Molecular Biology

Jiang Qihui (Vivi Kasim)

September 06, 2022 – November 29, 2022
 Schedule
Date Topics
Sepember 6 Chapter 1-2 (Introduction; Relationship between Biology & Other Natural Sciences)
September 13 Chapter 4-5 (DNA, Chromosome & Genome; DNA Replication, Repair &
Recombination)
September 20 Chapter 6-7 (From DNA to Protein; Control of Gene Expression)
September 27 Chapter 3, Chapter 8-9 (Protein; Techniques used in Molecular Biology)
October 11 Chapter 8-9 (Techniques used in Molecular Biology, Discussion, Presentation (2 Groups))
October 18 Chapter 17-18 (Cell cycle, Cell Death)
October 25 Chapter 20, 22 (Cancer, Stem Cells)
November 1 Cell cycle & Cancer
November 8 Special Topic: Cell-cell Communications
November 15 Special Topic: Cancer Metabolism
November 22 Special Topic: Cancer Stem Cell
November 29 Presentation (4 Groups)
 Assessment
• Attendance: 24 points (2 points x 12 meetings)
• Participation and/or Quiz: 16 points
• Reports: 20 points
• Discussions (presentations & problems solving): 30 points & 10 points

** Class will be held online before students could come to CQU.

 Textbooks

Molecular Biology of The Cell, Lewin’s Genes XI

6th Edition
 CONTENTS
Introduction: From Cells to Genome
Relationship between Biology and other Natural Sciences
DNA, Chromosomes & Genomes
DNA Repair & Replication
From DNA to Protein
Control of Gene Expression
Protein
Techniques used in Molecular Biology
Cell Cycle
Cell Death
Cancer
Stem Cells
Cell cycle & Cancer
Special Topic: Cell-cell Communications; Cancer Metabolism; Cancer Stem Cells
 Molecular Biology
I. Introduction:
From Cells to Genome

Jiang Qihui (Vivi Kasim)

 What is “Biology”?
Biology:
bio—bios—life
logia —logia—study of

 Carl Linnaeus (Sweden) first used “biologi” in

Bibliotheca botanica.
 In 1802-22, Gottfried Reinhold Treviranus announced:
The objects of our research will be the different forms &
manifestations of life, the conditions and laws under which these
phenomena occur, & the causes through which they have been effected. The
science that concerns itself with these objects we will indicate by the
name biology [Biologie] or the doctrine of life [Lebenslehre].
(Six-volume treatise Biologie, oder Philosophie der lebenden Natur)
 What is “Molecule”?

 An electrically neutral group of two or more atoms held together

by chemical bonds.
 Molecules are distinguished from ions by their lack of electrical
charge.
 However, in quantum physics, organic chemistry,
& biochemistry, the term molecule is often used
less strictly, also being applied to polyatomic ions.
 What is “Molecular Biology”?

Concerns the molecular basis of biological activity between

biomolecules in the various systems of a cell, including the
interactions between DNA, RNA, and proteins and their
biosynthesis, as well as the regulation of these interactions.
 What is “Molecular Biology”?

“searching below the large-scale manifestations of classical biology

for the corresponding molecular plan. It is concerned particularly
with the forms of biological molecules and … is predominantly
three-dimensional and structural—which does not mean, however,
that it is merely a refinement of morphology. It must at the same
time inquire into genesis and function.”
William Astbury, Nature, 1961
 What is “Molecular Biology”?
Why we should learn Life Sciences

molecular biology?
Medical
Zoology Pharmaceutical Developmental
sciences / Biomaterials Others
Botany sciences Biology
Biomedicine

Biochemistry Cellular Biology

 The study of the chemical substances
& vital processes occurring in living
organisms Genetics
 Focus heavily on the role, function, & Functions  The study of genetics & heredity

try
 Focus on the effect of
structure of biomolecules

G e ne t
genetic differences on organisms
Molecular biology emi
h
Bioc

ics
 Study of molecular basis of
replication, transcription Protein Genes
Molecular
translation & cell function
Biology
 What is life? What is living things?
Are they
different?
What is the common things
between them?

