cbcs syllabus - sardar patel university

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SARDAR PATEL UNIVERSITY

M.SC. BIOTECHNOLOGY

I SEMESTER

Core Papers:

PS01CBIT01: Molecular Biology

PS01CBIT02: Bioinstrumentation

PS01CBIT03: Cell biology and Genetics

Elective Paper:

Any one from the list

PS01CBIT04: Practicals of PS01CBIT01 & PS01CBIT02

PS01CBIT05: Practicals of PS01CBIT03 & PS01EBITXX

PS01CBIT06: Viva Voce

II SEMESTER

Core Papers:

PS02CBIT01: Bioprocess & Biochemical engineering

PS02CBIT02: Microbial Genetics

PS02CBIT03: Genetic engineering & Bioinformatics

Elective Papers:





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III SEMESTER

Core Papers:

PS03CBIT01: Microbial Biotechnology

PS03CBIT02: Immunology

PS03CBIT03: Enzymology

Elective Paper:





IV SEMESTER

Core Papers:

PS04CBIT01: Plant Biotechnology

PS04CBIT02: Environmental Biotechnology

Elective Papers:

Any two from the list

OR

DISSERTATION


PS04CBIT04: Practicals of PS04EBITXX & PS04EBITXX


OR


PS04EBIT04: Dissertation


List of Elective Papers:

PSCOEBIT01: Biostatistics PSCOEBIT02: Phytoresource utilization and conservation PSCOEBIT03: Microtechniques PSCOEBIT04: Animal Biotechnology PSCOEBIT05: Biochemistry PSCOEBIT06: Human physiology PSCOEBIT07: Genomics and proteomics PSCOEBIT08: Stem cell technology and developmental Biology PSCOEBIT09: Bioethics, Bio safety and IPR

PSCOEBIT10: Food biotechnology

PSCOEBIT11: Toxicology

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SARDAR PATEL UNIVERSITY

I SEMESTER

PS01CBIT01: MOLECULAR BIOLOGY

Unit-I

DNA structure: Chemistry of DNA, Forces stabilizing DNA structure, Helix parameters, Forms

of DNA (A, B, C, D, T, and Z), Watson –Crick and Hoogsteen base pairing, Physical properties

of ds DNA (UV-Absorption spectra, Denaturation and Renaturation, Cot curves, DNA

hybridization), Chemicals that react with DNA.

DNA topology: DNA supercoiling, Supercoiled forms of DNA, Superhelical density, energetics

of supercoiled DNA, Biology of supercoiled DNA (Topological domains of DNA, DNA

topoisomerases, Mechanisms of supercoiling in cells, Mechanism of action of Topoisomerase I

and II, effect of supercoiling on structure of DNA and role of supercoiling in gene expression

and DNA replication)

DNA-protein Interactions: General features, Interaction of Helix-turn Helix motif, B-sheet, Zn-

DNA binding domains, etc with DNA.

Unit-II

Organization of DNA into chromosomes: Packaging of DNA and organization of chromosome

in bacterial cells; Packaging of DNA in eukaryotic nucleosome and chromatin condensation,

assembly of nucleosomes upon replication, Chromatin modification and genome expression.

DNA replication: Mechanism of DNA polymerase catalyzed synthesis of DNA, Types of DNA

polymerases in bacteria and their role. Initiation of chromosomal DNA replication and its

regulation in prokaryotes, assembly of replisome and progress of replication fork, termination of

replication. Types and function of eukaryotic DNA polymerases, initiation of replication in

eukaryotes, role of telomerases in replication of eukaryotic chromosomes. Inhibitors of DNA

replication (blocking precursor synthesis, nucleotide polymerization, altering DNA structure).

Unit-III

Transcription: RNA polymerases, features of prokaryotic and eukaryotic promoters, assembly

of transcription initiation complex in prokaryotes and eukaryotes and its regulation; synthesis

and processing of prokaryotic and eukaryotic transcripts. Transport of RNA within eukaryotic

cell.

Translation: Structure and role of t-RNA in protein synthesis, ribosome structure, basic features

of genetic code and its deciphering, translation (initiation, elongation and termination in detail in

prokaryotes as well as eukaryotes).

Unit-IV

Processing of proteome Posttranslational processing of proteins (protein folding, processing by

proteolytic cleavage, processing by chemical modification, Inteins), Protein degradation.

Regulation of gene expression in prokaryotes: Operon concept, positive and negative

regulation. Examples of lac-, ara-, his- and trp- operon regulation; antitermination, global

regulatory responses; Regulation of gene expression in eukaryotes: Transcriptional, translational

and processing level control mechanisms.

Reference books:

Genes IX: Lewin

Molecular Biology of the Gene: Watson et al.

Genomes 3: T. A. Brown

Molecular Genetics of Bacteria: Snyder & Champness

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PS01CBIT02- BIOINSTRUMENTATION

Unit -I

Electrochemistry: pH and buffers, potentiometric and conductometric titration. Principle and

application of light, phase contrast, fluorescence, scanning and transmission electron

microscopy, scanning tunneling microscopy, atomic force microscopy, confocal microscopy,

cytophotometry and flow cytometry. Preparation of microbial, animal and plant samples for

microscopy.

Unit- II

Principle methodology and applications of gel – filtration, ion –exchange and affinity

chromatography; Thin layer and gas chromatography; High performance liquid chromatography,

FPLC.

Electrophoresis: Principle and applications of Native and SDS PAGE; Agarose and 2D gel

electrophoresis.

Unit III Spectroscopy: UV, Visible, IR, NMR and ESR spectroscopy. Atomic absorption and plasma

emission spectroscopy; MS and MALDI-TOF.

Unit IV

Centrifugation: Basic principle and application; Differential, density and Ultracentrifugation.

Principle of biophysical method and used for analysis of biopolymer structure; X ray diffraction,

fluorescence,

Principle and applications of tracer technique in biology: Radioactive Isotopes and half life of

isotopes; Effect of radiation on biological system; autoradiography; Cerenkov radiation;

radiation dosimetry; scintillation counting.

