NANYANG JUNIOR COLLEGE H2 Biology

Organisation and Control of Prokaryotic Genome

ORGANISATION AND CONTROL OF PROKARYOTIC GENOME

Learning Outcome
Candidates should be able to
Core Topic 3 – Genetics of Viruses and Bacteria
(e) Describe the structure of a bacterial chromosome including the arrangement of DNA within
bacterial cells.
(f) Describe the process of binary fission, transformation, transduction and conjugation in bacteria
and explain the role of F plasmids in bacterial conjugation. (Knowledge of Hfr is not required.)
(g) Distinguish between structural and regulatory genes. A structural gene is a region of DNA that
codes for a protein or RNA molecule that forms part of a structure or has an enzymatic function
(e.g. lacY, lacZ lacA, but excludes lacI). A regulatory gene codes for a specific protein product
that regulates the expression of the structural genes (e.g. lacI).
(h) Distinguish between the concept of repressible and inducible systems of gene regulation using
trp and lac operon as examples respectively (attenuation of trp operon is not required).
(i) Describe the concept of a single operon (using lac operon as an example).

Core Topic 4 – Organisation and Control of Prokaryotic and Eukaryotic Genome

(a) Compare the structure and organisation of prokaryotic and eukaryotic chromosomes, in terms
of size, packing of DNA, linearity / circularity, presence of introns and type of regulatory
sequences.
(h) Outline the differences between prokaryotic control of gene expression with the eukaryotic
model.
Use the knowledge gained in these sections in new situations or to solve related problems.

Content Outline
1. Introduction
2. Organisation of Prokaryotic Genome
3. Structure of Bacterial Chromosome
4. Prokaryotic Reproduction - Binary fission
5. Genetic Transfer in Prokaryotes
(a) Transformation
(b) Transduction
(c) Conjugation
6. Control of Prokaryotic Gene Expression
(a) Transcriptional control
(b) Translational control

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References
1. Campbell N. A. and Reece J.B. (2008). Biology. Chapter 17: From Gene to Protein. Eighth
Edition. Pearson Education, Inc.
2. Campbell N. A. and Reece J.B. (2008). Biology. Chapter 18: Regulation of Gene Expression.
Eighth Edition. Pearson Education, Inc.
3. Campbell N. A. and Reece J.B. (2008). Biology. Chapter 27: Bacteria and Archaea. Eighth
Edition. Pearson Education, Inc.
4. Brooker R.J. et. al. (2008). Biology. Chapter 12: Gene Expression at the Molecular Level. First
Edition. The McGraw-Hill Companies.
5. Brooker R.J. et. al. (2008). Biology. Chapter 13: Gene Regulation. First Edition. The McGraw-
Hill Companies.
6. Brooker R.J. et. al. (2008). Biology. Chapter 18: Genetics of Bacteria and Viruses. First
Edition. The McGraw-Hill Companies.
7. Brooker R.J. et. al. (2008). Biology. Chapter 27: The Bacteria and Archaea. First Edition. The
McGraw-Hill Companies.
8. Karp G. (1999). Cell and Molecular Biology – Concepts and Experiments. Chapter 12: The Cell
Nucleus and the Control of Gene Expression. Second Edition. John Wiley and Sons, Inc.
9. http://dnalc.bii.a-star.edu.sg/dnaftb/31/concept/index.html

1. Introduction
All forms of life are groups within three domains called Bacteria, Archaea and Eukarya.
Eukarya comprise of eukaryotes while Bacteria and Archaea comprise of prokaryotes.
Individual prokaryotic cells may exist as single units or remain associated with each other after
cell division, forming pairs, chains or clumps. Bacteria are widespread on Earth, and several
species are known to cause many types of infectious diseases. Many species of archaea are
also known, though they are less common than bacteria. In this chapter, the focus is on
bacteria.

