Structure of B. Sc (Biological Sciences) program under CBCS
DISCIPLINE:: GENETICS
SEMESTER / PAPER / COMP/ELEC / CODE / PAPER TITLESemester1 / Paper I / Compulsory / DSC 2 A / General Genetics
Semester2 / Paper II / Compulsory / DSC 2 B / Molecular Genetics
Semester 3 / Paper III / Compulsory / DSC 2 C / Recombinant DNA Technology
Semester 4 / Paper IV / Compulsory / DSC 2 D / Statistical Methods in Genetics
Semester 5 / Paper V / Compulsory / DSE 2 E / Population Genetics
Semester 6 / Paper VI
or
Paper VI
or
Paper VI / Elective A
Elective B
Elective C / DSE 2 F / Human Genetics
or
Animal Genetics & Breeding
or
Plant Genetics & Breeding
Semester 7 / Paper VII / Compulsory / DSE 2 G / Genome Informatics
Semester 8 / Paper VIII
or
Paper VIII / Elective A
Elective B / DSE 2 H / Genetic Diagnostic Techniques
or
DNA Cloning Techniques
Semester I
DSC 2 A (Paper I): General Genetics
Unit 1: Mendelian Genetics and Extensions
1.1 Mendelian Principles of inheritance - Law of segregation, Law of independent assortment; Chromosome theory of inheritance.
1.2 Incomplete dominance and codominance; Multiple alleles, Lethal alleles, Pleiotropy, Penetrance and Expressivity;
1.3 Two gene interactions – Epistatic, nonepistatic interactions; Polygenic inheritance – continuous variation, genetic variance and heritability, QTL .
1.4 Genes and environment –norm of reaction, phenocopies, developmental noise
Unit 2 Sex Linked Inheritance and Sex Determination
2.1 Sex Linked Inheritance - Sex linked inheritance in drosophila and human; Sex limited and Sex influenced inheritance
2.2 Sex Determination - Sex determination in drosophila – genic balance theory;
2.3 Sex determination in eukaryotes –heterogametic, homogametic, haplodiploidy, role of environmental factors, mosaics, gynandromorphs,
2.4 sex determination in melandrium; Sex determination in mammals- human Y chromosome
Unit 3 Extrachromosomal Inheritance
3.1 Mitochondrial inheritance (petite mutations);
3.2 Chloroplast inheritance (Variegation in Four o’clock plant);
3.3 Maternal inheritance-shell coiling in snail, ephestia pigmentation;
3.4 Infective heredity- symbionts in Drosophila,Kappa particles in Paramecium.
Unit 4: Linkage, crossing over and chromosome mapping
4.1 Linkage and chromosome mapping in eukaryotes – cytological basis of crossingover; recombination frequency, two factor and three factor crosses; interference and coincidence; Mitotic recombination; tetrad analysis in chlamydomonas.
4.2 Linkage and chromosome mapping in prokaryotes – bacteria and bacteriophages – transformation, transduction, conjugation; gene mapping in bacteria.
4.3 Genetic definition of gene - Complementation test, limitations of cis-trans test, intragenic complementation,rII locus of phage T4,concept of cistron
Unit 5: Cell Division - Variation in Chromosome number and structure
5.1 Mitosis and meiosis - Mitotic and meiotic transmission of chromosomes
5.2 Specialized chromosomes - Lampbrush chromosomes. Polytene chromosomes: Supernumerary chromosomes.
5.3 Variation in chromosome structure - Deletion, Duplication, Inversion, Translocation, Position effect
5.4 Variation in chromosome number - Euploidy and Aneuploidy
Practicals:
1. Mendel’s laws through seed ratios & Drosophila mutants.
2. Statistical tests in genetic analysis - application of laws of probability (product rule, sum rule, binomial probability); chi square test and its application in the analysis of genetic data.
3. Study of linkage, recombination, chromosome mapping using test cross data.
4. Pedigree analysis for dominant and recessive autosomal and sex linked traits.
5. Study of human genetic traits: Sickle cell anemia, XerodermaPigmentosum, Albinism, red-green Colour blindness, Widow’s peak, Rolling of tongue, Hitchhiker’s thumb and Attached ear lobe.
