Molecular Biology

Teacher

Gagan Kumar Panigrahi

Category

Core Courses

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Course Name : Molecular Biology (Zoology)

Code(Credit) : CUTM1507(3-2-1)

Course Objectives

• This course covers the structure function, and makeup of the molecular building blocks of prokaryotic and eukaryotic organisms.
• It focuses on the interactions and interrelationship of DNA, RNA and protein synthesis and how these interactions are regulated.

Learning Outcomes

• Student would understand and apply general concepts of molecular biology to specific problems
• Student would understand the biological processes such as DNA replication, transcription and translation.
• Student would understand the consequences of dysfunctioning of these processes and develop ideas for possible solutions

Course Syllabus

Module-1: Bio molecules
Introduction to nucleic acids: Nucleotide and Nucleoside, Types of nucleic acids: DNA & RNA
DNA: Watson & Crick model of DNA, Different forms of DNA (A, B and Z forms)
RNA: Different forms of RNA, Protein coding RNA (mRNA), Functional RNA (rRNA and tRNA), Regulatory RNA (si RNA, mi RNA, sn RNA), Carbohydrates, Proteins, Lipids

Practice 1
Isolation and spectrophotometric estimation of DNA.

Practice 2
Isolation and spectrophotometric estimation of RNA.

Assignment 1
The history of DNA and RNA world

Assignment 2
Significance of wobble and degeneracy in genetic code


Module-2: DNA replication

Overview of DNA replication: Different models of DNA replication, Semi-conservative mode of DNA replication, rolling circle mode of DNA replication, Theta mode of DNA replication
Enzymes involved in DNA replication and their roles: DNA polymerases, DNA gyrase, DNA helicase, DNA ligase, Primase
Replication process: DNA replication in prokaryotes and eukaryotes

Practice 3
Visualization of DNA/RNA using agarose gel electrophoresis

Practice 4
Preparation of equilibrated phenol

Assignment 3
The codon AGG normally codes for argine but in altered translation it codes for stop. Where does it occur and what is its significance?

Assignment 4
Changes in mitochondrial DNA (double-stranded circular DNA genome) as one proceeds from lower to higher eukaryotes.


Module-3: DNA mutation

Mutation: Causes of mutation and effects of mutation
Types of mutation: Missense mutation, Nonsense mutation, Insertion or Deletion, Duplication, Frameshift mutation, Repeat expansion

Practice 5
Quantitative estimation of RNA using Orcinol reaction
Practice 6
Demonstration of DNA & RNA by MGP

Assignment 5
t-RNA as an adapter molecule

Assignment 6
How tRNA recognizes several codons?


Module-4: DNA Repair

DNA Repair: Direct repair, Excision repair, Mismatch repair, Nonhomologous end-joining, SOS response
DNA repair errors: Defects in DNA repair and its consequences

Practice 7
Preparation of liquid culture medium (LB) and raise culture of E. coli

Practice 8
Preparation of solid agarose medium (LB) and raise colonies of E. coli

Assignment 7
All newly synthesized bacterial proteins start (initiate) with formylmethionine (may be abbreviated as fmet). How is formyl group removed from the fmet polypeptide in bacteria?

Assignment 8
Insights on operon and highlight what controls induction and repression.


Module-5: Transcription and post transcriptional processing

Transcriptional machinery: The transcription Unit, Enzymes and transcription factors
Transcription process: Process of transcription in prokaryotes and eukaryotes
Post transcriptional processing: Processing of mRNA, Synthesis and processing of functional RNA (rRNA & tRNA)
Reverse transcription: The process of synthesis of cDNA

Practice 9
Demonstration of DNA replication, transcription and translation using Photograph, slides and/or videos.

Assignment 9
Significance of catabolite repression

Assignment 10
Role of positive regulators (activators) and negative regulators (repressors).


Module-6: Regulation of gene transcription

Transcription regulation in prokaryotes: The operon concept: The lac operon, The trp operon
Transcription regulation in eukaryotes: Activators, repressors, enhancers, silencer elements
Gene silencing: Transcriptional and post-transcriptional gene silencing

Assignment 11
Palindromic sequence of DNA and its significance.


Module-7: Translation and post translational processing

Component of translation and their roles: mRNA: The precursor of molecule of translation, Ribosomes: The site of protein synthesis, tRNA: the carrier molecule of translation
Translation: Process of translation in prokaryotes and eukaryotes
Post translational modifications: Co- and post-translational modifications of proteins

Practice 10
Application of in silico tools (BIOVIA’s DISCOVERY STUDIO) to study the three dimensional structure of proteins.

