Semester I Biochemistry papers - Sardar Patel · PDF fileSemester I Biochemistry papers ... Core Theory PS01CBIC01 Cell biology and Genetics ... (Practicals of PS01 CBIC01 and PS01

Semester I Biochemistry papers

Semester II Biochemistry papers

Biochemistry

Core

Theory

PS01CBIC01 Cell biology and Genetics

PS01CBIC02 Bioinstrumentation

PS01CBIC03 Cellular Metabolism

One

Elective

Theory

One elective paper from the list

Practical

PS01CBIC04 Practical –I (Practicals of PS01 CBIC01 and PS01

CBIC02) PS01CBIC05 Practical –II (Practicals of PS01 CBIC03 and PS01

EBIC0x) Viva-Voce PS01CBIC06 Viva -voce

Biochemistry

Core

Theory

PS02CBIC01 Molecular Biology

PS02CBIC02 Biochemical and Environmental Toxicology

PS02CBIC03 Enzymology

One

Elective

Theory


Practical

PS02CBIC04 Practical –I (Practicals of PS02 CBIC01 and PS02



Semester III Biochemistry papers

Semester IV Biochemistry papers

List of Elective Papers

PSCOEBIC01: Biostatistics

PSCOEBIC02: Phytoresource utilization and conservation

PSCOEBIC03: Microtechniques

PSCOEBIC04: Plant Biotechnology

PSCOEBIC05: Plant Biochemistry

PSCOEBIC06: Bioinformatics

PSCOEBIC07: Pharmacognosy

PSCOEBIC08: Microbial Physiology

PSCOEBIC09: Biochemistry of Horticultural commodities

Biochemistry

Core Papers

PS03CBIC01 r-DNA technology

PS03CBIC02 Immunology

PS03CBIC03 Human Physiology

One

Elective


Practical PS03CBIC04 Practical –I (Practicals of PS03 CBIC01 and PS03



SUBJECT COURSE COURSE

CODE COURSE TITLE

Biochemistry

Core

papers

PS04CBIC01 Animal Biotechnology PS04CBIC02 Nutritional & Clinical Biochemistry

Two

Elective

Two elective

papers from the

list

PS04CBIC03 Practical –I based on PS04CBIC01and PS04CBIC02 PS04CBIC04 Practical –II based on PS04EBIC0x and PS04EBIC0x

PS04CBIC05 Viva -voce

OR

Biochemistry

Core papers

PS04CBIC01 Animal Biotechnology PS04CBIC02 Nutritional & Clinical Biochemistry PS04CBIC03 Practical –I based on PS04CBIC01and PS04CBIC02

Dissertation PS04CBIC04 Dissertation

PS04CBIC05 Viva -voce

I SEMESTER

Core papers

PS01CBIC01: CELL BIOLOGY & GENETICS

Unit I

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

Cell 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.

Unit II

Chloroplast and Mitochondria: 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. 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.

Unit III

Cytoskeletal elements– composition and organization of microtubules, microfilaments and

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

Apoptotic pathway and cell death

Unit IV

Fundamentals of genetics: Mendelian analysis- Mendels laws of inheritance; Quantitative

inheritance. Multiple alleles and physical basis of heredity.

Linkage and tetrad analysis: Linkage and crossing over in higher organisms; tetrad analysis;

mitotic recombination and gene conversion in haploid organisms. Molecular mechanisms of

recombination.

Reference Books:

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

& Sons, Inc.,USA.

Cell and Molecular Biology (1987), 8th Edn. De Robertis, E. D. P. and De Robertis, E.

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

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

Scientific American Books, N.Y.

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.

Genetics: P K Gupta

Genetics: Suzuki et al

PS01CBIC02- 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, SDS, Agarose and 2D gel electrophoresis.

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

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

emission spectroscopy; MS and MALDI-TOF.

