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UNIVERSITY OF MUMBAI
M.Sc. Semester I and II BIOTECHNOLOGY Syllabus
Credit Based and Grading System To be implemented from the Academic year 2012-2013 SEMESTER- I

Syllabus for the M.Sc. Sem. I & II Program: M.Sc. Course: Biotechnology
(Credit Based Semester and Grading System with effect from the academic year 20122013)

Course Code I

UNIT Proteins

Biochemistry

Credits

L / Week 1 1

II PSBT101 III IV Course Code I II PSBT102 III IV Course Code I II PSBT103 III UNIT UNIT

Signal transduction 4 Lipids Neurochemistry Immunochemistry Immuno-globulins Complement system MHC and Regulation of immune response Cytokines Genomes and Transcriptomes Gene evolution and the Human Genome Mapping Genomes Transcription Initiation in prokaryotes and eucaryotes Synthesis and processing of RNA Biophysics DNA Topology Protein Secondary Structure 4 Advances in Microscopy Membrane mimicry Credits 4 Credits 4 Credits

1 1 L / Week 1 1 1 1 L / Week 1 1 1

IV Course Code I II PSBT104 III IV UNIT

1 L / Week 1 1 1 1

PSBTP101 PSBTP102

Biochemistry Immunochemistry

2 2

4 4

PSBTP103 PSBTP104

Genomes and Transcriptomes Biophysics

2 2

4 4

SEMESTER II Course Code I PSBT201 II III IV Course Code I PSBT202 II III IV Course Code I II PSBT203 III IV Course Code I II PSBT204 III IV X-Ray Crystallography Spectroscopy UNIT DNA vectors Model organisms Advanced Analytical Techniques Analytical Techniques Gene amplification technique 4 1 1 Credits UNIT UNIT UNIT Metabolomics Carbohydrate and Lipid metabolism Protein metabolism Nucleic Acid metabolism Plant metabolism Clinical Immunology Hypersensitivity and Autoimmunity Transplantation Tumor immunology Immuno-deficiency Genomics and Molecular biology Translation in eucaryotes Regulation of Genome Activity 4 1 1 L / Week 1 1 Credits 4 Credits 4 Credits L / Week 1 1 1 1 L / Week 1 1 1 1 L / Week 1 1

PSBTP201 PSBTP202 PSBTP203

Metabolomics Clinical Immunology Genomics and Molecular biology

2 2 2

4 4 4

PSBTP204

Advanced Analytical Techniques

Semester- I Course Code PSBT101 Proteins : Primary structure of proteins and their determination end group analysis; cleavage of disulphide bond; separation, purification, characterization of polypeptide chain; specific peptide cleavage reactions. Unit I Secondary structure Ramachandran plot, helical structure, beta structure; Tertiary structure- fibrous (Collagen) and globular (Myoglobin) structure. Protein stability, protein denaturation. Quaternary structure (Haemoglobin) subunit interaction, 1 Title Biochemistry Credits 4

symmetry, subunit composition determination Signal transduction Unit II Cell signalling pathways that control gene activity- TGF-Beta and activation of Smads: Regulation of TGF-Beta by negative feedback loops. Cancer and loss of TGF-Beta signalling, Lipids Unit III Lipoproteins structure, function, disorders and dysfunction in Alzheimers disease. Neurochemistry Unit IV Anatomy and functions of neuron, organization of brain, neuronal pathways and systems, propagation of nerve impulse, ion conducting channels, synapses and gap junction, neurotransmitters, neurotoxins 1 1 1

Course Code PSBT102 Immunoglobulins

Title Immunochemistry

Credits 4

Hematopoiesis, Immunoglobulin fine structure, Immunoglobulin Unit I superfamily ,Multigene organization of Ig gene, Variable region gene rearrangement, Generation of antibody diversity, Class switching among constant region. Synthesis, assembly, and secretion of immunoglobulins
5

Complement system Unit II Activation, Regulation, Biological consequence of complement activation, Complement deficiency MHC and Regulation of immune response Cellular distribution of MHC molecule, Antigen processing and Unit III presentation exogenous and endogenous antigen processing. Self MHC restriction of T cells. Presentation of non-peptide antigens. Activation of B and T lymphocytes, T-cell regulation. Cytokines Unit IV Properties, receptors, antagonists, diseases, therapeutic use of cytokines 1 1 1

Course Code PSBT103

Title Genomes and Transcriptomes Gene evolution and The human genome Human genome project, the content of human nuclear genome,

Credits 4

Unit I

tandemly repeated DNA, interspersed genome-wide repeats. Human mitochondrial genome. Genome evolution-Acquisition of New Genes (gene duplication, from other species, transposable elements), Non-coding DNA Mapping Genomes

Unit II

Genetic Mapping: DNA markers for genetic mapping, Physical Mapping: Restriction Mapping, Fluorescent in situ hybridization (FISH), Sequence tagged site (STS) mapping. Transcription Initiation in prokaryotes and eukaryotes

