|
|
|
Biochemistry & Molecular Biology – Direct Intake
3rd and 4th Year Special Degree Syllab
Third Year
1. MB 3020: Molecular Cell Biology (45L, 3C)
2. MB 3021: Gene Expression (30L, 2C)
3. BC 3001: Biosynthesis of Macromolecular Precursors (30L, 2C)
4. BC 3020: Enzyme Catalysed Reactions (30L, 2C)
5. BC 3021: Food Chemistry (30L, 2C)
6. BC 3030: Practical Biochemistry and Molecular Biology (240P, 8C)
7. BT 3053: Introduction to Bioinformatics (15L/30P, 2C)
8. BT 3067: Phylogenetic Analyses (15L, 1C)
9. CH 3022: Bio-Organic Chemistry (45L, 3C)
10. CH 3057: Biological Chemistry (30L, 2C)
11. CH 3054: Nutritional and Clinical Biochemistry (30L, 2C)
12. ZL 3058: Immunology (30L, 2C)
13. Appropriate elective course/s (15L/30L, 1C/2C)
Fourth Year
1. MB 4001: Genomics and Proteomics (45L, 3C)
2. MB 4002: Transgenic Technology (45L, 3C)
3. MB 4003: Molecular Evolution, Modelling and Computer Based Drug Design (30L/30P, 3C)
4. BC 4001: Biochemistry and Molecular Biology Research Project (8C)
5. BC 4002: Biochemistry and Molecular Biology Seminar and Essay (3C)
6. BC 4003: General Paper (3C)
7. BC 4004: Optional Topics in Biochemistry and Molecular Biology (60L, 4C)
8. BC 4005: Advanced Topics in Biochemistry and Molecular Biology (30L, 2C)
9. ZL 4060: Molecular Immunology (15L, 1C)
Detailed Syllabus
Third Year
MB 3020: Molecular Cell Biology (45L, 3C)
Dependencies: MB 2001, BT 1002
Syllabus: Anatomy and function of gene: Mutations and genetic analysis to identify and study gene structure and gene function, Inactivating the function of specific genes in eukaryotes, Identifying and locating human disease genes; Molecular and Cellular interactions: Molecular aspects of nucleo cytoplasmic transport of RNA and proteins, Organellar and cellular targeting, Protein processing and protein sorting; Molecular Developmental Biology: Molecular events during animal and plant development, molecular basis of cellular induction and cell differentiation, Homeo box genes in development and sex determination; Viruses and sub viral agents: Viral infection strategy, Diversity of replication strategy, Strategies for viral gene expression, Sub viral agents; Bacterial Genetics; Bacterial conjugation, Recombination, Transformation, Bacteriophage genetics, Transduction; Molecular biology of apoptosis: Molecular and biochemical mechanisms involved in programmed cell death and ageing
Assessment: End of semester theory examination
Suggested Readings: Molecular Cell Biology (H. Lodish et al), An Introduction to Genetic Analysis (A.J.F.Griffith, J. H. Miller, D.T. Suzuki et al.)
MB 3021: Gene Expression (30L, 2C)
Dependencies: None
Syllabus: Gene structure; Prokaryotic and eukaryotic gene transcription; Transcription factors, activators and repressors, Mechanism of activation and repression; DNA modifications, Chromatin remodelling; Transcription of class I, II and III genes, Posttranscriptional modifications (capping, splicing and polyadenylation); Transcriptional regulation (Myc-Max system, Yeast GAL system), Posttranscriptional regulation, Regulatory RNAs, Regulation of gene expression in development
Assessment: End of semester theory examination
Suggested
Readings:
Genes VIII
(B.
Lewin)
BC 3020: Enzyme Catalysed Reactions (30L, 2C)
Dependencies: None
Syllabus: General properties of enzymes; Enzyme nomenclature, Substrate specificity, Cofactors and coenzymes, Catalysis mechanisms; Acid-base catalysis, Covalent catalysis, Metal ion catalysis, Electrostatic catalysis, Catalysis through proximity and orientation effects, Catalysis by preferential transition state binding, Active site residues of different enzymes and positioning, Substrate kinetics, Kinetics of enzyme inhibition, Substrate inhibition, Nonproductive binding, Competing substrate, Multisubstrate system, Allosterism and cooperativity, Primary and secondary isotope effects on enzyme catalyzed reactions, Study of the mechanisms for selected enzyme catalysis reactions: Structure-activity studies, Structure based inhibitor design, Introduction to combinatorial chemistry.