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

flurorescence

Unit IV 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

PS01CBIC03 - CELLULAR METABOLISM

Unit I

Concepts of energy transformation in metabolic reactions, Biological oxidations, free energy

changes and redox potentials, phosphate potential,The mitochondrial respiratory 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 II

Glycolysis, citric acid cycle its function in energy generation and biosynthesis of energy rich

bonds, pentose phosphate pathway and its regulation, Gluconeogenesis, interconversions of

sugars, Biosynthesis of glycogen, starch and oligosaccharides.

Unit III

Fatty acid biosynthesis : Acetyl CoA carboxylase, Fatty acid synthase, desaturase and elongase.

Fatty acid oxidation, : a, b, w oxidation and lipoxidation. Lipid biosynthesis : Biosynthesis of

triacylglycerol, phosphoglycerides , sphingolipids and cholestrerol. Ketone bodies –formation

and degradation

Unit IV

Biosynthesis and degradation of amino acid and their regulation. Specific aspect of amino acid

metabolism.Urea cycle and its regulation. Biosynthesis of purines and pyrimidines,

Degradation of purines and pyrimidines, Regulation of purines and pyrimidines

biosynthesis, Structure and regulation of ribonucleotide reductase ,biosynthesis of

ribonucleotides, deoxyribonucleotides and polynucleotides

Reference Books :

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

Inc., NY.

Biochemistry : Lubert Stryer WH Freeman & Co., NY.

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

Text book of Biochemistry with clinical correlations by Delvin

Elective paper

Any one from the list

II SEMESTER

PS02CBIC01 - 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

PS02CBIC02: BIOCHEMICAL & ENVIRONMENTAL TOXICOLOGY

Unit I

Definition and scope of toxicology: Eco-toxicology and its environmental significance.

Toxic effects: Basic for general classification & nature. Dose-Response relationship:

Synergism and Antagonism, Determination of ED50 & LD50. Acute and Chronic exposures.

Factors influencing Toxicity, Pharmacodynamics & Chemodynamics.

Diagnosis of toxic changes in liver and kidneys: Metabolism of Haloalkanes, Haloalkenes &

Paracetamol with their toxic effects on tissues.

Unit II Xenobiotics Metabolism: Absorption & distribution. Phase I reactions. Oxidation,

Reduction, Hydrolysis and Hydration. Phase II reaction/Conjugation : Methylation,

Glutathione and amino acid conjugation. Detoxification.

Biochemical basis of toxicity: Metabolism of Toxicity : Disturbances of Exitable membrane

function. Altered calcium Homeostasis. Covalent binding of cellular macromolecules &

Genoatoxicity. Tissue specificity of Toxicity.

Toxicity testing : Test protocol, Genetic toxicity testing & Mutagenesis assays : In vitro Test

systems – Bacterial Mutation Test : Reversion Test, Ames Test, Fluctuation Tests and

Eukaryotic Mutation Tests. In vivo Mammalian Mutation tests – Host mediated assay &

Dominant Lethal Test. Use of Drosophila in toxicity testing. DNA repair assays.

Chromosome damage test. Toxicological evolution of Recombinant DNA – derived proteins.

Unit III Pesticide toxicity: Insecticides: Organochlorines, Anti cholinesterases – Organophosphates and

Carbamates, Fungicides. Herbicides, Environmental consequences of pesticide toxicity.

Biopesticides.

Food Toxicity: Role of diet in cardio-vascular disease and cancer. Toxicology of food

additives.

Unit IV Metal Toxicity: Toxicology of Arsenic, mercury, lead and cadmium. Environmental factors,

affecting metal toxicity effect of light, temperature & pH.

Air pollution: Common air Pollutant & their sources. Air pollution & ozone. Air pollution due

to chlorofluorocarbons (CFCS) and asbestos.

