Gene Expression and Population Genetics 2022F

GENE EXPRESSION
Cletus A Wezena (PhD)

UDS
Gene on DNA
 Chromosomal DNA contains 1000s of different genes.
 Each gene is considered a single unit of heredity.
 Genes can be made up of as short as 76 nucleotides (bp) to
as long as 80000 bp.
 Genes control all traits observed in different organisms
and are passed from one generation to the other as DNA.
 The biological information carried by a gene is contained
in its nucleotide sequence.
 The biological information contained in the gene (DNA) is
essentially a set of instructions for the synthesis of RNA
which can be used to direct the synthesis of proteins or
enzymes.
 These proteins and enzymes ultimately determine the
expression of traits.
Gene on DNA
 The extraction of genetic information from DNA to
produce functional RNA, proteins or enzymes is termed
gene expression.
 Genes are discrete segments of DNA molecules, often
separated from one another by intergenic DNA.
 The arrangement of genes on DNA varies in different
organisms or species.
 In viruses and bacteria, genes are closely packed on DNA

with very little intergenic regions.
 In higher organisms, genes are spread out on the DNA
molecule often separated by very long intergenic regions.
 In humans, genes make up less than 30% of the total DNA.

Gene on DNA
 The biological information of a gene is carried by just one
of the two polynucleotides of the double helix.
 The strand carrying the generic information is called the
template strand and acts as the blueprint for the synthesis
of a complentary RNA molecule in the process of
transcription.
 Transcription is the first step of gene expression.
 The template strand is also called the `antisense‘ or
noncoding strand of DNA.
 The strand that is complementary to the template strand is
called the `sense‘ or coding strand.
 Two genes that occur on the same chromosome and for
that matter the same DNA molecule do not necessarily
have the same polynucleotide as their template strand.
Gene on DNA
 In some cases, genes are group into distinct clusters on the
DNA molecule. These clusters may be made up of related
genes or completely unrelated genes.
 Two important clusters made up of related genes are
operons and multigene families.
 An operon is a cluster of genes coding for a series of
enzymes that work in concert in an integrated biological
pathway.
 Operons occur commonly in bacteria e.g lac operon of E.
coli which is a cluster of three genes involved in lactose
metabolism.
 Multigene family is a cluster of related genes which have
identical or similar peices of biological information –
homologous genes.
 Multigene families occur across all species.
Gene on DNA
 Some genes are also discontinous on the DNA molecule
because their biological information is split into distinct
units separated by intervening segments of DNA.
 The sections containing biological information are called

exons and the intervening senseless sequences are called
introns.
 Many eukaryotic genes contain introns and exons.

GENE EXPRESSION
Gene expression
 The extraction of genetic information from DNA to
produce functional RNA, proteins or enzymes is termed
gene expression.
 There are two sequential stages of gene expression:
 Transcription, which is the synthesis of a single RNA

molecule from a double stranded DNA molecule, is the
first step in gene expression.
 Translation involves the use of transcribed RNA (mRNA)

as a template for the assembly of amino acids into proteins
and is the second and final step of gene expression.
Transcription
 The template strand of every gene is used to direct the
synthesis of a specific RNA molecule, the sequence of
which is determined by gene and complementary base-
pairing.
 The new RNA transcript is build in a step-by-step fashion
in the 5‘-3‘ direction.
 The new transcript is antiparallel to the template strand
but parallel to the sense or coding strand which actually
is the gene on the DNA molecule.
 The enzyme that catalyzes the process of transcription is

called a DNA-dependent RNA polymerase (RNA pol).
 RNA polymerases are large proteins made up of several
different subunits that can occur in several forms.
Transcription
 In E. coli, there is one RNA polymerase that occurs in two
forms:
 The holoenzyme and the core enzyme:
 The holoenzyme is made up of five subunits of four

different polypeptides – α2ββ`δ. This form of RNA
polymerase functions in the initiation of transcription.
 The core enzyme has the same structure as the holoenzyme

except that it lacks the δ polypetide. This form of the is
involved in transcript synthesis.
 RNA polymerases of eukaryotes are more complex and

diverse than those of prokaryotes.
Transcription
 In most eukaryotes, there are three different types of RNA
polymerases: RNA polymerases I, II and III each
transcribing different sets of genes.
 RNA polymerase I transcribes genes that control rRNA

