II SEMESTER SYLLABUS 

MSC BIOTECHNOLOGY-I YEAR

SEMESTER- II

BT 201 T-MOLECULAR BIOLOGY-THE GENOME

1. Course Objectives (C.Obj)

a. To give insights into genome organization of prokaryotes and eukaryotes

b. To impart knowledge on the process of genome replication in prokaryotes andeukaryotes

c. To enable basic understanding of DNA damage and repair pathways

d. To give insightsinto genome rearrangements and recombination mechanisms 

2. Course Outcomes (C.O)

a.  Knowledge on organization of prokaryotic and eukaryotic genome

b. Understanding of DNA replication in prokaryotes and eukaryotes

c. Comprehension of DNA damage and repair pathways involved

d. Knowledge of mechanisms of DNA recombination and genome rearrangements and their role in genome evolution

Course Plan/Schedule

UNIT 1 Genome Organization 

1.1 Historicalperspective: DNA as a genetic material, structure of DNA, Genome size, C-value paradox 3

1.2 Organization of prokaryotic genome and eukaryotic nuclear genome (Chromosome number, Gene size, Gene density) 2

1.3 Unique sequences, repeated sequences – interspersed and tandem repeats; satellite DNA, mini satellites and microsatellites 3

1.4 Gene families (Clustered and Dispersive – Hemoglobin gene and Histone gene clusters) 3

1.5 Pseudogenes– processed and unprocessed 2

1.6 Organization of Mitochondrial and Chloroplast genomes 3

UNIT 2 Genome Replication 

2.1 DNA Replication– enzymes involved in the replication of DNA, Origin of replication fork 3

2.2 Replication of Prokaryotic genome and plasmid DNA 2

2.3 Replication of nuclear genome of eukaryotes, mitochondrial and chloroplast 3

2.4 Regulation of genome replication (Prokaryotes and Eukaryotes) 3

2.5 Replication associated errors 3

2.6 Inhibitors of DNA replication 2

UNIT 3 DNA Damage and Repair 

3.1 Spontaneous and Induced mutations, physical and chemical mutagens 2

3.2 DNA damages (oxidative damages, depurinations, depyrimidinations, O6-methylguanines, cytosine deamination, single and double strand breaks) 3

3.3 Types of mutagenesis–transition, transversion, frameshifts, missense and non-sense mutations 2

3.4 Repair mechanisms– Photo-reactivation, Excision repair (base excision repair, nucleotide excision repair), mismatch repair, SOS repair, recombination repair 4

3.5 Proof reading activity of DNA polymerases, Direct reversal of damaged DNA, Post-replication repair 2

3.6 Cellular responses to DNA damage, DNA repair defects and disorders 3

UNIT 4 Genome Rearrangements and Recombination 

4.1 Homologous recombination (Holliday junctions, rec BCD pathways), Site-specific recombination, Non-Homologous recombination 3

4.2 Mechanism and Regulation of Meiotic Recombination ,Whole genome duplication  3

4.3 Mechanism of Gene Duplication and Amplification: Insertion, deletion and translocation of sequences (Eg– flip-flop inversion, yeast mating type, TetrahymenaDNA) 3

4.4 Transposable genetic elements:Types of mobile elements, mechanisms of transposition, Transposable elements in prokaryotesand eukaryotes 3

4.5 RetrotransposonclassI and classII, Retrogenes, Transposons and their role in genome evolution 2

4.6 DNA rearrangements and Genome instability  2

PRACTICALS  

BT 251 P- MOLECULAR BIOLOGY– THE GENOME

S.No. Topics to be covered 

1 Isolation of Genomic DNA from bacteria 

2 Isolation of Genomic DNA from plants 

3 Isolation of Genomic DNA from human blood 

4 Determine purity of DNA by agarose gel electrophoresis 

5 Determination of melting temperature of DNA 

6 Re-association Kinetics and estimation of Cot values 

7 Induction of mutations by chemical agents 

8 Determination of DNA damage by Comet assay 

 REFERENCE BOOKS

1. Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, 

Keith Roberts and Peter Walter.

