SYLLABUSpupdepartments.ac.in/syllabi/Academic Session 2016-17... · Web viewEstimation of DNA by DPA method and RNA by Orcinol method. Isolation of plasmid and genomic DNA of E. coli

SYLLABUSM.Sc. (Hons.) Biotechnology

Sessions 2016-17 and 2017-2018The course will consist of four semesters, two in each year. In each of the semesters I, II and III, there would be four theory papers and two practical papers. In semester IV, there would be two theory papers and one practical paper. In addition to this, students would undertake research as project work on problems relevant to Biotechnology in semester IV. As the project work is time bound and to be completed with in the stipulated period of IVth semester, a maximum of three students can work under the supervision of a teacher. Only those faculty members fulfilling the qualifications as per UGC guidelines can supervise the project work. The students will undertake in-plant training of 4-6 weeks at various industries/institutions/R & D centers at the end of semester II, which would be evaluated in semester III and IV. During the M.Sc. course, the students would visit at least two industries/R & D centers to become familiar with the industrial operations and sophisticated scientific equipments, etc. Hands-on training to the students on sophisticated equipments like CHN analyzer, biochemical analyzer, HPLC, HP-TLC, GC, AAS, fluorescence microscope, phase contrast microscope, inverted microscope, electron microscope, electrochemical analyzer, electrochemical work station, fiber optic spectrofluorimeter, RT-PCR, gel documentation system, ELISA reader, ultracentrifuge, CO2 incubator, ultrasonicator, fermenter (10 L capacity), protein purification system (AKTAPRIME+), boiler, etc. during the practical classes is mandatory. Each theory paper shall have 4 hours teaching and 3 practical hours per week. Each theory paper shall be of 100 marks of which 75 marks shall be allocated to theory paper set by external examiner and 25 marks to the internal assessment. The internal assessment would comprise of one assignment of 5 marks, one seminar of 5 marks and test of 10 marks (average of the two tests shall be considered), and attendance of 5 marks. The awards of internal assessment shall be dispatched by the Head of the department before the commencement of semester examinations. The seminars would be allotted to all the students from the respective syllabi of theory papers in such a way that each student would be assessed by the teacher of the subject. The subjects and distribution of marks shall be as under:

Semester-ITheory Papers Paper I: Macromolecular Biochemistry & Metabolomics 100 Marks Paper II: Advanced Molecular Genetics & Genomics 100 Marks Paper III: General Microbiology 100 Marks Paper IV: Immunology & Immunotechnology 100 Marks Practical Papers Practical Paper I: Pertaining to theory paper I and II 100 Marks Practical Paper II: Pertaining to theory paper III and IV 100 Marks Total 600 Marks

Semester-II Theory Papers Paper V: Genetic & Metabolic Engineering 100 Marks Paper VI: Molecular Biophysics & Macromolecular Modeling 100 Marks Paper VII: Bioprocess & Biochemical Engineering 100 Marks Paper VIII: Advanced Fermentation Technology 100 Marks Practical Papers Practical Paper III: Pertaining to theory paper V and VI 100 Marks Practical Paper IV: Pertaining to theory paper VII and VIII 100 Marks Total 600 Marks

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Semester-III Theory Papers Paper IX: Enzymology & Enzyme Technology 100 Marks Paper X: Food Biotechnology 100 Marks Paper XI: Advanced Environmental Biotechnology 100 Marks Paper XII: Entrepreneurship & Legal Biotechnology 100 Marks Practical Papers Practical Paper V: Pertaining to theory paper IX and X 100 Marks Practical Paper VI: Pertaining to theory paper XI and XII 100 Marks Total 600 Marks

Semester-IIITheory Papers Paper XIII: Animal Cell & Plant Tissue Culture Technology 100 Marks Paper XIV: Computational Biology & Applied Bioinformatics 100 Marks Practical Paper Practical Paper VII: Pertaining to theory paper XIII and XIV 100 Marks In-Plant Training* Satisfactory/Unsatisfactory Project Work** Satisfactory/Unsatisfactory Total 300 Marks

*In-plant training seminars shall be evaluated by a board of three teachers and the result would be communicated by Head of the Department before commencement of semester IV examinations. *Project work would be evaluated by one examiner and the result would be communicated by Head of the Department after the evaluation of project work by the examiner. 4

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M.Sc. (Hons.) Biotechnology Part ISemester I

PAPER-IMACROMOLECULAR BIOCHEMISTRY & METABOLOMICS

M. Marks: 75 Lectures to be delivered: 60 Time allowed: 3 Hours Pass Marks: 40% (Theory and

Practical separately)

INSTRUCTIONS FOR THE PAPER SETTERSThe question paper will consist of three sections A, B and C. Section A and B will have four questions from the respective sections of the syllabus and carry I5 marks each. Section- C will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 15 marks in all. INSTRUCTIONS FOR THE CANDIDATES

1. Candidates are required to attempt two questions each from sections A and B and the entire Section C.

2. The use of scientific calculators is allowed.

SECTION- A1. Introduction to macromolecules: Macromolecules and their monomeric subunits, fitness

of the aqueous environment for living organisms, ionization of water, water as a reactant, pH, Handerson-Hasselbalch equation, biological buffers, amino acid titration curves, four levels of architecture of proteins, interactions stabilizing 3D structure of proteins, purification and protein functions, peptide synthesis by automated solid phase.

