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UNIVERSITY OF MUMBAI
Syllabus for the M.Sc. Part - II
[Sem ester III and IV]
Program: M.Sc.
Course : Life Sciences
Specialization :
Biochemistry
Choice Based Credit and Grading System
The Academic Year 2017 -18
(Credit Based Semester and Grading Sys tem with
effect from the academic year 2013 -2014)
2
M.Sc. Semester III and IV - Life Sciences Syllabus
Restructured for Credit Based Semester and Grading System
To be implemented from the Academic year 201 7-2018
SEMESTER III
Theory
Course Code UNIT TOPIC HEADINGS Credits L / Week
PSLSC BMT301
(Biomathemati
cs and Cell
Biology
Techniques) I Biomathematics
4
II Cell and Molecular Biology
Techniques
III Animal Tissue Culture
IV Plant Tissue Culture
PSLS CBMT302
(Bioenergetics
and
Carbohydrate
Metabolism) I Bioenergetics and Carbohydrate
Metabolism
4
II Lipid Metabolism
III Amino Acid Metabolism
IV Metabolic Engineering and
Systems Biology
PSLSC BMT303
(Biomolecular
Structure) I Chemical Bonds and
Spectroscopic Techniques
4
II Protein and Nucleic Acid
Structure
III Supramolecular Assemblies and
DNA -protein Interactions
IV Biomolecular Structure and
Disea ses
Course Code UNIT TOPIC HEADINGS Credits L / Week
PSLSC BMT304
(Research
Methodology
and Quality
Control ) I Research Methodology
4
II Scientific Writing
III ISO
IV GLP and GMP
Practic al
PSLSC BMP301 Biomathematics and Cell Biology Techniques 2
PSLSC BMP302 Bioenergetics and Carbohydrate Metabolism 2
PSLSC BMP303 Biomolecular Structure 2
PSLSC BMP304 Literature Review 2
3
SEMESTER IV
Theory
PSLSC BMT401
(Molecular Cell
Biology) I Cell Division and Apoptosis
4
II Biomembrane and Cell Matrix
III Protein Trafficking and Targeting
IV Gene Silencing and Epi genetics
PSLSC BMT402
(Nitrogen
Metabolism
and Plant
Biochemistry) I Nucleotide Metabolism
4
II Nitrogen Assimilation in Plants
III Photosynthesis and Secondary
Metabolism
IV Free radicals and Antioxidant
Biology
PSLSC BMT403
(Biomolecular
Function) I Protein folding and Engineering
4
II Kinetics and Mechanism in
Biological Systems
III Metabolomics and
Transcriptomics
IV Nanobiology
PSLSC BMT404
(Drug
Development
and
Environmental
Toxicology) I Natural products
4
II Activity Guided Drug
Development
III Environmental toxicology
IV Environmental monitoring
Practical
PSLSC BMP401 Molecular Cell Biology 2
PSLSC BMP402 Nitrogen Metabolism and Plant Biochemistry 2
PSLSC BMP403 Biomolecular Function and Environmental
Toxicology 2
PSLSC BMP404 Project 2
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M.Sc. Part – II Life Sciences Syllabus
Restructured for Credit Bas ed Semester and Grading System
To be implemented from the Academic year 201 7-2018
Semester I II Detail ed Syllabus
Course Code Title Credits
PSLSC BMT301 Biomathematics and Cell Biology Techniques (60L) 4
Unit I: Biomathematics (15L)
Biomathematics : Binomial Theorem (without infinite series),
Determinants, Matrices, Rank of Matrices by Diagonalisation method Limit
and derivatives, Differentiation (including differe ntiability), Successive
Differentiation, Integration – Definite and Indefinite (ordinary, method of
substitution, special trigonometric function, partial fraction) Application of
integration to find area, Differential equations ‐‐homogeneous and Linear
ODE’s and its simple applications to biological problems.
Unit II: Cell and Molecular Biology Techniques (15L)
Cell Biology Techniques: Principles, Instrument overvie w, and Applications
of flow cytometry, Fluorescence Resonance Energy Transfer (FRET); Surface
Plasmon resonance .
Proteomics: Peptide synthesis and Protein sequencing methods, detection
of post -translation modification of proteins; 2 -D gel electrophoresis; Mass
spectrometry; X -ray diffraction methods; Static and dynamic light
scattering (SLS and DLS); Capillary electrophoresis; Protein chips;
Differential scanning calorimetry; Isothermal titration calorimetry.
Genomics: Oligonucleotide synthesis; DNA chip s/microarrays; DNA
hybrid ization; DNA sequencing methods; S trategies for genome
sequencing; M ethods for analysis of gene expression at RNA and protein
level; Site directed mutagenesis; Gene knockdown; Differential display;
Serial analysis of gene expressi on (SAGE) .
Unit III: Animal Tissue culture (15L)
Basic of animal tissue culture: Methods of cell dissociation/separation and
preparation of primary cell culture, characteristics of c ells in vitro , cell
culture growth parameters, detection, prevention and determination of
contamination in tissue culture.
Culture: Short term culture, Specialized cells: bone marrow myogenesis, in
vitro skin cell culture, ethrogenesis - leukemia cells, cho ndriogenesis - in
vitro , cryopreservation of tissues and cell lines.
Analysis and Production: cell synchronization, cell transformation in vitro ,
Mass cultivation - cytodex and biofermentors. cell cloning and Transgenic
animals.
