid
How, then, do flowering plants provide nutrition for the embryo cell produced by double fertilization. Photo source:
to grow? Greg Lawler/Alamy.
This is where the central cell of the female gametophyte,
which contains two haploid nuclei, comes into play. During In rice, the endosperm In a mature peanut seed, all
pollination, the two sperm travel down the pollen tube and fills most of the seed and of the endosperm’s stored
the embryo is small. resources have already been
enter the ovule (Fig. 30.19). One of the sperm fuses with the transferred to the embryo.
egg to form a zygote, just as occurs in all plants. The other sperm,
however, unites with the two haploid nuclei in the central cell to
form a triploid (3n) cell. This triploid cell undergoes many mitotic Seed coat Cotyledon
divisions, forming a new tissue called endosperm. In angiosperm (2n, previous (part of the
diploid embryo)
seeds, it is the endosperm that supplies nutrition to the embryo.
generation)
The process in which two sperm from a single pollen tube fuse
with the egg and the two haploid nuclei in the central cell is called Endosperm Shoot of
double fertilization. (3n) embryo
Double fertilization and endosperm formation offer a
distinct advantage. In pines and other gymnosperms, the female Embryo (2n) Root of
gametophyte provides food for the embryo. This provisioning embryo
Female gametophyte
occurs whether or not the egg is successfully fertilized, and so is tissue (1n) is too small to
see, even at this scale.
potentially a significant waste of resources. In angiosperms, the
636 SECTION 30.3 F LO W E R I N G P L A N T S
FIG. 30.21 Developmental transition from flower to fruit. Fruits, in this case a plum, develop from ovaries and provide a means of dispersing
seed. Sources: (left to right) Gert Tabak/Getty Images; Trevor Sims/age fotostock; McPHOTO/age footstock.
peanut has virtually no endosperm left at the time it is dispersed. ripening of the banana. Tomatoes and bananas are usually picked
Almost all the resources that were previously held within the in an immature state and are subsequently ripened by exposure to
endosperm have been transferred into two large embryonic ethylene. The fruits can therefore be transported while they are
leaves, called cotyledons, which form the two halves of the part still hard and less prone to damage. Because ethylene synthesis
of the peanut we eat. Thus, the embryo itself contains all of the requires oxygen, the unripe fruits are typically stored in a low-
stored resources that will nourish the growth of the seedling at oxygen environment. Without this precaution, the ethylene
germination. produced by the ripening of even a single fruit could set off a chain
reaction in which all the stored fruit would ripen at once.
Fruits enhance the dispersal of seeds. The tremendous diversity of form seen in fruits reflects the
The transformation of a flower into a fruit is as remarkable as the many ways in which angiosperm seeds are dispersed (Fig. 30.22).
metamorphosis of a caterpillar into a butterfly (Fig. 30.21). As The winged fruit of an ash tree is carried away on the wind, and a
the fertilized egg develops to form an embryo and the endosperm coconut can float on ocean currents for many months, protected
proliferates around it, the ovary wall develops into a fruit, from exposure to salt water by its thick outer husk. The burdock
stimulated by signaling molecules produced by the endosperm. fruit has small hooks that attach to fur (or clothing)—this small
In a tomato, for example, the fleshy fruit is a mature ovary that hitchhiker was the inspiration for Velcro. Other fruits are not
encloses the seeds. In some plants, other parts of the flower dispersed, but instead open to expose their seeds. For example,
may also become incorporated into the fruit. For instance, the as milkweed fruits mature and dry out, they split apart to release
fleshy part of an apple is formed from the outer part of the ovary hundreds of seeds, each with a tuft of silky hairs that floats
combined with the base of the petals and sepals. Other fruits, like them away on even a light breeze. Still others, such as Impatiens
pineapple, develop from multiple flowers. (jewelweed), produce fruits that forcibly eject their seeds.
Fruits serve two functions: They protect immature seeds from Animals are probably the most important agents of seed
being preyed on by animals, and they enhance dispersal once the transport, in many cases attracted by the nutritious flesh of the
seeds are mature. In the case of fruits dispersed by animals, it fruit. In fleshy fruits, the seeds are protected by a hard seed coat
is essential that the fruit not be consumed before the seeds are and pass unharmed through the animals’ digestive tract. In some
able to withstand a trip through their disperser’s digestive tract. species, this passage actually enhances germination rates. In many
Thus, immature fleshy fruits are physically tough and their tissues cases, however, the seed is consumed, and successful dispersal
highly astringent. As they ripen, the fruits are rapidly transformed occurs only when the animals gather more seeds than they eat.
in texture, palatability, and color. Ripening converts starches to Squirrels are a good example, storing many acorns that never
sugars and loosens the connections between cell walls so that the get eaten. Humans are an important dispersal agent—we can
fruit becomes softer. transport seeds long distances, sometimes far outside their usual
In a number of species, including apples, bananas, and range. In some cases, accidentally introduced plant species can
tomatoes, a gaseous hormone called ethylene triggers fruit disrupt native plant communities.
ripening. It is the production of ethylene that explains why
placing a ripe apple and an unripe banana together hastens the j Quick Check 6 From what flower structure(s) is a fruit derived?
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 637
? CASE 6 AGRICULTURE: FEEDING A GROWING POPULATION these conditions, the new wheat varieties produced so many seeds
that stalks became top heavy, falling over in the wind. Borlaug
How did scientists increase crop yields during the knew that an answer to this problem was to cross his plants with
Green Revolution? wheat varieties that had shorter, sturdier stems. But given the
Human civilization and plant reproduction are closely selective advantage of height in natural populations, where was he
intertwined. Not only do seeds and fruits make up a significant to find such a plant? Japanese wheat breeders had identified and
portion of our diet, the direct manipulation of plant reproduction preserved a mutant dwarf plant that had arisen spontaneously, and
plays a critical role in agriculture. Plant breeding began as the Borlaug obtained seeds of this dwarf variety.
artificial selection for plants with seeds that were easy to harvest Much hard work and many thousands of hand pollinations lay
and has today become a highly quantitative field in which ahead. But by 1963, more than 95% of Mexican wheat cultivation
controlled crosses between plants are used to combine favorable made use of Borlaug’s high-yielding semidwarf wheat varieties,
638 SECTION 30.4 A S E X UA L R E P RO D U C T I O N
resulting in wheat yields six times greater than in 1944, the year without sex” —for example, an embryo can form directly from
he began work in Mexico. In 1965, the seeds were exported in large a diploid sporophyte cell. Dandelions are an example of plant
numbers, first to India and Pakistan and soon to the rest of the species that produce seeds in the absence of sex. Apomixis would
world. Used in combination with greater investments in fertilizer be of tremendous utility in agriculture if it could be turned on
and irrigation, these varieties prevented the famines that had been or off at will. The reason for this is that, once a desirable variety
predicted by many as a result of rising human populations. For his was developed, additional seeds could be produced without
work in alleviating world hunger, Borlaug was awarded the Nobel introducing new genetic variation. This ability to breed true would
Peace Prize in 1970. be useful in self-incompatible species such as apple and blueberry.
Most plants that reproduce asexually do so without producing
seeds; instead, a new plant grows out of part of the parent plant.
30.4 ASEXUAL REPRODUCTION In these cases, dispersal of offspring occurs in different ways. In
mosses and liverworts, for example, tiny plantlets form by mitosis at
Many plants can also reproduce asexually, producing new the base of shallow cups. Raindrops landing in this cup can dislodge
individuals without the formation and fusion of gametes. While the tiny plantlets, splashing some away from the parent plant.
asexual reproduction avoids the challenges associated with However, most plants that reproduce asexually do so by
fertilization, asexually formed plants must still disperse if they growing to a new location and only then producing a new plant.
are to avoid competition for resources with the parent plant. You need look no further than a front lawn to find evidence of
Sexual reproduction relies on spores and seeds; how do asexually such vegetative reproduction. Grass forms horizontal stems
produced individuals move across the landscape? underground from which new upright grass shoots are produced
at a distance from the site where the parent plant originally
Asexually produced plants disperse with and without germinated. Strawberries, bamboo, and spider plants (a common
seeds. houseplant) also spread vegetatively by forming horizontal stems.
Some species of flowering plants are able to use seeds to disperse In many cases, the connections that were needed initially to
asexually formed individuals. In these species, seeds can develop produce a new plant become severed. When this happens, genetic
even in the absence of fertilization, a process called apomixis. A evidence is needed to determine if a plant is the result of sexual or
variety of underlying mechanisms exists that can result in “seeds asexual reproduction.
FIG. 30.23 Vegetative growth of aspen trees. Each distinct group of trees, distinguished by
leaf color, is a group of genetically identical individuals produced by vegetative
reproduction. Source: Scott Smith/Corbis.
CHAPTER 30 P L A N T R E P RO D U C T I O N : F I N D I N G M AT E S A N D D I S P E R S I N G YO U N G 639
Vegetative reproduction also occurs in woody plants. For of thousands of years by continuing to produce new
example, when a redwood tree falls over, new upright stems stems. The current record holder is an aspen clone in Utah,
can form along the now-horizontal trunk. Perhaps the most consisting of nearly 50,000 stems, that is estimated to be
impressive example of the ability to spread vegetatively is the 80,000 years old.
quaking aspen (Populus tremuloides), a common tree of the Plants can reproduce vegetatively because of the way they
Rocky Mountains that produces brilliant yellow foliage in build their bodies. As we will see in the next chapter, growth
autumn (Fig. 30.23). Aspens reproduce vegetatively by producing and development occur throughout a plant’s life, and this is the
upright stems from a spreading root system. Although each shoot plant characteristic that allows plants to produce new upright
lives for less than 200 years, a single individual can persist for tens “individuals” from roots or horizontal stems. •
Core Concepts Summary is called an ovule. Ovules, when fertilized, develop into
seeds. page 625
30.1 Alternation of generations evolved in plants by Pollination is the transport of pollen to the ovule, where
the addition of a diploid sporophyte generation that fertilization takes place. page 625
allows plants to disperse spores through the air.
Seeds contain the diploid embryo, a seed coat, and, in
The life cycle of the algal sister groups of land plants has one gymnosperms, nourishment in the form of the female
multicellular haploid generation. page 620 gametophyte. page 625
The life cycle of land plants is characterized by an alternation The pollen and ovules of gymnosperms are produced in separate
of haploid and diploid generations, one generation specialized structures, whereas the pollen and ovules of angiosperms often
for fertilization and the other for dispersal. page 621 form in one structure, the flower. page 625
Gametes are haploid cells produced by mitosis from cells in A trend in the evolution of plants is the progressive reduction in
the multicellular haploid generation, which is referred to as size and independence of the gametophyte and the increasing
the gametophyte generation. page 622 role of the sporophyte. page 627
Spores are haploid cells produced by meiosis from the
multicellular diploid generation, which is referred to as the 30.3 Angiosperms (flowering plants) attract and reward
sporophyte generation. page 622 animal pollinators, and they provide resources for seeds
only after fertilization.
Bryophytes have a free-living haploid gametophyte that
makes gametes and a dependent diploid sporophyte that Flowers consist of four whorls of organs: ovule-bearing carpels,
makes spores that are released into the air. page 622 pollen-producing stamens, petals, and sepals. page 629
In spore-dispersing vascular plants, both the gametophyte Many flowers attract animals because they provide a reward, such
generation and the sporophyte generation can survive on as food, shelter, or chemicals. Animals, in turn, transfer pollen.
their own. page 623 page 631
Bryophytes and spore-dispersing vascular plants rely Many flowering plants have genetic and structural mechanisms
for fertilization on swimming sperm released into the to prevent self-fertilization. page 632
environment. page 623 Double fertilization, which is unique to angiosperms, is the
formation of a diploid zygote and triploid endosperm. The
30.2 Pollen allows the male gametophyte to be endosperm nourishes the embryo that develops from the zygote.
transported through the air, while resources stored page 635
in seeds support the growth and development of the
The fertilization of an ovule triggers the development of the
embryo.
ovary wall into a fruit, a structure that enhances seed dispersal.
Pollen is the male gametophyte that develops within the page 636
spore wall, and so can be transported through the air.
page 625 30.4 Many plants also reproduce asexually.
The female gametophyte of seed plants is retained and Asexual reproduction produces new individuals without the need
nourished by the sporophyte. The female gametophyte, for uniting gametes. Dispersal of offspring, however, remains
together with the surrounding layers of protective tissues, important. page 638
PASS 2
664400 SSEEC
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T E R N AT I O N O F G E N E R AT I O N S
Apomixis is the formation of seeds from diploid cells, in the 3. Explain how the organs in the different whorls of
absence of fertilization. Seeds formed by apomixis are thus angiosperm flowers interact to promote fertilization.
genetically identical to the parent plant. page 638
4. Contrast the investments that angiosperms and
Vegetative reproduction can occur when a plant spreads gymnosperms make and the structures that they produce to
horizontally and develops new upright shoots. page 638 enhance pollination.
5. Diagram the structure of a mature angiosperm and a
mature gymnosperm seed, indicating the ploidy (1n, 2n, 3n) of
Self-Assessment each tissue and its role in seed development and germination.
1. Explain how the evolution of alternation of generations is 6. Describe two ways that plants can reproduce asexually
an adaptation for reproduction on land. and explain how each of these help to disperse offspring.
2. Diagram the relationship between the sporophyte
and gametophyte generations in bryophytes, ferns, Log in to to check your answers to the Self-
gymnosperms, and angiosperms. Show the relative sizes Assessment questions, and to access additional learning tools.
and physical interactions (if any) of the two generations.
CHAPTER 31
Plant
Growth and
Development
Core Concepts
31.1 In plants, upward growth by
stems occurs at shoot apical
meristems, populations of
totipotent cells that produce
new cells for the lifetime of
the plant.
31.2 Hormones are chemical signals
that influence the growth and
differentiation of plant cells.
31.3 Lateral meristems allow plants
to grow in diameter, increasing
their mechanical stability and
the transport capacity of their
vascular system.
31.4 The root apical meristem
produces new cells that allow
roots to grow downward into
the soil, enabling plants to
obtain water and nutrients.
31.5 Plants respond to light, gravity,
and wind through changes in
internode elongation and the
development of leaves, roots,
and branches.
31.6 Plants have sensory systems
that control the timing of
developmental events.
Dietrich Rose/Getty Images.
641
642 SECTION 31.1 S H O OT G RO W T H A N D D E V E LO P M E N T
FIG. 31.1 Shoot organization. (a) A tropical vine and (b) barrel cacti look very different, but their shoot systems are built from (c) the same
repeating units of nodes and internodes. Sources: a. Le Do/Shutterstock; b. LianeM/Alamy.
a. b. c. Leaf
FIG. 31.2 The shoot apical meristem. The shoot apical meristem consists of undifferentiated cells that divide rapidly, giving rise to all the cells in
stems and leaves. (a) The seedling is rowan (Sorbus acuparia). (b) The photo shows a longitudinal section of the shoot apical meristem
of coleus (Solenostemon scutellariodes). (c) This scanning electron micrograph shows the shoot apical meristem of tomato (Solanum
lycopersicum). Sources: a. Ian Gowland/Science Source; b. M. I. Walker/Science Source; c. Siobhan Braybrook.
a. c.
Developing leaves (leaf primordia)
200 µm
Shoot apical
meristem
b.
Shoot apical meristem
FIG. 31.3 Stem elongation. Internodal elongation results from cells increasing many times in length, but only a small amount in width.
Elongating Growth
internodes
Fully expanded
internodes
Cell wall
Cytoplasm
Time Vacuole
Nucleus
exactly the same distance from the ground as they were on the The shoot apical meristem controls the production
day you inscribed them. The letters, however, will be wider—a and arrangement of leaves.
phenomenon we discuss later in this chapter. The earliest vascular plants were simple branching stems, and
photosynthesis took place along the length of the stem. As evolution
The development of new apical meristems allows
stems to branch.
Vascular plants evolved the ability to branch even before they FIG. 31.4 Axillary buds. In seed plants, branching results from
evolved roots or leaves. Branching was important to these first axillary buds that are produced at nodes. Photo source:
plants because it allowed them to produce more sporangia. Jacqueline S. Wong/ViewFinder Exis, LLC.
Branching allows present-day plants to support greater numbers of
both reproductive structures and leaves.
Shoot apical
In spore-dispersing vascular plants, branches form when the meristem
shoot apical meristem divides in two, giving rise to two stems,
each with its own shoot apical meristem. In seed plants, branches
grow out from axillary buds, which are meristems that form Axillary bud
at the base of each leaf (Fig. 31.4). Axillary buds have the same
structure and developmental potential as the apical meristem
Leaf
and express the same meristem identity genes. When a branch
develops, the axillary bud becomes the shoot apical meristem
of the new branch. Thus, most plants have many shoot apical
meristems: one at the tip of each stem and branch. Axillary buds
are formed at the same time as leaves, but they remain dormant
until triggered to grow, and they persist even after leaves are shed.
Thus, axillary buds provide seed plants with many points along
their stem where new branches can form.
CHAPTER 31 P L A N T G RO W T H A N D D E V E LO P M E N T 645
are restricted to the region close to the shoot tip. Other signaling
FIG. 31.8 Arrangement of vascular bundles. In most seed plants, molecules, or their precursors, enter the vascular system and are
the vascular bundles are arranged in a ring near the outside transported the entire length of the plant. Because plants grow
of the stem. Photo source: Steve Gschmeissner/Science Source. and develop in many places at once, signaling molecules that can
move from one part of the plant to another play an important role
in coordinating growth and development.
Gibberellic acid Synthesized in the growing regions of both Stimulates stem elongation and cell division.
roots and shoots.
O H
Mobilizes seed resources for developing
embryo.
O
OH Stimulates cytokinin synthesis.
HO
H
HO O
Cl
Zeatin
Abscisic acid Synthesized in root cap, developing seeds, Maintains seed dormancy.
and leaves. Stimulates root elongation.
OH COOH
O Transported from roots to leaves in xylem. Triggers closing of stomata.
Antagonistic with ethylene.
bend and grow toward light. Auxin also plays an important role in the outermost cell layer toward the shoot tip. High levels of auxin
establishing spatial patterns of shoot development. In particular, in the outermost layer of cells trigger the growth of new leaf
auxin influences the spacing and placement of leaf primordia and primordia. The movement of auxin into leaf primordia depletes
the formation of the vascular bundles connecting young leaves to auxin from surrounding regions and thus prevents new leaf
the mature vascular system of the stem. primordia from forming nearby. As the shoot continues to grow,
Auxin’s role in patterning results from the fact that its already formed leaf primordia become displaced from the shoot
direction of movement across a group of cells can be controlled. tip and spread farther and farther apart. This allows auxin moving
The net movement of auxin in a single direction creates regions upward in the outermost cell layer to accumulate to levels needed
of high and low concentrations of auxin. These gradients in to trigger new leaf primordia close to the shoot tip.
auxin concentration can guide the growth and development of Let’s now consider how auxin transport guides the formation
individual cells. of vascular bundles that connect the leaf to the stem. As auxin is
Let’s consider first how auxin movement influences the transported into leaf primordia, it promotes cell expansion and
placement of new leaf primordia. Auxin is synthesized in rapidly the young leaves grow. However, auxin does not remain in the
dividing cells within the shoot meristem and is transported in developing leaf. Instead, auxin that has accumulated at the tip of
CHAPTER 31 P L A N T G RO W T H A N D D E V E LO P M E N T 649
FIG. 31.9 Polar transport of auxin. The polar transport of auxin results in the movement of this hormone from the tip of each developing leaf to
the base of the plant.
Direction of
auxin transport
Developing
leaves
the connection to vascular tissues in the cell (the side farthest away
stem is not yet complete. from the shoot tip). Thus,
auxin can exit only through
the basal end of the cell.
Uncharged auxin
Negatively charged auxin
PIN transport proteins
the young leaf is transported back toward the stem, but this time the plasma membrane. However, because the pH of the cytoplasm
through cells in the interior of the leaf. As auxin moves through is higher than the pH of the cell wall, auxin loses a proton. As a
these cells, it causes the cells both to elongate and to produce result, auxin has a net negative charge when inside the cell and
more of the membrane transport proteins needed for auxin to cannot move easily across the plasma membrane. For auxin to
exit the cell. The cells that initially, by chance, have the highest leave the cell, an auxin-specific plasma membrane transport
auxin levels become highly efficient at transporting auxin toward protein known as PIN is required. By restricting the placement of
the stem. This, in turn, creates distinct “channels” through which PIN proteins to only one face of each cell, plants can control the
auxin drains from the leaf. These continuous strands of elongate direction of auxin movement across an otherwise undifferentiated
procambial cells eventually develop into veins and vascular group of cells. For example, if PIN proteins are inserted only on
bundles containing mature xylem and phloem. the side of cells farthest away from the shoot tip, auxin movement
These two examples illustrate how the movement of auxin will be toward the roots. In fact, the prevailing direction of auxin
in a single direction establishes spatial patterns that can guide transport in plants is from shoot apical meristems to the root tips.
further differentiation and development. But they leave open the
question of how undifferentiated cells control the movement of
auxin in the first place.
? CASE 6 AGRICULTURE: FEEDING A GROWING POPULATION
The coordinated movement of auxin across many cells in a What is the developmental basis for the shorter stems
single direction is referred to as polar transport (Fig. 31.9). Polar of high-yielding rice and wheat?
transport allows auxin to move independent of gravity at rates In natural ecosystems, competition for sunlight creates a strong
faster than the hormone could move by diffusion alone. However, selective advantage for growing tall. Compare the slender vine in
it requires an input of energy. Fig. 31.1, which grows in a dense forest, with the compact barrel
Polar transport depends on the difference in pH between the cactus that grows where there is little danger of being shaded
cell wall and the cytoplasm. In the cell wall, auxin carries no net by a neighboring plant. Whereas the ancestors of today’s crops
charge and thus can enter surrounding cells by diffusing across competed for sunlight by growing taller, a key element of the
650 SECTION 31.3 S E CO N DA RY G RO W T H
of these new cells are lateral meristems, which form along the Gro
wth
length of a stem. Lateral meristems are similar to shoot apical
meristems in their ability to produce new cells that grow and
differentiate. However, lateral meristems differ from their apical
counterparts in several ways. First, lateral meristems surround the
stem, rather than occur at its tip. Second, because lateral meristems
form only after elongation is complete, the new cells they produce
grow in diameter but not in length. Finally, as a stem becomes
thicker, the number of meristem cells needed to encircle the stem
also increases. Thus, lateral meristems become larger over time.
Plants produce two distinct lateral meristems that together
Wood Bark
result in secondary growth. One of these, the vascular cambium
(plural, cambia), is the source of new xylem and phloem. The
xylem produced by secondary growth is familiar to you: It’s wood.
Plants with secondary growth are often described as woody,
whereas plants that lack secondary growth are described as
herbaceous. Most of the mass of a large tree consists of wood,
generated from the vascular cambium.
As the plant’s diameter increases, the epidermis formed during
primary growth eventually ruptures. Thus, plants with secondary
growth have a second lateral meristem, the cork cambium,
which renews and maintains a protective outer layer. This outer Secondary growth involves the formation of a
layer protects the stem against herbivores, mechanical damage, continuous vascular cambium that produces
secondary xylem toward the center of the
desiccation, and, in some species, fire.
stem and secondary phloem toward the
outside. The cork cambium maintains a
The vascular cambium produces secondary xylem protective outer layer.
and phloem.
The vascular cambium forms at the interface between xylem and
phloem. In stems, the vascular cambium derives from procambial This is because the undifferentiated and actively dividing cells
cells within each vascular bundle and parenchyma cells in between of the vascular cambium are weak and easily pulled apart. All of
the bundles. In forming vascular cambium, both types of cell take the material produced to the outside of the vascular cambium,
on a new identity, becoming meristem cells. including the secondary phloem, makes up the bark.
The vascular cambium produces new cells that differentiate Plants must produce more secondary xylem than secondary
on both its sides. Those to the inside of the vascular cambium phloem to replenish the water lost by leaves at high rates during
become secondary xylem, and those on the outside become the uptake of CO2 for photosynthesis (Chapter 29). As the vascular
secondary phloem (Fig. 31.11). The vascular cambium forms a cambium forms new secondary xylem cells along its inner face,
continuous layer, one cell thick, which surrounds the xylem and the newly formed cells push the vascular cambium outward, much
runs nearly the entire length of the plant. When you peel the bark the way the elongation of newly formed cells pushes the shoot
off a stem, it separates from the wood at the vascular cambium. apical meristem upward. The vascular cambium accommodates
652 SECTION 31.3 S E CO N DA RY G RO W T H
FIG. 31.13 Outer bark. (a) Outside and (b and c) inside, showing how successive cork cambia are produced. The growth of many,
discontinuous cork cambia results in the patchy bark of pine and walnut trees. Sources: a. Alan Majchrowicz/age fotostock; b. Biosphoto/Dr. Keith
Wheeler/Science Photo Library.
a. Outside of tree, ponderosa pine (Pinus ponderosa) b. Cross section of bark, walnut (Juglans regia) c.
Cork cambium
Cork
Secondary phloem
CHAPTER 31 P L A N T G RO W T H A N D D E V E LO P M E N T 653
FIG. 31.15 Wood structure. These scanning electron micrographs show (a) a gymnosperm, Douglas fir (Pseudotsuga menziesii), and (b) an
angiosperm, English elm (Ulmus procera). Sources: a. Scanning electron micrograph courtesy of the N.C. Brown Center for Ultrastructure Studies, State
University of New York College of Environmental Science and Forestry, Syracuse, NY; b. Andrew Syred/Science Source.
a. Gymnosperms b. Angiosperms
In gymnosperms, In angiosperms,
tracheids have fibers provide
both a mechanical mechanical
and a transport support, allowing
function. vessels to be
specialized for
water transport.
Tracheid
Vessels
Fiber
654 SECTION 31.4 RO OT G RO W T H A N D D E V E LO P M E N T
As in stems, the hormone auxin plays a central role in specifying single layer of cells just inside the endodermis (Fig. 31.17). The
which cells differentiate into vascular tissues. Auxin produced in pericycle is immediately adjacent to the vascular bundle, so the
shoot meristems is transported downward through the mature stem new root is connected to the vascular system from the beginning.
and into the roots by the phloem. At the end of the fully formed Because the new root meristem develops internally, the new root
phloem, auxin moves by polar transport from cell to cell until it must grow through the endodermis, cortex, and epidermis before
reaches the root apical meristem and the root cap. As auxin moves reaching the soil.
through the elongation zone, it triggers the formation of procambial One consequence of initiating new root meristems from the
cells that subsequently become phloem and xylem. pericycle is that new roots can form anywhere along the root. As
In this way, the production of auxin by developing leaves a result, plants have tremendous flexibility in the development
and the polar transport of auxin from cell to cell ensures that the of their root systems and roots can proliferate locally in response
vascular system is continuous between roots and leaves. Phloem to nutrient abundance. For example, the presence of nitrate, the
extends closer to the root tip than do fully lignified xylem conduits. most common form of nitrogen in soil, triggers the formation
The root apical meristem does not need direct access to the xylem of lateral roots. Only a relatively small number of a plant’s roots,
because it can obtain water and nutrients directly from the soil however, continue to elongate and branch indefinitely. Most new
but depends entirely on the phloem for carbohydrates needed for roots are active for only a short time, after which they die and are
growth. shed. This turnover of fine roots allows the root system to respond
So far, we have described only the primary growth of roots. to changes in the availability of water and nutrients but represents
However, roots can undergo secondary growth as well. Through a major expenditure of carbon and energy.
secondary growth, roots increase in diameter and add new xylem Up to this point, we have described how new roots form from
and phloem. As in stems, the vascular cambium forms at the existing roots. New roots can also be produced by stems. Many
interface between the xylem and the phloem. Indeed, the vascular plants that lack secondary growth produce horizontal stems that
cambium must be continuous from the shoot to the roots to grow on or beneath the soil surface. In these plants, new roots
ensure that the secondary xylem and phloem provide an unbroken form at each successive node, so the uptake capacity of the root
connection between the roots and the leaves. In older roots with system is directly coupled to the elongation of the stem.
extensive secondary growth, a cork cambium is also formed. As When the stem of a plant is severed, new roots often form at
in stems, the cork cambium renews the outer layers of cells that the cut end. The formation of new root meristems is stimulated by
protect the living tissues from damage and predation. auxin, which is produced by the young leaves and accumulates by
polar transport at the cut end. Because their cut stems can form
The formation of new root apical meristems allows new roots, plants are able to survive damage and in some cases
roots to branch. even proliferate afterward. Many commercially important plants
Compared to stems, roots branch extensively. Even a plant are propagated through cut stems.
that has only a single stem aboveground will have many tens
j Quick Check 3 How is root development similar to and how is it
of thousands of elongating root tips. A major reason that roots
different from stem development?
branch so much is that most of the water and nutrients are taken
up in a zone near the root tip where root hairs are most abundant.
Thus, branching is necessary to create enough root surface area to The structures and functions of root systems are
supply the water and nutrient needs of the shoot. diverse.
For a root to branch, a new root apical meristem must be How a plant’s roots are distributed in the soil has a tremendous
formed. In roots, new meristems develop from the pericycle, a impact on the ability of the root system to supply the shoot with
FIG. 31.17 Branching in roots. New root meristems develop from the pericycle, and the developing lateral root grows through the root cortex
before reaching the soil. The light micrographs show willow (Salix) roots. Source: Science Source.
Emerging Epidermis
lateral root
Cortex
Lateral
Vascular root 100 μm
cylinder
656 SECTION 31.5 T H E E N V I RO N M E N TA L CO N T E X T O F G RO W T H A N D D E V E LO P M E N T
water. Some plants produce very deep roots that provide access to produce new leaves and shoots quickly following either damage or
groundwater that is independent of the variability of rainfall. For a period of drought or cold that has killed the shoots. Cassava and
example, roots have been observed in mine shafts and caves more sweet potato are examples of economically important species with
than 50 m below the soil surface. Producing and maintaining these storage roots.
non-photosynthetic structures is costly for the plant. Perhaps the most unusual rooting structures are the
At the other extreme are plants that produce shallow and “breathing” roots produced by trees that grow in water. For
spreading root systems. For example, barrel cacti produce roots that example, black mangroves produce pencil-sized roots that extend
penetrate less than 10 cm into the soil but extend out several meters vertically upward out of the sandy soil (Fig. 31.18d). Breathing roots
from the base of the plant. These roots cast a wide but shallow net to do not actually breathe; instead, they contain internal air spaces
capture as much water as possible from intermittent rain showers. that provide an easier pathway for oxygen to diffuse into the roots
Some plants produce distinctive roots whose principal than through the waterlogged soil. For this reason, breathing roots
role is not the absorption of water and nutrients from the soil must extend above the surface of the water.
(Fig. 31.18). For example, climbing plants such as poison ivy produce
roots along their stems that allow them to adhere to the sides of
trees (Fig. 31.18a). The conspicuous prop roots produced by some 31.5 THE ENVIRONMENTAL CONTEXT
tropical trees provide mechanical stability that allows these plants to OF GROWTH AND DEVELOPMENT
grow tall despite their slender stems (Fig. 31.18b).
Many plants produce swollen roots that store resources such The capacity for continued growth allows plants to respond to
as starch (Fig. 31.18c). Plants with belowground storage can changes in their environment by growing more in one direction
than another. To respond in a manner that
enhances fitness, however, plants must first
gain information about the world around them.
FIG. 31.18 Root diversity. (a) Climbing roots of poison ivy; (b) prop roots of a Pandanus
Plants rely on three types of sensory receptors:
tree; (c) storage roots of yams; and (d) breathing roots of black mangrove
Photoreceptors sense the availability of light
(shown at low tide). Sources: a. Doug Wechsler/age fotostock; b. A Jagel/age fotostock;
needed to drive photosynthesis; mechanical
c. PhilipYb/Shutterstock; d. Patrick Lynch/Alamy.
receptors sense physical influences such as
a b gravity and wind; and chemical receptors detect
the presence of specific chemicals, as well as
chemical gradients.
We saw in Chapter 9 how a signal can be
conveyed to a cell by a change in the shape of a
receptor molecule on the cell surface or within
the cell. Sensory receptors in plants work in a
similar manner. For example, the absorption of
light by a photoreceptor changes the chemical
properties of the photoreceptor, similar to the
photoreceptors in your eye. When a plant’s
sensory receptor is activated, it produces a signal
that triggers changes in the cell’s metabolism or
alters patterns of gene expression. Hormones
d c play a key role in translating information
gained by the plant’s sensory receptors into an
appropriate developmental response.
FIG. 31.19
light. Plant stems are also negatively gravitropic, meaning they were exposed, they did. This experiment established the shoot tip
grow upward against the force of gravity. In contrast, plant roots as the site where the light is perceived but left open the question of
grow down and away from the light. Thus, roots are positively what kind of signal caused the plants to bend (Fig. 31.19).
gravitropic and negatively phototropic. Photoreceptors allow plants to detect and respond to
Observing that grass seedlings bend toward light, Charles light. If a plant is exposed to light from only one side, only
Darwin and his son Francis conducted experiments to determine the photoreceptors on the illuminated side are activated.
what part of the plant detects light. When they covered just the Phototropism in plants involves a photoreceptor that absorbs
tip of the young plants, the plants no longer grew toward the light, blue wavelengths of light. The absorption of blue light by the
but when they buried them in fine black sand so that only their tips photoreceptor is thought to trigger a change in the placement of
657
658 SECTION 31.5 T H E E N V I RO N M E N TA L CO N T E X T O F G RO W T H A N D D E V E LO P M E N T
the plant
grows straight
upward. FIG. 31.21 Root orientation with respect to gravity. Starch-
filled statoliths settle to the bottom of cells, triggering
a redistribution of auxin to the lower side of the root,
where it slows elongation, causing the root to bend
b. downward. Photo source: Courtesy Dr. Christophe Jourdan.
Light
from
side
Auxin R
oo
tg
row
th
ow
Auxin
th
Auxin
Root growth
Vascular tissue
Shoot gr
Apical meristem
Root cap
Gravity
side of the shoot. stem to bend toward the light.
Statoliths
FIG. 31.22
How do seeds detect the Lettuce Seeds Germinating After Exposure to Red and Far-Red
Light in Sequence
presence of plants growing SEQUENCE OF SUBSTRATE-LEVEL
Dark (control)
GERMINATION (%)
8.5
Red 98
BACKGROUND To study the effect of light on seed germination,
scientists exposed lettuce seeds that had been kept continually in Red, far-red 54
the dark to different wavelengths of light and then counted what Red, far-red, red 100
fraction of the seeds germinated. Red light had the greatest ability Red, far-red, red, far-red 43
to stimulate germination, but surprisingly, far-red light inhibited Red, far-red, red, far-red, red 99
germination such that fewer seeds germinated than in the control
Red, far-red, red, far-red, red, far-red 54
seeds, which were kept in darkness. In the rush to conduct more
experiments, petri dishes with the light-treated seeds piled up Red, far-red, red, far-red, red, far-red, red 98
by the sink until someone noticed that the seeds that had been Time →
experimentally treated with far-red light were now germinating.
HYPOTHESIS This observation suggested that the inhibitory effect CONCLUSION Seed germination in lettuce is triggered by exposure
of far-red light can be overcome by a subsequent exposure to red to red light and is inhibited by exposure to far-red light in a reversible
light. fashion. As a result, plants are able to track changes in the relative
amount of red and far-red light, which provides information on the
EXPERIMENT The scientists exposed lettuce seeds to red and presence or absence of plants overhead (see Fig. 30.23).
far-red light in an alternating pattern, ending with either red light
or far-red light. They then placed the seeds in the dark for two days FOLLOW-UP WORK Additional studies showed that this result
and afterward counted the number of seeds that had germinated. was due to a single pigment in a photoreceptor, now known as
phytochrome, that is converted into an active form by red light and
RESULTS When the lettuce seeds were exposed to red light last, reversibly converted into an inactive form by far-red light.
nearly 100% of the seeds germinated. By contrast, when the last
exposure of the seeds was to far-red light, the percentage of seeds SOURCE Borthwick, H. A., et al. 1952. “A Reversible Photoreaction Controlling
that germinated was dramatically reduced. Seed Germination.” Proceedings of the National Academy of Sciences 38: 662–666.
thus sink to the bottom of the cell. The weight of these organelles than it is in the shade of another plant. When scientists first began
pressing on the cytoskeleton or membranes is thought to be the to study the effects of light on seed germination, they found that
signal that causes auxin to move toward the lower side of the red light is particularly good at stimulating germination, while far-
plant. In roots, gravity is a critical source of information regarding red light inhibits germination. A simple “flip-flop” experiment by
orientation. Specialized gravity-sensing cells in the root cap contain H. A. Borthwick and colleagues showed that the inhibitory effect
large starch-filled organelles known as statoliths (Fig. 31.21). of far-red light could be overcome by a subsequent exposure to
red light (Fig. 31.22). Ultimately, it was shown that only a single
Seeds can delay germination if they detect the photoreceptor was needed to detect both far-red and red light.
presence of plants overhead. Phytochrome is a photoreceptor that switches back and
For a small seed that has few stored reserves, germinating in the forth between two stable forms depending on its exposure to
shade of another plant could be fatal. But how can a seed detect light (Fig. 31.23a). Red light causes phytochrome to change into a
the presence of plants overhead? form that absorbs primarily far-red light (Pfr); far-red light causes
As sunlight passes through leaves, the red wavelengths are phytochrome to change back into the form that absorbs red light
absorbed by chlorophyll but the far-red wavelengths are not. The (Pr). Because red light stimulates seed germination, we know that
ratio of red to far-red light is thus much higher under an open sky Pfr is the active form of phytochrome. That is, red light causes
659
660 SECTION 31.5 T H E E N V I RO N M E N TA L CO N T E X T O F G RO W T H A N D D E V E LO P M E N T
FIG. 31.24 Seedlings grown in the light and the dark (left) or in full sun and shade (right). Photo source: Nigel Cattlin/Science Source.
Node
Node
Node
Node
Node
Node
by other plants that could grow to shade it in the future. Thus, production of ethylene, the production of ABA in drought-exposed
phytochrome provides an early-warning system that competitors roots leads to roots that penetrate deeper into the soil.
are nearby.
Exposure to wind results in shorter and stronger stems.
Roots elongate more and branch less when water In the 1980s, scientists studied the model plant Arabidopsis
is scarce. thaliana to learn which genes are expressed in response to different
The developmental sensitivity of plant shoots to their hormones. The experimental treatment involved spraying plants
environment is mirrored underground. When a plant experiences with different solutions containing different hormones; control
drought, it produces more roots, and these roots penetrate farther plants were sprayed with water. The hormone treatments were
into the soil, in part because they produce fewer lateral branches. successful in that several genes were strongly up-regulated.
By producing deeper roots, a plant increases its chances of However, the same genes were also turned on in the plants sprayed
reaching moister soil. with water. Further experiments showed that what the plants were
The root cap appears to play an important role in allowing responding to was neither the hormones nor the water, but the fact
roots to sense and respond to the amount of water in the soil. that their stems were bent back and forth when the plants were
Because the root cap is not well connected to the plant’s vascular sprayed. This led to the discovery of touch-sensitive genes in plants,
system, the water status of its cells provides a good indication of which are activated by mechanical perturbation.
the moisture content of the soil. As soils dry, root cap cells produce This discovery confirmed what foresters and horticulturists
a hormone called abscisic acid, abbreviated as ABA (Table 31.1). had long known. Plants exposed to wind produce stems that are
Abscisic acid stimulates root elongation, leading to roots that shorter and wider than ones grown in more protected sites. In fact,
penetrate deeper into the soil. It also triggers stomata to close, commercial greenhouses often install fans, in part so that their
reducing the demand for water. plants will produce stems robust enough that the plants can thrive
Abscisic acid stimulates root elongation by suppressing ethylene when moved outdoors. Flexing a stem back and forth triggers an
synthesis. Ethylene slows root elongation by influencing the increase in the synthesis of ethylene. As noted in section 31.4, cells
orientation of cellulose in the cell wall. Cells treated with ethylene treated with ethylene expand more in diameter and less in length,
expand in diameter rather than in length. Thus, by inhibiting the resulting in shorter and thicker stems.
662 SECTION 31.6 T I M I N G O F D E V E LO P M E N TA L E V E N T S
FIG. 31.25 Control of flowering by daylength. Short-day plants flower only when hours of daylight are below a certain number. Long-day plants
flower only when hours of daylight are above a certain number. Photo sources: (top left) Darlyne A. Murawski/Getty Images; (bottom left) Liz Van
Steenburgh/Shutterstock; (top right) Dr. Jeremy Burgess/Science Source; (bottom right) Biosphoto/Dr. Jeremy Burgess/Science Photo Library.
FIG. 31.26 Flowering strategies for short-day and long-day plants. (a) A short-day plant that germinates in the spring flowers in the late
summer when day length falls below a critical value. (b) A long-day plant flowers in the summer after a critical day length is reached.
(c) A long-day plant that requires vernalization does not flower until the critical day length is reached in the second summer.
14 Plant flowers.
Hours of daylight
Plant germinates.
Plant germinates.
12
8
Dec June Dec Dec June Dec
Plant germinates.
12
10
Vernalization
8
Dec June Dec June Dec
Plants use their internal circadian clock and phytochrome tells the plant whether it is light or dark during a
photoreceptors to determine day length. specific phase of the circadian cycle.
To determine day length, one first needs to know what time The actual mechanism used by plants to determine day length
it is, specifically how long it has been since the sun came up, relies on the fact that the plant’s circadian clock affects the
and then whether it is light or dark outside. Plants, like all transcription of many genes. For example, in Arabidopsis thaliana, a
organisms, have an internal circadian clock. Circadian clocks are long-day plant, a gene whose protein product is critical for triggering
biochemical mechanisms that oscillate with a 24-hour period flowering is transcribed at increasingly higher rates throughout
and are coordinated with the day–night cycle. Phytochrome is the day, peaking ~16 hours after dawn. After that, the rate of
the photoreceptor responsible for synchronizing the plant’s transcription declines. The protein product of this gene is targeted
internal oscillator with the first light of dawn. The circadian clock for rapid degradation unless light is present. Thus, whether the
tells the plant how long it has been since the sun came up, while protein builds up to a level sufficient to trigger flowering depends on
664 CO R E CO N C E P T S S U M M A RY
day length. During long days, the protein reaches levels needed to flower, when the chances for successful pollination and seed
trigger flowering because peak production occurs during daylight, development are greater (Fig. 31.26c). Even parts of the plant
when the protein is not targeted for destruction. During short that form long after the cold stimulus is past seem to “remember”
days, the protein product does not reach levels needed to trigger that they received the required cold treatment. This “memory”
flowering because the gene is transcribed at high rates only after the of winter is important because many plants that overwinter grow
sun has gone down, so the protein is rapidly degraded. rapidly in the spring. What is the basis of this “memory”?
