BHARATHIAR UNIVERSITY: COIMBATORE-641046
M.PHIL./Ph.D. - (FT/PT) – BIOCHEMISTRY
PART I: SYLLABUS
(For the candidates admitted from the academic year 2018-19 onwards)
PAPER- I RESEARCH METHODOLOGY
UNIT I: Biostatistics
Scientific writing - Writing methodology, results and discussion.
Correlation & regression.
Sampling distribution- students T test, χ2 test.
Experimental design – CRD,RBD.
Analysis of experimental results- ANOVA, Duncan’s Multiple range test.
UNIT II: Immunotechnology
Fluroscent antibody assay- Histochemical localization
RIA-principle and applications.
ELISA techniques - Principles and applications.
Immuno radiometric Assay - Principles and applications.
Stem cells- Embryonic stem cells, Adult cells, stem cell therapy. Gene therapy.
UNIT III: DNA Technology
Flow cytometry- Principle, abnormal chromosome analysis, karyotying, COMET assay DNA
fragmentation analysis.
PCR Methodology- designs of primers- RTPCR, Q-PCR, PCR in genomic analysis and diagnostic
application.
PFGE- Principles, techniques & applications.
UNIT IV: Protein Technology
Natural Products- Detection of bioactive molecules by gas chromatography.
Mass spectrometry - Principles and application.
HPLC and HPTLC - Principle, instrumentation and application.
Capillary Electrophoresis- Principles, instrumentation and application.
X-ray diffraction, NMR & their uses in protein structure prediction
Principle and Instrumentation-UV Visible Spectroscopy, Fluorescent Microscopy.
UNIT V: Bioinformatics
Biological databases – DNA sequence databases & protein sequence databases.
Genome database- Mouse genome database.
SRS- Similarity searching pairwise sequence alignment- BLAST, FASTA
Dynamic programming-local and global alignment, Needleman alignment.
Multiple sequence alignment- Phylogeny.
Structure database- Secondary structure prediction, Choufeat passman, Neural network methods.
Predicting 3-dimensional folds (Threading), Homology modeling, Molecular docking.
REFERENCE:
1. S.P. Gupta(2004). Statistical methods.Sulthan Chand & sons, Educational publishers, New Delhi.
2. Janis Kuby(2000) Immunology 3rd
edition.
3. Richard A.Goldsby (2000) 5th edition. Immunology W.H.Freeman & Co. Newyork
4. D.A.Skoog & J.J. Leary, 1992. Principles of Instrument analysis 4th edition, Saunders College Pub.
5. Rastogi C.S.(2003)Bioinformatics- Concepts, skills, and applications. CBS Publishers.
6. David Freifelder (2003). Molecular biology 2nd edition. Narosa publishing house, New Delhi.
PAPER- II ADVANCED PAPER IN BIOCHEMISTRY
UNIT I
Hormonal Regulation of Metabolism
Nucleic acid metabolism: Purine and Pyrimidine metabolism
protein metabolism urea cycle, aliphatic and aromatic amino acid metabolism
Inborn errors of metabolism- Albinism, Phenylketonuria, Maple syrup urine disease and Homocystinuria.
UNIT II
Cell Biology and Molecular Biology
RNA editing, mi RNA and RNAi, and its applications.
Antisense RNA technology,signal sequence. hypothesis protein glycosylation, Protein
degradation- ubiquitin pathway.
General principles of cell communication G- Protein-coupled receptors-structure and
functions, cAMP and other second messengers –phosphatidyl inositol, diacyl
glycerol,inositol1,4,5 triphosphate Ca2+; Receptor Tyrosine Kinases- structure and
functions, importance of Ras, MAP Kinase cascade.
UNIT III
Genomics and Proteomics
Human Genome project - history, techniques, and applications; NGS principle and applications.
Anatomy of Prokaryotic and Human Genome; Genetic mapping and genetic markers-
RFLP, Mini- and Microsatellite, STS and EST, SSCP, R APD, AFLP, SNPs. Analyzing
Gene expression - DNA microarray. Epigenetics.
Proteome analysis- 2D gel electrophoresis; Protein-protein interactions- yeast two-hybrid system and
protein microarrays.
UNIT IV
Biotechnology
Plant Biotechnology- Micropropagation, Organogenesis, somatic embryogenesis, artificial seeds,
Haploidy: Protoplast fusion and somatic hybridization. Transgenic plants.
Animal Biotechnology- Primary cell culture and cell line, tissue culture, organ culture; three Dimensional
culture; Feeder layer; cell separation; cell synchronization; cryopreservation and revival, Transgenic
animals.