synthesis.
 RNA polymerase II transcribes genes that control the

synthesis most proteins
 RNA polymerase III transcribes genes that control the

synthesis small RNAs like tRNA.
Transcription in E. coli
 Transcription in E. coli proceeds in three steps:
 Initiation
 Elongation
 termination
Transcription in E. coli - initiation
Important features of transcription initiation in E. coli:
RNA polymerases transcribes a gene not at random DNA
segment.
Thus the initiation of transcription occurs at a specific
position on the DNA molecule which is just in front
(upstream) of the gene of interest.
This initiation point is signalled by a portion of the gene
called the promotor on the coding strand.
The promotor of a gene is a short sequence of nucleotides
that is recognised by an RNA polymerase as the point of
transcription initiation and to which it binds.
Therefore, promotors of genes occur upstream of the gene

and nowhere else.
Important features of transcription initiation in E. coli:
Every gene must have a promotor sequence before it can be
transcribed or expressed.
Since all E. coli genes are transcribed by one type of
polymerase, it means all the genes in this organism must have
the same or similar promotor sequences.
In E. coli, the promotor sequence is made up of two distinct
components: the -35 box and the -10 box.
The consensus sequences of the -35 and -10 boxes are 5‘-
TTGACA-3‘ and 5‘-TATAAT-3‘ respectively.
Major variations in the -35 and -10 boxes can completely

block transcription.
 The δ subunit of the RNA polymerase recognises the
promotor for specific promotor binding.
 When the holoenzyme binds to the promotor, it leads to

the formation of a structure called closed promotor
sequence.
 Formation of the closed promotor sequence causes strand
separation at the -10 box of the promotor and unwinding
of the DNA double helix.
 This leads to the formation of an open promotor
sequence.
 At this stage the δ component of the holoenzyme
dissociates and the polymerase becomes a core enzyme.
 The core enzyme is able to build an new RNA molecule

Transcription in E. coli - elongation
 During this stage the RNA pol migrates along the DNA
molecule melting and unwinding the double helix as it
progresses.
 RNA pol sequentially attaches ribonucleotides to the 3‘
end of the growing RNA transcript.
Three points of these stage are worthy:

 The transcript is larger than the gene – there is always a
leader sequence and a trailer sequence.
 Only a small region of the DNA double helix is unwound
at a time as it reanneals immediately after point template
usage. This reduces strain on the parent molecule.
 The rate of elongation is not constant. Occasionally, the
RNA pol may pause, accelerate, reverse on a short stretch
etc.
Transcription in E. coli - termination
 Termination of transcription is not random but occurs at
specific positions after the target gene.
 There is no consensus sequence for termination of
transcription.
 Termination is controlled by a complex of termination
signals.
 Most genes in E. coli contain complementary palindromes

which are able to base pair not only between two strands
but also within the same strand.
 Base pairing within the strand causes cruciform structures

in the double helix or a stem-loop struture in the single
stranded RNA structure which leads to termination of
transcription.
Crusciform
DNA
Stem-loop
RNA
 After termination of transcription, the holoenzyme is

reformed and is ready to transcribe another gene.
Transcription in eukaryotes
 The process of transcription in eukaryotes is similar to that
which occurs in E. coli.
 The main differences are that, initiation of transcription is

more complex and termination does not involve the
formation of palindrome activity.
Initiation of eukaryotic transcription:
As in E. coli initiation depends on the RNA polymerase
recognizing and binding to the promotor sequence of the
gene.
Each of the three different eukaryotic polymerases

recognize separate and different promotor sequences.
At the promotor sequence, several different nucleotide

sequences are important in the initiation process.
The main sequence however is the RNA polymerase
binding site.
There are however other important upstream sequences for

RNA polymerase II binding site:
This comprises of the TATA box with the consensus
sequence 5‘-TATAAAT-3‘. This is also called the -25 box.
The polymerase will bind to the TATA box to initiate

transcription but with the help of special proteins called
transcription factors.
Transcription factors for pol II are designated TFIIA,
TFIIB etc to distinguish them from TFI and TFIII of polI
and polIII respectively.
To initiate pol II transcription, TFIID binds first to the
TATA box with the help of TFIIA. TFIIB next binds
followed by TFIIH and then the polymerase. To complete the
initiation complex, TFIIE and TFIIF will then bind.
RNA polymerase II binding site:
Among all the transcription factors, TFIIH plays a very
important role in forming the open promotor complex by
acting as a helicase and opening the double helix.
It is also responsible for activating the polymerase to start

transcription.
With the formation of the open promotor sequence, TFIIB,
TFIIE and TFIIF dissociate from the complex.
The polymerase is now free to proceed with chain

formation.
Chain elongation proceeds as in E.coli.