Assessment: End of semester theory examination
Suggested Readings: The Organic Chemistry of Enzyme Catalysed Reactions (R. B. Silverman)
BC 3021: Food Chemistry (30L, 2C)
Dependencies: BC 1008
Syllabus: Introduction to food components: Major and minor constituents in food, Water, Interaction of food components, Factors that cause changes in food components; Food carbohydrates: Classification; Sugars and their derivatives: Occurrence in food, Structure and properties of glucose, lactose, maltose and sucrose; Oligosaccharides: raffinose and stachyose; Starch: Occurrence in food, Properties of amylose and amylopectin, Gelatinization of starch; Cellulose and hemicelluloses; Pectins: Occurrence in fruits and vegetables, Physico-chemical properties, Application in food industry; Food gums and their application in food industry; Methods used in the determination of carbohydrates; Food lipids: Classification of lipids, Properties of fatty acids, Triglycerides and polar lipids; Fats and oils: Rancidity, Autoxidation of fats, Mechanism of action of antioxidants, Refining and modification of fats, Effects of food lipids on health, Analysis of fats and oils; Proteins: Factors that cause denaturation of proteins, Enzymes, Meat protein, Milk proteins, Egg protein, Wheat protein, Methods used in the determination of proteins in food, Interaction of proteins with other food components; Flavour compounds and pigments in food: Occurrence of natural flavour impact compounds in food, Methods used in flavour analysis, Development of flavour during cooking and processing, Structure and properties of chlorophyll, Anthocyanins, Carotenoids and curcumins; Micronutrients: Structure and properties of vitamins and minerals in food, Methods of analysis; Food Additives: Preservatives, Antioxidants, Artificial food colours and flavours, Natural and synthetic emulsifiers and stabilizers, Safety of food additives, Methods used in analysis of food additives
Assessment: End of semester theory examination
Suggested Readings: Food, The Chemistry of its Components (T.P. Coultate), Integrated Food Science and Technology for the Tropics (A.I. Ihekoronye & P. O. Ngoddy), Nutritional Biochemistry (S. Ramakrishnan & S. Venkat Rao), An Introduction to the Chemistry and Biochemistry of Fatty Acids and their Glycerides (F. D. Gunstone), Polysaccharides in Foods (J. M.V. Blanshard & J. R. Mitchell)
BC 3030: Practical Biochemistry and Molecular Biology (240P, 8C)
Dependencies: BC 1006, BC 1008, BC 2009, MB 2003
Syllabus: Column chromatography , Ion exchange and Gel filtration, High performance liquid chromatography, Phytochemical screening, Determination of Vitamin C, Sequence determination of dipeptide, Florescence quenching, Computational chemistry, Determination of chloride, Calcium ions in blood serum, Determination of estrogen levels in chicken, Determination of serum Na+, K+, Mg2+ and Ca2+ levels using atomic absorbtion spectrophotometery, Lipid profiles, Determination of total protein in blood, SDS-PAGE (Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis), Aspartate transaminases, Creatine kinase assays, Analysis of abnormal constituents in urine, Blood glucose and glycosylated hemoglobin analyses, Isolation of RNA from animal and plant tissues, Northern blotting, Synthesis of cDNA by reverse transcription, RT-PCR; DNA labeling, DNA hybridization and hybrid detection; Construction of genomic and cDNA libraries in plasmids and lambda phage. Screening of phage libraries, Isolation of recombinants and in-vivo excision; DNA sequencing and sequence analysis; Yeasts transformation, Gene complementation in yeasts; Plant transformation, Cell culture and transfection; Expression of recombinant proteins; Western blotting and ELISA
Assessment: End of each semester practical examination (4C x 2)
Suggested Readings: Practical Biochemistry and Molecular Biology (J. Sambrook, E.F. Fritsch & T. Maniatis), Molecular Cloning: A Laboratory Manual
Dependencies: BT 3053
Syllabus: DNA data in evolutionary biology: biological context of inter and intra specific differentiation, different molecular techniques and different types of data, sampling, processing DNA data; Molecular cytogenetics; Concepts of cladistics and phenetics; Major analytical methods of DNA data: distance and character state methods; Phylogenetic inference using different methods: Neighbor Joining, Maximum Parsimony, Maximum Likelihood, Bayesian analysis; Phylogenetic trees and the concepts; Bootstrapping; Applications of molecular phylogenetics in organismal phylogeny, evolutionary biology, character evolution, timing the evolutionary trees, phylogeographic and biogeographic studies, evolutionary and developmental genetics and biodiversity conservation.
Assessment: End of semester theory examination. Assignments will be carried out to practice Neighbor Joining, Maximum Parsimony, Maximum Likelihood and Bayesian analytical approaches.