This mechanism explains why interrupting the dark period One common mechanism acts through chromatin remodeling.
with a brief exposure to light alters the flowering response. In The DNA of all eukaryotic organisms is bound with proteins
an early set of experiments, both short-day plants and long-day to form chromatin. We saw in Chapter 19 that modifications
plants were grown under a photoperiod that would normally to chromatin, such as DNA methylation, can change gene
cause the short-day plants to flower and the long-day plants expression. In Arabidopsis, for example, vernalization results in
to produce only leaves. A brief exposure to light during the chromatin remodeling that turns off a gene whose protein product
dark period reversed this result. The short-day plants no longer represses flowering. Chromatin remodeling is stable through
produced flowers, but the long-day plants did. Furthermore, the mitotic divisions, explaining why newly formed parts of a plant
night interruption was effective only when the light contained “remember” winter. However, the slate is wiped clean during
red wavelengths, and the effects of red light could be reversed meiosis, and the requirement for vernalization is reinstated with
if exposure to far-red light immediately followed. These results each generation.
indicate that the light is detected by phytochrome. We now
understand that the night interruption acts like a switch Plants use day length as a cue to prepare for winter.
that converts phytochrome into its active form. In that form, We have seen how plants use day length to control when flowers
phytochrome can then affect the stability of proteins whose are produced. Day length also triggers other developmental
synthesis follows a circadian rhythm. events, particularly ones that allow plants that persist for more
Other experiments demonstrated that day length is sensed by than a year to prepare for winter. One such developmental
the leaves and not by the buds where the flowers will form. When change is the formation of storage organs, for example in roots.
conditions are right for flowering, the protein florigen is synthesized Carbohydrates that accumulate in these structures can support the
in leaves and transported through the phloem to the growing points growth of new leaves and stems the following spring.
of a plant. In this way, florigen is a chemical signal or hormone that A second developmental change in response to day length is
converts shoot meristems into floral meristems. the formation of overwintering buds. As the days begin to shorten,
plants stop producing photosynthetic leaves and begin forming
Vernalization prevents plants from flowering until bud scales. Bud scales surround and protect the meristem from ice
winter has passed. and water loss. The formation of bud scales accompanies a series of
In some species, flowering is induced only if the plant has metabolic changes that allow meristems to remain in a dormant
experienced a prolonged period of cold temperatures, a process state throughout the winter. For example, plugs are produced that
known as vernalization. A requirement for vernalization block the plasmodesmata between the meristem and the rest of
prevents long-day plants from flowering during their first summer, the plant. These plugs prevent any growth-stimulating compounds
and instead forces them to wait until the following spring to from reaching the meristem. •
Core Concepts Summary Stems contain zones of cell division, elongation, and maturation.
Most of the increase in size occurs in the zone of cell elongation.
31.1 In plants, upward growth by stems occurs at shoot page 643
apical meristems, populations of totipotent cells that In seed plants, branching occurs at axillary buds at the base of
produce new cells for the lifetime of the plant. each leaf. page 644
Stems are built from repeating modules consisting of nodes, Leaves differ from stems in that they differentiate fully and thus
where one or more leaves are attached, and internodes, which have no capacity for continued growth. page 645
are the regions of stem between the nodes. page 642 Leaves develop from leaf primordia produced by the shoot apical
meristem. page 645
The shoot apical meristem, located at the tip of each stem, is
the source of new cells from which the stem and the leaves are In most seed plants, the stem’s vascular bundles are organized as
formed. page 642 a ring. page 646
CHAPTER 31 P L A N T G RO W T H A N D D E V E LO P M E N T 665
Shoot apical meristems and axillary buds can be transformed Roots alter their development in response to conditions in the
into floral meristems, at which point they lose their capacity for soil. page 655
continued growth. page 646
Some roots are involved in adhesion, storage, and gas diffusion.
31.2 Hormones are chemical signals that influence the page 656
growth and differentiation of plant cells.
31.5 Plants respond to light, gravity, and wind through
Traditionally, five plant hormones have been identified: changes in internode elongation and the development of
auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid. leaves, roots, and branches.
page 647
Plant stems grow toward the light and away from gravity as a
Xylem and phloem differentiate from procambial cells. result of redistribution of auxin. page 656
page 649
Roots grow away from light and toward gravity as a result of
The polar transport of auxin through PIN proteins guides redistribution of auxin. page 656
the formation of leaf primordia and the development of
vascular channels (xylem and phloem) that connect leaves Starch-filled statoliths allow roots to sense and respond to
and stems. page 649 gravity. page 659
Gibberellic acid causes internodal elongation of shoots. Phytochrome is a photoreceptor that allows plants to
page 650 determine the amount of red versus far-red light. Because light
filtered through leaves has lower levels of red wavelengths,
Apical dominance is the suppression of the outgrowth of axillary
phytochrome allows plants to detect the presence of plants
buds caused by hormones produced by roots (strigolactone) and
overhead. page 659
shoots (auxin). page 650
Seedlings germinating in the dark produce elongated internodes
31.3 Lateral meristems allow plants to grow in diameter, and suppress leaf expansion to increase their ability to reach the
increasing their mechanical stability and the transport soil surface before their stored resources are depleted. page 660
capacity of their vascular system.
Some plants respond to the presence of neighboring plants by
The formation of two lateral meristems—the vascular cambium elongating more rapidly and suppressing branching, which allow
and the cork cambium—allows plants to grow in diameter. them to maximize height growth. page 660
page 651
Mechanical stress, such as the bending of stems in the wind,
The vascular cambium produces secondary xylem toward the results in stems that are short and wide. page 661
center and phloem toward the outside. page 651
31.6 Plants have sensory systems that control the timing
The cork cambium produces a protective outer layer. page 652
of developmental events.
Gymnosperm tracheids function in both mechanical support
Many plants are photoperiodic, meaning that their flowering is
and water transport. Angiosperm xylem produces fibers that
controlled by the day length. page 662
influence the strength of wood and vessel elements that
function in water transport. page 653 Plants measure day length through an interaction between
photoreceptors and their internal circadian clock. page 663
31.4 The root apical meristem produces new cells that
allow roots to grow downward into the soil, enabling Vernalization is a prolonged period of exposure to cold
plants to obtain water and nutrients. temperatures necessary in some temperate-zone species before
flowering can be induced. page 664
The root apical meristem is the source of new cells that allow
roots to elongate. page 654 Decreases in photoperiod trigger plants to prepare their
meristems for winter by producing bud scales and reducing
The root apical meristem has a cap that protects it from damage
internode elongation. page 664
as the root grows through the soil. page 654
The root’s vascular tissues are located in the center of the root,
surrounded by the pericycle, the endodermis, the cortex, and the Self-Assessment
epidermis. page 654
1. Diagram the zones of cell division, elongation, and
Lateral roots develop from new root apical meristems that form maturation, and explain why this organization allows stems to
in the pericycle. page 655 grow without a predetermined limit to their length.
PASS 1
666666 SSEELCFT-IAOSN
S E3S0S.M
1 EN
AT
2. Name one role of the plant hormone auxin and 8. Give an example of how a plant’s ability to sense its
describe how auxin is transported within a plant. environment improves the plant’s chances for survival and
reproduction.
3. Explain why a plant that has a vascular cambium
also has a cork cambium. 9. Explain why a short-day plant that germinates in the
spring will not flower until late summer and why a long-day
4. Explain why the vascular cambium forms a
plant that germinates at the end of summer will not flower
continuous sheath that runs from near the tips of the
until late the following spring.
branches to near the tips of the roots, whereas the cork
cambium is discontinuous in both space and time. 10. Describe how vernalization can have an effect in cells that
were not formed at the time of the cold treatment.
5. List three structural differences between roots and
shoots that allow roots to grow through the soil. Explain
how you would tell whether an isolated piece of a plant Log in to to check your answers to the Self-
came from the shoot or from the root. Assessment questions, and to access additional learning tools.
Plant
Defense
Keeping the World Green
Core Concepts
32.1 Plants have evolved
mechanisms to protect
themselves from infection
by pathogens, which include
viruses, bacteria, fungi, worms,
and even parasitic plants.
32.2 Plants use chemical,
mechanical, and ecological
defenses to protect themselves
from being eaten by
herbivores.
32.3 The production of defenses
is costly, resulting in trade-
offs between protection and
growth.
32.4 Interactions among plants,
pathogens, and herbivores
contribute to the origin and
maintenance of plant diversity.
Don Johnston/Getty Images.
667
668 SECTION 32.1 P ROT E C T I O N AG A I N S T PAT H O G E N S
FIG. 32.3 Parasitic plants. (a) Mistletoe carries out photosynthesis, but relies on its host plant for water and nutrients. (b) Rafflesia, which
produces the world’s largest flower, also obtains everything it needs from its host. (c) Cuscuta, or dodder, parasitizes the stems of many
plants. It does not photosynthesize and instead receives everything it needs from its host. Sources: a. © Mark Boulton/NHPA/Photoshot;
b. Paul Kennedy/Gettty Images; c. Clive Varlack/clivevbugs/AGPix.
a b c
50 cm
670 SECTION 32.1 P ROT E C T I O N AG A I N S T PAT H O G E N S
FIG. 32.4 The plant immune system. (a) In basal resistance, plasma membrane receptors recognize molecules produced by broad classes of
pathogens. (b) Specific resistance depends on R genes that allow plant cells to identify and deactivate AVR proteins produced by
specific pathogens.
Pathogens
Pathogen secrete AVR
proteins that
AVR can enter
Receptor protein plant cells.
protein
Plant cell
A receptor protein in the plant In the absence of a When an R protein binds with an AVR
cell’s plasma membrane binds matching R protein, the protein, it prevents the AVR protein from
with a pathogen-derived molecule AVR protein blocks the blocking the plant’s basal resistance and
and triggers a defense response. plant’s basal resistance. directly activates defensive genes.
giant flowers. The ability to parasitize other plants has evolved mount an appropriate response. A key feature of the immune
independently multiple times. Currently, more than 4000 species system is that plants, like animals, can recognize a cell or virus as
of parasitic plants have been identified. foreign. How do they accomplish this?
How do parasitic plants find an appropriate host? Mistletoe Plant cells have protein receptors (Chapter 9) that bind to
fruits, which are eaten and dispersed by birds, have a sticky layer molecules produced by pathogens and recognize them as foreign
that adheres to the stems and branches of trees that the plant will to the plant body. Binding changes the conformation of the
parasitize. Dodder, a parasitic vine (Fig. 32.3c), orients its growth receptor, triggering a cascade of reactions that enhance the plant’s
toward a potential host plant, guided by volatile organic compounds ability to resist infection.
produced by the species it infects. One of the most destructive plant The plant immune system has two components (Fig 32.4).
pathogens is witchweed (Striga species), which infects the roots of The first consists of receptors located on the plasma membrane
a number of crop species, including corn, sorghum, and sugarcane. (Fig 32.4a). These receptors recognize highly conserved molecules
Striga seeds remain dormant in the soil until their germination is generated by broad classes of pathogens. Examples of these
triggered by chemicals released from the roots of host species. Striga molecules are flagellins, present in the flagella of bacteria, and
infects more than 40% of all agricultural areas in Africa, driving chitin, a component of the fungal cell wall. When one of these
down crop yields, in some cases to zero. molecules binds to the plant’s receptor, an array of defense
mechanisms is triggered that help protects the plant from
Plants are able to detect and respond to pathogens. infection. Protection from pathogens conferred by this component
Most plants are at risk of infection by only a small subset of of the immune system is called basal resistance.
the many known plant pathogens. Host plants of a particular The second component of the plant immune system allows
pathogen are the species that can be infected by that pathogen. plants to resist pathogens that have evolved means of overcoming
Not all infections significantly damage the host plant, however. basal resistance. Pathogens produce proteins called AVR proteins
Virulent pathogens can overcome the host plant’s defenses and that enter into plant cells and facilitate infection (“AVR” stands
lead to disease. In contrast, avirulent pathogens damage only a for “avirulence”). Some AVR proteins block defense responses
small part of the plant because the host plant is able to contain the triggered by the basal resistance of plants, while others cause the
infection. Whether an interaction is virulent or avirulent depends cell to secrete molecules that the pathogen needs to support its
on the genotypes of both the pathogen and the host plant. own growth. The second component of the plant immune system
In your own body, the innate immune system provides a first targets these AVR proteins.
line of defense against pathogens (Chapter 43). Plants, too, have Like basal resistance, this component of the immune system
an immune system that allows them to detect pathogens and also consists of receptors, but in this case they are located inside
CHAPTER 32 PL ANT DEFENSE: KEEPING THE WORLD GREEN 671
the cell rather than on the plasma membrane (Fig. 32.4b). Plants
harbor hundreds of these receptors, called R proteins, each FIG. 32.5 Hypersensitive response. A tobacco plant infected with
expressed by a different gene—these genes are collectively called tobacco mosaic virus responds by producing a region
R genes (the “R” in both cases stands for “resistance”). Each of dead tissue that surrounds the site of infection and
R protein recognizes a specific AVR protein. When an R protein prevents the virus from spreading to other parts of the
binds with a pathogen-derived AVR protein, it both prevents the plant. Source: Norm Thomas/Science Source.
AVR protein from blocking the plant’s defenses and activates
additional defenses. Because this component of the immune
system depends on interactions between specific plant and
pathogen genes, it is commonly called the gene-for-gene model
of plant immunity. Protection from pathogens conferred by this
component of the immune system is called specific resistance.
The large number of R genes is the result of an evolutionary
arms race that occurs as pathogens evolve ways to evade their
host’s detection systems. Pathogens improve their success rate
when mutation results in an AVR protein that does not bind with
any of the R proteins produced by its host plant. For example,
P. infestans, the pathogen responsible for the Irish potato famine,
produces many more AVR proteins than related Phytophthora
species. The large number of AVR proteins found in P. infestans
increases the probability that at least one of these proteins is not
detected by the infected plant. Conversely, when pathogens are
successful, natural selection favors plant populations that produce
new R proteins capable of binding to the AVR proteins of the
invader.
FIG. 32.7
FIG. 32.6 Vascular wilt diseases. Pathogens that
are transmitted through the xylem can kill
their host if plant defenses also block water Can plants develop immunity to
transport to the leaves. (a) Panama disease,
which affects bananas, is caused by a fungal specific pathogens?
pathogen. (b) Pierce’s disease, which affects
BACKGROUND Tobacco is susceptible to an infectious disease that causes its
grapes, is caused by a pathogenic bacterium.
leaves to turn a mottled yellow, hence the name of the disease—tobacco mosaic
Sources: a. Guy Blomme/Bioversity International;
disease. In the 1890s, experiments with filters showed that the infectious agent was
b. Bruce Fleming/Cephas Picture Library.
smaller than a bacterium, a finding that led to the discovery of viruses. Some plants
a succumb to the disease, but others do not. Are the plants that survive the initial
infection immune from further attacks?
HYPOTHESIS Plants that survive infection with tobacco mosaic virus (TMV) have
acquired immunity and therefore resist further attack.
RESULTS Plants that had been previously exposed to TMV showed no signs of
infection when exposed to the virus a second time.
7 days
TMV
Tobacco
plant
CONCLUSION Tobacco leaves that have never been exposed to TMV can acquire
resistance to the pathogen if another leaf on the same plant has been previously exposed.
This result indicates that a signal has been transmitted from the originally infected leaf to
the undamaged parts of the plant, and that the transmitted signal subsequently triggers
the development of an immune response that protects the plant from further infection.
FOLLOW-UP WORK Plants are now known to acquire immunity to a wide range of
pathogens in addition to viruses.
SOURCE Ross, A. F. 1961. “Systemic Acquired Resistance Induced by Localized Virus Infections in Plants.”
Virology 14 : 340–358.
CHAPTER 32 PL ANT DEFENSE: KEEPING THE WORLD GREEN 673
FIG. 32.9 The formation of a crown gall tumor. Rhizobium radiobacter, a soil bacterium, can insert genes into the plant genome, altering the
growth and metabolism of the plant in ways that enhance the growth of R. radiobacter bacteria.
Bacteria
enter the
plant
through
a wound.
Wound Plant Tumor
chromosome
Plant nucleus
containing the genes that are integrated into the host cell’s genome, themselves against organisms from caterpillars to cows only
as well as all the genes needed to make this transfer. Some of the increased. Given that they are unable to run away, plants would
transferred genes—including ones that result in the synthesis of seem to be the ideal food. But plants have evolved a diversity
the two plant hormones auxin and cytokinin (Chapter 31)—cause of mechanisms that deter would-be consumers. Because these
infected cells to proliferate and form a gall. Other transferred genes mechanisms deplete resources that could otherwise be directed
induce cells in the gall to produce specialized compounds that the toward growth and reproduction, plants have also evolved means
bacteria use as sources of carbon and nitrogen for growth. Note that of deploying their defenses in a cost-effective manner. Here,
because plant cells do not move (in contrast to animal cells), there is we explore the mechanical, chemical, developmental, and even
no possibility that the tumor-forming cells will spread to other parts ecological means by which plants protect themselves in a world
of the plant. teeming with hungry herbivores.
Biologists interested in genetically modifying crops and other
plants make use of R. radiobacter’s ability to insert genes into Plants use mechanical and chemical defenses to avoid
the host genome. The first step is to replace the genes in the Ti being eaten.
plasmid that are usually inserted into the plant genome. Genes Milkweeds (Asclepias species) are commonly found in open fields
for gall formation are removed, and genes of interest are inserted. and roadsides across North America. They illustrate well how
Examples of genes that have been transferred into plants in this plants protect themselves from herbivorous animals. In fact, most
way include genes whose products increase the plant’s nutritional generalist herbivores, which eat a diversity of plants, do not use
value or confer resistance against disease. In addition, researchers milkweeds as a food source. Only specialists, such as caterpillars of
need a way to identify which cells have taken up the genes, and so the monarch butterfly (Danaus plexippus), can feed on these well-
a marker gene, for example one conferring antibiotic resistance, is defended plants.
typically included. In this way, cells that survive an application of In part, milkweed’s defenses are mechanical. The leaves of many
the antibiotic are known to have successfully incorporated the Ti milkweed species are covered with dense hairs. An insect crawling
plasmid into their genome. on a leaf must make its way through as many as 3000 hairs per
square centimeter, a journey likely more daunting to an insect than
wading into a blackberry thicket is to a human. Monarch caterpillars
32.2 DEFENSE AGAINST HERBIVORES may spend as much as an hour mowing off these hairs before they
begin to feed. This long handling time represents a significant cost.
The first land plants were followed closely in time by the ancestors To understand why monarch caterpillars make this investment, let’s
of spiders and scorpions. Fossils show that these earliest land look at milkweed’s other defenses.
animals soon began to feed on plant fluids and tissues. As plants A network of extracellular canals filled with a white, sticky
diversified, so did herbivores, and the pressure on plants to defend liquid called latex runs through the milkweed leaf, both within
CHAPTER 32 PL ANT DEFENSE: KEEPING THE WORLD GREEN 675
FIG. 32.10 How monarch caterpillars feed on milkweed. Young monarch caterpillars disarm milkweed defenses by digging trenches, while
older, larger caterpillars sever major veins. Both methods prevent the sticky latex from flowing into the feeding area.
Large latex
canals
Flow of latex
the major veins and extending into the regions between veins Most plant species have mechanical or chemical defenses
(Fig. 32.10). Latex canals are under pressure in the intact leaf. against herbivores, or even both. Mechanical defenses are varied.
Thus, when the leaf is damaged, the latex flows out, sticking to Hairs are common on leaves, and, as anyone who has ever rubbed
everything it comes into contact with and rapidly congealing on against a stinging nettle knows, these hairs are sometimes armed
exposure to air. A feeding insect is in danger of having its tiny with chemical irritants. Grasses and some other plants have a hard,
mouthparts glued together, with potentially fatal consequences. mineral defense consisting of silica (SiO2) plates formed within
Small monarch caterpillars cut trenches into the leaf that prevent epidermal cells. Silica wears down insect mouthparts, so the insects
latex from flowing onto the region where they are feeding. Larger feed less efficiently and grow more slowly. On a larger scale, some
caterpillars sever the midvein, relieving the pressure within the tropical trees have prickles, spines, or thorns (Fig. 32.11). Even
latex canals downstream of the cut. The caterpillars are then able something as simple as how tough a leaf is can have a large impact
to feed without risk on the part of the leaf that lies beyond the on the probability of the leaf’s being eaten. In fact, leaves are most
severed midvein. likely to be eaten while they are still growing and their tissues not
Milkweed latex is not only sticky but also toxic. In particular, fully hardened. Nonetheless, the most spectacular diversity in plant
milkweed latex contains high concentrations of cardenolides, defenses lies in the realm of chemistry.
steroid compounds that cause heart arrest in animals. (In small
doses, these compounds are used to treat irregular heart rhythms in Diverse chemical compounds deter herbivores.
humans.) Monarch caterpillars do not metabolize the cardenolides The cardenolides produced by milkweeds are only one example
that they consume, but instead sequester them within specific from the vast chemical arsenal available to plants for protection.
regions of their bodies as a chemical defense against their own Some plants produce alkaloids, nitrogen-bearing compounds that
predators. Because of the presence of these cardenolides, monarch damage the nervous system of animals. Commonly bitter tasting,
caterpillars and even the adult butterflies are highly toxic to alkaloids include such well-known compounds as nicotine, caffeine,
most birds and other animals that would otherwise eat them. morphine, theobromine (found in chocolate), quinine (a treatment
The protection conferred by these chemicals helps explain why for malaria), strychnine, and atropine. Alkaloids are a costly defense
monarch caterpillars have evolved to feed on leaves that are both because they are rich in nitrogen, an essential and often limiting
metabolically difficult and time-consuming to eat. element that plants need to build proteins for photosynthesis.
676 SECTION 32.2 D E F E N S E AG A I N S T H E R B I VO R E S
Menthol
OH
OH
Salicylic acid
the plant tissue. Insects that feed on plants that produce protease
inhibitors have reduced growth rates. FIG. 32.12 Ants attracted by an extrafloral nectary. These ants
receive a food reward and also consume any insect eggs
Some plants provide food and shelter for ants, which or larvae they encounter on the plant. Source: Alex Wild/
actively defend them. alexanderwild.com.
While many plants have mechanical defenses against herbivores
and nearly all have at least one form of chemical defense, a
smaller number of species have evolved ecological defenses
against herbivory. These plants “employ” animals as bodyguards
in exchange for shelter or nourishment, much the way that many
plants provide food or other rewards to animals that transfer
pollen and disperse seeds (Chapter 30).
Nectar is typically associated with flowers. However, many
plants produce nectar in glands located on their leaves (Fig. 32.12).
These extrafloral nectaries attract ants, which move actively
throughout the plant in search of nectar. When the ants encounter
the eggs or larvae of other insects, they consume these as well.
The value of this relationship to the plant is easily demonstrated:
When ants are prevented experimentally from patrolling certain
branches, those branches suffer higher rates of herbivore damage.
678 SECTION 32.2 D E F E N S E AG A I N S T H E R B I VO R E S
only during the past 25 million years. The fossil record shows that Plants can sense and respond to herbivores
as grasslands expanded, grazing mammals evolved along with For more than 15 years, biologists have studied how coyote tobacco
them. Horses, for example, originated as small browsers that fed (Nicotiana attenuata), a relative of tobacco native to dry open
on the leaves of small trees and shrubs. As grasslands expanded, habitats of the American West (Fig. 32.15), defends itself against
larger horse species with teeth adapted to eating grass evolved. herbivores. These studies provide a fascinating window into how
Why would specialized teeth be advantageous? The small plates of plants allocate resources toward defense under natural conditions.
silica in grass cell walls increases their strength and may provide
mechanical defense against herbivores. Horses and other grazers
that feed on these grasses wear down their tooth enamel grinding
against the silica, so teeth with a thick enamel layer are favored FIG. 32.15 Nicotiana attenuata, the coyote tobacco. This species
by natural selection. It is not clear whether grasses evolved in has been developed as a model organism for studying
response to grazing or to disturbances such as fire, but without how plants protect themselves against herbivores.
question, their distinctive pattern of meristem activity minimizes (a) Nicotiana attenuata in a Utah desert; (b) Manduca
the damage caused by grazing mammals. sexta, a specialist herbivore, feeding on N. attenuata.
Sources: a. Danny Kessler, Max Planck Institute for Chemical Ecology,
Jena, Germany; b. Celia Diezel, Max Planck Institute for Chemical
TO DEFENSE a
FIG. 32.16
2
EXPERIMENT One set of plants was placed downwind of other
1
plants in which two leaves were torn, simulating herbivore
damage, and a set of control plants was placed downwind of an 0
Control Damaged Experimental
empty chamber. The concentrations of defensive compounds in all plants plants plants
sets of plants were measured and compared.
Air flow CONCLUSION Volatile chemicals released from damaged plant
tissues can trigger the production of defensive chemicals in
undamaged plants.
SOURCE Baldwin, I. T., and J. C. Schulze. 1983. “Rapid Changes in Tree Leaf
Chemistry Induced by Damage: Evidence for Communication Between Plants.”
Experimental plants Control plants Science 221: 277–279.
(undamaged) (undamaged)
Nicotiana attenuata is attacked by a wide variety of herbivores, to leaves in the xylem, the activation of this inducible defense
both generalists and specialists. A major component of requires the transport of signaling molecules in the phloem from
N. attenuata’s defense against being eaten is the production of the the sites of insect damage to the roots.
alkaloid nicotine. Nicotine is an effective defense against many Nicotiana attenuata is also attacked by a specialist herbivore,
generalist herbivores. However, nicotine is also an expensive form the tobacco hornworm caterpillar, Manduca sexta. These
of chemical defense because it contains nitrogen, a nutrient whose caterpillars, which can reach 7 cm in length, have evolved the
availability can limit growth. Thus, N. attenuata plants that have ability to sequester and secrete nicotine. By this means, these
not been exposed to herbivores produce only low levels of nicotine caterpillars are able to consume leaves with high levels of nicotine.
as a constitutive defense. When N. attenuata is attacked by a If nicotine is not an effective defense against this voracious
generalist herbivore, nicotine concentrations in leaves increase herbivore, what can N. attenuata do to protect itself?
dramatically—typically fourfold, but in some cases as much as It turns out that N. attenuata can recognize specific chemicals
tenfold. Because nicotine is synthesized in roots and transported in the saliva of M. sexta. When damaged by most herbivores—or a
680
CHAPTER 32 PL ANT DEFENSE: KEEPING THE WORLD GREEN 681
pair of scissors—N. attenuata responds by producing nicotine. But related species found on nutrient-poor sandy soils. They found
when attacked by M. sexta, N. attenuata does not waste time and that species from the nutrient-rich clay soils invested less heavily
resources synthesizing nicotine. Instead, it protects itself in an in defenses than did species from the sandy sites. Because the clay-
entirely different way, by attracting other insects that will attack soil species divert fewer resources to defense, they grow faster in
its herbivores, as we discuss next. either soil type compared to sandy-soil species—as long as they are
grown under a net that excludes herbivores (Fig. 32.17). However,
Plants produce volatile signals that attract insects that when grown out in the open, each species grows best in the soil
prey upon herbivores. type on which it is naturally found.
How does N. attenuata attract its insect allies? A hint comes from The clay-soil species grow poorly on sandy soils when not
the smell of a newly mown lawn. This distinctive smell originates protected by a net because, without ample soil nutrients available,
from chemicals released from the cut blades of grass. Some of the they are unable to replace tissues consumed by herbivores.
chemicals released when plants are damaged represent nothing Conversely, when grown on the nutrient-rich soils, species from
more than the exposure of cell interiors to the air. Others, however,
are produced specifically in response to damage. When N. attenuata
is attacked by M. sexta caterpillars, it produces volatile signals that FIG. 32.17 A trade-off between growth and defense. Plants from
attract insects that prey on the eggs and larvae of M. sexta. The nutrient-rich clay habitats can overcome herbivory by
adage “The enemy of my enemy is my friend” seems to hold true growing fast, whereas plants from low-nutrient sandy
when it comes to protecting plants from herbivore damage. habitats grow slowly and invest more in defense. The
Studies first conducted in the 1980s showed that undamaged photos show that, without defenses, clay-soil plants are
plants increase their synthesis of chemical defenses when prone to being eaten by herbivores. Source: Paul Fine
neighboring plants are attacked by herbivores (Fig. 32.16).
Clay soil plants growing in sandy soils
Although these plants were described in the popular press as
“talking trees,” the plants under attack are not altruistically
warning their neighbors. Instead, subsequent studies suggest that
the undamaged plants are detecting the signals released by their
neighbors that are directed at other insects, then ramping up their
own defenses. Recent work demonstrates that even the sound
of a neighboring plant being chewed on by insects can trigger
defensive responses in a nearby plant.
Such plants would grow relatively slowly because their resources 0.6
6
are being used to build defenses rather than to produce new leaves
and roots. By contrast, plants from nutrient-rich habitats would
favor growth over defense because they can more readily replace 0.4
Increase in leaf area
the sandy habitats are poor competitors because they allocate consistent with an important role for plant–insect coevolution in
resources that could have been used for growth to defensive generating diversity. Further evidence that defense has influenced
compounds and structures. What we see is a classic example of a plant diversification comes from plant genes and secondary
trade-off. compounds. For example, the R genes that are instrumental in
pathogen recognition form one of the largest gene families in
j Quick Check 4 Does the trade-off between growth and defense
plants, while chemical defenses against herbivores include about
favor a single species that dominates in all soil types or different
6000 alkaloids and more than 10,000 terpenoid compounds. Such
species specialized for each habitat?
observations suggest that plants are locked in an evolutionary arms
race with herbivores and pathogens. This arms race is very much in
Exposure to multiple threats can lead to trade-offs. evidence in the efforts by farmers to limit crop losses by reducing
In the real world, plants are routinely confronted with more than the numbers of the pathogens and herbivores in fields and orchards.
one threat. A plant may be attacked simultaneously by both a
pathogen and an herbivore, or it might be in danger of being shaded The evolution of new defenses may allow plants
by a fast-growing neighbor at the same time that it must defend its to diversify.
leaves from being eaten. Given that the resources a plant can draw American scientists Paul Ehrlich and Peter Raven observed that
on are limited, how do plants respond to multiple threats? closely related species of plants were fed upon by closely related
Often, the response to multiple threats suggests a trade- species of butterflies. In 1964, they cited this observation as
off. For example, a plant exposed to a pathogen may be less evidence that plants and their herbivores are caught up in an
able to respond to a later herbivore attack. If tobacco plants are evolutionary arms race: Plants evolve new forms of defense, and
exposed to tobacco mosaic virus and systemic acquired resistance herbivores evolve mechanisms to overcome these defenses. In
is activated, they become more susceptible to the hornworm particular, Ehrlich and Raven hypothesized that the evolution of
caterpillar, Manduca sexta. Studies indicate that plants do not novel defenses has been an important force in the diversification
defend themselves as vigorously against subsequent herbivore of both plants and herbivorous insects.
attacks because of crosstalk between the signaling pathways for A novel form of defense may allow a plant population to expand
responding to biotrophic pathogens and those for responding to into new areas. If the population in a new area remains separated
herbivores. from the original population, it may evolve into a new species.
There can also be trade-offs between the threat of competition Similarly, a novel means of overcoming plant defenses may allow
with neighboring plants and the threat of attack by herbivores. For an insect or pathogen population access to new plant resources. If
example, when the phytochrome receptor in plants detects the these insects or pathogens became separated from their original
presence of neighboring plants (Chapter 31), plants allocate more population, then they might also evolve into new species. Ehrlich
resources to growing tall, but they also produce fewer defensive and Raven’s “escape and radiate” hypothesis thus predicts a burst of
chemicals in response to herbivore damage. Interactions among diversification following the evolution of novel defenses.
the signaling molecules associated with each of these processes This hypothesis makes intuitive sense, but it could only
underlie this trade-off. be tested with the advent of phylogenetic trees based on DNA
sequence comparisons (Chapter 23). Biologists knew that latex
or resin canals evolved independently in more than 40 different
32.4 DEFENSE AND PLANT DIVERSITY groups of plants. Reasoning that these features represent a novel
defense, they asked whether the groups that evolved latex or resin
Many plants spend a significant fraction of their resource and canals were more diverse than closely related groups that lacked
energy budgets on defensive chemicals and structures. Despite these forms of defense. In 14 of the 16 groups examined, the groups
this commitment, insects consume approximately 20% of all new with the protective canals were significantly more diverse than
plant growth each year, while pathogens destroy a substantial their closest relatives that lacked latex or resin canals. This pattern
additional amount. The magnitude of this loss means that supports the hypothesis that the evolution of latex and resin canals
pathogens and herbivores must be a potent force in both ecology provided plants with the freedom to expand into new habitats.
and evolution, limiting the success of some species while allowing Escalation of defenses, however, is not the only possible
some of their competitors to prosper. In nature, plant fitness may evolutionary outcome. Phylogenetic research shows that, as
be strongly influenced by the capacity to deter herbivores and milkweeds diversified, many of the newly evolved species
resist pathogens. produced fewer chemical defenses such as latex canals and
Interactions between plants and their consumers are thought cardenolides. Instead, these species are found in resource-
to have influenced patterns of plant diversification. Just like rich habitats and replace tissues by growing quickly following
pollinating insects, plant-eating insects diversified along with damage. The presence of specialized herbivores such as monarch
angiosperms (the flowering plants). The coincidence of timing is caterpillars that can disarm milkweeds’ defenses may help explain
CHAPTER 32 PL ANT DEFENSE: KEEPING THE WORLD GREEN 683
The bacterium Rhizobium radiobacter infects plants by inserting Herbivores and pathogens are a major concern for agriculture.
some of its genes into the plant’s genome, resulting in the page 683
formation of a tumor and providing a way to genetically Crop protection includes the use of chemical pesticides,
engineer plants. page 673 integrated pest management, application of spores or toxins
from Bacillus thuringiensis to plants, and inserting genes that
32.2 Plants use chemical, mechanical, and ecological encode for toxins from B. thuringiensis to make Bt-modified
defenses to protect themselves from being eaten by plants. page 684
herbivores.
Plant defenses against herbivory include dense hairs, latex,
and chemicals. page 675
Self-Assessment
Alkaloids are nitrogen-bearing compounds that interact with
1. Describe how pathogens enter and move within the plant
the nervous system of animals. page 675
body.
Terpenes, volatile compounds that give rise to many of the
essential oils we associate with plants, deter herbivores. 2. Distinguish between biotrophic and necrotrophic plant
page 676 pathogens.
Tannins bind with proteins, reducing their digestibility. 3. Name and describe the two components of the plant
page 676 immune system.
Ant-plants, such as the bullhorn acacia, provide food and 4. Describe and contrast the hypersensitive response and
shelter for ants, which defend their host plant. page 677 systemic acquired resistance.
686 SELF-ASSESSMENT
5. Describe a feature of Rhizobium radiobacter that 9. Draw a phylogenetic tree that illustrates an “escape and
makes it a useful tool in biotechnology. radiate” pattern of diversification for plants that evolve novel
defenses.
6. Describe three ways that plants protect themselves
from being eaten by herbivores. 10. Describe one benefit and one disadvantage of herbicide and
pesticide use in agriculture.
7. Explain why there are often trade-offs between plant
growth and plant defense.
Log in to to check your answers to the Self-
8. Explain how pathogens and herbivores can increase
Assessment questions, and to access additional learning tools.
plant diversity.
CHAPTER 33
Plant Diversity
Core Concepts
33.1 Angiosperms make up
approximately 90% of all plant
species found today.
33.2 Bryophytes form persistent,
photosynthetic gametophytes
and small, unbranched
sporophytes; today they
grow in environments where
the ability to pull water from
the soil does not provide an
advantage.
33.3 Spore-dispersing vascular
plants today are primarily
small plants that grow in moist
environments, but in the past
included tall trees.
33.4 Gymnosperms produce seeds
and woody stems and are most
common in seasonally cool or
dry regions.
33.5 Angiosperms are distinguished
by flowers, fruits, double
fertilization, and xylem
vessels; their diversity is the
result of traits that increase the
efficiency of completing their
life cycle and building their
bodies.
Gaby Wojciech/age fotostock.
687
688 SECTION 33.1 P L A N T D I V E R S I T Y : A N E VO LU T I O N A RY OV E RV I E W
Five hundred million years ago, the land surface supported ultraviolet radiation and temperature fluctuations, and they can use
little more than a green crust made up of a mixture of water currents to transport sperm and disperse offspring. Surviving
photosynthetic and non-photosynthetic microbes. Then, through on land required the evolution of new ways of growing and
the process of natural selection, a group of freshwater algae reproducing. Here, we highlight key adaptations that allowed plants
began the transition to survival on land. Fast-forward 465 million to photosynthesize and reproduce on land, explored in Chapters
years—to the present time—and plants are everywhere. Much 29–31, and discuss how plant diversity changed as new ways of
of what makes up a plant, including roots, leaves, tree trunks, growing and reproducing evolved.
and seeds, evolved quickly. Within the first quarter of the time
since these algal ancestors began to colonize the land, all of Four major transformations in life cycle and structure
these features were present. But one thing was missing: flowers. characterize the evolutionary history of plants.
Flowering plants, also known as angiosperms, do not appear The first major transformation was the evolution of alternation
on the scene until the last quarter of this history, and yet today of generations (Fig. 33.1; Chapter 30). To understand this
they make up a remarkable 90% of all plant species. Many of the change, let’s first consider the presumed ancestral life cycle. The
plant groups that diverged before angiosperms appeared are still algal relatives of plants produce multicellular bodies made up
present, but where they live and grow has been shaped by the entirely of haploid cells. These algae form gametes by mitosis,
evolution of flowering plants. and fertilization results in a zygote, which is the only diploid
cell. The algal ancestor of land plants is thought to have released
male gametes (sperm) into the surrounding water and relied on
33.1 PLANT DIVERSITY: AN water currents to carry the zygote away from the parent plant.
EVOLUTIONARY OVERVIEW The zygote then underwent meiosis, producing haploid cells that
developed into new multicellular algae.
The closest living relatives of plants are green algae that grow in Like their green algal relatives, the first land plants would
streams and ponds (Fig. 33.1). Some features found in plants are have produced a multicellular body composed entirely of haploid
also present in the close algal relatives, including cellular structures cells and that produces gametes. During periods of rain, the male
such as plasmodesmata and the enzymes used to reduce CO2 loss gametes could swim to female gametes in surface water layers.
during photorespiration. But for the most part, plants are quite But zygotes dispersed this way would not be able to travel very far
distinct from their aquatic progenitors. The reason is that, when from the parent plant. To enhance dispersal, land plants evolved
plants moved onto land, they had to survive in a new medium, air. alternation of generations: The multicellular haploid generation
Algae can rely on water for hydration, support, and protection from alternates with a multicellular generation composed of diploid
FIG. 33.1 Phylogenetic tree of land plants. The number of species is shown in parentheses.
Note that 90% of all land plant species are angiosperms.
cells. Specifically, the diploid zygote develops by mitosis into a large. These plants could only reproduce where and when surfaces
multicellular spore-producing plant, called a sporophyte, while were sufficiently wet. Eliminating this dependence—through the
still attached to and supported by the haploid gamete-producing evolution of pollen and seeds—is the third major evolutionary
plant, called a gametophyte. In the first diverging groups of event in the history of plant diversification.
plants, the multicellular diploid generation produces many The life cycle of seed plants differs from that of spore-
haploid spores by meiosis and, because it is typically erect, can dispersing vascular plants in a number of important ways
release these spores into the air where they can be carried off by (Chapter 30): (1) Spores are not dispersed; instead, they germinate
a breeze. Furthermore, because the walls of the spores contain and develop into morphologically distinct male and female
sporopollenin, a polymer that is highly resistant to decay, the gametophytes while still attached to the sporophyte. (2) Male and
spores can survive prolonged exposure to air. Thus, the sporophyte female gametes are brought together by the transport of the male
generation and the formation of spores represent evolutionary gametophyte, which is so small that is fits within the spore wall,
innovations that enhance dispersal on land. forming a pollen grain. (3) Following fertilization, the embryo and
The first plants lacked roots and thus would have depended surrounding tissues develop into a seed, a multicellular structure
entirely on surface water both for fertilization and to maintain that replaces unicellular spores as the dispersal unit. In seed
the hydration of their cells. As a result, these plants would have plants, alternation of generations persists, but the dominant phase
been small, with their photosynthetic tissues and gamete- of the life cycle is the sporophyte, and pollen and seeds carry out
producing structures remaining in close contact with the ground. tasks previously accomplished by swimming sperm and spores.
Photosynthesis would have taken place only when conditions The effect of this transformation is a life cycle that is freed from
were wet enough to keep cells well supplied with water. Only the dependence on surface moisture for fertilization and in which
sporophyte generation is likely to have extended above the surface, embryos are dispersed along with resources that they can draw
to increase the chances of spores being carried off by a breeze. upon during germination.
This situation radically changed with the second major event The fourth evolutionary event is the evolution of the
in the evolutionary history of plants: the evolution of vascular flowering plants, also referred to as the angiosperms. Angiosperms
plants. These plants produce elongate cells for the internal are seed plants and thus their life cycle contains all the traits just
transport of water and other materials. Xylem cells transport water described. In addition, four new reproductive features are thought
and dissolved nutrients, and phloem cells transport carbohydrates to have contributed to angiosperm diversity and success. The
produced by photosynthesis (Chapter 29). The cell walls of the first is the flower, a reproductive structure that attracts animal
xylem conduits contain lignin, a chemical that greatly strengthens pollinators, increasing the efficiency of pollen transfer compared
the cellulose wall. Conduits made rigid by lignin allow vascular to wind pollination. The second is the carpel—the closed “vessel”
plants to pull water from the soil and to transport it efficiently in which seeds develop and that gives angiosperms their name.
through their stems. As a result, vascular plants are taller and able Because pollen must grow through the carpel to reach the female
to photosynthesize over a much wider range of conditions than gametophyte, interactions between pollen and carpel genotypes
plants dependent solely on surface moisture. The phloem conduits can affect the probability of fertilization. A third feature is
that transport sugars allow roots to grow into the soil, where there double fertilization, in which one sperm nucleus from the male
is no sunlight to power photosynthesis. gametophyte fuses with the egg, and a second sperm nucleus
In many vascular plants, xylem and phloem are formed only fuses with two haploid nuclei from the female gametophyte. The
as stems and roots elongate; they cannot be added to an already first union results in the diploid zygote, and the second gives rise
formed stem. However, some vascular plants evolved the ability to endosperm, which forms the nutritive tissue within the seeds
to produce additional or “secondary” xylem and phloem through of angiosperms. A consequence of double fertilization is that
the formation of a vascular cambium, a layer of actively dividing angiosperms do not expend resources for the next generation until
and differentiating cells that surrounds stems and allows them to the egg is fertilized. A fourth feature is the development of fruits,
increase in diameter (Chapter 31). A second layer of dividing cells, structures that surround seeds and attract animals to enhance
the cork cambium, maintains an intact layer of protective outer seed dispersal.
bark. Vascular and cork cambia provide the support and water Angiosperms are also distinguished by the presence of
transport capacity needed for plants to grow tall and to support wood containing xylem vessels (Chapter 29). Most other seed
increasing numbers of leaves. Thus, the evolution of secondary plants produce only tracheids, which both support the stem
growth opened the way to the development of trees and forests. and transport water. In contrast, angiosperms have thick-
As plants moved onto land, they retained their ancestral pattern walled, elongate fibers that support the stem and xylem vessels
of releasing swimming sperm into the environment. As a result, that transport water. Because xylem vessels are not a stem’s
the gamete-producing generation remained small, constrained by sole source of support, they can be wide and long, allowing
the requirement for surface moisture for fertilization, even as the angiosperms to transport water through their stems at higher
evolution of vascular tissues allowed the sporophyte to become rates than plants with tracheids. Their uptake of CO2 for
690 SECTION 33.2 B RYO P H Y T E S
photosynthesis increases as well because CO2 uptake is directly plant species increased dramatically. Thus, angiosperms’ hold on
linked to water lost to the atmosphere. As a result, angiosperms plant diversity is the result of both squeezing out other groups and
compete well for light and space and are the dominant plants in increasing the number of species that can coexist.
most terrestrial ecosystems. One way that angiosperm evolution may have increased the
overall number of plant species on Earth was by transforming the
Plant diversity has changed over time. environments into which they diversified. Climate models suggest
If we tabulate the numbers of species within each major branch on that angiosperms may have been necessary for the formation of
the phylogenetic tree shown in Fig. 33.1, one fact stands out: Of tropical rain forests as we know them today. Without the higher
the nearly 400,000 species of plants present today, approximately rates of transpiration exhibited by angiosperms, many tropical
90% are angiosperms. Furthermore, angiosperms are relative regions would have higher temperatures and lower rainfall. The
newcomers (Fig. 33.2). They appeared in the fossil record about warmer, drier conditions would have been less conducive to the
140 million years ago. The oldest known evidence of land plants luxuriant plant growth found in tropical rain forests. The new
is found in rocks approximately 465 million years old. Thus, for tropical forests, with their dense shade and humid understories,
more than 300 million years, terrestrial vegetation was made up provided new habitats into which both angiosperms and non-
of plants other than angiosperms. During this period, lycophytes, angiosperms could evolve. Thus, although early angiosperms
ferns and horsetails, and gymnosperms, as well as many groups outcompeted many species for space and light, their evolution also
of now-extinct plants, dominated the land, forming forests and stimulated radiations of new species in at least some of the groups
landscapes unlike those that surround us today. that preceded them.
