SYLLABUSOF

M.Sc., MOLECULARBIOLOGY

FROM2006 - 2007 ONWARDS

2

SEMESTER – ITHEORY:Paper - I : MLB 101 : Biochemistry – IPaper – II : MLB 102 : Molecular PhysiologyPaper – III : MLB 103 : Molecular Cell BiologyPaper - IV : MLB 104 : Microbiology

PRACTICALSPractical- I : MLB 105 : Biochemistry – I and Molecular PhysiologyPractical - II : MLB 106 : Molecular Cell Biology and Microbiology

SEMESTER – IITHEORYPaper - I : MLB 201 : Nucleic AcidsPaper - II : MLB 202 : Genetic EngineeringPaper - III : MLB 203 : Genetics and CytogeneticsPaper - IV : MLB 204 : Biostatistics, Computer Applications and

Bioinformatics

PRACTICALSPractical- I : MLB 205 : Nucleic Acids & Genetic EngineeringPractical - II : MLB 206 : Genetics and Cytogenetics and Biostatistics, Computer

Applications and Bioinformatics

3

SEMESTER – IScheme of Study and Examination

Code ofthe Paper Paper Subject

(Hrs / week) Total No.of hrs/

Semester

Duration ofexamination

(hrs)

Max. Marksof

examination

Continuousevaluation

TotalMarksTheory Practical

MLB101 I Biochemistry – I 4 -- 52 3 80 20* 100MLB102 II Molecular Physiology 4 -- 52 3 80 20* 100MLB103 III Molecular Cell Biology 4 -- 52 3 80 20* 100MLB104 IV Microbiology 4 -- 52 3 80 20* 100MLB105 Pract .I Biochemistry – I &

Molecular Physiology-- 8 104 4 40 10** 50

MLB106 Pract .II Molecular Cell Biology &Microbiology

-- 8 104 4 40 10** 50

TOTAL MARKS 500* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical Record + 5 marks for visit to Industries/Laboratories

4

SEMESTER – IIScheme of Study and Examination

Code ofthe Paper Paper Subject

(Hrs / week) Total No.of hrs/

Semester

Duration ofexamination

(hrs)

Max. Marksof

examination

Continuousevaluation

TotalMarksTheory Practical

MLB201 I Nucleic Acids 4 -- 52 3 80 20* 100MLB202 II Genetic Engineering 4 -- 52 3 80 20* 100MLB203 III Genetics and Cytogenetics 4 -- 52 3 80 20* 100MLB204 IV Biostatistics, Computer

Applications &Bioinformatics

4 -- 52 3 80 20* 100

MLB205 Pract .I Nucleic Acids & GeneticEngineering

-- 8 104 4 40 10** 50

MLB206 Pract .II Genetics & Cytogeneticsand Biostatistics,Computer Applications &Boinformatics

-- 8 104 4 40 10** 50

TOTAL MARKS 500* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical Record + 5 marks for visit to Industries/Laboratories

5

QUESTION PAPER FORMAT

BANGALORE UNIVERSITYM.Sc., (I & II Semester) Examination

MOLECULAR BIOLOGY

Paper:Time: 03 Hours Max. Marks: 80

Instructions: 1. Answer all the parts 2. Draw diagrams wherever necessary

A. Write short notes on the following: (5x2=10)1-5

B. Write critical notes on the following: (5x8=40)6-10

C. Answer any two of the following (2x15=30)11-14

6

SEMESTER – I

MLB – 101 BIOCHEMISTRY – I52 hrs

Unit - IChemical bonding: Covalent bonds, ionic bonds, hydrogen bonds, co-ordinate bonds; Electrostatic attractive forces, van der Waalsforces, hydrophobic forces; Involvement of molecular orbitals in chemical bond formation, sigma and pi bonds; Bond strength, bondenergy and bond radius; Formation of chemical bonds with carbon and other elements.Geometry of carbon compounds, tetrahedral structure, conformation and configuration, optical activity, asymmetric centers or chiralcenters, stereoisomers, cis-trans configuration. 05 hrs

Unit – IIpH: Weak acid and weak base; Dissociation constant, ionization of water and equilibrium constant, properties of water, hydrogen ionconcentration, Henderson-Hasselbalch equation.Buffers: Concept, importance and preparation. 04 hrs

Unit - IIIBio-organic reactions : Acid–base , Covalent and Metal ion catalysis; Concept of nucleophiles and electrophiles, Nucleophilicsubstitution reactions and their importance. 02 hrs

Unit - IVChemistry of Biomolecules:Carbohydrates: Classification, chemistry of mono, oligo and polysaccharides. Functions of homo and hetero polysaccharides.Lipids: Classification, brief outline of the chemistry of fatty acids, phospholipids, sphingolipids.Amino acids: Classification, properties, protein and non-protein amino acids, essential and nonessential amino acids. Modifiedamino acids and their functions.

06 hrsUnit - VProteins:Structural Organization and Classification

7

Concept of peptide bond; steric interference, Ramachandran plot and its importance. Primary, secondary, tertiary and quaternarystructure; Secondary structural forms such as alpha-helix, beta sheet conformation, sequence driven conformation, helix turn helix,beta turn beta and combination of them as structural motifs, structure prediction; Concept of motif and domain; Forces for tertiaryfolding and its stabilization; Protein-protein interaction, denaturation and renaturation; Determination of isoelectric point; Estimationof protein purity. Protein sequencing methods; Concept of protein microarray methods. specific and molecular activity of proteins.Role of chaperones and isomerases in 3-D folding of proteins. 10 hrs

Unit - VIEnzymes:Chemistry and structure: Basic organization 3-D structure of simple enzyme and multimeric enzyme and multienzyme complex;Structural features such as substrate binding site, catalytic site, allosteric site; Mechanism of enzyme activation, inducedconformational changes.Cofactors and Activators: Characteristic features of cofactors, coenzymes and their role in chemical reactions, concept of apozymes,prosthetic groups and holozyme. 07 hrs

Unit - VIIEnzyme Kinetics: Rate of reaction, kinetic order rate equations, turn over, Kcat, Vmax, Km, Michaelis-Menten equation,Lineweaver-Burk plot, activation energy, binding energy, transition states, equilibrium, kinetics of enzyme inhibitors.Mechanism of Enzymatic Catalysis: Principles and concepts of specificity, binding, entropy reduction, desolation, transitional stateand induced fit processes; Acid-base catalysis, covalent catalysis, metal catalysis; Single substrate reaction and double substratereaction.Factors: pH, temperature, concentration of substrates.Pre-pro enzymes and Regulation of Enzyme activity: Concept of feed back inhibition and allosteric regulation.

08 hrs

8

Unit – VIIIBiochemical mechanisms: Introduction, mechanistic role of the following in living systems :- thiamine pyrophosphate (TPP) indecarboxylation of alpha keto acids and in the formation of alpha ketols; Pyridoxal phosphate (PLP) in transamination,decarboxylation, dealdolisation and elimination reactions of amino acids; Lipoic acid in the transfer of acyl group, co-enzyme A (co-ASH) in the transfer of acyl group, biotin in the carboxylation reaction; Tetrahydropholic acid in one carbon transfer reaction; VitaminB12 co-enzymes in molecular rearrangement reactions and in the synthesis of methionine and methane; Nicotine amide and flavin co-enzymes in biological redox reaction.Biochemical Techniques: Principle and application of Spectrophotometry, X-Ray diffraction, NMR, Centrifugation, Chromatograpyand Electrophoretic techniques. 10 hrs

Reading References:1. Boyer, R.F. [Ed.] (1986) Modern Experimental Biochemistry; Addison Wesley2. Buchanan, B.B., Wilhelm Gurssem & Jones R.L. (2000), Biochemistry & Molecular Biology of plants. American Society of

Plant Physiologists, Rock Ville, USA, Maryland.3. Colowick, S.P. et al., [Eds.] (1987) Methods in Enzymology; Vol. 152, Academic press.4. Conn, E.E and Stumpf, P.K, G.Bruencing and R.G. Dol (1995). Outlines of Biochemistry. John Wiley, Singapore.5. Conn, E.E and Stumpf, P.K. (1976), Outlines of Biochemistry, John Wiley and sons Inc, New York6. Dey, P.M. and J.B.Harborne (1997), Plant Biochemistry: Academic press, Inc.San Dugo, California V7. Engel, P.C. (1981), Enzyme Kinetics; The steady state approach Champman and Hall8. Hans – Walter Heldt, (2005), Plant Biochemistry, 3rd edition, Academic Press, An Imprint of Elsevier9. Irwin H.Segal (1976), Enzyme Kinetics ; Interscience – Wiley10. Keithwilson and John Walker, (Ed) (2005). Principles and techniques of Biochemistry and Molecular Biology Cambridge

University Press.11. Mathews and Van Holde (1995), Biochemistry 2nd Edition, Benjamin/Cummings publishing company Inc.12. Nelson, D.L. and Cox, M.M. (2004), Principles of Biochemistry, CBS publishers and Distributors. New Delhi.13. Roberts , D.V. (1977), Enzyme Kinetics ; Cambridge University Press.14. Stryer, L.(1995), Biochemistry (4th Edition) W.H.Freeman and company, New York15. Thomas M. Devlin, (2006) Text Book of Biochemistry with clinical correlations, 6th edition, Wiley – Liss Publication.16. Voet , D and Voet, J.G. (2004), Biochemistry, 2nd edition J.Wiley and sons17. Wilson, K and J. Walker (1995), Practical Biochemistry; Principles and Techniques; Cambridge University Press.

9

18. Zubey G.L. (1998). Biochemistry, Wn. C. Brown publisher, Sydney19. Zubey, G.L. Parson, W.W. and Vance, D.E. (1994), Principles of Biochemistry Wn. C. Brown publishers. Oxford.

MLB – 102 MOLECULAR PHYSIOLOGY52 hrs

Unit – IMembrane Transport: Overview, molecules across biomembrane by passive diffusion, protein mediated transport, uniport transport,GLUT1 uniport transport, Human GLUT proteins.Pumps: Different classes, structure and functional properties; ATP-driven ion pumps; Ca2+ ATPase pump, Calmodulin mediatedpump, Na+/K+ ATPase pump, V-class H+ ATPase pump.Carriers: Glucose and amino acid transport proteinsABC transporter: Bacterial permeases, ABC small molecular pumps; Flippare mechanismIon channels: Nongated ion channels, co-transport by symporters and antiporters, voltage gated ion channels.08hrs

Unit – IIProtein sorting: The machinery of protein sorting: Translocation of secretary proteins across the membrane of endoplasmicreticulum, insertion of proteins into the membrane of endoplasmic reticulum, protein modification and folding, export of bacterialproteins. Targeting proteins to mitochondria and chloroplast.Vesicle traffic: Secretory pathway, molecular mechanism of vesicular traffic, early and late stages of secretory pathway.

07 hrs

Unit-IIIExocytosis: Transport of molecules from the trans Golgi network to the cell surface, and role of annexins in exocytosis,Endocytosis: Receptor for low density lipoproteins, ligands for endocytosis, endosomes for dissociation of receptor – ligandcomplexes, the endocytic pathway, specialized vesicles to deliver cell components to lysosomes, degradation.Transcytosis : Endocytosed ligands across an epithelial cell layer 06 hrs

10

Unit – IVDefense system: Plant pathogen interaction, R-genes and R-gene mediated disease resistance. Plant defense reaction and response.Control of pathogens by genetic engineering. Chaperones and Prions. 06 hrs

Unit – VAmino acid Metabolism: Amino acids as neurotransmitters, aromatic amino acid biosynthesis, aspartate derived amino acidbiosynthesis, proline metabolism: and its utility in evolving stress tolerance in plants. 05 hrs

Unit –VILipid Metabolism: Fatty acid biosynthesis, desaturases, synthesis of unusual fatty acids, membrane lipids and their function,synthesis and catabolism of storage lipids. 05 hrs

Unit – VIICellular Receptors and Signal Transduction: Concept of cellular signaling, characteristic signaling molecules, extra cellular andintracellular forms, paracrine, synaptic and endocrine form of signaling, concentration and their effects, cellular status and potential(programmed) in receiving and responding to signals, cellular receptors and their characters. Cell surface receptor proteins -ionchannel linked, G-protein linked and enzyme linked; Intracellular receptors - kinds and mechanism: mechanism of binding,activation and signal transduction. Role of Inositol Phosphotidyl, diacyl-glycerol molecules and Calmodulin, cAMP and cGMPs,kinases, phosphatases in signal transduction. 10 hrs

Unit – VIIIMolecular mechanism of plants and animal adaptation to temperature and osmotic pressure with reference to high and low altitude.

