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Module 1: Introduction to Cell

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Cell Voice

A Preview of the Cell

Cellular Organization
There are four levels of organization: Cells → Tissues → Organs → Organ Systems

Cells are smallest unit of life (e.g., skin cell)

Tissues are many of the same cells (e.g., skin tissue)

Organs are many of different tissues (e.g., stomach)

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 Organ systems are many different organs (e.g., digestive system)

Cell in News

Once heart attack occurs, some of the heart tissues dies, resulting to detrimental effect to
the heart

Research shows that cells are still in the progress of being understood

The Cell Theory: A brief History

Robert Hooke (1665) observed compartment in cork and named them cells

These cells changed the world of biology

Observations were limited by LPO (30x)

Antonie van Leeuwenhoek produced better lenses (300x)

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 Hooke’s Investigation/Experiment

Leeuwenhoek’s Investigations/Experiments

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 Credited for observing the live cells for the first time (e.g., bacteria)

He sent his observations in forms of letters, sending to Royal Society of London

Slow Early Progress in Cell Biology

Two factors restricting progress

Microscopes with limited resolution

Descriptive nature of cell biology: the focus was more on observation than on
explanation of those observations

Microscopes: essential tools in early cell biology

1830’s, compound microscopes were used

Increased magnification (up to 1000x) and resolution

1 micrometer structures can be seen

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 These microscopes are bright-field (either binocular or monocular)

Robert Brown used a compound microscope to identify the nucleus, found inside plant
cells

Matthias Schleiden concluded all plant tissues are composed of cells

Thomas Schwann made the same conclusion for animals

1827-1833: Robert Brown

He noticed that pollen gains in water jiggled around (called it the brownian motion)

Discovered the nucleus that’s found in the human cheek cell

He has other contributions to different fields of science

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 The Cell Theory
Schwann (1839) postulated the cell theory

[1st postulate] All living organisms consist of one or more cells

[2nd postulate] The cell is the basic unit of structure for all organisms

Schwann’s postulates did not answer the curiosity of where did cells come from

Virchow (1855) added

[3rd postulate] All cells arise only from preexisting cells

Matthias Schleiden: 1838

He was a german scientist that was fascinated with plant cells, using compound
microscope and studied these cells

Investigated and experimented with plants, stated plants are made of cells

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 Dear friend of Theodor Schwann

Theodor Schwann: 1839

German scientist that studied plant and animal cells and intrigued with their similarities

Determined all animals are made of cells

Published 1st statement of the cell theory: all living things are made of cells and cell
products

Rudolf virchow: 1855

A physician who researched on cancer cells and concluded “Ominis cellula e cellula”

Translation: All cells are from other pre-existing cells

Figure 1-1: Size-Shape-Function Relationship in Cells

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 Different sizes and shapes of cells

Different size and shapes of cells led people to find the correlation between the structure
(size and shape) and function of the cells

Structure leads to function

Cell f is a human ovum that is being fertilized by the sperm cell

Cell g is a series of intestinal cells

Cell h is a xylum

The Emergence of Modern Cell Biology

3 historical strands weave together into modern cell biology, each with important
contributions to understanding cells

Cytology strand on cellular structure and emphasizes optical techniques

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 Biochemistry strand on cellular function

Genetics strand focuses on information flow and heredity

In recent years, cell biology is the summation of contributions from cytology,

biochemistry, and genetics

The Cytological Strand Deals with Cellular Structure

Historically, this strand deals primarily with cell structure and observation via optical
techniques

The Light Microscope

Earliest tool of cytologists

Allowed identification of organelles within cells

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 These are membrane-bound structures (e.g., nuclei, mitochondria, chloroplasts, and
etc.)

