Molecular Biology
Teacher
Dr. 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.
Course Outcome
| COs | Course Outcome | Mapping COs with POs
(High-3, Medium-2, Low-1) |
| CO1 | Students will understand and apply general concepts of molecular biology to specific problems | PO1-3, PO7-1, PO9-2 |
| CO2 | Students will understand the biological processes such as DNA replication, transcription and translation. | PO1-3, PO4-2, PO9-2 |
| CO3 | Students will understand the consequences of dysfunctioning of these processes and develop ideas for possible solutions. | PO1-3, PO4-2, PO9-2, PO5-2 |
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
Text Books:
1. Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M., & Losick, R. (2004). Molecular Biology of the Gene (International Ed.).
Reference Books:
1. Brown, T. A. (2006). Genomes 3. Garland Science
2. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter: Molecular Biology of the Cell, IV Edition.
3. Cooper G. M. and Robert E. Hausman R. E. The Cell: A Molecular Approach, V Edition, ASM Press and Sinauer Associates.
4. De Robertis, E.D.P. and De Robertis, E.M.F. (2006). Cell and Molecular Biology. VIII Edition. Lippincott Williams and Wilkins, Philadelphia.
5. Karp, G. (2010) Cell and Molecular Biology: Concepts and Experiments. VI Edition. John Wiley and Sons. Inc.
6. Lewin B. (2008). Gene XI, Jones and Bartlett
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
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