UNIT V
Intellectual Property Rights (IPR) and Bioethics
Introduction to IPR and Patent.
World Trade Organization- Trademarks and copyrights.
Bioethics- Ethics in Bioscience, ethics in clinical trials and good clinical practice.
REFERENCE:
1. Geoffrey zubay (1993), Biochemistry, 3rd edition, Columbia University. Wm.C.Brown
publishers., England.
2. Gerald Karp (2000). Cell and Molecular Biology, concepts and Experiments. 4th editions,
John Wiley & sons, NewYork.
3. Lodish et. al (2000) Molecular Cell Biology, 5th edition, W.H. .Freeman and company,
NewYork.
4. D.Balasubramanian (1996). Concept in Biotechnology, Universal press India.
5. Freshney R.I(2000). animal Cell Culture, A practical Approch, John Wiley Publications,
NewYork.
6. David W.Mount, (2001), Bioinformatics sequence and genome analysis, cold spring
Harbor Laboratory press.
7. Pennigtons S.R and Dunn .M.J(2002), Proteomics, viva books pvt ltd.
PAPER III – 1. PLANT BIOCHEMISTRY AND PLANT THERAPEUTICS
UNIT I
Plant Therapeutics : Bioactive principles in herbs, plants with hepatoprotective , nephroprotective,
hypoglycemic, anticancer, antibacterial, antiviral and antimalarial ,anti-inflammatory properties.
UNIT II
Free radicals –types, sources, importance, producti on, free radicals induced damages, lipid
peroxidation , measurement of free radicals, disease caused by radicals, reactive oxygen
species, antioxidant defence system, enzymic and nom-enzymic antioxidants, role of
antioxidants in prevention of diseases ,phytochemicals as antioxidants.
UNIT III
Alkaloids, flavanoids, terpenoids, phenols-Occurrence ,distribution & functions ,Production of
secondary metabolite in plants, stages of secondary metabolite production, uses of tissue
culture techniques, elicitation, biotransformation- production of pharmaceutical compounds.
UNIT IV
Principles-callus, meristem and organ culture, culture methods, culture media & preparations ,plant
regeneration, protoplast technology, micropropogation in plants, somatic embryogenesis, somoclonal
selection.
UNIT V
Carbon reactions in C3,C 4 & CAM cycle - Calvin cycle, photorespiration, Nitrogen fixation-
symbiotic & non-symbiotic, role of nif and nod genes in nitrogen fixation, Techniques for plant
transformation: Agrobacterium-mediated gene transfer, the process of T-DNA transfer, Direct
gene transfer methods.
REFERENCES:
1. Khan, I. A and Khanum.A 2004. Role of Biotechnology in medicinal & aromatic plants, Vol 1
and Vol 10, Ukkaz Publications, Hyderabad.
2. Purohit. S.S. 2005 Agricultural Biotechnology, Dr.Updesh Purohit Publishers, Jodhpur.
3. Slater.A. Scott. N.W and Fowler. M.R 2004.Plant Biotechnology-The genetic manipulation
of plants, Oxford University Press, Oxford.
4. Singh. M.P and Panda .H 2005.Medicinal Herbs with their formulations, Daya
Publishing House, Delhi
PAPER III – 2. CLINICAL BIOCHEMISTRY & CLINICAL TOXICOLOGY
UNIT I
Effects of physiochemical and biological factors on heavy metal toxicity, toxic mechanism Carcinogenesis, teratogenesis & immunotoxicity. Bioassays for heavy metal toxicity, pathological and Histopathological examinations for heavy metal toxicity.
UNIT II
Diagnostic enzymes in hepatobiliary disease, myocardial infraction, atherosclerosis, renal dysfunction. Cancer markers for oral, prostate, colorectal, breast and GI tract cancer, oncofetal cancer markers.
UNIT III
Formation of free radicals, auto-oxidation initiated by oxygen radicals, Influence of free radicals in metal toxicity. Free radical hepatotoxins- CCl4 model .free radicals and cancer.Oxidative process in tissue injury. Detection of free radicals and radical ions. Role of free radicals in diseases.
UNIT IV
Enzymic antioxidants- Chemistry, mechanism, the antioxidant effect of SOD, catalase, Glutathione Peroxidase. Non Enzymic antioxidants- source, chemistry, toxicity, biochemical, functions, bioavailability, bioassays, Antioxidant effects of Vit A, Vit C, Vit E, glutathione, and selenium.