Once the flowering plants gained an ecological foothold,
however, the number of angiosperm species increased at an
unprecedented rate. As the number of angiosperm species rose, 33.2 BRYOPHYTES
the number of species in other groups fell. Yet the total number of
Liverworts, mosses, and hornworts diverged before the evolution
of xylem and phloem (Fig. 33.1). The hypothesis shown in
Fig. 33.1 implies that liverworts, mosses, and hornworts evolved
FIG. 33.2 The diversity of vascular plant groups through time. independently for hundreds of millions of years and that they
First appearing about 140 million years ago, angiosperms do not form a monophyletic group. Recall from Chapter 23 that
have come to dominate the fossil record. Source: Adapted from a monophyletic group includes a common ancestor and all of its
A. H. Knoll and K. J. Niklas, 1987, “Adaptation, Plant Evolution, and the descendants, whereas a paraphyletic group includes a common
Fossil Record,” Review of Palaeobotany and Palynology, 50:127–149. ancestor and some of its descendants. However, it is important to
recognize that the phylogenetic relationship between liverworts,
80
mosses, and hornworts remains uncertain. Because these three
groups share many features, we refer to them collectively as
70 Angiosperms bryophytes.
Conifers
As the living representatives of the first plant groups to
Mean number of species per fossil assemblage
Cycads
60 Gingkos diverge after plants moved onto land, bryophytes provide us
Ferns and horsetails with insights into how plants gained a foothold in the terrestrial
Lycophytes
environment. The insights from bryophytes are particularly
Extinct seed plant groups
50 Extinct spore-dispersing plant groups welcome because the first plants are poorly represented in the
fossil record. Only tiny spores and fragments of a cuticle-like
covering record these early events. Of course, we must not lose
40
sight of the fact that bryophytes have continued to evolve as the
Angiosperms conditions for life on land have changed over the past 400+ million
30 years. Where bryophytes grow today and what they look like have
been shaped by their long coexistence with vascular plants.
20 Lycophytes Conifers j Quick Check 1 Look at Fig. 33.1 and determine whether green
algae, bryophytes, and vascular plants are monophyletic or
Ferns and horsetails paraphyletic.
10
Cycads
Bryophytes are small, simple, and tough.
400 350 300 250 200 150 100 50 2 Mosses are the most widely distributed of the bryophyte groups
Millions of years ago and the most diverse, with about 15,000 species. You may have
CHAPTER 33 PL ANT DIVERSIT Y 691
FIG. 33.3 Bryophyte diversity. Bryophytes include (a) mosses (Polytricum commune is shown); (b) liverworts (Pellia ephiphylla, a thalloid liverwort,
is shown); and (c) hornworts (Anthoceros species). Sources: a. NHPA/Photoshot; b. ARCO/Reinhard H/age fotostock; c. Daniel Vega/age fotostock.
a b c
seen moss growing on a shady log or on top of rocks by a stream. do not provide an advantage—for example, on the surfaces of rocks.
However, mosses grow in all terrestrial environments, from Many bryophytes live on the branches and trunks of trees rather
deserts to tropical rain forests. Liverworts (about 8000 species) than on the ground. Plants that grow on other plants are called
and hornworts (about 100 species) are less widespread and also less epiphytes (from the Greek words epi, “on,” and phyton, “plant”).
diverse. In considering the diversity of these three groups, let’s Bryophytes are well suited to growing on other plants because they
start by reviewing some of their features that allow them to carry do not depend on the soil as a source of water.
out photosynthesis on land.
Bryophytes have small, simple bodies (Fig. 33.3). Some The small gametophytes and unbranched sporophytes
produce only a flattened photosynthetic structure called a thallus. of bryophytes are adaptations for reproducing on land.
Others consist of slender stalks and have a leafy appearance. The easily visible and persistently photosynthetic bryophyte
However, these leaflike structures are quite different from the bodies described above are those of the haploid, gamete-producing
leaves of vascular plants in that they are only one to several cells generation. Because bryophytes release swimming sperm into
thick and lack internal air spaces. Both thalloid and leafy species the environment, their mode of fertilization also limits their
are found in the liverworts, whereas all mosses are of the leafy size. Bryophyte sperm must swim through films of surface
type and all hornworts are of the thalloid type. water or be transported by the splash of a raindrop. Sperm can
Because bryophytes do not produce lignified xylem conduits, travel in this manner only a relatively limited distance and only
they cannot pull water from the soil. Instead, they absorb water, if water is present. A few mosses grow to be more than half a
nutrients, and CO2 through their surfaces. For this reason, meter tall, but these giants of the bryophyte world are found only
bryophytes have little or no waxy cuticle to protect their in the understory of very wet forests. In most bryophytes, the
photosynthetic tissues. Bryophytes can absorb enough water to gametophyte grows to only a couple of centimeters in height.
remain metabolically active when the environment is wet, but Following fertilization, the diploid sporophyte develops
they must be able to tolerate desiccation when the environment is while remaining physically attached to and, in varying degrees,
dry. Thus, while the small size and lack of differentiated structures nutritionally dependent upon the gametophyte. Recall that the
might suggest that bryophytes are delicate, nothing could be diploid, spore-producing generation represents a new component
further from the truth. Bryophytes can be found from the equator of the life cycle that evolved as plants moved onto land. This
to both the latitudinal and altitudinal limits of vegetation, and sporophyte generation addresses the challenges plants face in
from swamps to deserts. dispersing offspring through the air. In most bryophytes, the
Before the evolution of vascular plants, bryophytes likely unbranched sporophyte extends several centimeters above the
covered much of the land surface. However, because bryophytes gametophyte, greatly increasing the chances of a gust of wind
are small and they can only photosynthesize when surface water is dispersing spores through the air.
present, they are poor competitors for light and space with vascular In mosses and liverworts, the sporophyte is short-lived, drying
plants. Today, bryophytes thrive in local environments where roots out after the spores are dispersed. However, in hornworts, the
692 SECTION 33.2 B RYO P H Y T E S
FIG. 33.4 Moss specializations. (a) The yellow moose-dung moss, Splachnum luteum, attracts insects that then
transport its spores. (b) Dawsonia superba has internal transport tissues that allow it to grow more than
40 cm tall. Sources: a. Biopix: A Neumann; b. blickwinkel/Alamy.
a b
sporophyte can live nearly as long as the gametophyte because it Another example of convergent evolution is the presence of
can produce new cells at its base, similar to the way grass blades cells specialized for the transport of water and carbohydrates.in
elongate (Chapter 32). Thus, bryophytes illustrate an important some of the largest bryophytes (Fig 33.4b). The structure of these
trend in the evolution of plants, an increase in the persistence of cells indicates that they evolved independently from the xylem
the spore-producing generation. and phloem of vascular plants. In particular, the water-conducting
cells in bryophytes do not have lignified cell walls and thus are not
Bryophytes exhibit several cases of convergent sufficiently rigid to pull water from the soil. Nevertheless, because
evolution with the vascular plants. of these elongated cells, water and carbohydrates can move from
Bryophytes are interesting partly because they are so different one part of the plant to the other efficiently.
from the more familiar vascular plants. However, given that Stomata are present on the sporophytes of some mosses
they have long evolved in parallel with vascular plants, it is not and hornworts, particularly in regions where a waxy cuticle also
surprising that bryophytes have evolved similar solutions to develops. As discussed in Chapter 29, stomata are pores in the
environmental challenges, a process referred to as convergent epidermis of vascular plants that open and close, providing an
evolution (Chapter 23). For example, some mosses depend on active means of controlling water loss. Bryophyte stomata may
insects to transport their spores (Fig. 33.4a). The brightly colored play an additional role: A sporophyte with open stomata will dry
sporangia of these mosses emit volatile chemicals that mimic out quickly, so its spores are more easily released into the air.
compounds released by rotting flesh or herbivore dung. Attracted Further study is needed to determine if these stomata are the
by these chemicals, insects land on the sporangia, and their legs result of convergent evolution.
become covered with spores. When the insect subsequently
lands on a real pile of dung, some of the spores fall off into what j Quick Check 2 If the stomata of bryophytes and of vascular plants
is, for them, an ideal site for supporting the growth of a new are not an example of convergent evolution, what is an alternative
gametophyte. explanation for their appearance in these groups?
CHAPTER 33 PL ANT DIVERSIT Y 693
Sphagnum moss plays an important role in the global fossil fuels. Thus, any increase in the decomposition rate of these
carbon cycle. naturally formed peats has the potential to increase significantly
In most ecosystems, bryophytes make only a small contribution the CO2 content of Earth’s atmosphere.
to the total biomass. The one exception is peat bogs, wetlands in What might cause an increase in the decomposition rate? Peat
which dead organic matter accumulates rather than decomposes. bogs are vulnerable to changes in the water table. As water levels
A major component of peat bogs is sphagnum moss, any of the fall, the peat becomes exposed to the air, allowing it to be broken
several hundred species of the genus Sphagnum. These mosses down by microbes. Most peat bogs are located in northern latitudes,
play a key role in creating wet and acidic conditions that slow where the effects of climate change are predicted to be greatest. If
rates of decomposition. They have specialized cells that hold onto rising summer temperatures result in higher rates of transpiration
water, much like a sponge, and they secrete protons that acidify from surrounding forests, the result could be a lowering of the water
the surrounding water (Fig. 33.5). Unlike many plants with roots, table and a relatively rapid release of CO2 from this moss-dominated
sphagnum moss thrives under wet, acidic conditions. In addition, ecosystem. Thus, peat bogs have the potential to accelerate rates of
sphagnum mosses produce phenols, organic compounds that slow climate change over the next century.
decomposition under waterlogged conditions.
Peat bogs occupy only 2% to 3% of the total land surface, but
they store large amounts of organic carbon—on the order of 65 33.3 SPORE-DISPERSING
times the amount released each year from the combustion of VASCULAR PLANTS
Vascular plants first appear in the fossil record approximately
425 million years ago. The evolution of xylem and phloem gave
FIG. 33.5 Sphagnum moss. Peat bogs have low rates of organic vascular plants advantages in size and hydration. They were able
decomposition due to the wet and acidic conditions to outcompete bryophytes for light and other resources and to
created by sphagnum moss. Sources: (top) Duncan Shaw/ become the dominant plants on land.
Science Source; (middle) All Canada Photos/Alamy; (bottom) Vascular plants can be divided into two groups according
blickwinkel/Alamy. to how they complete their life cycle. Lycophytes, as well as
ferns and horsetails, disperse by spores and rely on swimming
sperm for fertilization, just like bryophytes. Gymnosperms and
angiosperms are seed plants: They disperse seeds and rely on the
aerial transport of pollen for fertilization. In this section, we focus
on the spore-dispersing vascular plants: lycophytes, and ferns and
horsetails. In both groups, the sporophyte dominates in physical
Peat bog size; the gametophyte is only a few centimeters across, thalloid
in structure, and typically tolerant of desiccation. Thus, our
discussion emphasizes the sporophytes of these plants.
Small
cylinder
FIG. 33.7 An early lycophyte preserved in the 400-million-
of xylem year-old Rhynie chert. The fossil has helically arranged
leaflike structures, adventitious roots (that is, roots that
arise from the shoot and not from the root system), and
Epidermis a central strand of xylem, features much like those of
with cuticle living lycophytes. Sources: (top) Photo by William Chaloner, Crown
Copyright; (bottom) Photo by John Hall © Botanical Society of America.
Hairlike
rooting
structures
FIG. 33.8 Lycophyte diversity. Living lycophytes include about 1200 species, in three major groups: (a) Lycopodium annotinum, showing
yellow sporangia-bearing leaves at the shoot tips of this 5-to-30-cm tall plant; (b) Selaginella wildenowii, in a close-up showing the
flattened arrangement of its 3-mm-long leaves; and (c) Isoetes lacustris, an aquatic lycophyte that grows from 8 to 20 cm tall.
Photo sources: a. Philippe Clement/Nature Picture Library; b. blickwinkel/Alamy; c. Biopix: JC Schou.
a b c
FIG. 33.10
Isoetes
X Lepidodendron
X Psilophyton
Adder’s tongue ferns
Whisk ferns
Extant horsetails
X Calamites
X Archaecalamites
2.5 mm
X Sphenophyllum
Ferns
A small stem of Calamites, an ancient giant horsetail
X Progymnosperms
Seed plants
Secondary xylem
Vascular cambium present
Vascular cambium lost Hollow center
X Extinct
Vascular cambium
5 mm
696
CHAPTER 33 PL ANT DIVERSIT Y 697
FIG. 33.11 Diversity of ferns and horsetails. (a) The adder’s tongue fern Ophioglossum, (b) the whisk fern Psilotum, (c) the horsetail Equisetum,
(d) a marattioid fern, (e) an aquatic fern (Salvinia), and (f) a polypod fern (in the middle of the photo is Athyrium felix-femina, the
common lady-fern). Photo sources: a. Jonathan Buckley/age fotostock; b. Biophoto Associates/Science Source; c. CuboImages srl/Alamy; d. Courtesy Gary
Higgins; e. FLPA/Chris Mattison/age fotostock; f. Ron Watts/First Light/Corbis.
Lycophytes a b c
Ferns and horsetails
Gymnosperms
Angiosperms
Adder’s tongue
ferns (114 species)
Whisk ferns (15 species)
Earlier branching
Leptosporangium leptosporangiate
ferns (1030 species)
and became buried, the combined action of high temperature and and their cells accumulate high levels of silica, earning them the
pressure converted the dead organic matter first into peat and then name “scouring rush.” Today, horsetails are small plants, most less
into the carbon-rich material we call coal. Thus, a major source of than a meter tall. However, tree-sized versions grew side by side
energy we use today derives originally from photosynthesis carried with the ancient lycophyte trees (see Fig. 33.9).
out by lycophyte trees.
FIG. 33.13 A tree fern and an aquatic fern. (a) Silver tree ferns (Cyathea meullaris) grow 10 m tall or more. (b) Azolla ferns floating on the
surface of still freshwater. Each fern is about 10 mm in diameter. Sources: a. AA World Travel Library/Alamy; b. Huetter, C/age fotostock.
a b
they were the most diverse group of plants (Fig. 33.2). Then, as
angiosperms evolved, their diversity markedly decreased. It is not
clear why angiosperm evolution should have so affected ferns and
horsetails, which had coexisted with a variety of seed plant groups
for more than 200 million years.
However, the most diverse group of ferns today evolved after
the rise of the angiosperms. These are the polypod ferns (about
9300 species; see Fig. 33.11f). Thus, many of the fern species
In contrast, many ferns produce large leaves—in some cases present today are likely to have evolved to occupy habitats newly
up to 5 m long, although typically the photosynthetic surfaces are created by the development of angiosperm forests. Approximately
divided into smaller units called pinnae. Yet, because ferns are 40% of living ferns are epiphytes, many of them growing in
not capable of secondary growth, their stems remain slender and tropical rain forests dominated by angiosperm trees.
frequently grow underground, with only the leaves emerging into Polypod ferns may owe some of their evolutionary success to
the air. Many ferns exhibit little stem elongation and produce their an enhanced capacity for spore dispersal. Horsetails, whisk ferns,
leaves in tight clumps. However, some species, such as bracken and a few other fern groups make large sporangia similar to those
fern, produce spreading stems with widely spaced leaves. Because produced by early vascular plants. Most ferns, however, have a
bracken is toxic to cattle and other livestock, its tendency to distinctive sporangium (called a leptosporangium) whose wall is
invade pastures is a serious problem. only a single cell thick. Polypod ferns have leptosporangia with a
Despite the absence of secondary growth, some ferns can grow line of thick-walled cells that run along the sporangium surface.
quite tall. Tree ferns, which can grow more than 10 m tall, produce When the spores mature, the sporangium dries out and these cells
thick roots near the base of each leaf that descend parallel to the contract, forcibly ejecting spores into the air.
stem to the ground. These roots increase the mechanical stability
of the plant and also allow it to transport more water (Fig. 31.13a). An aquatic fern contributes to rice production.
Other ferns grow tall by producing leaves that twine around the Azolla is a free-floating aquatic fern that has been used for
stems of other plants, using the other plant for support. At the other centuries in Asia as a biofertilizer of rice paddies (see Fig. 33.13b).
extreme are tiny aquatic ferns such as Salvinia (see Fig. 33.11e) and Its success as a fertilizer is due to its symbiotic association with
Azolla (Fig. 33.13b) that float on the surface of the water. nitrogen-fixing cyanobacteria. Azolla is common worldwide on
still water such as ponds and quiet streams. Its leaves contain an
Fern diversity has been strongly affected by the internal cavity in which colonies of nitrogen-fixing cyanobacteria
evolution of angiosperms. become established. The cyanobacteria provide Azolla with
The fossil record shows that ferns originated more than a source of nitrogen, while the fern provides shelter and
360 million years ago, and between 300 and 100 million years ago carbohydrates. The cyanobacteria are reported to have higher rates
CHAPTER 33 PL ANT DIVERSIT Y 699
of nitrogen fixation when they are housed within an Azolla leaf fertilization and the formation of a seed. Seeds in turn enhance
than when they live freely in the environment. dispersal. The nutrient-rich tissue in the seed makes it more
When added to newly planted rice fields, this fast-growing fern likely that the embryo will grow into a photosynthetically self-
suppresses weed growth by forming a dense, floating layer. At the sufficient plant. Before these innovations, the ancestors of seed
same time, it provides organic nitrogen that eventually finds its plants evolved the ability to form large woody stems through
way into the developing rice plants. The floating fertilizer factories the formation of both a vascular and a cork cambium. Therefore,
provided by Azolla may have made possible the long history of rice woody stems and roots are the ancestral condition in seed plants.
cultivation in Asia. Although the fossil record shows that there were once
many different groups of seed plants, today there are only two:
gymnosperms and angiosperms. Gymnosperms total only a bit
33.4 GYMNOSPERMS more than 1000 species, whereas angiosperms total 380,000
species or more. Despite their much lower diversity, in cool or dry
Seed plants have come to dominate terrestrial environments since parts of the world, gymnosperms such as pine trees can make up
their first appearance about 365 million years ago. While the coal- more of the forest canopy than do angiosperms. In this section,
swamps of 300 million years ago were populated by spore-producing we examine the evolutionary history of the four groups of living
giants, the understory of these strange forests included plants that gymnosperms (Fig. 33.14) and explore how their diversity and
produced pollen and seeds. By the time of the dinosaurs, seed plants distribution has been affected by the rise of the angiosperms.
had become the largest and most abundant plants on Earth.
What factors have contributed to the success of seed plants? Cycads and ginkgos are the earliest diverging groups
One is that they do not require external water for fertilization. of living gymnosperms.
Instead, the male gametophyte is transported through the air in It’s easy to confuse cycads with palm trees because both have
pollen. As a result, seed plants are able to reproduce successfully unbranched stems and large leaves (Fig. 33.15). However, the
in both rain forest and desert. Pollination, if successful, leads to presence of cones rather than flowers clearly marks cycads as
gymnosperms. Cones are modified branch tips inside
which reproductive structures develop, with pollen and
ovules produced in separate cones. In cycads, the cones
FIG. 33.14 Seed plant diversity. The phylogenetic tree shows a hypothesis of
are large and woody, and thus provide protection for the
evolutionary relationships among gymnosperms. Photo sources: (top
developing pollen and seeds.
to bottom) Robert Davis/age fotostock; Michael P. Gadomski/Science Source; Pete
Cycads have low photosynthetic rates and they grow
Ryan/Getty Images; Patti Murray/age fotostock.
slowly. Although they have large stems, their vascular
cambium produces little additional xylem, and most
Lycophytes
of their bulk is made up of unlignified (nonwoody)
Ferns and horsetails
Gymnosperms
cells in the center of the stem (pith) and surrounding
Angiosperms the vascular tissues (cortex). Cycads are able to grow
in nutrient-poor environments by forming symbiotic
associations with nitrogen-fixing cyanobacteria. Cycads
Cycads (~300 species) are also able to survive wildfires because their apical
meristem is protected by a dense layer of bud scales.
The approximately 300 species of cycads occur
most commonly in tropical and subtropical regions.
Ginkgo (1 species) Most species have a limited and often fragmented
distribution, suggesting that they were much more
widespread in the past. Most cycad populations are small
and often vulnerable to extinction. Cycads may owe
Conifers (~630 species) their persistence in part to the fact that they rely on
insects for pollination, as well as to their ability to live
in nutrient-poor and fire-prone environments. Insects
transfer pollen more efficiently than wind, and therefore
insect-pollinated species with small populations are able
Gnetophytes (~90 species)
to reproduce successfully. Many cycads are pollinated by
beetles, which are attracted by chemical signals produced
by the cones. The large seed cones provide shelter for the
Angiosperms (>380,000 species) insects, and the pollen cones provide them with food.
700 SECTION 33.4 GYMNOSPERMS
FIG. 33.15 Cycads. (a) Most living cycads have thick, unbranched stems that support large leaves and cones. Shown here is Encephalartos
friderici-guilielmi. (b) Many cycads, such as Encephalartos transvenosus, have large cones. (c) Mature seeds are large (here are shown
those of Cycas circinalis) and contain a relatively large female gametophyte that provides nutrition for the embryo and germinating
sporophyte. Sources: a. A. Laule/age fotostock; b. & c. Andrew Knoll, Harvard University.
a b
Following fertilization, brightly colored, fleshy seed coats attract fleshy seeds, perhaps a feature inherited from their common
a variety of birds and mammals that serve as dispersal agents. seed plant ancestor. Ginkgos date back about 270 million years,
Because of their small numbers and fragmented distribution, and during the time of the dinosaurs, they were common trees
two-thirds of all cycads are on the International Union for the in temperate forests. Like cycads, ginkgos declined in abundance,
Conservation of Nature’s “red list” of threatened species, the diversity, and geographic distribution over the past 100 million
highest percentage of any group of plants. years, as a result of both changing climates and angiosperm
Cycads are an ancient group, with fossils at least 280 million diversification.
years old. During the time of the dinosaurs, they were among the Ginkgos have long been cultivated in China, especially near
most common plants. Cycad diversity and abundance declined temples, and it is unclear whether any truly natural populations
markedly during the Cretaceous Period, at the same time the exist in the wild. Today, however, Ginkgo once again is found all
angiosperms rose to ecological prominence. A recent study shows over the world, as its ability to tolerate the pollution and other
that present-day cycad species date from a burst of speciation that stresses of urban environments has made it a tree of choice for
took place approximately 12 million years ago. At that time, the street plantings.
positions of the continents and ocean circulation patterns were
changing in such a way that climates became increasingly cooler Conifers are woody plants that thrive in dry
and more seasonal. This climate change provided new habitats for and cold climates.
emerging species while dooming older species to extinction. The approximately 630 species of conifers are, for the most part,
A second group of gymnosperms has only a single living trees. Conifers include the tallest (over 100 m) and oldest (more
representative: Ginkgo biloba. This species forms tall, branched than 5000 years) trees on Earth (Fig. 33.17). Well-known conifers
trees, with fan-shaped leaves that turn brilliant yellow in autumn include pines, junipers, and redwoods. Most conifers have strong
(Fig. 33.16). Ginkgo is wind pollinated, but, like cycads, develops apical dominance, and thus develop a single straight stem from
CHAPTER 33 PL ANT DIVERSIT Y 701
FIG. 33.16 Ginkgo biloba. (a) The fan-shaped leaves of Ginkgo turn yellow in autumn. (b) The fleshy seeds enclose a large female gametophyte,
as in cycads. Sources: a. JTB/Photoshot; b. Kathy Merrifield/Science Source.
a b
which extend much smaller horizontal branches. Conifers have of the great questions in the evolutionary history of plants is why
traditionally served as masts for sailing ships, and today are used conifers were displaced from tropical latitudes by the angiosperms
for telephone poles. Conifer xylem consists almost entirely of but continued to thrive in cold and dry environments.
tracheids, and so its wood is strong for its weight, making it well An important difference between angiosperms and conifers
suited as a building material. Conifers supply much of the world’s is that angiosperms transport water in the xylem vessels,
timber, as well as the raw material for producing paper. whereas conifers transport water in tracheids. In wet and warm
Most conifers are evergreen, meaning that they retain their environments, the xylem vessels of angiosperms can be both wide
often needle-like leaves throughout the year. In some species, and long, increasing the efficiency of water transport through
the leaves are remarkably long lived, remaining green and their stems. Thus, one hypothesis is that the evolution of xylem
photosynthetic for decades. Many conifers produce resin canals in vessels gave angiosperms a competitive advantage in moist
their wood, bark, and leaves that deter insects and fungi. Conifer tropical environments. With more water flowing through their
resins are harvested and distilled to produce turpentine and other stems, angiosperms could have higher rates of photosynthesis and
solvents. In addition, conifer resins are the source of a number of
important chemicals, including the drug taxol used in the treatment
of cancer. Amber, prized for its beauty, is fossilized resin. FIG. 33.17 Conifers. Giant sequoia (Sequoiadendron giganteum)
Conifer reproduction tends to be slow: After pollination, it can can reach 85 m in height and have stems that are 8 m in
take more than a year before the seeds are ready to be dispersed. diameter. Source: Charles J. Smith.
Pollen is produced in small cones, and seeds in larger cones. The
seed cones become woody, providing protection, as the fertilized
ovules develop slowly into seeds. Conifers are wind pollinated, and
most species also rely on wind for seed dispersal. However, some
conifers, such as junipers and yews, produce seeds surrounded
by fleshy and often brightly colored tissues that attract birds and
other animals.
Conifers dominate the vast boreal forests of Canada, Alaska,
Siberia, and northern Europe. Conifers tend to become more
abundant as elevation increases, and they are common in dry
areas, such as the western parts of North America and much of
Australia. Only a small number of conifer species are found in
tropical latitudes, most commonly at higher elevations. Before
the rise of the angiosperms, however, conifers were more evenly
distributed across the globe, including in the lowland tropics. One
702 SECTION 33.5 ANGIOSPERMS
Eudicots
Pollen with (75%)
three apertures
Instead, the formation of separate cell types for water different species and from closely related individuals (including
transport and mechanical support may have given the early self) suggests that these genetic recognition systems contribute to
angiosperms greater flexibility of form. Vines and sprawling shrubs the reproductive isolation required for speciation (Chapter 22).
are two examples of growth forms exhibited by early diverging It is important to recognize that diversity results from both
angiosperms. Both growth forms allow plants to grow toward high rates of species formation and low rates of species loss. The
small patches of sunlight that filter through the forest canopy. In fossil record suggests that the persistence of species may play
the heavily shaded tropical rain forest understory, this ability may a particularly important role in angiosperm diversity. Wind-
have provided a distinct advantage. pollinated plants can reproduce only when their populations have
a relatively high density. Since no wind-carried pollen is likely to
Angiosperm diversity results from flowers and xylem fall on isolated individuals, species with low population density are
vessels, among other traits, as well as coevolutionary more likely to go extinct. In contrast, animal pollinators actively
interactions with animals and other organisms. searching for rare species are much more likely to find them, and
The fossil record provides evidence that for the first 30 to 40 so animal-pollinated angiosperm populations can persist at low
million years of their evolution, angiosperms were neither population densities.
diverse nor ecologically dominant. In fact, fossil pollen indicates Another reason rare species may be more persistent is that
that, between about 140 and 100 million years ago, gnetophytes they are less likely to encounter soil pathogens and seed predators.
diversified just as much as angiosperms. Later in the Cretaceous These threats to survival tend to gather near an adult of the same
Period, beginning about 100 million years ago, angiosperm diversity species. The seeds of rare species are more likely to land away
began to increase at a much higher rate. Trees belonging to the from an individual of the same species and thus suffer less from
magnoliids, the branch of the angiosperm tree that today includes this density-dependent mortality than do more common species.
magnolias, black pepper, and avocado, emerged as ecologically However, this ecological strategy works only if rare isolated
important members of forest canopies. More important, however, individuals can remain in contact with a large enough population
was the divergence of the two groups that would come to dominate of potential mates, underlining again the key role of flowers and
both angiosperm diversity and the ecology of many terrestrial animal pollinators in persistence.
environments: the monocots and the eudicots. If animal pollination has so many advantages, why did
Before looking at the diversity of these two groups, let’s approximately 20% of angiosperm species subsequently evolve
consider how characteristics of angiosperms may have promoted a dependence on wind for pollination? Wind-pollinated species
their diversification. While many factors likely have contributed, grow primarily in seasonal environments, where fewer animal
we’ll focus on two themes. The first is that angiosperms are more pollinators are available than in tropical forests, and the pressures
efficient at building their bodies and completing their life cycle than resulting from soil pathogens and seed predators may be much less.
are other plants. Recall that the xylem of angiosperms has vessels That angiosperm diversity is the result of multiple factors is
supplying water required for photosynthesis and fibers providing reinforced by the observation that some of these “angiosperm”
mechanical support. Because water transport and mechanical features are also present in other groups of plants. For example,
support are separated, angiosperms are able to grow efficiently into cycads rely on animal pollination, whereas gnetophytes produce
a wide variety of forms, ranging from short-lived herbaceous plants xylem vessels, and yet neither group is particularly diverse.
to trees with large spreading crowns. This diversity of shapes and The initially slow but increasingly rapid buildup of angiosperm
sizes reduces competition for light and space. diversity may reflect the compounding effect of coevolutionary
Angiosperms complete their life cycle as efficiently as they interactions with pollinators and dispersers, as well as adaptive
build their bodies. Not only are animal-pollinated plants able to radiations triggered by chemical arms races with pathogens
reduce their production of pollen, but also double fertilization and herbivores (Chapter 32). This is what is meant by the adage
reduces the costs of reproduction by allowing angiosperms to delay “Diversity begets diversity,” a phenomenon further explored in
provisioning their offspring until after fertilization. Angiosperms Chapter 47.
can thus reproduce quickly and with a minimum of resources. One
possible consequence is that angiosperms can make use of habitats Monocots are diverse in shape and size despite not
and resources that are only fleetingly available, such as ephemeral forming a vascular cambium.
pools or open areas that appear following a fire. Monocots or monocotyledons make up nearly one-quarter
A second theme focuses on the ways in which angiosperms of all angiosperms. Monocots come in all shapes and sizes and are
interact with other types of organisms. The interaction of flowers found in virtually every terrestrial habitat on Earth (Fig. 33.21).
and animal pollinators contributes to angiosperm diversity. Plants Coconut palms, hanging Spanish moss (a relative of pineapple), and
whose flowers attract different pollinators tend to more readily tiny floating duckweeds, less than 2 mm across, are all monocots,
diverge to form new species than wind-pollinated species. In as are the sea grasses of tropical lagoons and the lilies and daffodils
addition, the ability of carpels to block the growth of pollen from in the garden. Some monocots grow in arid regions—including
CHAPTER 33 PL ANT DIVERSIT Y 705
a b
FIG. 33.21 Monocot diversity and phylogeny. This diverse group
of angiosperms includes (a) Agave shawii, a desert
succulent; (b) Leucojum vernum, a spring wildflower;
(c) bamboo, a forest grass; and (d) Costus species,
which grow in the rain forest understory. (e) Monocot
phylogeny indicates that orchids (~22,000 species)
and grasses (~11,500) make up much of monocot
diversity. Photo sources: a. Biosphoto/François Gohier; b. Kerstin
Hinze/naturepl.com/NaturePL; c. Axle71/Dreamstime.com;
d. Tropicals JR Mau/PhotoResourceHawaii.com.
FIG. 33.22
HYPOTHESIS Grasslands expanded as climate changed over the past 50 million years.
OBSERVATIONS AND EXPERIMENTS Grasses commonly make phytoliths, small structures of silica (SiO2) in their cells. These preserve well,
providing a direct record of grass expansion. Moreover, mammals that feed on grasses evolved high-crowned teeth, which also preserve well,
giving us an indirect record of grassland history. Finally, C4 grasses, which are adapted to hot sunny environments with limited rainfall, have a
distinctive carbon isotopic composition imparted by the initial fixation of CO2 by PEP carboxylase (Chapter 29). Measurements of 13C and 12C
in mammal teeth, soil carbonate minerals, and more recently, tiny amounts of organic matter incorporated into phytoliths, allow scientists to
track C4 grasslands through time.
produced creeping, horizontal stems as they grew along the within an environment that makes only modest demands for
shores of lakes and other wetlands. Many monocots today, water transport.
including the earliest diverging groups of monocots, grow in such We may never know for sure in what environment the
habitats, and many of the features of the monocot body plan are monocots first evolved. We thus turn our attention to one of the
well adapted to environments with loose substrates, flowing most diverse groups within the monocots: the grasses. Many
water, and fluctuating water levels. For example, their leaf base grasses produce stems that grow horizontally and branch, allowing
provides a firm attachment that prevents leaves from being pulled them to cover large areas. Grasses have linear leaves that elongate
off by flowing water. Furthermore, many monocots produce from the base, allowing them to survive grazing as well as fire
strap-shaped leaves that elongate from a persistent zone of cell and drought. Many grasses have evolved the ability to tolerate dry
division and expansion located at the base of the leaf blade. By environments by producing roots that extend deep into the soil.
continually elongating from the base, monocot leaves can extend In addition, C4 photosynthesis has evolved within the grasses
above fluctuating water levels. Finally, it is easier to imagine multiple times. As described in Chapter 29, C4 photosynthesis
evolutionary changes that affected the vascular system occurring allows plants to avoid photorespiration and thus photosynthesize
706
RESULTS Studies of phytoliths, mammal tooth structure, and carbon isotopic composition of teeth enamel from the North American
midcontinent clearly show that grasslands expanded 20 to 15 million years ago, and C4 grasslands expanded later, about 8 to 6 million
years ago.
3.0
Relative importance
2.5
2.0
1.5
1.0
100
Percent of grass
species that live
in open habitat
80
60
40
Based on analysis of
20
phytolith assemblages
0
100 The shading shows the maximum
that is C4 plants
80
value (bottom of shaded area)
60 recorded at each point in time.
40
Based on carbon isotope composition
20 of horse tooth enamel
50 45 40 35 30 25 20 15 10 5 0
Millions of years ago
CONCLUSION In North America, grasslands expanded as atmospheric CO2 levels declined and climates became drier. Other continents
show evidence of a similar linkage of grassland expansion to climate change.
FOLLOW-UP WORK At present, atmospheric CO2 levels are increasing rapidly, which may affect the competitive abilities of C3 and C4
grasses. Scientists are working to understand how global change will influence grasslands and other vegetation.
SOURCE Stömberg, C. A. E. 2011. “Evolution of Grasses and Grassland Ecosystems.” Annual Review of Earth and Planetary Sciences 39: 517–544.
with greater efficiency. Grasses are among the most successful of all angiosperm species (Fig. 33.23). Eudicots are well
group of plants, becoming widespread within the past 20 million represented in the fossil record, in part because their pollen is
years as climates changed (Fig. 33.22). Today, nearly 30% of easily distinguished. Each eudicot pollen grain has three openings
terrestrial environments are grasslands. from which the pollen tube can grow, whereas pollen from all
other seed plants has only a single opening. Eudicots take their
j Quick Check 4 What are some of the distinctive features of
name from the fact that they produce two cotyledons, whereas
monocots?
monocots produce one. But, because the magnoliids and early
angiosperm groups also have two cotyledons, this largest of all
Eudicots are the most diverse group of angiosperms. angiosperm groups is referred to as the “eu-” or “true” dicots.
Eudicots first appear in the fossil record about 125 million years Many eudicots produce highly conductive xylem. High rates
ago and, by 90 to 80 million years ago, most of the major groups of water transport, and thus high rates of photosynthesis, may
we see today were present. Today, there are estimated to be explain why eudicot trees were able to replace magnoliid trees as
approximately 160,000 species of eudicots, nearly three-quarters the most ecologically important members of forest canopies. In
707
708 SECTION 33.5 ANGIOSPERMS
milkweeds, potato, tobacco, What can be done to protect the genetic diversity
mints (60,000 species) of crop species?
Of the more than 400,000 species of plants on Earth today, we eat
Sunflower, carrots, honeysuckle
(10,000 species) surprisingly few. Of those we do eat, nearly all are angiosperms.
The only exceptions are the female gametophyte of a small
number of gymnosperms (pine nuts and ginkgos), as well as
addition, many eudicot trees lack strong apical dominance and the young leaves of a few ferns. Most of the plants we eat come
produce crowns with many spreading branches. Today, tropical from species that are grown in cultivation, and many of these
rain forest trees are an important component of the diversity of cultivated species have, as a consequence of artificial selection,
CHAPTER 33 PL ANT DIVERSIT Y 709
FIG. 33.24 “Centers of origin” where different crop species were domesticated.
Corn, tomato,
bean, cotton
Cabbage, lettuce, Cotton, potato,
olives, oats, wheat peanut
Wheat, barley Potato
Grapes Rubber, chocolate
Sorghum, wheat,
coffee
lost the ability to survive and reproduce on their own. Of the to collect seeds from around the globe. Vavilov’s observations of
approximately 200 such domesticated species, 12 account for over cultivated plants and their relatives led him to hypothesize that
80% of human caloric intake. Just three—wheat, rice, and corn— plants had been domesticated in specific locations from which
make up more than two-thirds. they had subsequently expanded as a result of human migration
Crop breeders select for varieties that grow well under and commerce (Fig. 33.24). Vavilov called these regions “centers
cultivation and are easy to harvest, but a consequence of selective of origin,” and he believed that they coincided with the centers of
breeding is a decrease in genetic diversity. Thus, not only do we diversity for both crop species and their wild relatives. In World
depend upon a small number of species for food, agriculture itself War II, during the siege of Leningrad in which more than 700,000
contributes to a narrowing of plant diversity. Because pathogens and people perished, scientists at the Vavilov Institute sought to
pests continue to evolve, any loss in genetic diversity of crop species protect what was then the world’s largest collection of seeds. Their
creates substantial risks. For example, in 1970, the fungal pathogen dedication—at least one of the self-appointed caretakers died of
Bipolaris maydis, a disease-causing organism that had previously starvation, despite being surrounded by vast quantities of edible
destroyed less than 1% of the U.S. corn crop annually, destroyed seeds—illustrates the priceless nature of the genetic diversity on
more than 15% of the corn crop in a single year. The severity of the which our food supply rests.
epidemic was due to the genetic uniformity of the corn varieties Today, seed banks help preserve the genetic diversity of crop
planted at that time. In natural plant populations, genetic variation species and their wild relatives. However, seed banks can store
for pathogen resistance makes it highly unlikely that a newly only a fraction of the genetic diversity present in nature. To
evolved pathogen strain will be able to infect every plant. help make up the difference, some have suggested establishing
Nicolai Vavilov, a Russian botanist and geneticist, was one protected areas that coincide with Vavilov’s centers of origin. As
of the first to recognize the importance of safeguarding the we discuss in Chapter 49, new threats lie just over the horizon.
genetic diversity of both crop species and their wild relatives. In Meeting these threats will require that every genetic resource be
the early twentieth century, he mounted a series of expeditions brought to bear. •
V I S UA L S Y N T H E S I S Angiosperms:
FIG. 33.25 Structure and Function
Reproduction Integrating concepts from Chapters 29 –31, and 33
Many angiosperms rely on animals
for pollination and dispersal.
1 Flowers: Animals in
search of nectar and
other rewards carry 2 Pollination: Animal pollination is more efficient
pollen from one flower than releasing pollen into the wind. Animal-pollinated
to another. plants can reproduce even when they are rare,
increasing the number of species that can coexist.
Seed
Apple 3 Double fertilization:
blossom Angiosperms supply resources for
seed development only after the
Triploid Ovary egg has been fertilized, during the
endosperm formation of triploid endosperm.
Embryo
Ovule
Triploid cell
Diploid
4 Fruits: Following zygote Pollen tube
fertilization, flowers nucleus
develop into
structures that
enhance seed
dispersal, often by
attracting animals that
carry the fruits away. Growth
Fruit Meristems allow angiosperms to grow and develop throughout their life.
Shoot apical
meristem
Seed
Root apical
meristem
710
Photosynthesis
Efficient water transport through stems allows angiosperms
to support high rates of photosynthesis.
Carbohydrates
H2O CO2
H2O
Nutrients
Nutrients
Carbohydrates
Endomycorrhizae: Plants
H 2O exchange carbohydrates for
nutrients with mycorrhizal
fungi, an example of a
symbiotic relationship.
711
712 CO R E CO N C E P T S S U M M A RY
Core Concepts Summary Three hundred million years ago, lycophytes included large
trees that dominated swamp forests. Today, lycophytes are small
33.1 Angiosperms make up approximately 90% of all plants that either grow in the forest understory as epiphytes or
plant species found today. occur in shallow ponds. page 694
There are thought to be nearly 400,000 species of plants living Ferns and horsetails are morphologically diverse. Ferns produce
today. Of these, approximately 90% are angiosperms. page 690 large leaves that uncoil as they grow; horsetails have tiny leaves;
and whisk ferns with no leaves at all. page 697
The other 10% of plant species is distributed among the other
six major groups of plants. page 690 Although ferns have a long history, most present-day species
Angiosperms first appear in the fossil record about 140 million are the result of a radiation that occurred after the rise of the
years ago, more than 300 million years after plants first moved angiosperms. page 698
onto land. page 690
33.4 Gymnosperms produce seeds and woody stems
The evolution of angiosperms resulted in a rapid and dramatic
and are most common in seasonally cool or dry regions.
increase in total plant diversity. page 690
As angiosperm diversity increased, other plant groups, such as Of the many groups of seed plants that have evolved, only two
gymnosperms and ferns, declined in diversity. page 690 can be found today: the gymnosperms, with fewer than 1000
species, and the angiosperms, with more than 380,000 species.
Moist tropical rain forests dominated by angiosperms provided page 699
new types of habitat into which other plants could evolve.
page 690 Gymnosperms are composed of four groups of woody plants:
cycads, ginkgos, conifers, and gnetophytes. page 699
33.2 Bryophytes form persistent, photosynthetic
Cycads produce large leaves on stout, unbranched stems.
gametophytes and small, unbranched sporophytes;
Although they once were widely distributed, they now
today, they grow in environments where the ability to
occur in small, fragmented populations, primarily in the
pull water from the soil does not provide an advantage.
tropics and subtropics. Many cycads are insect pollinated, and
Bryophytes constitute a paraphyletic group consisting of three all form symbiotic associations with nitrogen-fixing bacteria.
groups of plants: mosses, liverworts, and hornworts. page 690 page 699
Bryophytes are small plants that produce one of two Ginkgo is the single living species of a group that was distributed
morphological types: a flattened thallus or an upright leafy globally before the evolution of the angiosperms. Ginkgo is wind
type. They do not form roots, but instead absorb water through pollinated and produces tall, branched trees. page 700
their surfaces. page 691
Conifers include the tallest and longest-lived trees on Earth.