Biosensors: Principle and application

Reference Books:

Shrama BK, Instrumental method of chemical analysis

DA Skoog. Instrumental methods of analysis

Plummer, An introduction to practical Biochemistry

Chatwal and Anand, Instrumentation

Boyer, Modern experimental Biology

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PS01CBIT03: CELL BIOLOGY & GENETICS

UNIT-I

An overview of Cells and Cell Research; Structure and Organization of pro-and eukaryotic cells.

Application s of electron microscopy in Cell biology; Transmission and Scanning electron

microscopes: components and principle of image formation; Cell membranes: freeze fracturing

and freeze etching of cellular membranes, molecular organization, Cell permeability - transport

across membranes: facilitated diffusion, active transport and receptor mediated endocytosis.

Nucleus – Structure of the nuclear envelope, organization and regulation of nuclear pore

complex. Transport across nuclear membrane, internal organization of the nucleus and nucleolus,

the nucleus during mitosis. Chloroplast and Mitochondria: similarities and dissimilarties,

structural organization in relation to function, genome, transport of metabolites across the

membranes, import and export of proteins through membrane compartments and biogenesis –

Envelope, stroma and thylakoids; Molecular organization of thylakoids.

UNIT-II

Endomembrane system: endomembrane concept, membrane flow, Structural organization of ER

and Golgi, targeting of proteins to ER, , insertion of proteins into ER membrane, Protein folding

and exporting of proteins and lipids from ER to golgi protein sorting and export from golgi to

different cellular compartments, mechanism of vesicle transport and vesicle fusion.

Cytoskeletal elements– composition and organization of microtubules, microfilaments and

intermediate filaments. Role in cell division, wall formation and transport.

Intercellular communications: Cell wall –structure, composition, function and biogenesis.

Plasmodesmata, Tight junctions, Gap junctions – Structure and role in movement of molecules.

Cell Cycle – Phases of Cell Cycle, functional importance of each phase, Molecular events during

cell cycle, Check points, Cyclins and protein kinases, MPF (maturation promoting factor),

Regulation of cell cycle.

UNIT-III

Fundamentals of Genetics: Mendelian analysis, Mendel’s Laws of Inheritance, The principle of

segregation, Test cross and back cross; The principle of Independent assortment, pedigree

analysis. Probability & Statistics in Genetics: Probability in genetic analysis; probability of

combination of events, mutually exclusive events, use of binomial distribution in Genetics; The

Chi-square goodness of fit test and its use in Genetics. Interaction of genes: Incomplete

dominance, co-dominance, lethal genes, epistasis, pleiotropy polygenic traits and quantitative

inheritance; Sex chromosomes and sex-linked inheritance: Transmission of sex- linked traits, sex

determination; Linkage and chromosome mapping and its significance: Linkage, Crossing over-

two point crosses, three –point crosses tetrad analysis, chromosome maps.

UNIT-IV

Maternal effects and cytoplasmic inheritance: Maternal effects in snails, Streptomycin resistance

in Chlamydomonas, mitochondrial mutations in yeast, Kappa particles in paramecium, plastid

inheritance in Mirabilis jalapa, male sterility in plants; Alterations in chromosome number and

structure: Ploidy: Aneuploidy and euploidy, polyploidy and its significance: alteration in

chromosome structure: Deletions, duplications, inversions and translocations; Mutations: Types

of mutations, mutagens, molecular basis of mutations; transposable elements; Reverse mutations

& suppressor mutations.

Reference Books:

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Cell and Molecular Biology (1987), 8th

Edn. De Robertis, E. D. P. and De Robertis,

E. M. F. Jr., Lea & Febiger, USA (Indian Edn.: K. M. Varghese Company, Bombay).

Essential Cell Biology – Second Edition (2004), Bruce Alberts, Dennis Bray, Alexander

Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, Garland Publishing

Inc., New York.

Molecular Biology of the Cell (2002) Bruce Alberts, Dennis Bray, Alexander Johnson,

Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson, Garland Publishing Inc.,

New York.

Cell and Molecular Biology: Concepts and Experiments (1996) Gerald Karp, John Wiley

& Sons, Inc.,USA.

Cell and Molecular Biology (2002), Phillip Sheeler and Donald E. Bianchi, John Wiley &

Sons, Inc, Canada (Indian print by Replika Press Pvt. Ltd., Kundli).

The world of the Cell – Fourth Edition (2000) Wayne M. Becker, Lewis J. Kleinsmith

and Jeff Hardin, Addison Wesley Longman, Inc. (Benjamin/Cummings Imprint).

The Cell – A Molecular Approach (Third Edition) (2004) Geoffrey M. Cooper and

Robert E. Hausman, ASM Press, Washington, D. C.

Molecular Cell Biology (1986) Avers. C.J., Addision-Wesely Publishing Co., Inc., New

York, USA.

Molecular Cell Biology 3rd edn, (1995) Lodish, Baltimore, Berk, Lawrence, et al,

Scientific American Books, N.Y.

Biochemistry and Molecular Biology of Plants (2000) Eds. Buchanan, Grissem and

Jones, American Soc. Plant Biologists, Waldorf.

Genes (2000), edn7, Lewin B, Oxford Univ. Press, Oxford.

Cell Biology: A Laboratory Handbook- Third Edition. Volumes 1 – 4 (2006), Edited by

Julio E. Celis, Elsevier Academic Press, U. K.

David. E. Sadava. 1993. Cell Biology. Jones and Bartlett Publishers, Boston.

Strickberger M. W. Genetics. Third Edition. Macmillan Publishing co. New York.

Robert Weaber & Philip W. Hedrick. Basic Genetics, Second Edition. W. M. C. Brown

Publishers Dubuque lowq.

Anna C. Pai & Helen M. Roberts. Genetics – its concepts & implications, Prentic – Hall

Inc. Engle clifts, New Jersey. USA

Edmund W. Sinnot, L. C. Dunn & T. Dobzhansky, Principles of Genetics. McGraw Hill

Book company Inc. New York, USA.