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Applications: Stem cells & t herapeutic cloning, Tissue engineering and 3D
printing
Unit IV: Plant Tissue Culture (15L)
Basics of plant tissue culture : Totipotenc y, macro and micro nutrients,
media.
Culture: micropropogation, Callus culture, Somaclonal variation,
Suspension cell culture, Protoplast culture, Somatic hybridization, Cybrids,
Somatic embryogenesis and synthetic seed production. Cryopreservation.
Reco mbinant technology: Plant transformation by Agrobacterium
tumfaciens [including mechanism of T DNA transfer in wild type
Agrobacterium], A. rhizogenes its plasmid, Biolistics: chloroplast
transformation: advantages and disadvantages of the technique.
Applic ations of transgenics : vaccine subunits, edible vaccines, from hairy
root cultures.
Transgenic plants : Stress resistance [salt, water, and temperature],
Improved nutrition shelf life and Novel applications for industrial purpose,
biodegradable plastics, a nd novel horticultural traits [flower colour,
varigation].
Examples of secondary metabolite production ( industrial scale ): [shikonin,
taxol (biosynthesis and bioreactor production) capsasin/ berbrine].
Practical :
PSLSC BMP301 Biomathematics and Cell Bi ology Techniques (60L)
1. Mathematical sums to be solved in biomathematics
2. Site directed mutagenesis
3. 2-D Gel electrophoresis (Demonstration)
4. Expression of foreign protein in E. coli
5. Establishment of Primary Culture (ATC) using a sui table
source.
6. In vitro Culture - Washing & Sterilization, Preparatory
steps for tissue culture, surface sterilization of plant
material, basic procedures for Aseptic tissue transfer,
incubation of culture.
7. Preparation of Culture media & Reagents - Media
composition, Nutrition, Hormones.
8. Tissue Culture – Callus culture, Cell suspension
9. Preparation of plant protoplast and test for viability
10. Plant micro -propagation – micro -culture of plants.
11. Nucleic acid isolation and blotting
A. Isolation of RNA from E. Coli
B. Spectrophotometric characterization of RNA
C. Capillary blotting (Southern/Northern) of nucleic
acids from agarose gels 2 04
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D. Preparation of cDNA and RT -PCR
12. Demonstration of proteomic and geno mic techniques .
References:
1. Primrose, S.B. and Twyman, R.M. (2006) Principles of Genetic Manipulation and
Genomics. Seventh Edition. Blackwell Publishing, USA.
2. Winnacker, E -L.(1987) From Genes to Clones. VCH Publishers, USA.
3. SambrookJ.and Russell D .2001.Molecular Cloning: A Laboratory Manual, 3rd edition.
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
4. A K Vasil. Cell culture and somatic cell genetics of plants (Vols.1to3) - A,Press.
5. Ed. John R.W Masters Animal cell culture -Practi cal approach 3rd edition, Oxford
university press -2000
6. In vitro cultivation of Animal cells. Elsevier India PVT LTD -17-A/1 Main Ring Road,
New Delhi -110024
7. R. Sasidhara, Animal Biotechnology MJP publishers -Chennai.
8. Industrial Biotrasformations by A. Liese, K. Seelbach and C. Wandrey; Wiley – VCH.
9. Role of Biotechnology in Medicinal and Aromatics Plants by Khan and Khanum Vol. 1
to 3. Plant Tissue Culture by M. K. Razdan.
10. Animal Cell Culture by Ian Freshney
11. Basic Cell Culture. Ed.J.M.Davis 2nd.Ed 2007. Oxfor d press
12. Animal Cell Culture SudhaGangal
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Course Code Title Credits
PSLSC BMT302 Bioenergetics and Metabolism (60L) 4
Unit I: Bioenergetics and Carbohydrate Metabolism (15L)
Bioenergetics : Concept of free energy, standard free energy, determination
of ∆G for a reaction; Relationship between equilibrium constant and
standard free energy change, biological standard state & standard free
energy change in coupled reactions; Biological oxidatio n-reduction
reactions; Redox potentials; Relation between standard reduction
potentials & free energy change; High energy phosphate compounds –
introduction, phosphate group transfer, free energy of hydrolysis of ATP
and sugar phosphates alongwith reasons for high ∆G .
Carbohydrate Metabolism: Glycolysis in higher organisms and
microorganisms; Pentose phosphate pathway and its regulation;
Gluconeogenesis, glycogenesis and glycogenolysis, glyoxylate and Gamma
aminobutyrate shunt pathways; Cori cycle; Anaplero tic reactions; Entner -
Doudoroff pathway; Glucuronate pathway; Metabolism of disaccharides;
Hormonal regulation of carbohydrate metabolism ; Inborn errors of
carbohydrate metabolism .
Unit II: Lipid Metabolism (15L)
Fatty acid catabolism: Hydrolysis of tri -acylglycerols; α -, β-, ω- oxidation of
fatty acids; Oxidation of odd numbered fatty acids – fate of propionate;
Role of carnitine; Degradation of complex lipids; Formation of ketone
bodies; Energetics of beta oxidation .
Fatty acid biosynth esis: Acetyl CoA carboxylase; Fatty acid synthase; ACP
structure and function; Lipid biosynthesis; Biosynthetic pathway for tri -
acylglycerols, phosphoglycerides, sphingomyelin and prostaglandins;
Metabolism of cholesterol and its regulation; Biosynthesis o f bile acids and
steroid hormones; Alternative pathway for isoprenoid biosynthesis in
chloroplast ; Inborn errors of fatty acid metabolism .