Bacteria vary in shape. Major cell shape types are spherical, cocci, rod-shaped bacilli, comma-
shaped vibrios, and coiled spirilli and spirochaetes. A slimy layer of mucilage covers the
bacteria and this usually play a role in diseases or aid in the development of biofilms. Most
prokaryotes possess a protective cell wall, which contain peptidoglycan, which is composed of
carbohydrates cross-linked by peptides. Gram-positive bacterial cells have walls rich in
peptidoglycan, while Gram-negative cells have less peptidoglycan in their walls and are
enclosed by lipopolysaccaharide envelope. These two groups of cells can be distinguished by
Gram stain.

Motility enables microbes to change positions within their environment, which aids in locating
favourable conditions for growth. Some micro-organisms swim by means of flagella; other
twitch or glide by the use of thread-like pili, or adjust their buoyancy in water by means of
intracellular vesicles.

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2. Organisation of Prokaryotic Genome

Most bacterial species contain a large, circular chromosome.
 The chromosome inside a bacterial cell is highly compacted and found within the nucleoid
and is not bounded by a membrane
 A typical chromosome is a double-stranded DNA (a few million base pairs in length) that
is associated with DNA binding proteins (non-histone scaffolding proteins).
 Most bacterial species contain a single type of chromosome, but it may be present in
multiple copies.
 Several thousand different genes are interspersed throughout the chromosome.
Structural genes (i.e. sequences that encode proteins) account for majority of bacterial
genome. The non-coding sequences are located between adjacent genes, i.e.
intergenic sequences.
 Short, repetitive sequences (less than 10 nucleotides long) are found in multiple copies
and usually interspersed within the intergenic regions of the chromosome. They are
involved in processes such as DNA folding, DNA replication, gene expression of rRNA
and tRNA sequences and genetic recombination.
 Each chromosome possesses only one origin of replication. The origin of replication is a
sequence that functions as an initiation site for the assembly of several proteins that
are required for DNA replication. On the contrary, each eukaryotic chromosome has
several origins to allow several replication bubbles to be initiated simultaneously,
increasing the rate of DNA replication.
 The chromosome is usually attached to the cell membrane of bacteria.
 In Escherichia coli, the chromosomal DNA consists of about 4.6 million base pairs,
representing about 4400 genes. This is 100 times more DNA than is found in a typical
virus, but only about one-thousandth as much DNA as in a human somatic cell.
 In addition to the chromosome, bacteria also have several plasmids, which are small,
circular pieces of DNA that exist independently of the bacterial chromosome.
Plasmids occur naturally in many strains of bacteria and in a few types of eukaryotic cells,
such as yeast.
 Plasmids are self-replicating, i.e. their replication is independent of the bacterial
chromosome, as it contains its own origin of replication.
 Plasmids are not necessary for survival of bacteria. However, in many cases,
certain genes within a plasmid confer advantages to bacteria’s survival in stressful
environments
 Most plasmids fall under five different categories:
 Fertility plasmids (F plasmids), also known as F factors, allow bacteria to mate
with each other. Through the mating process, F plasmid facilitates genetic
recombination, which may be advantageous in a changing environment that no
longer favours existing strains in a bacterial population.
 Resistance plasmids, also known as R factors, contain genes that confer
resistance against antibiotics and other types of toxins.
 Degradative plasmids carry genes that enable the bacterium to digest and utilize
an unusual substance, e.g. digest of an organic solvent such as toluene.
 Col-plasmids contain genes that encode colicines, which are proteins kill other
bacteria.
 Virulence plasmids carry genes that turn a bacterium into a pathogenic strain.

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3. Structure of Bacterial Chromosome

 To fit within the bacterial cell, the chromosomal DNA must be compacted several folds.
Part of this compaction process involves the formation of loop domains. A loop domain
is a segment of chromosomal DNA that is folded into a structure that resembles a loop.
DNA binding proteins anchor the base of these loops.
 Supercoiling leads to further compaction of the looped bacterial chromosome.
 The chromosome in living bacteria is negatively supercoiled. The force of negative
supercoiling may promote DNA strand separation in small regions, enhancing genetic
activities such as replication and transcription.
 DNA gyrase and topoisomerase I control the degree of supercoiling in bacterial
chromosome.