2. Structure, functions and properties of carbohydrates and nucleic acids: Nomenclature and classification of carbohydrates, polysaccharides (cellulose, starch, chitin, pectin, hyaluronic acid), glycoconjugates (proteoglycans, glycoproteins and glycolipids), nature of glycosidic bond, properties of monosaccharides, analysis of carbohydrates, purine, pyrimidines, nucleosides and nucleotides, structure of DNA and RNA, internucleotide bonding, properties of DNA, nucleoproteins and viruses, solid phase synthesis of DNA.

3. Structure, function and properties of lipids: Fatty acids (saturated, unsaturated and essential), neutral lipids, phospholipids, sphingolipids, and isoprenoids, eicosanoids and phosphatidyl inositol as intracellular messanger, separation and analysis of lipids.

4. Enzymes: Classification, nomenclature and properties of enzymes, enzyme kinetics, Michaelis-Menten equation, turn over number, enzyme catalysis with two substrates (ternary complex or ping-pong mechanism), enzyme inhibition, isozymes, catalytic antibodies, purification.

5. Biological membranes, bacterial cell wall, membrane channel and pumps: Micelles, liposomes, properties of biological membranes, fluid mosaic model, membrane mediated transport, Donnan effect, sodium-potassium pump, calcium pump, calcium-sodium exchanger, symporters and antiporters, physical and chemical composition of bacterial cell wall and biosynthesis.

6. Biosignalling: Molecular mechanism of signal transduction (specificity, amplification, desensitization/adaption, and integration), Molecular circuits (receptors, enzymes, channels and regulatory proteins).

SECTION-B

7. Metabolomics & protein metabolism: Metabolic flux analysis; Metabolic control analysis;

Redirecting metabolic flow.

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8. Carbohydrate metabolism: Glycolysis, TCA cycle, pentose phosphate pathway, ED-pathway,

gluconeogenesis, glycogenolysis and glycogen storage and diseases, uronic acid pathway,

regulation of carbohydrate metabolism, oxidative phosphorylation.

9. Lipid metabolism: Oxidation of fatty acids, synthesis of fatty acids including essential fatty

acids, biosynthesis of neutrallipids, phospholipids and cholesterol, regulation of fatty acid

metabolism.Nucleic acid metabolism: Biosynthesis anddegradation of purines and

pyrimidines, nucleotides and their regulation, disorders of nucleic acid metabolism.

10. Biosynthesis of essential amino acids, regulation of amino acid biosynthesis, metabolic

breakdown of amino acids leading to Krebs cycle intermediates, urea cycle, disorders of

phenylalanine breakdown (PKU) and inherited defects of urea cycle.

11. Calcium, phosphorous, vitamins and hormone metabolism: Structure and functions of fat

soluble and water soluble vitamins, hormones, biological functions of calcium (Structure,

function, signaling function and enzymatic functions) and phosphorous, disorders of

calcium-insulin-vitamin D, phosphorous, parathyroid hormones and calcitonin.

12. Plant metabolism: Photosynthetic pigments, cyclic and non-cyclic electron flow, C-3 cycle

and C-4 cycles, CAM, glyoxylate pathway, calvin cycle, nitrogen fixation and role of

nitrogenase complex.

Recommended Readings: 1. Biochemistry by L. Stryer, W.H. Freeman and Company, New York (2002). 2. Harper's Illustrated Biochemistry by R.K. Murray, D.A. Bender, K.M. Botham, P.J.

Kennelly, V.W. Rodwell and P.A. Weil, McGraw-Hill Companies, Inc., India (2012). 3. Lehninger Principles of Biochemistry by D.L. Nelson and M.M. Cox, Macmillan worth

Publisher, New York, USA (2012). 4. Metabolomics: Methods and Protocols by W. Weckwerth, Humana Press, USA (2006). 5. Metabolomics: The Frontier of Systems Biology by M. Tomita and T. Nishioka, Springer

Verlag, Japan (2005). 6. The Handbook of Metabonomics and Metabolomics by J. Lindon, Jeremy Nicholson and

Elaine Holmes, Elsevier, UK (2006).

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PAPER-IIADVANCED MOLECULAR GENETICS & GENOMICS



INSTRUCTIONS FOR THE PAPER SETTERSThe question paper will consist of three sections A, B and C. Section A and B will have four questions from the respective sections of the syllabus and carry I5 marks each. Section- C will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 15 marks in all. INSTRUCTIONS FOR THE CANDIDATES

1. Candidates are required to attempt two questions each from sections A and B and the entire Section C.

2. The use of scientific calculators is allowed. Section - A

1. Genes and Genomes: DNA, RNA, Supercoiling, Topoisomerases, bacteriophage genomes: HIV and lambda. Genome anatomies of prokaryotes and eukaryotes: Repetitive DNA, Transposons, Pathogenicity islands, ribozymes

2. Replication & Mutation: Origin, initiation, elongation and termination. Homologous recombination, Site-specific recombination, Mutagenesis - causes and effects, DNA repair mechanisms

3. Transcription-Prokaryotic & Eukaryotic: initiation, elongation and termination.Post transcriptional modifications: Intron splicing, capping, polyadenylation, and maturation. Transcriptional inhibitors, post transcriptional gene silencing.

4. Translation-Prokaryotic & Eukaryotic: Genetic code, Polypeptide biosynthesis: role of tRNA and ribosomes, initiation, elongation and termination. Post translational modifications: Protein folding, secretion, localization, proteolytic cleavage, chemical modifications, inteins, degradation (ubiquitinylation, proteosome). Translation inhibitors

5. Regulation of Prokaryotic gene expression: operons e.g. Lac, Ara, Trp and Hut, Signal transduction. Small non-coding RNA, Stringent response, Quorum sensing.

