GONO BISHWABIDYALAY

Nolam,Mirzanagar,savar,Dhaka-1344

DEPARTMENT OF MICROBIOLOGY
An Assignment On : Chapter : 6 Control of Gene Expression in
Prokaryotes And Chapter : 7 Gene Mutation And Repair
Mechanisms
Course Title : Molecular Genetics
Course Code :Microbiol - 3502

Submitted To Submitted By

Dr. Donald James Gomes Name : Md Shamim Hossain

Professor Exam Roll : 1222

Department Of Microbiology Batch No : 33rd

University Of Dhaka Semester : 5th

Reg. No : G/Micro-2062/18

Submission Date : 24-06-2020

 Chapter : 6 Control of Gene Expression in
Prokaryotes

Question No 1. Differentiate among constitutive, inducible and repressible

gene expression systems.

Ans :

Constitutive gene :

A gene that is transcribed at a relatively constant level regardless off the cell environmental
conditions

 Such genes are called constitutive genes or house keeping genes.

 The constitutive genes are expressed at more or less constant rate in almost all the cells
and they are not subjected to regulation.
 The products of these genes are required all the time in cells.
 Neither inducible nor repressible and active at all time
 Essential genes for living cells
 The activity of constitutative genes is controlled by how efficiency RNA polymerase
binds to their promoter regions
 Example : Ribosomal proteins , tRNAs, RNA polymerase , glycolysis enzymes

Inducible gene :

Genes whose expression is regulated in this manner are called inducible genes .

 Normal states switched off but turn on only in the presence of their substance
 The expression of the inducible gene increased in response to an inducer.
 Inducers are small molecules.
 Some proteins produced by E.coli, e.g. β- galactosidase are said to be inducible because
they are only produced in significant amounts when a specific inducer “Lactose” is
present.
  Tryptophan pyrrolase of liver is induced by tryptophan.
 Lac operon : regulates production of proteins needed for digesting lactose

Repressible gene :

Gene whose expression is turned off by the presence of some substance (Co-repressor)

 Normal state switched on but Co-repressor turns off the transcription

 Repressor is inactive under normal conditions
 Co-repressor binds to the repressor
 Trp operon : regulates production of proteins needed to make tryptophan (an amino acid)
 Enzymes in anabolic pathway
 Example : Trp operon

Question No 2. Distinguish between induction and repression in a manner that

makes it clear that you know what each is and how they differ .

Ans :

Induction
1. It turns the operon on
2. It starts transcription and protein synthesis
3. It is caused by a new metabolites which
needs enzymes to get metabolised
4. It operates in a catabolic pathway
5. Repressor is prevented by the inducer from
joining the operator gene
6. Example : Lac operon
Repression
1. It turns the operon off
2. It stops transcription and protein synthesis
3. It is caused by an excess of existing
metabolite
4. It operates in a anabolic pathway
5. Aporepressor is enabled by a corepressor to
join the operator gene
6. Example : Trp operon
Question No 3. Draw a picture illustrating the general structure of an operon
and identify its parts.

Ans :

Figure : The general structure of an operon

Question No 4. Briefly describe the lac operon and how it controls the
metabolism of lactose.

Ans :

The lac operon consists of three structural genes involved in lactose metabolism, the lacZ gene,
the lacY gene, and the lacA gene. Each of these three genes has a different role in the
metabolism of lactose. The lacZ gene codes for the enzyme β-galactosidase, which breaks the
disaccharide lactose into galactose and glucose, and converts lactose into allolactose. The lacY
gene, located downstream of the lacZ gene, codes for lactose permease. Permease is necessary
for the passage of lactose through the E. coli cell membrane. The lacA gene, located downstream
of lacY, encodes the enzyme thiogalactoside transacetylase whose function in lactose
metabolism has not yet been determined. All of these genes share a common overlapping
promoter and operator region. Upstream from the lactose operon is the lacI gene that encodes the
lac operon repressor. The repressor binds at the operator region and inhibits transcription of the
lac operon by preventing RNA polymerase from successfully initiating transcription. When
lactose is present in the cell, the enzyme β-galactosidase converts some of it into allolactose.
Allolactose binds to the lac repressor, altering its shape and reducing the repressor’s affinity for
the operator. Since this allolactose-bound repressor does not occupy the operator, RNA
polymerase can initiate transcription of the lac structural genes from the lac promoter .
Question No 5. What is the difference between positive and negative control?
What is the difference between inducible and repressible operons .