Useful tools in early microscopy

Microtome (mid-1800s) allowed preparation of very thin slices of samples

Variety of dyes for staining cells (around the mid-1800s)

The tools improved the limit of resolution

Smaller the limit of resolution a microscope has, the greater its resolving power

Visualization of Cells
Light microscopy is also called a brightfield microscopy due to white light passing
through a specimen

These specimens must be chemically fixed and reserved

Some preparations may distort tissues

e.g., fixing, staining, embedding in plastic

Various types of microscopy have been developed to allow observation of living cells

Contributing Factors/Settings to Cell Visualization

Phase contrast/differential interference contrast microscopy exploit differences in the
phase of light passing through a structure with a refractive index different than the
surrounding medium

Fluorescence microscopy detect fluorescent dyes, or labels, to show locations of

substances in the cell

Confocal scanning uses a laser beam to illuminate a single plane of a fluorescent-labeled

specimen

Helps us to create 3d images and assembling multiple scans

Samples are prepared in slides and viewed under a dichromatic mirror

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 There is a fine limit in what can the unaided eye, light microscope (10^-6), and electron
microscope (10^-9) can see

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 Comparison of the different types of microscopy

The Electron Microscope

This microscope uses a beam of electrons rather than light

This beam is deflected and is focused using an electric and a magnetic field

Limit of resolution of electron microscopes is around 0.1 - 0.2 nm

Magnification is much higher than light—up to 100,000x

Invented by Ernst Ruska and Max Naul 1939 Germany

Electron Microscopy
In TEM, electrons are transmitted through the specimen

Specimens are examined in vacuum so they have to be specially prepared

This gives of a 2D view of the object

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 This type of electron microscopy requires little preparation

Has a high degree of magnification and resolution

In SEM, the surface of a specimen is scanned, by detecting electrons deflected from the
outer surface

Focuses on image formation

Samples are scanned in vacuum or near-vacuum conditions

Samples are dehydrated and surrounded with gold

Produced a 3D image that’s B&W

Ample degree of magnification and resolution

Specialized approaches in electron microscopy allow for visualization of specimens in

3D and one allows visualization of individual atoms

These structures were possible to be illustrated with the help of electron microscopy

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 Electron microscopes are also used to observe ultra structures (nanometer range) of
specific parts of the cell

A and B are viewed using a SEM while C and D are viewed using a TEM

The Biochemical Strand Covers the Chemistry

of Biological Structure and Function
Began exploring cellular function while cytologists were studying cells microscopically

Much of this dates from the work of Fredrich Wohler (1828)

Showed that a non-living or biochemical compound made in a living organism

could be synthesized in the lab (he made urea using ammonium cyanate in a
laboratory)

Developments in early biochemistry

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 Louis Pasteur (1860s) showed that yeasts could ferment sugar into alcohol

Buchners (1897) showed that yeasts extracts could do the same

Led to the discovery of enzymes, the biological catalysts

Early discoveries
Steps of pathways of fermentation and others were elucidated in the 1920s and 1930s

Gustav Embden and Otto Meyerhof described the steps of Glycolysis in the early 1930s

Krebs cycle was described after

Glycolysis and Krebs cycle are important in cellular metabolism for energy

Important advances
Radioactive isotopes are used to trace the fate of specific atoms and molecules (led to
elucidation of the Calvin cycle, 1950s)

Subcellular fractionation (e.g., centrifugation) is used to separate/isolate different

structures and macromolecules

Ultracentrifuges are capable of very high speeds (100,000 revolutions per minute)
[discovered in late 1920s]

Chromatography techniques are used to separate molecules from a solution based on

size, charge, or chemical affinity

Electrophoresis uses an electrical field to move proteins, DNA or RNA molecules

through a medium based on size/charge

Mass spectrometry is used to determine the size and composition of individual proteins

Led to proteomics

The Genetic Strand Focuses on Information

Flow
This strand has important roots in the 19th century

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 Gregor Mendel’s experiments with peas (1866) laid the foundation of understanding the
passage of hereditary factors from parents to offspring

Hereditary factors = genes

Chromosomes and the genetic material

Walther Flemming (1880) saw threadlike bodies (chromosomes) in the nucleus

Called the process of cell division: mitosis

Wilhelm Roux (1883) and August Weisman (shortly after) suggested chromosomes
carried the genetic material—showing consistency from generation to generation

The chromosome theory

Hugo de Vries, Carl Correns, Ernst von Tschermak formulated the chromosome theory
of heredity

Proposing that Mendel’s genes are located on chromosomes

Morgan, Bridges, and Surtevant (1920s) were able to connect specific traits to specific
chromosomes in the model organism (Drosophila melanogaster), the common fruit fly

Progress in understanding DNA

Friedrich Miescher (1869) first isolated DNA, which he called nuclein

Used unusual samples (e.g., salamander sperm)

DNA is known to be a component of chromosomes by 1914

Composed of only 4 different nucleotides (1930s)