“LIFE
Living things ”
curious, intricately organized chemical factories that take-in the matter
from their surroundings and use these raw materials to generate copies
of themselves

There must be something in common

between the living things
 Central mystery of the nature of life
cell wall
cell membrane
cytoplasm
nucleus
lysosome
chloroplast

Cells
• small, membrane-enclosed units
• filled with a concentrated aqueous solution of chemicals
• endowed with the extraordinary ability to create copies of themselves by
growing and then dividing in two
 Cells
Cells are fundamental units of life
Deeper understanding of
cells & their evolution

Grand historical problems of life on Earth

the mysterious origins of cells
the stunning diversity of cells
its invasion of every conceivable habitat

The key to every biological problem must finally be sought in the

cell; for every living organism is, or at some time has been, a cell.
E.B. Wilson (pioneering cell biologist)
The core of biology

Variety in Constancy in
individual fundamental
particulars mechanisms
Universal features of cells—heredity

Like father, like son

（龙生龙，凤生凤— lóng shēng lóng, fèng shēng fèng ：
a dragon born dragon, a phoenix born phoenix ）

Parent organism hands down extraordinary detail information

specifying the characteristics that the offspring shall have

Each species reproduces itself faithfully,

yielding progeny that belongs to the same species
Heredity is the central to the definition of life:
it distinguishes life from the other processes
How heredity is stored & passed to next generation?

“Living organism & computer”

 Living organism & computer

Store Proteins
Information Commands
mRNA
In the form of
Genome binary codes: 0 & 1
Actions
A, T, G, C
Functions
Activity
Phenotype
 Living organism & computer
Store
Information

In the form of
Genome binary codes: 0 & 1

A, T, G, C

Storable & readable in Storable & readable in

different species different devices
 Common hereditary mechanism
1. Same hereditary information storage—
DNA
2. Same way for replicating hereditary information—
templated polymerization
3. Same way for transferring hereditary information→functions—
central dogma
4. Same intermediary form—
RNA
5. Same catalyst—
protein
6. Same translational pathway (same code)—
codon
1. Same hereditary information storage: DNA
Living cells:
store information, just like computers,
& it is estimated that they have been
evolving and diversifying for over 3.5
billion years

DNA:
long, unbranched, paired polymer chains, formed always of the same
four types of monomers: adenine, thymine, cytosine, guanine
The archives of one type of cell is readable
by the information-handling machinery of another

DNA is the information store for heredity

2. Same way for replicating hereditary
information: templated polymerization
DNA polymer is extended by adding monomers at one end
Could the DNA strand being synthesized in any order? YES? NO?
the bases from the existing strand bind to the bases of the
strand being synthesized

All cells replicate their hereditary information directionally through

templated polymerization according to a strict rule:
complementary structures of the bases
 DNA replication
A C
T G

Bonds between base-pairs:

weaker compared to the sugar-phosphate links
Which one is stronger?
Allows the two DNA strands to be pulled
apart without breaking their backbones

The existing strands could serve as template

for replication
 3. Same way for transferring hereditary
information into functions: central dogma

REVERSE
TRANSCRIPTION
 4. Same intermediary form: RNA
 Ribose nucleic acids
 4 bases: adenine, guanine, cytosine, uracil
 Unstable, compared to DNA
 Single strand
 messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA)
 microRNA (miRNA), piwi RNA (piRNA), short interfering RNA (siRNA)

The cell’s archive of genetic information in the form of DNA is fixed,

but the RNA transcripts are mass-produced and disposable
 Other function of RNA

Single-stranded, thus they could form internal associations &

fold up into a specific shape, which in turn could recognize other
molecules by binding to them selectively, & even catalyze chemical
changes in the molecules that are bound. CATALYTIC RNA
 5. Same catalyst: protein
 Long, unbranched polymer chains
 Formed by stringing together monomeric building blocks drawn from a
standard repertoire that is the same for all living cells
 Form most of the cell’s mass (except water)
 Polypeptide created by joining its monomers (amino acids, 20 types in total),
in a particular sequence
 Can bind with high specificity to other molecules
 Can act as enzymes to catalyze reactions making or breaking covalent bonds
 Maintaining structures, generating movements, sensing signals, etc.

** Some special RNA (e.g., ribozyme)

could also act as enzyme
 6. Same translational pathway (same code)
Polynucleotide consisting 4 types of
Only these 24 kinds (+4 nucleotides
kinds in DNA) of monomers
that orchestrated all the Polypeptide consisting 20 types of
functions in living organism amino acids

Read out in group of 3 nucleotides at a time

mRNA

CODON
20 amino acids (+ initiating codon
43 = 64 possibilities of codon
and terminal codon)

More than 1 codon correspond to the same amino acid

The most common features between organisms:

All the functions of living organisms are

conducted by 8 nucleotides and 20 amino
acids!
 From gene to protein
Whole DNA (containing the specification for thousands of proteins)

An individual segment of DNA

mRNA molecules

Proteins
 Gene
An individual segment of DNA

mRNA (isoform 1, 2, 3,…) RNA with catalytic functions

RNA with regulatory functions RNA with structural functions

Gene: the segment of DNA sequence corresponding to a single protein or set of

alternative protein variants; or to a single catalytic, regulatory, or structural RNA

Species with one of the smallest genome known: Mycoplasma genitalium

530 genes:
 43 genes coding for transfer, ribosomal & other non-
messenger RNAs
 339 genes coding for protein
 580,070 nucleotide pairs  145,018 bytes (one chapter of
our text book)
 Regulation of genes expression