M. Sr & R. W. Owen. General Genetics, W. H. Freeman & Company, Sanfrancisco.

P. K. Gupta, Genetics. Rastogi Publications. Shivaji Road Meerut, India.

Elective paper: Any one from the list

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II SEMESTER

PS02CBIT01: BIOPROCESS AND BIOCHEMICAL ENGINEERING

Unit -I Introduction to bioprocess technology, Isolation, preservation and improvement of industrially

important organisms. Substrates for fermentation processes, Medium optimization

Unit -II Bioreactor design: Laboratory, pilot and large scale reactors. Plug flow reactors, enzyme

reactors. Sterilization of media and air. Scale up and Scale down, Mass transfer of oxygen:

Agitation and aeration, Determination of KLa, factors affecting KLa, fluid rheology. Inoculum

development, aseptic inoculation and sampling.

Unit -III Bioprocess kinetics: Kinetics of growth and substrate utilization in batch, fed batch and

continuous systems.

Control of process parameters: Instrumentation for monitoring bioreactor and fermentation

processes, Sensors, Controllers, fermentation control systems and architecture, Incubation and

sequence control, advanced control. Dynamic modeling of fermentation processes.

Unit -IV Downstream processing: Methods of Cell separation, Disruption and product purification.,

Fermentation Economics

Reference Books

Principles of Fermentation Technology : Whitekar & Stanbury

Comprehensive Biotechnology : Murray Moo Young

Methods in Industrial Microbiology : Sikyta

Fermentation Microbiology and Biotechnology, El Mansi and Bryc

PS02CBIT02: MICROBIAL GENETICS

Unit-I

Mutation and DNA Repair: Mutation, Spontaneous mutations (Randam v/s adaptive nature of

mutation, Luria and Delbruck experiment, Newcombe experiment, Lederberg’s experiment,

Mutation rate and its determination, Origin of spontaneous mutations), DNA damages

(Deamination of bases, alkylation, damage due to reactive oxygen, UV induced damage) and it

repair pathways (Methyl-directed mismatch repair, Nucleotide excision repair, Base excision

repair, recombinational repair, SOS inducible repair, specific repair for oxidative DNA damage,

pyrimidine dimers and alkylation induced damage and adaptive response).

Plasmid Biology: Types, compatibility, replication, control of copy number and plasmid

segregation.

Unit II

Recombination: Types of recombinations, Models for Homologous recombination, Molecular

mechanism of homologous recombination, Homologous recombination in eukaryotes, Mating-

type switching. Molecular mechanism for site-specific recombination, Biological roles of site-

specific recombination.

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Conjugation: Conjugation by E. coli F factor ( Structure of F-factor, Regulation of F-factor

fertility, establishment of cell contact, DNA mobilization and transfer and separation of mating

pair, Hfr conjugation and chromosomal transfer, F-prime conjugation and merodiploids,

Conjugation of fertility inhibited F-like plasmids, Nonconjugative, mobilizable plasmids, Broad

Host Range self-transmissible plasmids, Chromosome mobilization by Non-F plasmids, Plasmid

based conjugation in other bacteria (Salmonella, Pseudomonas, Streptomyces and Streptococcus.

Interrupted mating and conjugational mapping.

Agrobacterium genetics: Ti-plasmid, Interkingdom gene transfer (Key early experiments, vir

regulon, protein secretion apparatus, conjugation model of T-DNA transfer, Integration

products).

Unit III

Transformation: Mechanism of Natural competence and transformation in Bacillus subtilis,

Streptococcus pneumoniae and Haemophilus influenzae. Transformation by inducing artificial

competence, Gene linkage and mapping by transformation.

Transduction: Generalized transduction in P22, P1, T4, and Mu bacteriophages, homologous

recombination with recipients chromosome, measuring transduction (cotransduction of markers,

marker effects, abortive transduction, transduction of plasmids) Applications of generalized

transduction. Specialized transduction in and its applications.

Viral genetics:Bacteriophages (T-series, -biology, Miniphages (M-13, X 174, Mu),

Bacteriophage recombination (complementation, fine structure analysis).

Unit IV

Fungal genetics: Tetrad analysis and Mitotic recombination

Restriction-Modification systems: Role of Restriction-Modification systems, Types of RM

systems, Modification, Restriction and Regulation.

Transposable elements: Types of transposable elements, Structure, genetic organization and

mechanism of transposition of Tn5, Tn3 and related transposons, Bacteriophage Mu, Tn7 and

IS911, Integrons, Retrotransposons, Conjugative and Mobilizable transposons. Assays of

transposition.

Molecular biology of tumor: Control of cell proliferation, oncogene activation, role of tumor

suppressor genes.

Apoptosis

Reference books:

Genes IX: Lewin

Molecular Biology of the Gene: Watson et al Vth

edition.

Modern Microbial Genetics: Uldis Streips and Ronald Yasbin.

Microbial genetics: Stanley Molay, John Cronan and David Freifelder.

Molecular Genetics of Bacteria: Snyder and Champness.

Molecular Genetics: Stent and Calendar

Principles of Genetics: Snustad and Simmons

Molecular Biology of the Cell: Alberts et al.

PS02CBIT03: GENETIC ENGINEERING & BIOINFORMATICS

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Unit -I

Genetic Engineering

Introduction to the scope of genetic engineering. Overview of the principles and progress in

genetic engineering. Basic steps involved in recombinant DNA technology: Isolation of DNA

from various sources, fragmentation methods, ligation strategies, introduction of the chimeric

DNA into various host cells and selection and screening of recombinant clones. Manipulation

and characterization of cloned DNA: Basic PCR, Reverse Transcriptase, inverse, nested, real

time and mega primer PCR.

Unit II

DNA sequencing and sequence assembly. Maxam-Gilbert’s and Sanger’s methods, Shot gun

sequencing, sequencing strategies for large genomes. DNA mapping and DNA fingerprinting:

Physical and molecular mapping, Hybridization and PCR based methods of fingerprinting. Site

directed mutagenesis: Methods and applications.