Proteins, composed of 20 different amino acids, thought more likely to be genetic

material

DNA is the genetic material

Experiments with bacteria and viruses began to implicate DNA as the genetic material
(1940s)

Beadle and Tatum formulated the one gene-one enzyme concept

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 Each gene is responsible for the production of a single particular protein

Watson and Crick (with Rosalind Franklin) proposed the double helix model for DNA
structure (1953)

Many advanced toward DNA replication, RNA production, and the genetic code
happened in the 1960s

Important techniques in Genetics

Ultracentrifugation and electrophoresis are used for separating DNA and RNA
molecules

Nucleic acid hybridization is a variety of techniques that uses the ability of nucleic acid
bases to bind to each other

Recombinant DNA technology, restriction enzymes cut DNA at specific places allowing
scientists to create recombinant DNA molecules, with DNA from different sources

i.e., technology that allows the creation of new DNA molecules by combining two
DNA molecules from two different sources

DNA sequencing are methods for rapidly determining the base sequences of DNA

Now possible to sequence entire genomes

Bioinformatics merges computer science with biology to organize and interpret

enormous amounts of sequencing and other data

Yast two-hybrid system allows determination of how proteins interact within a cell

Nanotech - development of tiny tools, sensors, and computer-aided analysis of the results

OMICS Studies

Transcriptomics - study of all transcribed genes

Metabolomics - analysis of all metabolic reactions happening at a given time

Lipidomics - study of all lipids of the cell

“Facts” and the Scientific Method

Facts are tenuous and dynamic

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 Scientific method is used to assess new info

Formulate a hypothesis

Data are collected and interpreted and the model is accepted or rejected based on the
data interpretation

Occam’s razor stated that the simplest explanation consistent with the observations
is most likely to be correct

Consistency is key if you want bette results in the world of science

Research approaches in cell biology

In vitro - using purified chemicals and cellular components

In vivo - using live cells or organisms

In silico - using computer analysis of large amounts of data

The model organisms used for the study of cell biology

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 Model organism is a species that studied, characterized, and manipulated that contains
particular and useful characteristics

Different model organisms result from the particular purpose/aim of the experiment

If you want to study a drug or medicine or therapy, you can first experiment them on
mice, and follow with the other model organisms depending on the aim

Explaining observations
Hypothesis is a statement consistent with most data, may take the form of a model
(explanation that appears to account for the data); must be testable

Theory is a hypothesis that has been extensively tested by many investigators, using
different approaches, widely accepted

Law is a theory that has been tested and confirmed over a long period of time with
virtually no doubt of its validity

Cell and Organelles

Introduction
Topics of focus

Properties and strategies of cells

Eukaryotic cell in overview

Agents that invade cells

Properties and Strategies of Cells

Several general characteristics of cells have arose more generally

Organizational Complexity

Molecular components

Sizes and shapes

Specialization

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 All Organisms Are Bacteria, Archaea, or
Eukaryotes
Biologists recognized two types of cells: Prokaryotes and Eukaryotes

Prokaryotes are a simpler type of bacteria

Eukaryotes are more complex types characteristics of plants, animals, fungi, algae, and
protozoa

Main distinction: membrane-bound nucleus of eukaryotic cells (eu - true; karyon -

nucleus)

Changing View of Prokaryotes

Term prokaryote is unsatisfactory in describing the non-nucleated cells

Sharing of gross structural feature is not necessarily evidence of relatedness

Using rRNA sequence analysis, prokaryotes can be divided into bacteria and archaea

Three domains
Bacteria and archaea are as divergent from one another as humans and bacteria are

Three domains

Archaea

Bacteria

Eukarya (Eukaryotes)

All domains have unique characteristics

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 Properties of each domain

Each domains are different form one another but they all relate with a common factor:
life

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 It is believed that all three domains of life originate from a common ancestral cell

Bacteria
Most commonly encountered single-celled, non-nucleated organisms (called bacteria)

e.g., E. coli, Pseudomonas, Streptococcus

Archaea
Originally called archebacteria

Before they were observed to be different

Lives in extreme habitats and have diverse metabolic strategies

Types

Methanogens - obtain energy from H and convert CO2 into CH4

Halophiles - occupies extremely salty environments

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 Thermacidophiles - Thrive in acidic hot springs