Reference Books:

Handbook of Clinical Biochemistry by R. Swaminathan Oxford Press

Environmental chemistry by Stanley E. Manahan

Environmental Toxicology by David A. Bright and Pamela Welbourn

Emergency Toxicology by Peter Viccellio

Introduction to Food Toxicology by Takayuki Shibamoto and Leonard S. Bjeldknes Acad. Press

2nd

edn.

PS02CBIC03: ENZYMOLOGY

Unit I

Structure and functions of enzymes: Properties of Amino Acids; Basis of protein structure;

Chemical & acid-base properties of proteins ; Specificity of enzyme action; monomeric and

oligomeric enzymes ; Co enzymes and Cofactors; Units of activity, Specific activity of enzyme

and methods of enzyme assay. Protein sequencing; Enzymes Purification: methods and strategies

for small and large scale purification

Unit II

Enzyme kinetics: Uni-substrate enzyme kinetics and factors affecting the rate of enzyme

catalyzed reactions ; Forms and derivation of M.M. equation, significance of V max and Km.

Enzyme inhibition – Type of inhibition, competitive, non competitive and uncompetitive

kinetics. Two substrate system kinetics-sequential and ping pong.

Unit III

Enzyme catalytic efficiency – factors associated with catalytic efficiency such as proximity,

orientation-distortion or strain, and base nucliophitic catalysis with example.

Detailed mechanism of catalysis of chymotrypsin, Lactate dehydrogenase and Triose

phosphate isomerase.

Protein ligand binding, cooperative Hill and satchard plots.

Allosteric enzymes, sigmoidal kinetics and their physiological significance, symmetric and

sequential modes for action of allosteric enzymes and their significance.

Unit IV

General mechanism of enzyme regulation, Reversible and irreversible covalent modification of

enzymes. Feed Back inhibition and Feed Forward stimulation; Enzyme repression, induction and

degradation, control of enzymatic activity by products and substrates.

Enzyme engineering and its applications. Synthetic enzymes.

Reference Books:

Fundamentals of Enzymology: 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.

Elective paper


III SEMESTER

Core papers

PS03CBIC01: rDNA TECHNOLOGY

Unit I

Basic techniques involved in r-DNA technology.

Concept and emergence of r-DNA technology. Relevance and future prospects.

Principles involved, preparation and purification of genomic DNA from eukaryotic and

prokaryotic organisms, plasmid DNA and bacteriophage DNA preparation.

Generation of DNA fragments: Methods available and their advantages and

Disadvantages; Ultrasonication; Restriction enzyme digestion and shearing of DNA.

Cloning vectors – Plasmid and phage biology; vectors based on plasmids, cosmids, λ,

M13, phagemids, yeast artificial chromosomes (YACs), Bacterial Artificial

Chromosomes (BACs) and animal viruses.

Unit II

DNA modifying enzymes: Ligation: reaction kinetics and factors affecting ligation.

Introduction of DNA/RNA in bacteria, yeast, fungi and in other eukaryotic host

systems.

Selection and screening of recombinant clones: Direct and indirect methods; probe

selection and labelling; methods based on nucleic acid hybridization; immunochemical

methods; reporter genes and other emerging methods for clone identification. In vitro

translation.

Unit III

Generation of genomic and cDNA libraries.

Methods and strategies for preparation and screening of genomic and cDNA libraries ;

Advantages and disadvantages of various methods. Applications of the genomic and

cDNA libraries.

Characterization of cloned DNA :

Mapping and DNA fingerprinting: Physical and molecular mapping.

Methodology, merits and demerits and applications of Restriction mapping; RFLP;

RAPD; AFLP; SSR; REMAP and SCAR analysis.

Unit IV

DNA sequencing: Principles and methods for DNA sequencing. Sequencing of whole

genomes; data submission and validation.

Polymerase Chain Reaction: Principle and basic types of PCR; Reverse Transcription and

Real Time PCRs; Factors affecting PCR; Applications and precautions.