6. Regulation of Eukaryotic gene expression: chromatin modification and imprinting in regulation, Regulation of cell cycle, Apoptosis, Signal transduction, Developmental and Cancer genetics.

Section - B7. Genome Sequencing: DNA and RNA sequencing, Maxam-Gilbert, Sanger’s,

Pyrosequencing, New generation sequencing, whole genome sequencing and assembly by shotgun and clone contig approach. Introduction to Genome Sequence Databases - Genbank, EMBL, DDBJ, Introduction to Protein Sequence Databases (Uni-Prot, Swiss Prot).

8. Techniques: PCR, Real Time PCR, DNA fingerprinting, DNA footprinting, RAPD, RFLP, DNA denaturation, hybridization, cot/rot curves,

9. Preparation and applications of DNA and Protein Microarray, MS, MALDI-TOF, 2DGE, flow cytometry

10. Functional genomics: Comparative genomics-gene evolution, exon shuffling, domain analysis.

11. Introductory Pharmacogenomics: ADME, effect of genetic variation on drug responses, β2 adrenergic receptor, MDR, Cytochrome P450

12. Transcriptome analysis: Preparation and applications of EST and SAGE.

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RECOMMENDED READING Latest Editions:1. Biochemistry: Molecular Basis on Cell structure and Function, by Lehminger, A.L.,

Kalyani Publications, New Delhi, 19832. Genes VII, by Benjamin Lewin, John Wiley and sons, New York, 2000.3. Genes IX by Benjamin Lewin, Jones Bartlett Publ. 20084. Microbial Genetics; by D. Friefelder, Narosa Publishing House, New Delhi, 1989.5. Molecular Biology: by D. Friefelder, Narosa Publishing House, New Delhi, 1998.6. Molecular Biology and Human Diseases; by A Macleod and S. Sijkora, Blackwell

Scientific Publications Ltd., London, 1984.7. Molecular Microbial Ecology Manual: Ed, ADLSK Kerman, J.D. Van Elsas, F.J. de

Bruigin, Kluwer Academike Publ. 1995.8. Molecular Biology of Gene: By J.D. Watson, N.H. Hopkin, J.W. Roberts, J.A. Steing

and A.M. Weings, Benamin Cummings Publication Co., Amsterdan, 1988.9. Genomes 3 by T.A.Brown. Garland Science Publ; 2007.10. Proteome Research: New Frontiers in Functional Genomics. Eds. MR Wilkins, RD

Appeal and DF Haochshauser, Springer Publ. 1997.11. Molecular Genetics of Bacteria, J.W. Dale, Wiley and Sons Ltd. 3rd Edn. 1998.

PAPER-IIIGENERAL MICROBIOLOGY



INSTRUCTIONS FOR THE PAPER SETTERSThe question paper will consist of three sections A, B and C. Section A and B will have four questions from the respective sections of the syllabus and carry I5 marks each. Section- C will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 15 marks in all.

INSTRUCTIONS FOR THE CANDIDATES1 Candidates are required to attempt two questions each from sections A and B and the entire Section C. 2 The use of scientific calculators is allowed.

SECTION-A1. Introduction: Historical development and relevance of microbiology to biotechnology. 2. Microscope and microscopy: principles and applications of bright field, fluorescence,

phasecontrast, TEM, SEM.3. Microbial groups: Prokaryotes (bacteria, archaebacteria, cyanobacteria, mycoplasma,

actinomycetes), eukaryotes (molds, slime molds, yeast, algae, fungi, protozoa) and viruses (bacterial, plant and animal); a general account of characteristics, structure and functions.

4. Principles of microbial nutrition: Requirements for carbon, nitrogen, sulfur, growth factors, etc. role of oxygen in nutrition, nutritional categories among micro-organisms.

5. Methods of microbiology: Pure culture techniques, preparation of culture media, types of media; sterilization techniques; methods for culturing anaerobes; cultural characteristics, maintenance and preservation of culture.

6. Strain improvement: Methods of improvement and stability of biotechnologically important cultures.

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SECTION-B7. Microbial growth: Definition, mathematical nature and expression of growth,

measurement and efficiency of growth; factors affecting growth; synchronous and diauxic growth; continuous culture; sporogenesis and spore generation.

8. Concept of energy generation: Aerobiosis, anaerobiosis and concept of autotrophs; fermentative types of microorganisms.

9. Microbial genetics: Modes of bacterial recombination, conjugation, transformation and transduction in bacteria.

10. Microorganisms as geochemical agents: Fitness of micro organisms as agent of geochemical change; cycles of matter and microbial interactions.

11. Biological nitrogen fixation: Microbiology of symbiotic and non-symbiotic nitrogen fixation; root nodule formation and its functions; nitrogen fixation by cyanobacteria, structure and function of Heterocyst.

12. Microbiology and epidemiology of food poisoning and food borne infections: Mode of transmission and their prevention.

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Recommended Readings: 1. Alcamo’s Fundamentals of Microbiology by J.C. Pommerville, Jones & Bartlett Learning,

USA (2012). 2. Brock Biology of Microorganisms by M.T. Madigan, J.M. Martingo, D.A. Stahl and D.P.

Clark, Pearson Education Limited, USA (2011). 3. General Microbiology by R.Y. Stanier, J.L. Ingraham, M.L. Wheelis and P.R. Painter,

Mac Millan, Hong Kong (2005). 4. Microbiology by M.J. Pelczar, E.C.S. Chan and N.R. Krieg, Tata McGraw-Hill

Education, India (1993). 5. Microbiology: A Human Perspective by E.W. Nester, D. Anderson, Jr. Roberts and C.

