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Syllabus
SEMESTER II
MSCMB201
MOLECULAR BIOLOGY
(60 Hrs)
Module 1
DNA replication and DNA repair:
Initiation of DNA replication in prokaryotes, semiconservative, primer, template, origin of
replication, replication-fork, leading & lagging strand, enzymes involved at different stages, co-
ordinated synthesis of leading and lagging strands
Relationship between replication and cell cycle, inhibitors of DNA replication (blocking
precursor synthesis, nucleotide polymerization, altering DNA structure, A brief account of DNA
proof reading and repair mechanisms.
Types of DNA damage- deamination, oxidative damage,, alkylation, pyrimidine dimers; Repair
pathways- photo-reactivation, excision repair, post replication repair, SOS repair, methyl
directed mismatched repair, very short patch repair. 15 hrs
Module 2
Transcription:
The transcriptome, prokaryotic RNA polymerase; molecular composition, and mechanism of
transcription. Initiation of prokaryotic transcription; Bacterial promoters, Closed and open
initiation complexes, promoter clearances. Sigma factors, concept of mRNA, termination; rho-
dependent and independent termination processing of RNA in prokaryotes. Inhibitors of RNA
synthesis; Degradation of bacterial mRNA.
Eukaryotic RNA polymerases-classification and transcription units. Initiation at RNA pol I, II, and
III promoters. Elongation and termination in eukaryotic Post transcriptional modification of
eukaryotic tRNA, and rRNAs, role of RNPs, RNase-P, polynuceotide kinase in modification. Post
transcriptional modification of eukaryotic mRNAs; capping, and tailing. Intron splicing;
Properties and role of snRNPs in splicing, mechanism of splicing by class-I (GU-AG), and class-II
(GU-AC) introns, spliceosome, alternative splicing. RNA editing; degradation of mRNAs,
Transportation of RNA within eukaryotic cells. 15 hrs
Module 3
Translation:
Prokaryotic ribosomes; molecular components, in vivo assembly, dissociation of subunits, and
polysomes. Eukaryotic components and their assembly. Organelle ribosomes and different
types of RNA in protein synthesis
Genetic code- Deciphering of the genetic code; Nierenberg and Khorana's work. General
features of the code. Co-linearity of genes and proteins. Coding properties of tRNA; wobble
hypothesis and departure from wobble hypothesis. Suppresser genes and suppresser
mutations. Mitochondrial genetic code.
Amino acid activation, mechanism of translation (prokaryotes and eukaryotes)– initiation,
elongation and termination, inhibitors of protein synthesis and their mode of action, protein
trafficking, signal hypothesis, post translational modification of proteins. 15 hrs
Module 4
Regulation of Gene Expression:
Prokaryotes- control of transcription- interaction with promoter regions,enzyme induction and
repression, constitutive synthesis of enzymes;, operon concept, catabolic repression, instability
of bacterial RNA, inducers and co-repressors, Negative gene regulation- E.coli lactose operon;
Positive regulation- E.coli arabinose operon; Regulation by attenuation- his and trp operon;
antitermination- N protein and nut sites; modification of RNA Polymerase; modification by
sigma factors; modification of core enzyme.
Patterns of gene expression in Lambda phage; Structure and functions of λ repressor, Cro, and
λcII.
SECTION A
Answer all the questions from 1 -4. For questions 1-4, attempt either (a) and (b) OR (c) and
(d).
1a. Describe the events leading to the co-ordinated synthesis of leading and
lagging strand of DNA.
.
1b. Write a note on the inhibitors of different stages of DNA replication 7+7
OR
1c. Discuss the different types of DNA damage. Add a note on mismatch
repair.
OR
2c. Write an account of the assembly of spliceosome components on pre
mRNA and explain the mechanism of splicing.
2d. Describe the features and mechanism of alternative splicing with relevant 7+7
examples.
3b. Write a detailed account of ribosomes and their role in protein synthesis. 7+7
OR
3c. Describe the events leading to in initiation of translation in prokaryotes.
3d. Discuss the events leading to the synthesis of secretory proteins 7+7
OR
4c. Write a note on i) regulation of genes by antisense RNAs. Add a note on
applications of this technology.