Unit I II Amino Acid Metabolism (15L)
Amino acid catabolism: Proteolysis; General reactions of amino acid
metabolism - Transamination, decarboxylation, oxidative & non -oxidative
deamination of amino acids; Acetyl CoA, alpha ketogutarate, acetoacetyl
CoA, succinate, fumarate and oxaloaccetate pathway; Ur ea cycle and its
regulation; Ammonia excretion.
Biosynthesis of Amino A cids: Biosynthesis of aromatic amino acids and
Histidine; One carbon atom transfer by folic acid (Biosynthesis of glycine,
serine, cysteine, methionine, threonine); Conversion of amino acids to
specialized products; Inborn errors of protein metabolism .
TCA cycle: Central role of TCA cycle in energy generation and biosynthesis
of energy rich bond; Integration/regulation of carbohydrate, lipid and
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protein metabolism .
Unit : IV Metabolic Engineering and Systems Biology (15L)
Metabolic Engineering: Historical perspective and introduction;
Importance of metabolic engineering; Paradigm shift; Information
resources; Scope a nd future of metabolic engineering; Plant and microbial
metabolic engineering ; Metabolically engineered organisms ; Metabolic flux
analysis .
Systems Biology : Concepts and working principles of System Biology -
Practical applications of System Biology in Lif e Sciences - Introduction to
System Biology platforms ; Proprietary system Biology platform ; Different
Markup languages used in systems biology. Introduction to NGS
technology.
Practical :
PSLSC BMP302 Bioenergetics and Metabolism (60L)
1. Estimation of inorganic phosphorus by Fiske and
SubbaRao method
2. Determination of pyruvate by 2,4 -dinitrophenyl
hydrazine method
3, Isolation of cholesterol and lecithin from egg yolk
4. Assay of alanine and aspartate aminotransfera ses
5. Fractionation of cell organelles from animal/plant
tissues and identification by marker enzymes
6. Effect of metal ions on the activity of enzymes/proteins
7. Determination of Molar absorption coefficient of
tyrosine 2 04
References
1. L. Stryer, Biochemistry, W.H. Freeman and Co. 5th 2002
2. Voet, Donald, Voe Judith, Pratt, Charlotte W. Fundamentals of Biochemistry: Life at
the molecular Level 2nd Edition. Publisher: Asia, John Wiley & Sons. 2006.
3. Nelson David L., Cox Michale. Lehninger Principles of Biochemistry 5th
Edition.Publisher: New York. W. H. Freeman. 2008.
4. Text Book of Biochemistry with clinical correlation by Thomas M. Devlin, John Wiley -
Liss, Hobokhen NJ publishers (2006)
5. Zubey, Biochemistry GL WCB Publishers.
6. Stephanopoulos Gregory N., Aristidou Aristos A., Nielsen Jens. Metabolic
Engineering: Principles and Methodologies. Publisher: New Delhi, Reed Elsevier India
Pvt. Ltd. 2006.
7. Purich Daniel L., Allison R. Donald. The Enzyme Reference: A Comprehensive
Guidebook to Enzyme Nomenclature, Reactions, and Methods. Publisher: California,
Academic Press.
8. Andres Kriete (Editor), Roland Eils (Editor). System Biology: Computatio nal Systems Biology
(Hardcover)
9. Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits,
Chapman & Hall/CRC Press, Mathematical and Computational Biology, 2nd edition,
2006.
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Course Code Title Credits
PSLSC BMT303 Biomolecular Structure (60L) 4
Unit I: Chemical Bonds and Spectroscopic Techniques (15L)
Inter atomic interactions, ionic, covalent and metallic bonds; Importance of
weak, non -covalent bonded interactions in biomolecules, such as Van der
Waals forces and hydrogen bonding; En ergies and geometrics of these
interactions and their roles in structure and conformation of biomolecules .
Spectroscopic techniques: Principle, methodology and applications of
Infrared, Raman, ESR, Atomic absorption spectroscopy .
Optical Activity: Importa nce of chirality in biomolecules; Principles and
applications of CD and ORD .
Unit II: Protein and Nucleic Acid Structures (15L)
Structure and Stability of Proteins: Myoglobin, Hemoglobin, Lysozyme,
Ribonucle ase A, Carboxypeptidase and Chymotrypsin ; Conformation of
proteins by Ramachandran plot; N and C terminal analysis of proteins .
Covalent modification of proteins: Acetylation, p hosphorylation,
adenylation, methylation, ribosylation , lipidation .
Synthetic p rotein modifications: Protein -based hybrid structures and
protein polymer systems ; applications of protein polymer systems ; Amino
acid targeting for synthetic protein modification; Synthetic approaches for
polymer -protein hybrid structure; Non-covalent app roaches for polymer -
protein conjugates; Protein -nanopartcle hybrids via surface conjugation;
Biocatalytic approaches for biohybrid structures .
DNA structure: A/B/Z/D forms of double helical structure of DNA; Triple
helix; DNA supercoiling and topoisomerase s.
Unit III: Supramolecular Assemblies and Complex proteins (15L)
Viruses: Viral assembly; Capsid; Capsomere , eg., TMV, HIV, Adenovirus ,
Influenza .
Nucleic Acid Binding Motifs in Proteins: Leucine zipper; Zinc fingers; Helix -
turn -helix; Beta barrel; OB fold and their role in regulation of gene
expression .