Regulation of individual genes expression:

1. Manufacturing its full repertoire of possible protein at full tilt all
the time
2. Adjust the rate of transcription & translation of different genes
independently

Genome of the cell dictates not only the nature of the cell’s protein,
but also when & where they are to be made
Genome: the totality of the genetic information of a cell as embodied
in its complete DNA sequence
 Other common features
 All cells requires free energy---will be discussed later
 All cells function as biochemical factories:
All cells have to contain and manipulate a similar
collection of small molecules:
simple sugars
nucleotides
amino acids
ATP, and other universally required
substances
 All cells are enclosed in plasma membrane across which
nutrients and waste materials must pass to maintain its
integrity as a coordinated chemical system
 Cell membrane

lipid (hydrocarbon, -CH2-

Amphiphilic phospholipid molecule: CH2-CH2-), water
Aggregate spontaneously in the avoiding
water to create a bilayer that forms phosphate, water loving
small closed vesicles
Cell boundary:
Not totally impermeable
Have membrane transport proteins
embedded in their membrane,
transport specific molecules from one
side to another
The core of biology

Variety in Constancy in
individual fundamental
particulars mechanisms
Diversity of genome—variety of free energy sources
 Organotrophic
Living organisms that obtain their free energy by feeding on other living things
or the organic chemicals they produce
Example: animals, fungi, bacteria in human gut, etc.

 Living organism that obtain their free energy from non-living world:
Phototrophic:
Feeding on sun-light
Oxygen in the atmosphere is their biosynthetic activities’ by-product
Examples: plants, bacteria, algae

Lithotrophic: Feeding on rock

Aerobic or anaerobic---similar to the circumstances of early
days of life on Earth, before oxygen had accumulated
Diversity of genome—variety of free energy sources
Phototrophic (feeding on sun-light)
Oxygen in the atmosphere is their biosynthetic activities’ by-
product Example: plants, bacteria, algae
nitrogen fixation
photosynthesis
formation of spores

Anabaena cylindrica
Diversity of genome—variety of free energy sources
Lithotrophic: (feeding on rock)
Aerobic or anaerobic---similar to the circumstances of early days of life on Earth,
before oxygen had accumulated

H2, CO, Mn2+, Fe2+, Ni2+, CH2, NH4+ &

phosphorous containing compounds

other
bacteria
organisms: tube Symbiosis with bacteria
submarine geyser
worm, etc. that could oxidize sulfur
 The tree of life
How to classify living organisms?
Traditionally:
comparing their outward appearances

Nowadays:
genome analysis– a simpler, more direct and much more powerful way to
determine evolutionary relationships
The number of differences between the DNA sequences of two organisms can
provide a direct, objective, quantitative indication of their evolutionary distance
 Mutation & conservation of genes

Mutations
Neutral
Better Serious damage (no change in Highly conserved genes /
function) sequence
Endless
repetition Not perpetuated A matter of chance in
Perpetuated
(cannot survive) competition with its cousins
Natural selection Highly optimized essential
Perpetuated or not protein, RNA molecule, or
functional regulatory region
Evolution:
• New ways to exploit the environment more effectively
• To survive in competition with others
• To reproduce successfully
Mutation & conservation of genes

A part of the gene of one of the rRNA components

Essential genes / sequences are highly conserved;

highly conserved genes are usually essential
 Generation of new genes
occurs randomly; mainly due to errors
during DNA replication

a pair of initially identical genes in a single

cells; the two genes may then diverge in the
course of evolution
a hybrid gene consisting of DNA segments
that originally belong to separate genes is
generated as a result of break & rejoin of 2
or more genes

Transfer of a piece of DNA from the

genome of one cell to that of another (even
another species)
Could occur naturally and in laboratory
Ex:
mitochondria Nothing comes from nothing 
chloroplast No gene is entirely new
Homologous genes: orthologs & paralogs
Repetition &
Gene duplication divergence

Generation of two genes

in a single cells:
each copy is free to mutate
and gain different function
within the same cells

After billion of years:

Many gene families
in a single genome
 The three major divisions
of the living world

First eukaryotic cells formed after a particular type of

ancient archaeal cell engulfed an ancient bacterium
 Common gene families to all
three primary branches of the tree of life