Unit III

Bioinformatics

Introduction to Bioinformatics: Overview, Internet and bioinformatics, Applications

Databases: Databases in Bioinformatics, various biological databases, Protein and Nucleotide

sequence Data bases. Protein sequence, structure and Classification databases

Sequence analysis: Pairwise alignment, local and global alignment, Multiple sequence

alignment,

Gene prediction: Gene prediction methods: Signal sites Predictions

Unit IV

Protein Computational Biology:

Structural classification of proteins, structure alignment and comparison and Protein Structure

prediction, Active site prediction, Protein modelling and drug design

Phylogenetic analysis: molecular basis of evolution, Phylogenetic trees & different methods for

phylogenetic inference

Reference Books:

Bioinformatics: A Beginners Guide, Clavarie and Notredame

Bioinformatics: David Mount

Bioinformatics: Rastogi

Introduction to Bioinformatics:Arthur M. Lesk

M.Sc. Biotechnology Syllabus w.e.f. June 2009 (I-IV Semesters)

Bioinformatics: Principles and applications, Ghosh and Mallick

Bioinformatics: Genes, Proteins and Computer, C A Orengo

Protein Structure Prediction: Methods and Protocols, Webster, David (Southern Cross

Molecular Ltd., Bath, UK)


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III SEMESTER

PS03CBIT01: MICROBIAL BIOTECHNOLOGY

Unit -I

General concept of Microbial biotechnology and Fermentation economics

Microbial production of

Antibiotics: penicillin, streptomycin

Enzymes: proteases, amylases

Organic acids: Citric acid, acetic acid

Unit- II

Microbial production of .......

Amino acids: Glutamic acid, Lysine

Industrial Alcohol,

Beer and wine

Vitamins: Vit B12, B2

Ergot alkaloids

Unit-III

Biotransformations of steroids

Production of single cell protein from bacteria, fungi and algae: Nutritional value and

safety.

Edible Mushrooms: Cultivation of edible and medicinal mushrooms.

Bioplastics

Single cell oil

Unit -IV

Microbial Exopolysaccharides: Xanthan, Alginate

Microbial Flavours: Diacetyl, Methyl ketones, Terpenes, Vanillin

Fermented food and dairy products: Starter cultures, science and technology of bread,

cheese and yogurt manufacture.

Reference Books :

Biotechnology: Rehm and Reid.

Comprehensive biotechnology: Murray Moo Young.

Microbial Technology: Pepler

Microbiology and technology of fermented foods: R. W. Hutkins. Blackwell publishing.

Topic related review papers

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PS03CBIT02: IMMUNOLOGY

Unit -I

Innate and adaptive immunity: role of cells, receptors and proteins in innate immunity, ubiquity

of the innate system.

Cells and organs of the immune system: Hematopoiesis, primary and secondary lymphoid

organs.

Complement: components of the system, activation, regulation, biological consequences and

deficiency diseases. Inflammation and anti-inflammatory agents.

Unit -II

Antigens and antibodies: properties of immunogens, haptens, epitopes, structure and classes of

immunoglobulins, biological activities and effector functions, monoclonal antibodies and

abzymes.

Antibody diversity: models, organization of Ig genes, mechanism of gene rearrangement,

generation of diversity; expression, synthesis and class switching, antibody engineering.

Production of polyclonal and monoclonal antibodies: Principles, Techniques and applications

Antigen-antibody interactions: Agglutination and precipitation techniques, Radio Immunoassay,

ELISA, Immunofluorescence assays: Florescence activated cell sorter (FACS) technique,

Cytotoxicity assay, Cytokines assays: ELISA and ELISPOT

Unit- III

Major histocompatibility complex and antigen presentation: MHC- organization, inheritance,

genes, molecules and peptide binding, expression, disease susceptibility,immune responsiveness,

self MHC restriction, cytosolic and endocytic pathway for antigen processing.

T-cell receptor, T-cell maturation, activation and differentiation: TCR- genetic organization and

rearrangement of genes, TCR-complex, peptide binding, thymic selection, activation and

differentiation of T cells.

Generation, activation and differentiation of B cells: B cell maturation, activation and

proliferation, germinal centers, regulation of the responses.

Cell mediated cytotoxicity: Effector T cells, cytotoxic T cells, NK cells, ADCC.

Unit -IV

Hypersensitivity reactions: classification and types of hypersensitivity reactions.

Immune tolerance and autoimmunity: establishment and failure of tolerance, autoimmune

diseases, mechanisms for the induction, animal models, treatment.

Transplantation immunology: basis and manifestation of graft rejection, immunosuppressive

therapy, immune tolerance.

Experimental systems in immunology.

Reference books:

Kuby-Immunology: T. J. Kindt, R. A. Goldsby and B. A. Osborne; W. H. Freeman

Janeway’s Immunology: K. Murphy, P. Travers and M. Walport; Garland Sciences

Immunology: Ivan Roitt, J. Brostoff and D. Male; Mosby

Essential immunology: Ivan Roitt; Oxford: Blackwell

Topic related review articles.

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PS03CBIT03: ENZYMOLOGY

Unit- I

Introduction to enzymology and historical developments in enzymology

Protein Structure: Primary, secondary, tertiary and quaternary structure, techniques used in

enzyme characterization

Enzyme classification: IUB enzyme classification. Enzyme Activity: Principle and techniques of

enzymatic analysis, factors affecting enzyme activity, Extraction and Purification of enzyme:

Objectives and strategy, separation techniques, test of purity.

Unit- II

Enzyme Kinetics: Bioenergetics and Catalysis

Single substrate kinetics: Equilibrium and Steady state kinetics, significance of Km, Vmax &

Kcat. Pre-steady state and Relaxation kinetics.

Multisubstrate kinetics: General rate equation, compulsory order, random order and ping-pong

mechanisms and their primary and secondary plots.

Enzyme inhibition and its kinetics: Reversible and irreversible inhibition, competitive, non-

competitive and uncompetitive, mixed, partial, substrate and allosteric inhibition.

Thermal kinetics: Effect of temperature on reaction rate, enzyme stability, Arrhenius equation

and activation energy.