Metalloproteins: General principles of metal coordination; Storage and
transport metalloproteins (Rubredoxin, Plastocyanin, Ferritin,
Ceruloplasmin) ; Signal -transduction metalloproteins (Calmodulin,
Troponin); Metalloenzymes (Carbonic anhydrase, SOD, Hydrogenase) .
Transport proteins: Oxygen transport proteins from vertebrate and
invertebrate (haemoglobin, hemo eryhtrin , cytochrome C) , Albumin .
Unit IV: Biomolecular Structure and Diseases (15L)
Structural and functional aspects of proteins and DNA : Relationships
between structure and function and their role in human disease ; DNA -
protein interactions; Protein -RNA interactions; P rotein -protein
interactions; Protein aggregation; Non-enzymatic glycosylation (Protein -
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sugar interaction) ; Methods to study these interactions.
Molecular basis of disease : methods for prevention, diagnosis, and
treatment ; Advanced techniques used in the diagnostics of diseas es due to
structural alteration.
Diseases: Huntington's disease, Sickel -cell anemia ; Cataract; Alzheimer's
disease ; p53 in cancer ; Von Hippel -Lindau syndrome ; Metabolic syndrome
(Diabetes) .
Practical :
PSLSC BMP303 Biomol ecular Structure (60L)
1. Protein purification methods:
A. Isolation of casein from milk
B. Purification of an enzyme by ion exchange
chromatography/affinity chromatography
C. Use of ammonium sulphate precipitat ion and
dialysis
D. Use of gel filtration
E. SDS -PAGE
2. Polyacrylamide gel electrophoresis under non
denaturing conditions
A. Silver staining
B. Activity staining of enzymes
C. Determination of effect of acrylamide
concentration on the mobility of proteins
3. Determination of melting temperature (Tm) of DNA .
4. Analysis of DNA
A. Estimation of DNA and RNA by UV absorption
method
B. Determination of purity of nucleic acids
C. Conformational analysis of plasmid DNA by
agarose gel electrophoresis (Oxidative/carbonyl
stress induced damage) .
5. Spectrofluo rimetric analysis of proteins
6. Determination of N - and C -terminal amino acids
(demonstration) .
7. Protein aggregation studies by Congo Red and
Thioflavin T .
8. Generation and measurement of non -enzymatic
glycosylat ed products (Protein/DNA) .
9. Assay of transport protein (BSA) – esterase activity .
10. Analysis of protein -sugar -DNA interactions 2 04
References:
1. K. Wilson and I. Walker , Practical Biochemistry, 5th edition, University press (2000)
2. Shawney , Practical B iochemistry
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3. P. Asokan , Analytical Biochemistry. China publications, (2003)
4. David Frifelder , Physical Biochemistry, W. H. Freeman; 2nd edition (1982)
5. Sheehan, D. (2009) Physical Biochemistry: Principles and Applications. John Wiley &
Sons Ltd., UK.
6. Brand en, C. I. and Tooze, T.(1999) Introduction to Protein Structure. Garland
Publishing, USA.
7. Lesk, A. M. (2004) Introduction to Protein Science: Architecture, Function and
Genomics. Oxford University Press, UK.
8. Creighton, T.E. (1983) Proteins: Structures and Molecular Properties. W.H. Freeman
and Co., USA.
9. Pain, R.H. (2000) Mechanism of Protein Folding. Oxford University Press, UK.
10. Arai, M. and Kuwajima, K. (2000) Advances in Protein Chemistry. Academic Press,
USA
11. The Chemical Reactions of Living Cells: David E Metzler
12. William J. Marshall, Stephan K. Bangert, Elizabeth S.M. Ed. S.M (ed) Marshall , Clinical
Biochemistry: Metabolic And Clinical Aspects by (2008) Publisher: Elsevier Science
Health Science Div
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Course Code Title Credits
PSLSC BMT304 Research Meth odology and Quality Control (60L) 4
Unit I: Research Methodology (15L)
Meaning of Research; Objectives of research, motivation in research; Types
of research – Descriptive, Ana lytical, Applied, Fundamental, Quantitative,
Qualitative, Conceptual, Empirical and Other Types of Research; Research
Approaches; Research Methods vs. Methodology; Research and Scientific
Method; Research Process: Steps of research process; Criteria of Goo d
Research; Sampling, Sample size determination, Plan for data collection,
Methods of data collection, Plan for data processing and analysis; Ethical
considerations during research
Unit II: Scientific writing (15L)
Meaning of Scientific and non scientific writings; Structures of Research
proposals, Synopsis, Dissertations, Thesis, Research paper writings
(Abstract, Introduction, Review literature, methodology, Results,
Discu ssions, Summary, Conclusion, Bibliography etc); Presentations:
Graphical, Tabular, Animation, Power point etc
Unit III: ISO (15L)
Introduction: Over View of standards in ISO9000 Family
Key principles: Key principles of ISO 9000 - Quality Management System
ISO 9001: Detailed study on ISO 9001:2015 standard, based on a seven
principles of quality management, including a strong customer focus, the
motivat ion and implication of top management, the process approach and
continual improvement
Application: Sector specific Application of ISO 9001 - Quality Management
System adapted by various industries
Unit I V: GMP/ GLP (15L)
Introduction: Good Manufacturing Practices (GMO) and Good Laboratory
Practices (GLP) in Pharmaceutical Industries.
Overview of GMPs is enforcement by the U.S. Food Drug Administration
(US FDA) unde r Title 21 CFR
Documentation requirement for GMP and GLP
Case studies for Documentation related to SOP preparation and CAPA
(Corrective action Preventive Action).
