MSc Life Sci Part II Biological Macromolecules1 Syllabus Mumbai University by munotes
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UNIVERSITY OF MUMBAI
Syllabus for the M.Sc. Part - II
[Sem III and IV]
Program: M.Sc.
Course : Life Sciences
Specialisation:
Biological Macromolecules
(Credit Based Semester and Grading S ystem with
effect from the academic year 2013 -2014)
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M.Sc. Part – II Life Sciences Syllabus
Restructured for Credit Based and Grading System
To be implemented from the Academic year 201 7-2018
SEMESTER III
Course Code UNIT TOPIC HEADINGS Credits L / Week
PSLSC BMT301
(Biomathemati
cs, Research
Methodology
and Cell
Biology
Techniques) I Biomathematics
4
II Research Methodology
III Cell and Molecular Biology
Techniques
IV Animal and Plant Tissue Culture
PSLSC BMT302
(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 Complex Proteins
PSLSC BMP301 Biomathematics, Research Methodology and
Cell Biology Techniques 2
PSLSC BMP302 Bioenergetics and Carbohydrate Metabolism 2
PSLSC BMP303 Biomolecular Structure 2
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SEMESTER IV
PSLSC BMT401
(Molecular Cell
Biology) I Cell Division and Apoptosis
4
II Biomembrane and Cell Matrix
III Protein Trafficking and Targeting
IV RNAi and Epigenetics
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 BMP401 Molecular Cell Biology 2
PSLSC BMP402 Nitrogen Metabolism and Plant Biochemistry 2
PSLSC BMP403 Biomolecular Function 2
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M.Sc. Part – II Life Sciences Syllabus
Restructured for Credit Based and Grading System
To be implemen ted from the Academic year 201 7-2018
Semester I II Detail ed Syllabus
Course Code Title Credits
PSLSC BMT301 Biomathematics, Research Methodology 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 differentiability), Successiv e
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: Research methodology (15L)
Meaning of Research, Objectives of resear ch, Motivation in research;
Types of research – Descriptive, Analytical, Applied, Fundamental,
Quantitative, Qualitative, Conceptual, Empirical and Other Types of
Research; Research Approaches; Research Methods vs. Methodology;
Research and Scientific Meth od; Research Process: Steps of research
process; Criteria of Good Research; Sampling, Sample size determination,
Plan for data collection, Methods of data collection, Plan for data
processing and analysis; Ethical considerations during research.
Systematic review and meta analysis
Unit III: Cell and Molecular Biology Techniques (15L)
Cell Biology Techniques: Principles, Instrument overview, 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
scatte ring (SLS and DLS); Capillary electrophoresis; Protein chips;
Differential scanning calorimetry
Genomics: Oligonucleotide synthesis; DNA chips/microarrays; DNA
hybridization; DNA sequencing methods, strategies for genome
sequencing; methods for analysis of gene expression at RNA and protein
level; DNA microarrays; Site directed mutagenesis; Gene knockdown;
Differential display; Serial analysis of gene expression (SAGE)
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Unit IV: Animal and Plant Tissue Culture (15L)
Plant tissue culture: Basic concepts in cell culture - cell culture, Cellular
Totipotency, Somatic Embryogenesis
In vitro culture: approaches & methodologies - preparation steps for tissue
culture, surface sterilization of plant tissue mater ial, basic procedure for
aseptic tissue transfer, incubation of culture.
Tissue culture methodologies : introduction - Callus Culture, Cell Suspension
Culture, Protoplast culture and hybridization, Organoge nesis, plant micro
propagation , cryopreservation.
Animal tissue and cell culture:
In vitro culture: approaches & methodologies - preparation steps for tissue
culture, basic procedure for aseptic tissue transfer, incubation of culture.
