MaulanaAbulKalamAzadUniversityofTechnology,WestBengal
Maulana Abul Kalam Azad University of Technology, West BengalDepartment of BiotechnologyM. Sc. in Genetics Syllabus 2019-20
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemester ICodeCourse hemistry3-0-03MSUGN-102Laboratory Technique & Safety3-0-03MSUGN-103Cell & Molecular Basic yticalTechniques0-0-63MSUGN-192Lab on Cytogenetics0-0-63MSUGN-193Data analysis using software0-0-42CMSUGN-181SeminarSemester Total124
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemester IICodeCourse TitleContact onary Biology andPopulation GeneticsClinical netic Engineering3-0-03MSUGN-205Applied Bioinformatics3-0-03MSUGN-206BChoice based courses(from MOOCS basket)PracticalCredit2MSUGN-291Genetic Engineering Lab0-0-63MSUGN-292Immunology Lab0-0-63CMSUGN-281SeminarSemester Total124
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemester MSUGN-301Human Genetics andGenetic Counselling3-0-03MSUGN-302Developmental Biology3-0-03MSUGN-303Genomics & Proteomics3-0-03MSUGN-304IPR, Biosafety & Bioethics3-0-03MSUGN-305Choice Based course(From Elective Basket) *2-0-02MSUGN-306Choice Based course(from MOOCS basket)B2PracticalMSUGN-391Lab on Applied Bioinformaticslab0-0-63MSUGN-392Lab on Molecular Genetics andDevelopmental Genetics0-0-63CMSUGN-381Project Proposal PresentationSemester Total* Elective subjects BasketCodeMSMC-305AMSMC- 305BMSMC-305CMSMC-305DMSMC-305ESubjectPrinciples of EcologyResearch methodology and WritingMolecular diagnosticsEnzyme technologyPlant Molecular Biology224
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemester – IVCodeCourse TitleContactHrs./wkCreditL-T-PMSUGN-481Project Work22MSUGN-482Industry/lab visit1MSUGN-483Journal ClubPresentationSemester Total1Total CourseCredit2496
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemester –IMSUGN-101: Biochemistry credits 3Unit 1: Basic chemistryFormation of chemical bonds, molecular orbital (MO) theory and linearcombination of atomic orbitals (LCAO), basics of mass spectrometry, molecules, Avogadronumber, molarity, chemical reactions, reaction stoichiometry, rates of reaction, rate constants,order of reactions, kinetic versus thermodynamic controls of a reaction, reaction equilibrium(equilibrium constant); light and matter interactions (optical spectroscopy, fluorescence,bioluminescence, paramagnetism and diamagnetism, photoelectron spectroscopy;chemical bonds (ionic, covalent, Van der Walls forces); electronegativity, polarity; VSEPRtheory and molecular geometry, dipole moment, orbital hybridizations; acids, bases and pH Arrhenious theory, pH, ionic product of water, weak acids and bases, conjugate acid- base pairs,buffers and buffering action etc; chemical thermodynamics - internal energy, heat andtemperature, enthalpy (bond enthalpy and reaction enthalpy), entropy, Gibbs free energy ofATP driven reactions, spontaneity versus driven reactions in biology; bond rotations andmolecular conformations - Newman projections, conformational analysis of alkanes, alkenesand alkynes; functional groups, optically asymmetric carbon centers, amino acids, proteins,rotational freedoms in polypeptide backbone (Ramachandran plot).Unit 2: Protein StructureWater – properties of water, essential role of water for life on earth pH, buffer, maintenance ofblood pH and pH of gastric juice, pH optima of different enzymes (pepsin, trypsin andalkaline phosphatase), ionization and hydrophobicity, emergent properties of biomoleculesin water, biomolecular hierarchy, macromolecules, molecular assemblies; Structure-functionrelationships: amino acids – structure and functional group properties, peptides andcovalent structure of proteins, elucidation of primary and higher order structures,Ramachandran plot, evolution of protein structure, protein degradation and introduction tomolecular pathways controlling protein degradation, structure-function relationships inmodel proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.; basic principlesof protein purification; tools to characterize expressed proteins; Protein folding: Anfinsen’sDogma, Levinthal paradox, cooperativity in protein folding, free energy landscape ofprotein folding and pathways of protein folding.Unit 3: EnzymeEnzyme Classification, Enzyme catalysis – general principles of catalysis; quantitation ofenzyme activity and efficiency; enzyme characterization and Michaelis-Menten kinetics;relevance of enzymes in metabolic regulation, activation, inhibition and covalent modification;single substrate enzymes; restriction enzymes and nucleoside monophosphate kinase;regulatory strategies with specific example of haemoglobin; isozymes; role of covalentmodification in enzymatic activity; zymogens.Unit 4: GlycobiologySugars-mono, di, and polysaccharides with specific reference to glycogen, amylose. lipids- structureand properties of important members of storage and membrane.6
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BUnit 5: Nucleic acidNucleosides, nucleotides, nucleic acids - structure, a historical perspective leading up to theproposition of DNA double helical structure.Unit 6: BioenergeticsBioenergetics-basic principles; equilibria and concept of free energy; coupled interconnectingreactions in metabolism; oxidation of carbon fuels; Ca signaling pathways; glycolysis andgluconeogenesis; Citric acid cycle, entry to citric acid cycle, citric acid cycle as a source ofbiosynthetic precursors; Oxidative phosphorylation, Photosynthesis – chloroplasts and twophotosystems; proton gradient across thylakoid membrane.Unit 7: Vitamins & cofactorsCalvin cycle and pentose phosphate pathway; glycogen metabolism, reciprocal control ofglycogen synthesis and breakdown, elucidation of metabolic pathways; logic and integration ofcentral metabolism; entry/ exit of various biomolecules from central pathways; principles ofmetabolic regulation; steps for regulation.Texts/References:1. David L. Nelson; Michael M. Cox. Lehninger Principles of Biochemistry2. L Stryer, Biochemsitry, Freeman publishing.MSUGN-102: Laboratory Techniques & Safetycredits 3Unit 1 : Laboratory safetyBasic goal of Chemical hygiene and lab safety, Occupational Safety and healthadministration (OSHA), Safety precaution, Health hazard, Chemical and biologicalhazard, Personal protective equipment.Unit 2: ChromatographyPaper Chromatography, Thin-layer chromatography, Displacement chromatography, Gaschromatography, High performance / pressure liquid chromatography, Ion exchangechromatography, Size-exclusion chromatography, Affinity chromatography.Unit 3: Electrophoresis and blottingTheory and application of Polyacrylamide and Agarose gel electrophoresis; Capillaryelectrophoresis; 2D Electrophoresis; Immunoelectrophoresis, Isoelectric focussing, Disc gelelectrophoresis; Gradient electrophoresis; Pulsed field gel electrophoresis, Western blot,Eastern blot, Southern blot, Northern blot.Unit 4 :RadioactivityRadioactive & stable isotopes; Pattern and rate of radioactive decay; Units of radioactivity;Measurement of radioactivity; Geiger-Muller counter; Solid & Liquid scintillation counters(Basic principle, instrumentation & technique); Applications of isotopes in biochemistry;Autoradiography.7
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BUnit5:CentrifugationBasic principles; Mathematics & theory (RCF, Sedimentation coefficient etc); Types of centrifuge,Micro centrifuge, High speed & Ultracentrifuges; Preparative centrifugation; Differential &density gradient centrifugation; Applications (Isolation of cell components); Analyticalcentrifugation; Determination of molecular weight by sedimentation velocity & sedimentationequilibrium methods.Unit 6: MicroscopyOptical microscopy, Electron microscopy, Confocal microscopy, AFM, Flow cytometry,Instrumentation, Applications.Unit 7: Advanced molecular biology techniquesDNA and