Among 4873 protein-coding gene families

(50 species of bacteria, 13 archae, 3 unicellular eukaryotes)
 Eukaryotes
 Nucleus
 Nuclear envelope (double layer of membrane, surrounds the nucleus and separates DNA from the
cytoplasm) & other internal membranes
 10x bigger in linear dimension, 1000x bigger in volume compare to prokaryotes
 Cytoskeleton—provides mechanical strength, shape and the ability to control movement
 Phagocytosis (no tough cell wall such as in bacteria)
 Hybrid genomes
 Big genome sizes
 Rich in regulatory DNA
(98.5% noncoding DNA in human vs 11% in E. coli)
 Defines program for multicellular development
 Eukaryotic genomes
Comparison of the genome size between model organisms
 Eukaryotic genomes
Genome defines the program
of multicellular development

Snapdragon Antirrhinum, mutation in a single gene coding for

regulatory protein causes leafy shoots to develop in place of flowers
All cells are descendants of a single fertilized eggs,
& contain identical copies of genetic information
Phagocytosis—Eukaryotic cells may have
originated as predators
Eukaryotic cytoskeleton:
• A system of protein filaments
crisscrossing the cytoplasm
• Controls its shape
• Gives mechanical strength
• Drives & guides its movement
A human neutrophil engulfing a red blood cells

A Didinium is Lack of tough cell wall 

engulfing its prey Animal cells & protozoa can
change their shape rapidly &
engulf other cells & small
objects (phagocytosis)
Modern eukaryotic cells evolved from a symbiosis
Mitochondria

 Double layer membrane

 Take up O2 and harness energy by oxidizing food molecules
 Similar size to small bacteria
 Own genome, ribosome & tRNA
 Originated from symbiosis between an ancestral cell (anaerobic) & aerobic bacteria—
the bacteria provides the host with energy, and receive shelter & nourishment
Eukaryotes have hybrid genome: the nuclear DNA of humans contains
many genes coding for proteins essential for mitochondria functions
Modern eukaryotic cells evolved from a symbiosis
Chloroplast

 Don’t need to chase the prey anymore,

 Photosynthesis—provides energy
 Have tough, protective cell wall,
 Own genome
 Lost the ability to change shape rapidly
Eukaryotes have hybrid genome:
the nuclear DNA of plant cells contains ALSO many genes coding for
proteins essential for chloroplast functions
Similarities and differences of amino acids

Times from the last common ancestors

 Model organisms (1)
Yeast
Easy to grow
Closely related to plant & animal
Vegetative & sexual reproduction
Small but sufficient genome
(13 million nucleotide pairs)
6600 proteins Arabidopsis thaliana
Ex: for studying cell cycle Model plant
Complete genome sequence: 1997 Can be grown indoors
Can be grown in large numbers
Produces offspring after 8-10 w
Produces thousands of offspring
220 million nucleotide pairs
29000 proteins
 Model organisms (1)
Caenorhabditis elegans

Drosophila melanogaster
Life cycle: only few days
Survive in freezer
Simple body plan
Exact number of body cells (959)
Fertilized eggs to adult  9 d
130 million nucleotide pairs
Vastly easier and cheaper to breed
21000 proteins 200 million nucleotide pairs
Ex: for studying cell cycle, cell death 15000 proteins
Giant chromosome
Ex: for studying genome
 Model organisms (2)
Frogs (Xenopus)
Xenopus tropicalis (Western clawed frog) Xenopus laevis (African clawed frog)

Diploid genome Duplicated genome,

36 chromosomes DNA 2x / cell compared to X.

tropicalis
72 chromosomes
The eggs are big
Easy to manipulate

Another related species:

Fertilized out of the animal
Xenopus ruwenzoriensis Ex: human disease gene
Sixfold duplication of original genome cell division
108 chromosomes
embryonic development
Are estimated diverged within the past 120
million years
signal transduction
genetic studies, etc.
 Model organisms (3)
Zebra fish (Danio rerio) Easy to manipulate
 Fertilized out of the animal
 Genome is compact (half of human or mouse)
 Generation time: 3 months
 Many known mutants
 Transparent embryo—
can observe the behavior of individual cells in the living organism
 Ex: embryonic development

Mouse (Mus musculus)

 Foremost model organism of molecular genetics, human disease, gene function, etc.
 Similarity in genome
 Small, easy to handle, rapid breeding (weaning: 4 weeks, mature: 6-7 weeks)
 Mutations mimicking the effects of corresponding mutations in human
 Transgenic mouse, knockout mouse
 Other model organisms
Dogs Minipigs Primates
(beagle dog, etc.) (Wuzhishan minipig, etc.) (Marmoset,
etc.)

For pharmacokinetics,  Toxicology

toxicity experiments, etc.  Pharmacology  Body size: 19-25 cm
 Pulmonology  Tail: 27-35 cm (tail)
 Cardiology  Weight: 220-450 g
 Aging  High similarity with human
 Organ transplantation in pathological characteristics
 Bio-material development  For studying: social behavior,
 Tissue-organ Repair reproduction, disease model
 Disease model (e.g. Hepatitis A, parasitosis),
etc.
END