05 hrs

Reading References:1. Buchanan, B.B, Gruissem, , W. and Jones, R.L. (2004). Biochemistry and Molecular Biology of plants. I.K. International

Pvt., New Delhi.2. Conn, E.E., Stumpf., Bruenning, G and Doi, R.H. (1987). Outlines of Biochemsitry. John Wiley and Sons, New York.3. Flochachka and Sumarea. M. (1989). Molecular Mechanism of Adaptations, Academic Press, New York.4. Gerald Karp. (1996). Cell and Molecular Biology – Concepts and Experiments. John Wiley and Sons, Inc., New York.5. Gupta, P.K. (2004). Cell and Molecular Biology. Rastogi Publications, Meerut.

11

6. Harvey Lodish, Arnold Berk, Paul Matsudaira, Chris A. Kaiser, Monty Krieger, Matthew P. Scott, S. Lawrence Zipursky andJames Darnell. (2003). Molecular Cell Biology, W.H. Freeman and Company, New York.

7. Hopkins, W.G. (1995). Introduction to plant physiology. John Wiley & Sons Inc. New York, USA.8. Moore, T.C. (1989). Biochemistry and physiology of plant hormones. 2nd edition. Springer-Verlag, New York , USA.9. Stumpf, P.K. and Conn, E.E. (Eds) (1988). The biochemistry of plants- A Comprehensive treatise. Academic press, New

York.10. Schmidt – Nelson, R. (1987). Annual Physiology, Adaptation and Environment, 5th Edition, Cambridge University Press,

London11. Taiz, L. and Zeiger, E. (2003). Plant Physiology. 3rd edition. Panima Publishing Corporation, New Delhi/Bangalore12. Taiz, L. and Zeiger, E. (1998). Plant Physiology. 2nd edition. Sinauer Associates, Inc., Publishers, Massachusetts, USA.13. Wilkins, M.B. (eds.) (1989). Advanced Plant Physiology. Pitman Publishing Ltd., London.

MLB – 103 MOLECULAR CELL BIOLOGY52 hrs

Unit – ICell wall: Cell wall composition, biosynthesis and assembly. Membrane structure - Fluid mosaic model. Ultra structure and functionof membranous organelles: Endoplasmic Reticulum, Golgi Apparatus, Vacuoles, Lysosomes, Chloroplast and Mitochondria

08 hrs

Unit - IICytoskeleton: Microfilaments, Microtubules and Intermediate filaments. Actin and tubulin gene families, dynamics of actin andtubulin, role of microtubules in intracellular movement, mitosis and cytokinesis 06 hrs

Unit - IIIRibosomes: Structure of prokaryotic and eukaryotic ribosomes. Riboproteins, rRNA , 3-D modular structure. Ribosome biogenesis.Important structural motifs in ribosomes and their functions. 06 hrs

Unit - IVNucleus: Nuclear membrane, nuclear pore complex, transport mechanism of nuclear laminins and their role. Composition of nuclearsap, nucleolar sap and nucleoplasm.,

12

Nucleolus: Organization, chemistry, function and biogenesis 05 hrs

Unit – VMolecular organization of Eukaryotic chromosome: Molecular organization of nucleosome, nucleosomal thread, solonoid andcoiled coil structures. Molecular features of telomere, kinetochore, euchromatin and heterochromatin; Role of scaffold and matrixproteins (SARS and MARS); Mechanism and factors for chromosomal condensation and relaxation. 08 hrs

Unit – VIChloroplast: Genome size, number, organization of genes; Chloroplast mRNA and tRNA, ribosomes, biogenesis of plastids, role oflight and phytochrome in the development of plastids; Import of proteins from cytoplasm.Mitochondria: Genome size, number and organization of genes; Molecular organization of inner and outer membrane, attachmentsites and their function; mitochondrial matrix and its chemical composition and physiological functions. Organization of electrontransport system in the inner membranes, elementary particles and their organization and functions. Mitochondrial protein synthesis;Transport mechanism of cytosolic proteins into mitochondria, Biogenesis of mitochondria.08 hrs

Unit – VIICell Cycle: Genetic regulation of cell cycle; Molecular basis of cellular check points.

05 hrs

Unit - VIIIApoptosis: Programmed cell death (PCD), signals and causes for inducing apoptosis, regulation of gene activity during apoptosis,role of cysteine-containing-aspartate specific proteases (CASPASes), Apoptotic Protease Activating Factors (APAF) mechanism ofapoptosis at biochemical level, importance of apoptosis in development and organogenesis. Programmed cell death (PCD) in plantsand its relation to senescence, senescence associated genes (SAGs), hypersensitivity as a cause for apoptosis, Necrosis, tumournecrosis factor, death signals, cell death by activating Caspases 06 hrs

Reading references:1. Alberts. B., Bray, D., Lewis, J., Raff, M., Roberts, K and Watson, J.D. (1994). Molecular Biology of the cell. Garland

Publisher Inc., New York2. Bishop J.A. (1982). Retroviruses and cancer genes. Advances in cancer research.

13

3. Brachet J. (1985). Molecular Cytology . Academic Press New York4. Celis J E (Eds): Cell Biology : A Laboratory Hand Book . Vol I & II Academic Press.5. Elliot and Elliot. (2001). Biochemistry and Molecular Biology. Oxford University Press.6. Gerald Karp. (1996). Cell and Molecular Biology. John Wiley and Sons. Inc7. J.Daneil H and Lodish D. (1995). Molecular cell Biology. Baltimore Scientific American Book8. Knudson A.G. (1998). Anti – Oncogenes and Human cancer . Proceedings of the National academy of xciences USA 90:10

0114-109219. Lodish,H., Ber, A., Zipuoskry, L.S., Matsudaira, P., Bahimore, D and Damell J. (2001) Molecular Biology W.H Freeman G

Co. 4710. Pollard J.P. and W.C. Earnshaw. (2002). Cell Biology, Sunders11. Sudberry P. (2002). Human Molecular Cytogenetics. Prentice Hall Publication12. Wolfe. A. (1995). Chromatin structure and function. Academic press; New York

MLB – 104 MICROBIOLOGY52 hrs

Unit - IIntroduction to viruses: Structure, properties, importance and classification.Bacterial viruses:Structural organization, replication and assembly of dsDNA phages: T4 phage, T7 phage and Lambda phage; ssDNA phages:Øx 174 phage and M13 phage; RNA phages: Ms2 phagePlant viruses:Occurrence, distribution, structural organization of capsid and genome organization and replication, disease caused by the viruses andmethods to contain the viruses. DNA viruses: Gemini Virus, Cauliflower Mosaic Virus. RNA viruses: Tobacco Mosaic Virus, PotatoVirus - X and Y, Gamphrena Virus (Rhabdovirus), Plantain-B Virus. 10 hrs

Unit - IIBacteria:Occurrence, distribution, shape, size, pathogenesis of bacteria and control measures. Gram negative and positive bacteria. Ultrastructure of E-coli. Basic mechanism of bacterial membrane transport : Passive, facilitated passive transport, Active transport-pumps,carriers; group translocation, translocation of sugars, ions, amino acids, and their regulation. Flagella and Cilia: Structural

14

organization of flagella and cilia and molecular mechanism of movements. Fimbriae and sex pili: Structural organization andfunctions of Fimbriae and Sex pili; Chromosome: Genome size and organization (nucleoids). Cell division: Molecular Mechanismof cell division and its regulation; genes involved in cell division. 08 hrs.

Unit - IIIRecombination in bacteria: a) Conjugation, Discovery, nature of donor strains and compatibility, interrupted mating and temporalmapping, Hfr, F’, heteroduplex analysis, mechanism of chromosome transfer, molecular pathway of recombinations andgenemapping. b) Transformation in Gram +ve and Gram –ve bacteria, natural transformation systems, biology of transformation,transformation and gene mapping, chemical mediated and electro tansformations c)Transduction Discovery, generalized andspecialized transduction, phage P1 and P22 mediated transduction, mechanism of generalized transduction, abortive transduction,mechanism of specialized transduction, gene mapping, fine structure mapping.

05 hrs

Unit - IVAgrobacterium: Morphology, Ti plasmids, and T-DNA, their characteristic features, mechanism of T-DNA transfer into plant cells,Ti- mediated crown gall development, mechanism of plant cancer development.Bacterial plasmids: Characteristic features and classes of plasmids- sex factor F+/- containing plasmids, R-plasmids, Pathogenicplasmids (K-plasmids, Hly and Enteric plasmids), Col-plasmids, Degradative plasmids, Tumour inducing plasmids, Cryptic plasmids,metal resistance plasmids- and their characters. Transmission of Colicin and drug resistant R plasmids. 04 hrs

Unit - VCyanobacteria: Structural features, cell structure, organization of membranes for photosynthesis, nitrogen fixation, genomes andreproductive methods and use of cyanobacteria as fertilizers.Transposable elements: Insertional elements (IS), Tn elements (Transposons); Structural features, numbers, sizes, replication andmechanism of transpositions, Transposon mediated drug resistance. 04 hrs

Unit - VIFungi:Yeast: Detailed account of Saccharomyces cervisiae, cell biology, reproductive biology, genetics of mating types, nuclear andcytoplasmic inheritance. Importance of Saccharomyces and its related members in genetic engineering and commercial uses.

15

Mycorhizae and Vam fungi: Composition, structural features and their importance.05 hrs

Unit - VIIMicrobial metabolism:Bacterial photosynthesis: Phototrophs, .chemotrophs, chemical composition of photosynthetic components. Mechanism of lightreaction and dark reaction - Reductive pathway, pentose pathway and pyruvate synthase pathway. Mechanism of chemosynthesis.Bacterial carbohydrate metabolism: Embden-Meyerhoff and Parnas pathway, Entner-Duodorff pathway and Warburg-Dickenspathway, Pentose and Hexose phosphoketolase pathway. Aerobic pathways leading to citrate cycle and oxidative phosphorylation

06 hrs

Unit - VIIIGenetically Engineered Microbes (GEMS): Gene manipulated microbes, Production of therapeutic agents:Gene engineering and production of - Human interferons, human growth hormones, DNase-I, alginate lyase. Production of humanizedand regular antibodies in E.coli and yeast. Anti HIV agents. Use of GEMS for the production of proteins, antibodies and othermetabolites of importance.Biofertilizers:Use of microbes and genetically engineered microbe in enriching soil with fertilizers.Nif genes: Nitrogen fixing genes and organization, Genetic engineering of Nitrogen fixing gene clusters in Klebsiella pneumoniae.Regulation of nif genes. Hydrogenase genes:Cloning and expression of Hup+ genes (Hydrogenase gene) and its importance. Genetic engineering of nodulation genes and itsimportance in agriculture.Cloning of antibiotic genes from pseudomonads: Cloning and expression of antibiotic genes and its importance.

10 hrs

Reading References:1. Atlas R.M. (1998) Microbiology : Fundamental and application (IIeds) Mac millan Publishing company2. Bruijin et al ., (1998). Bacterial genomes, Chapman and Hill3. Dale J.W. (1994). Molecular genetics and Bacteria. John Wiley and sons4. Hayes W. (1970). The genetics of Bacteria and their viruses. The English Book society of Blackwell Scientific Publication,

Oxford

16

5. Hunderson et al., (1999). Cellular Microbiology Wiley6. Lewin B (2002). Genes VIII, Oxford7. Prescot L.M., Hanley, J.P. and Klein, D.A. (1999). Microbiology, WCB Mc Graw Hill , Con MY8. Roger L.P., John T., Knowler and Daviol P. Leadr. (1992). The Biochemistry of Nucleic acids, 11th edition. Chapmann and

Hall9. Samuel Singer (2001). Experiments in Applied Microbiology, Academic Press New York.10. Stnely R. Maloy, John E. Cronan, Jr., David Freifelour (1994). Microbial genetics. Jones and Barlett Pub. Bosten.11. Sullia S.B. and S.Shantharam (1998). General Microbiology , Oxford IBH Publishing Con, New Delhi.