Amino acid Sequencing, DNA CHIP, Microarray, Substractive Hybridization, RNaseprotection assay, ELISA, Mass spectroscopy, Infra red spectroscopy, NMR, CircularDichroism, Microarray, Flow cytometry.Text/References :1. Cantor & Schimmel : Biophysical Chemistry (Part I, II & III)2. A. Lehninger : Principles of Biochemistry3. Freifelder D., Physical Biochemistry, Application to Biochemistry and MolecularBiology, 2nd Edition, W.H. Freeman & Company, San Fransisco, 1982.5. D. Holme & H. Peck, Analytical Biochemistry, 3rd Edition, Longman, 1998.MSUGN-103: Cell and Molecular Biologycredits 3Unit 1: Organization of cellUniversal features of eukaryotic cells; cell chemistry and biosynthesis: chemical organization ofcells; internal organization of the cell - cell membranes: structure of cell membranes andconcepts related to compartmentalization in eukaryotic cells; intracellular organelles:endoplasmic reticulum and Golgi apparatus, lysosomes and peroxisomes, ribosomes,cellular cytoskeleton, mitochondria, chloroplasts and cell energetics; nuclearcompartment: nucleus, nucleolus and chromosomes.Unit 2: Chromatin structure:Chromatin organization - histone and DNA interactome: structure and assembly of eukaryoticand prokaryotic DNA polymerases, DNA-replication, repair and recombination; chromatincontrol: gene transcription and silencing by chromatin-Writers,-Readers and –Erasers;Transcriptional control: Structure and assembly of eukaryotic and prokaryotic RNAPolymerases, promoters and enhancers, transcription factors as activators and repressors,transcriptional initiation, elongation and termination; post-transcriptional control: splicing andaddition of cap and tail, mRNA flow through nuclear envelope into cytoplasm, breakdown ofselective and specific mRNAs through interference by small non-coding RNAs (miRNAs andsiRNAs), protein translation machinery, ribosomes- composition and assembly; universalgenetic codes, degeneracy of codons, Wobble hypothesis; Iso- accepting tRNA;mechanism of initiation, elongation and termination; co- and post-translationalmodifications, mitochondrial geneticcode8
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, ffickingMolecular mechanisms of membrane transport, nuclear transport, transport acrossmitochondria and chloroplasts; intracellular vesicular trafficking from endoplasmicreticulum through Golgi apparatus to lysosomes/cell exterior.Unit 4: Cell cycle and its regulationCell division: mitosis, meiosis and cytokinesis; cell differentiation: stem cells, theirdifferentiation into different cell types and organization into specialized tissues; cell-ECM andcell-cell interactions; cell receptors and trans-membrane signalling; cell motility and migration;cell death: different modes of cell death and their regulation.Unit 5: Manipulating and studying cellsIsolation of cells and basics of cell culture; observing cells under a microscope, different typesof microscopy; analyzing and manipulating DNA, RNA and proteins.Unit 6: Genome instability and celltransformationMutations, proto-oncogenes, oncogenes and tumour suppressor genes, physical, chemicaland biological mutagens; types of mutations; intra-genic and inter-genic suppression;transpositions- transposable genetic elements in prokaryotes and eukaryotes, role oftransposons in genome; viral and cellular oncogenes; tumor suppressor genes; structure,function and mechanism of action; activation and suppression of tumor suppressor genes;oncogenes as transcriptionalactivators.Unit 7: Plant breeding and geneticsSeed technology, Types of seed, Suicide seeds, terminator gene technology, Seed/Genebank, Hybrid and self seed, crop improvement, seed certification, Plant promoter andtranscription factors, Crop finger printing, plant breeding and GM crop,Text/References1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002).Molecular Biology of the Cell. New York: Garland Science.2. Lodish, H. F. (2000). Molecular