UNIT V
Medicinal plants-bioactive principles in medicinal plants. Methods of extraction, isolation, separation and screening of pharmacologically active plants-CNS,CVS, Hypoglycemic, Hepatoprotective, anti-allergic, anticancer, immunoactive plants. Plants protecting against oxidative stress, and chemotherapeutic products.
REFERENCES:
1. Biochemistry oxygen toxicity, Annual review of Biochemistry Enrique cadinar, Vol 58,1989.pp 78-110
2. Free radicals in biology by William a.Pryor,Academic press 1980.,pp 96-150.
3. Heavy metal toxicity testing in environmetal samples, Reviews of environmental contamination and
toxicology in chul, Kong ,Gabrial Bitton,Benkoopan,vol 142.1995.pp 130-136.
4. Methods of plant analysis,Phytochemical analysis by J.B.Harborne,chapman & Hall Ltd.1973 pp 1-26.
5. Pharmocology of medicinal plants and natural products by S.A.Dhanukar,R.A.Kulkarani,
W.N.Rege, Indian Journal of Pharmacology,2000 S81-S118.
6. Selenium dependent enzymes-glutathione peroxidase. Annual review of Biochemistry by
Thresser,stadman ,Vol 49.1980 pp 103-108.
7. Superoxide radicals & SOD by Irwin Fridowich Annual review of Biochemistry,Vol 64.1995 pp 97-106
8. Vitamins –Annual research review by Horrobin ,Eden Press Pub.,Vol.3. 1980.pp 59-82,91-
105,218-291.
PAPER III – 3. ENZYMES AND ENZYME TECHNOLOGY
UNIT I
Protein structure, functions, compositions and conformation of proteins. Enzyme catalysis
(catalysis by serine proteases). Enzyme Kinectics. Proteins in solution and in membranes.
Liposomes and their preparation.
UNIT II
Sources of enzymes for industry, extraction of enzymes for scientific and industrial purpose.
Downstream processing of enzymes, Uses of soluble enzymes. Study of enzymes in aqueous
biphasic systems. Effects of pH and temperature on enzyme activity.
UNIT III
Major types of enzyme immobilization. Techniques employed for immobilizing enzymes, kinetics
of immobilized enzymes. Advantages and disadvantages in the utilization of soluble enzymes
immobilized enzymes and immobilized cells. Different types of reactors of immobilized enzymes
and their applications.
UNIT IV
Application of ELISA and EMIT in Clinical analysis. Different types of Biosensors-
potentiometric, amphometric, piezo electric and immuno biosensors. Electro analytic applications
of enzymes, Methods of coenzyme regeneration .Biochips and Biocomputers.
UNIT V
Restriction endonucleases and their Uses, DNA ligase, DNA polymerase and their uses in
Biotechnology, site directed mutagenesis, enzyme catalysis in organic solvents, artificial enzymes,
ribozymes and Abzymes.
REFERENCES:
1. Robert.K.Scopes-Protein purification practice, Sprincer verlag,1982
2. C.Branden and J.Tooze-Introduction to protein structure, Garland pub, New York.
3. Alanwisheman-Handbook of Enzyme Biotechnology II, John Wiley & Sons,1985
4. J. Tampion and M.D. Tampion-Immobilized cells, Principles and applications. Cambridge
University Press, New York, 1987.
5. M.F. Chaplin & C. Bucke, Enzyme Technology, Cambridge University press, New York,
1990.
6. M.J.C. Crabbe, Enzyme Biotechnology, Ellis Horwood, New York
7. Review of Enzyme function in organic solvents.L.J.Biochem, 203, 25-32.1992.FEBS.1992
PAPER III – 4. DNA TECHNIQUES &CLINICAL APPLICATIONS
UNIT I
Constructing restriction maps, Reporter Genes, Assay of Chloramphenicol, acetyltransferase and β-
galactosidase activity. PCR, Primer design, Cloning of PCR Products, Types of PCR, Anchored, Alu and RT-PCR. RAPD, Microsatellite and Quantitative PCR. Multimutation screening using PCR and ligation– Principles and Applications. Molecular diagnosis of viral and bacterial pathogens using PCR.