Loop domains

The compaction of a bacterial chromosome: As a way to compact the large, circular chromosome, segments are
organised into smaller loop domains by binding to proteins at the base of the loops. These loops are made more
compact by DNA supercoiling.
(adapted from http://genomebiology.com/content/figures/gb-2004-5-12-252-2.jpg on 1 March 09)

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Differences between Structure & Organization of Prokaryotic & Eukaryotic Chromosomes

Feature Prokaryotic Chromosome Eukaryotic Chromosome

Size Smaller, typically between
105 to 107 base pairs.
Packing of DNA Formation of loop domains
which are anchored by DNA
binding proteins, followed
by negative supercoiling.
Linearity / circularity Usually a single, large and
circular chromosome.
Larger, haploid
complement is typically
between 107 to 1011 base
pairs.
DNA wrapped around histones
to form nucleosomes which are
joined by linker DNA, to form the
beads-on-string structure. This is
further coiled to form the
solenoid structure which is
further coiled to form loop
domains anchored by non-
histone / scaffolding proteins.
The loop domains are further
coiled and condensed to form
the metaphase chromosome.
Usually several linear
chromosomes – number is
species-dependent.

Presence of Introns Absence of introns. Presence of introns

interspersed between
exons within a gene.
Type of regulatory Presence of promoters and Presence of promoters,
sequences operators enhancers, silencers

Type of non-coding Absence of telomeres and Presence of telomeres

sequences centromeres and centromeres
Proportion of coding Contain higher proportion Contain higher proportion
sequences to non- of coding sequences than of non-coding sequences
coding sequences non-coding sequences. than coding sequences.
/ Gene density

Other differences at Genome level:

 Ploidy state
 Presence / absence of plasmids
 Number of Origins of Replication

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4. Prokaryotic Reproduction – Binary Fission

Bacterial cells divide by binary fission. Binary fission is a form of asexual reproduction.The
cells of some species, such as E. coli, can divide every 20-30 minutes. Repeated cellular
divisions of the bacterial cell may form a clone of genetically identical cells called a bacterial
colony.

Process of Binary Fission

http://fig.cox.miami.edu/~cmallery/150/mitosis/c7.12.11.fission.jpg

 Before the bacteria cell divides, semi-conservative replication of parental DNA begins at
the origin of replication to give rise to two origins.
 As the chromosome continues to replicate, each origin moves rapidly toward the
opposite end of the cell and adhere to the cell membrane.
 While the chromosome is replicating, the cell elongates. Elongation of the cell also
separates the two identical copies of the chromosomes.
 When replication is complete and the cell has reached about twice its initial size, its cell
membrane invaginates, and deposits new cell wall materials, dividing the parent cell
into two genetically identical daughter cells. Each cell inherits a parental strand of
DNA.
 If the bacterial cell contains plasmids, these will replicate independently of the bacterial
chromosome. When a plasmid is found in multiple copies in a cell, binary fission usually
results in each daughter cell containing one or more copies of the plasmid.

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5. Genetic Transfer in Prokaryotes

Even though bacteria reproduce asexually, they exhibit a great deal of genetic diversity. Within
a given bacterial species, the term strain refers to a lineage that has genetic differences
compared to another strain. For e.g., one strain of E. coli may be resistant to an antibiotic while
another strain may be sensitive to the same antibiotic.

Genetic diversity in bacteria comes primarily from two sources. First, mutation can occur that
alter the bacterial genome and affect the traits of bacterial cells. For e.g., a mutation may give
rise to a bacterial strain that requires the amino acid histidine from an outside source for
growth, although other stains of the same species can make this amino acid.

The second way that diversity can arise is by genetic transfer / horizontal gene transfer, in
which genetic material is transferred from one bacterial cell to another. Genetic transfer
can occur in three very different ways: transformation, transduction and conjugation.

(a) Transformation
Transformation is the alteration of a bacterial cell’s genotype by the uptake of naked,
foreign DNA from the surrounding environment. Usually, this DNA was released into
the environment when another bacterium had died. Many bacteria possess cell-surface
proteins that recognize and transport DNA from closely related species into the cell.
This foreign DNA can then be incorporated into the genome, either by insertion or
recombination via crossing over at homologous regions.