6. Incomplete dominance and gene interaction through seed ratios
7. Blood Typing: ABO groups & Rh factor.
8. Study of aneuploidy: Down’s, Klinefelter’s and Turner’s syndromes.
9. Permanent Slides showing Translocation Ring, Laggards and Inversion Bridge.
10. Mitosis & Meiosis through temporary squash preparation.
11. Squash preparation of salivary glands to observe polytene chromosomes.
12.Smear technique to demonstrate sex chromatinin buccal epithelialcells.
Suggested Readings
1. Gardner, E.J., Simmons, M.J., Snustad, D.P. (1991). Principles of Genetics, John Wiley & sons, India. 8th edition.
2. Snustad, D.P. and Simmons, M.J. (2010). Principles of Genetics, John Wiley & Sons Inc., India. 5th edition.
3. Klug, W.S., Cummings, M.R., Spencer, C.A. (2012). Concepts of Genetics. Benjamin
Cummings, U.S.A. 10th edition.
4. Griffiths, A.J.F., Wessler, S.R., Carroll, S.B., Doebley, J. (2010). Introduction to Genetic
Analysis. W. H. Freeman and Co., U.S.A. 10th edition.
Semester - II
DSC 2 B (Paper – II): Molecular Genetics
Unit 1: Nucleic acids – Structure and Organization
1.1 DNA as carrier of genetic information -Griffith’s, Hershey & Chase, Avery, McLeod & McCarty, Fraenkel-Conrat’s experiment.
1.2 Structure of DNA and RNA Genetic Material: DNA Structure - Watson and Crick model, Salient features of double helix, Types of DNA;
1.3 RNA Structure-mRNA, tRNA and rRNA
Unit 2 Genome organization
2.1 Organization of DNA: denaturation and renaturation, cot curves;
2.2 Prokaryotes, Viruses, Eukaryotes genome organization;
2.3 Organelle DNA -mitochondria and chloroplast DNA;
2.4 Transposable elements – prokaryotic and eukaryotic.
2.5 Organization of DNA in Chromosomes - Nucleosome – Chromatin structure -Euchromatin, Heterochromatin -Constitutive and Facultative heterochromatin.
Unit 3: DNA replication, Mutation, Recombination & Repair
3.1DNA replication - General principles –bidirectional, Semiconservative and semi discontinuous replication, RNA priming;
3.2DNA replicaton - Various models of DNA replication, including rolling circle, θ (theta) mode of replication, replication of linear ds-DNA, replication of the 5’end of linear chromosome; Enzymes involved in DNA replication.
3.3DNA Mutation – types of mutation; molecular basis of mutations; mutagens – physical and chemical agents; Detection of mutations – ClB method
3.4DNA Recombination & Repair: enzymes involved in recombination-Holliday model; types of DNA repair
Unit 4: Transcription & Translation
4.1Transcription in prokaryotes; Transcription in eukaryotes
4.2Processing and modification of RNA- Split genes - spliceosome machinery, splicing pathways; eukaryotic mRNA processing(5’ cap, 3’ poly A tail); Ribozymes, exon shuffling; RNA editing and mRNA transport.
4.3Translation - Ribosome structure and assembly, mRNA; Charging of tRNA, aminoacyl tRNA synthetases; genetic code - key experiments establishing Genetic code (deciphering & salient features- wobble hypothesis); central dogma
4.4Translation - Various steps in protein synthesis, proteins involved in initiation, elongation and termination of polypeptides; Post-translational modifications of proteins.
Unit 5: Regulation of Gene Expression
5.1 Regulation of gene expression in prokarytoes - principles of transcriptional regulation; Prokaryotes - Regulation of lactose metabolism and tryptophan synthesis in E.coli.
5.2 Regulation of gene expression in eukaryotes –heterochromatin, euchromatin, chromatin remodeling: regulation of galactose metabolism genes in yeast
5.3 DNA binding activators and co-activators, repressors, enhancers and silencers; DNA binding domains, transcription factors, heat shock proteins, steroids and peptide hormones; regulatory RNAs, riboswitches
5.4 Post-transcription gene silencing by RNAinterference
Practicals:
1. Preparation of LB medium and raising E. coli.
2. Isolation of genomic DNA from E. coli.
3. DNA isolation from cauliflower head.
4.Ultraviolet absorption spectrum of DNA and RNA
5.Determination of DNA and RNA concentration by A260nm
6.Determination of melting temperature and GC content of DNA.