UNIT II
Prokaryotic Expression system, pUR, pT 7-7, pET, pQE, expression vectors, pRIT, pGEX, pMAL vectors. Expression Strategies, Preparation of expression vector, Foreign DNA ligation, transformation and characterization of protein by N-terminal sequencing and by LCMS
UNIT III
Eukaryotic vectors, vectors for the propagation of cloned DNA in yeast –episomal vectors, integrating vectors, engineering a foreign gene for intracellular expression, yeast (S.cerevisiae) promoter systems & terminators, yeast signal sequences, culture and transformations methods of commonly used S.cerevisiae strain, Induction, and analysis of intracellular expressions.
UNIT IV
Purification of expressed proteins from E.coli, purification of soluble recombinant proteins, Preparation of cell lysate, ion-exchange chromatography, gel filtration, metal chelate affinity chromatography (MCAC), and immunoaffinity column. Purification of inclusion bodies, In vitro refolding of proteins, verifying protein integrity. Techniques for measuring protein stability and processing of secreted protein.
UNIT V
Probes-non radioactive labeling of nucleic acids-systems, substrated, labeling methods-Nick translation, oligo or random primer, and PCR labeling. The efficiency of the methods. Detection of probes- Autoradiography- chemiluminogenic and different chromogenic substrates. Molecular diagnosis of genetic disease-cystic fibrosis, muscular dystrophy, Huntington's disease, Fragile-X- syndrome, Retinoblastoma, Alzheimer's disease, Amyotrophic lateral sclerosis.
REFERENCES:
1. Recombinant DNA Technology-Raymond .L.Rodringuez & Robert C. Tait- Benjamin Cummings pub.1983.
2. Recombinant DNA Mrthodology-WU,Grossman,Moldave-Academic Press1989
3. DNA Cloning 1, 2, 3& 4 –D.M. Glover & B.D. Hames-IR L Press.
4. Molecular Cloning Vol.1, 2, 3-Sambrook, Fritsch & T. Maniatis-Cold spring Harbor
Laboratory press, 1989.
5. Gene and Biology of Cancer-Harold Varmus, Robert A. Wrinbert-Scientific
American library, 1993.
6. PCR-C.R. Newton & A. Graham. Bios Scientific Publishers .1995
7. PCR 1& 2 – A Practical Approach-M.J. Mc Pherson, B. D. Hames and G.R. Taylor-
Oxford University Press,1995
8. Molecular Biology- A Project approach – Susan J. Ka rcher. Academic Press, 1995.
9. Essential Molecular Biology-Vol.I and II. T. A. Brown.
10. PCR-based Diagnostics in infectious Disease. Garth .D. Ehrilich, Steven .T. Greenberg.
Blackwell Scientific Publication.
11. Non-isotope probing, Blotting and Sequencing, 2nd edition, Edited by
Larry.J.Kricka, Academic Press, 1995.
PAPER III – 5. ENVIRONMENTAL BIOCHEMISTRY
UNIT I
Concept of an ecosystem. Structure and functions of ecosystem. Producers, consumers and decomposers. Energy flow in an ecosystem. Ecological succession. Food chains, food webs and ecological pyramids. Introduction, types, characteristic features, structure and function of the following ecosystem. Forest ecosystem, Grassland ecosystem, Desert ecosystem, Aquatic ecosystems (Pond, streams, lakes, rivers, oceans, estuaries.)
UNIT II
Causes, effects and control measure of, Air pollution, Water pollution ,Soil pollution, Noise pollution, Thermal Pollution, Bioleaching,
UNIT III
Introduction – Definition, genetic, species and eco system diversity. Value of Biodiversity : Consumptive use, Productive uses social, ethical, aesthetic and option values. Biodiversity at global, National and local levels. Hot spots of biodiversity, Threats to biodiversity Endangered and endemic species of India Conservation of biodiversity: In-situ and Ex-situ conservation of biodiversity-Conservation of Germplasm.
UNIT IV
Enzymes: Immobilization of enzymes, enzymes engineering ,isolation and culturing of microorganisms from contaminated area. Production of enzymes ,fermentation ,antibiotics, use of microbes to treat sewage water and industrial effluents and mining.
UNIT V
Pollution Control: Cleaner technologies, reducing environment impact of industrial effluents, chemical pesticides, herbicides and fertilizers. Renewable source of energy through through waste materials; biogas, energy crops, cellulose current levels of biodiversity.
REFERENCES:
1. Elements of biotechnology, P.K.Gupta, Rastogi and Company, Meerut, India.
2. An Introduction to Genetic Engineering, Desmond S.T.Nicoll-Cambridge University.
3. Biotechnology, Kesar, Trehar Wiley, Eastern India.
4. Microbiology, Michael Pelczar, Tata-Mc Graw Hill Publishing Company, New Delhi.
5. Recombinant DNA-a short course, J.D.Watson, Scientific American Bank.
PAPER III – 6. CANCER BIOLOGY AND IMMUNOLOGY
UNIT I
Biology of cancer-Phenotype of a cancer cell. Causes of cancer-DNA tumor viruses, RNA tumor viruses, cell cycle and its control. Role of protein kinases, checkpoints, kinase inhibitors and cellular response.