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PSLSC BMP304 Dissertation in Literature Review (60L)
1. Project dissertation of literature review
2 04
References:
1. Kothari, C.R., 1985, Research Methodology - Methods and Techniques, New Delhi,
Wiley Eastern Limited.
2. Das, S.K., 1986, An Introduction to Research, Kolkata, Mukherjee and Company Pvt.
Ltd.
3. Misra R.P., 1989, Research Methodology: A Handbook, New Delhi, Concept
Publishing Company
4. Kumar, R., 2005, Research Methodology - A Step -by-Step Guide for
Beginners,(2nd.ed.), Singapore, Pearson Education.
5. Bhattachraya, D.K., 2006, Research Methodology,( 2nd.ed.),New Delhi, Excel Books.
6. Panneerselvam R., 2012, Research Methodology, New Delhi, PHI Learning Pvt. Ltd.
7. ISO 9000 quality systems handbook fourth edition by David Hoyle
8. International standard iso9001 : quality management systems — requirements fif th
edition 2015 -09-15.
9. Pharmaceutical quality assurance for students of pharmacy, @nd edition
Dec.2007.by Mr. manohar a. Potdar. NiraliPrakashan.
10. How to Practice GMPs 7th ed. by P.P. Sharma , Seventh edition 2015.
11. Hand Book, Good Laboratory Practices: Qua lity practices for regulated non -clinical
research and development, 2nd Edition, 2009.
12. The Oxford Book of Modern Science Writing (Oxford Landmark Science) 2009 by
Richard Dawkins (Author, Editor)
13. Writing Science: How to Write Papers That Get Cited and Pro posals That Get Funded
(2012) by Joshua Schimel (Author)
14. The Best of the Best of American Science Writing (The Best American Science
Writing) 2010 by Jesse Cohen (Author)
15. From Research to Manuscript A Guide to Scientific Writing (Second Edition) By Katz ,
Michael J. (Springer Publication)
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M.Sc. Part – II Life Sciences Syllabus
Restructured for Credit Based Semester and Grading System
To be implemented from the Academic year 201 7-2018
Semester I V Detail ed Syllabus
Course Code Title Credits
PSLSC BMT401 Mole cular Cell Biology (60L) 4
Unit I: Cell Division and Apoptosis (15L)
Cell division and cell cycle: Meiosis: its regulation, steps in cell cycle , and
control of cell cycle. Cell-cell fusion in normal and abnormal cells.
Programmed Cell Death : Regulation of Apoptosis; Induction and Inhibition
by Genes and proteins involved in apoptosis; Receptors with death
domains and their signalling pathways; Ro le of apoptosis in development
and disease ; Caspase -independent pathways eg., Necrosis, necrotopsis,
autophagy, mitotic catastrophy .
Carcinogenesis : Characteristics of cancerous cells; Agents promoting
carcinogenesis; molecular basis of cancer therapy, Tu mor markers - AFP,
CEA, hCG ; Telomere replication; Telomerase and its role in cancer and
aging .
Unit III: Biomembrane and Cell Matrix (15L)
Biomembranes: Structure and assembly; Orientation of memb rane
proteins, their solubilisation with detergents and enzymes; Membrane
reconstitution; Liposomes and their application in biology and medicine
Nuclear pore complex: Structure; Assembly and disassembly; RNA
transport; Role in macromolecular exchange and regulation; nuclear
import –export cycle
Molecules of the matrix: Proteins of the microfilament, microtubules and
intermediary filaments; Structure, properties and assembly of actin and
tubulin, examples and roles of these filaments in cell structure and
function, eg., dynamics and roles of kinesin and dynein; Organization of
proteins on microvillus ; Cell-cell/cell -matrix interactions .
Unit I II: Protein Trafficking and Targeting (15L)
N-glycosylation in the ER and Golgi (quality control, UPR, ERAD and
proteosomal degradation
Intracellular and membrane protein trafficking and targeting; Secretory
pathways in prokaryotes and eukaryotes; Endocytic pathways; Signal
sequences; Co -translational transport (protease protection assay);
Targeting of mitochondrial, chloroplast, peroxisomal and nuclear proteins;
Vesicle biogenesis and ER to Golgi transport; ER translocation of
polypeptides (soluble and transmembrane); ER chaperons; SNAPs and
SNAREs; Methods of studying P rotein Transport; Disorders of protein
transport
Unit IV: Gene silencing and Epigenetics (15L)
Gene silencing : Historical background; RNA interference as regulatory
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mechanism in eukaryotes; Slicer and dicer; Synthesis and function of RNAi
molecules in plants; Gene silencing mechanisms; RNAi -based gene therapy ;
Chromatin remodelling in human disease and diagnosis
Epigenetics: Background, ch romosomal inheritance taking fission yeast as
an example; DNA methyltransferases, DNA methylation maintenance;
Histone modification and regulation of chromatin structure; Bivalent
histones; Histone demethylation ; Epigenetic therapy; Epigenetic regulation
of gene expression
Practical :
PSLSCP 401 Molecular Cell Biology (60L)
1. Preparation of lipid bilayer vesicles (liposomes) using
the purified lipids
2. Effect of detergents on membranes
3. Protease prot ection assay to study protein transport
and secretion
4. Isolation of DNA and demonstration of apoptosis of
DNA laddering
5. MTT assay for cell viability and growth
6. UV damage and repair mechanism in Escherichia coli or
Serratia marcescens
7. Synthesis of siRNA
8. Histone modification assays 2 04
References
1. Kleinsmith and Harden , The World of the cell, Becker, Academic Internet Publishers;
5th edition (2006)
2. Geoffrey M. Cooper and Robert E. Hausman. The Cell: A Molecular Approach, Fourth
Edition
3. Harv ey Lodish. Molecular cell Biology. W. H. Freeman; Sol edition (2007)
4. Alberts B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002)
Molecular Biology of the Cell. Garland Publishing, Taylor & Francis Group, USA.