Tissue culture methodologies : introduction - Source of tissue, prima ry
culture, differentiation of cells, growth kinetics, animal cell lines and their
origin and characterization
Cloning & Selection of specific cell types – cloning, somatic cell fusion and
HAT selection, Medium suspension fusion, selection of Hybrid clone ,
production of monoclonal antibodies, stem cell culture
Organ Culture - Culture of embryonic organs, whole embryo culture,
culture of adult organs
Practicals:
PSLSC BMP301 Bionanalytical Techniques and Cell Dynamics (60L)
1. pka values of Ala or Gly by Titration Curve
2. Determination of melting temperature ( Tm) of
DNA
3. Spectroflourimetric analysis of proteins
4. Preparation of lipid bilayer vesicles (liposomes)
using the purified lipids
5. Effect of detergents on membranes
6. Fracti onation of cell organelles from
animal/plant tissues and identification by marker
enzymes
7. Estimation of inorganic phosphorus by Fiske and
SubbaRao method
8. Protease protection assay to study protein
transport and secretion
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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 oxidation -reduction
reactions; Redox potentials; Relation between stand ard 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 organ isms and
microorganisms; Pentose phosphate pathway and its regulation;
Gluconeogenesis, glycogenesis and glycogenolysis, glyoxylate and Gamma
aminobutyrate shunt pathways; Cori cycle; Anaplerotic reactions; Entner -
Doudoroff pathway; Glucuronate pathway; Me tabolism 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 biosynthes is: 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 of 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 ca tabolism: 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; Urea 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 a cids 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 and f uture 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 Life Sci ences - Introduction to
System Biology platforms Proprietary system Biology platform ; Different
Markup languages used in systems biology. Introduction to NGS
technology.
Practicals:
PSLSC BMP102 Bioenergetics and Metabolism (60L)
1. Determination of pyruvate by 2,4 -dinitrophenyl
hydrazine method
2. Isolation of cholesterol and lecithin from egg
yolk
3. Measurement of free radicals by
spectrophotometric method
4. Analysis of free radical scavengers and
antioxidant enzy mes (Assay of any one -
peroxidase, catalase, phenol oxidase, ascorbic acid
oxidase )
5.Determination of N - and C -terminal amino acids
(demonstration)
6. Effect of metal ions on the activity of
enzymes/proteins
7. Protein purification methods:
A. Isolation o f casein from milk
B. Purification of an enzyme by ion exchange
chromatography/affinity chromatography
C. Use of ammonium sulphate precipitation and
dialysis
D. Use of gel filtration
E. SDS -PAGE
8. Polyacrylamide gel electrophoresis under non
denaturing co nditions
A. Silver staining
B. Activity staining of enzymes
C. Determination of effect of acrylamide
concentration on the mobility of proteins 2 04
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Course Code Title Credits
PSLSC BMT103 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 bi omolecules, such as van der
Waals forces and hydrogen bonding; Energies and geometrics of these
interactions and their roles in structure and conformation of biomolecules .
Spectroscopic techniques: Principle, methodology and applications of
Fluorescence, I nfrared, Raman, ESR, Atomic absorption spectroscopy; NMR;
Use of lasers for spectroscopy .
Optical Activity: Importance of chirality in biomolecules; Principles and
applications of ORD and CD
Unit II: Protein and Nucleic Acid Structures (15L)
Structure and Stability of Proteins: Myoglobin, Hemoglobin, Lysozyme,
Ribonuclease A, Carboxypeptidase and Chymotrypsin ; Conformation of
proteins by Ramachandran plot; N and C terminal analysis of proteins
Covalent modifi cation of proteins: Phosphorylation, adenylation,
methylation, ribosylation
DNA structure: A/B/Z/D forms of double helical structure of DNA; Triple
helix; DNA supercoiling and topoisomerases
Unit III: Supramolecular Assemblies and Complex proteins (15L)
Viruses: Viral assembly; Capsid; Capsomere , eg., TMV, HIV, Adenovirus
Prokaryotes and Eukaryotes: Ribosomal assembly; Biosynthesis and
processing of rRNA; Macromolecular interactions in regulating translation .
Nucleic Acid Binding Motifs i n Proteins: Leucine zipper; Zinc fingers; Helix -
turn -helix; Beta barrel; OB fold and their role in regulation of gene
expression
Unit IV: Complex Proteins (15L)
Metalloproteins: General principles of metal coordination; Heme - and non -
heme proteins .
Transport proteins: Oxygen transport proteins from vertebrate and
invertebrate (haemoglobin, hemocyanin, cytochrome C)
Bacterial two -component signalling systems and their role in regulat ing
sugar transport, catabolite repression, phosphotransferase system,
chemosensory mechanisms and sensory modulation of C -N metabolism.
Practicals:
PSLSC BMP103
Biomolecular Structure (60L) 2 04
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Semester IV Detail Syllabus
Course Code Title Credits
PSLSC BMT201 Molecular Cell Biology (60L) 4
Unit I: Cell Division and Apoptosis (15L)
Cell divisi on and cell cycle: Meiosis: its regulation, steps in cell cycle, and
control of cell cycle. Cell-cell fusion in normal and abnormal cells.
Apoptosis : Factors inducing apoptosis; Genes and proteins involved in
apoptosis; Receptors with death domains and the ir signalling pathways;
Role of apoptosis in development and disease.