They are considered to have descended from a common ancestor that also gave rise to
eukaryotes long after diverging from bacteria

Limitations on Cell Size

Cells vary in size and shape

Smallest bacteria are about 0.2 - 0.3 µm in diameter

Some highly elongated nerve cells may extend a meter or more

Despite extremes, cells in general fall into predictable size ranges

Normal range of bacteria: 1 - 5 µm in diameter

Animal cells: range of 10 - 100 µm

There are three main limitations on cell size

Need for adequate surface area relative to volume

Rate of diffusion of molecules

Need to maintain adequate locate concentrations of substances required for

necessary cellular functions

Surface area:Volume Ratio

This is often the major limit on cell size

Surface area is important because exchanges between the cell and its surrounding stake
place there

Cell’s volume determines the amount of exchange that must take place, across the
available surface area

Problem with maintenance

Volume increases with the cube of its length

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 Surface area increases with the square of its length; i.e., larger cells have
proportionately smaller surface areas

Beyond a certain threshold a large cell would not have a large enough surface area to
allow for intake of enough nutrients and release of enough wastes

Cells specialized for absorption

Those specialized for absorption have characteristic to maximize surface area/volume
ratio

e.g., cells lining the small intestine have microvilli, fingerlike projections that
increase the surface area

Diffusion Rates of Molecules

Many molecules move through the cell via diffusion

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 This is the unassisted movement of a substance from a region of high concentration
to a region of low concentration

Rate of diffusion decreases as size of molecule increases

This makes the limitation the most important for macromolecules (proteins and
nucleic acids)

Avoiding limitations
Eukaryotes can avoid the problem of slow diffusion rates via carrier proteins to actively
transport through the cytoplasm

Some cells use cytoplasmic streaming (cyclosis in plants) to actively move cytoplasmic
contents

Other cells move molecules through the cell in vesicles that are transported along
microtubules

The need for Adequate Concentrations of

Reactants and Catalysts
For a reaction to occur, appropriate reactants must collide with and bind to a particular
enzyme

The frequency of such collisions is greatly increased with higher concentrations of

enzymes and reactants

As cell size increases, the number of molecules increase proportionately with volume

Eukaryotic Cells Use Organelles to

Compartmentalize Cellular Function
Compartmentalization of activities within specific regions of the cell is the solution to
the concentration problem

Most eukaryotic cells have a variety of organelles

Organelles = membrane-bounded compartments that have a special function

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 e.g., cells in a plant lead have most of the materials needed for photosynthesis
compartmentalized into chloroplasts

Presence of a Membrane-Bounded Nucleus

A eukaryotic cell has a true, membrane bounded nucleus

Nuclear envelope consists of two membranes

Nucleolus is the site of rRNA synthesis and ribosome assembly

Nucleoid is a compact structure that holds the genetic information of bacterial and
archaeal cell and is attached to the cell membrane

Bacteria, Archaea, and Eukaryotes Differ from

Each Other in Many Ways
There are shared characters among cells of each domain

However , each type of cell has a unique set of distinguishing properties

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 A prokaryote and its compartments; 3-D model (a) and electron micrograph (b)

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 Electron micrograph of Nucleus (found in prokaryotes)

Eukaryote Organelles
Nearly all eukaryotes make use of internal membranes to compartmentalize specific
functions and have numerous organelles

e.g., ER, golgi complex, mitochondria, chloroplasts, etc.

Each organelle contains the materials and molecular machinery needed to carry out the
functions for which the structure is specialized

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 The Cytoskeleton
Several non-membranous, proteinaceous structures for cellular contraction, motility, and
support are found in cytoplasm of eukaryotic cells

e.g., microtubules, microfilaments, and intermediate filaments

All key component of the cytoskeleton, which imparts structure and elasticity to
most eukaryotic cells

Cytoskeleton provides scaffolding for transport of vesicles within the cell

Exocytosis and Endocytosis

Eukaryotes exchange materials between compartments within the cell and exterior of the
cell

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 Possible through exocytosis and endocytosis, processes involving membrane fusion
events unique to eukaryotic cells

Organization of DNA
Bacterial DNA is present in the cell as a circular molecule with few proteins

Eukaryotic DNA is organized into linear molecules with large amounts of proteins
(histones) and packed together to become chromosomes