17

FIRST SEMESTER PRACTICALS MLB – 105 BIOCHEMISTRY – I

AND MOLECULAR PHYSIOLOGY

PART – A1. Preparation of Buffers2. Protein isolation (crude) from plant, animal and microbial sources3. Estimation of Protein – Colorimetric method4. Estimation of amino acids – Ninhydrin method5. Determination of Specific activity of Enzyme- Invertase6. Determination of Km using Line weaver – Burk plot

PART – B7. Extraction of lipids - Plant and animal sources8. Salicylic acid chromatography of lipid extracts9. TLC of lipids and identification of different lipids10. Separation of amino acids by paper chromatography and TLC

MLB – 106 MOLECULAR CELL BIOLOGY AND MICROBIOLOGYPART – A

1. Preparation of meiotic chromosomes using Haemotoxylin/Feulgen stain – Poecilocera picta

2. Vital staining of mitochondria3. Isolation of mitochondrial DNA4. Isolation of chloroplast DNA5. Preparation of salivary gland chromosomes – Drosophila melanogaster

6. Vital Staining – Animal and Plant, Dye exclusion techniquePART – B

7. Growth curve of E.coli8. Isolation of bacterial plasmids

18

9. Isolation of cyanobacteria10. Bacterial respiration11. Estimation of oxygen during photosynthesis12. Plasmid transformation

19

SECOND SEMESTER

MLB – 201 NUCLEIC ACIDS52 hrs

Unit - IChemistry and properties of Nucleic Acids: Discovery of genetic material, chemistry and structural features of nucleotides.Quantitative relationship between bases, ionic state, sugar puckering, base configuration with respect to the sugar. Comparativeproperties of DNA and RNA with respect to size, quantity, distribution, turnover, Watson-Crick base paring, Non-Watson–Crick basepairing by hydrogen bonds. Procedures and protocol for DNA melting and annealing by DNA:DNA hybridization and DNA:RNAhybridization, kinetics of melting and reannealing. Cot curves and Cot ½ values and rot and rot ½ curves, kinetic complexity andchemical complexity. Importance of kinetic class of DNA.

08 hrsUnit - IIStructural forms of DNA:dsDNA: (ds= double stranded) Structural features of Watson-Crick B-DNA model, the basis for A=T and G=C base pairing byhydrogen bonds, nature of sugar phosphate backbone, projection of bases, hydrophobic interaction between stacking of base pairs,tortional twist, thermodynamic compatibility. Structural features of Z-DNA and A-DNA and important differences between B, Z andA forms and their importance.ssDNA: (ss = single strand) the nature and properties of ssDNA and its structural form.tsDNA: (ts = triple strand) Structural features of tsDNA, sequences responsible for forms, inter and intra-strand triple helices anddisease due to tsDNA formation.qsDNA: (qs = quadruplex strand): Characteristic features of four stranded DNA, basis for four stranded forms, the structure and therole of telomeric DNA. Supercoiled DNA: Structural features of negative and positive supercoiling. Role of topoisomerases inmaintaining the supercoiling.Other forms of DNAs: Structural distinguishing features of Cruciform DNA, Flexible DNA, Curved DNA and their importance.

08 hrs

Unit - IIIReplication of DNA:

20

Replication of single stranded DNA: Mechanism of ssDNA replication of Ø x174 and M13 phage; structural features of origin,primosomal assembly and primosomal complex, factors and DNA-polymerases , replication mechanism, and the enzymes involved.Replication of Prokaryotic DNA: Replicons, number of replicons per genome. Structural feature of E.coli genomic Origins (ORI)and Termination regions (TER). Factors and characteristic features of different DNA-polymerases involved in replication apparatus(replisome); subunits and their functions, primosomal assembly, primer formation, assembly of subunits into functional DNA-polymerase-III. Mechanism of replication: Replication of leading strand and replication of lagging strand, fidelity, rate, and regulationof replication in bacteria. Repair of replication error. 09 hrs

Unit - IVReplication of Eukaryotic DNA: Organization of chromosomal replicons, number and structural features of eukaryotic origins withexamples from yeast plasmids and yeast chromosomes. Characteristic features of DNA polymerases – alpha and delta, their chemicalcomposition and associated subunits. DNA-Pol associated factors : RF-A, RF-C, PCNA, MF-1 and their role. Mechanism ofreplication : Replication of telomeric DNA – telomerase, components and the mechanism.

07 hrs

Unit – VGenetic Code: The language of information transfer, genetic and biochemical analysis of genetic code, Features of genetic code andevolution of genetic codeDNA damage and Repair: Causes for DNA damage. Kinds of errors in DNA: natural, chemical and radiation, their effects asheritable mutations, frequency of mutations, kinds of mutations and their importance in evolution. Repair mechanism of DNAdamage, genes and the factors involved in repair mechanism.

07 hrs

21

Unit - VIIChemistry and Structural forms of RNA: Characteristic features and classification of RNA. Genetic RNA: A brief review of RNAviruses, structure and replication of RNA genome: Picorna virus, Rabies virus and Retrovirus (HIV).Viroidal and virusoidal RNA: Structure and characteristic features of viroids and their RNA. Concept of ribozyme and mechanismof ribozyme action. Characteristic features of few satellite viral RNAs.Ribosomal RNAs: Structural features of prokaryotic and eukaryotic rRNA systems, size, kinds of rRNA and base modifications.Precursors and processing, assembly and organization of the rRNA into ribosomes, important structural motifs and their functions

06 hrs

Unit - VIIItRNA: Structure and nature of prokaryotic and eukaryotic tRNAs, base modifications, organization of tRNA into 3-D structure,different motifs and their functionl features. Aminoacylations, aminoacyl-tRNA synthetases and their features, concept of secondcodon, mechanism of aminoacylation of tRNA. Anticodons and operation of Wobble mechanism and its importance. PrecursortRNAs and processing of tRNAs.snRNAs, scRNAs and ncRNAs: Structure, kinds, genes, their associate proteins and the function of snRNAs, scRNAs and snoRNAsin precursor RNA processing miRNAs, siRNAs and tmRNAsmRNAs: Structural features of prokaryotic and eukaryotic mRNA. Concept of introns and exons, exons as protein motifs and theirorigin and evolution. 07 hrs

Reading References:1. David. A. Micklos, Greg.A. Freyer and David A. Crotty, (2003). DNA Science A First Course, 2nd edition, Cold Sprind Harbor

Laboratory Press, New York.2. Flint. S.J, L.W. Enquist, R.M. Krug, V.R. Racaniello and A.M. Skalka, (2000) Principles of Virology, ASM Press, Washington

D.C3. Gerald Karp (1996). Cell and Molecular Biology – Concepts and Experiments. John Wiley and Sons, Inc., New York.4. Gupta, P.K. (2004). Cell and Molecular Biology. Rastogi Publications, Meerut.5. G.M. Malacinski and D. Friefelder (2005). Essentials of Molecular Biology vol – I, Jones and Bartlet Publishers.6. Griffiths AJF, H.J. Muller., D.T. Suzuki, R.C. Lewontin and W.M. Gelbart (2000). An introduction to genetic analysis. W.H.

Freeman , New York7. Harvey Lodish, Arnold Berk, Paul Matsudaira, Chris A. Kaiser, Monty Krieger, Matthew P. Scott, S. Lawrence Zipursky and

James Darnell. (2003). Molecular Cell Biology, W.H. Freeman and Company, New York.

22

8. Lewin B. (2003). Genes VIII Oxford University Press. Oxford9. Miglani G.S. (2002). Advanced Genetics, Narosa Publishing House , New Delhi.10. Watson, Baker, Bell, Gann, Levine and Losick. (2006). Molecular Biology of the Gene, 5th edition, Pearson Education.11. Watson, J.D. T.A.Baker, S.P. Bell, A.Lann. M.Levine and R.Losick. (2004). Molecular Biology of genes, V edition, Perason

Education RH Ltd., India

MLB – 202 GENETIC ENGINEERING52 hrs

Unit – IIntroduction: Phases of genetic studies, historical account, definition and objectives

02hrsUnit – IIMolecular tools, restriction and modifying enzymes, other nucleases, polymerases, ligase, kinases and phosphatases. Isolation andpurification of DNA and RNA. 06 hrsUnit – IIICloning Vectors: Plasmids, phages, cosmids, artificial chromosomes and expression vectors. Cloning hosts: E.coli, Saccharomyces,plant and animals cells. Cloning protocols: General transformation, electroporation, pofectamine, gene-gun method.

06 hrs

23

Unit – IVGene isolation: Methods of construction of genomic and cDNA libraries, direct cDNA cloning, positional cloning. RFLP mapping,chromosome walking and jumping 06 hrs

Unit – VScreening and characterization of clones: Molecular probes and methods of labelling, principles of hybridization and hybridizationbased techniques (colony plaque, Southern, Northern and in situ hybridizations). Expression based screening,

07 hrs

Unit – VIDNA sequencing: Maxam and Gilbert’s method, Sanger’s method, Automated DNA sequencing, Capillary gel electrophoresismethod and DNA sequence analysis. 05 hrs

Unit – VIIPolymerase chain reaction: Mechanism, methods-RT-PCR, RAPD, AFLP, ISSR, real time PCR and its application

08 hrs

Unit – VIIIDNA Engineering techniques: Gel electrophoresis of nucleic acids (denaturing and native), gel electrophoresis of proteins (SDSPAGE), pulse-field gel electrophoresis of DNA, oligonucleotide synthesis, Microarray technology, RNAi technology, blotting ofmacromolecules, Promoter characterization : Promoter analysis through reporter genes, electrophoretic mobility shift assay, DNA foot– printing, DNA fingerprinting, Mutagenesis: Site directed mutagenesis, Transposon mutagenesis, Construction of knock-out mutants,Gene transfer techniques (Physical and vector mediated methods), Transfection of cells: Principles and methods, Germ linetransformation in Drosophila and transgenic mice : Stratagies and methods, In vitro translation 12 hrs

24

Reading Reference1. Brown,T.A. (1995). Gene Cloning: An introduction . Chapman and Hall, London2. Glick,B.R. and Pastenak, J.J. (1994). Molecular Biotechnology: Principles and applications of recombinant DNA. ASM Press,

Washington D.C.3. Kreuzer, H. and A. Massey. (2001). Recombinant DNA and Biotechnology. ASM press, Washington DC4. Lodish, Berk, Zipursky, Matsudira, Baltimore and Darnell. (2005) Molecular cell Biology, W.H.Freeman and Company5. Mathew R Walker, Ralph Rapley. (1997) Route maps in Gene Technology, Blackwell Publishing.6. Micklos, D A, Freyer GA and Crotty D A (2003) DNA Science, Second edition, Cold Spring Harbour Laboratory Press, New

York.7. Primrose, S.B., R.M. Ywyman and R.W. Old. (2006). Principles of Gene manipulation and tenomics Seventh edition,

Blackwell Science,U.K.8. Watson, Baker, Bell, Gann, Levire and Losick, (2005), Molecular Biology of the Gene, 5th edition, Pearson Education

Publication.