Unit- III

Mechanism of Enzyme Action:

Enzyme activators, co-enzymes and co-factors in enzyme catalysis, Enzyme and substrate

specificity, Investigation of active Centre, Factors affecting catalytic efficiency, Experimental

approaches to determine enzyme mechanisms.

Enzyme mechanisms: Lysozyme, Chymotrypsin, Carboxypeptidase, Restriction endonuclease,

Aspartate transcarbomylase. Allosteric enzymes and sigmoidal kinetics: Protein ligand binding,

Co-operativity, MWC & KNF models,

Regulation of enzyme activity. Control of metabolic pathways.

Unit- IV

Isoenzymes and its physiological significance, Ribozymes and Abzymes, Enzyme engineering:

Chemical modification of enzymes: methods of modification of primary structure, catalytic and

allosteric properties, use of group specific reagents.

Enzyme Immobilization, Enzymes in non conventional media, Enzymes sensors, Enzymes as

analytical reagents

Reference Books:

Fundamentals of Enzymologist: Nicholes C. Price and Lewis Stevens, Oxford Univ.

Press.

Enzyme Structure and mechanism: Alan Fersht, Reading, USA.

Understanding Enzymes: Trevor Palmer

The chemical kinetics of enzyme action: K. J. Laider and P. S. Bunting, Oxford

University

Press, London.

Enzymes: M. Dixon, E. C. Webb, CJR Thorne and K. F. Tipton, Longmans, London.

Proteins: Thomas Creighton

Biochemistry: Lubert Stryer.


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IV SEMESTER

PS04CBIT01: PLANT BIOTECHNOLOGY

Unit -I

Cell & tissue culture in plants; callus cultures; in-vitro morphogenesis-organogenesis and

embryogenesis; Artificial Seeds, Micropropagation (Clonal propagation); Haploidy;

anther and ovule cultures, Embryo cultures; Protoplast isolation, culture and protoplast

fusion and somatic hybridization, Cybrids, Somaclonal Variation; in-vitro mutation

methods; Virus elimination, pathogen indexing; Cryopreservation.

Unit- II

Production of secondary metabolites; Sources of plant secondary metabolites; criteria for

cell selection, factors affecting the culture of cells; different bioreactors and their use in

secondary metabolite production; biochemical pathways for the production of different

secondary metabolites; and biotransformation.

Unit- III

Principles and methods of genetic engineering, and its applications in Agriculture.

Methods for genetic transformation and transgenic plants production through

Agrobacterim tumefaciens and A. rhizogenes; Gene transfer methods in plants; PEG-

mediated, microinjection, particle bombardment, electroporation, Molecular markers and

their importance in plant breeding, Marker Assisted Selection (MAS).

Unit- IV

Molecular plant pathology: Mechanisms of disease resistance in plants against pathogens;

Signalling pathways and molecular events during pathogen – plant interaction.

Biotechnology and intellectual property rights (IPR); Plant genetic resources GATT &

TRIPS; Patent for higher plant genes and DNA sequence

Reference Books:

Plant biotechnology – J Hammond, et. al., Springer Verlag.

Plant cell and tissue culture for production of food ingredients – T J Fu, G Singh, et. al.

Biotechnology in crop improvement – H S Chawla.

Practical application of plant molecular biology – R J Henry, Chapman & Hall.

Elements of biotechnology – P K Gupta.

An introduction to plant tissue culture – M K Razdan.

Plant propagation by tissue culture: The technology (Vols. 1 & 2) – Edwin George.

Handbook of plant cell culture (Vols. 1 to 4) – Evans et. al., Macmillan.

Plant tissue and cell culture – H E Street, Blackwell Scientific.

Cell culture and somatic cell genetics of plants (Vols. 1 to 3) – A K Vasil, A. Press.

Plant cell culture technology – M M Yeoman.

Plant tissue culture and its biotechnological applications – W Bary, et. al., Springer

Verlag.

Principles of plant biotechnology: An introduction to genetic engineering in plants – S H

Mantel, et. al.

Advances in biochemical engineering / Biotechnology – Anderson, et. al.

Applied and fundamental aspects of plant cell tissue and organ culture edited by Reinert

& Bajaj Y P S, Springer Verlag.

Plant cell and tissue culture – S Narayanswamy, Tata Mc Graw Hill Co.

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PS04CBIT02: ENVIRONMENTAL BIOTECHNOLOGY

Unit- I

Issues and scopes of environmental biotechnology.

Waste water treatment- Waste water characterization and its significance: COD, BOD,

Inorganic constituents, solids, biological components. Primary, secondary and tertiary

treatment of waste water. Principles and aims of biological wastewater treatment

processes. Biochemistry and microbiology of inorganic phosphorus and nitrogen

removal. Suspended growth technologies: Activated sludge, oxidation ditches, waste

stabilization ponds. Fixed film technologies: Trickling filters, rotating biological

contactors, fluidized bed and submerged aerated filters.

Unit- II

Toxicity testing in waste water treatment plants using microorganisms.

Anaerobic digestion: microbiological and biochemical fundamentals, factors influencing

anaerobic digestion. Anaerobic waste water treatment systems: RBC, UASB, anaerobic

filters. Merits and demerits of anaerobic treatment of waste.

Composting: Objectives, fundamentals, microbiology, factors influencing composting

and composting systems. Compost quality and uses. Vermicomposting.

Unit- III

Biodegradation of organic pollutants: Mechanisms and factors affecting biodegradation.

Pollution problems and biodegradation of simple aliphatic, aromatic, polycyclic aromatic

hydrocarbons, halogenated hydrocarbons, azo dyes, lignin and pesticides.

Bioremediation: Intrinsic bioremediation, Biostimulation and Bioaugmentation. In situ

and ex situ bioremediation technologies. Bioremediation of oil spills. Bioremediation of

heavy metal pollution, Phytoremediation. Use of GMO in bioremediation. Biological

treatment of waste gas (polluted air): biofilters, bioscrubbers, membrane bioreactors,

biotrickling filters.