Assignment 12
Significance of cistron and prokaryotic cistron differs from eukaryotic cistron

Session Plan

Session 1

Nucleic acids: Nucleotide and Nucleoside, Types of nucleic acids: DNA & RNA

Session 2

DNA: Watson & Crick model of DNA, Different forms of DNA (A, B and Z forms)

Session 3

RNA: Different forms of RNA, Protein coding RNA (mRNA), Functional RNA (rRNA and tRNA), Regulatory RNA (si RNA, Mi RNA, sn RNA)

Session 4

Bio molecules

Session 5

Enzymes involved in DNA replication and their roles (DNA polymerases, DNA gyrase, DNA helicase, DNA ligase, Primase)

Session 6

Practice 1: Isolation and spectrophotometric estimation of DNA. (2h)

Session 7

Practice 2: Isolation and spectrophotometric estimation of RNA (2h)

Session 8

Assignment 1: The history and evolution of DNA and RNA world

Session 9

Assignment 2: Significance of Shine-Dalgarno sequence

Session 10

DNA replication

Session 11

Mutation: Causes of mutation and effects of mutation

Session 12

Types of mutation

Session 13

DNA Repair: Direct repair, Excision repair, Mismatch repair, Nonhomologous end-joining, SOS response

Session 14

Defects in DNA repair and its consequences

Session 15

Practice 3: Visualization of DNA/RNA using agarose gel electrophoresis. (2h)

Session 16

Practice 4: Preparation of equilibrated phenol. (2h)

Session 17

Assignment 3: The codon AGG normally codes for argine but in altered translation it codes for stop. Where does it occur and what is its significance?

Session 18

Assignment 4: Changes in mitochondrial DNA (double-stranded circular DNA genome) as one proceeds from lower to higher eukaryotes

Session 19

The transcription Unit, Enzymes and transcription factors

Session 20

Process of transcription in prokaryotes and eukaryotes

Session 21

Processing of mRNA, Synthesis and processing of functional RNA (rRNA & tRNA)

Session 22

Reverse transcription: The process of synthesis of cDNA

Session 23

Transcription regulation in prokaryotes: The operon concept: The lac operon, The trp operon

Session 24

Practice 5: Quantitative estimation of RNA using Orcinol reaction. (2h)

Session 25

Practice 6: Demonstration of DNA & RNA by MGP. (2h)

Session 26

Assignment 5: t-RNA is considered to be an adapter molecule

Session 27

Assignment 6: How tRNA recognizes several codons?

Session 28

Transcription regulation in eukaryotes: Activators, repressors, enhancers, silencer elements.

Session 29

Transcriptional and post-transcriptional gene silencing.

Session 30

Component of translation and their roles.

Session 31

Process of translation in prokaryotes and eukaryotes

Session 32

Protein modification

Session 33

Practice 7: Preparation of liquid culture medium (LB) and raise culture of E. coli. (2h)

Session 34

Practice 8: Preparation of solid agarose medium (LB) and raise colonies of E. coli. (2h)

Session 35

Assignment 7: All newly synthesized bacterial proteins start (initiate) with formylmethionine (may be abbreviated as fmet). How is formyl group removed from the fmet polypeptide in bacteria?

Session 36

Assignment 8: Insights on operon and highlight what controls induction and repression.

Session 37

Inhibitors of replication (Antibacterial agent)

Session 38

Post-translational modifications

Session 39

Inhibitors of translation.

Session 40

Co-translational targeting and post-translational targeting.

Session 41

Protein targeting to Mitochondria.

Session 42

Practice 9: Demonstration of DNA replication, transcription and translation using Photograph, slides and/or videos.

Session 43

Practice 10: Preparation of solid culture medium (LB) and growth of E. coli by spreading and streaking. (2h)

Session 44

Assignment 9: Significance of catabolite repression.

Session 45

Assignment 10: Role of positive regulators (activators) and negative regulators (repressors).

Session 46

Protein targeting to chloroplast.

Session 47

Protein targeting to Endoplasmic Reticulum.

Session 48

Regulation of gene expression in prokaryotes.

Session 49

Regulation of gene expression in eukaryotes.

Session 50

Role of chromatin in regulating gene expression and gene silencing.

Session 51

Practice 10: Application of in silico tools (BIOVIA’s DISCOVERY STUDIO) to study the three dimensional structure of proteins.(2h)

Session 52

Assignment 11: Palindromic sequence of DNA and its significance

Our Main Teachers

Gagan Kumar Panigrahi

Assistant Professor, Department of Zoology
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