Archaeal DNA is circular with proteins similar to eukaryotic histone proteins

DNA packaging
Circular DNA is much longer than the cell itself and so must be folded and packed
tightly

Equivalently to packing about 60 feet of thread into a thumble

Most eukaryotes have more than 1000 times more DNA than prokaryotes and encode
only 5 - 10 times more proteins

Excess noncoding DNA (junk DNA) MAY have important functions in gene regulation
and evolution (currently not known that much)

Junk region of the DNA is an A-T region

Does not produce any proteins

Chromosomes
Solution to the problem of DNA packaging among eukaryotes

Contains equal amounts of histones and DNA

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 Segregation of Genetic Information
Prokaryotes and eukaryotes differ in how genetic information is allocated to daughter
cells upon division

Bacterial and archaeal cells replicate their DNA and divide by binary fission with one
molecule of the replicating DNA and the cytoplasm going into each daughter cell

Eukaryotes replicate DNA and then distribute their chromosomes into daughter cells by
mitosis, meiosis, and cytokinesis (cytoplasmic division)

Expression of DNA
Eukaryotes transcribe genetic information in the nucleus into large RNA molecules that
are processed and transported into the cytoplasm for translation

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 They go to the cytoplasm through the nuclear pores (the nuclear envelope is NOT a
continuous membrane)

Each RNA molecule typically encodes for one polypeptide

Bacteria transcribe genetic information into RNA, and these molecules produced
may contain information for several polypeptides

In both bacteria and archaea, RNA molecules become involved in protein synthesis
before transcription is complete

Cell Specialization Demonstrates the Unity and

Diversity of Biology
All cells resemble one another in fundamental ways

They differ from one another in important aspects

Unicellular organisms must carry out all the necessary functions in one cell

Multicellular organisms have cells which are specialized for particular functions

In basic structure-function relationships, there is a unity between cells

For specialization, there is a diversity

The Plasma Membrane Defines Cell

Boundaries and Retains Contents
All cells have a plasma membrane

Ensures that cells contents are retained

Consists of lipids (including phospholipids) and proteins and is organized into two layers

Amphipathic membrane components

Each phospholipid molecule consists of 2 hydrophobic tails and hydrophilic head

Lipid bilayer is formed when the hydrophilic heads face outward and the tails face
inward

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 Membrane proteins are also amphipathic, some, with polysaccharides attached to them,
are called glycoproteins

Proteins in the plasma membrane

Enzymes catalyze reactions associated with the membranes

Others serve as anchors for structural components of the cytoskeleton

Transport proteins move substances across the membrane

Receptors for external signals trigger processes within the cell

Transport proteins and receptors are transmembrane proteins

The Nucleus is the information Center of the

Eukaryotic Cell

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 Nucleus is the most prominent structure in eukaryotes

Contains DNA, surrounded by nuclear envelope

Nuclear envelope has pores, each of which is a transport channel, lined with a
nuclear pore complex

The Nucleus
Number of chromosomes is a species-specific characteristic

Chromosomes are most easily visualized during mitosis, whereas during interphase, they
are dispersed as chromatin and difficult to visualize

Nucleoli are also present in the nucleus

Intracellular Membranes and Organelles

Define Compartments
70% of the cell is water (cytosol)

Cytosol = gel-like fluid substance of the cytoplasm

Cytoplasm = everything in the cells that are outside of the nucleus

Number of heritable human disorders are caused by malfunctions of specific organelles

The Mitochondrion
Found in all eukaryotes and is the site of aerobic respiration

Comparable in size to bacteria

Most eukaryotes have hundreds of them and each of them are surrounded by an inner
and outer mitochondrial membrane

Similarity to bacterial cells

Contains small circular DNA

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 Mitochondrial chromosome encodes some RNAs and proteins needed for mitochondrial
function

They also have their own ribosomes, to carry out protein synthesis

Function
Oxidation of sugars and other fuel molecules in mitochondria extracts energy from food
and stores it in ATP

Most molecules for mitochondrial function are localized on the cristae or the matrix

Varied number and location

Number and location of mitochondria varies among cells according to their role in that
cell type

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 Tissues with high demand for ATP have many mitochondria, located within the cell at
the site of greatest energy needs

e.g., sperm and muscle cells

Mitochondria found in the sperm cells

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 Mitochondria found in muscle cells