Unit -IV

Biogeotechnology- Bioleaching of metals: Characteristics of commercially important

microbes, mechanisms of bioleaching, factors affecting bioleaching and current

biomining processes. Biobeneficiation of gold ores. Microbially enhanced oil recovery.

Biodesulfurization of coal: Removal of organic and inorganic sulfur from coal.

Microbial Insecticides: Bacterial, fungal and viral insecticides in pest management.

Biofertilizers: Nitrogen fixing and phosphate solubilizing biofertilizers.

Reference Books:

Comprehensive Biotechnology Vol-4, Murray Moo Young.

Biotechnology-Rehm and Reid.

Waste water microbiology by G. Bitton

Biodegradation and bioremediation by M.Alexander

Waste water treatment for pollution control, 2nd edition. Arceivala

Environmental Biotechnology by H. Jordening and Josef Winter

Topic related review articles

Elective paper: Any two from the list

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List of elective papers

PSCOEBIT01: BIOSTATISTICS

Unit I:

Data Collection and Presentation

Types of Biological Data: Qualitative Data -Nominal, Ordinal, Ranked; Quantitative Data:

Discrete and Continuous.

Understanding of Population and sample

Methods of Collection of Data: (i) Experimental Data and (ii) Survey Data- Simple random

sample(with and without replacement), stratified sampling and cluster sampling.

Tables: Frequency Distributions, Relative Frequencies.

Graphical Presentation: Bar charts, Histograms, Frequency Polygons, One way scatter plots, Box

plots, two-way scatter plots, line graphs.

Practicals Using MS-Excel.

Unit II:

Descriptive Statistics

Measures of Central Tendency: Mean, Median and Mode, quartiles, deciles and percentiles (both

for raw data and grouped data)

Measures of Dispersion: Range, Interquartile Range, Variance, Standard Deviation and

Coefficient of Variation.

Measures of Skewness and Kurtosis.

Practicals Using MS-Excel.

Unit III:

Probability and Probability Distributions:

Random Experiment: Elementary outcomes, events, and Sample Space.

Mathematical Definition of Probability, Marginal Probability, Marginal Probability and

Conditional Probability. Independent Events. Some simple laws of probabilities(Statements

only).

Random Variables: Discrete and Continuous. Some examples from biological sciences.

Probability Distributions: Binomial Distribution, Standard Normal Distribution ,General Normal

Distribution; Sampling Distributions- t, chi-square and F distributions.

Unit IV:

Testing of hypotheses:

Statistical hypotheses: Null and Alternative hypotheses. Simple and Composite hypotheses.

Statistical Tests: Acceptance region and Rejection Region. Types of errors and power of the test.

Goodness of fit tests.

Significance Tests for Normal Distribution: One sample tests for mean – z test and t-test.

Two sample tests for normal distributions: Tests for means (i) when variances are known (ii)

when variances are unknown. Tests for equality of variances.

Paired t-test for equality of means.

Confidence Intervals

Bivariate and Multivariate Data

Some examples on bivariate and multivariate data. Correlation: Simple, partial and multiple

correlation Coefficients.

Regression: Simple and multiple linear regressions. Logistic Regression

Analysis of Variance: Completely Randomized Design, Randomized Block Design

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PSCOEBIT02: PHYTORESOURCE UTILIZATION AND CONSERVATION

Plant Biodiversity : Concept, status in India, utilization and concerns.

Origin, evolution, botany, cultivation and uses of (i) Food, forage and fodder crops, (ii) fibre

crops (iii) medicinal and aromatic plants, and (iv) vegetable oil – yielding crops

Ethnomedicobotany: Basic approaches to study traditional knowledge on herbal medicine; Scope

and potential applications.

Collection methods of ethnomedicobotanical data: Field methods and scrutiny of Herbarium

specimens and folklore; verification of data; collection of materials for voucher specimen and for

phytochemical screening; application of ethnomedicobotany.

Creating indigenous knowledge base of traditional medicines of plant origin.

Forest products : Important timber yielding planting.

Timber types, identification diagnostic features, structure & quality

Important fire wood plants

Non Timber forest products bamboos, rattans, fibers pulp; gums, resins, tanins, lotex, fruits &

tubers.

Innovations for meeting world food demands.

Plants used as avenue trees for shade, pollution control and aesthetics.

Principles of conservation; extincitons; environmental status of plants based on International

Union for Conservation of Nature.

Strategies for conservation – in situ conservation : International efforts and Indian initiatives;

protected areas in India – sanctuaries, national parks, biosphere reserves, wetlands, mangroves

and coral reefs for conservation of wild biodiversity.

ex situ conservation : Principles and practices; botanical gardens, fields gene banks, seed banks,

in vitro repositories, cryobanks; general account of the activities of Botanical Survey of India

(BSI), National Bureau of Plant Genetic Resources (NBPGR), Indian Council of Agricultural

Research (ICAR), Council of Scientific & Industrial Research (CSIR), and the Department of

Biotechnology (DBT) for conservation, non-formal conservation efforts.

Reference Books : Anonymous. National Gene Bank: Indian Heritage on Plant Genetic Resources (Booklet).

National Bureau of Plant Genetic Resources, New Delhi.

Arora, R. K. and Nayar, E. R. Wild Relatives of Crop Plants in India. NBPGR Science

Monograph.

Baker, H. G. Plants and Civilization. C. A. Wadsworth, Belmont.

Bole, P. V. and Vaghani, Y. Field Guide to Common Indian Trees. Oxford University Press,

Mumbai.

Chandel, K. P. S., Shukla, G. and Sharma, N. Biodiversity in Medicinal and Aromatic Plants in

India : Conservation and Utilization. National Bureau of Plant Genetic Resources, New Delhi.

Cristi, B. R. CRC Handbook of Plant Sciences and Agriculture. Vol. I. In-situ conservation. CRC

Press, Boca Raton, Florida, USA

Council of Scientific & Industrial Research. The Useful Plants of India. Publications and

Information Directorate, CSIR, New Delhi.