Termination:
As with initiation, the three different polymerases of
eukaryotes employ different mechanisms of termination.
The process of transcription termination in eukaryotes even
though not fully understood, is significantly different from
that of E. coli.
In the case of termination of polymerase II transcription, the

process is completed with the addition of a poly-A tail to the
newly synthesized mRNA transcript.
During the elongation process, several modification

processes occur on the growing transcript, including the
addition of a series of adenines to the 3‘ end in a process
Termination:
What is thought to occur is that, activities during
polyadenylation causes the detachment of one of the
components of the transcription complex.
This will cause the destabilization of the complex leading to

its dislodge from the template at a point later.
Types of RNA synthesized
 The RNAs formed through the process of transcription can
be grouped into three major classes:
 Ribosomal or rRNA.
 Transfer or tRNA.
 Massenger or mRNA.
 rRNA and tRNA are the end products of gene expression

and perform their functions in the cell as RNA molecules.
 mRNA, on the other hand, undergoes the second step of

gene expression, translation.
 mRNA has no function beyond acting as an intermediate

between the gene and its final expression product, a
 rRNA and tRNA are often referred to as stable RNA,
indicating that these are stable and long-lived in the cell.
 mRNA in contrast, is short-lived with a short turn-over

rate.
 It must be noted that both rRNA and tRNA, even though

not translated, are very important in protein synthesis.
 mRNA serves as a link between the gene which is located

and transcribed in the nucleus and the polypeptide formed
through translation in the cytoplasm.
 rRNA is an essential molecular component of the
ribosome, the cells factory for protein synthesis.
 ribosome
 ribosome
 tRNA are reponsible for bringing the codon-specified
amino acid to the ribosome for protein synthesis. They are
carriers of amino acids and contain the anticodon.
Modification and processing of mRNA
 In bacteria, the mRNA molecules that are translated are
direct copies of the genes encoding them.
 In eukaryotes, the situation is different. The mRNA that is
translated is not only a processed version of the
transcribed mRNA from the gene in terms of direct
nucleotide variation, but is also modified in many ways to
prepare it for translation.
 The three main modification and processing events that
occur during or after synthesis of the mRNA include:
 Chemical modification to the two ends of the mRNA
molecule. This includes the addition of a 5‘ cap and the
polyadenylation.
 Removal of introns from the mRNA sequence (splicing).
 Rearly, the alteration of the nucleotide sequence of the
Chemical modification of mRNA ends
5‘ Capping:
All eukaryotic mRNA are capped.
A freshly forming mRNA will have at its 5‘ end a

triphosphate nucleotide ie pppNpN….
A mature modified mRNA rather has a 5‘ terminus as a

complex chemical structure described as m7GpppNpN…
This is called the cap structure.
m7G in the above structure is a special nucleotide carrying a

modified base called 7-methylguanine.
The cap is thought to play a role during translation
initiation.
5‘ Capping:
Poly(A) tail:
Most prokaryotic and all eukaryotic mRNAs are
polyadenylated.
Tails can contain as many as 250 As ie
pNpNpN(pApApA)npA.
The enzyme that catalysis polyadenylation is called a
Poly(A) polymerase.
It does this by first cleaving 10 - 30 nucleotides downstream
of the primary transcript to a specific signal, 5‘-AAUAAA-3‘
to produce and intermediate 3‘ end.
It then adds the many nucleotides with adenine as a base.
Polyadenylation is thought to protect the transcript from