The persistent component of the life cycle is the gametophyte.
Wind-pollinated and largely evergreen, they are found primarily
Sporophytes range from tiny and non-photosynthetic in
in cool to cold environments. page 700
some liverworts to relatively long-lived and photosynthetic in
hornworts. page 691 Before the angiosperms appeared, conifers were widespread.
Their almost complete absence in the tropics and persistence
There are several examples of convergent evolution between
in temperate regions may be due to their dependence upon
bryophytes and vascular plants, including insect dispersal of
wind pollination and having xylem formed entirely of
spores in some mosses and the evolution of internal transport
tracheids. page 701
cells in some mosses and liverworts. page 692
Sphagnum moss is the dominant plant of peat bogs. page 692 The gnetophytes are a small group, containing only three
genera and few species, that has independently evolved xylem
Sphagnum moss produces water-holding cells that allow
vessels. page 702
it to soak up water, and it acidifies the environment. Both
characteristics help slow decomposition, so large amounts of
organic carbon build up year after year. page 692 33.5 Angiosperms are distinguished by flowers,
fruits, double fertilization, and xylem vessels;
33.3 Spore-dispersing vascular plants today are their diversity is the result of traits that increase the
primarily small plants that grow in moist environments, efficiency of completing their life cycle and building
but in the past included tall trees. their bodies.
Only two groups of seedless vascular plants have living relatives Xylem vessels make it possible for angiosperms to have a
today: lycophytes, and ferns and horsetails. page 693 diversity of form and to grow toward light. page 704
PASS1
Angiosperm diversity may result as much from low rates of 2. Imagine a world in which mosses, liverworts, and
extinction as from high rates of speciation. page 704 hornworts form a monophyletic group. How would your ability
to infer what the first land plants looked like be affected?
Plants having flowers can reproduce even if they are far
apart, allowing rare species to persist and reproduce. 3. Describe three environments that allow bryophytes to
page 704
coexist with vascular plants.
4. Describe the habitats in which lycophytes are found
The angiosperm phylogeny indicates a major split between
today.
two diverse groups, monocots and eudicots. page 704
5. List three ways that ferns, which lack secondary growth,
Monocots include grasses, coconut palms, bananas, ginger,
are able to elevate their leaves and thus access more sunlight.
and orchids. page 704
6. Describe how fern diversity has been affected by the
Monocots have a single cotyledon, or embryonic seed leaf, evolution of the angiosperms.
and they do not form a vascular cambium. page 705
7. Contrast the ways in which the evolution of angiosperms has
Eudicots are characterized by pollen grains with three affected the distribution of cycads and of conifers.
openings through which the pollen tube can grow.
8. Explain how xylem produced by conifers differs from that
page 707
of angiosperms and how that difference may have influenced
Eudicots are diverse, and include many familiar plants such the present-day distribution of conifers.
as legumes, roses, cabbage, pumpkin, coffee, tea, and cacao.
9. Compare the movement of pollen from an animal-
page 708
pollinated angiosperm and a wind-pollinated conifer, noting
Modern agriculture is based on just a few plant species with what features of angiosperm reproduction increase the
low genetic diversity, making crops vulnerable to pests and efficiency (or lower the costs) of pollen transfer.
pathogens. page 709 10. Name two features that have contributed to the diversity
and success of angiosperms and discuss possible advantages of
these features.
Fungi
Structure, Function,
and Diversity
Core Concepts
34.1 Fungi are heterotrophic
eukaryotes that feed by
absorption.
34.2 Fungi reproduce both sexually
and asexually, and disperse by
spores.
34.3 Other than animals, fungi are
the most diverse group of
eukaryotic organisms.
715
716 SECTION 34.1 G RO W T H A N D N U T R I T I O N
In tropical rain forests, vascular plants make up most of the Hyphae permit fungi to explore their environment
biomass. Animals eat the plants, obtaining food for growth and for food resources.
reproduction, but they feed selectively: They consume leaves, Most fungi consist of highly branched, multicellular filaments
fruits, and seeds, but largely avoid a much more abundant called hyphae (Fig. 34.1). The hyphae are slender, typically
tissue—wood. In fact, most leaves also escape grazing and 10 to 50 times thinner than a human hair. The numerous long,
eventually fall, dead, onto the forest floor. Animals, too, may be thin hyphae provide fungi with a large surface area for absorbing
eaten by predators, but some die of other causes and contribute nutrients.
their remains to the soil. Given this constant rain of biological Hyphae maintain their slender form by growing only at their
materials, we might expect wood, leaves, and animal carcasses tips. Elongating hyphae thus penetrate ever farther into their
to accumulate in great piles, but a walk through the rain forest environment, encountering new food resources as they grow.
reveals that the forest floor is remarkably clean. What happened Where resources are low, growth is slow or may stop entirely.
to all the dead plant and animal tissues? On the other hand, when fungi encounter a rich food resource,
On land, the organisms principally responsible for the they grow rapidly and branch repeatedly, forming a network of
decomposition of plant and animal tissues are fungi, one of branching hyphae called a mycelium (plural, mycelia). Mycelia
the most abundant and diverse groups of eukaryotic organisms. can grow to be quite large—the largest known individual of the
Many of us have seen mushrooms and toadstools in a meadow or fungus Armillaria ostoyae covers over 2000 acres in the Blue
woodland, but most fungal biomass and most of the metabolic Mountains of Oregon and weighs many hundreds of tons. We may
work that fungi do occurs within the soil, out of sight. Fungi play be impressed by blue whales and redwoods, but in fact some fungi
a critical role in cycling carbon because of their ability to locate are the largest living organisms on Earth.
and break down the complex molecules and bulky tissues in A strong but flexible cell wall is key to hyphal growth and
plant and animal bodies. Moreover, because they form intimate nutrient transport. In fungi, cell walls are made of chitin, the
relationships with living plants and animals, fungi affect the same compound found in the exoskeletons of insects. Chitin is a
growth and reproduction of many other organisms. For example, modified polysaccharide that contains nitrogen. Because of their
fungi associated with plant roots dramatically increase plant chemical makeup, fungal cell walls are thinner than plant cell
productivity by enhancing the uptake of mineral nutrients walls. Fungal cell walls prevent hyphae from swelling as water
from the soil (Chapter 29). Other fungi are major agricultural flows into the cytoplasm by osmosis. Thus, the wall prevents cells
pests (Chapter 32). Fungi enable us to turn wheat into bread, from rupturing when exposed to dilute solutions such as those in
barley into beer, and milk into cheese, but still other fungi cause
athlete’s foot, yeast infections, and, especially in patients with
compromised immune systems, overwhelming infections that can
lead to death. FIG. 34.1 Fungal hyphae. These thin filaments have enormous
surface area that increases absorption of nutrients. Shown
here are hyphae of Trichophyton, a fungus that infects
34.1 GROWTH AND NUTRITION the skin of humans, as seen under a scanning electron
microscope. Source: Susumu Nishinaga/Science Source.
Fungi are heterotrophs, meaning that they depend on preformed
organic molecules for both carbon and energy. Unlike animals,
fungi do not have organs that enable them to ingest food and
break it down in a digestive cavity (Chapter 40). Instead, fungi
absorb organic molecules directly through their cell walls. This
mode of feeding presents two major problems. First, although
simple molecules like amino acids and sugars pass readily through
the cell wall, more complicated molecules do not. Fungi secrete a
diversity of enzymes that break down complex organic molecules
like starch or cellulose into simpler compounds that can be
absorbed. Fungi, then, digest their food first and take it into the
body afterward.
A second challenge is to find food in the environment. Other
heterotrophic organisms such as bacteria, protists, and animals
commonly move through their habitat, actively searching for
food. Fungi, however, have no means of locomotion, and so these
organisms use the process of growth itself to find nourishment.
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 717
Fungi are principal decomposers of plant tissues. Blanchette, Elizabeth Simpson, and Marilyn L. Fogel. Nitrogen cycling
Most fungi use dead organic matter as their source of energy and by wood decomposing soft-rot fungi in the “King Midas tomb,” Gordion,
raw materials. As noted in Chapter 25, on land the organic matter Turkey PNAS 2001 98 (23) 13346-13350. Copyright 2001 National
in dead tissues on and within soils far exceeds the amount in Academy of Sciences, U.S.A. Photos courtesy of Robert A. Blanchette,
the living biomass. Thus, the ground beneath our feet provides University of Minnesota.
and animals.
While some interactions between species benefit the fungus at the
expense of its host, others benefit both partners. In Chapter 29,
we saw that mycorrhizal fungi supply plant roots with nutrients
such as phosphorus and nitrogen from the soil and in return
receive carbohydrates from their host (Fig. 34.7). There are two
main types of mycorrhizae. The hyphae of ectomycorrhizal fungi
surround, but do not penetrate, root cells. In contrast, the hyphae
of endomycorrhizal fungi penetrate into root cells, where they
produce highly branched structures that provide a large surface
area for nutrient exchange. As we discuss in section 34.3, the
endomycorrhizal fungi constitute a monophyletic group dating back
over 400 million years. In contrast, ectomycorrhizae are present in
multiple groups and appear to have evolved more than once.
Other fungi, called endophytes, live within leaves. While
endophytes are much less studied than mycorrhizae, they may
be as widespread. Endophytic hyphae grow within cell walls
and in the spaces between cells. Long thought to be harmless,
endophytes are now recognized as beneficial. They may help beetles. These beetles maintain fungal gardens within tunnels that
the host plant by producing chemicals that deter pathogens and they excavate in damaged or dead trees.
herbivorous insects.
Mutually beneficial associations between fungi and animals Lichens are symbioses between a fungus and a green
are much less common, but a few examples are known, none more alga or a cyanobacterium.
striking than insects that actually grow fungi for food. The fungi Lichens are familiar sights in many environments, often forming
benefit because the insects provide shelter, food, and protection colorful growths on rocks or tree trunks (Fig. 34.8). Lichens
from predators and pathogens. Insect–fungal agriculture has look, function, and even reproduce as single organisms, but
evolved at least three times: in leaf-cutter ants that live in tropical they are actually stable associations between a fungus and
forests, in a group of African termites, and in some wood-boring a photosynthetic microorganism, usually a green alga but
FIG. 34.8 Lichens. A lichen is a mutualistic association between a fungus and a photosynthetic microorganism. Sources: (left to right) Wallace Garrison/
Getty Images; Stephen Sharnoff; Stephen Sharnoff.
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 721
FIG. 34.9 Lichen anatomy. The fungus provides structure, and photosynthetic algae form a thin layer under the surface. The scanning electron
micrograph shows a section through Xanthoria flammea. Photo source: Eye of Science/Science Source.
sometimes a cyanobacterium. Nearly 15% of all known fungal Surprisingly, these associations are not species specific. There
species grow as lichens. are approximately 13,500 known lichens, but only about 100
The dual nature of lichens was first proposed by a Swiss participating photosynthetic species. This means that different
botanist, Simon Schwendener, in 1867, but his hypothesis lichens can have the same algae or cyanobacteria. Conversely,
found little favor at the time. The existence of a composite a given fungal partner may associate with more than one
“organism” challenged the idea that life could be divided photosynthetic species without affecting the lichen’s outward
into discrete categories such as animals and plants and raised form. Because of the intimate association between lichen
the question of how an association of distinct species could morphology and fungal species, the lichen and fungus are assigned
function as an integrated whole. Given what we now understand the same scientific name.
about the widespread nature of mutualisms, the opposition to Lichens spread asexually by fragmentation or through the
Schwendener’s proposal may seem surprising. Yet it was only in formation of dispersal units consisting of a single photosynthetic
1939, when Eugen Thomas showed that lichens could be separated cell surrounded by hyphae. Sexual reproduction, at least by
into their individual parts and then reassembled, that their dual the fungi, is common, and the photosynthetic cells reproduce
nature became widely accepted. asexually by mitotic cell division. Whether sexual or asexual
Lichens consist mostly of fungal hyphae, with the reproduction is more important in allowing lichens to establish in
photosynthetic algae or cyanobacteria forming a thin layer just new habitats is not known.
under the surface (Fig. 34.9). The hyphae anchor the lichen Lichens are remarkable for their ability to grow on the surfaces
to a rock or tree, aid in the uptake and retention of water and of rocks and tree trunks. They are among the first colonizers of
nutrients, and produce chemicals that protect against excess light lava flows and the barren land left after glacial retreat. In these
and herbivorous animals. In turn, the photosynthetic partners habitats, lichens obtain nutrients from rainfall or by secreting
provide a source of reduced carbon, such as carbohydrates. organic acids that help release some nutrients from even rocky
Cyanobacteria living in lichens are capable of nitrogen fixation surfaces. Not surprisingly, lichens in these harsh environments
(Chapter 26) and thus can use atmospheric N2 as a source of grow slowly. Some lichens grow on soil, for example reindeer
nitrogen. The two partners exchange nutrients through fungal “moss,” which grows in the Arctic tundra and is eaten by caribou.
hyphae that tightly encircle or even penetrate the walls of the Reindeer moss is thought to compete successfully for space by
photosynthetic cells. As a result, lichens are able to thrive where secreting chemicals that hinder the growth of plants.
neither partner could exist on its own. Given their small size and exposure to the environment,
It remains an open question whether either partner can exist lichens must be able to tolerate drying out from time to time.
independently in nature. In cases where the fungal partner can All lichens have a high tolerance for desiccation, and can tolerate
be grown in the laboratory in culture, it produces a relatively wide fluctuations in temperature and light. In contrast, lichens are
undifferentiated hyphal mass. Thus, while the bulk of the lichen quite sensitive to air pollution, particularly sulfur dioxide (SO2 ).
structure comes from the fungus, chemical signals from the For this reason, lichen growth is sometimes used as an indicator of
photosynthetic partner influence the form and shape of the fungus. industrial pollution.
722 SECTION 34.2 R E P RO D U C T I O N
within soils or host organisms can spread locally but cannot disperse
34.2 REPRODUCTION over great distances, so fungi produce spores that can be carried by
the wind (Fig. 34.10a), in water, or attached to (or within) animals.
Like plants, fungi face two challenges in completing their life In early-diverging fungi that live in aquatic environments, spores
cycles. First, to maintain genetic diversity within populations, have flagella that allow them to swim. The great majority of fungi,
they must find other individuals to mate with. Second, they must however, live on land, and their spores lack flagella. Instead, the
be able to disperse from one place to another. The majority of spores are encased in a thick wall that protects them as they are
fungi reproduce both sexually and asexually. Sexual reproduction dispersed over habitats unsuitable for growth.
in many fungi is characterized by a feature of the life cycle that The probability that any given spore will come to rest in a
distinguishes it from all other eukaryotes, and some asexual favorable habitat is low, so fungi produce large numbers of spores.
fungi have a unique way to generate genetic diversity. Fungal Fungal spores remain viable, able to grow if provided with an
adaptations for dispersal broadly resemble those of plants. Fungi appropriate environment, for periods ranging from only a few
rely on wind, water, or animals to carry spores through the hours in some species to many years in others. Thus, spores allow
environment. Recall from Chapter 30 that spores are specialized fungi to use resources that are patchy in time as well as in space. In
cells well adapted for dispersal and long-term survival. fact, a shortage of resources is one of the cues that triggers spore
We most often come into contact with fungi through formation.
their reproductive structures. Fungal spores commonly cause Spores can form by meiotic cell division as part of sexual
respiratory illness, and mushrooms attract our attention reproduction, and they can also form asexually. Asexual spores
because they are delicious or poisonous. Yet many aspects of are formed by mitotic cell division and therefore are genetically
fungal reproduction are not easily observed. In this section, we identical to their parent. In many species, asexual spores are
emphasize the most general principles and patterns. produced within sporangia that form at the ends of erect hyphae,
allowing the release of the spores into the air. A close look at
Fungi proliferate and disperse using spores. a moldy piece of bread reveals that the surface is covered with
The tissues, living or dead, that support fungal growth often have a hyphae carrying sporangia containing asexual spores (Fig. 34.10b).
patchy distribution. For this reason, fungi must be able to disperse Fungal species vary in the extent to which they rely on
from one food source to another. The extensive networks of hyphae asexual as opposed to sexual spore production. In some groups,
FIG. 34.10 Fungal spores dispersed by wind. Sources: a. Biosphoto/Yves Lanceau; b. (top) Gregory G. Dimijian/Science Source; b. (bottom) Garry DeLong/Getty Images.
Sporangium
Spores
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 723
FIG. 34.11 Fruiting bodies, complex multicellular structures built from hyphae. Fruiting bodies of Hygrophorus miniatus, known commonly as
the vermillion waxcap. Photo source: Matt Meadow/Getty Images.
Fruiting body
Hyphae Spores
Mycelium
such as the group that includes the most common mushrooms, eject their spores, achieving velocities of more than 1 m/s that
sexual reproduction is the dominant means of spore production. allow the tiny spores to penetrate and travel beyond the
On the other hand, in a small number of fungi that includes the layer of unstirred air that surrounds the fruiting body. Once
endomycorrhizal species, spores produced by meiotic cell division airborne, the spores are transported efficiently through air
have never been observed. Although sexual reproduction appears (Fig. 34.12). Other fungi rely on external agents such as
to be absent in some fungal species, asexual fungi have other raindrops or animals to move their spores around. In section
mechanisms for producing genetic diversity, as discussed later in 34.3, we will encounter examples of the diverse dispersal
this section. mechanisms found in the fungi.
Multicellular fruiting bodies facilitate the dispersal The fungal life cycle often includes a stage in which
of sexually produced spores. haploid cells fuse, but nuclei do not.
Fungi employ an astonishing array of mechanisms to enhance Like other sexually reproducing eukaryotes, fungi have life
spore dispersal. Particularly conspicuous are the multicellular cycles that include haploid (1n) and diploid (2n) stages. The
fruiting bodies produced by some fungi, which are structures nuclei in fungal hyphae are haploid, and the fungal life cycle is
that allow the dispersal of sexually produced spores. (Fungal therefore similar to the life cycles of eukaryotic organisms that
fruiting bodies should not be confused with the fruits of exist normally in the haploid stage (see Fig. 27.3a). In these
flowering plants, which are unrelated and very different haploid-dominant organisms, asexual reproduction takes place
structures.) Mushrooms, stinkhorns, puffballs, bracket fungi, through the production of haploid spores by mitosis, while sexual
truffles, and many other well-known structures are fungal reproduction takes place as two haploid cells (often male and
fruiting bodies. female gametes) fuse to form a diploid zygote, which undergoes
Fruiting bodies are highly ordered and compact structures meiosis as its first division. However, sexual reproduction in
compared with the mycelia from which they grow, yet they are fungi differs from all other haploid-dominant organisms in one
constructed entirely of hyphae (Fig. 34.11). In fact, in many important respect: In fungi, the fusion of haploid cells is not
cases their mechanisms of spore dispersal demand a high degree immediately followed by the fusion of their nuclei.
of structural precision. Yet we know little of the developmental In most fungi, the sexual phase of the life cycle takes
processes that allow tip-growing hyphae to produce such complex place through the fusion of hyphal tips rather than specialized
and regular structures. reproductive cells, or gametes. For mating to occur, two hyphae
The fruiting bodies of many fungi rise above the ground or grow together and release enzymes that digest their cell walls at
grow from the trunks of dead trees, so the sexually produced the point of contact. Once the dividing wall is gone, the contents
spores are released high above the ground. But elevation by of the two hyphal cells merge, forming a single cell with two
itself is not enough to ensure dispersal. Thus, many fungi forcibly haploid nuclei. Eventually, the two haploid nuclei merge, forming
HOW DO WE KNOW?
FIG. 34.12
from Elsevier.
BACKGROUND Many fungi disperse their spores by ejecting
them forcibly into the air. For spores to be picked up by the wind,
however, they must escape a layer of still air called the boundary Fungal spores with outlines (blue) of computer-modeled shapes
layer that lies close to the ground. Escape from the boundary layer that minimize drag.
is easier if spores have a size and shape that minimize drag, the
RESULTS Nearly three-quarters of the examined spores had
resistance of air to the movement of an object.
shapes that came within 1% of the shape calculated to minimize
HYPOTHESIS In fungi that eject their spores into the atmosphere, drag (shown in the figure as blue outlines). Related species that do
natural selection favors spore shapes that minimize drag. not eject spores forcibly were less likely to have drag-minimizing
shapes.
EXPERIMENT Working from computer models for minimizing drag
CONCLUSION Natural selection has acted on fungi to facilitate
on airplane wings, scientists modeled spore shapes that minimize
spore dispersal by wind.
drag. These models took into account spore size as well as the
physical characteristics of the air through which spores travel. The
SOURCE Roper, M., et al. 2008. “Explosively Launched Spores of Ascomycete
scientists then measured spore shape for more than 100 species of Fungi Have Drag-Minimizing Shapes.” Proceedings of the National Academy of
spore-ejecting fungi. Sciences, USA 105:20583–20588.
a diploid zygote. The zygote divides by meiotic cell division, giving edible mushrooms found on market shelves consist entirely of
rise to sexually produced haploid spores. dikaryotic hyphae.
In most sexually reproducing organisms, when two gametes Dikaryotic fungi account for more than 98% of all known
merge, their nuclei fuse almost instantly to form a diploid zygote. In fungal species, suggesting that the separation of plasmogamy
fungi, however, the cytoplasmic union of two cells (plasmogamy) and karyogamy in time and space may confer an evolutionary
is not always followed immediately by the fusion of their nuclei advantage. One such advantage can be seen when we think about
(karyogamy). Instead, the haploid nuclei retain their independent the environments where fungi live. Mating takes place principally
identities, resulting in what is referred to as a heterokaryotic within the soil or inside the trunks of rotting trees, sites where
(“different nuclei”) stage (Fig. 34.13). In the heterokaryotic stage, hyphae are most likely to come into contact. Dispersal, however,
a cell contains nuclei from two parental hyphae, but the nuclei is most effective when spores can be released into the air. The
remain distinct. The heterokaryotic stage ends with pairs of nuclei separation of plasmogamy and karyogamy allows mating and
fusing, which leads to the formation of a diploid zygote. spore production to occur where each is most effective. In some
In some groups, the heterokaryotic stage consists of a single dikaryotic fungi, however, the separation of plasmogamy and
cell with many haploid nuclei. In other groups, plasmogamy is karyogamy is neither distant in space nor long in time. In these
followed by mitosis, which produces hyphae in which each cell fungi, the highly branched dikaryotic hyphae may serve primarily
contains two haploid nuclei, one from each parent. Heterokaryotic as a means of increasing the number of cells in which karyogamy
cells with two genetically distinct haploid nuclei are referred to will eventually take place, therefore leading to the production of
as dikaryotic, or n + n, cells. In fungi with dikaryotic cells, called more sexually produced spores.
dikaryotic fungi, there may be a small number of dikaryotic cells At present, we really don’t know why fungi proliferate n + n
or extensively developed hyphae made up of dikaryotic cells. Some cells rather than forming a multicellular diploid phase, and there
724
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 725
FIG. 34.13 Generalized fungal life cycle. In many fungi, plasmogamy and karyogamy are
separated by a heterokaryotic stage.
HAPLOID
(1n)
Dispersal and
germination Spores
Asexual cycle
Mycelium
Dispersal and
germination Plasmogamy
(fusion of cytoplasm)
Heterokaryotic cell
Meiosis
may be no single answer to the question of why the dikaryotic individual is determined by a mating-type gene. Fertilization can
fungi have this unique cell type. take place only between individuals that have different alleles at
the mating-type gene. In some species, there are only two mating-
j Quick Check 2 What is the difference between a diploid cell
type alleles. In this case, mating patterns are identical to those for
and a dikaryotic cell?
species with male and female sexes. If the two mating-type alleles
are spread evenly throughout the population, an individual should
Genetically distinct mating types promote be able to mate with 50% of the general population.
outcrossing. Some fungi have more than two mating-type alleles. These
Under most conditions found in nature, genetically diverse fungi have a greater likelihood of encountering a compatible
populations persist better than those lacking diversity. Indeed, genotype in the general population. That likelihood is even higher
sexual reproduction is widely viewed as a means of promoting for fungi in which mating type is determined by two different
genetic diversity for long-term ecological success in variable mating-type genes that each have multiple alleles. Fungi in the
environments (Chapters 11 and 42). With the exception of early- group that includes the common mushrooms can have as many
diverging aquatic groups, fungi do not produce male and female as 20,000 different mating-type alleles. In this case, the odds of
gametes. What prevents an individual from mating with itself? finding a compatible mate are close to 100%.
Fungi have different mating types that are genetically Genetic compatibility is a prerequisite for mating. How do
determined and prevent self-fertilization. The mating type of an fungi go about finding a suitable mate? The answer is that they
726 SECTION 34.3 DIVERSIT Y
Fungi
in some species elongated cellular outgrowths called rhizoids
penetrate into organic substrates. Rhizoids anchor the organism in
Complex Basidiomycetes place and absorb food molecules.
multicellular (25,000 species) Chytrids generally disperse by flagellated spores. Sexual
fruiting bodies
reproduction appears to be rare, but there is substantial life-cycle
diversity within this group. Chytrids lack a heterokaryotic stage
Dikarya
Regular septa but form flagellated gametes that swim through their aqueous
environment.
Most chytrids are decomposers, and a few of them are
Ascomycetes
pathogenic. Notably, infection by the chytrid Batrachochytrium
(48,000 species)
dendrobatidis may be a cause of a widespread decline in amphibian
populations (Chapter 49).
Complex
multicellular
fruiting bodies
FIG. 34.18 Two groups of dikaryotic fungi. (a) The morel (Morchella esculenta) is an ascomycete, whereas
(b) the shiitake mushroom (Lentinula edodes) is a basidiomycete. Sources: a. Matt Meadows/Getty
Images; b. Topic Photo Agency/age fotostock.
a b
The Dikarya contain two monophyletic subgroups (see to absorb nutrients from the substrate for a while before nuclear
Fig. 34.15), each named for the shape of the cell in which the key fusion occurs.
reproductive processes of nuclear fusion (karyogamy) and meiosis
take place. The Ascomycota, or ascomycetes, are sometimes Ascomycetes are the most diverse group of fungi.
called sac fungi because nuclear fusion and meiosis take place in Ascomycetes make up 64% of all known fungal species. They
an elongated saclike cell called an ascus (askos is Greek for “leather include important wood-rotting fungi, many ectomychorrizal
bag”). The Basidiomycota, or basidiomycetes, are popularly species, and significant pathogens of both animals and plants.
known as club fungi because the nuclear fusion and meiosis take Ascomycetes form the fungal partner in most lichens—
place in a club-shaped cell called a basidium. (“Basidium” is derived approximately 40% of all ascomycete species occur in lichens.
from the Greek basis, which means “base” or “pedestal”; the Ascomycetes loom large in human history, contributing the
reference is to the position of sexually produced spores at the tips baker’s and brewer’s yeasts used to make bread and beer,
of this club-shaped body.) the antibiotic penicillin, and model systems employed in
Although ascomycetes and basidiomycetes have the same laboratory investigations of eukaryotic cell biology and genetics.
basic life cycle, they diverged from each other as much as Ascomycetes are used to produce soy sauce, sake, rice vinegar,
600 to 500 million years ago and evolved complex multicellular and miso, and to transform milk into Brie, Camembert, and
structures independently of each other. The morel in the Roquefort cheeses. Athlete’s foot and other skin infections are
supermarket is an ascomycete, whereas the shiitake mushroom caused by ascomycetes, as are many more serious fungal diseases.
next to it is a basidiomycete (Fig. 34.18). In addition to asci Ascomycetes include both species that form multicellular
and basidia, the two groups differ in several other features. For fruiting bodies and ones that form unicellular yeasts. A
example, the septal pores that connect adjacent cells within remarkable feature of ascomycete fruiting bodies is that they
hyphae are distinct in the two groups, as are the ways in which contain both dikaryotic and haploid cells. The proliferation of
cells can plug the pores to minimize damage to a mycelium. Also, dikaryotic cells leads to the production of many asci, while the
when ascomycetes reproduce, mating cells form and their nuclei growth of haploid cells contributes to the bulk of the fruiting
fuse in relatively close succession. Thus, the heterokaryotic stage body. Two ascomycete lineages consist largely of yeasts. The
is brief. In contrast, in the basidiomycetes, the nuclei of two fused earliest branching members in these groups, however, produce
cells may remain separate for a long time. In this case, hyphae hyphae. Thus, the unicellular nature of yeasts is a derived feature
containing both types of nuclei (dikaryotic hyphae) can continue evolved through loss of hyphae and is not an ancestral condition.
730 SECTION 34.3 DIVERSIT Y
FIG. 34.19 The sexual cycle of a common ascomycete, the brown cup fungus (Peziza species). Photo source: Ed Reschke/Getty Images.
Spores
Dispersal and
germination
Eight HETEROKARYOTIC
spores (1n)
Fig. 34.19 illustrates the life cycle of a common ascomycete, of an ascomycete that grows as an ectomycorrhizal fungus on tree
the brown cup fungus. In ascomycetes, meiosis is followed by roots. Not only do truffles encase their spores in protective tissues,
a single round of mitosis, resulting in asci that contain eight but they also develop underground. How, then, can their spores
haploid spores. When mature, the spores are ejected from the be dispersed? Developing truffles release androstenol, a hormone
top of the asci, expelled by turgor pressure. In many ascomycetes, also produced by boars before mating. The hormone attracts female
fruiting bodies elevate the asci on one or more cup-shaped pigs, which unearth and consume the fruiting body. The spores pass
surfaces, from where the spores are easily caught and carried away through the pig’s digestive tract without damage and are released
by wind. into the environment in feces, thereby dispersing the spores.
In the fruiting bodies of some ascomycetes, the asci are Another ascomycete is thought to have played a role in the
completely enclosed by a layer of tissue and thus must be dispersed events that unfolded in Salem, Massachusetts, in 1692. That year,
by other organisms rather than by the wind. The truffles prized in several girls came down with an unknown illness manifested by
cooking provide an example. The edible truffle is the fruiting body delirium, hallucinations, convulsions, and a crawling sensation on
0
FIG. 34.20
Can a fungus influence the RESULTS Infected ants have repeated convulsions (indicated
by vertical bars in the graph), but uninfected ants show no such
behavior of an ant? behavior (not shown). Transitions from erratic wandering to a
“death grip,” in which the ant bites into a leaf (indicated by red
triangles in the graph and shown in the photograph), occurred at
BACKGROUND A curious death ritual unfolds in the rain forest of about the same time of day. Dissections showed that the ants’ death
Thailand. Spores of the ascomycete fungus Ophiocordyceps infect grip results from jaw-muscle wasting caused by the fungus.
Camponotus leonardi ants, growing hyphae inside their bodies. The
fungus eventually kills the ant, and fruiting bodies emerge from the 12
dead ant’s head to disperse spores that begin the life cycle anew. 11
Camponotus leonardi nests and forages for food high in the forest 10
canopy. Infected ants, however, undergo convulsions that cause 9
them to fall to the forest floor. The infected ants wander erratically 8
Individual ant
and are unable to climb more than a few meters above the ground 7
before convulsions make them fall again. In their final act, the ants 6
bite into the undersides of leaves and die. The fungus is then able 5
to complete its life cycle within the humid forest understory. Is 4 Each horizontal
3 entry records
the ants’ behavior, including both the convulsions and leaf biting,
2 behavioral events
induced by the fungi? for a single ant.
1
the skin. The girls were thought to be bewitched, and subsequent Basidiomycetes include smuts, rusts, and mushrooms.
accusations led to the infamous Salem witch trials. They were The basidiomycetes, which make up 34% of all described fungal
executed for witchcraft, but today many scholars prefer a simpler species, include three major groups (Fig. 34.21). Two of these—
diagnosis for the illness: poisoning by the ascomycete fungus the smuts and rusts—consist primarily of plant pathogens.
ergot. Ergot is a common pathogen of rye and related grasses, Smut fungi, which infect the reproductive tissues of grasses and
and ingestion of contaminated plants can lead to the symptoms related plants, take their name from the black sooty spores that
reported in Salem. Like many defensive compounds produced by they produce. Ustilago maydis, the corn smut, turns developing
plants, alkaloid molecules produced by ergot and their derivatives corn kernels into soft gray masses that are a culinary delicacy in
are used in medicine in low doses, such as in the treatment of Mexico. Because smuts infect seeds, their spread is magnified by
migraines. the harvest, storage, and eventual sowing of crop seeds. Before the
Ascomycetes are even known for producing so-called zombie introduction of chemical seed treatments in the 1930s, infection
ants, a topic explored in Fig. 34.20. by Tilletia (the stinking smut) commonly caused the loss of up to
731
732 SECTION 34.3 DIVERSIT Y
j Quick Check 4 When you eat a mushroom, what stage of its life
cycle are you consuming?
FIG. 34.22 Diverse fruiting bodies of basidiomycetes. (a) Stinkhorn (Dictyophora indusiata); (b) puffball (Calvatia gigantea); (c) bracket fungi
(Ganoderma australe). Sources: a. Bill Gozansky/age fotostock; b. Wally Eberhart/Getty Images; c. Bob Gibbons/Science Source.
a b c
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 733
FIG. 34.23 The sexual cycle of a basidiomycete that forms multicellular fruiting bodies.
Haploid
mycelia
Sexual cycle
Meiosis Karyogamy
Elevation alone does not ensure dispersal because the spores raindrops displace groups of spores (the “eggs” in the nest)
must penetrate a boundary layer of air that surrounds the fruiting onto nearby vegetation. Herbivores consume the spores when
body. Many basidiomycetes depend on surface tension to catapult they feed on the vegetation and transport them to a new dung
their spores through the air. The placement of their four spores pile. Stinkhorns produce spores in a stinky, sticky mass that
on the ends of short stalks is the key to this mechanism. Both the attracts insects, which then carry off spores that stick to their legs
spores and the supporting basidial cell actively secrete solutes that and body.
cause water to condense on their surfaces. At first, the droplets are
independent, but as they grow they eventually come into contact ? CASE 6 AGRICULTURE: FEEDING A GROWING POPULATION
with one another, and at this point the high surface tension of How do fungi threaten global wheat production?
water causes them to merge into a single, smooth droplet. This Throughout much of human history, crops have been vulnerable
change in shape shifts the center of mass of the water with such to infection by Puccinia graminis, the black stem rust of wheat.
force that it catapults the spore into the air. Puccinia graminis infects wheat leaves and stems through their
Basidiomycetes that form conspicuous fruiting bodies have stomata and then extends within the plant’s living tissues to fuel
diverse mechanisms for dispersing their spores. For example, its own growth. Rust-colored pustules erupt along the stem and
puffballs function like bellows: The impact of raindrops forces the then release a vast number of spores, leaving the host plant to
loose, dry spores out of a small hole at the tip of the ball (see Fig. wither and die. Crop losses from P. graminis can be devastating.
34.10a). Bird’s nest fungi function like splash cups: In this case, In the past, both the United States and the Soviet Union tried to
734 CO R E CO N C E P T S S U M M A RY
different host species. For example, to complete its life cycle, JPEG image, 2010, http://www.fao.org/agriculture/crops/rust/
P. graminis must infect wheat first and then barberry bushes stem/rust-report/stem-ug99racettksk/en/; (photos) Yue Jin,
(Berberis species). After a particularly severe outbreak of wheat USDA-ARS, Cereal Disease Laboratory.
(2007), and South Africa (2009). As you read this, Ug99 is poised to
reach the major wheat growing regions of Turkey and South Asia.
Even more rapid spread is possible if spores accidentally lodge on how plants defend themselves against rusts and what makes
cargo or airline passengers. Ug99 so virulent. The resurgence of P. graminis as a serious
Just before his death in 2009, Norman Borlaug urged the threat to world food production underscores the importance of
world to take this threat seriously. Today, plant breeders are safeguarding the genetic diversity of agricultural species so that
actively searching ancestral wheat varieties for genetic sources of the inevitable evolutionary battles with pathogenic species may be
resistance to Ug99, while other scientists are trying to understand waged successfully. •
Core Concepts Summary Most fungi have numerous branched filaments called hyphae,
which absorb nutrients. page 716
34.1 Fungi are heterotrophic eukaryotes that feed by
When fungi encounter a rich source of food, their hyphae form
absorption.
a network called a mycelium. page 716
Fungi are heterotrophs that depend on preformed organic
Fungal cell walls are made of chitin, the same compound found
molecules for both carbon and energy. page 716
in the exoskeletons of insects. page 716
Fungi break down their food and then absorb it. page 716
In early fungal groups, the hyphae form a continuous
Fungi use the process of growth to find and obtain food in their compartment, with many nuclei but with no cell walls, but in
environment. page 716 later evolving groups, nuclear divisions are accompanied by the
0
CHAPTER 34 F U N G I : S T RU C T U R E , F U N C T I O N , A N D D I V E R S I T Y 735
formation of septa that divide the cytoplasm into separate cells. Zygomycetes produce hyphae without septa and make up less
page 717 than 1% of known fungal species. page 728
Some fungi, such as yeasts, do not produce hyphae. page 717 The glomeromycetes are a group of fungi of low diversity but
tremendous ecological importance because of their association
Most fungi feed on dead organic matter. page 718
with plant roots. page 728
Fungi are critical elements of the carbon cycle, converting dead
Most fungi belong to the Dikarya (ascomycetes and
organic matter back into carbon dioxide and water. page 718
basidiomycetes), which form septa along hyphae. During the
Many fungi feed on living animals and plants, causing diseases. heterokaryotic stage, these fungi produce cells that contain two
page 718 haploid nuclei, one from each parent. page 728
Fungi have repeatedly evolved mutually beneficial relationships Ascomycetes include wood-rotting fungi, many ectomychorrizal
with plants and animals. page 720 species, plant and animal pathogens, the fungal partner in most
Lichens are stable associations between a fungus and a lichens, and baker’s and brewer’s yeasts. page 729
photosynthetic microorganism that look, function, and even Basidiomycetes include familiar toadstools and puffballs, as well
reproduce as single organisms page 720 as plant pathogens page 732
Genetically determined mating types prevent self-fertilization 7. Draw the life cycle of a basidiomycete, and indicate the
in many fungi. page 725 heterokaryotic stage.
Asexual fungal species have mechanisms for generating genetic 8. Name and describe several key innovations in the
diversity; these are thought to involve fusion of haploid nuclei, evolutionary history of fungi that allowed them to move from
followed by crossing over during mitosis and chromosome loss. water to land.
page 726 9. Explain how the evolution of vascular plants has
provided opportunities for fungal diversification.
34.3 Other than animals, fungi are the most diverse
group of eukaryotic organisms.
Log in to to check your answers to the Self-
About 75,000 fungal species have been formally described, but Assessment questions, and to access additional learning tools.
total diversity may be as high as 5 million species. page 726
Predator–Prey
A Game of Life and Death
In his 1850 poem In Memoriam A.H.H., Alfred, Lord Northwest. When sea star numbers fall, mussel numbers
Tennyson wrote of “Nature, red in tooth and claw.” increase. The mussels crowd out other species, such as
The phrase has endured as a powerful description barnacles and seaweed, which compete for space on the
of the brutality of wild nature. Thanks to nature rocks. The result is a drop in the overall number of species in
documentaries and our human fascination with wild that habitat.
animals, most of us have witnessed plenty of images of The same patterns have been found among birds of prey
this red-toothed nature: a lion chasing down a zebra, a in the Italian Alps. These raptors—including the goshawk
hawk scooping a mouse into its talons, a shark sinking and four types of owl—are the top predators of their food
its teeth into a sea lion. chains. Spanish researchers found that locations where the
Predator–prey interactions are important in every birds were present had a greater diversity of trees, birds,
ecosystem on Earth. After all, every living animal can be and butterflies than did
classified as either “predator” or “prey”—and often, both comparable control sites.
labels apply. To a fly, a toad is a fearsome predator. To a One reason that Predator–prey
snake, that same toad may be choice prey. the predator and prey dynamics have
Very few species enjoy the luxury of having no populations eventually
natural predators; these are called top predators. For achieve a delicate balance is influenced both
the vast majority of animals, the threat of predation is that both are well adapted the evolution of
simply a fact of life. Not surprisingly, that threat has been to their roles. Predation
a powerful evolutionary force. Predator–prey dynamics has exerted powerful individual organisms
have influenced both the evolution of individual evolutionary pressure that and the shape of the
organisms and the shape of the ecosystems in which has influenced anatomy and
they live. physiology over the long ecosystems in which
On Isle Royale, an island in Lake Superior, ecologists term. That pressure has they live.
have been studying moose and wolves since 1958 in the shaped predators by giving
longest-running study of a single predator–prey system them claws, teeth, venom,
in the world. The moose arrived on the island about 100 and powerful muscles for hunting prey.
years ago, presumably by swimming about 15 miles from Of course, predation pressure has also shaped the form
the nearest shoreline. They arrived to find a predator- and function of prey. Some animals, including some insects
free paradise, and the moose population quickly and frogs, have evolved toxins to deter would-be predators.
exploded. Then, about 1950, a pair of wolves crossed an These toxic species often exhibit warning colors that tell the
ice bridge to Isle Royale. As the wolf population grew, predators to steer clear. Other prey animals have evolved
the moose population declined, until a delicate balance camouflage colors and forms to help them hide from hungry
was established. carnivores. Still others have developed protective behaviors,
As a predator population grows, the prey population such as living together in herds for security against
shrinks—a seemingly logical relationship. But predator– predation.
prey interactions are complex and sometimes even Often, predator and prey evolve in lockstep, driving
counter-intuitive. Removing a top predator can actually each other’s adaptations. Clams may have evolved thicker
reduce biodiversity. Sea stars, for instance, prey on shells to protect themselves from hungry crabs. In turn, the
mussels in the rocky intertidal zone of the Pacific crabs evolved larger, stronger claws for cracking clamshells.
736
Wolves and moose on Isle Royale. The
populations of this predator and prey have
Canada been studied for more than 50 years, and the
Minnesota Isle Royale two have achieved a delicate balance over
time. Sources: (wolf) Samuel R. Maglione/Science
Source; (moose) Ron Erwin/age fotostock; (graph)
Data from J. A. Vucetich and R. O. Peterson, 2012, “The
Wisconsin
population biology of Isle Royale wolves and moose: an
Michigan
overview,” www.isleroyalewolf.org.
50 2500
Wolves
40 Moose 2000
Number of wolves
Number of moose
30 1500
20 1000
10 500
0
1959 1969 1979 1989 1999 2009
Year
This pattern of back-and-forth change is often described as When predators are nearby, prey species experience
an evolutionary arms race. And it has happened time and fear and anxiety. Stress hormones produced by prey animals
time again. can influence an animal’s physiology in a number of ways.