Carcinogenesis : Characteristics of cancerous cells; Agents promoting
carcinogenesis; molecular basis of cancer therapy, Tumor markers - AFP,
CEA, hCG ; Telomere replication; Telomerase a nd its role in cancer and
aging
Unit III: Biomembrane and Cell Matrix (15L)
Biomembranes: Structure and assembly; Orientation of membrane
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; Organizat ion of
proteins on microvillus .
Extracellular Matrix: Structure; Cell -cell/cell -matrix interactions;
Intracellular transport – cilia and flagella
Unit I II: Protein Trafficking and Targeting (15L)
N-glyco sylation 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 tran sport (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; Method s of studying Protein Transport; Disorders of protein
transport
Unit IV: RNAi and Epigenetics (15L)
Regulatory RNAs: Historical background; RNA interference as regulatory
mechanism in eukaryotes; Slicer and dicer; Synthesis and function of RNAi
molecules in plants; Gene silencing mechanisms; RNAi -based gene therapy ;
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Chromatin remodelling in human disease and diagnosis
Epigenetics: Background, chromosomal inheritance taking fission yea st 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
Practicals:
PSLSCP 201 Molecular Cell Biology (60L)
1. Nucleic acid isolation and blotting
A. Isolation of RNA from E. Coli
B. Spectrophotometric characterization of RNA
C. Capillary blotting (Southern/Northern) of
nucleic a cids from agarose gels
D. Preparation of cDNA and RT -PCR
2. Isolation of DNA and demonstration of apoptosis of
DNA laddering
3. MTT assay for cell viability and growth
4. UV damage and repair mechanism in Escherichia coli
or Serratia marcescens
5. Determination of Molar absorption coefficient of
tyrosine
6. Measurement of DNA by DPA method
7. Assay of alanine and aspartate aminotransferases
8. Measurement of activity of plant nitrate assimilation
enzymes
A. Isolation of nitrate reductase from plants
B. Effect of en vironmental factors and hormones
(CO 2, light, pH, growth hormones)
9. Plant pigments
A. Extraction of plant pigments from spinach
B. Separation by column chromatography
C. Determination of absorption spectra of plant
pigments 2 04
Course Code Title Credits
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PSLSC BMT202 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; Role 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; Anticancer drugs .
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 redu ctase and
nitrite reductase, incorporation of ammonia into organic compounds,
regulation of nitrate assimilation; Ammonium assimilating enzymes –
glutamine synthetase, glutamate synthase and GDH
Unit III: Photosynthesis and Secondary Metabolism (15L)
Photosynthesis: Light harvesting complexes; 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 (classification,
biosynthesis), lignin, tannins, pigments, phytochrome, waxes, alkaloids;
Biosynthesis of nicotine; Functions of alkaloids ;
Unit IV: Free radicals and Antioxidant Biology (15L)
Free radicals: Introduction & Chemistry of Reactive Oxygen/Nitrogen
Species (ROS/RNS); Sources of ROS/RNS; Cellular damage by ROS/RNS;
Disease states and free radicals; Transition metals as catalyst; ROS and
Signal T ransduction ; 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 Ant ioxidants; 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
Practicals:
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PSLSC BMP202 PRACTICAL VII: Nitrogen Metabolism and Plant
Biochemistry (60L)
1. 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 electrophor esis
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
hydrol ysis 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. 2-D Gel electrophoresis (Demonstration)
5. Study of nanoparticles
A. Synthesis of Silver nanoparticles
B. Spectroscopic characterisation 2 04
Course Code Title Credits
PSLSC BMT203 Biomolecular Function (60L) 4
Unit I: Protein folding and Engineering (15L)
Protein Folding: Folding pathways; Intermediates of protein folding;
Compact Intermediates; Hierarchical and non -heirarchical folding
mechanisms ; Molten globule structure; Role of chaperons, heat shock
proteins and enzymes in protein folding
Protein Engineering Design and construction of novel proteins and
enzymes; Conformation of proteins in general and enzymes in particular;
Effect of amino acids on structure of proteins; Energy status of a protein
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molecule, Struct ure- function relations of enzymes
Basic concepts for design of a new protein/enzyme molecule; Specific
examples of enzyme engineering – Dihydrofolatereductase
Unit II: Kinetics and Mechanism in Biological Systems (15L)
Enzym e 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 protein s; Bohr’s effect;
Models of Allostery - MWC and KNF models Hill’s equation coefficient
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 normalizatio n,
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,
Light scattering , Zeta potential),; Surface and composition (ECSA, EDAX,
AFM/STM),
Practicals:
PSLSC BMP203
Biomolecular Function (60L)
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