7. DNA estimation by diphenylamine reagent.
8 Isolation of total RNA from yeast cells
9. Estimation of RNA by Orcinol method.
10. Separation of nucleotide based by chromatography.
Suggested Readings
1. Watson J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M., Losick, R. (2007). Molecular Biology of the Gene, Pearson Benjamin Cummings, CSHL Press, New York, U.S.A. 6th edition.
2. Snustad, D.P. and Simmons, M.J. (2010). Principles of Genetics. John Wiley and Sons Inc., U.S.A. 5th edition.
3. Klug, W.S., Cummings, M.R., Spencer, C.A. (2009). Concepts of Genetics. Benjamin
Cummings. U.S.A. 9th edition.
4. Russell, P. J. (2010). Genetics- A Molecular Approach. Benjamin Cummings, U.S.A. 3rd
edition.
5. Griffiths, A.J.F., Wessler, S.R., Carroll, S.B., Doebley, J. (2010). Introduction to Genetic
Analysis. W. H. Freeman and Co., U.S.A. 10th edition.
Semester - III
DSC 2 C (Paper- III): Recombinant DNA Technology
Unit 1 Introduction to recombinant DNA technology
1.1 Restriction endonucleases and other enzymes used in manipulating DNA molecules
1.2 Cloning vectors for prokaryotes and eukaryotes: Plasmids and bacteriophages as vectors for gene cloning. Cloning vectors based on E. coli plasmids, pBR322, pUC8, pGEM3Z. Cloning vectors based on M13 and λ bacteriophage Vectors for yeast, higher plants and animals.
1.3 Joining of DNA fragments: Ligation of DNA molecules. DNA ligase, sticky ends, blunt ends, linkers and adapters. Synthetic oligonucleotides, synthesis and use.
1.4 Generation of genomic and cDNA libraries; DNA markers.
Unit 2 Gene transfer methods and selection for recombinants
2.1 Selection for transformed cells - Uptake of DNA by cells, preparation of competent cells.
2.2 Identification for recombinants - insertional inactivation, blue-white selection.
2.3 Introduction of phage DNA into bacterial cells. Identification of recombinant phages. Introduction of DNA into animal cells, Introduction of DNA into plant cells
2.4 Methods for clone identification: The problem of selection, direct selection, marker rescue. Gene libraries, identification of a clone from gene library, colony and plaque hybridization probing, methods based on detection of the translation product of the cloned gene.
Unit 3 PCR and DNA sequencing
3.1 Polymerase chain reaction: Fundamentals of polymerase chain reaction,
3.2 designing primers for PCR. Studying PCR products, Cloning PCR products. Real time PCR.
3.3 DNA sequencing: DNA sequencing by Sanger’s method, modifications based on Sanger’s method. Automated DNA sequencing. Pyrosequencing.
Unit 4 Expression of Cloned genes
4.1Expression of cloned genes - Vectors for expression of foreign genes in E. coli,
4.2 cassettes and gene fusions.
4.3Challenges in producing recombinant protein in E. coli.
4.4Production of recombinant protein by eukaryotic cells. Fusion tags and their role in purification of recombinant proteins.
4.5Site–directed mutagenesis and protein engineering.
Unit 5 Applications of genetic engineering
5.1Applications in production of recombinant pharmaceuticals - insulin, human growth hormone, factor VIII. Recombinant vaccines.
5.2 Genomics - organization of genomes, mapping and sequencing genomes.
5.3 Analysis of transcriptome- microarrays, EST
5.4 Proteomics- structural and functional proteomics
Practicals
1. Isolation of plasmid DNA from E. coli cells.
2. Digestion of plasmid DNA with restriction enzymes.
3.Estimation of size of a DNA fragment after electrophoresis using DNA markers
4. Construction of restriction digestion maps from data provided
5. Amplification of a DNA fragment by PCR.
6. Transformation of E. coli cells with plasmid DNA.
7. Hyper expression of poly histidine-tagged recombinant protein and purification using Ni-affinity resin.
8. Complementation of beta−galactosidase for Blue and White selection.
9. Recovery of DNA from low-melting temperature agarose gel
10. SDS gel electrophoresis of proteins
11. Southern blotting
12. Western blotting.
Suggested Readings
1. Gene Cloning and DNA Analysis (2010) 6th ed., Brown, T.A., Wiley-Blackwell publishing(Oxford, UK), ISBN: 978-1-4051-8173-0.