Evans, Mc Graw-Hill Education, India (2011). 6. Microbiology: An Introduction by G.J. Tortora, Pearson Education, India (2008). 7. Microbiology: Principles and Explorations by J.G. Black, John Wiley & Sons, USA

(2008). 8. Practical Handbook of Microbiology by E. Goldman and H.L. Green, CRC Press, USA

(2009). 9. Principles of Microbiology by R.M. Atlas, WC Brown Publishers, USA (1997).

PAPER-IVIMMUNOLOGY & IMMUNOTECHNOLOGY





SECTION-A1. Introduction and scope of immunology: History, types of immunity, innate immunity,

acquired immunity, active and passive immunity. 2. Antigens and MHC: Antigens-properties, T dependent and independent antigens, concept

of haptens, epitopes, super antigens; MHC-structure and function of major histocompatibility complex I and II, typing of MHC.

3. Cells and organs of immune system: Cells involved in immune system, organs of immune system, lymphocytes, macrophages, enumeration of various types of cells of immune system.

4. Humoral immune response: Immunoglobulins-types, structure, distribution, function, molecular biology of immunoglobulin synthesis, organization of immunoglobulin genes; B cells-development, B cell markers, activation.

5. Complement system: Classical and alternate pathway, consequences, methods of assessment of complement functions.

6. Cell mediated immune response: T cells and its development, markers on T cell, T cell activation, mechanism of cell mediated immune response; Interferons; Cytokines & their interactions and functions.

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SECTION-B7. Hypersensitivity: Mechanism of type I hypersensitivity, type II, III and IV immune

reactions; Disorders related to hypersensitivity Type I and Type II; Techniques to measure hypersensitivity.

8. Autoimmunity: Mechanism of autoimmunity, diseases (Rheumatoid arthritis, Diabetes, SLE, Pernicious anaemia) and treatment.

9. Immunomodulation: Adjuvants as immunomodulators, transplantation immunity, immunosuppression, mechanism; Immunosuppressive drugs; Cancer immunology.

10. Immunization and vaccines: Active and passive immunization; Vaccines-traditional and modern vaccines, vaccine delivery methods; Immune response to polio vaccines, Hepatitis vaccine and AIDS.

11. Immune response assays: Methods to assay humoral immune response (agglutination, immunodiffusion, immunoelectrophoresis, RIA, fluorescent assays, ELISA), immunoblot, methods of assay of cell mediated immune response; MLR; Blast transformation.

12. Hybridoma technology: Production of monoclonal antibodies, purification, characterization of antibodies (Physical methods), applications of monoclonal antibodies in diagnosis and therapy and in biomedical research, antibody engineering, abzymes.

Recommended Readings: 1. Cellular and Molecular Immunology by A.K. Abbas, A.H. Lichtman and Shiv Pillai,

W.B. Saunders Co., Philadephia (2003). 2. Fundamental Immunology by W.E. Paul, Lippincott Williams & Wilkins, USA (2008). 3. Immunology: A Short Course by E. Benjamin, John Wiley and Sons, USA (1996). 4. Immunology: A Short Course by R. Coico and G. Sunshine, Wiley-Blackwell, USA

(2009). 5. Immunology: An Introduction by I.R. Tizard, Saunders College Publishing, Philadelphia

(1995). 6. Kuby Immunology by J. Owen, J. Punt and S. Stranford, W.H. Freeman and Co., USA

(2012). 7. Lecture Notes Immunology by I. Todd and G. Spickett, Wiley-Blackwell, USA (2010). 8. Practical Immunology by F.R. Hay, O.M.R. Westwood and P.N. Nelson, John Wiley &

Sons, USA (2002). 9. Roitt’s Essential Immunology by P.J. Delves, S.J. Martin, D.R. Burton and I.M. Roitt,

Wiley-Blackwell, USA (2007). 10. The Experimental Foundation of Modern Immunology by W.R. Clark, John Wiley and

Sons, USA (1991). 11. The Immune System in Health and Disease by C.A. Janeway Jr, P. Travers, M. Walport

and M.J. Shlomchik, Garlan Science, USA (2001).

PRACTICAL PAPER-I Pertaining to: Theory Paper I: Macromolecular Biochemistry and Metabolomics Theory Paper II: Advanced Molecular Genetics & Genomics M. Marks: 100 Total practical hours: 60

Time: 4 hours 1. Qualitative and quantitative analysis of reducing and total sugars by biochemical and

biophysical techniques. 2. Determination of acid value, acid number and iodine number of a fat/oil. 3. Determination of cholesterol-total, free and esterified. 4. Isolation, qualitative and quantitative analysis of lipids. 5. Isolation of chloroplast by sucrose density gradient centrifugation. 6. Uric acid and urea estimation from serum and urine samples. 7. Detection of phenylketone urea. 8. Estimation of calcium and phosphorus in blood and urine.