degradation and extend its shelf-life in the cell.
Poly(A) tail:
Splicing:
Transcription produces a direct copy of the gene.
Therefore, if the gene contains introns, then the primary
transcript will also contains these introns.
Introns must be removed from the transcript and exons
joined together before a functional protein can be translated.
The process of removing introns and joining of exons is
called splicing.
Special splicing molecules called U-RNAs or small
nuclear RNAs conjugate in their numbers and then complex
with special proteins called small nuclear ribonuclear
proteins (snRNPs) to form the spliceosome.
The spliceosome is the enzyme complex that controls
splicing. There also self-splicing introns – ribozymes.
Splicing:
RNA editing:
This refers to the change in the nucleotide sequence of an
RNA molecule that involves deletion, addition or substitution
of particular nucleotides.
Translation
The Genetic Code
 The three major types of RNA molecules produced
through transcription work together to synthesize
proteins by the process of translation.
 All proteins are primarily a sequence of 20 different

amino acids (aa).
 The sequence of aas in the polypetide being synthesized

is specified by the sequence of nucleotides in the mRNA
molecule being translated.
 The rules which determine which sequence of nucleotides

specifies which aas are embodied in the genetic code.
 The sequence of nucleotides on the mRNA molecule is
read in groups of three called the codon.
Amino acids
The Genetic Code
 Depending on the sequence of nucleotides, there are two
different types of codons:
 One that specifies an aa eg CCC specifies the aa called
proline, AUG specifies methionine.
 One that ends the process of translation
 In both eukaryotes and prokaryotes, the codon AUG

begins almost all protein genes and it is therefore the
first codon on the mRNA molecule.
 Thus AUG is also called the start codon.
 Codons that occur at the end of mRNA (gene) and thus

end translation are called termination codons or stop
codons.
The Genetic Code
The Genetic Code
 Since there are four different nucleotides in the mRNA
molecule and three of these combine in a codon, there
must be 64 different types of codons.
 There are three stop codons (UAG, UAA and UGA)

meaning the other 61 specify amino acids.
Features of the genetic code:

 There are three features of the genetic code:
1. The genetic code is degenerate. There 61 aa coding
codons and only 20 aas. This means some codons specify
the smae aa eg GGU, GGC, GGA and GGG all specify the aa
glycine (note the wobble base).
All aas except for methione and tryptophan have more than
one codons.
The Genetic Code
Features of the genetic code:
2. The genetic code contains punctuation codons. This is to
say, it has start and stop codons at the begining and end of
the gene respectively. Because the start codon is AUG, the aa
methionine always occurs at the begining of most eukaryotic
proteins.
3. The genetic code is not universal. Human and bacterial

nuclear genes may follow the genetic code but mammalian
mitochondrial genes do not.
Translation - tRNA
 The genetic code, mRNA, the ribosome and tRNA are the
key players in the process of translation.
The role of tRNA

 tRNA molecules act as adaptors that form a physical and
informational link between the codon on the mRNA and
the aa sequence on the polypeptide.
 Structurally, tRNAs are small molecules of about 74 to 95
nucleotides.
 All tRNAs have the same basic structure called the
cloverleaf. The cloverleaf is the folded base pair structure
made up of the following components:
1. The acceptor arm which holds the specified aa.
2. The D or DHU arm because this component contains the
tRNA
3. The anticodon arm which carries the three nucleotide
sequence called the anticodon. The anticodon
complementarily base pairs with the codon.
4. The extra, optional and variable arm.
5. The TΨC arm.
tRNA
The role of tRNA
A tRNA molecule forms a covalent linkage with its aa and
can recognize and attach to a codon specifying that aa.
The are only about 31 – 40 tRNAs in a cell depending on
the organism.
This fewer number of tRNAs are able to base pair the 61
codons because of the wobble hypothesis
Since the genetic code is degenerate, two tRNAs that specify
the same aa are called isoacceptors.
The wobble hypothesis states that only the first two

positions of the anticodon pair strictly according to the
AU/GC rule. The third can tolerate certain mismatches.
In the above case, anticodon 3‘AAG5‘ can recognise the
codons 5‘UUC3‘ and 5‘UUU3‘.
tRNA
tRNA
Ribosomes
Ribosomes:
These are complex structures composed of rRNA and
proteins.
During translation, ribosomes attach to the mRNA
molecules and migrate along them, synthesizing the
polypeptide as they go.
Ribosomes are one of the most numerous cell organelles.
Both eukaryotic and prokaryotic ribosomes are made up of

two subunits: a smaller subunit and a larger subunit.
These subunits are designated 60s and 50s for the larger
subunits in eukaryotes and prokaryotes respectively and 40s
and 30s for the smaller subunits in eukaryotes and
prokaryotes respectively.