Plant Wealth of India. Special Issue of Proceedings India National Science Academcy B – 63

Rodgers, N. A. and Panwar, H. S. Planning a Wildlife Protected Area Network in India. Vol. 1.

The Report Wildlife Institute of India, Dehradun.

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Sahni, K. C. The Book of India Trees, Oxford University Press, Mumbai.

Sharma, O. P. Hill’s Economic Botany. Tata McGraw Hill Co. Ltd., New Delhi.

Swaminathan, M. S. and Kocchar, S. L. Plants and Society. Macmillan Publication Ltd., London.

Thakur, R. S., Puri, H. S. and Husain, A Major Medicinal Plants of India. Central Institute of

Medicinal and Aromatic Plants, CSIR, Lucknow. S.K. Jain: A Manual of Ethnobotany

S.K. Jain: Glimpses of Indian Ethnobotany

S.K.Jain, B.K. Sinha and R.C.Gupta: Notable plants in Ethnomedicine of India

J.K. Maheswari: Dictionary of Indian Folk medicine and Ethnobotany

S.K. Jain: Useful plants of India

Wiley Chichester, CIBA Foundation Symposium 185: Ethnobotany and the search for new drugs

PSCOEBIT03: MICROTECHNIQUES

Unit- I

Light microscopy:- Optical corrections, Properties and types of objectives. Oculars,

Illumination.

Types of light microscopes: Bright field, dark field, fluorescence, phase contrast, polarizing,

differential interference contrast. Micrometry.

Electron microscopy: Basic components of electron microscopes. Thermionic and field

emission electron guns.

Types of electron microscopes: TEM, SEM, STEM, ESEM and HVEM

Unit- II

Fixation and storage: Classification of fixatives, formulas. (plant, animal and microbial

samples) Factors affecting fixation. Procedures for fixation. Dehydration, infiltration and

embedding. Media for embedding. Microtomes: Rotary, sliding cryostat, ultramicrotome and

freezing ultra microtome.

Unit- III

Preparation of biological samples for light and electron microscopy: Sectioning,

maceration, squash and clearing technique. Freeze etching and freeze fracturing. Stains for light

and electron microscopy. Staining procedures. Photomicrography.

Unit- IV

Histochemistry: Histo chemical localization of metabolites:- Starch, proteins, lipids, total

carbohydrates, lignin, polyphenols, nucleic acid, histones, cutin, suberin and waxes. Localization

of enzymes: Peroxidase, acid phosphatase and succinic dehydrogenase.

Ultra structural cytochemistry:- Localization of tannin, protein, cell wall polysaccharide, lignin

and membrane. Immunocytochemistry

PSCOEBIT04: ANIMAL BIOTECHNOLOGY

Unit -I

Structure and organization of animal cells, tissues and biology of cultured cells.

General out-line of epithelial tissue, connective tissue, muscular tissue and nerve tissue.

Cell adhesion; Junctions; Extracellular matrix; Cytoskeleton; Cell cycle; Differentiation;

Cell signaling; Energy metabolism

Aseptic condition and requirement of other equipments; Incubation; Storage;Different

substrates.

Unit -II

Introduction to the balanced salt solutions and growth medium:

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Media –Physical properties, balance salt solutions, complete media, serum, Serum-Free

media.

Chemical, physical and metabolic functions of different constituents of culture medium.

Role of carbon dioxide. Role of serum and supplements. Serum and protein free media

and their application.

Unit -III

Primary and established cell line culture. Measurement of viability and cytotoxicity.

Biology; Characterization and growth of the cultured cells; Disaggregation of tissue and

primary culture; Maintenance of cell culture; Cell cloning and cell separation; Cell

differentiation; Cell synchronization and transformation; Measurement of cell death and

apoptosis.

Unit -IV

Basic techniques of mammalian cell culture in vitro

Culture of s[pecialized cells: Epithelia; Mesenchymal and connective tissues; Muscles;

Neuroectoderm; Endocrine; Hematopoietic cells; Tumor cells

Embryonic stem cells stem cell culture and their applications.

Embryo technology and transgenic animals

References :

Freshney, R. I: Culture of Animal Cells. Wiley-Liss.

Masters, J. R. W. (ed): Animal Cell Culture – Practical Approach, Oxford Univ. Press.

Basega, R. (ed): Cell Growth and Division: A Practical Approach. IRL Press.

Butler, M and Dawson, M. (eds.).: Cell Culture Lab Fax, Eds., Bios Scientific

Publications Ltd., Oxford.

Clynes, M. (ed).: Animal Cell Culture Techniques. Springer.

Mather, J.P and Barnes, D. (eds). : Methods in Cell Biology, Vol. 57, Animal Cell

Culture Methods. Academic Press.

PSCOEBIT05: BIOCHEMISTRY

Unit- I

Carbohydrates : Occurrence, classification, structure and functions, active groups and chemical

properties of sugars, Monosaccharides, disaccharides and polysaccharides,

Mucopolysaccharides, proteoglycans, glycolipids and blood group polysaccharides;

Carbohydrate metabolism: aerobic and anaerobic glycolytic pathways, TCA cycle and various

fates of Glucose 6 Phosphate in a cell - Gluconeogenesis, glycogen synthesis and breakdown.

Unit- II

Bioenergetics, Energy transformations in cell, ATP Cycle, High energy compounds; Electron

transport chain order and organization of carriers, proton gradient, iron sulphur proteins,

cytochromes and their characterization, respiratory controls and oxidative phosphorylation,

uncouplers and inhibitors of energy transfer. ATP- synthetase complex.

Unit -III

Structure and properties of lipids, fatty acids, phsopholipids and other derived lipids; structure

and functions of lipoproteins, cholesterol, steroids and prostaglandins, membranes; Lipid

metabolism: α, β and δ oxidation of fatty acids, metabolism of fatty acids with even and odd

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carbon atoms, saturated and unsaturated fatty acids. Metabolism and synthesis of phospholipids,

glycolipids and sphinglipids; Ketone bodies –formation and degradation, Mobilization of fats.