Ans :
Positive transcriptional control requires an activator protein to stimulate transcription at the
operon. In negative control,a repressor protein inhibits or turns off transcription at the operon.
An inducible operon normally is not transcribed. It requires an inducer molecule to stimulate
transcription either by inactivating a repressor protein in a negative inducible operonor by
stimulating the activator protein in a positive inducible operon.Transcription normally occurs in
a repressible operon. In a repressible operon, transcription is turned off either by the repressor
becoming active in a negative repressible operon or by the activator becoming inactive in a
positive repressible operon .

Question No 6. What is catabolite repression? How does it allow a bacterial

cell to use glucose in preference to other sugars?

Ans :
In catabolite repression, the presence of glucose inhibits or represses the transcription of genes
involved in the metabolism of other sugars. Since the gene expression necessary for utilizing
other sugars is turned off, only enzymes involved in the metabolism of glucose will be
synthesized. Operons that exhibit catabolite repression are under the positive control of catabolic
activator protein (CAP). For CAP to be active, it must form a complex with cAMP. Glucose
affects the level of cAMP. The levels of glucose and cAMP are inversely proportional—as
glucose levels increase, the level of cAMP decreases. Thus, CAP is not activated .
Question No 7. How does the interaction between the repressor protein and
the operator site differ between the lac operon and the trp operon? What role
does the ligand that binds to the repressor protein play in each case?

Ans :

The lac operon is used to degrade lactose , when glucose level is low .But in absence of trp , the
trp operon is switched on to fulfull the trp amino acid . Here the repression protein bind to the
operator site , that’s why the RNA polymerase enzyme cannot bind to the promoter region . on
the other hand lac operon is switched off , when adequate glucose is available. Repressor block
the RNA polymerase. When allolactose is available which acts as a inducer molecule that binds
to the repressor molecule then the promoter region is opened and lac operon switched on . but the
trp operon is switched off when host cells have available of trp .

In first case the ligand molecule binds the regulator protein, and decreasing its affinity , so it
unable to block the RNA polymerase to bind the operator reason , that’s why the ligand
molecules (allolactose) induces theblac operon (structural gene). Other case ,, the ligand
molecule binds to the upstream region of the trp operon , which has hairpin structure that
represses the binding of RNA polymerase . The upstream region folded and the RNA Polymerse
unable to bind. So the operon is switched off . that’s why the ligand molecule acted as
repressible mannar .

Question No 8. Describe the mechanism responsible for shutdown of the trp

operon when a plentiful supply of free tryptophan is available.
Ans :

RNAP transcribe ; nascent mRNA is formed quickly ;ribosome will initiate translation at start
codon near 5’ end regions 1 & 2 of mRNA may from loop transiently , but no polyU region
follow RNAP pauses , but continues transcribing Trp-enriched leader peptide is readily
synthesized (stop codon after 1) lots of Trp available for ribosome to incorporate rapidly loop
involving regions 1 & 2 melts regions 3 & 4 of mRNA form loop > polyU follows region 4 >
RNAP will terminate transcription before reaching trp structural gene .

Question No 9.What is attenuation? What is the mechanism by which the

attenuator forms when tryptophan levels are high and the antiterminator
forms when tryptophan levels are low?

Ans :
Attenuation is the termination of transcription prior to the structural genes of an operon. It is
aresult of the formation of a termination hairpin or attenuator. Two types of secondary structures
can be formed by the mRNA 5' UTR of the trp operon. If the 5' UTR forms two hairpin
structures from the base pairing of region 1 with region 2 and the pairing of region 3 with region
4, then transcription of the structural genes will not occur. The hairpin structure formed by the
pairing of region 3 with region 4 results in a terminator being formed that stops transcription.
When region 2 pairs with region 3, the resulting hairpin acts as an antiterminator allowing for
transcription to proceed. Region 1 of the 5' UTR also encodes a small protein and has two
adjacent tryptophan codons (UGG). Tryptophan levels affect transcription due to the coupling of
translation with transcription in bacterial cells. When tryptophan levels are high, the ribosome
quickly moves through region 1 and into region 2, thus preventing region 2 from pairing with
region 3. Therefore region 3 is available to form the attenuator hairpin structure with region 4,
stopping transcription. When tryptophan levels are low, the ribosome stalls or stutters at the
adjacent tryptophan codons in region 1. Region 2 now becomes available to base pair with region
3, forming the antiterminator hairpin. Transcription can now proceed through the structural
genes.
Chapter : 7 Gene Mutation And Repair Mechanisms

Question No 1. Define mutation. Why are mutations important?