(Adapted from http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-20/2019.jpg)

 E.g. A harmless ‘R’ strain of Streptococcus pneumoniae can be transformed to

pneumonia-causing ‘S’ cells by the uptake of DNA from a medium containing lysed
cells of the pathogenic ‘S’ strain.

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(Adapted from http://fig.cox.miami.edu/~cmallery/150/gene/sf11x1b.jpg)

 This transformation occurs when a live non-pathogenic ‘R’ cell takes up a piece of
DNA carrying the allele for ‘S’. The allele for ‘S’ codes for a smooth cell coat that
protects the bacterium from a host’s immune system, hence making the bacteria
pathogenic to its host cell.
 The foreign allele is then incorporated into the chromosome of the non-pathogenic
cell, replacing the allele for the “coatless” condition by genetic recombination via
crossing over.
 The cell is now a recombinant: its chromosome contains DNA derived from two
different strains.
 E. coli and some other bacteria appear to lack this transformation mechanism.
However, placing E. coli in a culture medium containing a relatively high
concentration of calcium ions will artificially stimulate the cells to take up small
pieces of DNA.
 In biotechnology, this technique is applied to introduce foreign genes into the E. coli
genome – genes coding for valuable proteins, such as human insulin and growth
hormone.

(b) Transduction
Transduction occurs when a phage (i.e. a virus that infects bacteria) infects a bacterial
cell and then transfers some of the cell’s DNA to another bacterium. The mechanism
of transduction is actually an error in a phage lytic cycle. During the synthesis of phage
DNA and proteins, the bacterial chromosome is degraded into small pieces. When the new
viruses are assembled, coat proteins occasionally surround a piece of bacterial DNA
instead of phage genetic material. This mistake creates an abnormal phage carrying
bacterial chromosomal DNA. There are two types of transduction, namely, generalized and
specialized. [Details of transduction found in Genetics of Viruses.]

 Generalized transduction

(Adapted from http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-20/2019.jpg)

 Bacterial genes are randomly transferred from one bacterial cell to another.
 Before the completed phages are released from its host cell (via the lytic cycle), a
small piece of the host cell’s degraded DNA could be accidentally packaged
within a phage capsid in place of the phage genome. Such a virus is defective
because it lacks its own genetic material.
 However, after its release from the lysed host, the phage can attach to another
bacterium (the recipient) and inject the piece of bacterial DNA acquired from the
first cell (the donor).

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 Some of this DNA can subsequently replace the homologous region of the
recipient cell’s chromosome, if crossing-over takes place, resulting in genetic
recombination.

(Adapted from http://diverge.hunter.cuny.edu/~weigang/Images/13-12_lysogeniccycle_1.jpg on 5 March 2009)

 Specialized Transduction
 Only bacterial genes adjacent to the prophage site are efficiently transferred to
another bacterium. Prophage refers to the phage genome that is inserted as
part of the bacterial genome.
 Lysogenic phages (i.e. those able to integrate their genome into the bacterial
chromosome as a prophage) pick up just a few adjacent bacterial genes as it exits
the chromosome as a prophage and transfers them to a new host cell.

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(Adapted from http://faculty.ircc.edu/faculty/tfischer/images/specialized%20transduction.jpg on 5 March 2009)

(c) Conjugation
Conjugation involves a direct physical interaction between two bacterial cells and the
transfer of genetic material from a donor bacterium to a recipient bacterium.

(Adapted from http://trc.ucdavis.edu/biosci10v/bis10v/week7/20f/Slide4.gif)

 The DNA transfer is one-way, i.e. one cell donates DNA, and the other cell receives
the DNA.
 The donor uses appendages called sex pili (singular: pilus) to attach to the recipient.