Unit- IV

Proteins structure: Classification of amino acids; Primary, secondary, tertiaryand quaternary

structure of proteins. Determination of protein structure and its analysis, Ramachandran plot.

Hydropathy plot, Protein folding. Metabolism : Biosynthesis and metabolism of individual

amino acids. Urea cycle. Nitrogen balance, Biosynthesis, degradation and regulation of Purines

and Pyrimidines. Interrelationship of protein, carbohydrate and Lipid metabolism; In born errors

of metabolism.

Reference Books:

Lehninger’s Principles of Biochemistry: D. L. Nelson and M. M. Cox, Macmillan, Worth

Pub. Inc., NY.

Harper’s Biochemistry: R. K. Murray and others. Appleton and Lange, Stanford.

PSCOEBIT06: HUMAN PHYSIOLOGY

Unit I

Blood-composition and functions of plasma, erythrocytes including Hb, leucocytes and

thrombocytes and plasma proteins. Hemoglobinopathies, thalassemias and anemias. Blood

clotting – extrinsic and intrinsic pathways of blood clotting, laboratory test to measure

coagulation and thrombolysis.

Unit II

Digestive system – Composition, functions and regulation of saliva, gastric, pancreatic intestinal

and bile secretions – digestion and absorption of carbohydrates, lipids, proteins nucleic acids,

minerals and vitamins.

Unit III

Excretory system – structure of nephron formulation of urine, glomerular filteration, GFR,

tubular reabsorption of glucose. The Muscular System – Types of muscles and their functions

Unit IV Nervous System- Structure of neuron, function and organization of nervous system, Nerve

impulse transmission.

Endocrine glands – secretion and function Reproduction, pregnancy and lactation. Hormonal

disturbances.

Reference Books:

Molecular Biology of the cells : Alberts et. al., Garland Publications Inc. NY

Cell and Molecular Biology by E D P de Robertis and E M F de Robertis.

Text book of Medical Physiology by A. C. Guyton and J. E. Harcourt.

Text book of Medical Physiology by Garong.

Text book of Biochemistry and Human Biology by Talwar.

Principles of anatomy and physiology by Tortora Grabowski, 10th edition

PSCOEBIT07: GENOMICS AND PROTEOMICS

UNIT I

The rise of ‘omics

Impact on other fields of study (e.g.metabolomics, toxicogenomics, chemical genomics,

pharmacogenomics) The structure, function and evolution of the human genome. Strategies for large-scale sequencing

projects. Human disease genes; approaches for determining gene expression patterns and

functions.

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UNIT II

Genomic mapping and sequence analysis Comparative genomics, synteny, genome evolution

Sequencing and individual variation Next generation sequencing and its utility for understanding individual variation and disease.

UNIT III

Protein structure and its prediction

Protein structure, secondary structure and super-secondary structure. Mechanisms of protein folding,

tertiary folds. Formation of bloomers. Relationship between protein structure and function. Prions.

Structure prediction and

human proteomics. Mutant proteins.

Use of computer simulations and knowledge-based methods in the design process. De-novo design.

Protein structure and drug discovery, Proteins in disease

UNIT IV

Comprehensive mutant libraries High throughput gene knockout, gene targeting, gene trapping, genome-wide mutagenesis

Mapping protein interactions Methods – two hybrid, phage display, mass spectrometry.

Reference Books:

PSCOEBIT09: Bioethics, Bio-safety and IPR

Unit I

Biotechnology and social responsibility, public acceptance issues in biotechnology, issues of

access, ownership, monopoly, traditional knowledge, biodiversity, benefit sharing,

environmental sustainability, public vs private funding, biotechnology in international relations,

globalization and development divide.

Introduction to bioethics: Social and ethical issues in biotechnology. Principles of bioethics.

Ethical conflicts in biotechnology- interference with nature, unequal distribution of risk and

benefits of biotechnology, bioethics vs business ethics.

Unit II

Biosafety: Definition of bio-safety, Biotechnology and bio-safety concerns at the level of

individuals, institutions, society, region, country and world with special emphasis on Indian

concerns.

Biosafety in laboratory institution: laboratory associated infection and other hazards, assessment

of biological hazards and level of biosafety.

Bio safety regulation: handling of recombinant DNA products and process in industry and in

institutions (Indian context).

Unit III

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Introduction to IPR: IPR, forms of IPR and Intellectual property protection. Concept of property

with respect to intellectual creativity, Tangible and Intangible property.

WTO: agency controlling trade among nations, WTO with reference to biotechnological affairs,

TRIPs. WIPO, EPO.

Unit IV

Concept related to patents novelty, non-obviousness, utility, anticipation, prior art etc. Type of

patents. Indian patent act and foreign patents.

Patentability, Patent application, Revocation of patent, Infringement and Litigation with case

studies on patent, Commercialization and Licensing.

Books Recommended:

1. Fleming, D.A., Hunt, D.L., (2000). Biotechnology and Safety Assessment (3rd Ed)

Academic press.ISBN-1555811804,9781555811808.

2. Thomas, J.A., Fuch, R.L. (1999). Biotechnology and safety assessment (3rd Ed). CRC

press, Washington. ISBN: 1560327219, 9781560327219

3. Law and Strategy of biotechnological patents by Sibley. Butterworth publication.(2007)

ISBN: 075069440, 9780750694445.

4. Intellectual property rights- Ganguli-Tat McGrawhill. (2001) ISBN-10: 0074638602,

5. Intellectual Property Right- Wattal- Oxford Publicatiopn House.(1997)

ISBN:0195905024.

6. Biotechnology - A comprehensive treatise (Vol. 12). Legal economic and ethical

dimensions VCH. (2nd

ed) ISBN-10 3527304320.

7. Encyclopedia of Bioethics 5 vol set, (2003) ISBN-10: 0028657748.

8. Thomas, J.A., Fuch, R.L. (2002). Biotechnology and safety Assessment (3rd

Ed)

Academic press.

9. B.D. Singh. Biotechnology expanding horizons.

10. H.K.Das. Text book of biotechnology 3rd

edition.

cbcs syllabus - sardar patel university

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