Modification of cloned DNA :

Techniques available, advantages and limitations of random and site-directed

mutagenesis. Applications of DNA modifications in genetic engineering.

Applications of recombinant DNA technology :

Applications of genetic engineering in improvement of plants, animals and microbes;

Gene therapy, pharmaceutical products and molecular diagnostics; Marker Assisted

Selection; Molecular Pharming.

Restriction and regulation for the release of GMOs. Patenting and IPR

Reference Books :

Recombinant DNA : Watson et. al.

Genetic engineering : Sandhya Mitra

Principles of gene manipulation : Old & Primrose

Gene cloning : T. A. Brown

Molecular cloning: Sambrook and Russel

From genes to clones: Ernst Whittaker

PS03CBIC02: IMMUNOLOGY

Unit I:

Adaptive immunity and innate immunity: inflammation, role of cells, receptors and proteins in

innate immunity, ubiquity of the innate system.

Cells and organs of the immune system: Hematopoiesis, cells of the immune system, primary

and secondary lymphoid organs.

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.

Unit II:

Antigen-antibody interactions: principles and applications.

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

deficiency diseases.

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.

Unit III:

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 centres, regulation of the responses.

Cytokines: properties, receptors, associated diseases, therapeutic applications.

Leukocyte activation and migration: CAM, chemokines, recirculation and extravasation,

inflammation and anti-inflammatory agents.

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. Cancer and immune system. Immunodeficiency.

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.

PS03CBIC03: 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.

Unit IV

The Muscular System – Types of muscles and their functions

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 Ganong.

Text book of Biochemistry and Human Biology by Talwar.

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

Elective paper


IV SEMESTER

Core papers

PS04CBIC02: ANIMAL BIOTECHNOLOGY

Unit 1: 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.

Unit 2: Equipments and materials for animal cell culture technology.

Aseptic conditions and requirement of equipment; Incubation; Storage;

Different substrates.

Introduction to the balanced salt solutions and growth medium:

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 3: 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 4: Basic techniques of mammalian cell culture in vitro.Culture of specialized 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.

Recommended 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.

PS04CBIC02: NUTRITIONAL & CLINICAL BIOCHEMISTRY

Unit I

Basic concept- composition of human body: Energy content of food .Measurements of energy

expenditure. Energy requirements of man, woman and factor affecting energy requirements,

Basal metabolic rate, factor affecting BMR.

Carbohydrates- Dietary requirements and sources of available and unavailable carbohydrates and

action of dietary fibers.

Disorders of carbohydrate metabolism: Diabetes mellitus.Glucose tolerance test, Glycogen

storage disease

Unit II

Proteins: protein reserves of body. Nitrogen balance studies and factor affecting it. Protein

quality and essential amino acids. Cereal proteins requirement at different stages of development

Disorder of AA metabolism-phenylalaniremia homocystineuria and tyrosinemia.

Disorders of purine and pyrimidine metabolism.

Protein energy malnutrition (PME)-Marasmus and Kwashiorkor disease.

Starvation –protein metabolism in prolonged fasting, high proteins, low caloric weight reducing

diets.

Unit III

Lipids-major classes of dietary lipids. Properties and composition of plasma lipo-proteins.

Essential fatty acid and their physiological function.

Clinical inter-relationship of lipids, lipoproteins and apolipoproteins.

Tests for apolipoproteins, HDL, LDL, cholesterols and Triglyceride disorder.

Obesity-factor leading to obesity –environmental and genetic. Role of leptin in regulation of

body mass.

Unit IV

Electrolytes and water balance

Food processing and loss of nutrients during processing and cooking.

Anti-nutrients-naturally occurring food born toxicants, Protease inhibitors, hepatotoxins

allergens, toxins from mushroom, animal and see goods

Reference Books:

Harper’s Illustrated Biochemistry by Murray, Granner and Rodwell 27th

edition McGraw Hill

Food and nutrition by Swaminathan

Nutritional biochemistry and metabolism by Linten .

