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BBCCT-123: Gene Expression and Regulation

BBCCT-123: Gene Expression and Regulation

IGNOU Solved Assignment Solution for 2022-23

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Assignment Code: BBCCT-123/TMA/2022-2023

Course Code: BBCCT-123

Assignment Name: Gene Expression and Regulation

Year: 2022-2023

Verification Status: Verified by Professor


Answer all the questions given below. All Questions carry equal marks.


Q1) (a) Write a brief note on prokaryotic RNA Polymerases.

Ans) RNA Polymerase, also called RNA Pol or RNAP, is a molecular biology enzyme that makes RNA from a template made of DNA. RNA polymerase copies the DNA sequence into an RNA sequence during transcription. It does this with the help of the enzyme helicase, which opens the broken DNA strands. The RNA Pol not only transcribes DNA, but it also helps attach and lengthen nucleotides, checks the transcribed RNA for mistakes, and helps figure out where the end of the DNA is.


RNAP makes functional mRNAs that code for proteins or functional RNAs that don't code for proteins, like tRNA, rRNA, and miRNA. RNA Polymerase is a very important enzyme that can be found in both bacteria and viruses. Depending on the type of organism, the size and number of subunits in the RNAP complex can be different.


Q1) (b) Explain the DNA foot printing technique.

Ans) DNA footprinting is a term for a group of ways to look at complexes of proteins and DNA and figure out where the binding site is. When a protein binds to a certain spot on a DNA sequence, footprinting can help find the spot. It can also give hints about how specific the binding is and how the protein-DNA complex is put together. Using purified proteins and a small piece of DNA to make a protein–DNA complex in the lab makes fingerprinting easier and more accurate. But there are also ways to study these complexes in vivo, which means inside the cell, though these methods are harder. When there are no proteins bound to the DNA, the footprinting techniques can sometimes tell us about the structure of the DNA itself.


Q2) Describe Rho-dependent and Rho-independent termination of transcription.

Ans) The word "termination" refers to the state, action, or process of reaching a decision. In biology, this phrase is often used to describe any process that ends or finishes a biological structure. The main difference between Rho-Dependent termination and Rho-Independent termination is that in Rho-Dependent termination, the Rho factor binds to the transcript and stops transcription by breaking hydrogen bonds between the transcript and the template, while in Rho-Independent termination, the hairpin loop structure and the resulting U-rich portion in the transcript stop transcription.


Rho-Dependent Termination

Rho-dependent termination is one of the two ways that prokaryotes stop the process of transcription. The helicase activity is shown by the protein Rho factor. The Rho protein binds to the RNA transcript and moves with the RNA polymerase in the 5′-3′ direction. This helps break the hydrogen bonds between the DNA template and the RNA transcript.


As the DNA/RNA hybrid gets close to the transcription bubble, Rho factor breaks it apart. This lets the transcript out of the bubble. When this happens, the transcription process is over. Most Rho-dependent terminators have been found in enteric bacteria, but they have also been found in Gram-positive microorganisms, which suggests that they may be common among microbes.


Rho-Independent Termination:

As RNA polymerase moves forward, an mRNA sequence is made. A second method, called Rho-independent termination, is used to stop transcription in prokaryotes. Most terminator regions have a pattern that repeats in the opposite direction. Right after the inverted repeat sequence is an Adenine-rich region.


Because the two parts of the inverted repeat sequence region complement each other, hydrogen bonds allow it to form a hairpin loop structure. The RNA polymerase can't do its job because of the hairpin shape. The next area will be the one with the most U.


In the U-rich regions, there are also weak interactions between the U bases of the transcript and the A bases of the template. Weak interactions between Adenine and Uracil separate the RNA transcript from the DNA template, which makes them less stable. At some point, the transcript moves away from the location of the transcription.


Q3) (a) Give a detailed account of prokaryotic transcription inhibitors.

Ans) Bacteria are microorganisms that belong to the prokaryotic domain, which is one of the three domains of life. Even though most bacteria live in a huge variety of ecological niches, a small number of them can make people sick. Due to how quickly these pathogens are becoming resistant to antibiotics, it is becoming more and more likely that we won't be able to treat many infections effectively. A recent report says that if we don't work together to find and make new antibiotics, by 2050 there will be more than 10 million deaths per year from infections that are resistant to antibiotics. This will cost the global economy about $1 trillion.


Q3) (b) With the help of neatly labelled diagrams explain the functions of ‘cap’ and “Poly-A” tail of eukaryotic m-RNA.

Ans) Chemical groups are added to both ends of a pre-mRNA to change it. The group at the beginning (5' end) is called a cap, and the group at the end (3' end) is called a tail. Both the cap and the tail protect the transcript and help it leave the nucleus and get translated on ribosomes, which are "machines" in the cytosol1 that make proteins.