25

MLB – 203 GENETICS AND CYTOGENETICS52 hrs

Unit - IChromosomal organization: Chromosome number, size, morphology, chromatid, centromere, telomere, secondary constriction,chromomere, heterochromatin. Special chromosomes: Lampbrush chromosomes, Polytene chromosomes and Accessorychromosomes. 08 hrsUnit -IIMolecular mechanism of cell division: Molecular organization of centrosome and spindle, dynamic instability of microtubules,kinetochore and microtubule interaction, synaptic pairing, chromosome movements during metaphase and anaphase, spindle withoutchromosomes and cytokinesis. 06 hrsUnit - IIIMolecular basis of sex determination: Molecular basis of sex determination and dosage compensation in Caenorhabditis elegans,Drosophila and human. 04 hrsUnit -IVSomatic cell genetics: Tissue culture and cell fusion, human and rodent cell hybrids and alignment of gene to chromosomes.Construction of fine scale map. 05 hrsUnit -VImprinting of genes, chromosomes and genomes: Definition, exception to the principle of equivalence of reciprocal hybrids,pronuclear transplantation experiments in mouse, uniparental chromosomal disomies in mouse, human triploids, sex determination inCoccids, X-chromosome inactivation in marsupial females and molecular mechanisms. 07 hrsUnit - VIMutations: Key concepts. Forward mutations: At DNA level – Transition and Transversion; At protein level – Silent, missense,nonsense, frameshift mutations, Reverse mutations: Exact reversion, equivalent reversion. Intragenic suppressors: Frameshift ofopposite sign and second site within a gene, second site missense mutation. Extragenic suppression: Nonsense suppression, missensesuppression, Frameshift suppression, Physiological suppression. Lethal mutation, loss and gain of functional mutations, amorphic,hypomorphic and isoallelic mutations. Chromosome based mutations

26

Chemical mutagens: Base analogues: Nitrous acid, hydroxylamine, hydrazine, alkylating agents. Detection of mutations: Bacteria –replica plating technique, Ames test; Drosophila – Sex – linked recessive lethals, autosomal recessive lethals, dominant lethal test;Small mammals – Micronucleus test, dominant lethal assay and host mediated assay. 10 hrs

Unit - VIIBiochemical genetics of Neurospora: Tetrad analysis and linkage detection in Neurospora, two point and three point crosses,chromatid and chiasma interference. Induction and detection of biochemical mutations in fungi, mitotic recombination in Neurosporacrassa and Aspergillus nidulans. Transposable elements in fungi and gene conversion.Biochemical genetics in Algae: Fine structure of an algal cell, algal chromosomes and ploidy. Chlamydomonas – unordered tetradanalysis – recombination and mapping. Nucleocytoplasmic interactions and gene expression in Acetabularia and plastid inheritance.Biochemical genetics of Protozoa: Ultrastructure of a protozoan cell. Reproduction and recombination in Plasmodium. Expressionof virulence factors in Plasmodium. 07 hrsUnit – VIIIMolecular population genetics: Patterns of change in nucleotide and amino acid sequences, molecular evolution, molecular clockand emergence of Non-DarwinismMolecular phylogenetics: Construction of phylogenetic tree. Phylogenetic inference : Distance methods, parsimony methods andmaximum likelihood method. Phylogenetic considerations based on nucleotide and amino acid sequences.

05 hrs

27

Reading references:

1. Alberts, B, Johnson, J Lewis, M.Raff, K Roberts and P.Watter. (2002). Molecular Biology of the cell IV eds Garland Science,New York

2. Beatty,, B.S. Mai and J. Squire (2002). FISH. Oxford Univ. Press, Oxford3. Chatterjee, R.N. (1998) Mechanisms and Evolutionary origins of gene dosage compensation. In Genome analysis in

Eukaryotes. Eds. R.N. Chatterjee, and L.Sanchez. Narosa Publishing House, New Delhi4. Dobzhansky Th., F.J. Ayala,, G.L. Stebbins and J.M. Balentine, (1976). Evolution. Surjeet Publication, Delhi5. Futuyma D.J. (1986). Evolutionary Biology, Sinauer Associates, INC, Sunderland6. Hollander A (Editor) (1971-76) Chemical mutagens: Principles and methods of their detection. Vols.1-3, Plenum press New

York7. Lodish, Berk, Matsudaira, Kaiser, Krieger, Scott, Zipursky and Darnell (2005) Molecular Cell Biology, 5th Editon, W.H.

Freeman and Company, NY8. Macgregor, H.C. (1993). An introduction to Animal Cytogenetics, Chapmann and Hall, London9. Singh, B.D. (2003). Genetics. Kalyani Publishers, New Delhi.10. Smith, J M (1998). Evolutionary Genetics, Oxford Univ. Press, Oxford11. Snustad D P, M J Simmons and J P Jenkins. (1997). Principles of Genetics. John Wiley and Sons, INC12. Verma R.S. (Editor) (1988) Heterochromatin: Molecular and Structural aspects. Cambridge University Press, Cambridge.

28

MLB - 204 BIOSTATISTICS, COMPUTER APPLICATIONS AND BIOINFORMATICS52 hrs

BIOSTATISTICS:Unit – IPopulation and sample, variable, constant and parameters, types of data, summarization of data through frequency distribution,histograms, bar diagrams, and cumulative frequency curve. Measures of central tendency: Mean, median and mode. Measures ofdispertion: Variance, standard deviation, co-efficient of variation, quartiles, percentiles and their graphical determination. Skewness-Pearson’s and Bowley’s measures. 05 hrs.

Unit-IIBivariate Data: Scatter plot, correlation, co-efficient, properties, fitting linear regression, regression co-efficient and interpretation.Probablity: Rules, conditional probability, independence of events, Bayes formula.Sampling: Sampling methods, standard errors of sample means. 05 hrs

Unit-IIIHypothesis Testing: Basic concepts, large sample tests for proportion, equality of two proportions and means of normal population,confidence intervals for mean and proportion, student’s – test, chi-square test of independent of attributes. ANOVA for one way andtwo way classification. Dunnett’s and Ducan multiple comparision test. 06 hrs

COMPUTER APPLICATIONS:Unit-IVComputer fundamentals, computer organization, computer hardware and computer software, programming languages, operatingsystem, input and output devices, computer memory. 05 hrs

Unit-VWord processing, spread sheet calculations and databases. An overview of MS office. Computer networks, internet and itsapplications. 03 hrs

29

BIOINFORMATICS:Unit - VIAn overview: Applications of Bioinformatics, Data available from various sources, data integration and analysis.Tools of bioinformatics: Web based softwares, commercial softwaresMolecular Biology and Bioinformatics: Systems approach to the central dogma of molecular biology. Definitions of various termsand their meaning and relation to bioinformatics.Molecules of Information: A brief account of nucleic acids, DNA, RNA, synthesis if nucleic acids, genes, organization of the samein chromosomes, cloning methods, PCR and DNA sequencing and concept how and in what form the information is encrypted.

10 hrs

Unit - VIIProteins: Introduction to protein structure : Secondary and tertiary structure prediction, protein 3D – structure analysis, proteinmodeling. Principles of homology and comparative modelingBiological database: Types of database, network and database, biological significance of database

06 hrs

Unit – VIIIMolecular mapping: DNA sequencing, gene mapping, application of mapping, DNA microarrays, design and data analysis,algorithm in assembling sequence fragments. QTL mapping, candidate gene mapping, physical mappingProteomics: Proteomic analysis, and tools used, metabolic pathways, genetic network, network properties, simulation of pathway.

Phylogenetic analysis: Concept of trees, phylogenetic trees, distance matrix methods, character based methods, evaluation methods.Working with phylogenetic trees.Prediction methods: Use of patterns, methods and tools to predict genes. Prediction of protein structure. Introduction to humangenome project. Pharmacogenomics and drug designing. 12 hrs

Reading references:1. Attwood, T.K. and Parry-Smith, D.J. (1999). Introduction to Bioinformatics, Pearson Education2. Bergeron. (2005). Bioinformatics computing. Pearson Education.

30

3. Campbel, (2004). Discovering Genomics, Proteomics and Bioinformatics, Pearson Education.4. Daniel. (2002). Biostatistics, John Wiley, ISE.5. Higgins, D and W.Taylor (2000). Bioinformatics Sequence, Structure and databanks , Oxford University Press, Oxford6. Leibler, D.C. (2002). Introduction to Proteomics, Tools for the new biology, Humana Press, New Jersey7. Leon and Leon (1999). Information Technology, Leon and leon Publications, Chennai.8. Lesk, A.M. (2002). Introduction to Bioinformatics, Oxford University Press, Oxford9. Misener, S and S.A. Krawetz, (2000). Bioinformatics: Methods and protocols , Humana Press, New Jersey10. Mount, D.W. (2001). Bioinformatics: Sequence and genome analysis. Cold Spring Harbour LaboratoryPress, Cold Spring

Harbour New York11. Primrose S.B., Twyman, R.M. (2006). Principles of Gene Manipulation and Genomics, 7th edition, Blackwell Publishing.12. Rashidi, H.H. and L.K. Buchler (2000). Bioinformatics Basics: Applications in Biological Science and Medicine, CRC Press,

New York13. Shortliffe, E.H. and L.E.Perreault (Eds.) (2001). Medical informatics: Computer applications in health care and Biomedicine.

Springer-Verlag, N.Y.14. Zar, H.A. (1999). Biostatistical analysis , Person Education

SECOND SEMESTER PRACTICALSMLB – 205 NUCLEIC ACIDS AND GENETIC ENGINEERING

PART-A1. Extraction of genomic DNA from plants, animals and microorganisms2. Restriction digestion of DNA3. Agarose gel electrophoresis of restriction fragment4. PCR amplification of DNA5. Extraction and separation of RNA

PART-B6. Preparation of cDNA library

31

7. Cloning and subcloning8. Screening of cDNA library9. Blotting techniques: Western blotting and Southern blotting10. DNA fingerprinting : RAPD assay11. Restriction site mapping12. DNA sequencing.

MLB – 206 GENETICS AND CYTOGENETICSAND BIOSTATISTICS, COMPUTER APPLICATIONS AND BIOINFORMATICS

PART-A1. Culture of Drosophila .2. Studies on inversion polymorphism in Drosophila3. Bacterial culture and preparation of competent cells4. Identification of mutants in Drosophila5. Studies on phylogenetic trees6. G and C banding techniques

PART-B7. Statistical analysis such as descriptive statistics, regression, t-test, Analysis of Variance, multiple regression using statistical

software such as SPSS, MINITAB8. Tests of significance based on Normal, t, Chi-square and F-distributions9. Correlation and regression

32

10. Spread sheet and statistical calculations using MS, EXCEL11. Internet, E-mail, browsing and searching12. Practical application of BLAST13. RNA Folding14. Identification of genes in genomes15. Multiple alignment of sequencing

33

SYLLABUS FOR III AND IV SEMESTER M.Sc., MOLECULAR BIOLOGY

SCHEME OF STUDY AND EXAMINATIONSEMESTER III

PaperCode Paper Title of the Paper

(Hrs / week) Total No. ofHrs/

Semester

Examination

Theory Practical Duration(Hrs)

Max.Marks

ContinuousEvaluation

TotalMarks

MLB301 I Biochemistry – II 4 -- 52 3 80 20* 100

MLB302 II Molecular Biology – I 4 -- 52 3 80 20* 100

MLB303 III MicrobialBiotechnology 4 -- 52 3 80 20* 100

MLB304 IV Molecular Biology ofDevelopment 4 -- 52 3 80 20* 100

MLB305 Pract.I Of paper I & II -- 8 104 4 40 10** 50MLB306 Pract.II Of paper III & IV -- 8 104 4 40 10** 50

Total Marks 500

* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical record + 5 marks for visit to Industries/Laboratories

34

SCHEME OF STUDY AND EXAMINATIONSEMESTER IV

PaperCode Paper Title of the Paper

(Hrs / week) Total No. ofHrs/

Semester

Examination

Theory Practical Duration(Hrs)

Max.Marks

ContinuousEvaluation

TotalMarks

MLB401 I Immunology 4 -- 52 3 80 20* 100MLB402 II Molecular Biology – II 4 -- 52 3 80 20* 100MLB403 III Genomics and Proteomics 4 -- 52 3 80 20* 100

MLB404 IV Plant & AnimalBiotechnology 4 -- 52 3 80 20* 100

MLB405 Pract.I Of paper I & II -- 8 104 4 40 10** 50MLB406 Pract.II Of paper III & IV -- 8 104 4 40 10** 50

Total Marks 500

* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical record + 5 marks for visit to Industries/Laboratories

1. TOUR: Tour marks should be considered under Continuous Evaluation.a) There will be a Compulsory Industries / Laboratories visit in all the semesters as per relevance to the subject.b) There will be a compulsory Tour 5 to 6 days to any of the industries outside Bangalore in IV Semester.