The interactions between eaters and eaten have also In snowshoe hares, levels of the stress hormone cortisol
influenced the evolution of physiological systems. The skills increase when predators such as lynx and coyote are
that a predator needs to hunt its prey and that its prey needs plentiful. The hormones trigger behaviors, such as alertness
to escape depend in large part on adaptations of their sensory and fearfulness, which help the hares avoid becoming a
systems, musculoskeletal systems, nervous systems, and lynx’s lunch. But the behavioral benefit comes at a cost:
even their circulatory and respiratory systems. Research has shown that stressed hares give birth to fewer
Consider sensory systems. Animals rely on visual, and smaller offspring.
auditory, tactile, and chemical stimuli to warn them of In short, predation has left a physical imprint on both
approaching predators—or to guide them to suitable prey. A predator and prey, from nose to tail—their body shapes, their
bat relies on sonar to locate insects. A spider responds to the behaviors, their physiology, even their muscle fibers have
flutter of silk when an insect becomes ensnared in its web. been influenced over time by predator–prey interactions.
Gazelles are always attentive, watching and listening for In the modern world, our own species, Homo sapiens,
signs of a cheetah or lion in the grass. occupies a unique position at the top of the food web. While
737
humans are occasionally killed by animals such as bears or that it was our hunting of other animals that led us to
sharks, we are, for the most part, no longer constrained by evolve big brains and the ability to work together. Perhaps
the fear of predation by other species. But it wasn’t always both factors played a role. Either way, the importance of the
so. Some scientists have proposed that fear of predation predator–prey system can’t be ignored. To understand our
among early humans led to the evolution of cooperative roots, it seems, we must take a good look at nature, red in
social behavior and large brains. Others have theorized tooth and claw.
? CASE 7 QUESTIONS
Special sections in Chapters 35– 41 discuss the following questions related to Case 7.
1. What body features arose as adaptations for successful predation? See page 742.
2. How have sensory systems evolved in predators and prey? See page 771.
3. How do different types of muscle fiber affect the speed of predators and prey?
See page 797.
4. How does the endocrine system influence predators and prey? See page 821.
5. How do hormones and nerves provide homeostatic regulation of blood flow as well as
allow an animal to respond to stress? See page 843.
6. Does body temperature limit activity level in predators and prey? See page 854.
7. Can the loss of water and electrolytes in exercise be exploited as a strategy to hunt
prey? See page 880.
738
CHAPTER 35
Animal Nervous
Systems
Core Concepts
35.1 Animal nervous systems
allow organisms to sense and
respond to the environment,
coordinate movement, and
regulate internal functions of
the body.
35.2 The basic functional unit of the
nervous system is the neuron,
which has dendrites that
receive information and axons
that transmit information.
35.3 The electrical properties
of neurons allow them to
communicate rapidly with one
another.
35.4 Animal nervous systems can
be organized into central and
peripheral components.
Thomas Deernick, MCMIR/Getty Images.
739
740 SECTION 35.1 N E RVO U S S YS T E M F U N C T I O N A N D E VO LU T I O N
FIG. 35.3 Animal nervous systems. (a) Sea anemones have a nerve net; (b) flatworms have paired ganglia; (c) earthworms, (d) insects,
(e) squid, and (f) frogs have a brain.
In earthworms, paired ganglia, each made up of many been retained over the course of evolution to code and reliably
interneurons, are located in each of the body’s segments transmit information. The ability to receive sensory information
(Fig. 35.3c). These segmental ganglia help to regulate the muscles from the environment, and transmit and process this information
within each body segment that move the earthworm’s body. Paired within a nervous system, is therefore shared across a wide diversity
ganglia near the head regulate the activity of motor neurons that of animal life, contributing to the success of multicellular animals.
control movements of the mouth for feeding. Ganglia serve to
regulate key processes in local regions and organs of the animal’s ? CASE 7 PREDATOR–PREY: A GAME OF LIFE AND DEATH
body. For example, local ganglia assist in processing information What body features arose as adaptations for successful
from the eyes (Chapter 36) or control the digestive state of an predation?
animal’s gut (Chapter 40). The homeostatic regulation of internal A notable feature of most animal nervous systems is that nervous
physiological processes is a fundamental role of nervous systems. system tissue, including specialized sense organs such as eyes,
Centralized collections of neurons forming a brain are becomes concentrated at one end of the body. For example, the
present in earthworms and other annelid worms (Fig. 35.3c), paired ganglia and eyespot of the flatworm are located at one end
insects (Fig. 35.3d), and mollusks (Fig. 35.3e). Sense organs also of its body, as are the brain and sense organs of the earthworm,
developed in the head region, from eyespots in flatworms that squid, and insect, as shown in Fig. 35.3. The concentration of
respond to light to more sophisticated image-forming eyes in nervous system components at one end of the body, defined as
octopus and squid. The evolution of a brain in these invertebrate the “front,” is referred to as cephalization. Cephalization is a key
animals enabled them to learn and perform complex behaviors. feature of the body plan of most multicellular animals, including
Many of these nervous system capabilities are shared with all vertebrates.
vertebrate animals. Cephalization evolved independently multiple times in
In common with certain invertebrates, such as arthropods different animal groups and is therefore thought to confer
and cephalopod mollusks, the evolution of a brain is a key feature certain advantages. Cephalization is thought be an adaptation for
of vertebrate nervous systems (Fig. 35.3f). It enabled these forward locomotion because it allows animals to take in sensory
organisms to evolve complex behaviors that rely on learning and information from the environment ahead of them as they move
memory and, in certain vertebrates, the ability to reason. At the forward. In addition, the nearness of the sensory organs to central
same time, animal brains became increasingly complex in the ganglia or the brain makes it possible to process this information
number of nerve cells they contain (fruit fly, about 0.25 million; quickly to enable a suitable behavioral response. As the quality
cockroach, about 1 million; mouse, about 75 million; humans, and amount of sensory information taken in increased, brain size
about 100 billion), in the number of connections between and complexity increased. Cephalization is also considered to be
neurons, and in the variety of shapes and sizes of nerve cells and an adaptation for predation, allowing animals to better detect and
specialized connections between them. capture prey.
Although animal nervous systems differ in organization and Although cephalization is a feature of many animals, it has
complexity, their nerve cells have fundamentally similar molecular been particularly well studied in vertebrates. In vertebrates, the
and cellular features and use fundamentally the same mechanisms brain, many sense organs, and mouth are all located in the head.
to communicate with neighboring cells. These mechanisms have Vertebrates also evolved several novel features, including a jaw,
CHAPTER 35 A N I M A L N E RVO U S S YS T E M S 743
teeth, and tongue. These are all thought to be adaptations for signals from other nerve cells or, in the case of sensory nerves,
predation, or more generally the acquisition and processing of food. from specialized sensory endings. These signals travel along the
As a result of evolutionary selection for enhanced sensory dendrites to the neuron’s cell body. At the junction of the cell
perception and the ability to respond to important cues in the body and its axon, the axon hillock, the signals are summed. If
environment, the brain, sensory organs, and nervous system the sum of the signals is high enough, the neuron fires an action
of many animals are complex in their organization. These are potential, or nerve impulse, that travels down the axon. An action
linked to more sophisticated abilities that allow for a broad range potential is a brief electrical signal transmitted from the cell body
of behaviors. These abilities are critical to the success of both along one or more axon branches.
predators and prey and underlie the complex interactions that Axons generally transmit signals away from the nerve’s cell
occur among members of a species when they mate, reproduce and body. The end of each axon forms a swelling called the axon
disperse, and care for their young. terminal. An axon terminal communicates with a neighboring
cell through a junction called a synapse. A space, the synaptic
cleft, separates the end of the axon of the presynaptic cell and the
35.2 NEURON STRUCTURE neighboring postsynaptic cell. The synaptic cleft is commonly only
about 10 to 20 nm wide.
We have seen that nerve cells can be classified as sensory neurons, How does a signal cross the synaptic cleft? Molecules called
interneurons, or motor neurons. Yet all three receive and transmit neurotransmitters convey the signal from the end of the axon
information, and all three share the same basic organization. to the postsynaptic target cell. The arrival of a nerve signal at the
Neurons have extensions that receive information and relay it axon terminal triggers the release of neurotransmitter molecules
to the cell body. They also have other extensions that transmit from vesicles located in the terminal. The vesicles fuse with the
information away from the cell body. Although all neurons share axon’s membrane, releasing neurotransmitter molecules into
this basic plan, they differ remarkably in size and number of the synaptic cleft. The molecules diffuse across the synapse
extensions, according to their specific function. and bind to receptors on the plasma membrane of the target
cell. The binding of neurotransmitters to these receptors causes
Neurons share a common organization. a change in the electrical charge across the membrane of the
Neurons all share some basic features. These include a cell body receiving postsynaptic cell, continuing the signal in the second
from which emerge two kinds of fiberlike extension, dendrites cell. Most neurons communicate by the hundreds to thousands
and axons (Fig. 35.4). These extensions are the input and output of synapses that they form with other cells. The massive number
ends of the nerve cell. Both types of cellular extension can be of interconnections enables the formation of complex nerve cell
highly branched, enabling neurons to communicate over large circuits and the transmission of information from one circuit to
distances with many other cells. A neuron’s dendrites receive others in the nervous system.
FIG. 35.4 Neuron organization. Nerve cells typically have dendrites that receive signals and axons that transmit signals.
1 Stimuli are
received by 2 Synaptic stimuli are Synapse
the dendrites
summed at the axon
and cell body.
hillock, where an action Axon Postsynaptic Synaptic cleft
potential is triggered if terminal cell
the sum of the arriving
signals is high enough.
Neuro-
transmitter
Axon
hillock
tial
Action poten Receptor
Presynaptic
Nucleus cell
Axon Postsynaptic
Cell body membrane
3 Action potentials are conducted to the axon terminal,
where they cause the release of neurotransmitters. These
bind to receptors on the postsynaptic cell membrane,
creating a new signal in the postsynaptic neuron.
Dendrites
744 SECTION 35.2 N E U RO N S T RU C T U R E
from the blood into the brain. This barrier prevents pathogens and by a wire. In this section, we discuss the electrical properties
toxic compounds in the blood from entering the brain. Because of neurons and how signals are propagated along neurons. We
nerve cells have limited capacity to regenerate after damage, also describe special features of some neurons that enable even
protection of the brain and spinal cord is critically important. faster signal transmission and more rapid responses by animals to
Nevertheless, lipid-soluble compounds such as alcohol and certain environmental cues.
anesthetics readily diffuse across the blood–brain barrier, and
thus they can affect the functioning of the brain and an animal’s The resting membrane potential is negative and results
mental state. They can also damage and even destroy neurons. in part from the movement of potassium ions.
During development, glial cells help orient neurons as they The inside surface of a neuron carries an electrical charge that is
develop their connections. They also provide electrical insulation due to the presence of charged ions, and the same is true of the
to vertebrate neurons that allows nerve signals to be transmitted outside surface. However, the electrical charge on the inside and
rapidly, a topic we discuss next. the electrical charge on the outside are not the same because
unequal numbers of charged ions are located inside and outside
the cell. When no signal is present, there are more negative ions
35.3 NEURON FUNCTION inside the cell, and the inside is thus negatively charged relative to
the outside.
We have seen that neurons send signals from one neuron to The charge difference between the inside and the outside of a
the next by releasing neurotransmitters that diffuse across the neuron due to differences in charged ions is the cell’s membrane
synaptic cleft and bind to receptors. In Chapter 9, we discussed potential, measured in volts. Other cells also have membrane
that this is a general mechanism of cell communication: A potentials, but only nerve cells and muscle cells respond to
signaling cell releases a chemical signal that binds to a receptor changes in their membrane potential. Therefore, these cells are
on a receiving cell. However, once the receptor has bound the considered electrically excitable.
neurotransmitter and is activated, in neurons the signal is not The key to producing an electrical signal in a nerve cell is the
propagated by a chemical signal diffusing through the cell, which movement of positively and negatively charged ions across the cell
would be much too slow. Instead, as we have seen, neurons send membrane. This movement creates a change in electrical charge
signals electrically from one end of the cell to the other. across the membrane that constitutes the electrical signal.
All neurons are electrically excitable cells that transmit Let’s first consider the membrane potential when the neuron
information in the form of electrical signals. Nerve signals is at rest and no signal is being received or sent. Under these
travel at high speeds, up to 200 m/s (450 mph). Although the conditions, the cell’s membrane voltage is negative on its inside
speed of nerve signals is fast by biological standards, it is slow relative to its outside (Fig. 35.7). The resting membrane potential
by comparison with the speed of electrical signals transmitted of the cell is said to be polarized. This means that there is a
FIG. 35.7 Neuron resting membrane potential. The resting potential of a neuron is negative and results primarily from the movement of K+ ions
out of the cell.
Extracellular
fluid
0
+
K+ movement
Voltage (mV)
0
-40 +40
+ + + + + + + + + + + + + + + + + + + + + -80
V +80
Resting potential
–70
– – – +– – – – – – – – – – – – – – – – – –
K channel Na+–K+ pump
–
K+ Na+
Cytoplasm Time
The Na+–K+ pump moves Na+ K+ channels allow K+ ions to Membrane potential
ions out of the cell and K+ “leak” out of the cell, resulting can be measured with
ions into the cell. in a negative resting potential small glass electrodes.
on the inside relative to the
outside of the cell.
746 SECTION 35.3 N E U RO N F U N C T I O N
buildup of negatively charged ions on the inside surface of the How is the action potential generated? At the axon hillock,
cell’s plasma membrane and of positively charged ions on its the summed membrane depolarization of the cell’s dendrites
outer surface. The negative voltage across the membrane at rest causes voltage-gated sodium channels to open, allowing
is referred to as the cell’s resting membrane potential. The Na1 ions to enter the cell. Voltage-gated channels open and
resting membrane potential ranges from –40 to –85 millivolts close in response to changes in membrane potential (Fig. 35.8;
(mV) depending on the type of nerve cell and most commonly Chapter 9). As Fig. 35.8 shows, they play a key role in how
is about –65 to –70 mV. The voltage of the cell’s interior can neurons fire action potentials.
be measured with respect to its outside voltage by small glass The influx of Na1 causes a flow of positive charge, like a
electrodes on the inside and outside of the cell. current, along the inside of the cell, toward more negatively
At rest, nerve (and muscle) cells have a greater concentration charged nearby regions. This flow of charge is reduced at longer
of sodium (Na1) ions outside the cell than inside, and a greater distances and quickly dissipates so that the membrane potential
concentration of potassium (K1) ions inside the cell than outside. returns to a resting state unless additional excitatory stimuli
This distribution of ions results in part from the action of the further depolarize the membrane.
sodium-potassium pump, discussed in Chapter 5. The sodium- If the excitatory signal is strong enough to depolarize the
potassium pump uses the energy of ATP to move three Na1 ions membrane of the nerve cell body to a voltage of approximately
outside the cell for every two K1 ions moved in (Fig. 35.7). The 15 mV above the resting membrane potential (about –55 mV),
action of the pump makes the inside of the cell less positive, and the nerve fires an action potential at the axon hillock. An action
therefore more negative, than the outside of the cell. potential is a rapid, short-lasting rise and fall in membrane
The exact value of the resting membrane potential, however, potential, as shown in Fig. 35.8. The critical depolarization
depends on the movement of K1 ions back out of the cell by voltage of –55 mV required for an action potential is the cell’s
passive diffusion through potassium ion channels (Fig. 35.7). As threshold potential. Nerve cells in different animals have
discussed in Chapter 5, ion channels are protein pores embedded slightly different resting and threshold potentials, but all operate
in the cell membrane. The most important ions that move across similarly with respect to firing an action potential. When
the cell membrane are sodium (Na1), potassium (K1), chloride the threshold potential is exceeded, the nerve fires an action
(Cl2), and calcium (Ca21). When a nerve cell is at rest, more K1 potential in an all-or-nothing fashion. This means that once the
ion channels are open, giving K1 greater permeability compared threshold potential has been exceeded, the magnitude of the
with all other ions. As a result, K1 ions move out of the cell. action potential is always the same and is independent of the
The movement of K1 ions from the inside to the outside causes strength of the stimulating input. At this point, a rapid spike in
positive ions to build up on the outside of the cell, whereas voltage to approximately 140 mV occurs over a very brief time
negatively charged ions (largely proteins) remain on the inside of period of 1 to 2 msec.
the cell, making the inside of the nerve cell more negative than An action potential results from dramatic changes in the
its outside. state of voltage-gated Na1 and voltage-gated K1 channels in the
The relative proportion of ions does not by itself determine axon membrane. As the cell membrane crosses its threshold
the resting membrane potential. This is because the number of potential, a large number of voltage-gated Na1 channels
charged ions that build up at the cell’s surface is a tiny fraction of suddenly open, allowing Na1 ions to rush inside the cell. The
the total number of charged ions and proteins located inside and rise in voltage that results causes additional voltage-gated Na1
outside the cell. It is the movement of K1 ions relative to other channels to open. This is an example of positive feedback, in
ions, particularly Na1 ions, that largely determines the resting which a signal (depolarization) causes a response (open voltage-
membrane potential. gated Na1 channels) that leads to an enhancement of the signal
(more depolarization) that leads to an even larger response
Neurons are excitable cells that transmit information (more open voltage-gated Na1 channels).
by action potentials. During the rising phase of the action potential, voltage-gated
When a nerve cell is excited, its membrane potential becomes K1 channels also begin to open, but these channels are slow
less negative—that is, the inside becomes less negative, or more to activate relative to the rapidly opening voltage-gated Na1
positive, than the outside of the cell. The increase in membrane channels. As a result, relatively few K1 ions leave the cell and
potential is therefore referred to as a depolarization of the the cell membrane potential continues to rise due to the large
membrane. This depolarization does not occur over the entire number of Na1 ions entering the cell.
cell at once. Rather, it starts at the terminal end of the dendrite, As you can see from Fig. 35.8, the rising phase of the action
in response to neurotransmitter binding to membrane receptors, potential (rapid depolarization) is followed by the falling phase
and travels to the cell body, losing strength along the way. If the (rapid repolarization). What causes this sudden reversal of the
depolarization is still strong enough at the axon hillock of the membrane potential? There are two important factors. First,
cell body, the cell fires an action potential that carries the signal voltage-gated Na1 channels begin to close once the membrane
from the cell body to the terminal ends of the axon. potential becomes positive. Second, voltage-gated K1 channels
CHAPTER 35 A N I M A L N E RVO U S S YS T E M S 747
FIG. 35.8 An action potential. An action potential results from the opening and closing of voltage-gated ion channels and allows the membrane
potential briefly to be positively charged.
0 Voltage-gated
Na+ channel
Voltage-gated
K+ channel
– – –
5
Membrane potential (mV)
+ + +
1 Summed input
depolarizes the cell
Threshold of membrane at the axon – – –
excitation hillock above the
threshold potential.
–70
Resting potential
1 2 3
Time (msec)
748 SECTION 35.3 N E U RO N F U N C T I O N
continue to open in response to the change in voltage. Because The duration of the refractory period varies for different kinds of
they are slower to respond than the voltage-gated Na1 channels, nerve cell but limits a nerve cell’s fastest firing frequency to less
the membrane voltage peaks and then falls as K1 ions diffuse than 200 times per second. Most nerve cells fire at lower rates.
out of the axon through the open voltage-gated K1 channels. It might seem that many Na1 and K1 ions need to diffuse
The voltage inside the axon does not return immediately to across the axon membrane to produce an action potential.
the resting membrane potential. Instead, it briefly falls below However, only about 1 in 10 million Na1 and K1 ions need to cross
the resting potential (in what is known as hyperpolarization the membrane. Thus, enough ions are always available to generate
or undershoot), then returns to the resting potential after repeated action potentials.
another few milliseconds as K1 channels close to restore the The nature of the action potential, which is both all-or-
resting concentration of Na1 and K1 ions on either side of the nothing and uniform in its electrical features, means that the
cell membrane. The continuous action of the sodium-potassium action potential itself contains little information. Most neurons
pumps also helps to reestablish the resting membrane code information by changing the rate and timing of action
potential. potentials. Generally, a higher firing frequency codes for a more
The period during which the inner membrane voltage intense stimulus, such as a brighter light or louder noise, or
falls below and then returns to the resting potential is the a stronger signal transmitted by the nerve cell to other cells
refractory period (Fig. 35.8). During the refractory period, it contacts.
a neuron cannot fire a second action potential. The refractory
period results in part from the fact that when voltage-gated Neurons propagate action potentials along their axons
Na1 channels close, they require a certain amount of time by sequentially opening and closing adjacent Na+ and
before they will open again in response to a new wave of K+ ion channels.
depolarization. In addition, open voltage-gated K1 channels Once initiated, an action potential propagates along the axon (Fig.
make it difficult for the cell to reach the threshold potential. 35.9). The local membrane depolarization initiated at the axon
FIG. 35.9 Propagation of action potentials. Local depolarization of the membrane triggers the opening of nearby voltage-gated Na+ channels,
producing an action potential that spreads along the membrane. The action potential moves in only one direction (shown here as left to
right) because of the refractory period.
– – – + + + + + + – – – – – – –
Cytoplasm
– – – + + + + + + – – – – – – –
+ + + – – – – – – + + + + + + +
Depolarizing Resting
K+
+ + + + + + + + – – – – + + + +
– – – – – – – – + + + + – – – –
– – – – – – – – + + + + – – – –
+ + ++ + + + ++ ++ – – – – + + + +
FIG. 35.11
Eye
potential? Tentacle
Giant
axon
BACKGROUND In order to record the voltage of the inside of
a nerve cell relative to the outside, a small electrical recording
device called a microelectrode can be inserted into a neuron. The
technique is more easily performed on large cells, such as the
squid giant axon. This axon, as its name suggests, is quite large, b.
measuring 0.5 mm in diameter (Fig. 35.11a). The large diameter A reference
electrode is
of the axon allows electrical signals to be propagated to the placed
0
-40 +40
muscles very quickly. Vertebrate neurons are much smaller; they -80
V +80 outside the
rely on myelin sheaths rather than large size for rapid conduction cell in
A microelectrode contact with
of electrical signals. is inserted into an the solution
axon. bathing the
EXPERIMENT In 1939, two British neurophysiologists, axon.
Alan Hodgkin and Andrew Huxley, inserted a microelectrode
into a squid giant axon and placed a reference electrode on
the outside (Fig. 35.11b). They then used a separate set of
Axon
electrodes (not shown) to depolarize the cell to threshold,
triggering an action potential. Axon
membrane
RESULTS Fig. 35.11c is a trace from Hodgkin and Huxley’s 1939
paper showing the resting membrane potential and the course of
an action potential recorded by the electrode inside a giant squid c.
axon. Note that the resting potential (–45 mV in squid) is negative +40
on the inside of the axon relative to the outside, and that the
action potential is a rapid spike in potential, with the inside of the
Voltage (mV)
cell quickly becoming positive, then negative again. The large size 0
of the spike was a surprise.
750
CHAPTER 35 A N I M A L N E RVO U S S YS T E M S 751
FIG. 35.12 A chemical synapse. Neurons communicate with other neurons or with muscle cells by releasing neurotransmitters at a synapse.
1 Synaptic
transmission begins
with action potential
conduction to the
axon terminal.
Axon
terminal
Ca2+ channel
2 Depolarization
of the axon Ca2+
terminal opens
voltage-gated
5 After inactivation,
Ca2+ channels. neurotransmitters are
re-absorbed into the
presynaptic terminal and
stored in vesicles until the
Acetylcholine next action potential arrives.
(neurotransmitter)
Presynaptic
3 Vesicles respond membrane
by fusing with the
presynaptic Synaptic
membrane, releasing cleft
neurotransmitters
into the synaptic
cleft.
Postsynaptic
membrane
Na+
Receptor
Chemical synapses are by far the more common type of with the presynaptic membrane and release neurotransmitter
synapse in animal nervous systems. The signals conveyed molecules into the synaptic cleft by exocytosis. The
at chemical synapses are neurotransmitters contained neurotransmitters diffuse rapidly across the cleft and bind to
within small vesicles in the axon terminal. When an action postsynaptic membrane receptors of the neighboring cell. The
potential reaches the end of an axon (Fig. 35.12), the resulting binding of neurotransmitters opens or closes ion channels,
depolarization induces voltage-gated Ca21 ion channels to open. causing a change in the postsynaptic cell membrane potential
These channels are found only in the axon terminal membrane. that allows the signal to propagate along the next neuron.
Because of their higher concentration outside the cell, Ca21 These postsynaptic membrane receptors are called ligand-
ions diffuse through these channels into the axon terminal. gated ion channels because when the neurotransmitter binds
In response to the rise in Ca21 concentration, the vesicles fuse as a ligand it causes the ion channel to open. This allows specific
752 SECTION 35.3 N E U RO N F U N C T I O N
FIG. 35.14 Summation of excitatory and inhibitory postsynaptic potentials. (a) Widely spaced EPSPs do not sum. Other EPSPs and IPSPs can
be summed (b) in time or (c) space, or even (d) cancel each other out.
a. b. c. d.
No summation: Multiple EPSPs Temporal summation: Spatial summation: Single Cancellation: An EPSP and an
widely spaced in time do not Multiple EPSPs arrive quickly EPSPs at two or more different IPSP may cancel each other so
set off an action potential. at a single synapse and set synapses set off an action no action potential is set off.
off an action potential. potential.
Presynaptic axon Postsynaptic cell
EPSP
EPSP IPSP
3 EPSPs, No Summation 3 EPSPs, Temporal Summation 3 EPSPs, Spatial Summation EPSP and IPSP
+40
Membrane potential (mV)
Resting Threshold
potential potential
–55
–70
0
EPSP EPSP EPSP EPSP EPSP EPSP EPSP IPSP
Time EPSP
EPSP EPSP IPSP
EPSP EPSP
EPSP
EPSP
The role of temporal and spatial summation is explored further in Acetylcholine is one of the key neurotransmitters produced
Chapter 36. in a variety of nerve cells. It is the excitatory neurotransmitter
More than 25 neurotransmitters are now recognized, and released by motor neurons to stimulate muscle fibers
more are likely to be discovered. The amino acids glutamate (Fig. 35.15). All vertebrate motor synapses rely on acetylcholine
(excitatory), glycine (inhibitory), and GABA (inhibitory) are key and are therefore excitatory only. The release of acetylcholine
neurotransmitters that operate at synapses in the brain. The produces a depolarization of the muscle cell membrane by
related amino acid derivatives dopamine, norepinephrine, and opening ligand-gated Na1 channels, causing the muscle to
serotonin are also neurotransmitters acting in the brain. Simple contract (Chapter 37).
peptides serve as neurotransmitters for sensory neurons. More
recently, two gases, nitrous oxide and carbon monoxide, have been j Quick Check 4 Acetylcholinesterase is the enzyme that breaks
discovered to function as messengers between some nerve cells down and inactivates acetylcholine. Some nerve gases used
even though they do not behave as standard neurotransmitters as chemical weapons block acetylcholinesterase. What effect
that bind to membrane receptors. would such nerve gases have on muscle contraction?
754 SECTION 35.4 N E RVO U S S YS T E M O RG A N I Z AT I O N
that extends from the brain. Nerves are composed mainly of axons
FIG. 35.15 Vertebrate motor endplate. The motor endplate is from many different nerve cells. For example, the optic nerve
an excitatory synapse between a motor nerve and contains axons that travel from nerve cells in the eye to the brain.
a muscle cell; acetylcholine is the neurotransmitter. Sensory and motor nerves make up the peripheral nervous
Source: David B. Fankhauser, Ph.D., Professor of Biology and system (PNS). These nerves communicate with the central
Chemistry, University of Cincinnati, Clermont College. nervous system (CNS), made up of the brain, a main nerve cord,
or—in the case of animals such as flatworms that lack a brain—
Motor neuron axon Muscle cell
centralized information-processing ganglia. Sensory organs at or
near the body surface transmit information by afferent neurons,
which send information toward the CNS. After processing the
information, the ganglia and brain send signals through efferent
neurons, which send information away from the CNS. The signals
delivered by efferent neurons in peripheral nerves coordinate
the activity of muscles and glands in different regions of the
animal’s body. This organization ensures that an animal achieves
a coordinated behavioral and physiological response to the stimuli
received from its environment, which is fundamental to its ability
to maintain homeostasis. Among multicellular animals with
nervous systems, only the diffuse nerve nets of cnidarians lack
Acetylcholine binds to muscle membrane
receptors, causing a depolarization of the defined central and peripheral components.
muscle cell and contraction. The peripheral nervous system also includes interneurons and
ganglia that integrate and process information in local regions of
the animal’s body. For example, vertebrates and invertebrates have
ganglia that lie outside segments of their primary nerve cord that
coordinate localized function within a region of their body, such as
35.4 NERVOUS SYSTEM the muscles that control the limb of a running insect, the muscles
ORGANIZATION that allow an earthworm to dig, or the secretory activity of a
particular region of the digestive system of a fish or a mammal.
The brain is the body’s command center: It receives sensory However, the bulk of information processing, particularly in
information from the eyes, ears, nose, tongue, skin, and internal animals that exhibit a greater capacity for learning and memory,
organs, and sends instructions to the rest of the body. Up to this occurs in the CNS.
point, we have examined how individual neurons send signals to Let’s look more closely at the organization of the vertebrate
other nerve and muscle cells. How are these neurons organized in nervous system. The central nervous system of vertebrates
the body to sense stimuli, process them, and issue an appropriate includes both the brain and spinal cord (Fig. 35.16). The spinal
response? How does the brain coordinate the movement of limbs cord is a central tract of neurons that passes through the vertebrae
necessary to walk or run, and adjust heart rate and breathing to transmit information between the brain and the periphery
in response to exercise? In this section, we look at how the of the body. The vertebrate spinal cord is divided into segments,
nervous system is organized to allow the brain and the body to each controlling body movement in a particular region along
communicate with each other. the animal’s length. Each spinal cord segment contains axons
from peripheral sensory neurons, a set of interneurons, and a set
Nervous systems are organized into peripheral of motor neuron cell bodies. These are distinct from, but often
and central components. associated with, the ganglia mentioned above that lie outside the
As animals evolved the ability to sense and coordinate responses spinal cord.
to increasingly complex stimuli, their nervous systems became In humans and other vertebrate animals, the peripheral
organized into peripheral and central components (Fig. 35.16). Your nervous system is organized into left and right sets of cranial
eyes, receptors for the sense of touch, and other sensory organs are nerves located within the head and spinal nerves running from
located on the surface of the body, where they can receive signals the spinal cord to the periphery. Most of the cranial nerves and
from the environment. In contrast, the brain, centrally located all of the spinal nerves contain axons of both sensory and motor
ganglia, and a main nerve cord are located in the interior. neurons. Cranial nerves link specialized sensory organs (eyes, ears,
Nerves form the lines of communication between these tongue) to the brain. Cranial nerves also control eye movement,
nervous system structures. In general, nerve cell bodies are facial expression, speech, and feeding. Some cranial nerves, such
grouped together in sensory organs, ganglia, and a main nerve cord as the olfactory and optic nerves, contain only sensory axons.
CHAPTER 35 A N I M A L N E RVO U S S YS T E M S 755
FIG. 35.16 Human central (yellow) and peripheral (blue) nervous systems.
Spinal cord
Spinal nerves
Axons
Blood
vessels
Connective
tissue
Structure of a nerve
Spinal nerves exit from the spinal cord through openings located sensing and responding to external stimuli, whereas involuntary
between adjacent vertebrae to thread through the trunk and limbs components typically regulate internal bodily functions. Both
of an animal’s body. These nerves receive sensory information nervous system components are found in invertebrate and
from receptors in nearby body regions along the length of the body vertebrate animals.
and send motor signals from the spinal cord back to those regions In insects and crustaceans, for example, nerve circuits from
(Fig. 35.16). the involuntary component regulate the animal’s digestive
system. Nerve circuits connecting sensory structures such as the
Peripheral nervous systems have voluntary antennae and eyes to the animal’s brain and muscles are part of
and involuntary components. the voluntary system.
As bodies with distinct internal organ systems evolved, two In vertebrates, the peripheral nervous system is divided into
separate components of the nervous system emerged. When somatic (voluntary) and autonomic (involuntary or visceral)
a gazelle senses a predator, some nerve circuits send a signal to components. The somatic nervous system is made up of sensory
run, an action that is under conscious control, while others signal neurons that respond to external stimuli and motor neurons
the heart to beat faster and blood vessels supplying muscles to that synapse with voluntary muscles. This system is considered
dilate, actions that occur unconsciously. Conscious reactions are voluntary because it is under conscious control. However, many
under the control of the voluntary component of the nervous reflexes are controlled lower in the spinal cord (discussed in the
system, and unconscious ones are under the control of the following section) or by the brainstem, independent of conscious
involuntary component. Voluntary components mainly handle control by the central nervous system.
756 SECTION 35.4 N E RVO U S S YS T E M O RG A N I Z AT I O N
FIG. 35.18 Temperature regulation by negative feedback in (a) a house and (b) a mammal. In negative feedback, a response (such as heat)
opposes the stimulus (cold), leading to a stable state (a steady temperature).
a. b.
+ +
+ +
Muscles
Effector Heater
(shivering)
– –
physiologist Claude Bernard, who is often credited with fluctuates. Nerve cells in the hypothalamus (located in the base
bringing the scientific method to the field of medicine. The term of the brain) act as the body’s thermostat (Fig. 35.18b). When a
“homeostasis” was coined by the American physiologist Walter decrease in the temperature in the environment causes a drop
Cannon, whose book The Wisdom of the Body (first published in in body temperature, the lowered body temperature signals the
1932) popularized the concept. hypothalamus to activate the somatic nervous system to induce
Maintaining steady and stable conditions takes work in shivering and the production of metabolic heat, as discussed in
the face of changing environmental conditions. That is, a cell Chapter 40. At the same time, the hypothalamus activates the
(or organism) actively maintains homeostasis. For example, autonomic nervous system, causing peripheral blood vessels to
many animals are often faced with long periods of drought that constrict. The reduction in blood flow near the body’s surface
challenge their ability to remain hydrated and maintain a stable reduces heat loss to the surrounding air. By contrast, an increase
water and ion balance. These animals must rapidly respond by in temperature signals sweat glands to secrete moisture and
changing the permeability of their skin and respiratory organs so peripheral blood vessels to dilate to aid heat loss from the skin.
that they can retain as much water as possible. Homeostatic regulation, therefore, relies on negative feedback
How does the body, and in particular the nervous system, to maintain a set point, which in this case represents an animal’s
maintain homeostasis? Homeostatic regulation often depends on preferred body temperature. The ability to maintain a constant
negative feedback (Fig. 35.18). In negative feedback, a stimulus body temperature is known as thermoregulation, and it is just one
acts on a sensor that communicates with an effector, which of many physiological set points that the body actively maintains,
produces a response that opposes the initial stimulus. For example, as we discuss in subsequent chapters.
negative feedback is used to maintain a constant temperature
in a house. Cool temperature (the stimulus) is detected by a Simple reflex circuits provide rapid responses
thermostat (the sensor). The thermostat sends a signal to the to stimuli.
heater (the effector), producing heat (the response). The response An animal that has perceived a predator has an advantage if it can
(heat) opposes the initial stimulus (cool temperature), and no move quickly. Fast responses are made possible by simple reflex
further heat will be produced until the temperature drops below circuits that bypass the brain. These circuits connect sensory
the temperature setting of the thermostat. In this way, a stable neurons (detecting the presence of the predator) directly with
temperature is maintained (Fig. 35.18a). motor neurons (providing the quick movement necessary to
In a similar way, humans and other mammals maintain escape the predator). Reflex circuits are common in both the
a steady body temperature even as the temperature outside somatic and autonomic components of the nervous system.
758 SECTION 35.4 N E RVO U S S YS T E M O RG A N I Z AT I O N
FIG. 35.19 The knee-extension reflex. The knee-extension reflex involves a sensory neuron, a single synapse, and a motor neuron.
Spinal cord
3
2 A stretch receptor in an
The sensory neuron synapses
with a motor neuron in the
extensor muscle responds by Stretch Extensor
spinal cord.
sending a signal along the receptor muscle
sensory nerve. 3
Neuron from
stretch receptor
5
Patella
2 4
Interneuron for
Motor neuron to reciprocal inhibition
1 extensor muscle
etched
originally stretched
of flexor muscle
Patellar 4 The motor neuron sends
tendon
an excitatory signal to the
Motor neuron to
flexor muscle
5 An inhibitory interneuron
Flexor muscle same extensor muscle, which inhibits contraction of the
responds by contracting. opposing flexor muscle.
1 A physician strikes the
patellar tendon with a reflex
hammer.
Simple spinal reflex circuits connect sensory and motor dendrite and cell body to the axon. In the spinal cord, the axon
neurons directly in the spinal cord of vertebrates. The large of the sensory neuron forms synapses with motor neurons that
Mauthner neurons of fish are an example of such a circuit. Sensory travel from the spinal cord back to the muscle where the stretch
neurons respond to threatening visual, tactile, or vibratory cues originated. The signal from the muscle stretch receptor stimulates
from the environment and transmit signals through the spinal the motor neurons to increase the activation of the muscle: the
cord to the hindbrain of a fish, activating a large Mauthner neuron muscle contracts, and the leg extends at the knee.
on the side opposite the stimulus. The Mauthner cell in turn This reflex arc does not include an interneuron: It is composed
rapidly activates motor neurons along the body, causing the fish of just two neurons and one synapse. Transmission is delayed
to bend away from the threatening stimulus to initiate a rapid by communication at synapses, so the muscle contracts quickly
escape. At the same time, the Mauthner cell and motor nerves on because only one synapse is required to relay the sensory
the other side of the fish are inhibited. The giant axons of squid information back to the muscle.
are part of a similar reflex circuit that allows squid to swim quickly As well as being a useful medical test, the knee-extension
away from a predator. reflex has a normal physiological role. In running or landing from a
The knee-extension reflex in humans is an example of a jump, the knee joint first flexes (bends), stretching the quadriceps
simple nerve circuit that includes only a single synapse between muscles. This action sends the same sensory signal to the spinal
two neurons—a sensory neuron and a motor neuron (Fig. 35.19). cord as when a physician’s hammer taps the muscle’s tendon. As
Physicians commonly use this reflex to evaluate the performance a result, after flexing, the knee reflexively extends (straightens).
of the peripheral nervous and muscular systems. The strike of the Knee flexion followed by extension allows rapid adjustments in
physician’s hammer below the kneecap activates the extensor muscle force and knee position that help stabilize the body during
muscles on the front of the thigh, including the quadriceps running and jumping.
muscle, causing the bent leg to straighten. Because muscles can only contract, opposing movements at
Let’s follow this reflex pathway. It starts with specialized a joint such as flexion and extension require flexor and extensor
“stretch” receptors located on the dendrites of a sensory neuron muscles on either side of the joint (Chapter 37). These are often
in the extensor muscles of the leg. These dendrites extend to activated out of phase (at different times) so that, when one set of
cell bodies in ganglia alongside the spinal cord. These cell bodies muscles is activated (contracting), the other is inhibited (relaxed).
have axons that extend into the spinal cord. The stretch receptors The alternating extension and flexion of a leg during walking
sense the stretch of the muscle that occurs during movement or and running provide an example. This pattern of joint and limb
in response to a physician’s strike of a reflex hammer. In response movement is achieved by reciprocal inhibition: When stretch
to a stretch, a signal is sent from the stretch receptor, through receptors of the knee extensor muscles are activated to stimulate
CHAPTER 35 A N I M A L N E RVO U S S YS T E M S 759
these muscles to extend the knee, they also inhibit the activity of control the movement of the right and left limbs. In this case,
opposing muscles that flex the knee (Fig. 35.19). interneurons cross the spinal cord to control the timing of activity
Reciprocal inhibition of opposing sets of muscles occurs by flexor and extensor muscles of the opposite limb. Reciprocal
in the spinal cord. Axons of the stretch receptor neurons not inhibition is also involved in the Mauthner cell circuit of fish to
only synapse with motor neurons of extensor muscles, but also ensure that only one side of the fish’s body bends away from
synapse with inhibitory interneurons that inhibit motor neuron the stimulus to escape. The local spinal circuits that provide
stimulation of the opposing flexor muscles. This inhibitory reflex reciprocal inhibition are therefore fundamental to the alternating
pathway contains two synapses, one between the sensory neuron motion of the body and limbs that characterizes the movements
and interneuron and the second between the interneuron and the of most animals.
motor neuron to the flexor muscle. In other cases, more complex circuits in the brain may act
to coordinate sensory input and motor output. These circuits
j Quick Check 5 Why is an interneuron needed to provide reciprocal
integrate other sources of sensory information, such as vision and
inhibition of the flexor muscle when an extensor muscle is activated?
balance, with conscious commands from the brain to voluntarily
Reciprocal inhibition also operates between the right and control motor behavior. In the next chapter, we look more closely
left sides of the body. For example, reciprocal inhibition helps to at these sensory circuits.•
Core Concepts Summary Glial cells provide nutritional and physical support for
neurons. page 744
35.1 Animal nervous systems allow organisms to
35.3 The electrical properties of neurons allow them
sense and respond to the environment, coordinate
to communicate rapidly with one another.
movement, and regulate internal functions of the body.
Neurons have electrically excitable membranes that code
Nerve cells, or neurons, receive and send signals and are the
information by changes in membrane voltage and transmit
functional unit of the nervous system. page 740
information in the form of electrical signals called action
Animal nervous systems include three types of neuron: potentials. page 745
sensory neurons that respond to signals, interneurons
Ion channels open and close in response to changes in
that integrate and process sensory information, and motor
membrane voltage, underlying the production of action
neurons that produce a response from muscle. page 740
potentials in nerve cells. page 746
Ganglia are localized collections of nerve cell bodies that
Action potentials fire in an all-or-nothing fashion; a brief
integrate and process information. page 741
refractory period follows. page 746
Simply organized animals, such as cnidarians, have a nerve
In vertebrates, glial cells also produce the myelin sheath that
net to coordinate sensory and motor function. page 741
insulates axons, increasing the speed of nerve impulses.
Forward locomotion led to the evolution of specialized sense page 749
organs in the head, along with concentrated groupings of
Action potentials are conducted in a saltatory fashion
nerve cells to form ganglia and a brain. page 741
in myelinated axons, firing at nodes of Ranvier, where the
axon membrane is exposed and not insulated by myelin.
35.2 The basic functional unit of the nervous
page 749
system is the neuron, which has dendrites that receive
information and axons that transmit information. Communication across the synapse occurs when an arriving
action potential triggers the release of neurotransmitters
Neurons share a common organization: They have dendrites
from vesicles within the axon terminal. page 751
that receive inputs, a cell body that receives and sums the
inputs, and axons that transmit signals to other nerve cells. Neurotransmitters released from presynaptic vesicles bind to
page 743 receptors in the postsynaptic membrane, causing either an
excitatory or an inhibitory stimulus. page 752
Most neurons communicate by chemical synapses formed
between an axon terminal and a neighboring nerve or Excitatory stimuli depolarize the membrane, producing an
muscle cell. page 743 excitatory postsynaptic potential (EPSP), whereas inhibitory
760 SELF-ASSESSMENT
stimuli hyperpolarize the membrane, producing an inhibitory 3. Diagram and label the basic features of a neuron,
postsynaptic potential (IPSP). page 752 indicating where information is received and where it is sent.
4. Graph an action potential, showing the change in
35.4 Animal nervous systems can be organized into electrical potential on the y-axis and time on the x-axis.
central and peripheral components. Indicate on the graph the phases when voltage-gated Na1 and
Animal nervous systems are organized into central and K1 ion channels are opened and when they are closed.
peripheral components called the central nervous system (CNS) 5. Explain what is meant by saying action potentials are
and peripheral nervous system (PNS). page 754 “all-or-nothing.”