2. Principles of Gene Manipulation and Genomics (2006) 7th ed., Primrose, S.B., and Twyman, R. M., Blackwell publishing (Oxford, UK) ISBN:13: 978-1-4051-3544-3.
3. Molecular Biotechnology: Principles and Applications of Recombinant DNA (2010) 4th ed., Glick B.R., Pasternak, J.J. and Patten, C.L., ASM Press (Washington DC), ISBN: 978-1-55581-498-4 (HC).
Semester - IV
DSC 2 D (Paper- IV): Statistical Methods in Genetics
Unit 1 Descriptive Statistics
1.1 Classification and tabulation of data – frequency distribution, graphical representation of data, histogram, frequency polygon, frequency curve.
1.2 Measures of Central tendency – definition and calculation of arithmetic mean, geometric mean, harmonic mean, median quantiles and mode in grouped and ungrouped data
1.3Measures of Dispersion - definition and calculation of range, quartile deviation, mean deviation, standard deviation and variance, coefficient of variation.
Unit 2 Elementary Probability
2.1 Mathematical definition of probability of an event, Use of permutations and combinations in calculations of Probability
2.2 Conditional probability, Additive and Multiplication law of Probability, Random Variables, Mathematical expectation and variances
2.3 Probability Distributions: Binomial, Poisson and normal distributions.
Unit 3 Correlation and Regression
3.1Correlation and Regression — Relationship between variables
3.2Covariance, Karl-Pearson's Correlation Coefficient, Spearman's rank Correlation Coefficient,
3.3 Least square technique for regression lines,
3.4 Regression Coefficients, Relationship between Correlation analysis and Regression Analysis.
Unit 4 Statistical Inference
4.1 Hypothesis Testing — Sample, Population, Statistics and Parameters,
4.2 Basic principles of hypothesis testing: test, critical region, type I error and type II error, level of significance. Null Hypothesis, Level of significance,
4.3 Chi–square, ‘t’ and ‘F’ variates - Applications in testing of hypothesis.
Unit 5 Analysis of Variance
5.1 Analysis of variance for one-way classified data,
5.2 Analysis of variance for two-way classified data with one observation for cell, analysis of variance
5.3 Analysis of variance for two-way classified data with one observation for cell, analysis of variance for two-way classified data with multiple but equal number of observations per cell.
Practicals
1.Frequency distribution
2.Various types of graphs
3.Mean, geometric mean, harmonic mean
4.Median, quartiles deviation, mean deviation
5.Standard deviation, variance and coefficient of varition
6.Testing of hypotheses regarding population mean
7.Testing of hypotheses about the difference between population means
8.Chi-square test
9.Testing of Correlation Coefficient
10.Fitting of simple linear regression
11.One-way ANOVA
12.Two-way ANOVA
Suggested Readings
1. Fowler, J., Cohen, L. and Jarvis, P. (1998). Practical Statistics for Field Biology. John Wiley and Sons, 2nd ed. .
2. Bland, M. (2006). An Introduction to Medical Statistics. Oxford University Press, 3rd ed.
3. Finney, D.J. (1980). Statistics for Biologists. Chapman and Hall Ltd.
4. Wayne, W, Daniel (1999). Biostatistics: A Foundation for Analysis in Health Sciences. John Wiley and Sons, 7th ed.
Semester – V
DSC 2 E (Paper V): Population Genetics
Unit 1 Hardy-Weinberg Equilibrium
1.1 Allele frequencies - deriving genotypic & allelic frequencies, deriving allelic frequencies from molecular data, changes in allele frequencies.
1.2 Polymorphism - phenotypic & genotypic polymorphisms, transient polymorphism, balanced polymorphisms
1.3 Random & Non-random mating – positive & negative assortative mating, role in population size & change in gene frequency.
1.4 Hardy-Weinberg method & its applications – calculating allelic frequencies, assumptions of Hardy-Weinberg equilibrium, proof of Hardy-Weinberg equilibrium, Generation time, testing for fit to Hardy-Weinberg equilibrium