2. Molecular Biology of the Gene by J.D. Watson, N.H. Hopkins, J.W, Robertis, A. 

Steitz& A.M. Weiner, Benjamin Cummings Publ. California

3. Molecular Cell Biology Lodish, H., Baltimore, D; Fesk, A, Zipursky S.L., Matsudaride, P. and Darnel American Scientific Books. W.H. Freeman, NewYork

4. Genes VII. Benjamin Lewis, OxfordUniv. Press, Oxford

5. Molecular Biology by D, FreifelderNarosa Publishing house New York, Delhi

6. Advance Molecular Biology Twyman, R.M., Bios Scientific publishers Oxford 

7. Molecular Biology by T.A. Brown

8. Essentials of Molecular Biology. D. Freifelder, Panima publishing co-operation

9. Genes & Genomes – A changing perspective by Singer &Berr, Universal Science Books, California.

10.DNA Damage Repair, Repair Mechanisms and Aging by Allison E. Thomas Nova Science Publisher's, 2010.

11. Chromosomal Translocations and Genome Rearrangements in Cancer by Janet D. Rowley,Michelle M. Le Beau, Terence H. RabbittsSpringer International Publishing, 2015.

BT 202 T– MOLECULAR BIOLOGY– GENES TO PROTEINS

1. Course Objectives:

a) To give an overview and impart conceptual understanding of prokaryotic and eukaryotic genes and their organization

b) To give molecular insights into transcription and RNA processing

c) To highlight the important mechanisms and components, their role in translation 

d) To create a understanding aboutgene regulation and epigenetics

2. Course Outcomes:

a) Lay foundation to gene and gene organization

b) Acquire knowledge abouttranslation

c) Provide understanding of the core principles of genetic code and protein synthesis

d) Facilitates understanding the gene regulation and epigenetics

Course Plan/Schedule:

UNIT 1 Prokaryotic and Eukaryotic genes 

1.1 Structure of Prokaryotic gene, operons, polycistronic mRNA, inducible operon (Lac operon), repressible operon (Trp operon) 3

1.2 Fine structure of eukaryotic gene (Core and proximal promoters & enhancers, exons, introns,UTRs), monocistronic mRNA 3

1.3 Number of genes: prokaryotic gene number (parasitic and non– parasitic), eukaryotic gene number (unicellular, multicellular, humans & male specific genes) 2

1.4 Essential genes– Proportion and distribution in the genome (prokaryotes and eukaryotes) 3

1.5 Functional RNA genes (rRNA, tRNA) 2

1.6 Regulatory small RNA coding genes (snoRNA, snRNA, miRNAs, lnc RNAs) 3

UNIT 2 Transcription and RNA processing 

2.1 Transcription factors, activators, specific factors (Zinc fingers, Leucine zippers, helix loop helix and homeodomain); Types of RNA polymerases 3

2.2 Transcription in prokaryotes (components; initiation, elongation and termination of transcription) 3

2.3 Transcription in eukaryotes (components; initiation, elongation and termination of transcription 3

2.4 Post-transcriptional processing, 5’-capping and poly-adenylation. 3

2.5 RNA editing and processing, Splicing mechanism- alternate splicing, self-splicing & trans-splicing 3

2.6 Transcription inhibitors and their applications 1

UNIT 3 Translation and Post translational modifications  

3.1 Properties of genetic code (universal code, degeneracy, redundancy) 2

3.2 Correspondence of amino acid sequence with nucleotide sequence in DNA (Single letter codefor amino acids) 1

3.3 Translation machinery in prokaryotes, initiation (IF-1, IF-2,IF-3) (t-RNA charging, disassociation & assembly of ribosomal subunits) 2

3.4 Elongation  (EF-Tu, EF-Ts, EF-G) (translocation, t-RNA identity, aminoacyl t-RNA, peptide bond formation), termination (RF-1, RF-2, RF-3) (termination codons) 2

3.5 Translation mechanism in eukaryotes, initiation (factors, assembly of ribosomes), elongation, termination 2

3.6 Translational activators and inhibitors  2

3.7 Post translational modifications of proteins: glycosylation, lipidation, acetylation, ubiquitination, protein splicing, chaperones, modification of amino acids, disulphide bond formation, peptide bond cleavage and isomerization 3

UNIT 4 Regulation of Gene expression and Epigenetics 

4.1 Control of gene expression at transcription and translation level, co-ordinated regulation of gene expression 2

4.2 Regulation of gene expression in eukaryotes- genes controlling yeast mating type, regulation of Xenopus 5s rRNA in oocytes, using a strategically placed enhancer as genetic switch – chicken globin genes 3