35

THIRD SEMESTER

MLB 301: BIOCHEMISTRY - II52 hrs

Unit I:Photosynthesis : Introduction, photosynthetic apparatus – structure, organization, LHC molecules and antenna molecules. Lightreaction - cyclic and non-cyclic photophosphorylation. Biochemical reactions –C4 and C3 pathways, CAM Pathway, Energetics ofCalvin pathway. Bacterial photosynthesis. Photorespiration - organells involved, biochemical pathway and its significance.

8hrsUnit II:Carbohydrate metabolism – Glycogen – degradation and biosynthesis. Glycolytic pathway, regulation of glycolysis,gluconeogenesis, hexose interconvertions. HMP pathway.5hrsUnit III:TCA cycle – pathway and energetics. Alternate pathways – glucuronate pathway and glyoxylate pathway5hrsUnit IV:Lipids: Definition, Classification, Structure and biological role of Fatty acids, Acyl glycerols, Phospholipids, Glycolipids, Steroids,Prostaglandins, Thromboxanes and Leukotrienes. 6hrsUnit V:Lipid Metabolism: Degradation of triacyl glycerols and phospholipids. Oxidation of saturated, unsaturated fatty acids. Alternateroutes of fatty acid degradation. Synthesis of triacylglycerols, phospholipids and biosynthesis and degradation of cholesterol.Metabolism of Prostaglandins and related compounds. 8hrsUnit VI:Thermodynamics – Concept of enthalpy and entropy, free energy and chemical potential. Free energy change, significance of freeenergy change. Laws of thermodynamics and their applications 4hrsUnit VII:

36

Biological oxidation: Basic concept of metabolic energy capture and transfer. High energy compounds – definition, examples.Stages in the production of energy. Biological redox couplers, Redox potentials, Oxidation-reduction reaction free energy changes inelectron transfer reactions. 8hrsUnit VIII:Mitochondrial electron transfer system – topology of electron carriers, chemical nature of electron carriers, sequence of electroncarriers, isolation of mitochondrial complexes, reconstitution experiments and study of specific inhibitors of ETC. Oxidativephosphorylation – ATP synthesizing system – F0-F1 ATPase. Coupling of electron transfer to ATP synthesis, study of the effects ofuncouplers, inhibitors and ionophores, mechanism of oxidative phosphorylation. 8hrs

References:

1. Bob B. Buchanan, Biochemistry and Molecular Biology of Plants (2004), Wilhelm Guissem and Russel L. Jones, I.K.International Pvt. Ltd, New Delhi

2. Conn E.E. and stumpf, G. Bruenning, R.H. Boi (1987), Outline of Biochemistry by John Wiley & Sons, New York3. David Rawn, J, (Ed.), (1989), Biochemistry Neil Patterson Publishers4. Donald and Judith Voet (2005), 2nd edition, J.Niley & Sons, Biochemistry5. Hall, D.O and K.K.Rao (Eds), (1999),Photosynthesis; 6th Ed., Cambridge University Press.6. Jocelyn Dow, Lyndsay Gordon, and Jim Morrison, Biochemistry: Molecules, cells and the body7. Lars Garby and Paul S Larsen (Eds), (1995), Bioenergetics and its foundation; Cambridge University Press.8. Lehninger et al., (Eds), (1997), Principles of Biochemistry; 2nd ed., Worth Publishers.9. Mathews, van Holde, and Ahern, (1995), 2nd edition, Biochemistry (Companion Web Site) with 28 chapters.

Benjamin/Cummings Publishing Company, Inc.,10. Peter R Bergethon (Ed), (1998), The Physical Basis of Biochemistry; Springer Verlag.11. Thomas Devlin (Ed),( 2002),Biochemistry with clinical correlations; Wiley-Liss.12. Tiaz and Zeiger, (2003). Plant Physiology, 3rd edition, Lincoln Taiz and Eduardo Zugier, Parima Publishing Corporation, New

Delhi13. Voet, D and Voet, J.G. (Eds.), (1999), Biochemistry;3rd ed., John Wiley and Sons.

37

MLB 302: MOLECULAR BIOLOGY – I52 hrs

Unit I:Concept of Gene: Kinds of genes, gene numbers, functional genes, crypticgenes, pseudo genes, processed genes, overlapping genes..Gene structure: Structural organization of genes in prokaryotes and eukaryotes-regulatory elements of the genes (proximal or internal,including promoter, operator, activator and enhancers), coding and terminal regions of the gene. 6hrsUnit II:Prokaryotic Gene Expression:

Transcriptional Apparatus: RNA polymerase structure, function; sigma factors and their role; and the mechanism oftranscription, initiation, elongation and termination.

Genetic regulation of sporulation in B.subtilis, role of sigma factors in sporulation.Gene regulation in prokaryotes: Lac operon, Tryptophan operon and Histidine operon -mechanismGenetic regulation in lambda phage: lytic and lysogenic pathway, co-repressor, transcriptional terminators and antiterminators,expression and regulation of early and late genes, site specific recombination. 8hrsUnit III:Eukaryotic Gene Expression: Characteristic features of RNA polymerases - RNA polymerase-I, II and III.RNAP-I promoter: rRNA gene clustering, structural organization. Regulatory region (core sequences and upstream controlelements), coding and terminal regions, Role of transcriptional factors (TFs). Mechanism of transcription-initiation, elongation andtermination. 7hrsUnit IV:RNAP-II promoter: Structural organization of regulatory, coding and terminal regions of house keeping genes; Genes in response tostimuli-light, chemicals and hormones, and genes regulated in stage and tissue specific manner.Characterization of TATA box, upstream elements, InR elements, enhancer elements, activator elements, response elements, silencerelements/repressor elements; downstream InR elements their position, structure and their function.Transcriptional factors (TFs), activating factors, enhancer proteins and repressors and RE binding factors and their DNA bindingsequence elements and composition of factors in different tissue types- general TFs, special TFs, activators and enhancers, repressors/silencers, mediator complexes response element binding factors.

38

Concept of activators, activator domains, co activators and mediators involved in gene expression.9hrs

Unit V:DNA binding proteins- Helix turn Helix, Helix loop helix,, Helix turn beta, Zinc finger, leucine zipper , homeodomains, beta barrels,bZIP and bHLH domains, mode of their binding and regulation of gene expression. 5hrsUnit VI:RNAP-III promoter: Regulatory elements, (internal promoters), coding and terminal regions of 7sLRNA gene, tRNA genes, and5SrRNA genes; Enzyme, transcriptional factors and assembly of TFS and the mechanism of transcription. 4hrsUnit VII:Regulation of gene expression at transcriptional level :Modes of regulation- Negative and positive type and silencer type of regulation. H2B1Histone gene in sea urchin, globin gene, Galgene regulation in yeast cells, Interferon regulated gene in animal cells, hormone regulated gene expression in animal cells, lightregulated gene expression in plants; silencing of gene activity in Wilmes tumor and yeast mating types . GA induced, auxin induced,ethylene and abscissin induced gene expression. 6hrsUnit VIII:Gene expression and Chromosome remodeling: Structural remodeling during and after transcription; effect of Histones ontranscription of class II genes, changes in nuclear positioning, Dnase-1 mapping, Histone acetylation-deacetylation, methylation anddemethylation, phosphorylation and dephosphorylation. Role of SW1/SNF and NURFs in remodeling of chromosomes. Organizationin the salivary gland chromosomes of Drosophila and lampbrush chromosomes of Xenopus laevis. Role of chromosomal remodelingcomplexes. 7hrsReferences :

1. Benjamin Lewin (2004), Gene VIII, Published by Pearson Prints Hall, Pearson Education inc.Upper saddle River, NewJerssey-07458

2. Bruce Alberts, Julian Lewis, Alexander Johnson, J. Lewis, M. Raff (1994), Molecular Biology of the Cell, Garland PublisherInc., New York

3. Buchnan and Grussem et al, (2000) Biochemistry and Molecular biology of Plants by 5th edition, Oxford University Campus4. Buchnan B.B., W,Gruissem et al and R.L.Jones (2004) Biochemistry and Molecular biology of Plants by I.K. Internationla

Pvt., Ltd., New Delhi5. Cooper, G M The cell : A molecular approach. 2nd edition, (2000), ASM Press, Washington

39

6. Eduardo Diego Patricio De Robertis, EMF De Robertis (1988), Cell and molecular biology, International Ed. Inst. Med. Ltd7. Gerald Karp (2003), Cell and Molecular Biology, 3rd edition, John Wiley & Sons Publishers.(Concepts and Experiments)8. Glick B.R. & J.J.Pasternal, (1994), ASM Press, Washington,D.C.Molecular Biotechnology9. Gupta, PK, (2004) Biotechnology and Genomics, Rastogi Publishers, Meerut10. Gurbachan S. Miglani(1998), Dictionary of Plant Genetics and Molecular Biology- 348 pages11. John Marsten Walker, Ralph Rapley (2000), Molecular Biology and Biotechnology

MLB 303 : MICROBIAL BIOTECHNOLOGY52hrs

Unit I:Use of microbes in industry and agriculture:Production of organic compounds by fermentation- Latest biotech methods employed in the production of Ethanol, Acetone andButanol, Gluconic acid, antibiotics and Enzymes;

Methods and protocols for each of the mentioned products:Shake flask method, Bioreactor method, solid state fermentation method, aerobic and anaerobic fermentation method, immobilizedcell bioreactor method; Media used, culturing under optimal conditions; Isolation and maintenance of microbial strains, and geneticimprovement of strains by genetic engineering and mutation modes: down stream processing-purification of products by adsorptionchromatography, affinity chromatography, freeze drying, and in situ recovery methods. 8hrsUnit II:Biotransformation methods: Biotransformation of D-Sorbitol to L-Sorbose, Biotransformation of antibiotics, steroids and sterols.Microbes used for recovery of metals and land reclammation from toxic wastes and chemicals, Bio-insecticides, Bioherbicides,Biofertilizers. Employment of genetically engineered microbes (GEMS):Expression of heterologous genes- completing a partial pathway giving new product. Employing transfer of entire set of genescontrolling entire path way of metabolism or creating new products and new reactants, redirecting the metabolic pathway, advantagesand disadvantages and limitations. 6hrsUnit III:

Commercial scale production by recombinant microbes:

40

Production of Restriction enzymes, DNA modifying enzymes- down stream processing methods, Synthesis of Ascorbic acid,Synthesis of Indigo, Synthesis of Amino acids, Synthesis and improvement of production of common and novel Antibiotics,Synthesis of polypeptide antibiotics, Synthesis of Biopolymers-Xanthum gum, Melanin, Animal adhesives; Synthesis of Rubberproducts.Large scale production of proteins by recombinant microbes:Principles of fermentation cultures, High density cultures. Use of bioreactors for large scale fermentation, harvesting, cell disruptionand downstream processing. 7hrsUnit IV:Production of enzymes: Sources and Principles and use of enzyme reactors: Cell culture, large scale production and purification ofthe products; quality control.

Extreme ezymes, Bispecifc enzymes, Ribozymes and Endozymes.Enzyme immobilization and its application: In detergent industry, leather industry, wool industry. Production of glucose fromCellulose; application in food , dairy, beverage and medicinal industry.