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9. Demonstration of protein modeling on computers. 10. Fractionation of rat liver. 11. Isolation of casein from milk. 12. Determination of starch content from wheat flour. 13. Demonstration of Hill reaction. 14. Applications of Handerson-Haselbalch equation for the preparation of buffer solutions. 15. To determine vitamin C content in a citrus fruit. 16. Determination of enzyme activity, Km & Vmax of α- amylase/invertase. 17. Determine of nucleic acid (DNA & RNA) by biophysical techniques. 18. Resolution of serum protein by starch gel electrophoresis. 19. Estimation of DNA by DPA method and RNA by Orcinol method. 20. Isolation of plasmid and genomic DNA of E. coli. 21. Isolation of plasmid and genomic DNA of yeast. 22. Isolation of RNA from bacteria and yeast. 23. Agarose gel electrophoresis of DNA and polyacrylamide gel electrophoresis of RNA. 24. Spectrophotometric estimation of nucleic acids. 25. Determination of purity of DNA and RNA preparation. 26. Demonstration of polymerase chain reaction and multiplex PCR. 27. Determination of Tm of DNA. 28. Determination of phosphate content of DNA and RNA. 29. Demonstration of two dimensional gel electrophoresis and denaturing gradient gel

electrophoresis. 30. Isolation of m-RNA from eukaryotic cells. 31. Demonstration of DNA sequencing and DNA finger printing. 32. Demonstration of random amplified polymorphic DNA (RAPD) analysis. 33. Pharmaco-genetically important enzyme polymorphisms. 34. Detection of chemical carcinogens by Ames test. 35. Isolation and characterization of Serratia marcesens with altered pigmentation. 36. Demonstration of equipment pertaining to spectroscopic and other analytical techniques:

radio, amino acid, DNA synthesizer, microarray reader, flow cytometer, etc. 37. Determination of conjugation mapping in E. coli.

PRACTICAL PAPER-II Pertaining to: Theory Paper III: General Microbiology Theory Paper IV: Immunology & Immunotechnology M. Marks: 100 Total practical hours: 60

Time: 4 hours 1. Staining techniques in Microbiology-simple, negative, differential, spore and capsule

staining. 2. Isolation and purification of microorganisms by streak plate method, pour plate method

and use of selective media. 3. Maintenance and preservation techniques of aerobic and anaerobic cultures. 4. Cultivation of anaerobic microorganisms in anaerobic jar and CO2 incubator. 5. Morphological, biochemical and physiological characterization of microorganisms for

taxonomic identification. 6. Isolation of cyanobacteria and cyanophages. 7. Strain improvement by physical and chemical mutagenesis. 8. Determination of coliform bacteria in water and food samples. 9. Determination of viability of microbial culture by microscopic technique. 10. Measurement of size of microorganisms by microscopic method. 11. Hanging drop preparation to check motility of microorganisms. 12. Construction of bacterial growth curve and determination of generation time.

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13. Microbial growth measurements by different techniques and determination of factors affecting growth of microorganisms.

14. Determination of viability of splenocytes. 15. Making a suspension of viable cells by counting. 16. Making of a blood smear and differentiate the various lymphocytes. 17. Various routes of immunization and study of organs involved in immunity. 18. Immunization of animals with particulate and soluble antigens. 19. Raising of antiserum. 20. Testing of antibody titer by the technique based upon the principle of precipitation,

agglutination, electrophoresis and fluorescence. 21. Detection of an antigen and antibody by ELISA technique. 22. To perform immunoblot assay. 23. Determination of phagocytic index. 24. To perform blast transformation test. 25. Measurement of cell cytotoxicity by MTT assay. 26. Isolation of antibody by physical methods.

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Semester IIPAPER-V

GENETIC & METABOLIC ENGINEERINGM. Marks: 75 Lectures to be delivered: 60 Time allowed: 3 Hours Pass Marks: 40% (Theory and




Section - A1. DNA replicating and modifying enzymes: Thermostable DNA polymerases,

restriction endonucleases and methylases, ligase, S1 nuclease, exonucleases, terminal transferase, reverse transcriptase, ribonucleases.

2. Techniques: Blotting and nucleic acid hybridization, Chemical gene synthesis, Site-directed mutagenesis. Protein engineering: Directed evolution and gene shuffling,

3. Vectors from plasmids, phages and viruses: phagemids, cosmids- Biology, derivation strategies and application, Host ranges, In vitro packaging.

4. Genetic Libraries-cDNA & Genome libraries: Construction, amplification &applications.

5. Transformation techniques: Chemical, physical and biological strategies; Recombinant selection and identification: direct and indirect methods; reporter genes, immunological methods, south-western screening, north-western screening, maxi and mini cells, In vitro translation systems.

6. Recombinant protein expression and purification: expression enhancement, recombinant gene design, downstream processing strategies; tagging and cleavage strategies.

Section - B7. Cloning in bacterial and yeast host: Salient features of cloning in Gram-positive

(Bacillus), Gram-negative (E. coli) and yeast (S. cerevisae&S. pombe), yeast two-hybrid system.

8. Cloning in animals: Cell lines and selectable markers, Transgenic animals. Cloning in plants: Tissue culture, Transgenic plants, Molecular pharming.

9. Development of industrial & environmental recombinant products, new materials & devices: Biosensors, Recombinant vaccines, Nucleic acid therapeutics. DBT biosafety guidelines.

10. Introduction to Metabolic engineering: Central metabolism of E. coli, Metabolic flux analysis, Metabolic control analysis, Redirecting metabolic flow, Strategies to increase metabolic flow.

11. Metabolic engineering for creating novel products: Indigo, Melanin and polyhydroxyalkanoates in E. coli, Carotenoids biosynthesis in Erwinia herbicola, 7-ACA in Cephalosporium acremonium.

12. Metabolic engineering for novel substrate utilization: S. cerevisiae for utilization of lignocellulosics: cellulose, hemicelluloses, pectin and xylose. Engineering for

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enhancing metabolite production: Overproduction of tryptophan and lysine in C. glutamicum.

Recommended Readings – Latest Editions :1. Advances in Biochemical Engineering/Biotechnology, Volume 73 (Metabolic

Engineering) by J. Nielsen, Springer-Verlag, USA (2001).2. From Genes to Genomes: Concepts and Applications of DNA Technology by J.W.