The Chloroplast
Site of photosynthesis in plants and algae

Large and can be quite numerous in the plant cells

Surrounded both inner and outer membranes and contain thylakoids, stacked into
grana

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 Function
Site of photosynthesis (Using solar energy and CO2 to produce sugars and other
organic compounds)

Chloroplasts are found in photosynthetic cells and contain most of the enzymes
needed for photosynthesis

Reactions that depend on solar energy, take place in or on the thylakoid membranes

Reactions involved in the reduction of CO2 to sugar occur within the stroma, a
semifluid in the interior of the chloroplast

Like mitochondria, chloroplasts contain their own ribosomes, and a small circular
DNA molecule that encodes some RNAs and proteins needed in the chloroplast

Reduces nitrogen from NO3 in soils to ammonia NH3, needed for protein synthesis

SO42- is also reduced to H2S, also needed for protein synthesis

One of several types of plastids found in plant cells

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 Plastids
Specialized for particular functions

Chromoplasts are for coloration in flowers, fruits, and other plant structures

Amyloplasts are for storing starch (amylose and amylopectin)

The Endosymbiont Theory

Did Mitochondria and Chloroplasts Evolve from Ancient Bacteria?

Both mitochondria and chloroplasts have their own DNA and ribosomes and can
produce some of their own proteins

Most proteins needed in these organelles are encoded by nuclear genes

Overall, there are many similarities between processes in mitochondria and

chloroplasts and those in bacteria

This theory suggests mitochondria and chloroplasts originated from prokaryotes

These gained entry into proteoukaryotes

These may have ingested bacteria by phagocytosis without then digesting them,
allowing a symbiotic relationship to occur

Similarities
All three have circular DNA without associated histones

rRNA sequences, ribosome size, sensitivities to RNA and protein synthesis

inhibitors, and type of protein factors used in protein synthesis are all similar

Both resemble bacteria in size and shape and are surrounded by double membrane,
the inner of which has bacteria-type lipids

The Endoplasmic Reticulum

Consists of tubular membranes and cisternae

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 Lumen is the internal space of the ER

ER is continuous with the other membranes in the cell

Rough Endoplasmic Reticulum

ER can be rough or smooth in appearance

Studded with ribosomes on the cytoplasmic side of the membrane

These ribosomes synthesize polypeptides that accumulate within the membrane or

are transported across it to the lumen

Free ribosomes are not associated with the ER

Smooth Endoplasmic Reticulum

Has no role in protein synthesis

Involved in lipid and steroid synthesis

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 Responsible for inactivating and detoxifying potentially harmful substances

Sarcoplasmic reticulum (ER for muscles) has critical functions in contraction

The Golgi Apparatus

Closely related to the ER in proximity and function, consists of cisternae

Important role in processing and packaging secretory proteins, and in complex

polysaccharide synthesis

Accepts vesicles that bud off of the ER

Contents of vesicles from the ER are modified and processed in this organelle

e.g., secretory and membrane proteins are mainly glycosylated

Processed substances then move to other locations in the cell through vesicles that
bud off of the Golgi complex

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 Secretory Vesicles
Once processed by the Golgi body, materials to be exported from the cell are
packaged into secretory vesicles

These move to the plasma membrane and fuse with it, releasing contents outside
the cell

The ER, Golgi, secretory vesicles, and lysosomes make up the endomembrane
system of the cell, responsible for the traffic of resources within the cell

The Lysosome
Single membrane organelles that store hydrolases

Hydrolases are enzymes that can digest any kind of biological molecule

Sequestered to prevent them from digesting the contents of the cell

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 Another enzyme: sulfatases, phosphotases, nucleatases, proteases

A special carbohydrate coating on the inner lysosome membrane protects it from

digestion

Called the suicidal bag of the cell due to its enzymatic content in order to prevent
rogue cells from growing

The Peroxisome
Resembles lysosomes in size and appearance

They are surrounded by a single membrane and perform several function depending
on the cell type

This is especially prominent in the liver and kidney cells of animals

Hydrogen peroxide

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 H2O2 is highly toxic to cells but can be formed into water and oxygen by catalase

Eukaryotes have metabolic processes that produce H2O2

These reactions are confined to peroxisomes that contain catalase, so that cells are
protected from the harmful effects of peroxide

Other functions
Peroxisomes detoxify other harmful compounds, and catabolize unusual substances