6hrsUnit V:Production of single cell proteins: Large scale production and application. Spirulina maxima (Cyanobacteria), Kluyveromycesfragilis (yeast), Candida lipolytica (yeast), Chaetomium cellulolyticum (fungus), Methylophilus methylotrophus (bacterium);Yeast expression systems for production of therapeutical agents: Hepatitis-B surface antigen, Hirudin. Human platelet derivedgrowth factor B, Bovine Lysozyme C2. 6hrsUnit VI:Bioengineering of proteins and its application: Outline of bioengineering of macromolecules a multidisciplinary approach; sitedirected mutagenesis and computer aided molecular modeling,Steps involved in protein engineering and protein modeling to the desired needs, such as in vitro mutagenesis or synthesis of entiregene, multienzyme with bi or poly functions by gene fusion, chemical modification of existing enzymes; enzymes with characterssuch as thermo stable, work under non-aqueous solvents, increased Vmax, low Km and high specificity, tolerant to bleach anddetergents. 8hrsUnit VII:Development of immunotoxins as magic bullets: Use of Ricin a plant toxin as immunotoxins; drug designing for blocking enzymeactivity, blocking receptors from binding to target molecules, for blocking nucleic acid synthesis in cancer or specific cell types.5hrs

41

Unit VIIIEnvironmental Biotechnology:Brief account of pollution control-use of cleaner technology, treatment of industrial effluents, toxic sites and land restoration throughalternate aforestation, Mycorhizae,; Bioremediation- cleaning of land and water of oil herbicides, biopesticides by bioengineeredmicrobes, solarization and compatible Biofertilizers, and restoration, conservation of biodiversity-by in situ and ex situ conservationtechnology, species conservation,, environment and energy- use of alternate fuel sources, use of renewable sources such as biomass,fuel generating microbes. 6hrs

References :

1. Atlas R.M. (1998) Microbiology : Fundamental and application (IIeds) Mac millan Publishing company2. Bruijin et al ., (1998). Bacterial genomes, Chapman and Hill3. Dale J.W. (1994). Molecular genetics and Bacteria. John Wiley and sons4. Hayes W. (1970). The genetics of Bacteria and their viruses. The English Book society of Blackwell Scientific Publication,

Oxford5. Glick, Molecular Biotechnology , MSM pub, B.R. Glick & J.J.Pasternak, (1994), ASM Press Washington, D.C.6. Hunderson et al., (1999). Cellular Microbiology Wiley7. Lewin B (2002). Genes VIII, Oxford8. Prescot L.M., Hanley, J.P. and Klein, D.A. (1999). Microbiology, WCB Mc Graw Hill , Con MY9. Roger L.P., John T., Knowler and Daviol P. Leadr. (1992). The Biochemistry of Nucleic acids, 11th edition. Chapmann and

Hall10. Samuel Singer (2001). Experiments in Applied Microbiology, Academic Press New York.11. Stnely R. Maloy, John E. Cronan, Jr., David Freifelour (1994). Microbial genetics. Jones and Barlett Pub. Bosten.12. Sullia S.B. and S.Shantharam (1998). General Microbiology , Oxford IBH Publishing Con, New Delhi.

MLB 304: MOLECULAR BIOLOGY OF DEVELOPMENT52 hrs

Unit I:

42

Plant System: Biochemical and molecular basis of Growth and differentiation;Concept of growth and differentiation vs. morphogenesis; Site and cell types involved in growth and differentiation. Kinetics ofgrowth, Spatial and material basis of growth and growth trajectory.Polarity fixation: A brief account of polarity development in a fertilized egg cell; and determination of polarity of apices in plantsystems - Red algae. 6hrsUnit IIGenetic basis: Identity of genes that control development in Arabidopsis; stages of development from embryo, axial pattern, apicalbasal pattern, radial pattern, tissue identity shoot promeristem, and requirement of gene expression for the development of the abovestructure in Arabidopsis. The role of Homeobox genes (concept of homeobox genes vs. homeodomain proteins).Interaction of Phytohomones: Interaction of auxins with cytokinins in inducing shoot formation, inhibition of Auxin induced newroot formation by cytokinins, Inhibition of GA inducted expression of genes by Abscisic acid, synergistic effects of Auxin andEthylene, synergistic effects of Auxins and Cytokinins, synergistic effects of Ethylene and Abscisin, overall effects of Phytohormoneson each other and their effects on plant development. 8hrsUnit III:Flowering: Characters of shoot meristems that change into floral meristems and development of four types of floral organs, theirrelated genes. Changes in shoot apex, phase changes, Photoperiodism, vernalization effect on growth and flowering.

Phytochrome induced responses: Biochemistry of phytochrome, its reponse to light and it effect on plant and floral development.Phytochrom induce responses: Phytochrome induced whole plant responses, biological clock, role of phytochrome in daily circadianrhythm.Phytochrome and gene expression: Different responses of gene expression to Phytochrome A and Phytochrome B, Phytochromeregulation of gene expression- role of cis-acting elements, response elements and trans-acting factors; mechanism of action throughmultiple signaling pathways; Role of cryptochromes, inhibitor genes of Photo morphogenesis, such as DET and COP genes.Biochemistry of signaling pathway of flowering, identification of hypothetical florigin, Chemical basis of flowering substance, site ofsynthesis, transport, distribution and site of action and mechanism of action. 10hrsUnit IV:Molecular genetics of flowering: a general account of genes that regulate floral organ development; Arabidopsis as model system ,influence of hormones and photoperiod on floral development; Floral organ identity genes, cadastral genes and meristems identitygenes, FLORICULA,APETALA (APA 1, APA 2, APETALA3), leafy (LFY), EMF ,DEFICIENS and AGAMOUS genes. Homeoticmutations and their effect on floral organs. Role of MADS box genes in floral organ identity. The role of CRY 1 and CRY 2 genes in

43

Photoperiodism Identity of Homeotic genes that control organ identity response factor. ABC model of determining floral identity,effect of hormones and photoperiod on floral development. Regulation of juvenility by TOEPOD genes. 8hrsUnit V:Tissue Engineering – Renewal of adult tissues such as epidermal cells, mammary gland cells, photoreceptor cells in Retina, Gut-intestine cells, Alveolar cells in lungs, Liver cells, Blood-endothelial cells, Muscle cells,versatile none cells and fibroblast multipotentcells, stem cells from basal lamina; application and prospects. 5hrsUnit VI:Caenorhabditis elegans: Genes and gene products involved in development. Development from zygote to adult, cell lineage, dauerlarval stages. Programmed cell death during development, development of transgenic worms, use of gene knock out experiments tounderstand the mechanism and its effects. Control of cell lineage –role of Lin genes and regulated PCD in development5hrsUnit VII:Drosophila- Life cycle, Oogenesis- development of oocyte, role of follicle and nurse cells in the programming of the egg cell.Fertilization and the trigger of a cascade of developmental activation, positioning of specific mRNA, role of maternal genes, Gapgenes, pair rule genes, segment polarity genes and Homeobox genes during development., structural organization, developmentalgenes and their regulation, syncytial blastoderm, cellular blastoderm, gastrulation stages, polarity fixation, segmentation , regulation ofgene expression . A general account of Homeobox genes and their role in identifying body organs.

6hrsUnit VIII:A brief account of Development of higher systems- from egg to multicellular level and early development stages and the genesinvolved in development; Mus-musculus as a laboratory model, Use of transgenic mice and gene knock out in understandingdevelopmental pattern of higher animals. 4hrs

References :

1. Bruce Alberts, Julian Lewis, Alexander Johnson, J. Lewis, M. Raff (1994), Molecular Biology of the Cell, Garland PublisherInc., New York

2. Buchnan and Grussem et al, (2000) Biochemistry and Molecular biology of Plants by 5th edition, Oxford University Campus3. Goodwin and Mercer- CBS, Plant Biochemistry4. Gupta PK, (2004) Cell and molecular Biology, Rastogi Publications, Meerut5. Lewin B (2002). Genes VIII, Oxford

44

6. Lodish,H., Ber, A., Zipuoskry, L.S., Matsudaira, P., Bahimore, D and Damell J. (2001) Molecular Biology W.H Freeman GCo.

7. Taiz, L. and Zeiger, E. (2003). Plant Physiology. 3rd edition. Panima Publishing Corporation, New Delhi/Bangalore8. Taiz, L. and Zeiger, E. (1998). Plant Physiology. 2nd edition. Sinauer Associates, Inc., Publishers, Massachusetts, USA.9. Wilkins, M.B. (eds.) (1989). Advanced Plant Physiology. Pitman Publishing Ltd., London.

THIRD SEMESTER PRACTICALSMLB 305: BIOCHEMISTRY-II AND MOLECULAR BIOLOGY - I

104 hrs

1. Extraction and analysis of lipids

45

2. Isolation of mitochondria and chloroplasts : Extraction and analysis of DNA and RNA. 3.Assay of mitochondrial enzymes. 4. Estimation of proteins from mitochondria and chloroplasts 5. Construction of expression vector, PCR protocols 6. Use of enzymes for biodegradation of wastes 7. Purification of enzymes by different protocols 8. Seed germination – by RAPD analysis.

MLB 306 : MICROBIAL BIOTECHNOLOGY ANDMOLECULAR BIOLOGY OF DEVELOPMENT

104 hrs

1. Study of working - Fermentor2. Estimation of fermentation ability under different condiations ( substrate and temperature)3. Estimation of percentage of alcohol in yeast fermentation4. Assay of microbial enzymes ( amylase, protease )5. Study of gene expression during embryonic development of Drosophila (LacZ )6. Isolation of mRNA from Drosophila ( early embryo )7. Analysis of protein profile during flowering.8. Seed germination – protein profile by iso-electrofocusing.

-----------------------------------------------------------------------------------------------------NOTE

Experiments involving dissection and sacrifice of animals are carried out through computer simulations, models and videodemonstration.

---------------------------------------------------------------------------------------------------

46

SYLLABUS FOR III AND IV SEMESTER M.Sc., MOLECULAR BIOLOGY

SCHEME OF STUDY AND EXAMINATIONSEMESTER III

PaperCode Paper Title of the Paper

(Hrs / week) Total No. ofHrs/

Semester

Examination

Theory Practical Duration(Hrs)

Max.Marks

ContinuousEvaluation

TotalMarks

MLB301 I Biochemistry – II 4 -- 52 3 80 20* 100

MLB302 II Molecular Biology – I 4 -- 52 3 80 20* 100

MLB303 III MicrobialBiotechnology 4 -- 52 3 80 20* 100

MLB304 IV Molecular Biology ofDevelopment 4 -- 52 3 80 20* 100

MLB305 Pract.I Of paper I & II -- 8 104 4 40 10** 50MLB306 Pract.II Of paper III & IV -- 8 104 4 40 10** 50

Total Marks 500

* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical record + 5 marks for visit to Industries/Laboratories

47

SCHEME OF STUDY AND EXAMINATIONSEMESTER IV

PaperCode Paper Title of the Paper

(Hrs / week) Total No. ofHrs/

Semester

Examination

Theory Practical Duration(Hrs)

Max.Marks

ContinuousEvaluation

TotalMarks

MLB401 I Immunology 4 -- 52 3 80 20* 100MLB402 II Molecular Biology – II 4 -- 52 3 80 20* 100MLB403 III Genomics and Proteomics 4 -- 52 3 80 20* 100

MLB404 IV Plant & AnimalBiotechnology 4 -- 52 3 80 20* 100

MLB405 Pract.I Of paper I & II -- 8 104 4 40 10** 50MLB406 Pract.II Of paper III & IV -- 8 104 4 40 10** 50

Total Marks 500

* 5 marks for Test + 5 marks for Assignment + 5 marks for Seminar +5 marks for Attendance.** 5 marks for Practical record + 5 marks for visit to Industries/Laboratories

2. TOUR: Tour marks should be considered under Continuous Evaluation.a) There will be a Compulsory Industries / Laboratories visit in all the semesters as per relevance to the subject.b) There will be a compulsory Tour 5 to 6 days to any of the industries outside Bangalore in IV Semester.