Proteins
Proteins
Translation in E. coli
 As in replication and transcription, translation is also split
into three stages: initiation, elongation and termination.
Initiation:
 This begins with the binding of the 30s unit of the
ribosome to the mRNA molecule at a specific point just
upstream of the start codon.
 This binding point is called ribosome binding site and has
the consensus sequence 5‘-AGGAGGU-3‘.
 This site is also called the Shine-Dalgarno sequence.
 The 30s subunit next migrates downstream until it
encounters the start codon (≈10 bases away).
 Translation starts when a charged tRNA base pairs with
the initiation codon that has been located by the 30s
Initiation:
The initiator anticodon usually carries a methionine but in
E. coli it is a modified methionine called N-formylmethionine
or fmet.
The resulting structure of mRNA, 30s subunit of ribosome
and tRNAfmet is called the initiation complex.
Other proteins called initiation factors with no link to the

ribosome are also involved in initiation.
IF1, IF2 and IF3 have been cited to play various minor roles
in the initiation of translation.
Initiation of translation
Elongation:
Once the initiation complex is formed, the large subunit of
the ribosome can attach to it.
Binding of the larger subunit creates three sites on the
complex to mark the end of initiation:
The peptidyl- or P-site
Aminoacyl- or A-site
Exit site
At this point, the tRNAfmet is paired with the start codon at
the P-site whiles the A-site is free for the next
complementary anticodon to bind the second codon.
Elongation begins with the recruitment of the next

anticondon to the A-site.
Elonagation:
Elongation begins with the recruitment of the second
anticondon to the A-site.
As with initiation, elongation also requires the help of

special proteins called elongation factors: EF-Tu and EF-Ts.
When both A- and P- sites of the ribosome are filled with
charged tRNA, the aas carried by the tRNAs are placed in
close contact.
A peptide bond next forms between the carboxyl group of
the fmet and the amino group of the second aa.
The reaction is catalysed by an enzyme called peptidyl
transferase.
Elonagation:
A second enzyme called tRNA deacylase breaks the
covalent bond between the tRNA and the fmet at the P-site,
freeing the uncharged tRNA at this site from the chain.
A dipeptide is formed which is only attached to the tRNA at
the A-site.
A process called translocation occurs next. This involves the
slipping of the ribosome three bases backwards on the
mRNA.
Translocation moves the second anticodon carrying the
dipeptide into the P-site, expelling the uncharged tRNA and
making the A-site vaccant.
The third anticodon can now enter the A-site to repeat the
process of chain build up.
Elongation of translation
Elonagation:
For the third and subsequent anticodons, an additional
elongation factor, EF-G is required for chain build-up.
Each mRNA molecule can be translated by several

ribosomes as long as the earlier ribosome has moved further
down the chain.
A polysome is an mRNA molecule that is being translated

by several ribosomes.
Termination:
This occurs when a termination codon enters the A-site of
the ribosome.
No anticodon base pairs with stop codons.
Rather, one of two release factors, RF1 or RF2 enters the
A-site and cleaves the completed polypeptide from the final
tRNA.
The ribosome will then release the polypeptide and the
mRNA and then dissociate into the subunits.
The polypeptide can then be processed and modified into a

functional protein.
Termination of translation
Translation in Eukaryotes
 Basically similar to E. coli translation but with slight
differences.
1. The small 40s subunit does not recognize a sequence
anologous to Shine-Dalgarno sequence but recognises the
cap of the mRNA.
2. After locating the cap, it moves downstream to find the
start codon to start translation.
3. Initiation is more complex and requires more factors.
4. Initiation requires the hydrolysis of ATP.
5. Termination involves the hydrolysis of GTP.

Control of gene expression
 Biological information represented in a single cell is
staggaring.
 Some of this information is needed in the form of

enyzmes and proteins by the cell or organism all the time.
 For instance proteins for DNA replication and gene

expression such as polymerases and ribosomes are
needed all the time.
 These proteins must therefore be expressed continiously
and all the time.
 Genes that control these type of proteins are called

house-keeping genes (constitutive genes).
 Other proteins are only needed in small amounts at
specific stages of the cell‘s or organism‘s life (facultative
genes).
 Examples will include hormones needed only at puberty in

eukaryotes and those needed to adapt to specific
environments.
 Therefore, all organisms are able to regulate the

expression of their genes, so that genes whose proteins
are not needed at a particular time are switched off.
Control of gene expression in Bacteria
 Control of gene expression in bacteria can occur at
different levels; transcription, posttranslational,
translation, posttranslational (protein structure and
function).
 The effect of the control of gene expression in any of

these levels has the ultimate effect of regulating the
amount of gene product present in the cell.
 The amount of gene product in the cell is essentially a

balance between two factors: the rate of synthesis and
the rate of degradation of the gene product.
 Thus regulation of gene expression at any of the above