The central nervous system includes the brain and one or 6. Explain why action potentials propagate along an axon
more main trunks of nerve cells, such as the spinal cord. The only in a single direction.
peripheral nervous system is distributed throughout the animal’s
7. Create a table that lists the sequence of events that
body and is composed of sensory and motor nerve cells.
create an action potential, identifying the membrane potential
page 754
at each stage, which channels are opening or closing, and in
In many invertebrates and vertebrates, the peripheral nervous which direction ions are moving across the cell membrane.
system is divided into voluntary and involuntary components.
8. Briefly describe how myelinated axons increase the speed
page 755
of signal transmission.
In vertebrates, the voluntary component is referred to as the
9. Diagram a chemical synapse, labeling the vesicles that
somatic nervous system, and the involuntary component is
contain neurotransmitter molecules and the receptors that
referred to as the autonomic nervous system. page 755
bind the neurotransmitter to produce either an inhibitory or
The autonomic system regulates body functions through an excitatory stimulus in the postsynaptic cell.
opposing actions of the sympathetic and parasympathetic 10. Describe how neurotransmitter binding to receptors on a
divisions. page 756 postsynaptic cell causes inhibition or excitation.
The nervous system helps to regulate physiological functions to 11. Describe how temporal summation of EPSPs from two
actively maintain stable conditions inside a cell or an organism, a presynaptic neurons results in a larger depolarization of
process known as homeostasis. page 756 the postsynaptic cell compared with how an inhibitory
Homeostasis is often achieved by negative feedback, in which presynaptic neuron causes an IPSP that negates the EPSP of
the response inhibits the stimulus. page 757 an excitatory neuron, and how spatial summation of three
excitatory presynaptic neurons produces an even larger
Simple reflex circuits can involve as few as two neurons: a depolarization of the postsynaptic neuron.
sensory neuron from the periphery that synapses with a motor
12. List which functions of an animal are controlled by voluntary
neuron in the spinal cord that sends a signal to a muscle.
and by involuntary components of the nervous system.
page 757
13. Diagram a simple circuit that includes a sensory neuron that
synapses with a motor neuron to produce a reflex. Indicate
Self-Assessment where in the nervous system this synapse is found.
Animal Sensory
Systems and
Brain Function
Core Concepts
36.1 Animal sensory receptors
detect physical and chemical
stimuli by changes in
membrane potential.
36.2 Specialized chemoreceptors
relay information about smell
and taste.
36.3 Hair cells convey information
about gravity, movement, and
sound.
36.4 The ability to sense light and
form images depends on
photosensitive cells with light-
absorbing proteins.
36.5 The brain processes and
integrates information from
multiple sensory systems, with
tactile, visual, and auditory
stimuli mapped topographically
in the cerebral cortex.
36.6 Cognition is the ability of
the brain to process and
integrate complex information,
remember and interpret past
events, solve problems, reason,
and form ideas.
Custom Medical Stock Photo—All rights reserved.
761
762 SECTION 36.1 A N I M A L S E N S O RY S YS T E M S
To see, your eyes detect light, which is a form of electromagnetic These cells either communicate with neurons, as for taste and
radiation. To hear, your ears detect sound waves. To smell, your sight, or are themselves neurons, as for smell. Note that the short-
nose detects odor molecules present in the air. In all these cases, hand term “sensory receptor” refers to the entire sensory cell or
your sense organs are detecting a physical or chemical stimulus sensory neuron, not just the membrane protein.
in the environment. The first half of this chapter explores how Sensory receptors represent a key cellular unit of the sensory
specialized sensory cells detect these signals and code them as component of animal nervous systems. In most multicellular
information that can be transmitted and processed by the nervous animals, the sensory receptors are organized into specialized
system. How is a dog able to distinguish thousands of different sensory organs that convert particular physical and chemical
odors? How is a hawk able to see a small rodent far below? How are stimuli into signals that are communicated to the brain. Cnidarians
humans able to detect small differences in the pitch of a sound? (including jellyfish, corals, and anemones) and roundworms
The second half of the chapter follows nervous system (including the laboratory organism Caenorhabditis elegans) evolved
pathways from these sensory cells to the brain, on the way sensory receptors that sensed physical contact, and cnidarians and
exploring basic principles of brain function. Processing of sensory flatworms were among the first multicellular animals to evolve
information in the brain takes place in regions specialized for simple light-sensing organs.
each sense, and within many of these regions information is The conversion of physical or chemical stimuli into nerve
represented in the form of topographic maps. impulses is called sensory transduction. For example, receptors
located in the ear convert the energy of sound waves into nerve
impulses that allow an animal to distinguish loud versus soft
36.1 ANIMAL SENSORY SYSTEMS sounds and high-pitched versus low-pitched sounds. Although the
sense organs of different animals share many similar properties,
Animals can sense the physical properties of their environment, differences have also evolved. Consequently, different animals
including light, chemicals, temperature, pressure, and sound, that perceive the world differently. Many insects, for instance, are
are useful in finding mates and food and avoiding predators and sensitive to ultraviolet light; nocturnal snakes can see at night
noxious environments. Early in evolutionary history, organisms by sensing infrared radiation; and dogs can distinguish odor
evolved specialized protein receptors located in the cell membrane compounds as much as 100 million times lower in concentration
that were able to detect these critical features in their environment. than humans can detect (Fig. 36.1).
For example, before the evolution of nerve cells and a nervous
system, bacteria evolved membrane receptors that sensed osmotic Specialized sensory receptors detect diverse stimuli.
pressures that might otherwise rupture their cell membrane. Animals have evolved a diverse array of sensory receptors that
Bacteria and sponges also evolved membrane receptors that detect respond to different stimuli, among them touch, light, and the
chemicals—including nutrients—in their environment. oscillations in air pressure we call sound waves. How is a physical
The senses of smell, taste, and sight in multicellular organisms phenomenon in the world outside an organism transformed into
with a nervous system also rely on membrane receptors. These a nerve impulse? The initial transformation takes place inside
receptors are embedded in specialized sensory receptor cells. the sensory receptor (Fig. 36.2). A physical or chemical stimulus
FIG. 36.1 Diverse sensory receptors. (a) Many insects can detect ultraviolet light. (b) Rattlesnakes can see at night by detecting infrared radiation.
(c) Dogs have a keen sense of smell. Sources: a. Russell Burden/Getty Images; b. Andy Hunger/age fotostock; c. Monika Ondrušová/Dreamstime.com.
a b c
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 763
FIG. 36.2 Sensory transduction, which converts an external stimulus into a change in membrane potential. (a) Chemoreceptors are located
in the antennae of the luna moth; (b) mechanoreceptors below the cuticle of a roundworm; and (c) photoreceptors in the eyes of a
vertebrate. Photo sources: a. Rolf Nussbaumer Photography/Alamy; b. Sinclair Stammers/Science Source; c. Eyal Nahmias/Alamy.
Pressure
A molecule in the
environment Light
Na+
Cuticle
Signal to Signal to
open ion close ion
channel channel
Protein Protein
receptor receptor
Cell is Cell is Cell is
depolarized. depolarized. hyperpolarized.
is converted into a change in the sensory receptor’s membrane receptors in their cell membranes that respond to molecules in the
potential. Recall from Chapter 35 that a cell’s membrane potential environment.
is the electrical charge difference between the inside and the In animals, chemoreceptors are sensory receptor cells that
outside of the cell membrane, and that a depolarization in respond to molecules that bind to specific protein receptors on
membrane potential is the first step in firing an action potential. the cell membrane (Fig. 36.2a). Many animals detect food in
Sensory receptors either fire action potentials themselves or their environment by sensing key molecules such as oxygen
synapse with neurons that fire action potentials, which are then (O2), carbon dioxide (CO2), glucose, and amino acids. Female
transmitted to the central nervous system. mosquitoes track CO2 levels to detect prey for blood meals,
In many cases, the sound wave, touch, or other stimulus and coral polyps respond to simple amino acids in the water,
causes ion channels in the cell’s plasma membrane to open. The extending their bodies and tentacles toward areas of greater
influx of ions changes the membrane potential by altering the concentration to feed. Other arthropods, such as flies and crabs,
distribution of charged ions on either side of the membrane. Let’s have chemosensory hairs on their feet. These animals taste
look at examples of how three different types of stimuli from the potential food sources by walking on them. Salmon rely on
environment—molecules, touch, and light—can be transformed chemoreception to detect chemical traces of the home waters of
into a nerve signal. the river where they hatched, and where they will return to mate
and spawn.
Chemoreceptors are universally present in animals. Chemoreception underlies the sense of smell and taste.
The most ancient type of sensory detection is chemoreception. All Consider taste as an example. In most cases, the binding of
organisms respond to chemical cues in their environment. Even molecules to a protein receptor on a taste receptor causes
the earliest branching groups of Bacteria and Archaea have protein the protein receptor to change conformation. That change in
764 SECTION 36.1 A N I M A L S E N S O RY S YS T E M S
conformation in turn triggers the opening of Na1 channels receptors for balance, gravity sensing, and hearing, discussed in
through G protein signal transduction pathways (Chapter 9). The section 36.3.
influx of Na1 ions depolarizes the receptor cell. In the case of taste
receptors, no action potential fires, but the depolarization travels Electromagnetic receptors sense light,
far enough down the receptor’s short axon to trigger the release of thermoreceptors sense temperature, and nociceptors
neurotransmitters. Other chemoreceptors, such as those involved sense pain.
in the sense of smell or located on antennae to detect chemicals in Electromagnetic receptors are sensory cells that respond to
the air, are sensory neurons that do fire action potentials. electrical, magnetic, and light stimuli. Of these, light-detecting
photoreceptors are the most common and diverse. Most animals
Mechanoreceptors are a second general class sense light in their environment. Photoreceptors have been
of ancient sensory receptors. common since the first ones evolved in cnidarians (jellyfish) and
Mechanoreceptors respond to physical deformations of their ctenophores (comb jellies) more than 500 million years ago.
membrane produced by touch, stretch, pressure, motion, and Light-detecting photoreceptors are the sensory receptors in
sound. Mechanoreceptors are found in all multicellular animals, eyes (Fig. 36.2c). Photoreceptors respond to individual photons of
and even bacteria have pressure-sensitive protein receptors in light energy. In most invertebrates, light causes Na1 channels to
their cell membrane. In both bacteria and multicellular organisms, open, depolarizing the cell. By contrast, vertebrate photoreceptors
evidence suggests that the protein receptor is also a sodium ion close Na1 channels in response to light, causing the cell to become
channel. Thus, deformation of the receptor membrane opens hyperpolarized. Most receptors excite neurons that they synapse
sodium channels directly, causing a depolarization of the endings with, but vertebrate photoreceptors are unusual in that they can
of the cell’s dendrites (Fig. 36.2b). Early pressure-sensitive protein either excite or inhibit neurons in the eye. Photoreception in the
receptors in bacteria sensed internal cell pressure: When water vertebrate eye is discussed in section 36.4.
moving into the cell by osmosis increases the risk of bursting Some fish, such as catfish, contain specialized
(Chapter 5), the stretching of the membrane opens channels that electroreceptors arranged in a lateral line along their bodies.
let water leave the cell. Other mechanoreceptors in roundworms Electroreceptors enable these fish to detect weak electrical signals
and anemones are linked to externally projecting cilia that sense emitted by all organisms. They likely evolved as an adaptation for
forces at the animal’s body surface. locating prey or potential predators in poorly lit habitats where
One well-studied example of a mechanoreceptor is a vision was less useful. Some specialized “weakly electric” fish
touch receptor in the roundworm Caenorhabditis elegans. actually generate an electromagnetic field by emitting pulses
Roundworms, also called nematodes, are one of the most diverse from an electric organ located in the tail. Disturbances in the
and widespread groups of animals on Earth. Deformation of the field detected by electroreceptors of the lateral line system signal
surface of the worm—its cuticle—exerts pressure on proteins the location of nearby prey. These fish also inhabit rivers with
connected to an ion channel. The mechanical force changes the poor visibility. The bill of the duckbilled platypus also contains
shape of the ion channel, causing it to open and produce a change electroreceptors that locate prey in dimly lit water.
in membrane potential. Finally, specialized receptors with dendritic branches in the
A mechanoreceptor in humans and other mammals is the skin can respond to heat and cold (thermoreceptors) or to pain
sensory receptor found in the skin that senses touch and pressure. (nociceptors). Thermoreceptors help to control an animal’s
The cell bodies of these neurons are located in ganglia near the metabolism, and they also regulate body temperature by controlling
spinal cord, with extensions going in two directions: to the skin patterns of blood flow that in turn alter rates of heat gain and loss
and to the spinal cord. In the skin, the neuron has branched (Chapter 40). As a result, they help to maintain homeostasis. Pain
tips containing ion channels sensitive to deformations of the receptors send action potentials to the brain or spinal cord when
membrane. These branched tips are the initial sensors of touch exposed to excessive heat, force, or chemical damage. A quick
and pressure. If the stimulus is strong enough, local depolarization withdrawal from the painful stimulus is the typical response.
leads to the firing of an action potential that travels all the way
to the spinal cord. Thus, in contrast to taste chemoreceptors, this Stimuli are transmitted by changes in the firing rate
type of mechanoreceptor transmits an action potential. The of action potentials.
axon is much too long for simple depolarization to spread to its Sensory reception depends on converting the energy of a physical
other end. or chemical stimulus into an action potential, either in the sensory
Mechanoreceptors are also found at the base of whiskers receptor itself or in the neuron it synapses with. How do these
that rodents, cats, dogs, and other mammals use to sense touch nerve impulses convey information to the brain? In effect, action
with their snouts. Stretch receptors found in muscles are also potentials can be considered a code that the brain deciphers.
mechanoreceptors that influence a muscle’s motor activation, To convert information from the environment into a code,
helping to control its length and force. A very different group of the nerve impulses conveyed by sensory organs carry out the
specialized mechanoreceptors called hair cells are the sensory following functions:
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 765
correlate with
the intensity of ignore background noise. Novel stimuli
the stimulus. are generally the most important for an
Low firing rate High firing rate
animal. Consequently, sensory receptors
initially respond most strongly when a
b.
stimulus is first received (Fig. 36.3b). If
the stimulus continues over a longer time
period, sensory receptors typically reduce
their firing rate through a process called
Adaptation to adaptation (this is not the adaptation that
Membrane
continuous
potential
FIG. 36.5 The senses of smell and taste. Olfactory receptors respond to chemical odors in the nasal passages and communicate directly with the
brain. Taste cells are chemosensory receptors located in taste buds.
Olfactory
3 Interneurons integrate
nerves the odorant information
received by olfactory
receptors before sending
Interneuron it to the brain.
Interneuron
dendrites 2 Action potentials
produced in response to
Nasal the binding of odorants
bone to membrane receptors
are sent to the olfactory
Axon interneurons.
Sensory
neurons
A taste bud
Stereocilia FIG. 36.7 The vestibular system. The vestibular system senses
angular rotations of the head from movements of fluid
within three semicircular canals that deflect hair cells. It
Hair detects gravity and posture by means of statoliths in two
cells statocyst chambers.
Resting Rotating
Stereocilia
cells at the “bottom” of the chamber, the statolith activates those
cells. Statoliths help anemones and jellyfish orient themselves Hair
cell
in the water and direct their tentacles. Statoliths of lobster and
crayfish can be replaced by magnetic particles and subjected to an
Sensory nerve Support cell
experimental magnetic field that repositions the statolith to the
top or sides of the chamber. In this case, the lobsters and crayfish
respond by swimming upside down or on their sides.
Semicircular
The mammalian inner ear contains organs that sense motions canals
of the head and its orientation with respect to gravity. These
organs make up the vestibular system (Fig. 36.7), which consists
of two statocyst chambers and three semicircular canals. These
statocyst chambers are similar to those of invertebrates, providing
a sense of gravity and body orientation with respect to motion.
Hair cells located within the semicircular canals sense angular
motions of the head in three perpendicular planes, providing a
sense of balance. When the head rotates, gelatinous fluid in the
Cochlea
semicircular canals is accelerated, deflecting the stereocilia of Statocyst chambers
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 769
FIG. 36.8 The human ear. (a) The tympanic membrane and bones of the middle ear transmit external sound vibrations to the oval window of the
inner ear. (b) Hair cells in the cochlea respond to the vibrations, sending signals to the brain that distinguish sound amplitude and pitch.
(c) A scanning electron micrograph shows the V-shaped arrangement of stereocilia on hair cells. Photo source: SPL/Science Source.
Cochlear branch of
vestibulocochlear
nerve
Basilar
Cochlea membrane Lower canal
External
auditory
canal
Tectorial
Pinna Oval membrane
window Stereocilia
Tympanic Middle Hair cell
membrane ear cavity
(eardrum)
Outer ear
Middle ear Basilar membrane Sensory
neurons
Inner ear
c. Hair cells
FIG. 36.11 Three types of eye. Photo sources: a. David M. Dennis/age fotostock; b. Eye of Science/Science Source; c. Danté Fenolio/Science Source.
10,000 or more. Dragonflies are predators, and their high number of perceive ultraviolet light. Many pollinating insects sense UV light
ommatidia is an adaptation for visually tracking their prey. to locate the flowers they prefer to visit for nectar (Fig. 36.12).
Within a single ommatidium, light is focused through a The single-lens eyes of vertebrates and cephalopod mollusks
lens onto a central region formed from multiple overlapping like squid and octopus work like a camera to produce a sharply
photoreceptors. Each ommatidium is sensitive to a narrow angle of defined image of the animal’s visual field (see Fig. 36.11c). In spite
light (about 1° to 2°) in the animal’s visual field. Compound eyes of of their similar outward appearance, there is clear evidence that
insects and crustaceans provide a mosaic image because individual single-lens eyes evolved independently in vertebrates and in some
light regions are sensed by separate ommatidia. It is likely that the mollusks (Fig. 36.13). Other invertebrates, such as some spiders
image is sharpened within the brain, but the resolution of images and annelid worms, also evolved single-lens eyes independently.
produced by compound eyes is not nearly as good as that produced An advantage of single-lens eyes compared to compound eyes
by single-lens eyes. Nevertheless, compound eyes are extremely is that the single lens can focus light rays on a particular region
good at detecting motion and rapid flashes of light, more than of photoreceptors, improving both image quality and light
300 per second compared with 50 per second for a human eye. sensitivity. As a result, animals with single-lens eyes can detect
Insect eyes also have good color vision, and many insects can prey effectively by their motion and shape.
FIG. 36.12 The same flower seen with visual and UV light. FIG. 36.13 Convergent evolution of single-lens eyes. Single-lens
Many pollinating insects see ultraviolet light, which eyes evolved independently in vertebrates (fish and
can dramatically alter the image that attracts them to a mammals) and in some mollusks (octopus and squid).
particular flower. Source: Bjorn Rorslett/Science Source.
Fish Mammals Clams Snails Octopus, squid
Seen with visual light Seen with UV light Single-lens
eyes
Vertebrates Mollusks
FIG. 36.16 Opsin bound to the light-absorbing pigment retinal. Retinal changes conformation from cis to trans when it absorbs a photon of
light. Rendered by Dale Muzzey.
Extracellular Opsin
fluid
Light wave
cis alkene
bond
cis-retinal
Retinal
trans-retinal
trans alkene
bond
Cytoplasm
Why do so many animals have two eyes? One reason is that two action potentials, but when stimulated by light they increase or
eyes provide a wider field of vision. Close one eye and you will see decrease the firing rate of neurons in the retina of the eye. That is,
the visual field of the other eye. With both eyes open, the visual the reduction in neurotransmitter triggers ESPNs in the dendrites
field is wider than the visual field of either eye alone. You’ll also of some connecting neurons, and ISPNs in others. Differences in
notice considerable overlap in the visual field of both eyes. This the firing rates of these neurons provide information about the
overlap exists in humans and other primates, as well as in other intensity and location of light.
mammals and birds of prey, and makes possible binocular vision, the
ability to combine images from both eyes to produce a single visual Color vision detects different wavelengths of light.
image. Binocular vision allows for depth and distance perception. Color vision is crucial for many invertebrate and vertebrate
Prey animals, such as some birds, antelope, and rabbits, have animals. It is achieved by photoreceptor cells called cone cells
eyes positioned more to the side, expanding their visual field up that contain opsins sensitive to different wavelengths of light
to 360°, but limiting or preventing binocular vision. Animals that (Fig. 36.17). The more numerous rod cells are also sensitive
require greater visual sharpness, such as predatory hawks, cats, to light, and most sensitive to blue-green light. Because all rod
and snakes, have eyes pointing forward, increasing their binocular cells have the same opsin (called rhodopsin), the brain interprets
field of view.
j Quick Check 4 What is the primary role of rod cells, and what are
0 the two roles of cone cells in the retina?
400 500 600 700
Violet Blue Cyan Green Yellow Red
Wavelength (nm) Local sensory processing of light determines basic
features of shape and movement.
The rods and cones detect the intensity, color, and pattern of light
the light detected by rod cells as shades of gray, not as blue- entering the eye through the lens. However, it is their interaction
green. The human retina contains about 6 million cone cells and with a highly ordered array of neurons in the retina that begins
about 125 million rod cells. Because of their greater number and the first steps of visual sensory processing (Fig. 36.19). The
sensitivity to light, rod cells enable animals to see in low light. retina consists of five layers of cells that form a signal-processing
Together, rod and cone cells constitute approximately 70% of network just in front of a pigmented epithelium. The rods and
all sensory receptor cells in the human body, highlighting the
importance of vision in perceiving our environment.
Vertebrate cone cells likely evolved from a rod cell precursor.
FIG. 36.19 Cellular organization of the human retina. The retina
Most non-mammalian vertebrates have four types of cone cell,
is made up of five layers of cells: rods and cones,
each with a different opsin, whereas most mammals have only
bipolar cells, ganglion cells, horizontal cells, and
two types of cone cell, and two opsins. It is likely that two opsins
amacrine cells.
were lost early in mammal evolution, when mammals were small,
nocturnal, and burrowing. Old World primates, apes, and humans,
as well as some New World primates, regained trichromatic (three-
color) vision by means of gene duplication, likely in response to
selection for better ability to locate fruit, a key part of their diet. Retina
Each human cone cell therefore has one of three opsins, which
absorb light at blue, green, or red wavelengths (Fig. 36.18).
Stimulation of cone cells in varying combinations of these three
opsins allows humans and other primates to see a full range of
color (violet to red). Fish, amphibians, reptiles, and birds also have Light
good color vision, including for many the ability to see ultraviolet. Ganglion cells Bipolar cells Rod and cone cells
rays
Cone cells require higher levels of light than rod cells to
become stimulated. The low sensitivity of cone cells to light makes
it hard to detect color at night. Cone cells are most concentrated
within the fovea of the retina, the center of the visual field of
most vertebrates (see Fig. 36.15). Cone cells provide the sharpest
vision. Animals with particularly sharp vision, such as hawks and
other birds of prey, have an extremely concentrated number of
cone cells in the fovea, approaching 1 million/mm2 (compared
with about 150,000/mm2 in the human fovea). Birds of prey can
see small prey on the ground from high in the air. Many birds also
have eyes with two foveae, one projecting forward for binocular
vision and one projecting to the side to enhance the sharpness of
Optic Amacrine cell Horizontal cell Cone Rod Pigmented
their side vision. nerve epithelium
HOW DO WE KNOW?
FIG. 36.20
EXPERIMENT Kuffler stimulated different regions of a cat’s retina with localized points of light while recording the action potentials
produced by ganglion cells.
RESULTS Kuffler found that there are two types of ganglion cell: on-center and off-center cells. On-center ganglion cells fire more
action potentials when light shines on the center of the cell’s receptive field compared to the surrounding region, and off-center cells
fire more when light is shown in the periphery and less on the center. These patterns are explained by lateral inhibition of input by the
photoreceptors and varying excitation or inhibition of bipolar cells to the ganglion cells in the retina.
On-center Off-center
ganglion cell ganglion cell
Light in Light in
center Periphery center Periphery
Center Center
Action
Light Light
potentials
Inhibition Excitation
Periphery Periphery
Light off Light off
center Center center Center
Light Light
FOLLOW-UP WORK In the 1960s, Hubel and Wiesel found similar center–surround neural receptive fields, though with enhanced
opposition, in part of the thalamus and in the visual cortex of the brain. Cells with these fields enable cats and other mammals to detect
shapes of a given orientation moving through their visual field. Similar center–surround receptive fields have also been found in the
somatosensory and auditory cortex, highlighting the use of lateral inhibition to enhance sensory acuity and edge detection. Other studies
have found similar center–surround sensory processing in invertebrates and other vertebrates.
SOURCES Kuffler, S. W. 1953. “Discharge Patterns and Functional Organization of Mammalian Retina.” Journal of Neurophysiology 16:37–68; Hubel, D. H. 1963. “The Visual
Cortex of the Brain.” Scientific American 209:54–62.
cones are at the back of the retina, so that light must pass through on to bipolar cells, which also do not fire action potentials, but
several layers before reaching these light-sensitive cells. Because rather adjust their release of neurotransmitter in response to
they are photoreceptors, rod and cone cells hyperpolarize in the input from multiple rod and cone cells. Depending on their
response to light but do not fire action potentials. They synapse receptors, some bipolar cells are inhibited when rod and cone cells
776
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 777
FIG. 36.22 Human brain development. (a) The brain develops from the forebrain, midbrain, and hindbrain. (b) Part of the forebrain develops
into the limbic system, which controls drives and emotions.
a. Three major brain regions b. Limbic system
Cerebral
cortex
Thalamus
Midbrain Hindbrain Hypothalamus
Cerebellum
Forebrain Midbrain
Pons Brainstem
Medulla
Spinal Spinal
cord cord Hippocampus
The brain develops
as three regions: a 25-day brain Adult brain
hindbrain, midbrain
and forebrain, with Forebrain Cerebral cortex, thalamus, hypothalamus
the forebrain
becoming elaborated Midbrain Midbrain (part of brainstem)
as the cerebral cortex
in humans and most
Hindbrain Pons and medulla (part of brainstem), cerebellum
other vertebrates.
brainstem maintain a wakeful state; low levels enable sleep. If the The brain is divided into lobes with specialized
midbrain is damaged, loss of consciousness and then coma result. functions.
The forebrain consists of an inner brain region that forms The cerebral hemispheres are the largest structures of the
the thalamus and the underlying hypothalamus, and a more mammalian brain (Fig. 36.23). They consist of a highly folded
anterior region that develops into the cerebrum, the outer left outer layer of gray matter about 4 mm thick that forms the
and right hemispheres of the cerebral cortex (Fig. 36.22a). The cerebral cortex, which is made up of densely packed neuron cell
thalamus is a central relay station for sensory information sent to bodies and their dendrites (Fig. 36.23a). The folds greatly increase
higher brain centers of the cerebrum. The hypothalamus interacts the surface area of the cortex and are the result of selection for an
closely with the autonomic and endocrine systems to regulate increased number of cortical neurons within the limited volume
the general physiological state of the body. In humans and most of the skull. Deep inside the cerebral cortex is the white matter,
other primates, the cerebral cortex is the largest part of the brain, which contains the axons of cortical neurons. The fatty myelin
overseeing sensory perception, memory, and learning. Whereas produced by glial cells surrounding the axon makes this region of
the forebrain is essential to normal behavior in mammals, it the brain white. These axons are the means by which neurons in
appears less important for other vertebrates. different regions of the gray matter communicate with neurons in
Other inner components of the forebrain constitute the other regions of the cortex and in deeper regions of the forebrain,
limbic system, which controls physiological drives, instincts, midbrain, and hindbrain.
emotions, and motivation and, through interactions with Major regions of the cerebral hemispheres are defined by
midbrain regions, the sense of reward (Fig. 36.22b). Stimulation clearly visible anatomical lobes separated in most cases by deep
of the limbic system can induce strong sensations of pleasure, crevices called sulci (singular, sulcus) (Fig. 36.23b). The frontal
pain, or rage. A posterior region of the limbic system, the lobe is located in the anterior region of the cerebral cortex (behind
hippocampus, is involved in long-term memory formation, your forehead). It is important in decision making and planning.
discussed in the next section. The parietal lobe is located posterior to the frontal lobe and is
Sensory information reaches the cerebral cortex from the separated from the frontal lobe by the central sulcus. The parietal
cranial nerves and nerves passing through the spinal cord. This lobe controls body awareness and the ability to perform complex
information passes through the brainstem, and then through tasks, such as dressing. The temporal lobe lies below the parietal
the thalamus, the central relay station for sensory information. lobe. It is involved in processing sound, as well as performing other
From the thalamus, information for each of the senses goes to a functions discussed below. Located behind the parietal lobe, at the
different region of the brain specialized to further process that back of the brain, is the occipital lobe, which processes visual
information, in a manner discussed next. information.
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 779
FIG. 36.23 Human brain organization. (a) The folding of the brain and (b) the lobes of the cerebrum.
Gray matter
(neuron cell
bodies)
Frontal lobe
Sulcus
Parietal lobe
White matter Occipital lobe
(neuron
axons with Temporal lobe
myelin and Cerebellum
glial cells) Auditory
cortex Brainstem
Visual
cortex
The surface of the brain is highly folded, The cerebrum is organized into lobes.
increasing the surface area of the cortex,
where neuron cell bodies are located.
The central sulcus separates the primary motor cortex somatosensory cortex integrates tactile information from
of the frontal lobe from the primary somatosensory cortex specific body regions and relays this information to the motor
of the parietal lobe (Fig. 36.24). “Command” neurons in the cortex. Both cortices make connections to the opposite side
primary motor cortex produce complex coordinated behaviors of the body by sending axons that cross over in the brainstem
by controlling skeletal muscle movements. The primary and spinal cord. As a result, the right cortex controls the left
k
Arm ow
He er
Trun
Nec ad
Hip
Wr
H
uld
Lit and
Elb
ist
t
Mi Ring le
Sho
dd Leg
Front I n d le
Th ex Foo
t
um
b
Left Right No Eye To e s
se
hemisphere hemisphere Fac Genitalia
Up
Primary motor per e
lip
Central cortex Lips
sulcus Primary Lowe
r lip
somatosensory
cortex Gum and
jaw
Tongue
nx
Phary
inal
- a b dom
a
Intr
Back
780 SECTION 36.6 M E M O RY A N D CO G N I T I O N
side of the body and the left cortex controls the right side of include object identification and naming. An individual with
the body. damage to the temporal lobe may lose the ability to recognize
faces, even though he or she may still recognize others by voice or
Information is topographically mapped into the other body features.
vertebrate cerebral cortex. The occipital lobe topographically maps visual information
The primary motor cortex and somatosensory cortex are received from the optic nerves. The topographic mapping of
organized as maps that represent different body regions, as information from retinal ganglion cells enables the brain to detect
shown in Fig. 36.24. The neurons that control movements of the patterns and motion that are precisely related to different regions
foot and lower limb are located near the mid-axis of the motor of the visual field. As a result, highly visual animals, such as
cortex. Those that control motions of the face, jaws, and lips humans, primates, and birds, are able to detect complex patterns
map to the side and farther down in the primary motor cortex. and movements in their environment.
There is a similar topographic map in the somatosensory cortex
for pressure and touch sensation. Regions such as the fingers,
hands, and face that are involved in fine motor movements and 36.6 MEMORY AND COGNITION
distinguishing fine sensations are represented by larger areas of
the cortex. The ability of the brain to process and integrate complex sources of
The auditory cortex in the temporal lobe is similarly organized information, interpret and remember past events, solve problems,
as a map. This region processes sound information transmitted reason, and form ideas is broadly referred to as cognition. In
from the cochlea of the ear. Neurons in the auditory cortex are this section, we consider memory and learning, as examples of
organized by pitch: Neurons sensitive to low frequencies are cognitive abilities.
located at one end and neurons sensitive to high frequencies at the
other. With the evolution of language in humans, regions farther The brain serves an important role in memory
back in the temporal lobe developed into language and reading and learning.
centers. These centers are linked by pathways to a specialized Memory is the basis for learning. An animal that can remember its
motor center controlling speech, located at the base of the primary encounter with a predator or noxious plant will avoid that danger
motor cortex of the frontal lobe. Functions of the temporal lobe in the future. A memory is formed by changes to neural circuits
FIG. 36.25 Synaptic plasticity. Memory and learning depend on long-term potentiation (LTP) of synapses within neural circuits.
New
dendrite
forming
within specific regions of the brain, specifically, by changes in Cognition involves brain information processing
the synaptic connections between neurons in a neural circuit. and decision making.
These changes enable an animal, for example, to recognize other Cognitive brain function ultimately gives rise to a state of
individuals in its social group or to recognize the threat of a consciousness—an awareness of oneself and one’s actions
predator. In humans and other primates, the hippocampus, a brain in relation to others. Consciousness allows judgments to be
structure in the limbic region, plays a special role in memory made about events and experiences in one’s environment. When
formation. We can remember much of the information we receive you suddenly see someone you recognize from long ago, rapid
for several minutes. However, unless reinforced by repetition neural associations within the cortex identify that person by
or by paying particular attention, the information is typically name, retrieve multiple memories of past events you shared
forgotten. The hippocampus transforms reinforced short-term with that person, and elicit conscious thoughts, including your
memories into long-term memories. Long-term memory is opinion of that person. At the same time, extraneous sensory
essential for learning. information is filtered and other thoughts recede, allowing you
The hippocampus forms long-term memories by repetitively to focus your attention on the person you have just seen and
relaying information to regions of the cerebral cortex. Although recognized.
the details remain uncertain, memory and learning depend on Mental processes are studied by relating changes in brain
establishing particular neural circuits in the hippocampus and activity to changes in an animal’s behavioral state. The study
cerebral cortex. These circuits can be activated to recall a memory of the brain is challenging because of the complexity of the
that is triggered by a particular sound, or sight, or other relevant circuits involved. Nevertheless, considerable progress is being
stimulus. Establishing a neural circuit requires establishing made through non-invasive neuroimaging techniques
a particular set of connections between neurons. Thus, the (Fig. 36.26). These techniques allow the interactions of different
formation of a memory circuit requires changes in synapses. Some brain regions within human and other animal subjects to be
synapses are weakened or removed altogether, and others are investigated while the subjects perform a particular mental or
formed or strengthened. motor task. The results of neuroimaging studies can be linked to
The ability to adjust synaptic connections between neurons is studies of the molecular and cellular properties of nerve cells, to
called synaptic plasticity (Fig. 36.25). Long-term potentiation
(LTP) is an example of synaptic plasticity that is believed to
underlie memory and learning. In response to repeated excitation,
FIG. 36.26 Non-invasive imaging of brain function. PET scan
neurons in excited circuits within the hippocampus release the
imaging reveals regions of metabolic brain cell activity.
neurotransmitter glutamate, opening Na1 and Ca21 channels. The
The reddish areas show the locations of (upper left) the
increased Ca21 stimulates signaling pathways leading to protein
visual area activated by sight, (upper right) the auditory
synthesis. New receptors are placed in the postsynaptic cell
area activated by hearing, (lower left) the tactile area
membrane and new dendrites are formed, strengthening synaptic
activated by touching braille, and (lower right) areas of
signaling between the two cells. These changes make the cells
the frontal cortex activated by generating words. Source:
more responsive to subsequent stimulation.
WDCN/University College London/Science Source.
Through repeated activation of neurons within the
hippocampus and associated regions of the cerebral cortex, neural
circuits are established that may be reinforced by LTP to create a
memory that can be retrieved over long periods of time. Although
memories may be associated with certain regions of the cortex,
they also rely on the interaction of nerve cells and networks
within multiple brain regions.
Although the brain regions involved in memory and learning
vary among different animals, the basic features of how memories
are constructed by means of synaptic plasticity within neural
circuits are likely broadly shared across animals capable of forming
memories. For example, the ability of an octopus to learn and
remember how to perform motor tasks rivals that of certain
vertebrates. Even the roundworm C. elegans has been found to be
capable of memory and learning: Individual roundworms learn to
avoid pathogenic bacteria in favor of bacteria that are nutritious.
advance our understanding of how nerve cells form and summarized her review of studies on animal cognition and
maintain neural circuits among different brain regions, and consciousness as follows:
of how these circuits are linked to particular behaviors and
cognitive processes. Our near-certainty about [human] shared experiences is
Do animals other than humans have a conscious state of based, amongst other things, on a mixture of the complexity
awareness? Although the conscious awareness of other animals of their behavior, their ability to “think” intelligently, and
is difficult to study, it seems clear that many animals exhibit on their being able to demonstrate to us that they have
conscious states of awareness that influence their experience a point of view in which what happens to them matters
and behavior. Donald Griffin, known for his codiscovery as an to them. We now know that these three attributes—
undergraduate of bat echolocation, advocated the view not only complexity, thinking, and minding about the world—are
that animals are conscious, but also that animal consciousness is also present in other species. The conclusion that they, too,
amenable to scientific study. Behavioral biologist Marion Dawkins are consciously aware is therefore compelling. •
Core Concepts Summary The statocysts of invertebrates are sensitive to gravity, orienting
an organism to “up” and “down.” page 767
36.1 Animal sensory receptors detect physical and The vestibular system of the vertebrate ear provides a sense of
chemical stimuli by changes in membrane potential. balance and gravity. page 768
Sensory receptors include chemoreceptors, The tympanic membrane in the outer ear transmits
mechanoreceptors, thermoreceptors, pain receptors, and airborne sound waves to the middle ear, where the signal is
electromagnetic receptors. page 764 amplified. The amplified sound waves are transmitted to
Action potential firing rate correlates with the strength of a the cochlea in the inner ear, where sound waves are converted
stimulus. Generally, strong stimuli induce high firing rates to fluid pressure waves. These waves are then sensed by hair
and weak stimuli induce low firing rates. page 764 cells that convert the signal to an electrical impulse. page 769
Animal sensory receptors increase their sensitivity to stimuli 36.4 The ability to sense light and form images depends
by temporal and spatial summation, enhance their acuity by on photosensitive cells with light-absorbing proteins.
lateral inhibition, and adapt to continuous stimuli. page 765
Opsin is a G protein-coupled receptor and the universal
36.2 Specialized chemoreceptors relay information photoreceptor protein in all animal eyes. page 771
about smell and taste. The eyecups of flatworms detect light and dark. page 771
Odorant molecules bind to membrane receptors on the The compound eyes of arthropods sense light using individual
surface of olfactory chemoreceptors. page 766 light-focusing elements called ommatidia, providing low acuity
Olfactory sensory cells are neurons that fire action potentials but rapid motion detection. page 771
when sending odor information to the brain. page 766 The single-lens eyes of vertebrates and cephalopod mollusks
In humans, five taste receptors—for sweet, bitter, sour, salty, focus images on a retina, which contains photoreceptor cells
and savory—are activated in combination to determine a and interneurons that process the light stimuli. page 773
specific taste. page 766 The protein opsin present in photoreceptor cells converts
Taste receptors are sensory cells that do not fire action light energy into chemical signals, altering the firing rate of
potentials but communicate by synapses with afferent neurons. page 774
neurons. page 766 Photoreceptor cells of the retina include rod cells, which detect
light intensity, and three types of cone cells, which detect
36.3 Hair cells convey information about gravity, different wavelengths of light and allow color vision. page 774
movement, and sound.
Photoreceptor cells, bipolar cells, ganglion cells, horizontal
Hair cells are specialized mechanoreceptors that detect cells, and amacrine cells form a network that processes visual
motion and vibration. page 767 information in the retina. page 775
CHAPTER 36 A N I M A L S E N S O RY S YS T E M S A N D B R A I N F U N C T I O N 783
The vertebrate brain is organized into a hindbrain, midbrain, and 2. Diagram a generalized sensory receptor cell and show
forebrain, with the forebrain elaborated into the cerebral cortex how it changes its firing rate in response to detected stimuli.
in birds and mammals. page 777 3. State a hypothesis that explains why all animals have
chemoreceptors.
The cerebrum is divided into frontal, parietal, temporal, and
occipital lobes, which are specialized for different functions. 4. Describe the three main stages by which the
page 778 mammalian ear detects and codes sound.
Somatosensory, motor, auditory, and visual information is 5. Compare and contrast the roles of rod cells and cone
topographically mapped to specific areas in the cerebral cortex. cells in the retina.
page 780 6. Describe the role of the cornea and lens in vertebrate
eyes.
36.6 Cognition is the ability of the brain to process and
7. Describe three different types of eye in animals.
integrate complex information, remember and interpret
past events, solve problems, reason, and form ideas. 8. Draw the brain, label the lobes, and describe their
primary functions.
The cerebral cortex integrates and processes information from
diverse sources, giving rise to problem solving, reasoning, and 9. Describe the importance of topographic mapping
decision making. page 780 of sensory input to the cortex, using the primary
somatosensory cortex as an example.
The brain stores memories of past experiences and enables
learning through the creation of more long-lasting neural 10. Explain how brain function can be understood by studying
circuits. page 781 patients with brain injuries.
Animal
Movement
Muscles and Skeletons
Core Concepts
37.1 Muscles are biological
motors composed of actin
and myosin that generate
force and produce movement
for support, locomotion,
and control of internal
physiological functionsl.
37.2 The force generated by
muscle depends on muscle
size, degree of actin–myosin
overlap, shortening velocity,
and stimulation rate.
37.3 Hydrostatic skeletons,
exoskeletons, and
endoskeletons provide animals
with mechanical support and
protection
37.4 Vertebrate endoskeletons
allow for growth and repair
and transmit muscle forces
across joints.
Gustoimages/Science Source.
785
786 SECTION 37.1 M U S C L E S : B I O LO G I C A L M OTO R S T H AT G E N E R AT E F O RC E A N D P RO D U C E M OV E M E N T
The ability to move is a defining feature of animal life, allowing which evolved at least 600 million years ago. Thus, basic features
animals to explore new environments and avoid inhospitable of muscle organization and function are conserved across the
ones, escape predators, mate, feed, and play. An animal’s motor vast diversity of eukaryotes. As we will discuss, the geometry and
and nervous systems (Chapters 35 and 36) work together to organization of these proteins largely determines how muscles
enable it to sense and respond to its environment. How are contract to produce force and movement.
movements produced, and how are they controlled? What
determines an athlete’s performance? How do muscles and the Muscles use chemical energy to produce force
skeleton work together to provide movement and support? And and movement.
how do muscles convert the chemical energy of ATP into force Muscles are composed of elongated cells called muscle fibers.
and movement during a contraction? This chapter explores the Muscle fibers use ATP generated through cellular respiration
organization and function of the muscles and skeletons that (Chapter 6) to generate force and change length during a
power the movements of larger multicellular animals and provide contraction. This conversion of chemical energy into muscle work
mechanical support of their bodies (Fig. 37.1). underlies much of the energy cost of animal movement discussed
in Chapter 40.
A force is a push or pull by one object interacting with another
37.1 MUSCLES: BIOLOGICAL MOTORS object. The forces generated by skeletal muscles, for example,
THAT GENERATE FORCE AND act as pulling forces at specific sites of the skeleton. The work
performed by a muscle is equal to force times length change. For
PRODUCE MOVEMENT
example, work is increased when either the force produced or
We rely on our muscles for all kinds of movement. Muscles the distance the skeleton is moved increases. Similarly, a muscle
function as biological motors within the body because they that produces a pulling force twice as much as another muscle but
generate force and produce movement. Some of these movements moves the skeletal segment only half the distance does the same
are obvious—running, climbing stairs, raising your hand, playing work as that other muscle.
the piano. We are less aware of others—moving food through Because muscles only exert pulling forces, pairs of muscles
the digestive tract, breathing in and out, pumping blood through are arranged to produce movements in two opposing directions at
the body. A muscle’s ability to produce movement depends on specific joints of the skeleton. For example, muscles pull on the
electrically excitable muscle cells containing proteins that can be bones of your leg and foot to swing them forward when you kick a
activated by the nervous system. ball. Opposing sets of muscles contract to swing your leg back and
The contractile machinery of muscles is ancient. The proteins flex your knee before and after the kick.
underlying muscle contraction are found in eukaryotes that lived Muscles can shorten very quickly, and they can produce large
more than 1 billion years ago, and the first muscle fibers common forces for their weight. The forces they produce can be many times
to all animals are found in cnidarians (jellyfish and sea anemones), an animal’s body weight, allowing animals to move quickly. Some
small muscles contract extremely quickly:
The muscles of many flying insects
contract 200 to 500 times per second.