4.3 Gene regulation exerted at the level of translation – silk fibroin gene, regulation at splice site selection – Drosophila sex determination 3

4.4 Gene regulation in eukaryotes (antisense RNA & RNAi) 2

4.5 Role of chromatin in regulating gene expression and gene silencing, DNA methylation, histone modification (acetylation, deacetylation, analysis of epigenetic modifications, epigenetic memory) 2

4.6 Genome wide mapping of chromatin factors and modifications 2

4.7 Role of nutrition and environment in epigenetic modifications  2

PRACTICALS

BT 252 P (B)

S.No Topics to be covered 

1 Isolation of plasmid DNA from bacteria 

2 Determination of purity and concentration of DNA– Spectrophotometric method 

3 Induction of lac operon 

4 Protein overexpression and isolation 

6 Protein analysis by SDS electrophoresis 

7 Isolation of mRNA from blood/tissue andcDNA synthesis 

8 Gene expression analysis byqRTPCR 

REFERENCE BOOKS

1. Molecular Biology of the Gene by J.D. Watson, N.H. Hopkins, J.W, Robertis 

2. A.Steitz& A.M. Weiner, Benjamin Cummings Publ. California 

3. Genes VII. Benjamin Lewin, Oxford Univ. Press, Oxford 

4. Molecular Biology by D. FreifelderNarosa Publishing house New York, Delhi, 

5. Molecular Cell Biology H.Lodish, D.Baltimore, A.Fesk,S.L.Zipursky, P.Matsudaride and Darnel American Scientific Books. W.H. Freeman, New York 

6. Advance Molecular Biology R.M.Twyman, Bios Scientific publishers Oxford 

7. Molecular Biology by T.A. Brown

8. Essentials of Molecular Biology. D. Freifelder, Panima publishing co-operation

BT 203 T- IMMUNOLOGY

1. Course Objectives (C.Obj)

a. To give an overview of different types of immunities, cells & organs involved in the immune system and to provide the insights into immunogenicity and antigenicity

b. To understand the structure and function of immunoglobulins and their generation

c. To gain knowledge on structure and function ofMajor Histocompatibility Complex

d. To provide the comprehensive understanding of the cell mediated immune responses & in-depth knowledge about autoimmunity & immunodeficiency disorders.

2. Course Outcomes (C.O)

a. Basic understanding and importance of the immune system 

b. The importance and applications of immunoglobulins in therapeutics can be known

c. Appreciate the importance of MHC in organ transplantation

d. Knowledge about the cell mediated immune responses and creates awareness regarding autoimmune and immunodeficiency disorders.

Course Plan/Schedule:

UNIT 1 Basics principles of Immunology 

1.1 Immunity– Types of Immunity, Innate immunity- Anatomic barriers, physiological barriers, phagocytic barriers, microbial antagonism, inflammation; Acquired Immunity– characteristics 3

1.2 Cells of the Immune System– lymphoid cells (B & T-Lymphocytes; T cell subsets; NK cells), Mononuclear phagocytes (monocytes, macrophages), Granulocytes (neutrophils, eosinophils, basophils, mast cells, dendritic cells); haematopoiesis and differentiation 3

1.3 Organs of the immune system: primary lymphoid organs (Bone marrow and Thymus); secondary lymphoid organs (lymph nodes, spleen, mucosal-associated lymphoid tissue and cutaneous asscociated lymphoid tissue) 3

1.4 Antigens– Immunogenicity versus Antigenicity, Factors that influenceimmunogenicity, Epitopes– Properties of Bcell epitopes and T cell epitopes, Haptens 3

1.5 Complement system– functions and components of complement system; complement activation; regulation of complement system 2

1.6 Deficiencies of innate immune mechanisms– Chronic Granulomatous Disease (CGD), Leukocyte-adhesion deficiency 2

UNIT 2 B-cell development and Immunoglobulins: Structure and Functions 

2.1 Basic structure of Immunoglobulins– The role of multiple myeloma in understanding Ig structure; Fine structure of Immunoglobulins– Immunoglobulin domains-variable region and constant region domains; isotypes, allotypes, idiotypes 3