 Transcriptional control: If the number of transcripts of
the gene synthesized per unit time decreases, the amount
of gene product will also decrease. The opposite is also
true.
 mRNA turnover: If mRNA molecules are degraded before
they are translated, synthesis of the gene product will be
limited.
 Translational: control could be exerted over the number
of ribosomes that can attach to a single MRNA or over the
rate at which a single ribosome translates a message.
 Posttranslational: Small molecules can bind noncovalently
to a protein and affect ist structure and function.
Control of gene expression is a very complex process and
may involve several of the above together but, most
Transcriptional control:
This usually involve the actions of regulatory proteins that
bind to the DNA and affect the transcriptional process of one
or more genes.
There are two common types of regulatory proteins:
repressors and activators.
Repressors bind to and inhibit transcription whereas
activators bind to and increase the rate of transcription.
A third group of regulatory proteins called effectors bind to

activators and repressors and regulate their binding to DNA.
The result is a decreases in transcription. Eg of effectors are
corepressors and inhibitors.
An inducer is another protein that binds activators and
Lac Operon- absence of lactose
Lac Operon- presence of lactose
Glucose repression of lac operon
Control of gene expression – Eukary.
 As in bacteria, control of gene expression in eukaryotes
can occur at different levels; transcription,
posttranslational, translation, posttranslational (protein
structure and function).
 However, unlike in prokaryotes, there is also a substantial

regulation of gene expression in the genome level in
eukaryotes.
 Even though similar patterns of regulation are employed

by both eukaryotes and prokaryotes at the transcriptional,
translational and posttranslational levels, the actual
process is more complex in eukaryotes.
Population Genetics
 Concerns genetic variation in populations, why it
exists, and how it changes over many generations.
 Shifts interest in variation from the individual to the

level of the population in which the individual exists.
 Integrate extensions of Mendel’s work with that of

Darwin’s and Molecular Biology.
 Most recently, genetic variation in populations has

been investigated at the molecular level in the
laboratory.
Components of population genetics
 Gene pool: the totality of all genes within a particular
population.
 Individuals receive from and contribute to this gene
pools.
 Population genetics studies the dynamics of this
gene pool generation after generation.
A population: a group of interbreeding individuals who

share the same gene pool, usually separated from
other populations by geographical barriers (eg.
Continents).
A deme: a subpopulation or local population with its

members far likelier to interbreed than the general
 Population geneticists study the genetic variation
observed in the gene pool and how the variation
changes from one generation to the other.
 Populations are dynamic and change from

generation to generation
 This change could be in:

 Size – ‘feast and famine’
 Geographical location – migration
 Gene pool
 Population geneticists develop mathematical theories

to predict the gene in gene pool due to changes in
size, or environment.
 Genes making up the gene pool can be:
 Polymorphisms: in several to many different forms

(each at least up to 1% of all alleles) – large
populations
 Monomorphisms: exists as a single allele (at least

99% of all alleles) – small populations eg A. Cheetah
 There is about 30% polymorphism in the human

gene pool but in every individual the polymorphism
may be less than 10%.
 Polymorphism can be view at the phenotypic level or

 Population genetics is concerned with allele and
genotype frequencies
 Allele frequency = # of copies of allele in population/

total # of all alleles of that gene in the population
 Genotype frequency = # of individuals with that

genotype in the population/total # of individuals in
the population
 Allelic and genotypic frequencies always add up to 1

or 100%.
Hardy-Weinberg Equation/Equilibrium
 Attempts to predict how allelic and genotypic
frequencies stabilize over the course of many
generations.
 Mathematical equation that relates allelic and
genotypic frequencies within the population.
 Predicts that under certain conditions, allele and

genotype frequencies will be stable over many
generations.
 Results from the random combination of
alleles/gametes to form new individuals (Punnett
sq.).
 But natural populations are dynamic and so allele

and genotype frequencies are bound to change.
 The conditions that predict Hardy-Weinberg
Equilibrium include:
 A large population size where sampling error does

not affect allele frequencies.
 The is random mating in the population.
 No net migration between different populations.
 No natural selection, thus no survival advantage for

any genotype.
 No new mutations occurring within the population.