Dale, M. von Schantz and N. Plant, John-Wiley & Sons Ltd., USA (2012).3. Genomes 3 by T.A. Brown, Garland Science, USA (2006).4. Lewin’s Genes X by J.E. Krebs, E.S. Goldstein and S.T. Kilpatrick, Jones and Bartlett

Publishers, USA (2011).5. Metabolic Engineering by S.Y. Lee and E.P. Popoutsakis, Marcel Dekker, Taylor &

Francis Group, USA (1999).6. Molecular Biology of Gene by J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M.

Levine and R. Losick, The Benjamin Cummings Publishing Company Inc., USA (2008).

7. Molecular Biotechnology: Principles and Applications of Recombinant DNA by B.R. Glick and J.J. Pasternak, ASM Press, USA (2010).

8. Molecular Cloning by M.R. Green and J. Sambrook, Cold Spring Harbor Press, USA (2012).

9. Principles of Gene Manipulation and Genomics by S.B. Primrose and R. Twymann, Wiley-Blackwell Publishers, USA (2006).

10. Production of Recombinant Proteins: Novel Microbial and Eukaryotic Expression Systems by G. Gellissen, Wiley-Blackwell, USA(2005).

11. Text book of Biochemistry with Clinical Correlations by T.M. Devlin, Wiley-Liss, USA (2002).

PAPER-VIMOLECULAR BIOPHYSICS & MACROMOLECULAR MODELING




INSTRUCTIONS FOR THE CANDIDATES1. Candidates are required to attempt two questions each from sections A and B and the entire

Section C. 2. The use of scientific calculators is allowed.

SECTION-A1. Bioenergetics and thermodynamics: High energy bonds, ATP-the currency of energy,

standard state in biochemistry, principles of coupled reactions–glycolosis, laws of thermodynamics, concept of Gibbs free energy, natural variables of enthalpy, entropy, internal energy and Gibbs free energy; Dependence of Gibbs free energy on temperature and pressure, Vanthoff equation, some limitations of thermodynamics in biology.

2. Chemical and enzyme kinetics: Order of reaction, renaturation of DNA, determination of reaction order, effect of temperature on reaction rates (The Arrhenius equation), theories of reaction rates, thermodynamic formulation of transition state theory, isotope effect in biochemical reactions, use of isotopes as tracers in biological sciences, fast reactions in

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solution, methods to study fast reactions, enzyme kinetics-multi substrate systems, allosteric interactions, effect of pH on enzyme kinetics.

3. Quantum mechanics and atomic structure: Bohr’s theory of hydrogen emission spectrum, de Broglies’s postulate, The Heisenberg uncertainty principle, The Schrodinger wave equation, quantum mechanical tunneling, atomic orbitals, electronic configuration, variations in periodic properties.

4. Principles, instrumentation and applications: UV-Vis spectrophotometry, spectrofluorimetry and atomic absorption spectroscopy.

5. Principles, instrumentation and applications: IR, NMR and ESR spectroscopy, chemical shift, spin-spin coupling, Fourier transform NMR, spin labeling, properties of ESR spectra, selection rules for allowed transitions, hyperfine splitting.

6. Principles, instrumentation and applications: ORD, CD, X-ray diffraction and mass spectrometry, MALDI-mass spectrometry, tandem mass spectrometry.

SECTION-B7. Macromolecular modeling: Useful concepts in molecular modeling coordinate system,

potential energy surface, molecular graphics and mathematical concepts. 8. Protein folding: Levithal paradox, molten globules, Ramachandran plots, propensities of

amino acids forming alpha helica, beta sheet and beta turns, folding motifs, characterization and trapping of partially folded intermediates, subdomains, role of protein disulfide isomerase, peptidyl prolyl isomerase and chaperons in in vivo protein folding, different amino acid sequences-similar protein folds.

9. Protein modeling and drug designing: Properties of some conformationally constrained amino acids, coiled coil, four helix bundle and beta sheet frame work, comparative modeling, sequence analysis and alignment, pharmacophore, isosteres, molecular docking and structure based drug designing.

10. Genetic algorithm and molecular dynamic simulations: Computer simulations by a genetic algorithm, implementation of the principles of genetic algorithm for RNA folding and protein folding, setting up and running a molecular dynamic simulations.

11. RNA modeling: RNA folding dynamics, RNA tectonics and modular modeling of RNA. 12. DNA modeling: Design and characterization of antisense oligonucleotides for the

treatment of various human diseases, modifications to the phosphate back bone (phosphorothioate nucleotides), alteration of the sugar ring at 2’ position, and base substitutions-molecular simulations, how TATA box selects its protein partner-molecular dynamic simulations.

Recommended Readings:1. Biochemistry by L. Stryer, W.H Freeman and Company, USA (2002). 2. Biophysical Chemistry-Principles and Techniques by A. Upadhyay, K. Upadhyay and N.

Nath, Himalaya Publishing House, India (2009). 3. Computational Studies of RNA and DNA by J. Sponer and F. Lankas, Springer Verlag,

USA (2006). 4. Instant Notes in Biochemistry by B.D Hames, N.M. Hooper and J.D. Houghter, Bios

Scientific Publishers Limited, UK (1997). 5. Introduction to Molecular Biophysics by J.A. Tuszynski and M. Kurzynski, CRC Press,

USA (2003). 6. Lehninger Principle of Biochemistry by D.L. Nelson and M.M. Cox, Macmillan Worth

Publisher, USA (2012). 7. Molecular modeling of Nucleic Acids by N.B. Leontis and J. Santalucia, Jr, American

Chemical Society, USA (1998). 8. Molecular Modeling of Proteins by A. Kukol, Springer-Verlag, USA (2008). 9. Molecular Modeling, Principles and Applications by A.R. Leach, Prentice Hall, USA

(2001).