48

FOURTH SEMESTER

MLB 401: IMMUNOLOGY52 hrs

Unit I:Types of immunity: (a) Nonspecific (Innate) immunity: Anatomic, Physiologic,Phagocytic barriers (b) Specific (Adaptive) immunity: Active immunity -Naturally and artificially acquired; Passive immunity - Naturally and artificiallyacquired and Adoptive immunity (c) Brief description of cell mediated immunityand humoral immunity 5hrsUnit II:Organs of the immune system: (a) Primary lymphoid organs: Bone marrow,Thymus (b) Secondary lymphoid organs: Spleen, Lymph nodes, Mucosal-associated lymphoid tissue.5hrsUnit III:Cells of the immune system: (a) Hematopoesis (b) Lymphoid cells – BLymphocytes, T Lymphocytes (TH, TC and TReg cells), NK Cells (c) Macrophages(d) Granulocytes (e) Mast cells (f) Dendritic cells (g) Clinical uses ofhematopoietic stem cellsMaturation, Activation and Differentiation of T and B Lymphocytes, Antigenprocessing and Presentation: Processing and presentation of endogenous andexogenous antigens, presentation of non-peptide antigens

8hrsUnit IV:Antigens: Immunogenicity and Antigenicity, Factors influencingimmunogenicity, Epitopes, Haptens

4hrsUnit V:Antibodies: (a) Classes of antibodies – IgA, IgD, IgE, IgG and IgM (b) Structureof IgG (c) Cellular kinetics of antibody synthesis (d) Organization and expressionof Ig genes - l - Chain multigene family, k - multigene family, Heavy chainmultigene family, V-J rearrangements of light chain, V-D-J rearrangements ofheavy chain, organization of Recombination Signal Sequences (RSSs). (e) Othermechanisms causing antibody diversity – Junctional flexibility, P-addition, N-addition, Somatic hypermutation, Combinatorial association of light and heavychains (f) Class switching (g) Monoclonal antibodies: Formation and selection ofhybridomas, Production and Clinical importance of monoclonal antibodies

10hrs

49

Unit VI:Major Histocompatibility complex: Structure of Class I and Class II MHCmolecules, Polymorphism of peptide binding region, Class I MHC – peptideinteraction, Class II MHC – peptide interaction

4hrsUnit VII:Vaccines: Primary and Secondary responses, active and passive immunization,Whole organism vaccines, Purified macromolecules as vaccines, Recombinant-Vector vaccines, DNA vaccines

3hrs

Unit VIII:Hypersensitivity: IgE mediated hypersensitivity (Type I), Antibody mediatedcytotoxic hypersensitivity, Immune complex mediated hypersensitivity (Type III),Delayed type hypersensitivity (Type IV)

5 hrsImmunodeficiencies: Primary immunodeficiencies – Lymphoidimmunodeficiencies, Myeloid immunodeficiencies, Secondaryimmunodeficiencies (AIDS) 4hrsAutoimmune diseases: Autoimmune haemolytic anaemia, Hashimoto’s disease,Grave’s disease, Myasthenia gravis, Pernicious anaemia, Systemic LupusErythematosus

4 hrs References:

1. Abul Abbas, Andrew Lichtman, and Jordan Pober, (2005), Cellularand molecular immunology, Saunders Publishers, 5th edition, 576pages plus CD

2. Abul Abbas, Saunders,(2006), Basic Immunology, UpdatedEdition 2006-2007 (Paperback) by Publishers; 2nd edition 336pages

3. Ashi K Chakravarty, (2006), Immunology and Immunotechnology, Ist edition, Oxford Press.

4. Charles Janeway, Jr. and Paul Travers, (2004), Immunobiology -the immune system in health and disease, by. Garland Science; 6edition, 800 pages

50

5. Gupta P K, (2004) Cell and Molecular Biology, RastogiPublications, Meerut

6. Ivan Roitt, Jonathan Brostoff, and David Male. Mosby, (2006),Immunology, London. 7th edition, 544 pages

7. Lodish et al., (2001) Molecular Biology, W.H.Freeman G Co. 478. Thomas Kindt, Barbara Osborne and Richard Goldsby, (2006),

Kuby Immunology. W. H. Freeman & Co., Sixth edition, 20069. William E Paul, Lippincott Williams & Wilkins;(2003)

Fundamental Immunology (Hardcover) by 5th Bk&Cdr edition,1502 pages

MLB: 402 MOLECULAR BIOLOGY - IIUnit I:

52 hrsControl of gene expression at Post transcriptional level:

1. Processing of rRNA: precursor rRNAs, types and structural andfunctional features of sno-RNAs and sno-RNPs and their role in splicing

rRNAs. Processing of pre-tRNAs: size of pre-tRNAs, the number, size andposition of tRNA introns; two types of splicing and the mechanism of

splicing.Pre-mRNAs processing: Characteristic features of pre-mRNAs or Hn RNAs,structure and sizes of hn RNAs; hnRNP proteins, mRNP proteins; introns andexons and their characters; Processing of pre mRNAs; Capping andpolyadenylation: Enzymes and the time of capping, mechanism of capping, itsimportance. Factors, site, enzymes and the mechanism involved in Poly(A)addition, importance of poly(A) tail; poly(A) binding proteins and their role.Splicing: Characteristic features of introns splice junction site and intron’sinternal sites, splicing signals and signal sites;SnRNAs, their structural and functional features and their associated proteins;Mechanism of splicing event, the role of specific snRNA and SnRNPs;spliceosomal assembly and the mechanism of splicing.Processing of Histone mRNA and the role of sn-U7 RNA.8 hrsUnit II:Alternate splicing: Concept of alternate splicing and its implications. Alternatesplicing of Fibronectins, collagens, Example from Dscam splicing in Drosophila,alternate splicing of vertebrate inner ear cochlea for registering sound waves, A

51

brief description of alternate splicing in sex determination of Drosophila.Alternate splicing in mouse/human immunoglobulin u-heavy chain mRNA.Trans splicing: trans-splicing in C.elegans and Trypanosome pre-mRNAs, andsome Adenoviral mRNAs, where the leader sequence is same in 25% or more ofthe mRNAs; splicing components and SL-RNA and other snRNA-RNPs involvedin the mechanism of transplicing.Pre-mRNA Editing: Editing Apo-lipoprotein mRNA and Glutamine receptormRNA, features and mechanism. Special features of few mitochondrial faultypre-mRNAs (called pre-edited mRNAs) in Trypanosomes and Leishmania;editosomes, and characters and their composition, genes for Guide RNA and themechanism of editing.Self-splicing introns: Group-I introns, Group-II introns, Group III introns,Twinintrons: their characters and functions;Informosomes: Stored mRNAs in mature egg cells , normal cells and seeds, roleof mRNPs, importance of poly(A) size, polyadenylation signal elements,reactivation of mRNAs by reactivation of Poly(A) addition and its regulation.

10 hrsUnit III:mRNA transport: Structures and proteins involved in the transport of rRNA,tRNA and mRNAs; mechanism of transport.mRNA stability and turn over: sequence elements found in the 5’ leadersequences and 3’ non-coding regions and their structural features, relationshipbetween such sequences and sequence derived structures and stability;mechanism of protection and the mechanism of degradation and causes; ex.Casein mRNA, Transferrin mRNA, Ferritin mRNA..

8 hrs

Unit IV:

Control of gene expression : Prokaryotic translationTranslation apparatus; ribosomal subunits, initiator-tRNAs aminoacyl-tRNAs,initiating factors, elongation factors, termination factors, and their characteristicfeatures, mechanism of chain initiation, elongation and termination; production ofspecific proteins on translation of a polycistronic mRNA. Mechanism oftranslation, Post translational processing of polycistronic polypeptides, andtargeting the protein to periplasmic space or to the membrane. Regulation ofprotein synthesis, autogenous regulation, stringent response type regulation.

6 hrsUnit V:

52

Eukaryotic translation: Translational apparatus- ribosomes, initiator-tRNAs, aa-tRNAs, initiation factors, elongation factors and termination factors, theircomposition and functions; mechanism of translation;Regulation of protein synthesis: Regulation of translation at mRNA level,regulation at chain initiation factor level, ex. Heme regulated translation,regulation of Ferritin synthesis, and Transferrin receptor synthesis and interferonmediated regulation. Membrane free site-actin filament associated synthesis,localized synthesis, synthesis on ER.

6 hrsUnit VI:

Post translational processing:Co translational processing- transferring the translating system onto ER andtransferring the protein into the lumen of ER, the role of SRP particles, dockingproteins, and signal sequences in targeting the protein and also in orienting the Nand C- terminal ends of the proteins. Mechanism of transfer of proteins into ERlumen. 5 hrsUnit VII:Post translational modification and targeting:Processing of proteins in the lumen of ER, transfer of the same into cis surface ofthe Golgi membrane, further processing, and transferring to mid and trans-golgimembranes, modification such as glycosylation, sorting and packing and deliveryof the same to specific destination, factors and the proteins involved and themechanism.Transfer of membrane free synthesized proteins into organelles such as nucleus,chloroplasts, mitochondria and glyoxysomes; the signal sequences and theenzymes and factors involved in the mechanism of transfer and targeting.Processing of Pre-pro-proteins: Regulated cleavage of polyproteins and pre-proproteins in stage specific and tissue specific manner. Splicing of proteins,Removal of introns and joining of exons- its mechanism.

6 hrsUnit VIII:Protein stability and turnover:Sequence based structural form, unstable proteins, protein degradation, andubiquitination of condemned proteins and degradation by proteosome; structureand features of Proteosomes and the mechanism of degradation.

3hrs

References:

53

1. Buchnan, B.B. and Wilhelm Grussem et al., (2000) Biochemistry andMolecular biology of Plants , American Society of Plant Physiologists,Rock Ville, USA, Maryland

2. Eduardo Diego Patricio De Robertis, EMF De Robertis (1980) Cell andmolecular biology

3. Gerald Karp, (1996) Cell and Molecular Biology – Concepts andExperiments. John Wiley and Sons, Inc., New York

4. Gurbachan S. Miglani (1998), Molecular Biology:Dictionary of PlantGenetics and Molecular Biology, - 348 pages

5. James Darnell, Harvey Lodish, Paul Matsudaira, Arnold Berk, S.Lawrence Zipursky, (1998) Molecular Biology of the cell

6. John Marsten Walker, Ralph Rapley (2000), Molecular Biology andBiotechnology

7. Russell L. Jones, Virginia (EDT) Walbot (1995), Annual Review of PlantPhysiology and Plant Molecular Biology - Page 22

8. Sambrook,J; Russel,D.W., (2001)Molecular Cloning: A Laboratorymanual, cold spring Harbor Laboratory press, cold spring Harbour, NewYork

9. William H Elliott, Daphne C Elliott (1997), Biochemistry and molecularbiology

MLB403: GENOMICS AND PROTEOMICS

52 hrsUnit ISequencing: Use of large scale sequencing and application in identifying species,varieties and relate phylogeny.

Physical map:Use bottom-up approach or Top down approach; Sorting out chromosomes byFluorescence activated chromosome sorting method (FACS), Use of PFGE-Pulsefield gel electrophoresis or CHEF-Counter clamped homogenous electrical fieldelectrophoresis, Use of molecular markers, use of chromosomal aberrations suchas deletions and fragmentation, preparation of YAC libraries or Bacmid libraries,RE mapping, chromosomal walking and jumping, contigs, use of in situhybridization (ISH) and FISH, use of EST tags (expressed sequence tags) andSTS tags (sequence tagged sites) use of positional cloning of cloned sequence of achromosome, and candidate gene approach, developing high resolution mapping,

54

identification of genomic sizes by Resolution-Gap mode. Development ofintegrated genomic map using all methods. 8hrsUnit II:Functional Genomics: Transcriptomes-overall transcripts of a given tissue andtissues; use of Northern blot, dot blot and reverse northern blot, use of subtractivelibrary, additive library, RNase protection and RT-PCR techniques; techniquesfor analysis of steady state gene expressions by EST tags and CDNA libraries,characterization of each of them and relating each of them to each kind in termsof nucleotide sequence to their amino acid sequence; detection of ORFs, geneknock outs, construction of two expression plasmid systems in one cell to find outgene interaction. 8hrsUnit III:

DNA Micro array techniques-spotted arrays, printing techniques and spottedarray techniques, difference between spotted arrays and Oligochips;Transcriptomics and data processing. Construction of DNA-chips to find outregulation of gene expression and to detect mutations. Gene expressionmeasurement through DNA micro arrays and SAGE , Protein levels through two-dimensional gel electrophoresis and mass spectrometry, includingphosphoproteomics and other methods to detect chemically modified proteins.

6hrsUnit IV:Comparative Genomics:Concept of orthologs and paralogs in gene evolution, protein evolution throughexon shuffling, comparative genomics of bacteria and large microbial genomes,comparative genomics of closely related bacteria in particular and microbes ingeneral, comparative genomics and physiological phenomena,; comparativegenomics of organelles, comparative genomics of eukaryotes to identify genesand regulatory elements, evolution of key proteins, and evolution of species;comparative genomics and molecular mechanism to generate new gene structures.