Biochemistry with clinical correlation: Devlin.

List of Elective papers

PSCOEBIC01 - 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) whenvariances are unknown. Tests for equality of variances. Paired t-test for equality

of means. Confidence Intervals Practicals using MSEXCEL.

Unit V:

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

PSCOEBIC02: PHYTORESOURCE UTILIZATION AND CONSERVATION

Unit I

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

Unit II

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.

Unit III

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.

Unit IV

Principles of conservation; extinctions; 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.

PSCOEBIC03: 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.

Unit II

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

emission electron guns.

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

Unit III

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.

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.

Enzymes: Peroxidase, acid phasphatase.

Immunocytochemistry

References:

Johansen D. A. Plant Microtechnique McGraw-Hill, New York Latest Edition

Berlyn and Miksche Botanical Microtechnique and Cytochemistry, The Iowa State Uni Press

R. Marimuthu Microscopy and Microtechniques MJP Publishers, Chennai

PSCOEBIC04: 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.

PSCOEBIC05: PLANT BIOCHEMISTRY

Unit I Introduction - The aim and scope of Plant Biochemistry

Structure and biochemical aspects of specialized plant cell organelles – cell plate, primary

and secondary cell walls, plasmodesmata, importance of vacuoles, characteristics of

meristematic cells.

Water relations of plants – role of water, absorption, adsorption, conduction and transpiration,

guttation, water balance and stress.

Mineral metabolism – role of different minerals absorption and translocation of inorganic and

organic substances.

UNIT 2 Photosynthesis - Light and pigments; Light dependent reactions of Photosynthesis; Carbon

metabolism – The Photosynthetic Carbon Reduction (PCR) cycle; Activation and regulation of

the PCR cycle, The C4 syndrome, Crustacean Acid Metabolism (CAM), Regulation of C4

photosynthesis and CAM; Translocation and distribution of photoassimilates, Photorespiration,

Factors affecting the rate of photosynthesis .

Respiration - Organization of mitochondrial electron transport system in plants, cyanide

resistant pathway and alternative oxidase, its role in regulation of mitochondrial electron

transport. Transport of metabolites across mitochondrial membrane. Regulation of pentose

phosphate pathway and its significance. Gluconeogenesis. Anaerobic respiration.

Nitrogen assimilation and Biological nitrogen fixation.

Unit 3 Plant Hormones – Growth regulating substances and their mode of action. Role of auxins,

gibberelic acid, abscisic acid, cytokinins and brassinosteriods in the regulatory cell extension,

germination, growth and development. Signal transduction and gene expression.

Secondary metabolism - Special features, formation and functions of phenolic acids, tannins,

lignins, flavonoid pigments, surface waxes, cutin and suberin – the plant protective waxes,

terpenes.

Signaling molecules in defense system in plants (ethylene, Jasmonic acid and Salicylic acid),

Pathogenesis Related (PR) Proteins

Unit 4

Photomorphogenesis and Physiology of flowering & Vernalization

(i) Responding to light: Photomorphogenesis: Phytochrome, Phytochrome in dark grown

seeding, Physiological effects of Phytochrome, Phytochrome in green plants, Phytochrome

under natural conditions, mechanism of Phytochrome action.

(ii) Temperature and Plant Development: Temperature in the Plant environment, Influence of

temperature on growth and plant distribution, and development.

(iii) Photoperiodism and Rhythmic Phenomena: Photoperodism; the Biological Clock,

Genetic approaches to photoperiodism, and rhythms; Photoperiodism in nature.