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 In most cases, the ability to form sex pili and donate DNA during conjugation is due to
the presence of an F factor (F = fertility). F factor can exist either as a segment of
DNA within the bacterial chromosome or as a plasmid. The F plasmid consists of
several genes that are required for the production of sex pili and also may carry genes
that confer a growth advantage for the bacterium.
 Bacterial cells containing the F plasmid are F+ cells and function as DNA donors
during conjugation. The F plasmid replicates in synchrony with the chromosomal DNA,
and division of an F+ cell usually gives rise to two offspring that are both F+.
 Bacterial cells lacking the F factor are designated F- cells. These cells function as
DNA recipients during conjugation as the F+ condition is transferable (i.e. F + cell
converts an F- cell to F+ during conjugation).
 After contacting a recipient cell, a sex pilus retracts, drawing the donor and
recipient cells closer together. A temporary cytoplasmic mating bridge then forms
between the two cells, providing an avenue for DNA transfer.
 Successful contact between a donor and a recipient cell stimulates the donor cell to
begin the transfer process. Genes within the F factor encode proteins that promote the
transfer of one strand of F factor DNA. This DNA strand is cut at the origin of
transfer, and then the strand travels through the pilus into the recipient cell. The
other strand remains in the donor cell and is replicated, restoring the F factor
DNA to its original double-stranded condition.

 In the recipient cell, the two ends of the newly acquired F factor DNA strand are
joined to form a circular molecule, which is then replicated to become double-
stranded. Each parental strand acts as a template for synthesis of the second
strand in its respective cell. The end result of conjugation is that the recipient cell has
acquired an F factor, converting it from an F - to an F+ cell. The genetic composition of
the donor strain has not changed.
 Other donor E. coli strains were later identified that can transfer portions of the
bacterial chromosome at high frequencies. After a segment of the chromosome is
transferred, it then inserts, or recombines, into the chromosome of recipient cell. Such
donor strains were named Hfr (for High frequency of recombination).

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(Adapted from http://nsm1.utdallas.edu/bio/Gonzalez/fall05/LECTURE02%20(OVERHEAD)_files/image020.jpg)

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6. Control of Prokaryotic Gene Expression

In bacteria, control of gene expression occurs most commonly at the level of transcription,
which means that bacteria regulate how much mRNA is made from most genes. A second way
for bacteria to regulate gene expression is to control the rate at which mRNA is translated into
protein, i.e. translational level of control. This form of gene regulation is relatively uncommon in
bacteria. Finally gene expression can be regulated at the post-translational level. For example,
we have learnt that activity of enzymes can regulated by feedback inhibition.

(a) Transcriptional Control

In prokaryotes, the cluster of genes that encode enzymes of a metabolic pathway
under the transcriptional control of a single promoter, in a region on the chromosome,
is called an operon.

A typical bacterial operon consists of regulatory sequences (non-coding DNA which

includes promoter, operator and terminator) and structural genes. A structural gene is
a region of DNA that codes for a protein or RNA molecule that forms part of a structure or
has an enzymatic function.

Not part of an operon, a regulatory gene codes for a specific protein product that
regulates the expression of the structural genes.

Operons are categorised as either inducible or repressible:

 The lac operon is an inducible operon as transcription is turned on by the
presence of a small effector molecule, i.e. lactose. The structural genes in this
operon code for inducible enzymes.
 The trp operon is considered to be a repressible operon because its small effector
molecule, i.e. tryptophan, represses transcription. The structural genes in this
operon code for repressible enzymes.

Each operon can be under dual control, i.e. negative or positive control. The term
negative control refers to transcriptional regulation by repressors, whereas positive
control refers to transcriptional regulation by activators.

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(i) The lac operon

lac
terminator

Structure of a lac operon (Adapted from Brooker)

Escherichia coli can be found in the human gut. Lactose is available to E. coli when we
drink milk. Lactose metabolism begins with its hydrolysis into monosaccharides. By
producing the appropriate enzymes only when the nutrient is available, the cell avoids
wasting energy and resources making proteins that are not needed.

The regulatory sequences found in the lac operon are:

 promoter, which is found upstream of structural genes. It is the site where
RNA polymerase binds to DNA prior to transcription of the structural gene.
 terminator, which is found downstream of structural genes. It is the site which
signals the end of transcription.
 CAP site, which is a DNA sequence recognised by an activator protein.
 operator, which is situated between the promoter and structural genes. It is a
serves as the binding site for the repressor.