In animals, they play roles in oxidative breakdown of fatty acids, especially longer
chain fatty acids (up to 22 C atoms)

Some serious human diseases result from defects in one or more peroxisomal
enzymes, normally involved in degrading long-chain fatty acids

Peroxisomes in plants

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 During germination of fat-storing seeds, glyoxysomes play a role in converting the
stored fat into carbs

Glyoxysomes are specialized peroxisomes

Leaf peroxisomes are prominent in photosynthetic tissue because of their role in

photorespiration, the light-dependent uptake of oxygen and release of CO2

Vacuoles
Some cells contain a membrane-bounded vacuole

In animal and yeasts cells, they are used to temporary storage or transport

Phagocytosis leads to the formation of phagosome

Phagosome = membrane bound particle

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 When this type of vacuole fuses with a lysosome, the contents are hydrolyzed to
provide nutrients to a cell

Plant vacuoles
Most mature plant cells contain a central vacuole

Main function of a central vacuole is to maintain the turgor pressure that keeps
the plant from wilting

Tissues wilt when the central vacuole no longer presses against the cell contents

Ribosomes
They are not exactly organelles due to the non-closure by a membrane

Found in all cells but differ slightly in bacteria, archaea, and eukarya in their size and
composition

Each cell type has a unique type or rRNA

Electron microscope is the microscopic technique to examine ribosomes

With their small size, they have sedimentation coefficients

Sedimentation coefficient: a measure of how rapidly a particle sediments in an

ultracentrifuge, expressed in Svedberg units (S)

Ribosomes have a values of 80S (eukaryotes) or 70S (bacteria and archaea)

Ribosome subunits
There are two subunits: large and small subunits

Sedimentation coefficients: 60S and 40S respectively

Bacteria and archaea have large and small subunits of 50S and 30S, respectively

The S values of large and small subunits does not add up to the value for the
complete ribosome, because S values depend on both size and shape

Ribosomes are much more numerous than most other cellular structures

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 Ribosomes in mitochondria and chloroplasts are similar size and composition to
those of bacteria

This is particularly true of the nucleotide sequences of their rRNAs

The Cytoplasm of Eukaryotic Cells Contains

the Cytosol and Cytoskeleton
Components of the Cytoskeleton
Cytoplasm is the interior of the cell

Cytosol is the semifluid substance in which the organelles are suspended

Synthesis of fats and proteins and the initial steps in releasing energy from sugars
takes place in the cytosol

Cytosol is permeated by the cytoskeleton

Cytoskeleton is a 3D array of interconnected microfilaments, microtubules, and

intermediate filaments

Gives the cell a distinctive shape and internal organization

Plays a role in cell movement and cell division

Serves as a framework for positioning and moving organelles and

macromolecules within the cell

Even some of the water within the cell may be bound to microfilaments and
microtubules

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 Microtubules
Largest structural elements of the cytoskeleton

Axoneme of cilia and flagella is a microtubule based structure

Forms the mitotic spindle fibers that separate chromosomes prior to cell division

Function and structure

Overall shape of the cell, distribution of organelles

Movement of macros and other substances within the cell

Distribution of microfilaments and intermediate filaments

Microtubules are cylinders of longitudinal arrays of protofilaments with a lumen

Each protofilaments is a linear polymer of tubulin with inherent polarity

Tubulin is a dimeric protein conssiting of α-tubulin and β-tubulin

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 Microfilaments
Smallest components of the cytoskeleton

Can form connections with plasma membrane to affect movement

Produces the cleavage furrow in cell division

Contributes to cell shape

Structure
Microfilaments are polymers of actin

Actin is synthesized as G-actin (globular monomer)

These subunits are polymerized into F-actin (filamentous monomer) with a

helical appearance

Microfilaments have polarity

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 Intermediate Filaments
Larger in diameter than microfilaments but smaller than microtubules

Most stable and least soluble components

May have a tension bearing role in some cells because they are found in areas subject
to mechanical stress

Structure
Intermediate filaments differ in protein composition from tissue to tissue

Six classes of intermediate filaments and animal cells from different tissues can be
distinguished on the basis of the types of intermediate filament proteins they contain

This is the intermediate filament typing

Common features of intermediate filament proteins

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 Through heterogenous in size and chemical properties, these proteins are similar in
that they all have a central rodlike segment