4d. Write short notes on chromatin remodelling as a means of gene regulation. 7+7
SECTION B
5. Write short notes on any four of the following: 3.5x4=14
a. Ori C
b. E.coli RNA Polymerase
c. Trans splicing
d. RNAi
e. Protein transport to lysosomes
f. CHIP technique
Department of Microbiology
Question Bank
Matrix
Instructions:
I. Answer all the questions from Modules 1 -4. For questions 1-4, choose either (a) and (b)
OR (c) and (d).
II. Write short notes on any four of the following:
[7mks]
Module I
a&b
a. Describe in detail the Meselson-Stahl experiment that led to the semiconservative mode of
DNA replication.
b. Write a note on the inhibitors of different stages of DNA replication.
a. Describe in detail the experiment that led to proving the semiconservative mode of DNA
replication.
b. Cell cylce regulates the frequency of DNA replication. Explain.
a. Describe in detail the Meselson-Stahl experiment that led to the semiconservative mode of
DNA replication.
b. Write a note on origin of DNA replication in prokaryotes and eukaryotes and the
events leading to the formation of Primosome.
a. Discuss the role of different enzymes and proteins involved in different stages of DNA
replication.
b. Give an account of different inhibitors of different stages of DNA replication.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Describe the relationship between the DNA replication and cell cycle.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Discuss the structure and functional features of DNA Polymerase III.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Write a note on origin of DNA replication in prokaryotes and eukaryotes and the
events leading to the formation of Primosome.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Write a note on the inhibitors of different stages of DNA replication.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Describe the relationship between the DNA replication and cell cycle.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Discuss the structure and functional features of DNA Polymerase III.
a. Write a detailed note on the different enzymes involved in different stages of DNA
replication.
b. Write a note on origin of DNA replication in prokaryotes and eukaryotes and the
events leading to the formation of Replisome.
a. Describe the events leading to the co-ordinated synthesis of leading and lagging
strand of DNA.
b. Write a note on the inhibitors of different stages of DNA replication.
a. Describe the events leading to the co-ordinated synthesis of leading and lagging
strand of DNA.
b. Describe the relationship between the DNA replication and cell cycle.
a. Describe the events leading to the co-ordinated synthesis of leading and lagging
strand of DNA.
b. Discuss the structure and functional features of DNA Polymerase III.
a. Describe the events leading to the co-ordinated synthesis of leading and lagging
strand of DNA.
b. Write a note on origin of DNA replication in prokaryotes and eukaryotes and the
events leading to the formation of Primosome.
c&d
c. Discuss the different retrieval systems of DNA repair.
d. Give an account on DNA damage.
c. Write a note on origin of DNA replication in prokaryotes and eukaryotes and the
events leading to the formation of Replisome.
d. Write a detailed note on SOS repair.
c. c. Write a note on the features of Oric C of E.coli. Add a note on the events leading to
d. the formation of Primosome.
d. Write a detailed note on Recombination repair.
c. c. Explain excision repair in detail
d. Write short notes on: i. Error prone repair ii. Photoreactivation repair
b. Discuss the different types of DNA damage. Add a note on nucleotide excision
repair.
c. Discuss the different retrieval systems of DNA repair.
c. Discuss the different types of DNA damage. Add a note on nucleotide excision
repair.
d. Write a detailed note on SOS repair.
c. Discuss the different types of DNA damage. Add a note on nucleotide excision
repair.
d. Write a detailed note on Post replication repair. Add a note on end to end DNA
joining/ repair of double strand break repair.
c. Discuss the different types of DNA damage. Add a note on nucleotide excision
repair.
d. Write short notes on: i. SOS repair ii. photoreactivation
c. Write a note on Excision repair. Add a note on the diseases caused by damage in
DNA repair.
d. Discuss the different retrieval systems of DNA repair.
c. Write a note on different types of Excision repair.
d. Write a detailed note on retrieval systems of repair.
c.Write a note on Mismatch repair. Add a note on the diseases caused by damage in
DNA repair.
d.Write a detailed note on photoreactivation. Add a note on end to end DNA
joining/ repair of double strand break repair.
c. Write a note on Excision repair. Add a note on the diseases caused by damage in
DNA repair.