Cell Biology. New York: W.H. Freeman.3. Krebs, J. E., Lewin, B., Kilpatrick, S. T., & Goldstein, E. S. (2014). Lewin’s Genes XI.Burlington, MA: Jones & Bartlett Learning.4. Cooper, G. M., & Hausman, R. E. (2009). The Cell: a Molecular Approach.Washington: ASM; Sunderland.5. Hardin, J., Bertoni, G., Kleinsmith, L. J., & Becker, W. M. (2012). Becker’s Worldof the Cell. Boston: Benjamin Cummings.6. Watson, J. D. (1987). Molecular Biology of the Gene (7th ed.). Menlo Park,CA: Benjamin/Cummings.7. Tropp et al, Principles of Molecular Biologycredits 3MSUGN-104: BiostatisticsUnit 1: Introduction to BiostatisticsBasic definitions and applications. Sampling: Representative sample, sample size, sampling biasand sampling techniques. Sampledistribution.Data collection and presentation: Types of data,methods of collection of primary and secondary data, methods of datapresentation, graphicalrepresentation by histogram, polygon, ogive curves and pie diagram.9
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BUnit 2: Measures of central tendency and Measure of dispersionMean, Medium and mode. Measures of variability: Standard deviation, standard error, range,mean deviation and coefficient of variation. Correlation and regression: Positive and negativecorrelation and calculation of Karl- Pearsons co-efficient of correlation. Linear regression andregression equation and multiple linear regression, ANOVA, one and two way classification.Calculation of an unknown variable using regression equation.Unit 3: Tests of hypothesisTests of significance: Small sample test (Chi-square t test, F test), large sample test (Z test) andstandard error. Introduction to probability theory and distributions, (concept without deviation)binomial, poison and normal (only definitions and problems) Computer oriented statisticaltechniques. Frequency table of single discrete variable, bubble spot, computation of mean,variance and standard Deviation. Randomized block design, complete block design.Text/References:1. Aitken, M., Broadhursts, B., & Haldky, S. (2009) Mathematics for BiologicalScientists. Garland Science.2. Billingsley, P. (1986). Probability and Measure. New York: Wiley.3. Rosner, B. (2000). Fundamentals of Biostatistics. Boston, MA: Duxbury Press.4. Daniel, W. W. (1987). Biostatistics, a Foundation for Analysis in the Health Sciences. NewYork: Wiley.MSUGN-105: Basic Genetics3 CreditsUnit 1: Introduction to GeneticsGreat milestones in Genetics; levels of Genetic analysis (Classical, Molecular & PopulationGenetics.Basic principles of Heredity – Segregation of a single gene, the principle; verification ofsegregation, segregation of two or more genes, test cross with unlinked genes.Patterns of Inheritance – Autosomal inheritance, Sex-linked inheritance andextrachromosomal inheritance-.Endosymbiont Theory, Genetic codes of Organelles,Respiration-defective Mitochondrial mutants, Cytoplasmic Male sterility in Plants, Cytoplasmictransmission of Symbionts.Mendelian principles of Inheritance – The Big experiment of Mendel, principle of independentassortment. Extensions; Modifications of Mendelian principles – Complete; Incompletedominance, Epistasis, Pleiotropic effects.Unit 2: Linkage, Recombination & Crossing OverRecombination is the basis of Gene mapping, Linkage mapping, Tetrad analysis, Genemapping in absence of Meiosis, Fine mapping.Genetic Variation – Genes; gene products, interaction between the alleles of one gene,interacting genes; proteins, applications of chi-square test to gene interaction ratios.Variations in Allele, Multiple alleles, Gene, Modifier genes, Partial penetrance; variableexpressivity, Lethal alleles, Phenotypes produced by Conditional alleles.Unit 3: Chromosomal variationPolyploidy [Classification (autopolyploids, allopolyploids), methods of production, cytologicaland genetic methods for identification, polyploid genetics (chromosome and chromatidsegregation), utility in crop improvementUnit 4: Drosophila GeneticsGenetic crosses. Chromosomal and Molecular basis of sex determination in Drosophila ,10