Unit III

DNA-Protein

interactions

during

Transcription

Initiation,

Regulation of Transcription initiation. Synthesis and Processing of RNA Synthesis of eukaryotic mRNAs by RNA polymerase II, Intron splicing. Unit IV Synthesis and processing of Non-coding RNAs: Transcript elongation and termination by RNA polymerases I and III, Introns in eukaryotic pre-rRNA and pre-tRNA. Processing of Pre-RNA. Degradation of mRNAs
6

Course Code PSBT104 DNA Topology

Title Biophysics

Credits 4

Different forms of DNA, - A/B/C/Z and RL form of double helical Unit I DNA, Triple Helix, Nucleic acid binding protein Leucine Zipper, Zinc fingers, OB fold, Beta Barrel, Helix-turn-helix, Helix-loophelix. Linking number, Supercoiling, Topoisomerases. Protein secondary structure Unit II Protein folding. The different pathways of protein folding and its co-relation with protein stability. Molecular chaperons Unit III Advances in Microscopy
Different versions of electron microscopy, Confocal Microscopy

Membrane mimicry Unit IV Liposome structure and their uses in drug targeting. solubilisation of the membrane by using different detergents. Membrane mimicry. 1

Practical Semester-I Biochemistry 1. Preparation of buffers used in laboratory(Phosphate, Citrate, acetate and Tris buffer) PSBTP101 2. Detection of LDH isozymes by electrophoresis. 3. Protein estimation by Bradfords method 4. Study of protein complexes using PAGE and detection with CBB and Silver staining. Immunochemistry 1. Perform serum electrophoresis (horizontal) 2. Perform iso-agglutination titre PSBTP102 3. Perform Affinity chromatography for purification of antibodies from serum. 4. Perform SDS and native PAGE for studying immunoglobulins structure Genomes and Transcriptomes PSBTP103 1. Restriction digestion reaction 2. Demonstration of ligation reaction. 3. Perform transformation of bacteria Biophysics 1. Viscosity PSBTP104 studies of proteins (Std BSA & varying 2 2 2 2

concentration of urea.) 2. Present a seminar on any research paper obtained from a recent (past
5 years) journal with reference to any topic of choice. (Internal)

Semester II Course Code PSBT201 Title Metabolomics Carbohydrate metabolism HMP, uronic acid pathway, glycogenolysis and glycogen storage Unit I diseases. Lipid metabolism Synthesis of essential fatty acids Protein Unit II metabolism 1 1 Credits 4

Biosynthesis of essential amino acids. Metabolic breakdown of amino acids leading to Krebs cycle intermediate. Disorders of amino acid metabolism Nucleic acid metabolism

Unit III

Biosynthesis and degradation of purines and pyrimidines with regulation, disorders of Nucleic acid metabolism. Plant metabolism

Unit IV

C-3

cycle

and

C-4

cycles,

CAM,

glyoxalate

pathway,

photosyhthetic formation of hydrogen Nitrogen fixation and role of nitrogenase

Course Code PSBT202 Hypersensitivity Unit I

Title Clinical Immunology

Credits 4

Gel and Coombs Classification; Type I, II, III, IV hypersensitivity Autoimmunity Organ specific, systemic, mechanism, treatment Transplantation

Unit II

Basis of Graft rejection, clinical manifestation of graft rejection; immunosuppressive transplantation. Tumor immunology therapy; immune tolerance; clinical

Unit III

Oncogenes and cancer induction, Tumor of immune system, Tumor antigens, Tumor evasion of immune system, Cancer

immunotherapy
9

Unit IV Course Code PSBT203

Immuno-deficiency Primary immunodeficiency and secondary immunodeficiency Title Genomics and Molecular Biology Translation in eukaryotes

1 Credits 4

Unit I

Post-translational Processing: Processing by proteolytic cleavage, Processing by chemical modification, Inteins, Protein Degradation. Regulation of Genome Activity Genome rearrangements, gene silencing by modification of

Unit II

histones and DNA . RNA in gene regulation, Regulation of Genome Activity During Development: Vulva development in Caenorhabditis elegans, Development in

Drosophila melanogaster. DNA vectors Unit III Expression vectors- for maximizing protein synthesis, to facilitate protein purification, to promote protein solubilization, to promote protein export. Vectors for making RNA probes. BACs, PACs. Model organisms S.cereviceae-Genome,existence of haploid and diploid cells, facilitating genetic analysis, generating mutations in yeast, Unit IV Arabidopsis- genome life cycle , ease of transformation epigenetics, response to environment. Mus musculus- mouse embryonic development and stem cells, ease of introduction of foreign DNA, epigenetic inheritance. 1 1

10

Course Code PSBT204

Title Advanced Analytical Techniques Analytical Techniques

Credits 4

Unit I

2-D Page, Capillary isoelectric focusing- electro spray ionizationmass spectrometry, MALDI-TOF-MS/MS, Biochips (DNA, Protein and Biosensors). Flow cytometry

Unit II

Gene amplification technique PCR and its types (nested, arms, inverse, real time, SSCP) X-Ray Crystallography Protein crystallization and visualization, Method of data collection,

Unit III

factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates. Spectroscopy

Unit IV

Basic principles, instrumentation and applications of IR, Raman, ORD, CD spectroscopy, NMR and ESR.