d. Write short notes on: i. mismatch repair ii. photoreactivation
1. Okazaki fragments
2. Ori C
3. Replisome
4. Very short patch repair
5. Base excision repair
6. Mismatch repair
7. Direct repair
8. Role of Lex A in SOS repair
9. Pyrimidine dimers
10. Meselson Stahl experiment
11. Photoreactivation
12. Origin of replication
13. SOS repair
14. DNA damage
15. Recombination repair
16. Excision repair
17. Mis match repair
18. Retrieval system
19. DNA Polymerases of prokaryotes
20. Single strand binding protein
Module II
a&b
a. Define Transcription unit. Write a note on bacterial Promoters.
b. Describe the different types of termination of prokaryotic transcription.
a. Describe the structure and function of bacterial DNA dependent RNA Polymerase.
b. Describe the events of transcription by RNA Polymerase II.
a. Describe the structure and function of bacterial DNA dependent RNA Polymerase.
b. Write a note on sigma factors. Explain how sigma factors alter gene expression in
prokaryotes.
a. Compare and contrast the structure and features of eukaryotic RNA polymerases.
b. Describe the different types of termination of prokaryotic transcription.
a. Compare and contrast the structure and features of eukaryotic RNA polymerases.
b. Describe the events of transcription by RNA Polymerase II.
a. Compare and contrast the structure and features of eukaryotic RNA polymerases.
b. Describe the events of transcription by RNA Pol I and RNA Pol III.
a. Compare and contrast the structure and features of eukaryotic RNA polymerases.
b. Write a note on sigma factors. Explain how sigma factors alter gene expression in
prokaryotes.
c&d
a. Explain post transcriptional modification of rRNA.
b. Describe the events involved in tRNA processing.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. Describe the events involved in mRNA processing.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. Explain spliceosome mediated RNA splicing.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. Write a note on the properties and role of SnRNAs and SnRNPs in splicing.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. What is trans splicing. Explain the mechanism.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. Describe the splicing of rRNA in Tetrahymena.
c. Write a detailed note on the mechanism of Group I and Group II intron splicing.
d. Write a detailed note on alternative splicing. Explain its role in eukaryotic gene
regulation
c. Compare and contrast the three different types of introns.
d. Describe the events involved in tRNA spicing of yeast.
c. Compare and contrast the three different types of introns. Explain autosplicing.
d. Describe the splicing of rRNA in Tetrahymena.
c. Compare and contrast the three different types of introns. Explain autosplicing.
d. Write a detailed note on alternative splicing. Explain its role in eukaryotic gene
regulation
a&b
a. Explain in detail the organization and functional sites of ribosomes.
b. Describe the salient features of genetic code. Add a note on wobble hypothesis.
a. Ribosome is the seat for protein synthesis. Explain.
b. What is wobble hypothesis. Discuss the basis of wobble hypothesis.
a. Explain in detail the organization and functional sites of ribosomes.
b. Write a detailed account of tRNA and its role in protein synthesis
a. Explain in detail the organization and functional sites of ribosomes.
b. Genetic code is Universal, Explain. Write a note on Mitochondrial genetic code.
a. Discuss the role of different mRNA, rRNA and tRNA species in protein synthesis.
b. Discuss the difference between initiator tRNA and internal tRNA in prokaryotes
a. Discuss the role of different RNA species in protein synthesis.
b. What is wobble hypothesis. Discuss the basis of wobble hypothesis.
a. Discuss the role of different RNA species in protein synthesis.
b. Write a detailed account of suppressor tRNAs and suppressor mutations.
a. Discuss the role of different RNA species in protein synthesis.
b. Genetic code is Universal, Explain. Write a note on Mitochondrial genetic code.
a. Describe the process of charging of tRNA. Add a note on the proofreading mechanism of
tRNA.
b. Describe the salient features of genetic code. Add a note on wobble hypothesis.
a. Describe the process of aminoacylation of tRNA. Add a note on the proofreading
mechanism of tRNA.
b. What is codon degeneracy. Discuss the basis of wobble hypothesis.
a. Describe the process of charging of tRNA. Add a note on the proofreading mechanism of
tRNA.
b. Write a detailed account of features of mRNA and rRNA with respect to their role in
protein synthesis.