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10. Physical Chemistry for the Biosciences by R. Chang, University Science Books, USA (2005).

11. Protein Structure-A Practical Approach, The Practical Approach Series by B.D Hames, IRL Press, Oxford University Press, UK (1997).

PAPER-VIIBIOPROCESS AND BIOCHEMICAL ENGINEERING






SECTION-A1. Introduction: Principles of upstream and downstream processing; Unit operations

involved in bioprocesses. 2. Bioreactors: Designing and development of a bioreactor; Aeration and agitation systems

for bioreactors; Bioreactor configurations; Mode of operation-batch, fed batch and continuous; Scale-up of bioprocess.

3. Inline and online monitoring of bioreactors: Physical and chemical variables; Instrumentation for monitoring and controlling in-line and online process variables in bioreactors.

4. Transport phenomenon in bioreactors: Mass transfer coefficient (KLa) for gases and liquids, determination of KLa, factors affecting KLa value in bioprocesses; Heat transfer-general considerations; Dimensionless groups; Fluid rheology.

5. Sterilization: Principles and practices; Thermal death kinetics of batch and continuous sterilization of media; Air sterilization in lab scale and industrial fermenters; Kinetics of fibrous air filters.

6. Shake-flask fermentations: Rotary and rocker shakers; Agitation and aeration in roller tubes, static and submerged cultures; Factors affecting oxygen solution rates in shake-flasks.

SECTION-B7. Isolation and extraction of bioproducts: Separation of cells-foam separation, flocculation,

agglomeration, filtration and centrifugation; Cell disruption-physical, chemical and mechanical methods; Liquid-liquid extraction-Salt/solvent precipitation, aqueous two-phase extraction and dialysis.

8. Recovery and purification of bioproducts: Chromatographic techniques-adsorption, ion exchange, molecular sieve, affinity, hydrophobic, high performance liquid chromatography, gas-liquid and gas-solid chromatography; Electrophoresis.

9. Finishing techniques in bioprocesses: Distillation; Electrodialysis; Evaporation; Drying; Crystallography.

10. Modeling of bioprocesses: General characteristics of models (Linear/non-linear, static/dynamic, lumped/distributed, continuous/discrete, deterministic/stochastic, white/black box); First principle models, black box models, hybrid models; Parameter

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estimation (Identifiability, optimization criteria and algorithms, validation); Artificial neural networks.

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11. Computer applications in bioprocesses: Components of a computer linked system; Data logging & data analysis; Process control by computer; Role of neural networking in bioprocess control.

12. Fermentation economics: Economic analysis of projects, project selection, R & D planning for projects; Techno-economic parameters for commercial evaluation of bioprocesses; Capital cost; Direct and indirect manufacturing costs, etc.

Recommended Readings: 1. Biochemical Engineering Fundamentals by J.E. Bailley and D.F. Ollis, Tata McGraw-

Hill, USA (2010). 2. Bioprocess Engineering Principles by P.M. Doran, Academic Press, USA (2012). 3. Bioprocess Engineering: Basic Concepts by M.L. Schuler and F. Kargi, Prentice Hall,

USA (2002). 4. Biotechnology by H.-J. Rehm and G. Reed, VCH, Germany (2001). 5. Comprehensive Biotechnology, Volume 1 and 2 by M. Moo Young, Pergamon Press, UK

(2011). 6. Manual of Industrial Microbiology and Biotechnology, R.H. Baltz, Julian E. Davies and

Arnold L. Demain, ASM Press, USA (2010). 7. Modern Industrial Microbiology and Biotechnology by N. Okafor, Science Publishers,

USA (2007). 8. Principles of Fermentation Technology by P.F. Stanbury, A. Whitaker and S. Hall, Aditya

Publishers, India (1997).

PAPER-VIIIADVANCED FERMENTATION TECHNOLOGY


Practical separately) INSTRUCTIONS FOR THE PAPER SETTERS

The question paper will consist of three sections A, B and C. Section A and B will have four questions from the respective sections of the syllabus and carry I5 marks each. Section- C will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 15 marks in all.



SECTION-A1. Raw materials: Conventional and non-conventional substrates for microbial and food

fermentations; Chemical and biological control of raw materials; Storage, transport and homogenization.

2. Starter cultures: Techniques for the development of inoculum for industrial fermentations; Procedures for aseptic inoculation of industrial fermenters.

3. Fermentation: Types (Submerged, surface and solid substrate fermentation), factors affecting fermentations.

4. Microbial transformation: Practical aspects, types of biotransformation, biocatalysis in organic solvents, steroid biotransformations, applications of biotransformations in biotechnology.

5. Recombinant fermentations: Strategies for fermentation with recombinant organisms, selection of host cells, instability of recombinant plasmids, assessment of plasmid stability in host cells, proposals to ensure stability of recombinant plasmids, examples of genetically modified organisms.

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6. Microbial polysaccharides: Fermentative production of xanthan gums, pullulan, dextran and cyclodextrins.

SECTION-B7. Biofuels: Fermentative production of liquid fuels-ethanol, acetone and butanol; Factors

affecting production of biofuels. 8. Pharmaceutical products: Fermentative production of penicillin, cephalosporins,

vancomycin, erythromycin and streptomycin; Vaccines-types, fermentative production of live/attenuated vaccines and recombinant vaccines.