During transcription, the 5' cap is added to the first nucleotide in the transcript. The cap is a changed version of the nucleotide guanine, and it keeps the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it so that a protein can be made.


The 3' end of RNA comes together in a strange way. During transcription, when a sequence called a polyadenylation signal appears in an RNA molecule, an enzyme cuts the RNA in half at that spot. A poly-A tail is made when another enzyme adds between 100 and 200 adenine (A) nucleotides to the cut end. The tail makes the transcript more stable and helps it get from the nucleus to the cytosol.


Q4) (a) What is RNA splicing? Explain the steps involved spilceosome machinery with a neat diagram?

Ans) RNA splicing is the process by which the newly made pre-mRNA, also called hnRNA (heterogeneous nuclear RNA), is changed into the mature mRNA. In the nucleus, hnRNA is changed into mRNA, which then goes to the cytoplasm to be translated or used to make proteins. It is a change made after the recording.


Q4) (b) Explain riboswitches with the help of their structures.




Q5) Write a detailed note on salient features of genetic code with suitable diagrams.

Ans) The genetic code shows how the order of amino acids in a polypeptide chain and the order of nucleotides in mRNA or DNA are related. 64 genetic codons tell our bodies how to make 20 amino acids. George Gamow came up with the term genetic code.

The Salient Features of Genetic Code are as follows:

  1. The genetic code is clear, which means that each codon is specific to a single amino acid. This means that a single codon cannot be used to represent more than one amino acid.

  2. Codons don't overlap because each nitrogenous base is only part of one codon. A single nitrogenous base doesn't make up more than one codon.

  3. Codons are Universal: All organisms, from the simplest to the most complex, use the same codons to make the same amino acids.

  4. Commaless: The genetic code can always be read. If just one nucleotide is added or taken away, the whole genetic code will be different.

The other features of genetic code are as follows:

  1. The triplet in the genetic code is made up of three nitrogenous bases that are close together.

  2. Codons are groups of three nucleotides that tell the cell what amino acid to make.

  3. Collinearity means that the order of the amino acids on the polypeptide chain is set by the order of the codons on the DNA or mRNA.

  4. A single amino acid can be described by more than one codon, but a single codon cannot describe more than one amino acid.

Q6) (a) Explain the structure and functions of tRNA using a neatly labelled diagram.

Ans) Holley et al. were the first to figure out the nucleotide sequence of yeast alanine tRNA. tRNA has a lot of unusual bases like dihydrouridine, pseudouridine, inosine, methylguanine, dimethylguanine, methylcytosine, ribothymine, and methylinosine. These unusual bases are made when the four nitrogenous bases A, U, C, and G are changed after transcription. The strange bases keep RNase from breaking down the tRNA molecule and play important roles.




 Q6) (b) Enlist protein translation factors.

Ans) Translation, also called protein synthesis, is the process by which ribosomes read the message in the mRNA and turn it into a polypeptide product. The mRNA template, ribosomes, transfer RNAs (tRNAs), and enzymatic factors are all parts of the translation process. Translation happens when ribosomes and tRNAs use mRNA as a template to make polypeptides. Proteins called "factors" coordinate and speed up this process. The things that affect translation have been put into three groups based on which stage of translation they affect. These are called Initiation factors, Elongation factors, and Release factors.


Q7) Describe the protein translation in prokaryotes with the help of a labelled diagram.

Ans) Making an initiation complex is the first step in the process of making proteins. In E. coli, this complex is made up of the small 30S ribosome, the mRNA template, three initiation factors that help the ribosome put itself together correctly, guanosine triphosphate, which is an energy source, and a special initiator tRNA carrying N-formyl-methionine. The start codon AUG on the mRNA interacts with the initiator tRNA, which has a formylated methionine on it. E. coli puts fMet at the beginning of every polypeptide chain it makes because it helps with initiation. Shine-Dalgarno sequence, also called the ribosomal binding site AGGAGG, is a leader sequence upstream of the first AUG codon in E. coli mRNA. It interacts with the rRNA molecules that make up the ribosome through complementary base pairing. This interaction keeps the 30S subunit of the ribosome in the right place on the mRNA template. At this point, the 50S subunit of the ribosome binds to the initiation complex, making the ribosome whole again. When a nonsense codon is found for which, there is no matching tRNA, the translation process stops. When these nonsense codons line up with the A site, release factors in prokaryotes and eukaryotes recognise them. This causes the P-site amino acid to separate from its tRNA, letting the newly made polypeptide out. The small and large subunits of the ribosome separate from the mRNA and from each other. Almost immediately, they join up with another translation initiation complex.