The structural genes in an operon code for enzymes and lie adjacent to one
another. When the RNA polymerase moves from one structural gene to the next, the
genes are transcribed into a single mRNA. The mRNA that is transcribed is described
as a polycistronic mRNA as it contains the coding sequences of two or more
structural genes. Introns are absent in the mRNA. This extended mRNA is then
translated into the various enzymes of a particular metabolic pathway.

The lac operon contains three structural genes:

 lacZ gene, which encodes β-galactosidase, the enzyme that hydrolyses lactose
into glucose and galactose. A side reaction of this enzyme is to convert a small
percentage of lactose into allolactose, a structurally similar lactose analogue;
 lacY gene, which encodes lactose permease, a membrane protein required for
transport of lactose into the cell; and
 lacA gene, which encodes galactoside transacetylase, an enzyme whose
physiological role is unclear, although it has been suggested that it prevents the
toxic build up of non-metabolizable lactose analogues in the cytoplasm.

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A regulatory gene, lacI gene, lies adjacent to the lac operon. It encodes the lac
repressor. This repressor is important for the regulation of the lac operon. The lacI
gene, which is constitutively expressed at fairly low levels, has its own promoter
called the i promoter. It is considered to be a regulatory gene because the sole
function of the encoded repressor protein is to regulate the expression of other
genes. The lacI gene is not considered a part of the lac operon.
 When the repressor binds the operator, the promoter is blocked from the
RNA polymerase, and transcription of the structural genes is prevented.
However, the operon is not permanently switched off as the binding of the
repressors to operators is reversible.
 The ability of the repressor to bind the operator and inhibit transcription depends
on the protein’s conformation, which is allosterically regulated by an inducer.
Thus, the concentration the inducer determines the activity of the operon.

The lac operon is an inducible operon. Its transcription is usually switched off but can
be turned on when a specific small effector molecule (lactose / allolactose) binds
allosterically and inactivates the repressor.

 In the absence of lactose or when lactose concentration is low:

 No allolactose binds to the lac repressor.
 lac repressor binds to the operator site and blocks RNA polymerase from
transcribing the structural genes, thus inhibits transcription.
 In reality, the repressor does not completely inhibit transcription. The structural
genes are transcribed at a basal level, so that very small amounts of the β-
galactosidase, lactose permease, and galactoside transacetylase are
synthesized. Even so, the levels are far too low for the bacterium to readily
use lactose.

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 In the presence of lactose:

 A small amount of lactose is transported into the cytoplasm via lactose
permease.
 β-galactosidase will convert the lactose to allolactose.
 The cytoplasmic level of allolactose will gradually rise until allolactose binds
to the repressor, which has four identical subunits, each one recognising a
single allolactose molecule.
 This results in a conformational change of the repressor, preventing it
from binding to the operator site.
 RNA polymerase is then able to transcribe the structural genes ,
synthesising enzymes that catabolise lactose molecules.

(Adapted from Campbell)

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 The lac operon is under dual control: negative control by lac repressor and
positive control by catabolite activator protein (CAP), also known as the cAMP
receptor protein (CRP).
 Catabolite repression is a form of transcriptional regulation influenced by the
presence of glucose (which is a catabolite).
 The ability of glucose to repress the lac operon depends on a small effector
molecule, cAMP, that is converted from ATP via adenylate cyclase.
 cAMP accumulates when the intracellular concentration of glucose is low.
When cAMP accumulates, it binds to CAP.
 This activates CAP and causes it to bind to the CAP site.
 Because CAP is an activator, it enhances the rate of transcription of the
structural genes in the operon and more enzymes are synthesized for
lactose metabolism.

(Adapted from Campbell)

 Thus, two factors regulate the synthesis of enzymes of this pathway:

 The state of the lac repressor determines whether transcription of the
structural genes occurs or not.
 The state of CAP determines the rate of transcription of the structural
genes, only when the operator is not bound by a repressor.

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 The concerted actions of the lac repressor and CAP allow bacteria to use the
sugars in their environment most efficiently. When both glucose and lactose are
present in the environment, the lac operon is shut off, because CAP remains
inactive and does not enhance the rate of transcription of the structural genes
beyond the basal rate. Metabolism of glucose is preferred rather than lactose.