8hrsUnit V:Proteomics: Concepts, Protein array from a given tissue or tissues, detectionand screening techniques.Use of 2-D PAGE, sensitivity and resolution and representation of 2-D gels,multiplexed analysis to show expression profiles,; use of multidimensional liquidchromatography, Mass spectrometry and high throughput protein annotation,Matrix assisted laser desorption (MALDI), Electrospary ionization (ESI),TIMEflight (TOF), collision induced dissociation (CID), special strategies forqualitative and quantitative analysis.

55

Protein array for expressional analysis, profiling and functional analysis; antibodyarray for the capture of specific protein, antigen array to measure antibodies in asolution, use of BIOchips.Structural Proteomics-use of X-ray diffraction crystallography and NMR, circulardichroism (CD), use of algorithms for comparisons, functional assignment.8hrsUnit VI:Protein-protein interactions:genetic approach, use of comparative genomics, use of library based screeningand analyzing interactions, invitro expression libraries, yeast two hybrid system,,matrix approach,, analysis of protein complexes by affinity purification and MS,protein localization in a cell.

5hrsUnit VII:

Metabolomics and metabolic engineering:Concepts, methods used and application. Cloning and expression of heterologousgenes to change metabolic pathway to the desired product or to improve thedesired metabolic product; altering feed back inhibition, altering the regulation ofa desired metabolic pathways..Metabolomics-for small-molecule metabolites, glycomics for sugars;interactomics for interactome

4hrsUnit VIII:Systems Biology; Markup Language; List of omics topics in biology; Generegulatory network; Metabolic network modeling ; Model Computer simulation;Important publications in systems biology Systems theory; Systems ecology ;Regulome; Biomedical cybernetics;Different methods for analyzing metabolites. Choosing analytical methods to theneed of an organism. Basic mass spectrometry-use of Gas (GC/MS and liquidchromatograph (LC/MS). Use of Tandem Mass spectrometry, sample selectionand sample handling, use of data base for preparing global biochemicalnetworking. 5hrs

References:1. Brown, T.A., Genomes (1999). John Wiley &Sons2. Daniel, C. Leibler, (2002). Introduction to Proteomics: tools for new

biology, Human Press, Totowa, NJ

56

3. Dennis, C and Gallaghar, R (2001). The human genome. Naturepublishing group, U.K.

4. Kohane IS, AJ Butte, A Kho (2002), Microarrays for an IntegrativeGenomics - group of 2 », - MIT Press Cambridge, MA

5. Liebler DC (2002), Introduction to Proteomics: Tools for the New Biology- group of 12 »

6. Liu, BH (1998), Statistical Genomics: Linkage, Mapping, and QTLAnalysis - books.

7. Maleolm and Goodship (2001). Genotype to Phenotype. 2nd ed. BiosScientific publishers.

8. Palzkill, Timothy : (2002) Proteomics, Kluer Academic Publishers9. Pechkova E, Nicolini, C (2003), Proteomics and Nanocrystallography10. Pennington, S; M.J. Dunn (eds) (2001) Proteomics: from protein

sequences to function. Springer Publications.11. Puhler,A(1993), Genetic engineering of microorganisms, WCH Germany12. Saito K, RA Dixon, L Willmitzer (2006), Plant Metabolomics - group of 2

»13. Sehena,M (1999), DNA microarrays: A Practical approach, Oxford

University Press, Oxford14. Simpson RJ, JL Hotchkiss (2003), Proteins and Proteomics: A Laboratory

Manual15. Strachen,T Read, AP. (1999), Human Molecular Genetics, 2nd edition,

John Wiley & Sons.16. Tomita M, T Nishioka , lavoisier (2005), Metabolomics: The Frontier of

Systems Biology - group of 3 »17. Tomita, Masaru (Editor ), Takaai, Nishioka (Editor ), Metabolomics18. Wilkins MR, RD Appel, DF Hochstrasser, KI Williams (1997), Proteome

Research: New Frontiers in Functional Genomics., Springer –verlag, NewYork

19. Zhou, T, Thomas, D.K.,Y.XU and Tiedge, J.M. and Wiley Liss (2004),Microbial functional genomics

MLB 404: PLANT AND ANIMAL BIOTECHNOLOGY

PART A : PLANT BIOTECHNOLOGY

52 hrs

57

Unit IPrinciples of Tissue culture: Preparation of media, its components, autoclavingprinciples, preparation of explants and culturing.Use of Phytohormones: Understanding of Phytohormones and their effects onplant morphogenesis, interaction of the same in morphogenesis. Strategies toinduce callus and plantlets from different types of explants.Culture Types: Methods of embryo culture and embryo rescue, Meristem culture,virus free plants, ovule culture, endosperm culture.Large scale Micropropogation, hardening and its application. Selection forsomaclonal variants and creation of somoclonal variants.

6hrsUnit II:Cryopreservation: Germplasm sources and techniques of CryopreservationHaploid plants: Use and mode of ovule and anther culture for haploid plants,application of Haploids in agriculture.Protoplast culture: Preparation of protoplasts and culturing technique, modes ofprotoplast fusion to produce cell hybrids and cybrids, chromosomal stability; itsapplication.Liquid culture: Production of unicellular cell population by liquid culture andapplication liquid culture in creating embryoids, mutants.Transgenic plants and Large scale tissue culture:Kinds of culture: agar cultures, suspension cultures, Batch cultures, continuousand Multistage Bioreactors, immobilized bioreactors; Improving and enhancingyield, development of high yielding clones, and use of elicitors.Large scale culture: Single cell, Solid callus and Liquid culture, maintenance ofthe liquid culture, extraction methods and scale up of the process-for secondarymetabolites; production of single cell proteins(SCPs).

8hrsUnit III:Transgenic Plants:Plant cell culture for biotransformation.Biochemical production of Agrochemicals, Medicinal, Cosmetic and foodadditives, Enzymes, Plantibodies and vaccines, Biopolymers andvitamins.Vectors for plant transformation- Binary vectors and Integration vectors-its characteristic features in detail.Construction of a gene in expression modeUse of selection marker gene and how to get rid of the harmful antibiotic or toxingenes Use of terminator technology.

58

Methods of gene transfer: Electroporation, Gene gun and Agrobacteriummediated.Ti and T-DNA, mechanism of DNA transfer and integration, design of vectors onthe basis of Ti-plasmids.Tissue regeneration and screening- methods .Organelle Engineering :Construction of vectors with proper regulatory elements.Transfer of genetically engineered DNA clones into chloroplasts ofChlamydomonas, and higher plants.. Targeting cytoplasmically made proteinsinto chloroplast. Targeting cytoplsmically made proteins into Mitochondria

8hrsUnit IV:

Disease Resistance transgenic plants :Disease Resistant to viruses -capsid gene, antisense to capsid gene, defectivetransport protein and RNA and RNAi and Ribozyme mediated resistance. DiseaseResistant to fungi by engineering Chitinase (b-1, 3-glucanase gene. Diseaseresistant to bacteria by Lysozyme gene. Resistant to pests- Bt-toxin gene, proteaseinhibitor genes. Use of biological insecticide (Baculoviruses) and herbicideresistant strains..Transgenic food crops:Increase in essential amino acids in cereal seed proteins (phaseolin promoter and2sAlbumin gene; E.coli dihydropicolinate synthase (DHPS gene) with signalsequence for chloroplast, for increasing lysine content. Increase and change in thequality of oils in Brassica species (increase in medium chain fatty acids andconverting unsaturated fatty acid to saturated fatty acids). Prevention ofdiscoloration of Food, Increase in sweetness and flavor in fruits. Increase inAmylopectin (by antisense to starch synthase). Improvement in amylase synthesisby ADPG pyrophosphorylase.Plants as Bioreactors: Production of plantibodies, Production of vaccines.Production of biopolymers. Production of water soluble oleosins.

8hrs

PART B: ANIMAL BIOTECHNOLOGYUnit V:Methods of animal cell preparation: Protocols used for cell cultures from thetissues and culture methods and maintenance, Large scale animal cell culture forcommercial production of specific proteins, Igs, Interferons, vaccines,Monoclonal Antibodies, Hybridoma cells and other down stream processes.Animal tissue culture: skin cultures, Neuronal cell cultures, muscle cell cultures,Cartilage culture, blastocysts cell culture, whole embryo culture, Stem cell

59

research: use of stem culture methods for transformation and tissuetransplantation. Kinds of stem cells and characters and potentials, methods toobtain such cells, culture and maintenance of cells; methods to induce stem cellsto differentiate into specific tissues; Application of stem cells in medicine,research and therapy; ethical problems. 6hrsUnit VI:Animal cell Transformation and immortalization: Methods employed foranimal cell transformation, viral mode, oncogene mode or genetic manipulationmode, Properties of transformed cells, causes and mechanism of transformation,genes involved in transformation, application of cancer cells in biotechnology.IVF in humans and animals: In vitro fertilization, oocyte culture, in vitrofertilization and embryo transfer (IVF-ET). Design of vectors for genesexpression in animal cells; Integrating vectors, episomal high copy numbervectors with inducible promoters. Production of recombinant viruses for targetingspecific tissues.Methods of transfer: Electroporation, PEG method, and transfection method.6hrs

Unit VII:Transgenic animals:Methods employed in introducing cloned genes; protocols for developingtransgenic animals; use of fertilized egg cells, use of blastocyst cells; success andfailures, problems. Transgenic sheep, goat, fishes, cattle, mice, pigs and birds.Applications and ethical issues.Animal cloning: Techniques used in animal cloning- transfer of whole 2n nucleito enucleated cells (ex. Xenopus and other frogs), cultured cell fusion, use ofembryonic cells, applications and ethics.

5hrsUnit VIII:Human gene therapy:Ex vivo and in vivo gene therapy, viral gene delivery system, non viral deliverysystem, pro-drug activation therapy, oligonucleotide correction methods.Cell mediated therapy - blocking cell receptors in Hodgkin’s melanoma, treatingcancer cells with Tissue specific Tumor infiltering lymphocytes (TILs) andinterleukins.Treating transformed hepatocytes for defects in clotting factors and other liverspecific defects. Development of vaccines against specific cancer types. Genetherapy for SCID (severe combined immunodeficiency), Antisense RNA astherapy.

60

Cancer therapy: use of specific vaccines, use of antisense or RNA interference.5hrs References:

1. Altman, A ( 1997), Agricultural Biotechnology2. Bhojwani SS, MK Razdan (1983), Advanced immunology - group of 2 »

Plant Tissue Culture: Theory and Practice, - elsevier.com3. Freshney RI, JRW Masters, J Masters (2000), Animal Cell Culture: A

Practical Approach, 5th edition, Wiley-Liss Publication4. Goldsby RA, TJ Kindt, BA Osborne (2000), Kuby immunology,

academicbooktrade.co.uk5. Houdebine, LM (2003), Animal Transgenesis and Cloning - group of 3 »6. Krimsky DS, RP Wrubel (1996), Agricultural Biotechnology and the

Environment: Science, Policy, and Social Issues - group of 3 »

FOURTH SEMESTER PRACTICALSMLB 405: IMMUNOLOGY AND MOLECULAR BIOLOGY - II

104 hrs1. Raising antibodies against BSA in rabbit2. Ouchterlony double diffusion3. Protein electrophoresis by using serum from control and antigen

immunized rabbits4. Identification of pathogens by ELISA. (Kit method)5. Preparation of genomic DNA.6. PCR amplification of an identified gene.7. Subcloning of a gene for expression in a prokaryotic expression vector8. Protein expression analysis

MLB 406: GENOMICS AND PROTEOMICS & PLANT AND ANIMALBIOTECHNOLOGY

104 hrs1. Study of proteins by native gel electrophoresis2. Study of proteins by SDS-PAGE3. Study of proteins by 2 D gel electrophoresis4. Western blotting.5. Computational analysis of the proteome of a given organism6. Transient expression of a cloned gene in animal cells by electroporation

and analysis7. Tissue culture, micropropagation, anther culture8. Protoplast culture and fusion

61

9. Plant transformation and molecular analysis by PCR

-----------------------------------------------------------------------------------------------------

NOTE Experiments involving dissection and sacrifice of animals are carried outthrough computer simulations, models and video demonstration.-------------------------------------------------------------------------------------------------------