11

Practical Semester-II Metabolomics 1. Detection of Phenylalanine for PKU by spot test and chromatography done with std. Phenylalanine. PSBTP201 2. Isolation of chloroplast by sucrose density gradient 2

centrifugation. 3. Uric acid estimation from serum/urine 4. Determination of acid number and iodine number of lipids Clinical Immunology 1. Perform Western blotting PSBTP202 2. Perform DOT-blot for protein 3. Demonstration Practical Flow Cytometry 4. Demonstration Practical- ELISA reader. Genomics and Molecular biology PSBTP203 1. Plasmid isolation 4. Extraction of genomic DNA from bacteria and blood 5. Expression of recombinant protein Advanced Analytical Techniques 1. PCR amplification. PSBTP204 2. Validation of Autoclave, Micropipette, Colorimeter, Spectrophotometer and measuring containers. 3. Calibration of pH meter and weighing balance 2 2 2

12

Reference book-list Paper101 and 201, References: Sr.No 1 2. 3 Title of the Book Biochemistry, 5 edition Biochemistry, 4th Edition Biochemistry, The chemical reactions of living cells, Volume I and II. Lehningers Principles of Biochemistry, fourth edition. Biochemistry third edition, 2004 Textbook of Biochemistry with clinical correlations, Fifth Edition Fundamentals of biochemistry Biochemistry, second ed.
th

Author J. Berg,J. Tymoczko & L. Stryer G. Zubay David E. Metzler

Publisher W. H. Freeman & Company Wm .C. Brown Elsevier

4. 5. 6.

Nelson and Cox Donald Voet and Judith Voet. Thomas Devlin

Macmilan Worth John Wiley and sons, Inc John Wiley and sons, Inc New Central Book Agency The Benjamin/ Cummins publishing Company Thomson Brooks/Cole McGraw Hills Library of Congress cataloging in publication data.

7. 8.

A C Deb Mathews, Van Holde

9. 10. 11

Biochemistry, fourth and fifth ed Harpers Illustrated biochemistry, 26th Edition Diagnostic Recognition of Genetic Disease

Campbell and Farrell R Murray, D Granner, P Mayes William l Nyhan, Nadia A Sakati

Paper 102 and 202, References: Sr.No 1. 2. Title of the Book Immunology, fifth Ed Immunology, sixth Ed Author Goldsby, T J. Kindt, Osborne, Janis Kuby Roitt, Brostoff, Male Publisher Freeman and company. Mosby, An imprint of Elsevier science Ltd W B Saunders company Thomson Elsevier

3. 4. 5.

Cellular and molecular immunology. Fourth edition Immunology, An introduction, fourth edition. Immunology the experimental series An introduction to Immunology Immunology essential and fundamental, Second edition

Abbas , Abul K & Lichtman Ian R Tizard Wener Luttmann, K Bratke, M. Kupper, D Myrtek C V Rao S Pathak & U Palan

6. 7.

Narosa Publishing house Parveen Publishing House

13

8. 9. 10

Elements of Immunology Immunology, fourth edition. Microarray and Microplates

S C Rastongi Gordan Reeve and Ian Todd S Ye and I N M Day

CSB Publishers and distributors Blackwell Publishing House Bios

Paper 103 and 203 References: Sr.No 1 2. 3 4. 5. 6. 7. Title of the Book Gene VII Genome, Second edition Principles of Gene Manipulation. Principles of genetics Biochemistry third edition, 2004 Molecular biology of the gene The Cell, a molecular approach Author Benjamin Lewin T A Brown Old and Primrose Simmons, Gardner Donald Voet and Judith Voet. T D.Watson and others G M Cooper Publisher Oxford Publishers Bios Scientific Blackwell Science John Wiley and sons, Inc John Wiley and sons, Inc Pearson education ltd. Library of Congress cataloging in publication data. Freeman John Wiley and sons, Inc CSHL Press Bios Scientific

8. 9. 10. 11

An introduction to genetic analysis Molecular cell biology Molecular cloning, Vol I, II , III Gene cloning and DNA analysis

Griffiths, A. and Miller J Lodish.H, Berk A Sambrook J, Russell. T A Brown

Paper104 and 204, References: Sr.No 1 Title of the Book Biochemistry, second ed. Author Mathews, Van Holde Publisher The Benjamin/ Cummins publishing Company John Wiley and sons, Inc Pearson education ltd. Oxford Publishers Narosa John Wiley and sons, Inc Thomson Student Edition Humana Oxford

2. 3 4. 5. 6. 7. 8. 9. 10

Biochemistry third edition, 2004 Molecular biology of the gene Gene VII Biophysics Biophysics, An Introduction Principles of instrumental analysis Basic Biophysics 2004 PCR protocols, 2 ed Introduction to Protein science Architecture, Function and Genomics
nd

Donald Voet and Judith Voet. T D.Watson and others Benjamin Lewin V Pattabhi, N Gautham R Cotterill Skoog, Holler, Nieman. Daniel M Bartlett & Stirling Arthur M Lesk

s
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