2.2 Immunoglobulin classes– IgG, IgM, IgA, IgD and IgE; functions of Ig classes; effector functions of antibodies, Organization and expression of immunoglobulin light and heavy chain genes 3

2.3 B-cell activation and proliferation by Thymus Independent and Thymus Dependent antigens; invivo sites for induction of humoral response; B-cell differentiation, classswitching and generation of plasma cells and memory cells 3

2.4 Antigen antibody interactions and applications (immunodiffusion tests, ELISASandwich, Indirect, Dot; Western Blot, Flow cytometry, immunoprecipitation, immunoelectrophoresis, immunoflourescence, immunoelectron microscopy) 3

2.5 Polyclonal antibodies; Monoclonal Antibodies– Production of Monoclonal Antibodies– Formation and selection of hybrid cells; Antibody engineering– human antibodies from phage display; antibodies in immunotherapy– Targeting of therapeutic immunomolecules 3

2.6 B-cell immunodeficiency disorders– X-linked agammaglobulinemia, selectiveimmunoglobulin deficiency 1

UNIT 3 Major Histocompatibility Complex (MHC) and Tumor Immunology 

3.1 General organization and inheritance of MHC; MHC Haplotypes 3

3.2 The structure of MHC class I and class II molecules; organization of MHC class I and class II genes, peptide binding of MHC molecules 2

3.3 Polymorphism of MHC class I and class II molecules; cellular distribution of MHC molecules; MHC molecules and immune responsiveness and disease susceptibility 3

3.4 Types of grafts; Mechanism of graft rejection; immunological basis of graft rejection; Graft versus host reactions 3

3.5 Human leukocyte antigen (HLA) typing by mixed lymphocyte reaction (MLR), microcytotoxicity tests and by PCR; Role of HLA typing in organ transplantation 3

3.6 Tumors of the immune system– Tumor antigens, Immune response to tumors, tumor escape mechanisms; Cancer immunotherapy approaches 2

UNIT 4 Cell-mediated Immune Responses 

4.1 Antigen processing by antigen presenting cells; the structure and functions of Tcell receptors (TCR); the TCR-peptide-MHC tri-molecular complexes 3

4.2 Cytokines– properties; cytokine receptors; Th1 and Th2 type of cytokines; Therapeutic uses of cytokines 3

4.3 Cell-mediated immune response: General properties of effector Tcells;Direct cytotoxic response; experimental assessment of cell-mediated cytotoxicity 3

4.4 Hypersensitivity– types; Delayed Type Hypersensitivity (DTH) and cytokines involved in DTH 2

4.5 Auto-immunity– mechanisms and auto-immune diseases-Insulin Dependent Diabetes; Rheumatoid Arthritis, Auto-immune Thyroid disease, Systemic lupus erythematosus (SLE) 3

4.6 T cell primary immunodeficiency disorders– Severe combined immunodeficiency (SCID), Di George syndrome; Secondary immunodeficiency disorders- acquired immune deficiency syndrome (AIDS) 2

PRACTICALS

BT 253 T- IMMUNOLOGY

S.No Topics to be covered 

1 ABO blood typing, Micro-hemagglutination Test

2 Double diffusion 

3 Single Radial Immunodiffusion 

4 Dot ELISA 

5 Western Blot by Enzyme-conjugated antibody 

6 Sandwich Enzyme Linked Immunosorbent Assay 

7 Cell-viability test by Trypan Blue 

8 Principle and procedure for enumeration of specific cell types by Fluorescent

Activated Cell Sorter (FACS) 

REFERENCE BOOKS

1. Essential Immunology– By I. Roitt, Publ: Blackwell

2. Immunology– By G. Reever& I. Todd, Publ: Blackwell

3. Immuno diagnostics– By S.C. Rastogi, Publ: New Age

4. Immunology: By Richard A. Golds, Thomas J Kindt, Barbaraa A. Osborne,Janis Kuby

5. Fundamental immunology– By William E.Paul.

6. Basic Immunology– By Bhoosreddy G.L. and Wadher B.J.

7. Text book of immunology– By Baruj Benacerraf

BT 204 T- MICROBIAL TECHNOLOGY

1. Course Objectives:

a) To give an overview of the fundamentals of microbial technology

b) To give basic understanding of fermentation processes

c) To create an understanding about microbial products

d) To highlight important applications of microbial technology

2. Course Outcomes:

a) Lay foundationto basics in microbial technology

b) Acquire knowledge of fermentation technology

c) Provide understanding of various products of industrial importance

d) Facilitates understanding the importance of microbial technology in industry

Course Plan/Schedule:

UNIT 1 Fundamentals of Microbial technology 

1.1 General concepts of microbial technology, principles of exploitation of micro-organismsand their products, Industrial microorganisms– Bacteria, Algae and Fungi 3

1.2 Screening of microorganisms for industrial products 2

1.3 Isolation and preservation of microorganisms for industrial products;isolation, selection and improvement of microbial cultures 3

1.4 Strain development– strategies of strain improvement,mutation, selectionandrecombination 2

1.5 Use of recombinant DNA technology and protoplast fusion techniques for strainimprovement, problems associated with strain improvement  3

1.6 Improvement of characters other than products and their application in the industry 3

UNIT 2 Processes for Microbial Fermentation 

2.1 Brief history of fermentation; Fermentation–general concepts; Fermentation design–Overview of aerobic and anaerobic fermentation process;Submerged and solid statefermentation 3

2.2 Factors affecting submerged and solid state fermentation (SSF); Substrates used in SSF and their advantages; Applications of fermentation 3

2.3 Importance of media in fermentation; media types: components and formulations  2

2.4 Substrates with sources for Carbon and Nitrogen,inoculum development 2

2.5 Storage of cultures forrepeated fermentations, production of microbial biomass  3

2.6 Factors affecting fermentation process 3

UNIT 3 Microbial products and Food additives 

3.1 Organic acids– Citric acid, Lactic acid, Acetic acid, Gluconic acid 2

3.2 Amino acids– Glutamic acid, Lysine, Aspartic acid 2

3.3 Enzymes– Proteases, Amylases, Lipases, Cellulases & Pectinases; Enzyme Biosensors 3

3.4 Food fermentations and food produced by microbes; Dairy products– Cheese, Yoghurt;Other products-bread, cheese, vinegar, fermented dairy products 3

3.5 Oriental fermented foods, microbial cells as food-single cell proteins; production ofalcohol and fermented beverages, beer and wine 3

3.6 Microbial and Chemical safety of food products; Food quality & control: Analysis offood 3

UNIT 4 Applications of Microbial technology 

4.1 Health care: Production of antibiotics–penicillin, streptomycin and erythromycin 3

4.2 Production of therapeutic drugs, recombinant vaccines–BCG, Hepatitis-B 3

4.3 Monoclonal antibodies, Insulin, Vitamins–B12, D & C, Riboflavin, Cyanocobalamin 3

4.4 Biofuel and Biodiesel production, methane, alcohol, hydrogen 3

4.5 Biomining–Extraction of Cu, Au and U from ore 2

4.6 Bioplastics (biopolymers), Bioremediation 2

PRACTICALS: 

BT 254 P: MICROBIAL TECHNOLOGY

S.No. Topics to be covered 

1 Production of Organic acids 

2 Production and estimation of alcohol 

3 Screening for amylase producing organisms 

4 Production and assay of amylase activity 

5 Preparation of wine from grapes 

6 Production of penicillin/ampicillin 

7 Production of antibiotics from bacteria 

REFERENCE BOOKS

1. Text Book of Biotechnology–By H.K. Das (Wiley Publications)

2. Biotechnology–By H.J. Rehm and G. Reed.VIH Publications, Germany

3. Biogas Technology- By B.T. Nijaguna

4. Biotechnology- By K. Trehan

5.Industrial Microbiology- By L.E. Casida

6.Food Microbiology- By M.R. Adams and M.O. Moss

7.Introduction to Biotechnology- By P.K. Gupta

8.Essentials of Biotechnology for Students- By Satya N. Das

9.Bioethics– Readings and Cases- By B.A. Brody and H. T. Engelhardt. Jr. (PearsonEducation)

10. Bioprocess Engineering-By Shuler (Pearson Education)

11. Essentials of Biotechnology-By Irfan Ali Khan and AtiyaKhanum (UkaazPublications)

12. Gene, Genomics and Genetic Engineering- By Irfan Ali Khan and AtiyaKhanum(Ukaaz Publications)