(Adapted from Brooker)

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(ii) The trp operon

E. coli synthesises tryptophan (an amino acid) from a precursor molecule in a series of
steps, each catalysed by a specific enzyme. When E. coli needs to make tryptophan
for itself because the nutrient medium lacks this amino acid, all the enzymes in the
metabolic pathway are synthesised at one time.

 The trp operon is a repressible operon because its transcription is usually turned
on but can be inhibited (repressed) when a specific small molecule (tryptophan)
binds allosterically to a regulatory protein.

 The trp repressor is the product of a regulatory gene called trpR, which is
located some distance away from the operon it controls, and it has its own
promoter.
 The trp repressor is synthesised in an inactive form with little affinity for
the trp operator.
 Only if tryptophan binds to the trp repressor does the repressor
protein change to the active form that can bind to the operator,
inhibiting transcription of the structural genes.

 Tryptophan functions as a co-repressor (as opposed to the inducer in lac

operon) that cooperates with a repressor protein to switch an operon off. As
more tryptophan accumulates, more tryptophan molecules can then bind to
the trp repressor, which can then bind to the trp operator and inhibit the
synthesis enzymes involved in the tryptophan biosynthetic pathway.

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(Adapted from Campbell)

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(b) Translation Control

(i) Translational repressors
A translational repressor recognises sequences within the mRNA, acting to inhibit
translation. These proteins bind to the mRNA to inhibit translation by:
 Binding near the ribosome-binding site and / or start codon and strategically block
the ribosome from initiating translation.
 Binding to the secondary mRNA structures, thereby stabilising these secondary
structures, thus preventing initiation of translation by ribosomes.

(ii) Synthesis of antisense RNA

Double-stranded RNA can form if a second strand of RNA whose sequence of bases
is complementary to the first strand is available. An antisense RNA is an RNA strand
that is complementary to a strand of mRNA. It can be synthesised from the non-
template (antisense) strand of the double-stranded DNA. When mRNA forms a
duplex with a complementary antisense RNA sequence, translation is blocked.
This may occur because:
 the ribosome cannot gain access to the nucleotides in the mRNA or
 antisense RNA-mRNA duplex is quickly degraded by ribonucleases in the cell
 For example, at high osmolarity, the expression of the ompF gene is inhibited by
the expression of an antisense gene, known as micF (mic: mRNA interfering
complementary). When micF gene is transcribed, micF RNA binds to ompF mRNA
via complementary base pairing. This thus prevents ompF mRNA from being
translated.

(Adapted from http://www.teknat.uu.se/forskning/bild.php?typ=forskningsprogram&id=113)

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 NANYANG JUNIOR COLLEGE
Organisation and Control of Prokaryotic Genome
Table of Comparison between Prokaryotic and Eukaryotic Control of Gene Expression
Level of Control Eukaryotic Gene Expression
Chromatin level  Histone modification
 DNA modification
Transcriptional level  Transcription initiation
 Effects of enhancers and
silencers
Post-transcriptional level  RNA processing (5’
capping, 3’ poly-A tail,
splicing)
 RNA transport
Translational level  Translation initiation
 Translational repressors
 Stability of mRNA
 Cytoplasmic
polyadenylation
 Localisation of mRNA
Post-translation level  Biochemical modification
 Structural modification
 Protein degradation
J2/2016
H2 Biology
Prokaryotic Gene Expression
 Not applicable since no
histones are involved in the
packing of DNA
 Not as significant since the
levels of packing of DNA is
not as complex as in
eukaryotes
 Regulation of transcription
via operon system
 No processing of RNA as
transcription and translation
usually occurs
simultaneously in
prokaryotes
 RNA transport is not
applicable as the nucleoid
region in prokaryotes is not
surrounded by nuclear
membrane
 Translational repressors
 Synthesis of anti-sense
RNA (this has been found to
occur in eukaryotes as well)
 (Other translational control
mechanisms may be
available, but are not
covered in this topic)
 Structural and biochemical
modification is not as
significant as prokaryotes
lack most of the organelles
required for protein
modification
 Protein degradation
 Feedback inhibition (this
occurs in eukaryotes as
well)
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