5. Karp, J.G. (2007) Cell and Molecular Biology. John Wiley & Sons, USA.
6. Kleinsmith, L.J.and Kish, V.M. (1996) Principles of Cell & Molecular Biology. Second
Edition. Harper Collins College Publishers, USA.
7. Pollard, T.D. and Earnshow, W.C.(2002) Principles of Cell and Molecular Biolog y,
Saunders, USA.
8. Ross Dalbey (Editor) , Protein Targeting, Transport, and Translocation:, Publisher:
Academic Press; 1 edition (May 13, 2002)
9. T Gesteland et al. The RNA World Eds CSHL Press
10. Eds. Fire et. al. RNA Interference Technology: From Basic Science to Drug
Development. Cambridge University Press,
11. Ed. Gregory J. Hannon . RNAi: A Guide to Gene Silencing. CSHL Press
12. Ed. Gordon G. Carmichael . RNA Silencing: Methods and Protocols CSHL Press
13. Ed. Ute Schepers , RNA Interference in Practice, Wiley -VCH GmbH & C o. KGaA.
14. B. M. Turner , Chromatin and Gene Regulation: Molecu lar Mechanisms in Epigenetics
16
Course Code Title Credits
PSLSC BMT402 Nitrogen Metabolism and Plant Biochemistry (60L) 4
Unit II: Nucleotide Metabolism (15L)
Nucleotide Metabolism: Role of nucleases and phosphodiesterases in the
degradation of nucleic acids; Biosynthesis and degradation of purines and
pyrimidine nucleotides and their regulation; Thymine biosynthesis; Ro le of
foluc acid in nucleotide biosynthesis; Purine salvage pathway; Role of
ribonucleotide reductase; Biosynthesis of deoxyribonucleotides and
polynucleotides; Inhibitors of nucleic acid biosynthesis; Inherited disorders
of nucleotide metabolism; Anticanc er drugs ; Nucleotide metabolism as
target for cancer, antiviral therapy and malaria.
Unit II: Nitrogen Assimilation in Plants (15L)
Nitrogen Fixation: N itrogenase complex; Electron transport chain and
mechanism of action of nitrogenase; Structure of ‘NIF’ genes and its
regulation; Hydrogen uptake and bacterial hydrogenases .
Nitrate assimilation in plants: S tructural features of nitrate reductase and
nitrite reductase, incorporation of ammonia into organ ic compounds,
regulation of nitrate assimilation; Ammonium assimilating enzymes –
glutamine synthetase, glutamate synthase and GDH .
Unit III: Photosynthesis and Secondary Metabolism (15L)
Photosynthesis: Light harvesting com plexes; plant mitochondrial electron
transport and ATP synthesis; alternate oxidase ; Carbon fixation by C 3, C4
and CAM pathways ; Photoprotective mechanisms ; Photorespiration;
Bioluminescence.
Special features of secondary plant metabolism, terpenes (clas sification
and biosynthesis), lignin, tannins, pigments, phytochrome, waxes, alkaloids;
Biosynthesis of nicotine; Functions of alkaloids .
Unit IV: Free radicals and Antioxidant Biology (15L)
Free radicals: Intro duction & Chemistry of Reactive Oxygen/Nitrogen
Species (ROS/RNS); Sources of ROS/RNS; Transition metals as catalyst; ROS
and Signal Transduction ; Glycation mediated free radicals; Carbonyl and
oxidative stress; Beneficial Aspects of Oxidative Metabolism . Oxidative
damage markers Methods of Detecting ROS/RNS ; Detection of free radicals
in biological systems; EPR spectroscopy principles and determination .
Antioxidants: Diet-Derived Antioxidants; Enzym atic and non -enzym atic
components of antioxidative defense mechanism (catalase, peroxidase,
superoxide dismutases, vitamins E and C, uric acid, glutathione, metal
chelators) ; Chemical scavengers; Antioxidant therapy .
Role of free radicals in development of diseases: Mechanisms of Protein
oxdidation, Lipid peroxid ation, DNA oxidation. Types of oxidized lesions and
their biological importance
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Practical :
PSLSC BMP402 Nitrogen Metabolism and Plant Biochemistry (60L)
1. Measurement of activity of plant nitrate assimilation
enzymes
A. Isolation of nitrate reducta se from plants
B. Effect of environmental factors and hormones
(CO 2, light, pH, growth hormones)
2. Measurement of free radicals by spectrophotometric
method (Total phenolics, DPPH assay, ABTS assay, FRAP
assay)
3. Analysis of free radical scavengers and a ntioxidant
enzymes (Assay of any one - peroxidase, catalase, phenol
oxidase, ascorbic acid oxidase , SOD )
4. Generation and measurement of oxidative and
carbonyl stress in proteins and DNA (Protein oxidation
method /DNA cleavage assay )