FIG. 37.1 Muscles and bones. Muscles and bones work together to produce movement.
Even in vertebrate animals, muscles can
Photo source: Tom Brakefield/Corbis.
contract as many as 50 to 100 times per
second. Other muscles, such as the closing
muscle of a clam, contract slowly, but
can do so for prolonged periods without
tiring. To see how muscles produce forces
and contract to change length, we now
consider how muscle fibers are organized
at the molecular level.
FIG. 37.2 Light micrographs of (a) skeletal muscle, (b) cardiac muscle, and (c) smooth muscle. Skeletal and cardiac muscles have a striated, or
striped, appearance; smooth muscle does not. Sources: a. Innerspace Imaging/Science Source; b. Manfred Kage/Science Source; c. SPL/Science Source.
a b c
In contrast to skeletal and cardiac muscle, smooth muscles Muscles, like the
appear unstriated under the light microscope because the biceps that flexes the Nerve
elbow joint, connect
organization of actin and myosin filaments in smooth muscles is to a rigid skeleton. Muscle Connective
irregular (Fig. 37.2c). Smooth muscles are found in the walls of bundle tissue
vertebrate and certain invertebrate (squid and octopus) arteries to
regulate blood flow, in the respiratory system to control airflow, Connective
and in the digestive and excretory systems to help transport food tissue
and waste products. Smooth muscles contract slowly compared
with cardiac and skeletal muscles. Consequently, bivalve mollusks Muscles are composed
rely on smooth muscle fibers to keep their shells closed for long Muscle of elongate cells called
fiber muscle fibers that are
periods without having to expend much energy. (cell) embedded in
surrounding
connective tissue.
Skeletal and cardiac muscle fibers are organized into
Nucleus
repeating contractile units called sarcomeres.
The visible bands in skeletal and cardiac muscles are an important Mitochondrion
clue to the mechanism that produces muscle contractions. Whole
muscles are made up of parallel bundles of individual muscle fibers
Individual fibers have many
(Fig. 37.3). Recall that a muscle fiber is a muscle cell. Each muscle myofibrils with a striated
fiber in turn contains hundreds of long, rodlike structures called appearance due to their regular
Myofibril molecular organization.
myofibrils. Myofibrils contain parallel arrays of actin and myosin
filaments that cause a muscle to contract.
788 SECTION 37.1 M U S C L E S : B I O LO G I C A L M OTO R S T H AT G E N E R AT E F O RC E A N D P RO D U C E M OV E M E N T
FIG. 37.5 Muscle sarcomere. (a) Longitudinal and (b) cross-sectional views of a sarcomere,
including two transmission electron micrographs. The sarcomere is the region
Muscle
between Z discs. It is the contractile unit of a muscle. Photo sources: a. Don W. Fawcett/
fiber
Science Source; b. Biophoto Associates/Science Source.
Myofibril
Sarcomere
b.
Z discs
Actin (thin) Myosin (thick)
a.
A longitudinal section shows the organization A cross section shows the regular hexagonal
of thick (myosin) and thin (actin) filaments. arrangement of thick and thin filaments.
Z disc Z disc
Sarcomere
CHAPTER 37 A N I M A L M OV E M E N T : M U S C L E S A N D S K E L E TO N S 789
FIG. 37.7 Cross-bridge cycle. The myosin head binds to actin and uses the energy of ATP to pull on the actin filament, causing muscle
shortening.
Thick
filament
Myosin ATP
head
Thin
filament
ADP
ADP Pi
Cross-bridge
The cross-bridge cycle is just that—a cycle (Fig. 37.7). Let’s The myosin head then binds a new ATP molecule (step 1
look at it in more detail: again), allowing it to detach from actin, and the cycle repeats. After
detachment, the myosin head again hydrolyzes ATP, allowing it to
1. The myosin head binds ATP. Binding of ATP allows the return to its original conformation and bind to a new site farther
myosin head to detach from actin and readies it for along the actin filament. With the release of ADP and Pi, the myosin
attachment to actin. head undergoes another cycle of force generation and movement.
2. The myosin head hydrolyzes ATP to ADP and inorganic Individual muscle contractions are the result of many
phosphate (Pi). Hydrolysis of ATP results in a conformational successive cycles of cross-bridge formation and detachment.
change in which the myosin head is cocked back. ADP and Pi During these cycles, muscle cells convert the chemical energy
remain bound to the myosin head. Because ADP and Pi are released by ATP into force and the kinetic energy of movement.
bound rather than released, the myosin head is in a high- Muscle fibers that contract especially quickly, such as those that
energy state. power insect wing flapping or produce the sound of cicadas and
rattlesnake tails, express myosin molecules that have high rates of
3. The myosin head then binds actin, forming a cross-bridge.
ATP hydrolysis, allowing faster rates of cross-bridge cycling, force
4. When the myosin head binds actin, the myosin head development, and shortening. Thus, myosin functions as both a
releases ADP and Pi. The result is another conformational structural protein and an enzyme.
change in the myosin head, called the power stroke. Because each thick filament can interact with as many as six
During the power stroke, the myosin head pivots forward actin filaments, at any one time numerous cross-bridges anchor
and generates a force, causing the myosin and actin the lattice of myosin filaments, while other myosin heads are
filaments to slide relative to each other over a distance detached to find new binding sites. When summed over millions
of approximately 7 nm. The power stroke pulls the actin of cross-bridges, these molecular events generate the force that
filaments toward the sarcomere midline. shortens the whole muscle.
CHAPTER 37 A N I M A L M OV E M E N T : M U S C L E S A N D S K E L E TO N S 791
j Quick Check 1 When an animal dies, its limbs and body become
stiff because its muscles go into rigor mortis (literally, rigor mortis FIG. 37.8 Excitation–contraction coupling. Depolarization
means “stiffness of death”). Why would the loss of ATP following (excitation) leads to shortening (contraction) of the
death cause this to happen? muscle. Photo source: Don W. Fawcett/Science Source.
Action
the muscle fiber (Chapter 35). Motor Muscle cell
p
How does membrane depolarization lead to the cross-bridge endplate
otentia
cycle? Actin and myosin filaments can form cross-bridges only Myofibrils
when the myosin-binding sites on actin are exposed. At rest, these
2
l
The depolarization
binding sites are blocked by the protein tropomyosin. The wave is conducted into the
of depolarization in the muscle cell initiates a chain of events interior of the fiber by
that moves tropomyosin away from these binding sites, allowing the infolding of
plasma membrane.
cross-bridges between actin and myosin to form and the muscle to
contract (Fig. 37.8). Sarcoplasmic
Let’s look at the chain of events that concludes with the reticulum
exposure of the myosin-binding sites in more detail. You saw in
Chapter 5 that eukaryotic cells contain several types of membrane- 3 Depolarization
bound internal organelle. The myofibrils of muscle cells are leads to the release
of Ca2+ from the
surrounded by a highly branched membrane-bound organelle sarcoplasmic
called the sarcoplasmic reticulum (SR), a modified form of the reticulum.
endoplasmic reticulum (Fig. 37.8). Depolarization initiated in the
plasma membrane is conducted to the SR through infoldings of Ca2+
Tropomyosin
the plasma membrane (Fig. 37.8). When the muscle is at rest, the
SR contains a large internal concentration of calcium (Ca2⫹) ions 4 Ca2+ binds to
transported in by calcium pumps in its membranes. troponin, which
causes movement
A muscular contraction is initiated when depolarization of the Actin Troponin of tropomyosin,
Myosin-binding sites
muscle fiber causes the SR to release Ca2⫹. The Ca2⫹ diffuses into on actin blocked exposure of
myosin-binding
the myofibrils and binds to a protein called troponin, causing the Myosin–binding sites sites on actin, and
troponin molecule to change shape. This conformational change on actin exposed formation of
of troponin, in turn, causes tropomyosin to move, exposing cross-bridges to
produce shortening
myosin-binding sites along the actin filament. Now myosin cross- of the muscle.
bridges can form with actin, producing a contraction. Note that at
this stage in the cross-bridge cycle, the myosin head has already
792 SECTION 37.2 M U S C L E CO N T R AC T I L E P RO P E RT I E S
hydrolyzed ATP, is bound to ADP and Pi, and is in the cocked-back blood flow to particular body regions, and the gut moves digestive
“ready” position. Binding to actin then allows the power stroke to contents through the gastrointestinal tract.
occur. In this way, contraction is initiated immediately following
depolarization and release of Ca21.
The process by which membrane depolarization leads to Ca21 37.2 MUSCLE CONTRACTILE
release from the SR and the formation of myosin-actin cross- PROPERTIES
bridges is called excitation–contraction coupling because
excitation of the muscle cell is coupled to contraction of the Actin and myosin are evolutionarily conserved across all animal
muscle, producing force and movement. Together, these events life, so all muscles have similar force-generating properties. The
are the molecular “switch” that causes a muscle to contract. The huge muscles of a weight lifter are evidence that larger muscles
muscle relaxes when neural stimulation ends. Acetylcholine can exert more force. Why is that? The summed force produced
is broken down or reabsorbed, and Ca21 is actively transported by individual myofibrils of activated muscle fibers determines the
back into the sarcoplasmic reticulum, allowing tropomyosin force the whole muscle can exert. This means that larger muscles
molecules to once again block myosin-binding sites along the with more fibers produce greater forces than smaller muscles
actin filaments. with fewer fibers. However, the force that a muscle produces also
depends on its contraction length and the speed of contraction, as
j Quick Check 2 Curare is a paralyzing compound that blocks the we discuss next.
action of the neurotransmitter acetylcholine at the muscle fiber’s
motor endplate. What effect do you think curare has on the release Muscle length affects actin–myosin overlap and
of calcium ions from the sarcoplasmic reticulum of the muscle cell? generation of force.
Why is it difficult to jump while standing on your toes? A muscle’s
ability to generate force depends in part on how much it is
Calmodulin regulates Ca2+ activation and relaxation
stretched before contraction begins. The sliding filament model
of smooth muscle.
for muscle contraction, like any good model, makes specific
How is the contraction of smooth muscle regulated? The smooth
predictions. In this case, it predicts that the amount of overlap
muscle that controls many internal organs can be activated by
between actin and myosin filaments within the sarcomere
the autonomic nervous system and also responds to stretch of
determines the number of cross-bridges that can form. The more
the muscle, local hormones, and other local factors such as pH,
overlap, the more force that can be produced. Conversely, when
oxygen, carbon dioxide, and nitric oxide by intracellular signaling.
a muscle fiber is pulled to long lengths and then contracts, it
For example, smooth muscle in the walls of arteries contracts
generates less force because the overlap between myosin and
when stimulated by the release of epinephrine to reduce blood
actin filaments is reduced. When a muscle fiber contracts at short
flow to a body region (Chapter 39), and smooth muscle within
lengths, it also produces less force because myosin filaments begin
the mammalian uterus contracts when oxytocin is released
to run into the Z disc at each end of the sarcomere, disrupting the
to stimulate contractions (Chapter 42). As in skeletal muscle,
geometry of the myosin filament lattice and hindering cross-bridge
these initiators trigger the release of Ca21 from the SR. However,
formation. At intermediate lengths, the muscle fiber generates
in smooth muscle, Ca21 also enters through voltage-gated and
maximum force because actin–myosin filament overlap is greatest.
stretch-receptor calcium channels in the cell’s plasma membrane.
These predictions were tested by experiments (Fig. 37.9).
Smooth muscle lacks the troponin–tropomyosin mechanism
This influence of muscle fiber length on force generated is
for regulating contraction. Instead, activation of smooth muscle
the reason that you can’t jump well if you are on your toes and
cells results when the protein calmodulin binds with Ca21
your ankles are fully extended: This position shortens your calf
released from the SR or entering through the cell’s membrane.
muscle fibers. Conversely, if your ankles are overly flexed, your
The calmodulin–Ca21 complex activates a myosin kinase that
calf muscles are lengthened, and again jumping force is limited.
phosphorylates the smooth muscle myosin heads, causing them
Through training, athletes and dancers learn techniques, such
to bind actin and begin the cross-bridge cycle. A second enzyme
as bending the knees before jumping, so that their leg muscles
dephosphorylates the myosin heads, disrupting their ability to
contract at intermediate lengths to maximize muscle-force output.
bind to actin, and the muscle relaxes.
The relationship between force and length of striated muscle
Smooth muscle contracts slowly compared with skeletal
also explains Starling’s Law for the function of the heart as a pump
muscle, using less ATP per unit time. The SR of smooth muscle
(discussed in Chapter 39), which ensures that the heart contracts
cells is less extensive and has many fewer calcium pumps than the
more strongly when it is filled by larger amounts of blood
SR of skeletal muscle cells. As a result, calcium is returned more
returning from the veins.
gradually from the myofibrils back to the SR, or pumped back out
through the cell’s membrane, slowing the relaxation of smooth j Quick Check 3 Why can you lift a larger load when your elbow is
muscle. Using the slow contractions of smooth muscle, clams hold slightly flexed and your biceps muscle is at an intermediate length
their shells closed for long periods, arteries contract and restrict than you can when your elbow is fully extended?
HOW DO WE KNOW?
FIG. 37.9
muscles?
Force (% of maximum)
80
60
Muscle force and shortening velocity are inversely example, your arm moves faster when you throw a light ball than
related. when you throw a heavy one. The reason is that the faster a muscle
In experiments carried out in the 1930s, A. V. Hill (who won fiber shortens, the fewer cross-bridges can form within it, reducing
the 1922 Nobel Prize in Physiology or Medicine for his work the force that each fiber and the muscle as a whole can produce.
on muscle energy use) observed that a muscle shortens fastest The term “muscle contraction” suggests that muscles shorten
when producing low forces (Fig. 37.10). To produce larger forces, when stimulated to generate force, but in fact muscles may also
the muscle must shorten at progressively slower velocities. For exert force and remain a uniform length or even be lengthened.
793
794 SECTION 37.2 M U S C L E CO N T R AC T I L E P RO P E RT I E S
FIG. 37.12 (a) Twitch and (b) fused tetanus muscle contractions. Source: Adapted from E. P. Widmaier, H. Raff, and K. T. Strang, 2011, Vander’s Human
Physiology, New York: McGraw-Hill.
0 Muscle fiber
action potential
3 Tetanus
–90
Relative force
2 Summation
force (Newtons)
0.3
Muscle fiber
Muscle
0.2 contraction Twitch
1
0.1
0 0
0 20 40 60 80 100 120 140 100 200 300 400 500 600 700 800 900 1000
Time (ms) Time (ms)
Latent
period
circumferential (circular) layers, allowing them to function as Measurements in animals indicate that skeletal muscles
muscle antagonists that control movement and shape. commonly produce tetanic contractions, which generate steady
In contrast, when muscles combine to produce similar and large forces. Tetanus is a normal physiological response of a
motions, they are termed muscle agonists. Muscles arranged as muscle, but it can also be induced by a toxin from the bacterium
agonists increase the strength and improve the control of joint Clostridium tetani, so named because it causes severe muscle
motion. For example, the three heads of the triceps are agonists of spasms, particularly of the jaw, chest, back, and abdomen.
each other (Fig. 37.11). A motor neuron and the population of muscle fibers that it
innervates are collectively termed a motor unit (Fig. 37.13).
Muscle force is summed by an increase in stimulation
frequency and the recruitment of motor units.
How do animals vary the amount of force exerted by a muscle? As
we have seen, skeletal muscles are stimulated by motor nerves, FIG. 37.13 Motor units. A motor unit consists of the motor neuron
which conduct action potentials to the neuromuscular junction. and the population of cells (fibers) it innervates.
The force exerted by a muscle depends on the frequency of
stimulation by the motor nerve. As action potentials become more
Motor
frequent, the amount of calcium that is released to activate cross-
neurons
bridge formation in the muscle fibers also increases.
A single action potential results in a twitch contraction of
a certain force (Fig. 37.12a). If sufficient time is allowed for the
muscle to pump Ca21 back into the sarcoplasmic reticulum, the Motor
contraction ends, force falls to zero, and a second stimulus can endplate
elicit a twitch contraction of the same force. However, if a second Myofibril Muscle
action potential arrives before the muscle has relaxed, a greater cell
FIG. 37.14 Slow-twitch (darkly stained) and fast-twitch (lightly stained) skeletal muscle fibers. These two types of fiber provide differences
in endurance and the speed of contraction. (a) Mammalian limb muscle; (b) muscles of two different fish species. Photo source: Biophoto
Associates/Science Source.
a. b.
Fast-twitch glycolytic fibers (large diameter)
Fast-twitch
glycolytic
fibers are
light yellow.
Mackerel Tuna
Fast-twitch
fibers
Slow-twitch Slow-twitch
oxidative fibers
fibers are
dark red.
Motor units can include relatively few to several hundred muscle depends on fast-twitch fibers to sprint or lunge at its prey. A key
fibers. The number of muscle fibers innervated by a given motor difference between the two types of fiber is that slow-twitch fibers
nerve, and hence the size of the motor unit, affects how finely a obtain their energy through oxidative phosphorylation (aerobic
vertebrate muscle’s force can be controlled. For example, finger respiration), and fast-twitch fibers obtain their energy mainly
muscles have small motor units allowing fine adjustments through glycolysis (Chapter 7).
in muscle force, whereas leg muscles have large motor units Although slow-twitch fibers develop force more slowly,
providing larger adjustments in force. Together with stimulation they have greater resistance to fatigue in response to repetitive
frequency, a vertebrate muscle’s force output depends on the stimulation—that is, their loss of force over time is less. Their
number of motor units (and therefore the number of muscle greater endurance is explained by the ability of their mitochondria
fibers) that are activated. Within each motor unit, muscle fibers to supply ATP to muscle fibers by aerobic respiration. Slow-twitch
generally share similar contractile and metabolic properties. fibers have many mitochondria and are well supplied by capillaries.
Differences in these properties can give muscles very different They contain an abundance of myoglobin, an oxygen-binding
capabilities, as discussed in the next section. protein related to hemoglobin that facilitates oxygen delivery
to the mitochondria (Chapter 39). The iron in myoglobin gives
j Quick Check 4 What are the two mechanisms by which the force
muscles with these fibers their red appearance. Slow-twitch
of contraction can be increased in vertebrate muscles?
muscle fibers express a chemically “slow” form of myosin with a
relatively low rate of ATP hydrolysis, limiting their speed of cross-
Skeletal muscles have slow-twitch and fast-twitch bridge cycling and force development.
fibers. White fast-twitch muscle fibers have fewer mitochondria and
The difference between a sprinter and a marathoner is not just capillaries, contain little myoglobin, and rely heavily on glycolysis
training, but also the properties of their muscles. There are to produce ATP. Fast-twitch fibers express a chemically “fast” form
different types of muscle fiber (Fig. 37.14), allowing variation in of myosin with a high rate of ATP hydrolysis, favoring rapid force
the way muscles contract. In vertebrates, these are most simply development and movement. However, fast-twitch fibers also
classified as red slow-twitch fibers and white fast-twitch fibers fatigue quickly. Because white fibers are larger than red fibers,
(Fig. 37.14a). Slow-twitch fibers are found in muscles that contract they generate more force. In general, most skeletal muscles are
slowly and consume ATP more slowly to produce force. An animal composed of mixed populations of red and white fiber types,
uses slow-twitch fibers to control its posture or move slowly and providing a broad range of contractile function.
economically. Fast-twitch fibers generate force quickly, producing Athletes who have more oxidative slow-twitch fibers excel at
rapid movements, but they consume ATP more quickly. An animal endurance and long-distance competitions. In contrast, athletes
CHAPTER 37 A N I M A L M OV E M E N T : M U S C L E S A N D S K E L E TO N S 797
who have larger numbers of fast-twitch fibers perform better red muscle that they can keep warm (Fig. 37.14b), enabling their
in sprint races and weight-lifting competitions. Because the muscles to contract longer and faster to enhance their swimming.
distribution and properties of muscle fiber types are strongly When escaping from a predator or attacking prey, fish recruit their
inherited, it is largely true that champions are born and not made. larger fast-twitch white trunk musculature for rapid swimming.
Nevertheless, aerobic training can significantly increase the energy The evolutionary arms race between predators and prey
output through oxidative phosphorylation of an individual’s muscle has resulted in selection for particular muscle fiber types and
fibers, just as weight lifting and speed training can enhance an other musculoskeletal specializations for rapid movement and
individual’s strength and sprinting ability. Contrary to popular maneuvering. Features of the skeleton that contribute to these
belief that weight lifting builds muscle by straining the muscle to specializations are discussed next.
build new fibers, it actually builds muscle by increasing the size of
existing muscle fibers through the synthesis of additional myosin
and actin filaments. This synthesis increases the cross-sectional area 37.3 ANIMAL SKELETONS
of the fiber and thus its force-generating capacity.
Most animal skeletons provide a rigid set of elements that meet
at joints (articulate) to transmit muscle forces for movement
? CASE 7 PREDATOR–PREY: A GAME OF LIFE AND DEATH
and body support. They also enable many animals to manipulate
How do different types of muscle fiber affect the their environment by digging burrows, building nests, or
speed of predators and prey? constructing webs to catch food. Animals have evolved three types
We have just seen that slow-twitch muscle fibers provide of skeletal system: hydrostatic skeletons, exoskeletons, and
endurance for sustained activity, whereas larger fast-twitch endoskeletons. All three types of skeleton have rigid elements
fibers produce greater speed and strength but fatigue quickly. that resist the pull of antagonist sets of muscles.
The relative distribution of these fiber types in the muscles of
different animals is influenced mainly by genetic heritage. This Hydrostatic skeletons support animals by muscles that
affects the locomotive behavior and capacities of both predator act on a fluid-filled cavity.
and prey animals. Whereas cheetahs have exceptional speed, their Hydrostatic skeletons evolved early in multicellular animals
muscles tire quickly. As their prey, antelope have muscles that with the first cnidarians (jellyfish and anemones) approximately
enable endurance long-distance running and contract rapidly for 600 million years ago. They are found in nearly all multicellular
maneuvering. animals as well as in many vascular plants. In animals that depend
Highly aerobic animals such as dogs and antelope have large on a hydrostatic skeleton, fluid contained within a body cavity
fractions of slow-twitch fibers and specialized fast-twitch muscle serves as the supportive component of the skeleton. Muscles exert
fibers that have a high oxidative capacity and use glycolysis for pressure against the fluid to produce movement.
rapid ATP synthesis. These muscle fibers allow the animals to move Two sets of opposing muscles surround the fluid, controlling
for extended periods of time at relatively fast speeds. In contrast, the width and length of the body cavity and, in many cases, of the
cats have mainly fast-twitch fibers, enabling them to sprint whole animal (Fig. 37.15a). Circular muscles reduce the diameter
and pounce quickly. Nevertheless, cats and other animals use of the body cavity, and longitudinal muscles reduce its length. A
particular muscles with high concentrations of slow-twitch fibers sea anemone can bend its body in various directions to feed or to
(these are the dark-staining fibers shown in Fig. 37.14a) for slower resist water currents by closing its mouth to keep its fluid volume
postural movements and stealth. Animals such as sloths and lorises constant and contracting its circular and longitudinal muscles.
that move slowly have mostly oxidative slow-twitch fibers and few Sea anemones extend themselves into the water column by
glycolytic fast-twitch fibers. contracting their circular muscles and relaxing their longitudinal
More generally, animals with high body temperatures and muscles. Controlling the amount of fluid in their body cavity also
high metabolic rates (birds and mammals) have larger numbers allows sea anemones to adjust their shape. When threatened, a sea
of oxidative fibers compared with animals that have lower body anemone rapidly retracts by contracting its longitudinal muscles
temperatures and lower metabolic rates (reptiles). As a result, and allowing water to escape from its body cavity.
lizards use glycolytic fast-twitch fibers to sprint for brief periods Similarly, earthworms burrow through the soil by moving a
but must then recover from the acid buildup produced by their series of hydrostatic segments along their body (Fig. 37.15b). By
muscles’ anaerobic activity in longer periods of rest (Chapter 40). contracting longitudinal muscles in a few segments, they shorten
In contrast, birds and mammals can sustain activity over longer those segments and also widen them to anchor those segments
time periods because they have oxidative muscle fibers supported against the soil. They then extend intervening segments between
by aerobic ATP supply. anchor points by contracting circular muscles, causing the
Most fish have a narrow band of slow-twitch red muscle fibers segments to lengthen and move the animal’s body through the soil.
that runs beneath their skin, which they use for slow steady Because of their simple but effective organization, hydrostatic
swimming. Tuna and some sharks have evolved deeper regions of skeletons are well adapted for many uses. In animals such as squid
798 SECTION 37.3 A N I M A L S K E L E TO N S
FIG. 37.15 Diverse examples of hydrostatic skeletal support. (a) In sea anemone; (b) in earthworm; (c) intervertebral discs; (d) articular
cartilage. Photo sources: a. Carole Valkenier/Getty Images; b. Nigel Cattlin/Alamy.
a. b.
Partition
between
Fluid-filled Blood
segments
body cavity vessel
Epidermis Gut
Longitudinal
muscles Longitudinal
Circular muscles muscle
Fluid-filled
body cavity Circular muscle
Body wall
c. d.
Spinal cord
Nerve root
Ligament
Vertebra
and jellyfish, the hydrostatic skeleton has become specialized for bony vertebrae of the backbone (Fig. 37.15c). Each disc has a wall
jet-propelled locomotion. Large circular muscles contract to eject reinforced with connective tissue that surrounds a jelly-like fluid.
fluid from the body cavity, propelling the animal in the opposite Intervertebral discs enable the backbone to twist and bend. Disc
direction. The muscles of other mollusks also exert pressure walls damaged by repeated stress can rupture, causing significant
against a hydrostatic skeleton. By this means, for example, a clam lower back pain. Articular cartilage, another fluid-filled tissue,
uses its muscular “foot” to burrow into the sediment, and an forms the joint surfaces between adjacent bones (Fig. 37.15d). The
octopus adeptly manipulates its flexible tentacles. (Clams also fluid within the cartilage resists the pressure between the ends of
have shells that form an exoskeleton to protect the body.) These articulating bones, cushioning forces transmitted across the joint.
same principles allow an elephant to control its trunk, and our
tongue to manipulate food and assist in speech. Exoskeletons provide hard external support
Even vertebrate animals with rigid endoskeletons have and protection.
hydrostatic elements that provide flexibility and cushion loads An exoskeleton is a rigid skeleton that lies outside the animal’s
transmitted by the skeleton. These include intervertebral discs soft tissues. The first mineralized skeletons arose with sponges
and cartilage. Intervertebral discs are sandwiched between the about 650 million years ago, but the more common exoskeletons
CHAPTER 37 A N I M A L M OV E M E N T : M U S C L E S A N D S K E L E TO N S 799
FIG. 37.16 Examples of exoskeletons. The shells of (a) a bivalve mollusk (b) and nautilus, made of calcium carbonate, surround and protect internal
soft body parts. The exoskeleton of arthropods, such as (c) a grasshopper, is made of stiff cuticle that surrounds internal muscles and
tendons and other internal body parts. Sources: a. Rita van den Broek/age fotostock; b. Reinhard Dirscherl/Getty Images; c. Jim Simmen/Getty Images.
a b c
subsequently evolved in other invertebrate groups adapted for cuticle of arthropods is soft, so the animal can grow before the
life in aquatic and terrestrial environments (Fig. 37.16). Because cuticle hardens. Mature cuticle consists of two layers. A thin outer,
they are on the exterior of the animal, exoskeletons provide hard waxy layer minimizes water loss. Water loss is especially dangerous
external support and protection, allowing muscles to attach from for terrestrial arthropods, given their small size. The much
the inside. However, a main disadvantage is that exoskeletons thicker inner layer, whether flexible or stiff, is tough and hard
limit growth. to break. The cuticle remains flexible at joints, allowing motion
Different invertebrates have different kinds of exoskeleton, between body segments. Because a rigid exoskeleton restricts
but all types have relatively few cells for their volume of tissue. growth, arthropods shed their cuticle at intervals, a process called
The shells of bivalve mollusks, such as clams and mussels, or the molting. Molting allows arthropods to expand and grow before
cephalopod mollusk Nautilus that has existed largely unchanged forming a new rigid exoskeleton.
for nearly 500 million years, form a hard, mineralized calcium Marine crustaceans, such as crabs and lobsters, incorporate
carbonate exoskeleton (Figs. 37.16a and 37.16b). The calcium calcium carbonate in their cuticle. Calcium carbonate makes
carbonate is reinforced by proteins and is therefore an example the exoskeleton hard and stiff, much like the hardened cuticle
of a composite material, one that combines substances with of terrestrial insects, helping to protect these crustaceans from
different properties. Because of its composite nature, the shell predators.
is less brittle and more difficult to break than if it were made While offering several protective benefits, exoskeletons pose
of just one substance. The shell expands as the organism grows risks as well. Animals are vulnerable when the newly formed
and epidermal cells deposit new layers of mineralized protein in exoskeleton has not yet hardened. Exoskeletons are also hard to
regular geometric patterns. You can see the growth rings if you repair. If a skeleton is damaged while growing, the animal must
examine a mollusk shell. Although some marine bivalves achieve produce an entirely new one. Because the exoskeleton is a thin-
large size over many years, growth is limited by the rate at which walled structure, it is prone to breaking if its surface area is very
new skeletal material can be deposited on the outside of the shell. large. Consequently, the imperviousness of the monstrous insects
Arthropods have more complex exoskeletons. More than half depicted in science-fiction films is improbable—they would easily
of all known animal species, including insects and crustaceans, break from a blow to their exoskeleton.
are arthropods. Arthropods are defined in part by their jointed
legs, and another important feature is their exoskeleton formed The rigid bones of vertebrate endoskeletons are
of a cuticle that covers their entire body (Fig. 37.16c). Arthropod jointed for motion and can be repaired if damaged.
exoskeletons, which first evolved in aquatic crustaceans, protect Endoskeletons first evolved about 350–500 million years ago
animals from desiccation and physical insults. Consequently, when the first vertebrates evolved cartilaginous endoskeletons.
exoskeletons were key to the success and diversification of insects Lampreys are descendants of these early vertebrates.
in terrestrial environments about 450 million years ago. Subsequently, bony fishes evolved a more rigid mineralized
The cuticle of insects is composed mainly of chitin, a internal skeleton, a defining feature of this diverse group of
nitrogen-containing polysaccharide. When initially formed, the vertebrates. Sharks and other elasmobranchs (the cartilaginous
800 SECTION 37.4 V E RT E B R AT E S K E L E TO N S
is also stiff so that forces are transmitted effectively from the joint
to the bone shaft. Bone marrow, a fatty tissue found between FIG. 37.20 Hinge and ball-and-socket joints. The elbow and knee
trabeculae and also within the bone’s central cavity, contains are examples of hinge joints. The shoulder and hip are
many important cells, including blood-forming cells, other stem examples of ball-and-socket joints.
cells (Chapter 20), immune system cells (Chapter 43), and fat cells.
Ball-and-socket
Bones grow in length and width, and can be repaired. Highly mobile
ball-and-socket
Bones can grow in length, at least until an animal reaches maturity. joints allow
Growth in length occurs at a growth plate (see Fig. 37.18), a region motion along
of cartilage between the middle region, called the diaphysis, and all three axes.
the end, called the epiphysis. The growth plate remains in place
when the rest of the cartilage is transformed into bone. The growth Hinge
plate adds new cartilage toward the bone’s diaphysis, enabling
bone length to continue to increase after birth (see Fig. 37.18). Hinge joints
At maturity, each growth plate fuses as the remaining cartilage limit motion
to one
is replaced with bone, preventing further growth in length. The primary
fusion of growth plates is typical of most mammals and birds. In axis.
amphibians and reptiles, the growth plates often do not fuse and
growth may continue at a slower pace over much of their lifetime.
Limb bones grow in diameter when osteoblasts deposit new
bone on the bone’s external surface. At the same time, bone is
removed from the inner surface, expanding the marrow cavity.
Bone removal is slower than bone growth, thickening the walls
during growth. Bone is removed from the marrow cavity by a
group of cells called osteoclasts that secrete digestive enzymes
and acid to dissolve the calcium mineral and collagen. These
dissolved compounds are reabsorbed and recycled for bone
formation in other regions of the skeleton. Through this process,
the vertebrate skeleton serves as an important store of calcium
and phosphate ions. For example, in female birds, calcium
removed from the skeleton is regularly used to form the eggshell.
A great advantage of endoskeletons compared with
exoskeletons is that a damaged endoskeleton can be repaired by
osteoblasts and osteoclasts forming and removing mineralized They allow you to flex and extend your fingers as well as spread
tissue in particular regions of the bone. Generally, physically them laterally or move them together when making a fist or
active younger adults have thicker bones than less active younger grasping objects.
adults because physical loading stimulates osteoblasts to produce Joints with a broader range of motion are generally less stable.
more bone during growth. However, in older adults, bone tissue is The shoulder is the most mobile joint in the human body, but it
gradually lost as osteoclasts remove more bone than is produced is also the most often dislocated or injured. In contrast, the ankle
by osteoblasts. Bone loss is particularly severe in women after joint of dogs, horses, and other animals is a stable hinge joint that
menopause, in part because of hormone shifts as well as reduced is unlikely to be dislocated, but its range of motion is limited to
physical activity, and can lead to osteoporosis, a condition that flexion and extension. Because muscles are arranged as paired sets
significantly increases the risk of bone fracture. of antagonists to move a joint in opposing directions, hinge joints
are controlled by as few as two antagonist muscles (generally
Joint shape determines range of motion and skeletal referred to as a flexor and an extensor). In contrast, ball-and-socket
muscle organization. joints have at least three sets of muscle antagonists to control
The shapes of the bone surfaces that meet at a joint determine motion in three different planes. As a result, a more complex
the range of motion at that joint. Joints range from simple hinge organization of muscles is needed to control the movements of the
joints that allow one axis of rotation to ball-and-socket joints arm at the shoulder joint or the leg at the hip joint.
that allow rotation in three axes (Fig. 37.20). The human elbow
joint and the ankle joint of a dog are examples of hinge joints. The Muscles exert forces by skeletal levers to produce
shoulder and hip joints are examples of ball-and-socket joints, joint motion.
which allow the widest range of motion, as when you throw or By serving as a rigid set of levers, the skeleton enables muscles
kick a ball. The joints at the base of each finger are intermediate: to transmit forces that cause joint rotation. Muscles that attach
CHAPTER 37 A N I M A L M OV E M E N T : M U S C L E S A N D S K E L E TO N S 803
FIG. 37.22 Functional anatomy. The armadillo forelimb skeleton is adapted for digging, whereas the horse forelimb is adapted for speed and
weight support. Sources: Based on M. J. Smith and R. J. G. Savage, 1956, “Some Locomotory Adaptations in Mammals,” Zoological Journal of the Linnean Society
42:603–622. Photos ( left to right): Morales/age footstock; J. L. Klein & M. L. Hubert / Science Source.
Armadillo Horse
Line of muscle
Armadillo forelimbs are force Horse limbs are long
relatively short for the r for the animal’s size,
animal’s size, have a lot have reduced weight
of weight in the foot, and L toward the hoof, and
have large r compared to have small r compared
L, which produce large to L, which produce
digging forces. L rapid limb movements.
distance from where the output force is exerted (small L) produce the muscle attachment site (small r) and a long distance from where
strong but slow movements. Moles, armadillos, and spade-foot the output force is exerted (large L) produce faster movements but
toads are examples of digging animals that have this type of muscle– with less force. These are found in animals adapted for high-speed
joint arrangement. In contrast, joints located a short distance from running, such as antelope, cheetahs, and horses. •
Core Concepts Summary Muscles exert more force when they contract at slow
velocities compared with when they contract at high
37.1 Muscles are biological motors composed of actin velocities. page 793
and myosin that generate force and produce movement Because muscles can transmit force only by pulling on the
for support, locomotion, and control of internal skeleton, they are arranged as antagonist pairs to produce
physiological functions. reciprocal motions of a joint or limb. page 794
There are two main types of muscle: striated (skeletal and In vertebrates, a motor unit consists of a single motor neuron
cardiac) and smooth. page 787 and the muscle fibers (cells) it innervates. page 795
Skeletal and cardiac muscle fibers appear striated when Muscle force is increased by increasing the motor neuron firing
viewed under the microscope because of the regular spacing of rate and, in vertebrates, by increasing the number of motor units
sarcomeres along their length. page 787 that are activated. page 796
Smooth muscle fibers, which regulate airflow for breathing, Vertebrate muscles have two types of fiber: red slow-twitch
blood flow through arteries, and the passage of food through fibers that contract slowly over longer time periods and white
the gut, lack regular sarcomere organization and appear smooth fast-twitch fibers that contract rapidly but fatigue quickly.
when viewed under the microscope. page 787 page 796
Skeletal muscle fibers are long thin cells composed of parallel
sets of myofibrils built up from smaller parallel arrays of actin
37.3 Hydrostatic skeletons, exoskeletons, and
and myosin filaments. page 787
endoskeletons provide animals with mechanical support
The sarcomere is the basic contractile unit of a skeletal and protection.
muscle. Sarcomeres are arranged in series along the length of a
myofibril. page 788 The rigid element of a hydrostatic skeleton is an incompressible
fluid within a body cavity, used to support the body and change
Muscles change length and produce force by the formation of shape. page 797
actin–myosin cross-bridges, causing myosin and actin filaments
to slide relative to each other. page 789 Invertebrate exoskeletons form an external rigid support system,
which protects the animal and limits water loss, but also limits
Muscles are stimulated by motor neurons at the fiber’s growth and repair. page 798
motor endplate, leading to depolarization of the muscle cell
that triggers the release of Ca21 ions from the sarcoplasmic Vertebrates have a bony endoskeleton that provides rigid
reticulum. Ca21 binds troponin, which moves tropomyosin off support and protection of body organs, and that can grow and be
the myosin-binding sites on actin, allowing myosin heads to repaired. page 799
form cross-bridges with actin. page 791 The vertebrate endoskeleton is organized into axial (central)
Excitation–contraction coupling is the process by which and appendicular (limb) components. page 800
depolarization of the muscle cell leads to its shortening.
Vertebrate endoskeletons consist of bone and cartilage.
page 792
page 800
37.2 The force generated by muscle depends on Bone is a composite tissue that consists of calcium phosphate
muscle size, degree of actin–myosin overlap, shortening mineral and type I collagen and that is rigid and hard to break.
velocity, and stimulation rate. page 800
Muscles exert their greatest force when actin–myosin Cartilage is a fluid-based gel reinforced by type II collagen and
filaments have maximal overlap, allowing the most cross- proteoglycans, providing cushioning support at joint surfaces
bridges to form. page 792 page 800
CCHHAAPPTTEERR 3377 AANNI IM
MAALL M
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OVEEM
MEENNTT:: M
MUUSSCCLLEESS AANNDD SSKKEELLEETO
TONNSS 880055
37.4 Vertebrate endoskeletons allow for growth and events to how muscles generate force and shorten when they
repair and transmit muscle forces across joints. are stimulated to contract, identifying the role that ATP plays.
Vertebrate bones develop by one of two processes: either 4. Draw a graph of the isometric force–length relationship
directly or by way of a cartilage model. page 801 of striated muscle, indicating where maximal overlap between
actin and myosin filaments occurs.
Cartilage forms much of the embryonic skeleton and
remains as growth plates within the bone to provide rapid 5. Draw a graph of the force–shortening velocity
growth after birth, as well as forming the bone’s joint relationship of striated muscle.
(articular) surfaces. page 801 6. Compare the force produced by a muscle over time
when it is stimulated by a single twitch stimulus with the
Bone has two basic structures: Compact bone forms the
force produced by multiple stimuli at low frequency, and then
solid walls of a bone’s shaft, and spongy bone forms a mesh
with the force produced when the stimulation frequency is
that supports the cartilage at the bone’s ends. page 801
increased.
Bone formation by osteoblasts and removal by osteoclasts is
7. Name the two basic structural elements common to all
a continuing process of growth, shape change, and repair.
animal musculoskeletal systems.
page 802
8. Compare and contrast three features of an exoskeleton
The shape of a bone’s joint surfaces largely determines the
and an endoskeleton.
range of motion and stability of a joint. page 802
9. Identify the two primary components of bone tissue and
Muscles produce joint movements by transmitting forces by
explain how each of these contributes to a bone’s strength,
means of rigid skeletal levers. page 802
stiffness, and resistance to fracture.
10. Diagram a limb bone, such as the tibia, showing the regions
Self-Assessment of articular cartilage, spongy trabecular bone, compact bone
tissue, and the marrow cavity.
1. Diagram a sarcomere, showing the basic organization of
thin (actin) and thick (myosin) filaments. Indicate on your
diagram the regions where myosin cross-bridges form Log in to to check your answers to the Self-
Assessment questions, and to access additional learning tools.
with actin.
2. Describe the sequence of events that occurs when an
action potential arrives at a muscle fiber’s motor endplate,
causing the muscle to be depolarized.
3. Describe the sequence of events involved in myosin
cross-bridge attachment and detachment. Relate these
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CHAPTER 38
Animal
Endocrine
Systems
Core Concepts
38.1 Animal endocrine systems
release chemical signals called
hormones into the bloodstream
that respond to environmental
cues, regulate growth and
development, and maintain
homeostasis.
38.2 Hormones bind to receptors on
or inside target cells, and their
signals are amplified to exert
strong effects on target cells.
38.3 In vertebrate animals, the
hypothalamus and the pituitary
gland control and integrate
diverse bodily functions and
behaviors.
38.4 Chemical communication
can also occur locally
between neighboring cells
or, through the release
of pheromones, between
individuals, coordinating social
interactions.
FLPA/Chris Mattison/age fotostock.
807
808 SECTION 38.1 A N OV E RV I E W O F E N D O C R I N E F U N C T I O N
We have seen how the nervous system allows an animal to physiological functions of the organism. In particular, we examine
sense and respond to its environment, coordinating the animal’s the mechanisms by which hormones trigger cellular responses in
movement and behavior (Chapters 35–37). The nervous system also their target organs. Because most hormones are evolutionarily
works closely with the endocrine system to regulate an animal’s conserved, their chemical structure is similar across a diverse array
internal physiological functions. This coordination is accomplished of animals. However, their functions often evolve rapidly, enabling
by signals sent from the nervous system to the endocrine system, hormones to serve new and broader roles.
which distributes chemical signals throughout the body. The
endocrine system is made up of an interacting set of secretory
glands and organs, located in different regions of the body, which 38.1 AN OVERVIEW OF
respond to nervous system signals as well as to blood-borne signals ENDOCRINE FUNCTION
from other organs to regulate internal bodily functions.