Biochemistry of fruit ripening, senescence and abscission

Seed Germination and Dormancy

References: Heldt, H. 2005. Plant Biochemistry (3rd Edn.) Indian Reprint, Elsevier, New Delhi. Dey, P. M. & Harborne, J. B. (Eds.) 1997. Plant Biochemistry, Academic Press, London Buchanan et al. 2004. Biochemistry & Molecular Biology of Plants. Taiz, L. and Zeiger, E. Plant Physiology, 4th Edition. Hopkins, W. G., Introduction to Plant Physiology. 3rd Edition. John Wiley & Sons, New York. Salisbury, F. B. and Ross, C. W., Plant Physiology, 4th Edition. Wadsworth Publishing Company, California. Lehninger, A. L., D. L. Nelson and M. M. Cox 2000: Principles of Biochemistry. CBS Publishers and Distributors, New Delhi. Marschner, H., Water relations of plants. Academic Press, New York. Briggs, W. R. (ed.) Plant hormones. Klywer Academic Publishers, Dordrecht. Kendrick, R. E. and Kroenber, G. H. M., Photomorphogenesis in plants, 2nd Edition, Kluwer Academic Publishers, Dordrecht. Thomas, B. & Vince-Prue, D. Photoperodism in plants, 2nd Edition. Academic Press, San Dieo. Thimann, K. V. Senescence in plants, CRC Press, Florida. Bewley, J. D. and Black, M. Seeds: Physiology of development and germination. Plenum, New York. Levitt, J. Responses of plants to environmental stresses. Academic Press, New York.

PSCOEBIC06: 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, Scoring matrices, multiple

sequence alignment, tools for sequence alignment, programming algorithms

Gene prediction: Gene structure in Prokaryotes and Eukaryotes, Gene prediction methods:

Neural Networks, Pattern Discrimination methods, Signal sites Predictions, Evaluation of Gene

Prediction methods.

Genomics: Comparative Genomics

Transcriptomics: Complete transcript cataloguing and gene discovery- sequencing based

approach, Microarray based technologies and computation based technologies.

RNA structure and prediction

Protein Computational Biology: Structural classification of proteins, Protein structure analysis,

structure alignment and comparison, Secondary and tertiary structure prediction and evaluation,

prediction of specialized structures, Active site prediction, Protein folding, Protein modeling and

drug design

Tools in Bioinfomatics: Protparam, Translate, Bioedit, findmod, Coils, TMHMM, Rasmol,

Deepview.

Proteomics: Types of proteomics, tools for proteomics- separation and isolation of proteins,

acquisition of protein structure information, databases and applications

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

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)

PSCOEBIC07: Pharmacognosy

Unit-I

Plants as sources of drugs, pharmaceauticals and pharmaceutical aids.

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

and potential applications.

Unit -II

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.

Unit-III

Pharmacognosy of drugs derived from alkaloids, glycosides, volatile oils, lipids, gums, resins,

tannins and saponins. Drugs of botanical origin: Structure, physical properties and chemistry of

secondary metabolites: phenols, phenolic glycosides, saponins, steroids, alkaloids.

Unit-IV

Vitamins and hormones and natural antibiotics.

Biosynthesis of important secondary metabolites such as Glycosides, alkaloids, terpenes and

phenols in plants.

Methods for screening natural sources for bioactive principles.

References Books: Dennis, D. T., D. H. Turpin, D. D. Lefebvre and D. B. Layzell : Plant Metabolism. Addison

Wesley Longman Ltd. England.

Doby, G. : Plant Biochemistry. Inter Science Publishers, New York

Dey, P. M. and J. B. Horborne: Plant Biochemistry. Academic Press, London.

Lehninger, A. L., D. L. Nelson and M. M. cox 2000: Principles of Biochemistry. CBS Publishers

and Distributors, New Delhi.

Sadasivam, S. and A. Manickam : Biochemical Methods. 2nd

edition. New Age International (P)

Ltd. New Delh.

Voet, D., J. G. Voet and C. W. Pratt : Fundamentals of Biochemistry. John Wiley & sons, Inc.

New York.