Ans :
The changing of the structure of a gene, resulting in a variant form that may be transmitted to
subsequent generations, caused by the alteration of single base units in DNA, or the deletion,
insertion, or rearrangement of larger sections of genes or chromosomes.

Mutations are changes in the DNA of an organism. Mutations can be beneficial, benign, or
malignant, depending on where in the genetic code they are located. Examples of beneficial
mutations include HIV resistance, lactose tolerance, and trichromatic vision.

Harmful mutations may cause genetic disorders or cancer. A genetic disorder is a disease caused
by a mutation in one or a few genes. A human example is cystic fibrosis. A mutation in a single
gene causes the body to produce thick, sticky mucus that clogs the lungs and blocks ducts in
digestive organs.
Question No 2. What is the difference between somatic mutations and germ-
line mutations?

Ans :

Germline Mutation Somatic Mutation

1. A germline mutation is any detectable and 1. A somatic mutation is any mutation in a

heritable change in the germ cell lineage somatic tissue of an organism , which results
in a genetically mosaic individual

2. Known as hereditary mutation 2. Known as acquired mutation

3. Occure in different cell stage that appear 3. Occur in the regular body body cells such
during the gametogenesis as liver muscle and skin cells

4. Found in all body cells of the new 4. Can be found in a part of the body or tissue
organism

5. Inheritable to the offspring 5. Not inheritable to the offspring

6. After each and every cell in the body of the 6. Influence is local; it typically affects a
new organism single cell

7. Have an effect on the evolution through 7. Have no effect on the evolution

natural selection

Question NO 3. What is the difference between a transition and a

transversion? Which type of base substitution is usually more common?
Why?

Ans :
Transition mutations are base substitutions in which one purine (A or G) is changed to other
purine , or a pyrimidine (T or C) is changed to the other pyrimidine . Transversions are base
substitutions in which a purine is changed to a pyrimidine or vice versa . Although transversions
would seem to be statistically favored because there are eight possible transversions and only
four possible transitions , about twice as many transition mutations are actually observed in the
human genome .

Question No 4. What are frame-shift mutations and how do they occur?

Ans :
A frameshift mutation is a genetic mutation caused by indels of a number of nucleotides in a
DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by
codons, the insertion or deletion can change the reading frame, resulting in a completely different
translation from the original.

A frameshift mutation occurs when nucleotides are inserted into or deleted from the DNA and
cause a "shift" in the reading of mRNA codons.

Question No 5. How do insertions and deletions arise?

Ans :
Strand slippage that occurs during DNA replication and unequal crossover events due to
misalignment at repetitive sequences have been shown to cause deletions and additions of
nucleotides to DNA molecules. Strand slippage results from the formation of small loops on
either the template or the newly synthesized strand. If the loop forms on the template strand, then
a deletion occurs. Loops formed on the newly synthesized strand result in insertions. If, during
crossing over, a misalignment of the two strands at repetitive sequence occurs, then the
resolution of the crossover will result in one DNA molecule containing an insertion and the other
molecule containing a deletion.
Question No 6. What is the difference between (i) a missense mutation and a
nonsense mutation, (ii) a forward mutation and a reverse mutation, and
(iii) a silent mutation and a neutral mutation?

Ans :

A base substitution that changes the sequence and the meaning of a mRNA codon, resulting in a
different amino acid being inserted into a protein, is called a missense mutation. Nonsense
mutations occur when a mutation replaces a sense codon with a stop (or nonsense) codon. A
nucleotide substitution that changes the sequence of an mRNA codon, but not the meaning is
called a silent mutation. In neutral mutations, the sequence and the meaning of an mRNA codon
are changed. However, the amino acid substitution has little or no effect on protein function.