a. Discuss the role of aminoacyl synthases and their role in tRNA activation.
b. Genetic code is Universal, Explain. Add a note on the features of genetic code.
a. Give an account of aminoacyl synthetases. Add a note on their role in protein synthesis.
b. Describe the salient features of genetic code. Add a note on wobble hypothesis.
a. What is the second genetic code. Explain with respect to tRNA charging.
b. What is wobble hypothesis. Discuss the basis of wobble hypothesis.
a. Give an account of aminoacyl synthetases. Add a note on their role in protein synthesis.
b. Write a detailed account of ribosomes and their role in protein synthesis.
a. Give an account of aminoacyl synthetases. Add a note on their role in protein synthesis.
b. Genetic code is Universal, Explain. Write a note on Mitochondrial genetic code.
c&d
c. Describe the events leading to initiation of translation in Prokaryotes.
d. Define protein trafficking. Write a detailed note on co-translational translocation of
proteins.
c. Compare and contrast the events of translation initiation in prokaryotes and eukaryotes.
d. Write a detailed note on the post translational modification of proteins.
c. Describe the events leading to initiation of translation in Prokaryotes.
d. Discuss the events leading to the synthesis of secretory proteins
c. Describe the events leading to initiation of translation in Prokaryotes.
d. What is signal hypothesis. Add a note on co-translational translocation of proteins.
c. Describe the events leading to in initiation of translation in eukaryotes.
d. Define protein trafficking. Write a detailed note on co-translational translocation of
proteins.
c. Explain the events involved in eukaryotic translation intitiation.
d. Give an account on the post translational modification of proteins.
c. Describe the events leading to in initiation of translation in eukaryotes.
d. Discuss the events leading to the synthesis of secretory proteins
c. Describe the events leading to in initiation of translation in eukaryotes.
d. What is signal hypothesis. Add a note on co-translational translocation of proteins.
c. Explain the events leading to elongation during protein synthesis.
d. Define protein transport. Write a detailed note on co-translational translocation of
proteins.
c. Explain the events leading to ribosomal translocation during protein synthesis.
d. Write a detailed note on the post translational modification of proteins.
c. Explain the events leading to ribosomal translocation during protein synthesis.
d. Discuss the events leading to the synthesis of secretory proteins
c. Explain the events leading to ribosomal translocation during protein synthesis.
d. What is signal hypothesis. Add a note on co-translational translocation of proteins.
c. Give an account of the inhibitors of protein synthesis.
d. Define protein trafficking. Write a detailed note on co-translational translocation of
proteins.
c. Give an account of the inhibitors of protein synthesis.
d. Write a detailed note on the post translational modification of proteins.
c. Give an account of the inhibitors of the various stages of protein synthesis.
d. Discuss the events leading to the transport of secretory proteins
c. Give an account of the inhibitors of protein synthesis.
d. What is signal hypothesis. Add a note on co-translational translocation of proteins.
short notes (3.5 mks) (choose one)
1. Decoding system
2. tRNA charging
3. aminoacyl synthetases
4. Ribosome translocation during protein synthesis
5. Translation initiation in prokaryotes
6. Translation initiation in eukaryotes
7. Inhibitors of protein synthesis
8. Protein transport to lysosomes
9. Wobble hypothesis
10. signal hypothesis
11. transport of proteins to Golgi apparatus
12. Initiation factors
13. EFTu- Ts cycle
14. Initiator tRNA
15. tRNA
16. Genetic code
17. Wobble hypothesis
18. Signal peptides
19. Protein modification in ER
20. Protein glycosylation
21. Ribosome functional sites
Module IV
a&b
a. Lac operon is both negatively and positively regulated. Justify.
b. Describe the regulation of arabinose operon. Explain.
c&d
c. Write a detailed note on Genome imprinting and X-inactivation.
d. Explain how sequential gene expression regulates the switching between lytic and lysogenic
life cycle of lambda phage.
c. Write a detailed note on Genome imprinting and X-inactivation.
d. Write short notes on: i. Zn finger ii. Leucine zipper
c. Write a detailed note on Genome imprinting and X-inactivation.
d. What is antisense technology. Write a note on the procedure and applications of this
technology.
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