9. Vitamins: Fermentative production of thiamin (B-1), riboflavin (B-2) and cobalamin (B-12).

10. Biosurfactants: Classification and chemical nature, fermentative production and factors affecting it, applications.

11. Biopesticides/bioinsecticides: Production and applications of microbial and viral biopesticides/bioinsecticides.

12. Biofertilizers: Industrial production of Rhizobium inoculants, Azotobacter, Azospirillium, blue-green algae, phosphate solubilizers and mycorrhizal fungi.

Recommended Readings:1. Biotechnology, Volume 3, 6, 7, 8a and 8b by H.-J. Rehm and G. Reed, VCH, Germany

(2001). 2. Comprehensive Biotechnology, Volume 1 and 2 by M. Moo Young, Pergamon Press, UK

(2011). 3. Comprehensive Food Fermentation Biotechnology, Volume 1 and 2 by A. Pandey, C.

Larroche, G. Gnansounou, C.R. Soccol and C.-G. Dussap, Asiatech Publishers, India (2010).

4. Fermentation Microbiology and Biotechnology by M. El-Mansi and E.M.T. El-Mansi, Taylor & Francis, USA (2012).

5. Manual of Industrial Microbiology and Biotechnology, R.H. Baltz, Julian E. Davies and Arnold L. Demain, ASM Press, USA (2010).

6. Microbial Biotechnology by A.N. Glazer and H. Nikaido, W.H. Freeman and Company, USA (1995).

7. Prescott and Dunn’s Industrial Microbiology by G. Reed, CBS Publishers and Distributors, India (2004).

PRACTICAL PAPER-III Pertaining to: Theory Paper V: Genetics & Metabolic Engineering Theory Paper VI: Molecular Biophysics & Macromolecular Modeling M. Marks: 100 Total practical hours: 60

Time: 4 hours 1. Isolation and amplification of gene of interest by polymerase chain reaction. 2. cDNA synthesis from mRNA. 3. Restriction mapping of plasmid DNA. 4. Comparative study of maps of commercially available vectors for bacteria, yeast,

mammalian and plant transformation. 5. Ligation for recombinant DNA production. 6. Transformation of E. coli and yeast by physical and chemical techniques. 7. Cloning and expression of recombinant genes in E. coli. 8. Recombinant protein analysis by polyacrylamide gel electrophoresis. 9. Isolation of DNA, RNA and plasmids and staining with ethidium bromide. 10. Electrophoretic separation of DNA fragments and their recovery from gel slabs. 11. Performance of Southern and Northern blotting. 12. Purification of mRNA by using immobilized technique.

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13. Mapping of restriction sites on a plasmid. 14. Transfer of nopalene dehydrogenase gene into cultured plant tissue by Agrobacterium

tumefaciens. 15. Cloning using restriction enzyme generated cohesive/blunt ends. 16. Sequencing of DNA fragment with Maxam-Gillbert method. 17. Determination of quality of bioproducts. 18. Qualitative and Quantitative analysis of proteins and nucleic acids by U.V.

spectrophotometer. 19. Determination of protein in presence of nucleic acid by spectrophotometer method. 20. Optical spectroscopy to characterize protein conformation and conformational changes. 21. Peptide mapping. 22. Measurement of CD spectra of proteins and nucleic acids. 23. Fluorimetric determination of Trp content of proteins. 24. NMR spectra for structure determination of ethanol. 25. Fraction of α-helix, β-chain (random coil) in a protein by IR spectroscopy. 26. Protein modeling on computer. 27. Polarimetric determination of sucrose in the presence of other sugars, and other sugars in

the presence of sucrose. 28. Environmental effects on absorption and emission spectra of protein. 29. Protein engineering with non-standard amino acid. 30. Incorporation of PM-mercaptoacetyl and CPM-SAC met method. 31. Molecular docking. 32. Demonstration of TSAR. 33. Setting up and running a molecular dynamic simulation.

PRACTICAL PAPER-IV Pertaining to: Theory Paper VII: Bioprocess & Biochemical Engineering Theory Paper VIII: Advanced Fermentation Technology M. Marks: 100 Total practical hours: 60

Time: 4 hours 1. Demonstration of a laboratory scale bioreactor (10 L). 2. Cell disruption by physical, chemical and mechanical methods. 3. Ammonium sulphate and solvent precipitation for protein concentration. 4. Dialysis and ultrafiltration for purification of bioproducts. 5. Paper, thin layer chromatography, HPLC and HPTLC of bioproducts. 6. Lyophilization of bioproducts. 7. Distillation and evaporation for the recovery of bioproducts. 8. SDS-PAGE analysis of proteins. 9. Molecular weight determination of proteins by electrophoresis and gel exclusion

chromatography. 10. Determination of thermal death kinetics of batch sterilization. 11. Determination of KLa during fermentation. 12. Rheological investigations on fermented broths. 13. Preparation of fungal starter culture by roll bottle technique. 14. Microbiological and biochemical evaluation of substrates. 15. Biocatalysis in organic solvents. 16. Fermentative production of organic acids using free and immobilized cells. 17. Fermentative production of ethanol using free and immobilized cells. 18. Production and recovery of microbial surfactants. 19. Production and recovery of pullulan. 20. Solid state fermentation for the production of microbial products. 21. Production of vitamins using free and immobilized cells. 22. Preparation and evaluation of Rhizobia inoculants. 23. Cultivation of blue green algae as biofertilizer.

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SYLLABUSpupdepartments.ac.in/syllabi/Academic Session 2016-17... · Web viewEstimation of DNA by DPA method and RNA by Orcinol method. Isolation of plasmid and genomic DNA of E. coli