But evolution occurs because variation exists in natural

populations and there is no stability of allele frequencies
Nonrandom mating mostly occurs
 In most human and natural populations, nonrandom
mating usually occurs.
 This leads to cases of:

 Assortative mating – two individuals likely to mate
because of similar phenotypic traits.
 Disassortative mating – where dissimilar phenotypes

mate preferentially.
 Inbreeding (in small populations)

 Outbreeding (hybridization)
 Inbreeding and outbreeding usually don’t affect allelic

frequencies but do affect the stability genotypes.
How do polymorphisms appear in pop.
 All new alleles are produced by rear mutations
 Mutations will most often produce a deleterious allele

because of changes in the stable wildtype gene.
 Deleterious mutations are therefore mostly lost

because they are selected against.
 The rear event of mutation produces harmful alleles

which are removed by natural selection.
 Together these opposing forces (mutation and

natural selection) keep harmful alleles at low levels
in the population
How are mutant genes established in pop
 Polymorphisms, new alleles or variations are
introduce into the population by mutations.
 New alleles produced by mutation can be either

beneficial, neutral or deleterious.
 New alleles could either be fixed or eliminated from

the population.
 Fixation or elimination of a new allele is as a result of

one of two types of evolutionary forces
Evolutionary forces
 Neutral forces: which include migration and
genetic drift. These are forces that affect allelic
frequency in a random manner. That is, without
regard to the survival of a particular phenotype.
These forces occur by chance.
 Adaptive forces: processes in which alleles that

confer greater survival or reproductive success
increase in frequency and those that do not
decrease. It includes natural selection.
Genetic drift
 Random changes in allele frequencies due to
sampling error.
 Genetic drift can either cause fixation or elimination

of alleles.
 It affects more small size populations than large size.
 Examples of cases of genetic drift include:

 Bottleneck effect
 Founder effect

Genetic drift
Natural Selection
 Proposed by Charles Darwin & Alfred Russel
Wallace
 Acts on phenotypes
 ‘struggle for existence’
 The modern statement of natural selection has the

following components:
 Genetic variation occurs within populations

 Some alleles are better adapted for survival.
 These can survive and contribute to gene pool of
next generation.
 Net effect is a population that is better adapted to
Natural Selection acts in 3 ways
 Directional selection:
 Favors one extreme of the phenotypic distribution
that is more adapted to the environment.
 Disruptive/diversifying selection:
 Favors the survival of two or more well adapted and
different phenotypic classes.
 Stabilizing selection:
 Favors an intermediate phenotype.
Natural Selection acts in 3 ways
Recombinant DNA technology
 Introduction
 Based on the concept of gene recombination.
 Involves a number of experimental protocols leading to the

transfer of genetic information(DNA) from one
organism to another.
 Involves the manipulation of genetic material (DNA) to

achieve the desired goal in a pre-determined way.
 The whole process is also called gene cloning and

expression.
Recom. DNA technology- Principle
 Extraction and purification of DNA from organism such as
bacteria, fungi or parasite (Plasmodium).
 Generation of DNA fragments and selection of the desired
piece of DNA (gene) to be manipulated.
 Insertion of the selected DNA into a cloning vector to create a
rDNA or chimeric DNA (recombinant vector).
 Vectors also called plasmids are special ‘vehicles’ (small
circular DNA) that can be forced to enter other cells nuclei.
 Introduction of the recombinant vectors into host cells.
 Recombinant vectors are vectors carrying foreign DNA
 Multiplication and selection of clones containing the
recombinant molecules.
 Expression of the gene to produce the desired product.
 Materials needed
 Restriction enzymes
 Enzymes for the manipulation of DNA.
 Are bacterial enzymes that can cut/split DNA at specific
sites.
 Naturally used by E.coli and other bacteria for destroying
invading bacteriophages by cutting the viral DNA into
pieces.
 Thus, the enzymes that restrict the viral replication are
known as restriction enzymes or restriction
endonucleases.
 DNA ligase
 Joins target pieces of DNA to vectors or plasmids or
plasmid vectors (all mean the same).
 Host cell
 The host cell is the living cell in which the rDNA molecule
(recombinant vector) can be grown/propagated (cloned).
 Host cells can be prokaryotic (bacteria) or eukaryotic.

