Molecular Biology

Introduction

What is molecular biology?

the study of gene structure and function
at the molecular level

Writing
in
Nature
in
1961,
William
Astburydescribed molecular biology as not so
much a technique as an approach, an approach
from the viewpoint of the so-called basic sciences
with the leading idea of searching below the largescale manifestations of classical biology for the
corresponding molecular plan. It is concerned
particularly with theformsof biological molecules
and [...] is predominantly three-dimensional and
structuralwhich does not mean, however, that it
is merely a refinement of morphology. It must at
the same time inquire into genesis and function.

Central Dogma

Information
in
nucleic acids (DNA
or RNA) can be
replicated
or
transcribed.
Information flow is
reversible
However, there is no
flow of information
from protein back to
RNA or DNA

Gene as a unit of
inheritance

In molecular terms, a gene is the entire

DNA sequence required for synthesis of
a functional protein or RNA molecule.
In addition to the coding regions
(exons), a gene includes control
regions and sometimes introns.

Alleles are alternate forms of a gene

Although most genes are transcribed into

mRNAs, which encode proteins, clearly some
DNA sequences are transcribed into RNAs
that do not encode proteins (e.g., tRNAs and
rRNAs).

However, because the DNA that encodes

tRNAs and rRNAs can cause specific
phenotypes when it is mutated, these DNA
regions generally are referred to as tRNA and
rRNA genes, even though the final products of
these genes are RNA molecules and not
proteins.

Genome is the collective body of genetic

information that is present in a species.

A genome contains all of the genes

required to build a particular organism .

Genome = chromosome or set of

chromosomes that contains all the
DNA
an
organism
(or
organelle)
possesses

Chromosomes : the physical

carries of the genes

During cell division, the material of

the nucleus became organized into
visible threads, which were named
chromosomes, meaning colored
bodies.

Prokaryotic cells:

No membrane bound organelles

Simple genome organization
Genes usually do not have introns
Between 500 and 4000 genes
Great degree of diversity
Unicellular

Eukaryotic cells

All organelles are membrane-bound

Complex genome organization
Large genome size
Between 6,000 and 30,000 genes
Genes have introns
Large amount of regulatory DNA
High degree of genetic redundancy
Unicellular or multicellular

Primary structure: the components

of nucleic acids

DNA and RNA underwent a long

evolution, from nuclein to thymus
nucleic acid to nucleic acid to
deoxyribonucleic acid and ribonucleic
acid

DNA was first called thymus nucleic

acid because it was isolated from the
thymus gland of cattle, while RNA was
first identified as yeast nucleic acid

Genome organization in Prok.

and Euk

Prokaryotes
Circular

DNA

Eukaryotes
Linear

DNA
nuclear DNA

Prokaryotic DNA

Eukaryotic DNA

DNA packaged in a
chromosome
Linear DNA
Associated proteins

Organization of DNA/RNA in chromosomes

Viral chromosomes

1. single or double-stranded DNA or RNA

2. circular or linear
3. surrounded by proteins

TMV

T2 bacteriophage

bacteriophage

Prokaryotic chromosomes
1. most contain one double-stranded circular
DNA chromosome
2. others consist of one or more chromosomes
and are either circular or linear
3. typically arranged in arranged in a dense
clump in a region called the nucleoid

Problem:
Measured linearly, the Escherichia coli genome (4.6 Mb) would be 1,000
times longer than the E. coli cell.
The human genome (3.4 Gb) would be 2.3 m long if stretched linearly.

Fig. 2.15
Chromosome released
from lysed E. coli cell.

Prokaryotic chromosome structure---solutions:

1.

Supercoiling

DNA double helix is twisted in space about its

own axis, a process is controlled by
topoisomerases (enzymes).
(occurs in circular and linear DNA molecules)

Fig. 2.17

Eukaryotic chromosome structure

Chromatin

complex of DNA and chomosomal proteins

~ twice as much protein as DNA

Two major types of proteins:

1.

Histones

abundant, basic proteins with a positive charge

that bind to DNA
5 main types: H1, H2A, H2B, H3, H4
~equal in mass to DNA
evolutionarily conserved

2.

Non-histones

all the other proteins associated with DNA

differ markedly in type and structure
amounts vary widely
>> 100% DNA mass
<< 50% DNA mass

Eukaryotic
Genes
Produce
Monocistronic
mRNAs and Contain Lengthy Introns

many
bacterial
mRNAs
are
polycistronic;
a
single
mRNA
molecule (e.g., the mRNA encoded
by the trp operon) includes the
coding region for several proteins
that function together in a biological
process.

In contrast, most eukaryotic mRNAs

are monocistronic; that is, each mRNA
molecule encodes a single protein.

This difference between polycistronic

and monocistronic mRNAs correlates
with a fundamental difference in their
translation.

mRNA life cycle

mRNA is synthesised by
RNA Polymerase
Translated (once or many
times)
Degraded by RNAses
Steady
state
level
depends on the rates of
both
synthesis
and
degradation

mRNA transcription in Eukaryotic

Prokaryote mRNA structure

Linear RNA structure

5 and 3 ends are unmodified
Ribosomes bind at ribosome binding
site, internally within mRNA (do not
require a free 5 end)
Can contain many open reading
frames (ORFs)
Translated from 5 end to 3 end
Transcribed and translated together

Eukaryote cytoplasmic mRNA

structure

Linear RNA structure

5 and 3 ends are modified
5 GpppG cap
3 poly A tail
Transcribed, spliced, capped,
poly Adenylated in the nucleus,
exported to the cytoplasm