UNIT II
Programmed cell death (Apoptosis)-Intracellular proteolytic cascade, cascade of caspase proteins, adapter proteins, Bcl-2, IAP family proteins, extra cellular control of cell division. TNF family of death receptor and its signaling.
UNIT III
Genetic basis of cancer-oncogenes, tumor suppressor genes, aberrations in signaling pathways. oncogenic mutations in growth promoting proteins, Mutations causing loss of growth –inhibition and cell cycle control, role of carcinogens and DNA repair in cancer.
UNIT IV
Immunity- Active, passive, humoral and cell mediated immunity. Therapeutic uses of cytokines and cytokine receptors. Test for lymophocyte function. B cell and T cell immuno deficiency diseases. Clinical laboratory methods for the detection of antigens and antibodies. Test for histocompatability antigens. Autoimmune disease- RA, SLE.
UNIT V
Techniques-FISH techniques, Real time PCR, Western blotting, ELISA. Immunocytochemistry, immunohistochemistry, flow cytometry, cell sorting, fluroscent microscopy and confocal microscopy, Cancer immunotherapy- Monoclonal Ab therapy.
REFERENCES:
1. Gerald Karp (2004) .Cell and Molecular Biology, Concepts and Experiments .4th
edition, John Wiley & Sons, New York.
2. Lodish et.al. (2004) Molecular Cell Biology,5th edition, W.H.Freeman and Company, New York.
3. Bruse Albert’s et.al. (2002) Molecular biology of the cell, 4th edition, Garland Science, New York.
4. Benjamin Lewin (2004) Genes VIII, Prentice Hall.
5. Sam brook, J., Fritish, E. F., and Maniatis, T., (1989). Molecular cloning: A Laboratory
Manual.Vol. 1, 2, 3. Cold Spring Harbor Laboratory Press, New York.
6. Beatty, B et al., (2002) FISH, A Practical Approach, Oxford University Press , Oxford.
7. Ormerod, M. (2000) Flow Cytometry: A Practical Approach, 3rd ed. Oxford University
Press, Oxford.
8. Paddock, S.W. (1998) Confocal Microscopy : Methods and Protocols, Humana Press , US.
PAPER III – 7. FREE RADICAL BIOLOGY AND ENDOCRINOLOGY
UNIT I
Basic Concepts .Definition of the analytical processes, integrated automation for clinical laboratory, development of standards for laboratory automation, Blood analyzer.
UNIT II
Formation of free radicals, auto oxidation initiated by oxygen radicals, influence of free radicals in metal toxicity, free radicals hepatoxins,CCl4 model. Free radicals & cancer. Oxidative process in tissue injury. Detection of free radicals by ESR Spectroscopy.
UNIT III
Enzymic Antioxidants-Chemistry, mechanism, antioxidant effects of superoxide dismutase, catalase Glutathione peroxidase.
UNIT IV
Sources , chemistry , toxicity, biochemical functions, bioassay, antioxidant effects of Vitamin A, Vitamin C, Vitamin E, Glutathione and Selenium. Trace elements- Introduction, sources, biochemical functions of zinc, copper, magnesium & iron.
UNIT V
Definition, general characteristics, biosynthesis, bioassay of steroid hormones, peptide hormones, adrenal hormones, thyroid hormones.Vasoactive peptide hormones and pheromones (social hormones).
REFERENCES:
1. Tietz N.W. (1994), Fundamentals of Clinical chemistry. W.B.Saunder’s company.
2. Harper’s Biochemistry (1993) 23 rd edition, Prentice Hall International Inc, USA.
3. Free Radicals in Biology by William A. Pyror, academic Press, 1980. pp 96-150.
4. Selenium dependent enzymes-glutathione peroxidase. Annual review of Biochemistry
by Thresser, C.Stadman,Vol . 49.1980. pp 103-108.
5. Superoxide radicals and SOD by Irwin Fridowich, Annual review of Biochemistry,
Vol. 64.1995.pp97-106.
6. Vitamins-annual research review by Horrobin, Eden Press Pub., and Vol.3.1980.pp 59-
82, 91-105,218-291.