They’re different in N-terminal and C-terminal segments

Protofilaments are tetramers that interact with one another to form an intermediate
filament

The Extracellular Matrix and the Cell Wall

Are “Outside” the Cell
Most cells are characterized by extracellular structures

For many animal cells, these structures are called the ECM and consist mainly of
collagen fibers and proteoglycans

For plant and fungal cells, these are cell walls, consisting mainly of cellulose
microfibrils

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 Bacterial Cell Walls
Composed of peptidoglycans, long chains of GlcNAc and MurNAc

Held together by peptide bonds between a small number of amino acids, forming a
netlike structure

There are additional substances specific to cell walls of major groups of bacteria

Motility and the ECM

Plant cells are nonmotile and thus suited to the rigidity that cell walls confer on an
organism

Animal cells are motile and therefore are surrounded by a strong but elastic network
of collagen fibers

Bacteria and archaea may be motile or not

Cell walls provide protection from bursting due to osmotic differences between
the cell and the surrounding environment

Primary function of ECM is support but the types of materials and patterns in which
they are deposited regulate a variety of processes

In animal cells, a network of proteoglycans surrounds the collagen fibers

In vertebrates, collagen is the most abundant protein in the animal body

Can also be found in tendon, cartilage, and bone

Additional functions of ECM

Processes are regulated by the ECM may include:

Cell motility and migration

Cell division

Cell recognition and adhesion

Cell differentiation during embryonic development

Plant cell wall

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 Primary cell wall is laid down during cell division and consists of cellulose fibrils
that are embedded in a polysaccharide matrix

It’s flexible and extensible to allow for increases in cell size

Once the cell reaches its final size and shape, the rigid secondary cell wall forms by
deposition of additional cellulose and lignin on the inner surface of the primary cell
wall

Cell communication
Plant cells are connected to neighboring cells via plasmodesmata

Plasmodesmata are large enough to allow the passage of water and small solutes
from cell to cell

Animal cells also communicate with one another through gap junctions

Tight junctions and adhesion junctions also connect animal cells

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 Viruses, viroids, and prions: Agents that
invade cells
There are several types of agents that invade cells, disrupt cell function and even kill
the host cell

Including the viruses and the less well-understood viroids and prions

A virus consists of a DNA or RNA Core

Surrounded by a protein coat
Viruses are noncellular parasitic particles incapable of a free-living existence

Has no cytoplasm, organelles or ribosomes, and consist of only a few

different molecules of nucleic acids and protein

They invade and infect cells, using synthetic machinery to produce more
virus particles

Viruses
Responsible for many diseases in humans, animals, and plants

Also important as research tools for cell and molecular biologists

Typically named after the disease they cause

Those that infect bacteria are bacteriophages or phages

Structure of viruses
Viruses are small; smallest = about size of a ribosome; largest = about quarter
size of a bacteria

Each virus has a characteristic shape, defined by its protein capsid

Viruses are chemically quite simple, consisting of a capsid of protein surrounding

a core, containing DNA or RNA, depending on the type of virus

Some capsids consist of a single type of protein, while more complex viruses
have capsids with a number of different proteins

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 Some viruses are surrounded by a membrane (aka enveloped viruses)

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 Are Viruses Living?
Living things have fundamental properties:

Metabolism (cellular reactions, in pathways)

Irritability (ability to perceive and respond to external stimuli)

Ability to reproduce

Viruses do not satisfy the first two and though they reproduce, can only do so via
the machinery of a living cell

Viroids are small, circular RNA molecules

Viroids are simpler than viruses

They have small, circular RNA and are known to be the smallest known
infectious agents

Viroid cause several diseases of crop plants

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 Viroids don’t exist freely and are transmitted when the surfaces of adjacent plant
cells are damaged

Prions are “Proteinaceous infective

particles”
Prions are proteinaceous infective particles that are responsible for neurological
diseases

Scrapie, in sheep and goats causes infected animals to rub against trees etc,
scraping of their wool in the process

Kuru is a progressive, degenerative disease of the CNS in humans

Mad cow disease affects cattle

Prions
Prions have abnormally folded versions of normal cellular proteins

Cannot be destroyed by cooking or boiling

In regions where the prion disease, chronic wasting disease, is found in deer and
elk, hunters must have meat tested for the prion before eating it

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