Zubay, G. : Biochemistry. Vol. 1 – 3. Wm. C. brown Publishers, Oxford, England

Chadwick,D.J. & Marsh, J.:Bioactive compounds from plants

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

J.B. Harborne: Phytochemical methods

J.C. Willis: Pharmacognosy

C.K. Kokate: Pharmacognosy

Trease, G.E and Evans, W.C.: Pharmacogonosy

PSCOEBIC08: MICROBIAL PHYSIOLOGY

Unit I

Microbial cell surfaces

Bacterial flagella and chemotaxis

Unit II

Bacterial differentiation: endospore formation, physiological and genetic aspects of sporulation

and spore germination

Bacterial cell division

Yeast cell division

Unit III

Microbial stress responses

Mechanism of action of antibiotics and mechanisms of drug resistance

Bioluminescence

Microbial toxins

Microbial reserve compounds

Siderophores; structure, function and significance

Unit IV

Bacterial biofilms

Quorum sensing

Bacteriocins

Microbial fuel cells

Host Parasite interactions

References:

Microbial Physiology – Moat, Foster and Spector, Wiley-Liss

Research reviews

PSCOEBIC09: Biochemistry of Horticultural commodities

Introduction: common fruits, vegetables, flowers and their quality characteristics

Fundamental Nature of Perishable Products - Aspects of Deterioration

Biochemistry of development, maturation, ripening and senescence of fruits and vegetables;

Biochemistry of flower development and senescence

Maturity indices and harvesting of fruits, vegetables and flowers

Metabolism of Harvested Products / Metabolic Control Mechanisms of Ripening and Senescence

Processes

Programmed cell death during plant senescence

Phytochemistry of fruits and vegetables

Carotenoids and colour in fruit and vegetables

Phenolic compounds and oxidative mechanisms in fruit and vegetables

Aroma biochemistry of fruits and vegetables

Gibberellins and fruit development

Phytochemistry of fruit and vegetables: an ecological overview

Biochemical analysis of major nutrient constituents

Postharvest Biology and Technology of fruits, vegetables and flowers

Postharvest handling and Physiology of fruits, vegetables, cut flowers and spices

Edible films and coatings for fruits and vegetables

Processing of horticultural commodities

References:

Gopinadhan, P., Dennis, P. M., Avtar, K. H. and Susan, L. (2008) Postharvest Biology and

Technology of fruits, vegetables and flowers.

Tomas-Barberan, F. A. and Robins, R. J. (1997) Phytochemistry of fruits and vegetables.

Salunkhe, D. K. and Kadam, S. S. (2005) Handbook of Fruit Science and Technology:

Production, composition, Storage and Processing.

Thompson, A. K. (1996) Postharvest Technology of Fruit and Vegetables

Milda, E. E., Kerry, C. H. (2009) Edible films and coatings for food applications.

Kenneth, V. T. (1980) Senescence in plants

Heldt, H. 2005. Plant Biochemistry (3rd Edn.) Indian Reprint, Elsevier, New Delhi.

Dey, P. M. & Harborne, J. B. (Eds.) 1997. Plant Biochemistry, Academic Press, London

Doby, G.: Plant Biochemistry. Inter Science Publishers, New York

Buchanan et al. 2004. Biochemistry & Molecular Biology of Plants.

Taiz, L. and Zeiger, E. Plant Physiology, 4th

Edition. Sinauer Associates, Inc.

Hopkins, W. G., Introduction to Plant Physiology. 3rd

Edition. John Wiley & Sons, New York.

Salisbury, F. B. and Ross, C. W., Plant Physiology, 4th Edition. Wadsworth Publishing

Company, California.

Lehninger, A. L., D. L. Nelson and M. M. Cox 2000: Principles of Biochemistry. CBS

Publishers and Distributors, New Delhi.

Documents

Semester I Biochemistry papers - Sardar Patel · PDF fileSemester I Biochemistry papers ... Core Theory PS01CBIC01 Cell biology and Genetics ... (Practicals of PS01 CBIC01 and PS01