Microorganisms are preferred as host cells, since they
multiply faster compared to cells of higher organisms.
 Examples of host cells include E. coli, Plasmodium, C.

elegans, Mammalian or human cells such as muscle cells,
bone marrow cells etc.
 Transformation
 This is the process of getting a recombinant vector into a
host cell.
 There are several means of doing this:

 Chemical transformation: host cell picks up vectors in
the presence of chemicals.
 Electroporation: host cell picks up vectors with the
help of electric shock.
Recombinant DNA technology
 Techniques involved:
 Polymerase Chain Reaction (PCR):
 Used to make many copies (clones) of a particular DNA or
RNA fragment.
 Just like DNA replication just that it occurs in a test tube
 Ingredients for PCR include: Taq polymerase, nucleotides,
primer pairs, tamplate DNA
 Gel electrophoresis: used to separate and detect a DNA

fragmen from a mixture of DNA fragments
 Cloning of human insulin gene to produce insulin in
bacteria

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Gene Expression and Population Genetics 2022F

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GENE EXPRESSION

Cletus A Wezena (PhD)

 In viruses and bacteria, genes are closely packed on DNA

 In humans, genes make up less than 30% of the total DNA.

 The sections containing biological information are called

 Many eukaryotic genes contain introns and exons.

 There are two sequential stages of gene expression:

 Transcription, which is the synthesis of a single RNA

 Translation involves the use of transcribed RNA (mRNA)

 The enzyme that catalyzes the process of transcription is

 The holoenzyme is made up of five subunits of four

 The core enzyme has the same structure as the holoenzyme

 RNA polymerases of eukaryotes are more complex and

 RNA polymerase I transcribes genes that control rRNA

 RNA polymerase II transcribes genes that control the

 RNA polymerase III transcribes genes that control the

Therefore, promotors of genes occur upstream of the gene

Major variations in the -35 and -10 boxes can completely

 When the holoenzyme binds to the promotor, it leads to

 The core enzyme is able to build an new RNA molecule

Three points of these stage are worthy:

 Most genes in E. coli contain complementary palindromes

 Base pairing within the strand causes cruciform structures

 After termination of transcription, the holoenzyme is

 The main differences are that, initiation of transcription is

Each of the three different eukaryotic polymerases

At the promotor sequence, several different nucleotide

There are however other important upstream sequences for

The polymerase will bind to the TATA box to initiate

It is also responsible for activating the polymerase to start

The polymerase is now free to proceed with chain

Chain elongation proceeds as in E.coli.

In the case of termination of polymerase II transcription, the

During the elongation process, several modification

This will cause the destabilization of the complex leading to

 rRNA and tRNA are the end products of gene expression

 mRNA, on the other hand, undergoes the second step of

 mRNA has no function beyond acting as an intermediate

 mRNA in contrast, is short-lived with a short turn-over

 It must be noted that both rRNA and tRNA, even though

 mRNA serves as a link between the gene which is located

A freshly forming mRNA will have at its 5‘ end a

A mature modified mRNA rather has a 5‘ terminus as a

m7G in the above structure is a special nucleotide carrying a

Polyadenylation is thought to protect the transcript from

 All proteins are primarily a sequence of 20 different

 The sequence of aas in the polypetide being synthesized

 The rules which determine which sequence of nucleotides

 In both eukaryotes and prokaryotes, the codon AUG

 Thus AUG is also called the start codon.

 Codons that occur at the end of mRNA (gene) and thus

 There are three stop codons (UAG, UAA and UGA)

Features of the genetic code:

3. The genetic code is not universal. Human and bacterial

The role of tRNA

The wobble hypothesis states that only the first two

Both eukaryotic and prokaryotic ribosomes are made up of

Other proteins called initiation factors with no link to the

Elongation begins with the recruitment of the next

As with initiation, elongation also requires the help of

Each mRNA molecule can be translated by several

A polysome is an mRNA molecule that is being translated

The polypeptide can then be processed and modified into a

3. Initiation is more complex and requires more factors.