The signals communicated by the nervous and endocrine The word “hormone” often popularly connotes teenagers and
systems differ greatly in their modes of transmission and the times the changes that occur to their bodies as they grow and mature.
over which they act. The nervous system sends signals rapidly by Hormones, as we will see, do play a key role in animal growth and
action potentials running along nerve axons, and communication development—but that is only one of their roles. Hormones play
occurs between adjacent nerve cells by means of neurotransmitters. diverse physiological roles in the body, in particular regulating an
The endocrine system, by contrast, relies on cells and glands that organism’s response to the environment and helping to maintain
secrete chemical signals called hormones, which influence the stable physiological conditions within cells or within the animal
actions of other cells in the body. Whereas some hormones act as a whole. We start by highlighting these functions before
locally, many others are released into the bloodstream, allowing addressing the molecular mechanisms of how hormones work in
them to circulate and influence distant target cells throughout the section 38.2.
body. As a result, endocrine communication is generally slower and
more prolonged than the rapid and brief signals transmitted by The endocrine system helps to regulate an organism’s
nerve cells. Hormones exert specific effects on particular target cells response to its environment.
within the body by binding to receptors on or in target cells. The Organisms face constant changes in their environment. These
downstream influence of hormones is amplified in a series of steps changes often present physiological challenges or stresses that
so that a small amount of hormone can have dramatic effects in the the organism must respond to by altering the functional state
body (Chapter 9). of its body. Changes in light or temperature, the threat of a
In this chapter, we explore the properties and actions of predator, or the presence of a potential mate stimulate responses
hormones that help to coordinate and maintain a broad set of of an animal’s nervous system and endocrine system. Endocrine
FIG. 38.1 Growth and development in (a) moths and caterpillars and in (b) grasshoppers.
a. b.
Metamorphosis Molting
Adult
Molting Molting
Eggs
Hatching
4th nymph Eggs
5th instar
1st nymph
4th instar
responses are commonly triggered by sensory signals received by exoskeleton is referred to as molting. Each molting produces
the nervous system that are relayed to the endocrine system. The a new larval stage. In some insects, such as moths, the animal’s
endocrine system, with its slower and more prolonged signaling, body also changes dramatically, undergoing metamorphosis at
reinforces physiological changes in the animal’s body that better a key stage in development (Fig. 38.1a). In other insects, such
suit the environmental cues received by its nervous system. as grasshoppers and crickets, the animal grows larger after each
When a gazelle sees or smells a predator, its endocrine system molting, but with little change in body form (Fig. 38.1b).
helps to ready its body for rapid escape. When a female cardinal Molting and metamorphosis are regulated by hormones
sees a bright red, singing male early in spring, endocrine signals released from tissues in the insect’s head. British physiologist
released from within the female cardinal’s brain initiate changes in Vincent Wigglesworth studied their effects on the blood-sucking
its reproductive organs and increase its behavioral responsiveness, insect Rhodnius. Normally, Rhodnius goes through five juvenile
encouraging it to select the male as its mate. And when particular stages before developing into its final adult body form. Like
smells stimulate a sense of hunger and digestive function in grasshoppers and crickets, it does not undergo metamorphosis.
animals such as dogs and humans, the animals are attracted Each of the developmental stages is triggered by a blood meal.
to food. In each of these cases, the endocrine system helps an Wigglesworth showed that he could prevent molting if the head
organism respond appropriately to environmental cues. of the insect were removed shortly after a blood meal (Fig. 38.2).
Rhodnius can survive for long periods despite having its head
The endocrine system regulates growth and removed. If the insect takes a blood meal and the head is removed
development. a week later, the animal’s body undergoes a molt and grows into its
Growth and development require broad changes in many different adult form. Wigglesworth hypothesized that a diffusing substance
organ systems. The release of circulating hormones from the from the animal’s head controls its molt. In the first case, this
endocrine system accomplishes these changes, regulating how substance does not have time to reach the body to trigger a molt,
animals develop and grow. For example, we discuss in Chapter 42 but in the second it does.
the importance of the sex hormones estrogen and testosterone The German endocrinologist Alfred Kuhn found a similar
in determining female or male sexual characteristics both in the result in experiments performed on moth caterpillars. Tying the
embryo and during puberty. caterpillar’s head off from the rest of the body prevented the body
As another example, let’s consider how the well-studied from molting. Wigglesworth and Kuhn considered the diffusing
endocrine system of insects regulates their growth and substance to be a brain hormone. Subsequent work showed that
development. Insects produce a rigid exoskeleton (Chapter 37), cells in a specialized region of the insect brain secrete the peptide
which must be periodically shed and replaced by a larger new now known as prothoracicotropic hormone (PTTH) (Table 38.1).
one to enable the insect to grow (Fig. 38.1). Shedding of the In Rhodnius, PTTH is released after a blood meal and acts to trigger
Corpora allata Juvenile hormone All body tissues Inhibits metamorphosis to adult stages; stimulates
(peptide) retention of juvenile characteristics
Prothoracic gland Ecdysone All body tissues Stimulates molt and, in absence or low levels of juvenile
(steroid) hormone, stimulates metamorphosis
Nervous system Ecdysone All body tissues Stimulates growth and regeneration in sea anemones,
(steroid) flatworms, nematodes, annelids, snails, and sea stars
Brain and eye stalks Chromatotropins Chromatophores Stimulates pigmentation changes in crustaceans
(peptides)
Reproductive gland Androgen Reproductive tract Regulates development of testes and male secondary
(peptide) sexual characteristics of crustaceans
HOW DO WE KNOW?
FIG. 38.2
Egg 1st nymph 2nd nymph 3rd nymph 4th nymph 5th nymph Adult
b.
Experiment 1 Experiment 2
3rd nymph
Adult
decapitated
formed
1 week after
0 1 hr 1 week blood meal
FOLLOW-UP WORK Subsequent studies by the German SOURCES Wigglesworth, V. B. 1934. “The Physiology of Ecdysis in Rhodnius
prolixus (Hemiptera). II. Factors Controlling Moulting and ‘Metamorphosis.’ ”
endocrinologist Alfred Kuhn confirmed the result in experiments Quarterly Journal of Microscopical Sciences 77:191–223; Nagasawa, H., et al.
performed on moth caterpillars. More recent molecular analyses 1984. “Amino-Terminal Amino Acid Sequence of the Silkworm Prothoracicotropic
Hormone: Homology with Insulin.” Science 226:1344 –1345; Kawakami, A.,
performed by Japanese molecular endocrinologists Nagasawa and
et al. 1990. “Molecular Cloning of the Bombyx mori Prothoracicotropic Hormone.”
colleagues (1984) and Kawakami and colleagues (1990) isolated Science 247:1333 –1335.
and sequenced the structure of the hormone from silkworm moths.
It is now known as prothoracicotropic hormone, or PTTH, because
it acts on the prothoracic gland of the insect to release the molting
hormone, ecdysone.
810
CHAPTER 38 A N I M A L E N D O C R I N E S YS T E M S 811
the animal’s molt by stimulating the release of a second hormone other neurosecretory brain cells secrete the peptide hormone PTTH,
from the prothoracic gland. which stimulates the release of ecdysone from the prothoracic
Two decades later, the German endocrinologist Peter Karlson gland, triggering the transition from larval to pupal and adult forms.
isolated and purified this second hormone, termed ecdysone. PTTH These studies reveal how small amounts of hormones released
triggers molting by stimulating the release of ecdysone, a steroid from key glands within the animal’s body regulate major stages of
hormone that coordinates the growth and reorganization of body growth and changes in body form during metamorphosis. When
tissues during a molt. The action of ecdysone is a good example of an animal’s body requires coordinated changes in multiple organ
how a hormone can precisely coordinate broad changes in body systems, hormonal regulation by the endocrine system plays a
organization and function, in contrast to the specific regulation that critical role.
nerves provide. Karlson was able to purify a small amount of ecdysone Hormones also regulate growth in humans and other
from large numbers of silk moth Bombyx caterpillars. He ultimately vertebrate animals. Growth hormone controls the growth
isolated a mere 25-mg sample from 500 kg of moth larvae! This tiny of the skeleton and many other tissues in the human body.
amount highlights the general principle that relatively few hormone Growth hormone is produced by the pituitary gland, which is
molecules can have a large effect on an organism. located beneath the brain. Tumors of the pituitary that cause an
In his studies of Rhodnius, Wigglesworth also noted that, overproduction of growth hormone lead to gigantism, and tumors
whatever the larval stage, the decapitated bug always molted into that result in too little growth hormone cause pituitary dwarfism.
an adult after its blood meal. By removing just the front brain The role of the pituitary gland in regulating body function is
region of the head, Wigglesworth was able to show that a region described later in the chapter.
in the head close to the brain releases a hormone that normally
prevents the earlier larval stages from molting into the adult form The endocrine system underlies homeostasis.
(Table 38.1). This hormone, called juvenile hormone, is released in Endocrine control of internal body functions is also central to
decreasing amounts during each successive larval molt. After the homeostasis, the maintenance of a steady physiological state
fifth and final stage, the level of juvenile hormone is so low that within a cell or an organism (Chapters 5 and 35). Without
it no longer blocks maturation, and at the final molt the insect some way to maintain a stable internal environment, changing
undergoes its final growth into the adult form (Fig. 38.3). environmental conditions would lead to dangerous shifts in an
The brains of insects, similar to the nervous systems of other animal’s physiological function. For example, an animal’s body
invertebrate and vertebrate animals, contain neurosecretory weight depends on the regulation of its energy intake relative to
cells. These cells are neurons that release hormones, which act energy expenditure. Disruption of hormones that regulate appetite
on endocrine glands or other targets within the insect instead of and food intake can lead to obesity on the one hand or to weakness
secreting neurotransmitters that bind to another neuron or to muscle. and lethargy on the other. Similarly, hormones that regulate the
In the case of insects, peptide hormones released from neurosecretory concentration of key ions in the body, such as Na1 and K1, are
brain cells act on the corpora allata (paired endocrine glands in fundamental to healthy nerve and muscle function (Chapters 35
insects) and the prothoracic gland (Fig. 38.3).Neurosecretory cells and 36) and fluid balance within the body (Chapter 41).
stimulate the corpora allata to produce juvenile hormone so that How does the body, and in particular the endocrine system,
molting larvae retain juvenile characteristics. At appropriate times, maintain homeostasis? Maintaining homeostasis depends on
Prothoracic
Brain gland
Juvenile hormone produced by the
+ corpora allata prevents molting into an
Ecdysone Ecdysone triggers adult form. When juvenile hormone drops
PTTH hormone molting. to low levels, the insect molts into an adult.
Juvenile +
Corpora allata – + – + – + – + – +
hormone
glucose and its release from muscle and liver cells. The result is oxytocin (stimulus) by the pituitary gland causes the uterine
that blood-glucose levels rise. In both cases, the stimulus (either muscles (effector) to contract more forcefully. The uterine
high or low blood-glucose levels) is sensed by cells of the pancreas contractions in turn stimulate (positive feedback) the pituitary
( b cells or a cells) and triggers a response (secretion of insulin or of gland to secrete more oxytocin, causing the uterine muscles to
glucagon, bringing blood-glucose levels back to the set point). Note contract more forcefully and more frequently.
that in each case the response feeds back to the secreting cells to
reduce further hormone secretion.
When the control of blood-glucose levels by insulin fails, 38.2 PROPERTIES OF HORMONES
a disease called diabetes mellitus results. When untreated,
diabetic individuals excrete excess glucose in their urine because Because hormones are released into the bloodstream, they have
blood-glucose levels are too high. Diabetes causes cardiovascular the potential to affect many organ systems. How do hormones
and neurological damage, including loss of sensation in the circulating in the blood target specific tissues? How can one
extremities, particularly the feet. hormone exert its effect on one cell type and another hormone
exert its effect on a different cell type? The answer lies in the
j Quick Check 1 Diabetes mellitus is a disease characterized
presence of receptors on cells within target organs that bind
by high blood-glucose levels. What two different physiological
specific hormones.
conditions can produce diabetes?
In some instances, it is necessary to accelerate the response Hormones act specifically on cells that bind
of target cells for a period of time. Positive feedback provides this the hormone.
enhancement (Fig. 38.6). In positive feedback, a stimulus causes Hormones circulating in the bloodstream bind to receptors
a response in the same direction as the initial stimulus, which located either on the surface of or inside target cells. Therefore,
leads to a further response, and so on. In positive feedback in the it is the presence or absence of a receptor for a given hormone
endocrine system, a stimulus leads to secretion of a hormone that that determines which cells respond and which ones do not.
causes a response, and the response causes the release of more For example, when the hormone oxytocin is released into the
hormone. The result is an escalation of the response. A positive bloodstream of mammals, it affects only cells that express a
feedback loop reinforces itself until it is interrupted or broken by receptor on the cell surface capable of binding oxytocin as it
some sort of external signal outside the feedback loop but from flows by in the bloodstream. These cells are uterine muscle cells
within the body. and secretory cells in breast tissue. When oxytocin binds these
Positive feedback occurs in mammals during birth cell-surface receptors, uterine muscle cells are stimulated to
(Chapter 42). In response to uterine contractions, the hormone contract, and secretory cells in breast tissue release milk during
oxytocin is released from the pituitary gland. The release of breastfeeding. The cells of other organs do not express the
receptor, so the hormone can exert its effect only on these specific
tissues and no others.
The binding of a hormone to its receptor triggers changes in
FIG. 38.6 Positive feedback. In positive feedback, a stimulus
the target cell, resulting in a cellular response (Chapter 9). The
causes a response, and that response causes a further
specific action of a hormone depends on the kind of response
response in the same direction.
that it triggers in the target cell. For example, the binding of a
hormone can alter ion flow across the cell membrane, activate
Stimulus
an intracellular signal transduction cascade that leads to changes
in the biochemical activity of a target cell, or initiate more
+ substantial changes in gene and protein expression.
peptide hormones and amine hormones, and the hydrophobic Because steroid hormones are hydrophobic, they diffuse
hormones are steroid hormones, examples of which are freely across the cell membrane to bind with receptors in the
illustrated in Fig. 38.7. cytoplasm or nucleus, forming a steroid hormone–receptor
Peptide hormones and amine hormones are both derived from complex (Fig. 38.8b). Hormone–receptor complexes that form in
amino acids (Figs. 38.7a and 38.7b). Peptide hormones are short the cytoplasm are transported into the nucleus of the cell. These
chains of amino acids, whereas amine hormones are derived from complexes most commonly act as transcription factors: They
a single aromatic amino acid, such as tyrosine or phenylalanine stimulate or repress gene expression and thereby alter the proteins
(Chapter 4). All steroid hormones are derived from cholesterol produced by the target cell. Consequently, steroid hormones
(Fig. 38.7c). Whereas peptide hormones (which are sometimes typically have profound and long-lasting effects on the cells and
large enough to be considered proteins) can evolve through tissues they target, on timescales of days to months.
changes in their amino acid sequence, steroid hormones cannot. The sex hormones estrogen, progesterone, and testosterone
Evolutionary changes in steroid hormone function depend instead (Table 38.2) are steroid hormones that regulate the development
on changes in their synthetic enzymes or changes in the receptors of the vertebrate reproductive organs. Cortisol is a steroid
they bind and the cellular responses they trigger. hormone that regulates a vertebrate animal’s response to stress
Peptide and amine hormones are more abundant than steroid and inhibits inflammation. Steroid hormones similar to cortisol are
hormones and are more diverse in their actions. Because most used medically to reduce the symptoms of certain inflammatory
peptide and amine hormones are hydrophilic and cannot diffuse
across the plasma membrane (exceptions are thyroid hormones),
nearly all these hormones bind to membrane receptors on the
surface of the cell (Fig. 38.8a). Peptide and amine hormones FIG. 38.7 (a) Peptide, (b) amine, and (c) steroid hormones.
alter the biochemical activity of the target by initiating signaling
a. Peptide hormones
cascades within the target cell, as discussed in Chapter 9: The
Oxytocin and ADH
bound receptor activates an enzyme or other molecule within Oxytocin are peptide
the cell, and it in turn activates another and so on. Typically, the hormones that are
Cys Tyr Ile Gln Asn Cys Pro Leu Gly 9 amino acids long.
activated enzymes are protein kinases, which phosphorylate Both are released
other proteins. These signaling cascades can lead to changes in by the posterior
Antidiuretic hormone (ADH) pituitary gland and
gene expression or they can alter metabolism by turning on or off
Cys Tyr Phe Gln Asn Cys Pro Arg Gly share a similar
metabolic enzymes. For example, a peptide or amine hormone structure (only 2
could trigger a cell to grow, divide, change shape, or to release amino acids differ).
another hormone. Peptide and amine hormones act on timescales
b. Amine hormones
of minutes to hours.
L-dopa Dopamine
There are many examples of peptide hormones. In vertebrates, HO HO
for instance, growth hormone stimulates protein synthesis and
HO O HO
the growth of many body tissues, particularly the musculoskeletal
NH2
system (Table 38.2, on pages 816–817). As we saw, insulin and NH2 OH
glucagon are peptide hormones released by the pancreas that
regulate glucose metabolism by the liver, muscles, and other Norepinephrine Epinephrine
tissues. Gastrin and cholecystokinin are peptide hormones that HO NH2 HO
regulate mammalian digestive function (Chapter 40). In addition NH
to serving as a neurotransmitter released by the sympathetic HO HO
OH OH
nervous system (Chapter 35), epinephrine and norepinephrine
(also known as adrenaline and noradrenaline) are amine
hormones, supporting an animal’s fight-or-flight response. Amine hormones are derived
from aromatic amino acids.
All four shown here are
The steroid hormones all
derived from phenylalanine.
share a similar structure and
are derived from cholesterol.
c. Steroid hormones
OH
Progesterone Testosterone Cortisol Cholesterol
O O
OH OH
HO HO
O O O
HO
CHAPTER 38 A N I M A L E N D O C R I N E S YS T E M S 815
b. Intracellular receptors
Receptor FIG. 38.9 Amplification of a hormonal signal.
Steroid hormone protein
Stress
New protein
mRNA
+
Steroid hormones are
hydrophobic and diffuse into
the target cell, where they Hypothalamus
bind a cytoplasmic or
nuclear receptor that allows
them to act as transcription Corticotropin
factors to alter the gene releasing factor
expression of the cell. 0.1 μg
+
Nucleus
Anterior pituitary
DNA
Hormone– At each step,
receptor the hormonal
complex signal is Adrenocorticotropic
amplified, so hormone (ACTH)
that a small 1 μg
amount of
+
disorders. However, they carry risks because they also suppress corticotropin
releasing
the immune system, increasing the chance of infection and factor leads to
Adrenal cortex
diminishing wound healing. a large effect
(in this case,
j Quick Check 3 Why do peptide and steroid hormones bind the production
of glucose by Cortisol
different kinds of receptor, and how does this difference affect the the liver). 40 μg
resulting signaling pathways in the target cell?
+
Hypothalamus Releasing factors (peptides) Anterior pituitary Stimulate secretion of anterior pituitary hormones
gland
Anterior pituitary gland Thyroid-stimulating hormone Thyroid gland Stimulates synthesis and secretion of thyroid
(TSH) (glycoprotein) hormones by the thyroid gland
Luteinizing hormone (LH) Gonads Stimulates production and secretion of sex hormones
(glycoprotein) in ovaries (estrogen and progesterone) and testes
(testosterone)
Posterior pituitary gland Oxytocin (peptide) Uterus, breast, brain Stimulates uterine contraction and milk let-down;
influences social behavior
Antidiuretic hormone (ADH; Kidneys, brain Stimulates uptake of water from the kidneys;
vasopressin) (peptide) involved in pair bonding
Thyroid gland Thyroid hormones (peptides) Many tissues Stimulate and maintain metabolism for development
and growth
Ovaries Estrogen (steroid) Uterus, breast, other Stimulates development of female secondary sexual
tissues characteristics and regulates reproductive behavior
Hormones released by the anterior pituitary gland in turn bind its effects, it causes the liver to convert glycogen and amino acids
cell receptors in the target organ. In this case, ACTH acts on cells to glucose. This action yields 56,000 times more glucose than the
of the adrenal cortex, stimulating their secretion of the hormone initial weight of releasing factors secreted by the hypothalamus.
cortisol. Cortisol acts on many different cells and tissues in the We can also see an example of amplification in invertebrates in
body, causing what is known as an acute stress response. Among the regulation of insect molting and metamorphosis (see Fig. 38.3).
CHAPTER 38 A N I M A L E N D O C R I N E S YS T E M S 817
Testes Testosterone (steroid) Various tissues Stimulates development of male secondary sexual
characteristics; regulates male reproductive behavior
and stimulates sperm production
Adrenal cortex Cortisol (steroid) Liver, muscles, Regulates response to stress by increasing blood
immune system glucose levels and reduces inflammation
Adrenal medulla (Nor-) Epinephrine Heart, blood vessels, Stimulates heart rate, blood flow to muscles, and
(peptide) liver elevation of blood glucose level as part of
fight-or-flight response
Pancreas Insulin (protein) Liver, muscles, fat, Stimulates uptake of blood glucose and storage
other tissues as glycogen
Somatostatin (peptide) Digestive tract Inhibits insulin and glucagon release; decreases
digestive activity (secretion, absorption, and motility)
Small intestine Cholecystokinin (peptide) Pancreas, liver, Stimulates secretion of digestive enzymes and
gallbladder products from liver and gallbladder
Pineal gland Melatonin (peptide) Brain, various organs Regulates circadian rhythms
This pathway has two signaling steps in which an endocrine gland binds to cell receptors in the target organ. Signaling cascades within
releases a hormone. First, the brain releases the hormone PTTH. these cells further amplify the hormone signal. Thus, amplification
That hormone signals the prothoracic gland, leading to the release applies both to signal transduction cascades within a cell and to
of a much larger amount of ecdysone, the hormone that regulates the chemical signals that are transmitted as endocrine hormones
growth and metamorphosis of the insect’s body. Ecdysone in turn between glands and tissues.
818 SECTION 38.3 T H E V E RT E B R AT E E N D O C R I N E S YS T E M
Hormones are evolutionarily conserved molecules (Fig. 38.10). The hypothalamus, in turn, relays these signals to the
with diverse functions. pituitary gland, which lies just below it. The pituitary gland is a
Most hormones have an ancient evolutionary history. The central regulating gland of the vertebrate endocrine system:
structures of many hormones are evolutionarily conserved. For It releases several hormones that coordinate the action of many
example, some vertebrate hormones can also be found in many other endocrine glands and tissues. These glands, illustrated in
invertebrates. Since the first vertebrate animals diverged from Fig. 38.10, control the growth and maturation of the body, regulate
invertebrates over 500 million years ago, some animal hormones
are even older. In many cases, their roles in many invertebrate
animals have yet to be discovered.
Typically, the same hormone serves different functions FIG. 38.10 The hypothalamus–pituitary axis. The hypothalamus
in vertebrates and in invertebrates, and may even serve sends signals to the pituitary gland, which in turn sends
different functions within distinct groups of vertebrates. signals to diverse cells and organs throughout the body.
Thyroid-stimulating hormone (TSH), a hormone released by
Hypothalamus
the anterior pituitary gland that targets the thyroid gland, Releasing factors
regulates metabolism in mammals but triggers metamorphosis
in amphibians and feather molt in birds. It has even been found Anterior pituitary Posterior pituitary
in snails and other invertebrates that lack a thyroid gland. Its gland gland
TSH, FSH, LH, ACTH, Oxytocin, ADH
function in snails appears to be stimulation of the number of
GH, prolactin
sperm or eggs produced.
Recent genomic analysis has shown that the receptors for
many hormones evolved well before the hormones with which
they now interact. Even though the structure of a hormone or
its receptor is often largely unchanged across diverse groups of
organisms, hormones and their receptors can readily be selected to
take on new roles as organisms evolve new behaviors and exploit
new environments. An example is the shift in function of TSH to
regulate metabolism in mammals and feather molt in birds from
its role stimulating sperm or egg production in snails.
Another intriguing finding is that many peptides originally
identified as hormones in various tissues have also been found TSH
to function as neurotransmitters in the nervous system. For Thyroid
example, oxytocin, which stimulates uterine contraction and the Thyroid hormones
release of milk, also serves as a neurotransmitter in the brain and
is believed to influence social behavior, as well as stimulate sexual Prolactin Oxytocin
arousal in mammals. Similarly, antidiuretic hormone, a peptide Breast
hormone that regulates water uptake in the kidneys (Chapter 41),
also functions as a neurotransmitter in the brain influencing ACTH
mammalian mating and pair-bonding behavior. Hence, the same
compound, expressed in two different cell types, may have ADH
entirely different functions. The roles of hormones as chemical
messengers are varied within an organism and easily changed over
GH
the course of evolution. Adrenal gland Kidney
Bones
Cortisol,
and soft
aldosterone,
tissue epinephrine Uterus
38.3 THE VERTEBRATE
Oxytocin
ENDOCRINE SYSTEM
FSH/LH
The vertebrate endocrine system regulates changes in the animal’s
physiological and behavioral states in response to sensory cues
received by its nervous system both from the environment and from
internal organs. Whereas certain sensory signals may communicate
directly to endocrine glands or tissues in the body, many are
processed within the brain and transmitted to the endocrine Testis Ovary
Testosterone Estrogens,
system by the hypothalamus, which is located in the forebrain progesterone
CHAPTER 38 A N I M A L E N D O C R I N E S YS T E M S 819
reproductive development and metabolism, and control of The pituitary gland is divided into anterior and posterior
water balance. These effects reflect the broad range of roles that regions (Fig. 38.11). This division is not arbitrary—the two regions
the endocrine and nervous systems perform in regulating body have distinct functions, organizations, and embryonic origins.
maturation and maintaining homeostasis. The anterior pituitary gland forms from epithelial cells that
The pituitary gland communicates with many cells, tissues, develop and push up from the roof of the mouth, whereas the
and organs of the body. Some of these, like the thyroid and adrenal posterior pituitary gland develops from neural tissue at the
glands, secrete hormones in response to signals from the pituitary base of the brain. Both sets of cells form pouches that develop into
gland and therefore have exclusively endocrine functions. Others, glands, which come to lie adjacent to each other. The anterior and
like the lungs, kidneys, and digestive tract, harbor endocrine cells posterior pituitary glands should therefore be thought of as two
that secrete hormones and also have other physiological roles in distinct glands, not one.
the body. Consequently, the vertebrate endocrine system is not Because of these developmental differences, the anterior and
localized in one part of the body, but is present throughout. posterior pituitary glands receive input from the hypothalamus
in different ways. As does the brain of arthropods, the vertebrate
The pituitary gland integrates diverse bodily functions hypothalamus contains neurosecretory cells, which are part
by secreting hormones in response to signals from the of the brain and therefore are neurons. As with invertebrate
hypothalamus. neurosecretory cells, these cells release hormones into the
The hypothalamus is the main route by which nervous system bloodstream. Some of these neurosecretory cells communicate
signals are transmitted to the vertebrate endocrine system. The with the anterior pituitary gland. In this case, they secrete
function of the hypothalamus is to transmit these signals to the hormones called releasing factors into small blood vessels that
pituitary gland, the endocrine gland that acts as a control center travel to and supply the anterior pituitary gland (Fig. 38.11). In
for many other endocrine glands in the body. response, cells of the anterior pituitary gland release hormones
into the bloodstream.
These hormones circulate
throughout the body and bind
FIG. 38.11 The anterior and posterior pituitary glands. The hypothalamus communicates with the anterior
to receptors on target cells,
pituitary gland by secreting releasing factors into the blood. The hypothalamus communicates
tissues, and organs.
with the posterior pituitary gland by extending axons of neurosecretory cells into it.
In contrast,
communication between
the hypothalamus and the
The hypothalamus of the
midbrain communicates posterior pituitary gland does
with the pituitary gland not involve hypothalamic
located below.
releasing factors. Instead,
the posterior pituitary
Neurosecretory gland contains the axons of
cells Hypothalamus neurosecretory cells whose
cell bodies are located in the
hypothalamus. These axons
release hormones directly into
the bloodstream, and these
hormones are transported in
the blood to distant sites (Fig.
38.11). Consequently, the
posterior pituitary is part of
Some neurosecretory Other neurosecretory
cells in the hypothalamus cells of the hypo-
the nervous system itself.
Releasing
secrete releasing factors factors thalamus extend their In response to signals from
into the bloodstream that axons all the way to the hypothalamus, distinct
cause cells in the anterior Anterior the posterior pituitary
pituitary gland to release pituitary gland, where they hormones are secreted by
hormones. gland release their hormones the anterior and posterior
into the bloodstream.
Blood pituitary glands (Table 38.2).
vessels The hormones released by the
Posterior
anterior pituitary hormone act
Hormones pituitary
gland on an endocrine gland to cause
release of other hormones.
Endocrine cells Hormones Hormones that control
820 SECTION 38.3 T H E V E RT E B R AT E E N D O C R I N E S YS T E M
the release of other hormones are called tropic hormones. In of two peptide hormones, thyroxine (T4) and triiodothyronine
response to thyroid-stimulating hormone (TSH), the thyroid (T3). These peptide hormones are sufficiently hydrophobic that
gland releases thyroid hormones that regulate the metabolic state they enter cells, binding to intracellular receptors to increase the
of the body. In response to follicle-stimulating hormone (FSH) resting metabolic rate of cells throughout the body. As levels of T3
and luteinizing hormone (LH), the ovaries release estrogen and and T4 rise, these hormones act as a brake on the release of TSH
progesterone and the testes release testosterone. In response to by the anterior pituitary gland. This regulation of TSH by negative
adrenocorticotropic hormone (ACTH), the adrenal glands release feedback is critical to maintaining stable TSH levels and a stable
cortisol, which has diverse effects that include stimulating glucose metabolic state of the body as a whole. Overproduction of thyroid
release into the bloodstream, maintaining blood pressure, and hormones (hyperthyroidism) creates symptoms that reflect an
suppressing the immune system. overly active metabolic state (increased appetite and weight loss),
The anterior pituitary gland also secretes the hormones whereas thyroid hormone deficiency (hypothyroidism) creates
growth hormone (GH) and prolactin. Growth hormone acts symptoms that reflect a metabolic state that is too low (fatigue
generally on the muscles, bones, and other body tissues to and sluggishness). Both conditions are diagnosed by blood tests
stimulate their growth, and prolactin stimulates milk production that monitor circulating levels of thyroid hormones, and both can
in the breasts of female mammals in response to an infant’s be treated by medication.
suckling at the mother’s nipple. Because the thyroid hormones T3 and T4 require iodine for
The hormones released by the posterior pituitary gland their formation, individuals who do not acquire enough iodine
include oxytocin and antidiuretic hormone (ADH; also called from their diets produce too little thyroid hormone. Additionally, in
vasopressin). These are two evolutionarily related peptide cases of iodine insufficiency, the anterior pituitary gland increases
hormones of similar structure. As we discussed earlier, oxytocin its production of TSH because it is no longer receiving negative
plays several roles related to female reproduction: It causes uterine feedback. Over time, in response to TSH the thyroid gland enlarges
contraction during labor and stimulates the release of milk during to form a goiter, which is observed as an enlargement of the throat.
breastfeeding. Antidiuretic hormone acts on the kidneys (Chapter The introduction of iodized salt has eliminated goiter formation and
41), regulating the concentration of urine that an animal excretes, hypothyroidism in many countries, but in many underdeveloped
which is critical to maintaining water and solute balance in the body. areas these remain significant public health problems.
In addition to their roles in reproduction and kidney function, The gonadotropic hormones are FSH and LH. They target the
oxytocin and antidiuretic hormone are released by cells in the female and male gonads—the ovaries and testes (see Fig. 38.10;
brain and may play roles in social behaviors. For instance, recent Table 38.2). In response to FSH and LH, the ovaries and testes each
evidence indicates that oxytocin may be important in regulating secrete sex hormones that regulate their own development as well
maternal behavior toward infants. Recent research suggests as the development of secondary sexual characteristics. Female
that oxytocin may also have a role in behaviors such as trust as a sex hormones include the steroids estrogen and progesterone. The
prelude to mating in vertebrate animals. These functions reflect principal male sex hormone is the androgen testosterone. These sex
the long evolutionary history of oxytocin, as it plays a role in the hormones are common to a vast majority of vertebrates, regulating
social behavior of insects. sexual differentiation, gonadal maturation, and reproductive
Recent evidence also suggests that antidiuretic hormone behavior. The role of these sex hormones in regulating reproductive
plays a parallel role in regulating male social behavior and parental function is discussed in greater detail in Chapter 42.
behavior in mammals. This is not surprising because oxytocin and Testosterone is a naturally occurring anabolic steroid that
antidiuretic hormone have very similar chemical structures (see stimulates the synthesis in the testes of proteins needed for sperm
Fig. 38.7). The integration of reproductive function with parental production and the development of male sexual features and body
and social behavior for the care of young is likely favored strongly tissue growth, particularly in muscles. Anabolic steroids promote
by natural selection. Receptors for these hormones are expressed protein synthesis to build body tissues and anabolic metabolism to
within the brain. Thus, in addition to acting on reproductive and store energy within cells. A variety of synthetic anabolic steroids
renal organs of the body, oxytocin and antidiuretic hormone affect that mimic the action of testosterone have been developed to treat
mammalian behavior by acting directly on the brain. muscle wasting due to loss of appetite and diseases such as cancer
and AIDS. Anabolic steroids are used illegally by some male and
Many targets of pituitary hormones are endocrine female athletes to promote muscle strengthening, undermining
tissues that also secrete hormones. fair competition. The risks to health of continued use of anabolic
As we have seen, some of the hormones released by the anterior steroids are considerable: liver damage, heart disease, and high
pituitary gland act on endocrine organs that themselves then blood pressure. Tissues become damaged because elevated
release hormones. These tropic hormones are TSH, FSH and LH, circulating levels of testosterone produced by anabolic steroids
and ACTH (see Fig. 38.10; Table 38.2). Here, we look at their target inhibits the normal synthesis of tropic hormones by the anterior
organs in more detail. pituitary gland.
TSH acts on the thyroid gland, which is located in the front ACTH released by the anterior pituitary gland is also a tropic
of the neck (see Fig. 38.10; Table 38.2) and leads to the release hormone. As noted in section 38.1 in explaining how amplification
CHAPTER 38 A N I M A L E N D O C R I N E S YS T E M S 821
strengthens the action of downstream hormones in a signaling gland responds to light sensed by a “third eye,” photosensitive cells
pathway, ACTH acts on the cortex (the outer portion) of the paired located at the skull’s surface between the animal’s actual eyes. In
adrenal glands (see Fig. 38.10; Table 38.2). The adrenal glands are both cases, melatonin levels rise at night. In diurnal animals (those
located adjacent to the kidneys (ad- meaning “near” and “renal” that are active during the day), the rise in melatonin levels at night
referring to the kidneys). In humans, each small adrenal gland lies causes the animals to sleep. In nocturnal animals (those that are
just above each kidney. During times of stress, such as starvation, active during the night), the rise in melatonin levels causes them
fear, or intense physical exertion, ACTH stimulates adrenal cortex to become active. The release of melatonin in response to daily
cells to secrete cortisol. The release of cortisol in response to stress (and seasonal) light cycles helps to maintain circadian rhythms
affects a broad range of bodily functions, including blood-glucose of the body. Circadian rhythms are cycles of about 24 hours in
levels (Chapter 41), immune function (Chapter 43), and blood which an animal’s biochemical, physiological, and behavioral state
pressure (Chapter 39). Whereas acute (short-term) responses that shifts in response to changes in daily and seasonal environmental
lead to the release of ACTH and elevated cortisol by the adrenal conditions. To overcome jet lag, travelers are advised to seek
cortex are healthy physiological responses that enable animals to sunlight and often to take melatonin before sleeping to help reset
respond to stressful situations, chronic (long-term) stress often their 24-hour circadian rhythm.
leads to a broad range of unhealthy conditions that include impaired In several animals, including ground squirrels, bats, bears, and
cognitive and immune function, sleep disruption, and fatigue. rattlesnakes, the pineal gland regulates hibernation, controlling the
animal’s metabolic state over longer time periods. In many animals,
Other endocrine organs have diverse functions. release of melatonin also regulates seasonal breeding cycles.
Although many endocrine organs receive signals from the
hypothalamic–pituitary axis, some respond instead to internal
physiological states of the body or to external environmental ? CASE 7 PREDATOR–PREY: A GAME OF LIFE AND DEATH
cues. One of these is the parathyroid gland, which is located How does the endocrine system influence predators
on the thyroid gland. The parathyroid gland secretes parathyroid and prey?
hormone (PTH). Working together with calcitonin, secreted by The endocrine system works closely with the nervous system to
the thyroid gland, PTH controls the levels of calcium in the blood enable animals to respond to external cues in the environment.
(Table 38.2). The two hormones act by regulating the actions of In Chapters 35 and 36, we discussed how prey animals, such as
bone cells (osteoblasts and osteoclasts; Chapter 37) that control gazelles, use visual and olfactory cues processed by the nervous
bone formation and bone removal. system to detect the distant movement of a predator, such as a
When circulating levels of calcium fall too low, the parathyroid lion (Fig. 38.12). We saw how the sympathetic nervous system,
gland releases PTH, which stimulates osteoclasts to reabsorb
bone mineral, halting bone formation and releasing
calcium into the bloodstream. When calcium levels
are too high, the production of PTH is inhibited and FIG. 38.12 Predator and prey. Animals rely on rapid integration of sensory
calcitonin is released to shift bone metabolism toward information with coordination of bodily functions to escape a predator
net bone formation, building bone that stores calcium or to catch their prey. Source: Federico Veronesi/Getty Images.
in the skeleton. Note that, as with blood-glucose
levels, calcium levels are maintained in a narrow range
by negative feedback: The response to the hormone
(increasing or decreasing levels of calcium in the
blood) is the opposite of the stimulus (low or high
levels of calcium in the blood) so that a stable set
point is maintained.
Several organs of the digestive system, including
the pancreas, stomach, and duodenum, produce
hormones that regulate appetite and digestion. Three of
these hormones are discussed in Chapter 40.
The pineal gland is located in the thalamic region
of the brain. In response to darkness, the pineal gland
secretes melatonin, a hormone that helps control an
animal’s state of wakefulness (Table 38.2). Melatonin
secretion is inhibited when environmental light cues
sensed by the retina are conveyed to the gland by
the autonomic nervous system. In other vertebrates,
such as lampreys, some fishes, and reptiles, the pineal
822 SECTION 38.4 OT H E R F O R M S O F C H E M I C A L CO M M U N I C AT I O N
FIG. 38.14 Pheromone action. (a) Pheromones are means of attracting mates, as in these ladybugs; (b) wolves secrete pheromones in their
urine that mark their territory; (c) honeybees swarm to defend their nest after a bee that stings a threatening animal releases an alarm
pheromone. Sources: a. Krzysztof Bisztyga/age footstock; b. Jorg & Petra Werner/Animals Animals/Earth Scenes; c. Steven Smith/Alamy.
a b c
Local chemical signals regulate neighboring be extremely rapid and brief compared to the other modes of
target cells. chemical communication.
Whereas hormones enter the bloodstream to be transmitted to
more distant target cells (Fig. 38.13a), other chemical compounds Pheromones are chemical compounds released into
act locally on neighboring cells (Fig. 38.13b). In order to take the environment to signal physiological and behavioral
up the chemical signal, these cells must have receptors for the changes in other species members.
compound to bind to before it degrades or diffuses into the Many animals release small chemical compounds into the
bloodstream. environment to signal and influence the physiology and behavior
Chemical compounds that act locally are said to have paracrine of other members of their species. These water- or airborne
function (Fig. 38.13b). If the compounds act on the secreting compounds are called pheromones. For example, bees and wasps
cell itself, they are said to have autocrine function—that is, the release pheromones to find a nest, locate food, and regulate the
chemical signals may stimulate or inhibit their own secretion. development and activities of other colony members. Even plants,
Growth factors (also referred to as cytokines and distinct from such as orchids, release pheromones. Some plant pheromones
the growth hormone released by the anterior pituitary gland) and attract pollinating bees or wasps by mimicking the chemical
histamine are examples of paracrine chemical agents released in signals released by the females of these species. There are many
small amounts that act locally on neighboring cells. different pheromones, which serve very different functions, as
Growth factors (Chapter 9) enhance the differentiation shown in Fig. 38.14.
and growth of particular kinds of tissue. For example, bone Female silk moths use pheromones to attract males over
morphogenetic proteins (BMPs) promote the formation of bone long distances. The sex pheromone bombykol, released from
in skeletal growth, and fibroblast growth factors (FGFs) stimulate a gland in the female’s abdomen, signals her location to males
the formation of connective tissue. Similarly, nerve growth factors looking for a mate. Sex pheromones play a key role in the mating
(NGFs) promote the survival and growth of nerve cells. When behavior of many invertebrate and vertebrate species. In most
tissues are damaged, specialized cells nearby release histamine. mammals, amphibians, and reptiles, pheromones are detected
This chemical signal triggers the dilation of blood vessels, allowing by a vomeronasal organ with chemosensory neurons in the nasal
blood proteins and white blood cells to move into the region region of the skull. The release of sex pheromones to attract a
to fight infection and induce repair (Chapter 43). The release mate and trigger ritualistic social and mating behaviors is one of
of histamine causes the swelling, redness, and warmth that the most common types of pheromone signaling (Chapter 45).
commonly surround a wound. Humans and nonhuman primates lack a vomeronasal organ, and
Another form of short-range chemical signaling is the most studies indicate that they do not produce pheromones.
release of neurotransmitters into the synapse between directly Other pheromones signal territorial boundaries or predatory
communicating nerve cells or between nerve cells and muscles threats. Dogs and other canids (this family includes wolves and
at neuromuscular junctions (Fig. 38.13b). Synaptic signaling can coyotes), as well as cats, secrete pheromones in their urine that
824 SECTION 38.4 OT H E R F O R M S O F C H E M I C A L CO M M U N I C AT I O N
FIG. 38.15 Trail pheromones in ants. Here, a chemical trail has FIG. 38.16 A brightly colored male cichlid fish. The behavior and
been laid down by worker ants signaling a food source markings of this fish are under hormonal control and
for the colony. Source: LatitudeStock–Patrick Ford/Getty Images. triggered by social context. Source: blickwinkel/Alamy.
a trail, or into and out of your house, you have seen worker ants
using pheromone cues that signpost the way to food.
Aquatic species also depend on pheromone signaling. Fish,
salamanders, and tadpoles release alarm pheromones into the
water to warn of a threatening predator. Prey species that share
the same habitat may even sense and respond to the release of
another species’ alarm pheromone.
Fish also release pheromones to coordinate mating and to
regulate social interactions. In dense populations of cichlid fish
living in Lake Tanganyika in central Africa, the ratio of brightly
colored breeding males (Fig. 38.16) to females is highly regulated.
Only about 10% of males are brightly colored and defend their
territory to attract and mate with females. This restriction on the
mark their territories. Social seabirds, such as cormorants and
number of dominant breeding males is regulated by behavioral
boobies, mark their nesting sites by pheromones.
cues and chemical pheromones. When a dominant male dies,
Ants and other social insects deploy alarm pheromones to
subordinate males fight for the vacated territory. When a new
warn of an attack by an advancing army from another colony. The
male assumes dominance, it becomes brightly colored to attract
release of alarm pheromones from a stinging bee causes other bees
females and defend its newly won territory. The dominant
to swarm and join the attack to defend their nest. In many other
breeding male reinforces its dominance by releasing pheromones
species, an animal under attack releases an alarm pheromone,
in its urine that signal females and subordinate males in its
warning its neighbors. Similarly, social mammals such as deer
breeding area. The color change is mediated by hormones released
warn of an approaching predator by means of alarm pheromones.
from t