A mutation is an alteration of the nucleotide sequence of a gene or a genome. Mutation can

happen in somatic cells or germline cells. Germline mutations pass from parents to offspring,
while somatic mutations do not pass into the next generations. Moreover, if we consider a locus
with two alleles, mutations can be forward or reverse mutations. A forward mutation is a
mutation that changes wild type allele to a detrimental allele. In contrast, reverse mutation
changes the already changed allele (mutant) to a wild type allele, reversing the forward mutation.

Question No 7. Briefly describe two different ways in which intragenic

suppressors may reverse the effects of mutations.

Ans :

Intragenic suppression is the result of second mutations within an already mutated gene that
restore a wild-type phenotype. The suppressor mutations are located at different sites within the
gene from the original mutation. One type of suppressor mutation restores the original phenotype
by reverting the meaning of a previously mutated codon to that of the original codon. The
suppressor mutation occurs at a different position than the first mutation, which is still present
within the codon. Intragenic suppression may also occur at two different locations within the
same protein. If two regions of a protein interact, a mutation in one of these regions could disrupt
that interaction. The suppressor mutation in the other region would restore the interaction.
Finally, a frameshift mutation due to an insertion or deletion could be suppressed by a second
insertion or deletion that restores the proper reading frame.
Question No 8. What are the causes of spontaneous mutations?

Ans :
A common cause of spontaneous point mutations is the deamination of cytosine to uracil in the
DNA double helix. Subsequent replication leads to a mutant daughter cell in which a T·A base
pair replaces the wild-type C·G base pair. Another cause of spontaneous mutations is copying
errors during DNA replication.

Mutations arise spontaneously at low frequency owing to the chemical instability of purine and
pyrimidine bases and to errors during DNA replication. Natural exposure of an organism to
certain environmental factors, such as ultraviolet light and chemical carcinogens (e.g., aflatoxin
B1), also can cause mutations.

Question No 9. What is tautomerization and how is it believed to contribute to

mutation?

Ans :
Tautomers are organic compound that are interconvertible by a chemical reaction called
tautomerization .

During tautomerization , the the functional group of the nucleotide base is imidine group,that’s
why the changing group pairs with alternative nucleotide base. As example tautomerized adenine
to cytosine tautomerized thyamine to guanine, through this manners the mutation is happened.

Question No 10. What is 5-bromouracil and how can it lead to a replicated

error?

Ans :
 5 bromouracil is a pyrimidine analogue, which pairs with guanine, cause mutation.
Actullay it is a derivative of uracil.
Uracil is main paired cytosine , but 5 - bromouracil not pires with cytosine, that makes the
new mutated nucleotide
Since 5-bromouracil can pair with either adenine or guanine, it also affects base pairing during
DNA replication, which leads to mutations. An analogue of adenine, 2-aminopurine, also causes
mutations in a similar way since it can pair with either T or C.

Question No 11. What is an alkylating agent? Name and give chemical

formula of three alkylating agents?

Ans :

Alkylating agent a type of drug that is used in the treatment of cancer. It interferes with the cell's
DNA and inhibits cancer cell growth.

Question No 12. What types of mutations are produced by ionizing and UV

radiation?

Ans :
The high energies of X-rays, gamma rays, and cosmic rays are all capable of penetrating tissues
and damaging DNA. These forms of radiation, called ionizing radiation, dislodge electrons from
the atoms that they encounter, changing stable molecules into free radicals and reactive ions,
which then alter the structures of bases and break phosphodiester bonds in DNA. Ionizing
radiation also frequently results in double-strand breaks in DNA. Attempts to repair these breaks
can produce chromosome mutations.

Ultraviolet (UV) radiation does not possess sufficient energy to induce ionizations. However, it
is readily absorbed by many organic molecules such as the purines and pyrimidines in DNA,
which then enter a more reactive or excited state. UV rays penetrate tissue only slightly. Thus, in
multicellular organisms, only the epidermal layer of cells usually is exposed to the effects of UV.
However, ultraviolet light is a potent mutagen for unicellular organisms.

Question No 13. What is the purpose of the Ames test? How are his– bacteria
used in this test?

Ans :
The Ames test allows for rapid and inexpensive detection of mutagenic and potentially
carcinogenic compounds using bacteria. The majority of carcinogenic compounds result in DNA
damage and are mutagens. The increase in reversion rate of his– bacteria to his+ is used to detect
the mutagenic potential of the compound being tested.