5. Plant pigments
A. Extraction of plant pigments from spinach
B. Separation by column chromatography
C. Determination of absorption spectra of plant
pigments 2 04
References
1. Campbell and Farrell: Biochemistry 4th ed. Brooks/Cole Pub Co.
2. Buchanan : Biochemistry and molecular B iology of Plant
3. Heldt - Plant Biochemistry
4. Lubert Stryer, Biochemistry , W. H. Freeman; 6 editions (2006).
5. Voet and Voet , Fundamentals of Biochemistry:
6. Kuchel and Ralston, Biochemistry 1998. 2nd ed. Schaum’s Outlines McGraw Hill.
7. Harper’s Biochemistry: M urray, et al. 2003. 28th ed. McGraw Hill.
8. Nelson & Cox , Lehninger’s Principle of Biochemistry
9. K.G Ramawat , Biotechnology: Secondary Metabolites (2000) Publisher: Science
Publishers, U.S.
10. P.M Dey and J.B. Harborne , Plant Biochemistry (1997) Publisher: Ac ademic Press
11. Prof David T. Dennis, Prof David H. Turpin, Dr Daniel D. Lefebvre a nd Dr David B.
Layzell(Editors), Plant Metabolism by (1997) publisher: Longman
12. Packer L and Helumt S. Oxidative Stress and Inflammatory Mechanisms in Obesity,
Diabetes, and the Metabolic Syndrome. CRC Press.
13. Milan Lazár , Free Radicals in Chemistry and Biology,
14. Barry Halliwell , Free Radicals in Biology and Medicine (Paperback), John Gutteridge
15. Barry Halliwell , DNA & Free Radicals (Textbook Binding), Okezie I. Aruoma (Editor)
18
Course Code Title Credits
PSLSC BMT403 Biomolecular Function (60L) 4
Unit I: Protein folding and Engineering (15L)
Protein Folding: Folding pathway s; Intermediates of protein folding;
Compact Intermediates; Hierarchical and non -heirarchical folding
mechanisms ; Molten globule structure; Role of chaperons (trigger factor,
prefoldin) , heat shock proteins (Hsp70, Hsp90), chaperonins (Group I & II)
and en zymes in protein folding (PDI, PPI). Protein folding disorders.
Protein Engineering Design and construction of novel proteins and
enzymes using site -directed mutagenesis and Random/directed evolution
strategies ; Conformation of proteins in general and enzy mes in particular;
Effect of amino acids on structure of proteins; Energy status of a protein
molecule, Structure - function relations of enzymes .
Basic concepts for design of a new protein/enzyme molecule; Specific
examples of enzyme engineering – Dihydrof olate reductase and Subtilisin .
Unit II: Kinetics and Mechanism in Biological Systems (15L)
Enzyme Kinetics: Enzyme catalysis and factors contributing to high catalytic
rates; Molecular aspects of catalysis for specific enzyme substrate
complexes (Lysozyme, carbonic anhydrase, carboxypeptidase and
chymotrypsin) ; Multisite binding of ligands to proteins; Bohr’s effect;
Models of Allostery - MWC and KNF models Hill’s equation coefficient ;
Kinetics of multi -substrate enzyme -cataly sed reactions; Ping -pong bi -bi,
random order and compulsory order mechanism.
Immobilised enzymes: Methods and applications .
Unit III: Metabolomics and Transcriptomics (15L)
Metabolomics: Modern Concept of metabolomics; Detection and
characterization of metabolites ; metabolite library; Metabolite isolation
and analysis by Mass Spectrometry, NMR, LIF, LC -UV; Metabolomics
databases and resource (e.g. MetaboLights) .
Plant metabolomics: Plant stress responses, nutrigenomics, and metabolite
dynamics ; Metabolite profiling in phenotyping and breeding ( Arabidopsis
ecotypes, rice) .
Transcriptomics: basic concepts and technology, data normalization,
clustering (Hierarchical, k -means, SOM), detection of over expression and
under expression (PCA). Modeling using Boolean Networks. EST, Unigene.
Unit IV : Nanobiology (15L)
Introduction: Nanoscience; Nanobiotechnology; Nanodevices; Applications
in various fields viz. Physical and Chemical, Materials and Life Sciences .
Application: Gold bonding proteins; Nanopharmaceuticals such as
liposomal formulations; Membrane nanodiscs; Biosensors; Nanowires .
Synthesis of nanostructure: Physical, chemical and biological methods .
Properties and Characterization of nanomaterials: Optical (UV -Vis /
Fluorescence), X -ray diffraction; Imaging and size (Electron microscopy,
19
Light scattering, Zeta potential) , Surface and composition (ECSA, EDAX,
AFM/STM).
Practical :
PSLSC BMP403 Biomolecular Function and Environmental Toxicology (60L)
1. Protein denaturation by Guanidine hydrochloride /urea
2. Enzyme inhibition
A. Inhibition of enzyme activity
B. Determination of Ki values
3. Immobilization studies:
A. Preparation of urease entrapped in alginate beads
and determination of percent entrapment
B. Study of the kinetics of the rate of urea hydrolysis
by urease entrapped alginate beads
C. Study of reusability and storage stability of urease
entrapped alginate beads
D. Immobilization of urease by covalent attachment
to solid support
4. Study of nanoparticles
A. Synthesis of Silver nanoparticles
B. Spectroscopic characterisation
5. Toxicity testing: Effect of chemicals on seeds
6. Cytotoxicity ass ay (onion root tip/pollen germination) to
estimate water contamination 2 04
References:
1. Lutz, S. and Bornschesser, U. T. (2008) Protein Engineering Handbook. Wiley -VCH,
2. Gary C. Howard , Modern Protein Chemistry: Practical Aspects Published: S eptember
12, 2001 by CRC Press
3. Thomas E. Creighton , Proteins: Structures and Molecular Properties Publisher: W. H.
Freeman 1992 Edition: Second Edition
4. Christian Müller (Editor) , Protein Engineering Protocols (Methods in Molecular
Biology) K, Publisher: Humana Press; Softcover reprint of hardcover 1st ed. 2007
5. Anders Liljas, Structural Aspects of Protein Synthesis Publisher: World Scientific Pub
Co Inc; 1 edition (November 2 004)
6. David S. Goodsell, Bionanote chnology: Lessons from Nature, 1st Edition, Wiley -Liss,
2004.
7. Nicholas C. Price, Lewis Stevens, and Lewis stevens , Fundamentals of Enzymology:
The cell and molecular Biology of Catalytic Proteins by (2000) Publisher: Oxford
University Press, USA
8. Alejandro G. Marangoni , Enzyme Kinetics: A modern Approach Book: Enz yme
Kinetics: A Modern Approach, (2003) Publisher: Wiley -Interscience Enzyme Kinetics
and Mechani sms by Taylor Publisher: Springer
9. W. Weckwerth , Meta bolomics: Methods and Protocols, Humana Press, USA (2006).
10. M. Tomita and T. Nishioka , Metabolomics: The Front ier of Systems Biology, Springer
Verlag, Japan (2005).
20
Course Code Title Credits
PSLSC BMT404 Drug Development and Environmental Toxicology
(60L) 4
Unit I: Natural products (15L)
History of natural drugs, Sources of natural drug ie Plants, Animals, Micro
organisms ; Primary metabolites: carbohydrates, proteins, nucleic acids and
lipids and their importance to plants ; Secondary metabolites: Types,
mechani sm of synthesis, Importance in plants and for mankind as
fragrance, pigments, flavours and medicines
Unit II: Activity Guided Drug Development (15L)
Plant collection and Extract preparations: Methods of Plant collection,
solvent extraction (cold, hot, critical fluid extraction etc), screening of
medicinal properties; Natural products: methods of identification
(Qualitative and Quantitative), isolatio n and purification (Chromatography),
Characterization (LC -MS, GC-MS, NMR, XRD, Elemental analysis etc); Bio
efficacy studies: In vitro testing - Antimicrobial, Antidiabetic, Antioxidant,
Antiinflammatory, antilarvicidal etc. Pre clinical and clinical trials .
Unit III: Environmental toxicology (15L)
Toxic chemicals in the environment (air and water): their effects and
biochemi cal interactions
Biochemical aspects: of arsenic, cadmium, lead, mercury, carbon
monoxide, ozone and PAN pesticide; Mode of entry of toxic substance, its
breakdown and detoxification; biotransformation of xenobiotics;
Insecticides / Pesticides in environme nt, MIC effects.
Carcinogens : in environment, chemical carcinogenicity, mechanism of
carcinogenicity, environmental carcinogenicity testing.
Epidemiological issues of toxic compounds and metal poisoning.
Unit IV : Environmental monitoring (15L)
Basics: Definition and environmental monitoring process; Sampling – land
(site) sampling, water sampling, air sampling.
Analysis : physical, chemical and biological analysis methods and process.
Monitoring pollution : Bioindicators, Biomarkers.
Toxicity: testing using biological material.
Biosensors : mech anism, principle and working.
Environment Impact Assessment : EIA complete process, Importance of EIA.
Principles of environmental mitigation and monitoring .
Remote sensing : Principles and its applications in Environmental
Monitoring.
Geographical Informati on System (GIS): Concept of GIS; Types of
Geographical Data.Importance of Geographical Information System in
environmental studies.
21
PSLSC BMP404 Dissertation of Research Project (60L)
1. Project studies: presentation an d preparation of report
of observations and results
2 04
References:
1. Chemistry of Natural Products by Sujata V. Bhat , B.A. Nagasampagi , Meenakshi
Sivakumar (Springer Publication)
2. Indian Uses of Native Plants by Edith Van Allen Murphey
3. Plant Taxonomy ( 2nd Edition) by Sharma
4. Plant Drug analysis by H. Wagner
5. Biochemistry and Mol ecular Biology of Plants by Bob B . Buchanan
6. Plant Secondary Metabolites
Volume 1: Biological and Therapeutic Significance
Volume 2: Stimulation, Extraction, and Utilization by Kamlesh Prasad,
7. Vasudha Bansal Herbal Cosmetics & Ayurvedic Medicines by P. K. Chattopadhyay
8. Textbook of Clinical Trials by David Machin, Simon Day, Sylvan Green
9. Plant Bioactives and Drug Discovery: Pr inciples, Practice, and Perspectives 1st Edition
Valdir Cechinel -Filho (Author) , Wiley Publication.
10. Drug Discovery from Plants By Angela A. Salim, Young -Won Chin, A. Douglas
Kinghorn (Springer publication)
11. Bioassay Methods in Natural Product Research a nd Drug Development By Lars
Bohlin, Jan G. Bruhn (Springer Publication)
12. An Introduction to environmental toxicology: Michael H.Dong.
13. Environmental biotechnology: Alan Scragg.
14. Remote Sensing and GIS: Basudev Bhatta