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BMolecular basis of dosage compensation in Drosophila.Unit 5: PedigreesGathering family history; Pedigree symbols; Construction of pedigrees, Presentation ofmolecular genetic data in pedigrees; Pedigree analysis of monogenic traitsReferences :(1) Daniel L. Hartl; Elizabeth W. Jones : Genetics – analysis of Genes &Genomes(2) Alan G. Atherly, Jack R. Girton& John F. McDonald : The Science of Genetics(3) Benjamin A. Pierce : genetics – a conceptual appro(4) D. Peter Snustad& Michael J. Simmons : Principles of Genetics(5) Griffiths, Wessler, Lewontin, Gelbart, Suzuki &Miller : Introduction to Genetic analysisMSUGN-191: Biochemistry and Analytical Techniquescredits 31.To prepare an Acetic-Na Acetate Buffer system and validate the Henderson-Hasselbachequation.2.To determine an unknown protein concentration by plotting a standard graph of BSAusing UV-Vis Spectrophotometer and validating the Beer- Lambert’s Law.3.Titration of Amino Acids and separation of aliphatic, aromatic and polar amino acids byTLC.4.An enzyme purification theme (such as E.coli Alkaline phosphatase or any enzyme ofthe institutions choice).a)Preparation of cell-free lysatesb)Ammonium Sulfate precipitationc)Ion-exchange Chromatagraphyd)Gel Filtratione)Affinity Chromatographyf)Generating a Purification Tableg)Assessing purity by SDS-PAGE Gel Electrophoresish)Assessing purity by 2-D gel Electrophoresisi)Enzyme Kinetic Parameters: Km, Vmax and Kcat.5.Biophysical methods (Circular dichroism spectroscopy, fluorescence spectroscopy).6.Determination of mass of small molecules and fragmentation patterns by MassSpectrometry11
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BMSUGN-192: Lab on Cytogeneticscredits31. Whole Blood Culture2. Lymphocyte Culture3. Blood Cell Determination4. Chromosome preparation: staining and observation5. Chromosome counting and determination of chromosome characteristicMSMB193: Data analysis using softwarecredits 21. Introduction to different statistical software.2. Determination of mean, median, mode of given data set.3. Determination of standard deviation and standard error of a given data set.4. Preparation of different types of graph from a given data set.5. Determination of statistical significance of the experimental data: Paired and unpaired t testand p value determination5. Nonparametric Mann-Whitney test, including confidence interval of difference of medians.6. Wilcoxon test with confidence interval of median.7. Usage of two and three way anova.8. Kaplan-Meier survival analysis12
M.Sc Genetics Syllabus 2019-20 Dept. of Biotechnology, MAKAUT,W.BSemesterIIMSUGN-201: Evolutionary Biology and Population GeneticsCredits 3Unit 1: Genetic constitution of a populationGenetic constitution of a population: (a) Gene frequencies and genotypes; (b) HardyWeinberg equilibrium; (c) Changes in gene frequency and continuous variation; (d)Mutation, Selection, Equilibrium. Polymorphisms; Values, means andvariance: (a) Metriccharacteristics, Population means; (b) Genetic components of variation; (c)Genotype andenvironment correlation; (d) Environmental variance.Unit 2: Basic definitions Gene pool, Gene drift, Migration & gene flow, Founder effects,extinction, Speciation, Reduction in gene flow and bottle-necks, Reproductive isolation.Unit 3: Quantitative trait lociQuantitative trait loci: (a) Major genes; (b) Methods of mapping QTLs; (c) Genetical andstatistical considerations; (d) QTLs in plants, fruit fly,mouse/rats, yeast; (e) Genomicmethods of mapping QTLs; (f) Haplotype mapping and genome-wide association studies(GWAS) ; (g) QT
KAUT,W.B SemesterI Code CourseTitle Contact Hrs./Wk Credit A Theory L-T-P MSUGN-101 Biochemistry 3-0-0 3
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