Q8) Write a detailed note on role of activators and repressors in gene expression and regulation with relevant examples.

Ans) Activators are regulatory proteins that help transcription by making it easier for RNA polymerase to interact with the promoter. Some transcription factors activate transcription. Most activators are DNA-binding proteins that bind to promoter elements or enhancers. An activator-binding site is a place on the DNA where the activator binds. An activating region or activation domain is the part of the activator that makes protein-to-protein interactions with the general transcription machinery.


Most activators work by binding sequence-specifically to a regulatory sequence on DNA near a promoter and making protein-protein interactions with general transcription machinery. This makes it easier for the general transcription machinery to bind to the promoter. There are different ways that the activity of activators can be controlled to make sure that they stimulate gene transcription at the right time and level. Activator activity can go up or down in response to signals from the outside world or from other parts of the cell.


Repressors are regulatory proteins that stop transcription by lowering the number of times transcription starts or by stopping RNA polymerase from moving along the DNA strand. This keeps the DNA from being turned into mRNA. Repressing transcription is what other transcription factors do. When an RNA-binding repressor binds to mRNA, it stops the mRNA from being turned into protein. Repression is the act of stopping someone from speaking or making them speak less. This suppression can happen in many ways.


When an inducer, a molecule that starts gene expression, is present, it can interact with the repressor protein and pull it away from the operator. The message can then be written down by RNA polymerase. A co-repressor is a molecule that can bind to the repressor and make it stick to the operator more tightly, which slows down transcription.


Q9) (a) Describe the concept of ‘operons’ in gene expression.

Ans) Operon is a genetic regulatory system found in bacteria and their viruses. It is made up of clusters of genes that code for proteins that work together. This makes it possible for the needs of the cell to be considered when controlling protein synthesis. By making it possible for proteins to be made only when and where they are needed, the operon helps the cell save energy, which is a key part of how an organism lives.


A typical operon is made up of a group of structural genes that code for enzymes that are part of a metabolic pathway, like the biosynthesis of an amino acid. These genes are all on the same stretch of DNA and are controlled by the same promoter. From the operon, a single unit of messenger RNA is copied, which is then turned into different proteins.

Q9) (b) With the help of a neatly labelled diagram explaining regulation of “lac operon”.

Ans) There are three genes in the lac operon: lacZ, lacY, and lacA. Under the control of a single promoter, these genes are turned into a single mRNA. The lac operon has genes that make proteins that help the cell use lactose. lacZ codes for an enzyme that breaks lactose into monosaccharides, which are single-unit sugars that can be used in glycolysis. In the same way, lacY codes for a transporter that is part of the cell membrane and helps bring lactose into the cell.


The lac operon also has a number of DNA sequences that control how the gene works. These are parts of the DNA that certain regulatory proteins can bind to control how the operon is transcribed.


 Q10) (a) Explain the physiology and consequences of SOS responses in prokaryotes.

Ans) The SOS response is known to play a major role in the development and spread of antibiotic resistance and other clinically important events in bacteria. It is also an important factor in the evolution of bacterial species and species variants. Sub-inhibitory levels of antibiotics can cause SOS, which can lead to horizontal gene transfer, the spread of antibiotic resistance, and the production of virulence factors.


DNA is very important. It is found in all living things on Earth, and it contains the information needed to make proteins and arrange them in a cell. If the DNA is broken, the cell will be in danger very quickly. In organisms with more than one cell, what happens when one cell goes haywire is so bad that, unless the damage is very simple and only affects the DNA, the damaged cell usually kills itself.


Q10) (b) Write a short note on hetero chromatin and euchromatin.



Heterochromatin is a part of the chromosomes that is heavily stained and has a high concentration of DNA-specific strains. They are a type of DNA that is packed in tightly in the nucleus. Because heterochromatin has a very dense structure, it is hard to get to the protein that is needed for gene expression. Because of the things listed above, it becomes hard to do the chromosomal cross over. So, heterochromatin is both inactive in terms of transcription and genetics.



Eukaryote is a type of chromatin that is not packed tightly. This part of the chromosome has a lot of genes. During transcription, Euchromatin is very active. About 90% of the human genome is made up of euchromatin. It includes everything from the centre of the nucleus to most of the dynamic genome.


In euchromatin, 147 base pairs of DNA are wrapped around the histone proteins. This is like the way that nucleosomes are made. So that transcription can happen, genes that have been turned on are grouped together in loose groups. Because their DNA isn't tightly wrapped around them, anyone can easily get to it. Euchromatin helps make the change from DNA to RNA happen. The process by which euchromatin changes into heterochromatin or vice versa is called the gene-regulating mechanism. A certain type of euchromatin is called "housekeeping genes."

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