Suggested Readings: Molecular Evolution: A Phylogenetic Approach (Page, R. D. M. and Holmes, E. C.) 1998; Inferring Phylogenies (Felsenstein, J.) 2004; Phylogenetic Trees Made Easy (Hall, B. G.) 2001; Molecular Systematics (Hills, D. M., Moritz, C. and Mable, B. K.) 1996, 2nd Edition.
Appropriate Elective Courses (15L/30L, 1C/2C)
(i) BT 3003: Plant Molecular Biology (30L, 2C)
(iii) BC 3022: Biotransformation & Bioremediation (30L, 2C)
Dependencies: None
Syllabus: Phase I, II and III reactions; Xenobiotics: Xenobiotic excretion, Examples of conversion reactions to nontoxic compounds; Bioremediation: Organisms involved in bioremediation, Bioremediation of PCBs, Pesticides, Radioactive compounds, Oil spills etc., Bioremediation types and methods
Assessment: End of semester theory examination
Suggested Readings: Molecular Biotechnology (B.R. Glick and J.J. Pasternak)
(iv) CH 3004: Laboratory Management (15L, 1C)
(v) CH 3008: Quality Management (15L, 1C)
Fourth Year
MB 4001: Genomics and Proteomics (45L, 3C)
Dependencies: None
Proteomics
Overview of proteomics; Methods used in proteome analyses: Protein Purification strategies (Ion-exchange Chromatography, Affinity chromatography, Fast protein liquid chromatography, Gel filtration, Hydrophobic interaction and hydroxyl apatite chromatography), 2D Gel Electrophoresis, SDS-polyacrylamide gel electrophoresis, Isoelectric focusing, Spot identification, 2D gel data analysis, Differential in-gel electrophoresis (DIGE), Drawbacks and limitation of 2D gel electrophoresis, Applications of 2D-PAGE, Characterization and identification of proteome using mass spectrometry, MALDI (Matrix-assisted Laser Desorption/Ionization), nESI (nanoelectrospray ionization), (MALDI-TOF (time of flight), Tandem mass spectrometry (MS/MS), Surface enhanced laser desorption ionization (SELDI), Protein sequencing by Edman degradation and protein sequence analyses; Protein Arrays: Types of protein Arrays, Data analysis, Applications of protein microarrays; Organelle and cellular proteomics; Protein and Enzyme Assays; E. coli and baculovirus expression systems, Eukaryotic expression systems
Genomics
Overview; Prokaryotic and eukaryotic genome organization; high throughput sequencing and sequence analyses, (prediction of gene structure, promoter regions, open reading frames, etc); comparative genomics, single nucleotide polymorphism (SNPs); gene mapping; databases (genomes, expressed sequence tags (EST), sequence tags sequence (STS) etc); DNA microarrays and its application
Assessment: End of semester theory examination
Suggested Readings: Discovering Genomics, Proteomics and Bioinformatics (A.M. Campbell & L.J. Heyer), High Throughput Techniques in Post Genomic Era (R.S. Dassanayake & Y. I. N. Silva Gunawardena)
MB 4002: Transgenic Technology (45L, 3C)
Dependencies: None
Syllabus: Gene transfer techniques in animals and plants; Generation of improved animals and plants for biotechnology and medicine; The use of transgenic animals, plants, bacteria, yeast and fungi as bioreactors; Generation of transgenic animal models for human disease studies; The use of transgenic animals for organ transplantation and gene therapy; Molecular Biotechnology and Ethical Issues
Assessment: End of semester theory examination
Suggested Readings: Molecular Biotechnology: Principles and Applications of Recombinant DNA (B.R. Glick & J.J. Pasternak), Molecular Cell Biology (H. Lodish, M.P. Scott, P. Matsudaira & J. Darnell)
MB 4003: Molecular Evolution, Modeling and Computer Based Drug Design (30L/30P, 3C)
Dependencies: BT 3053, BT 3067
Syllabus: Protein structure analyses and prediction: Open Reading Frame prediction, Protein secondary structure analysis and prediction, Signal sequences, Protein subcellular localization prediction, Transmembrane regions predictions. Functional Proteomics: Methods for determination of protein structure, Molecular motifs, Recognition and binding, Evolution, Antigenic regions; Molecular Evolution: Positive evolution, Negative evolution, Diversifying selections, Neutral selections; Microarray analysis: Processing array images, Filtering, clustering, Gene regulation, Evaluating analysis; Protein tertiary structure modeling: Ab-initio methods, Threading, Comparative modelling approaches, Visualization approaches; Molecular modeling: Force field methods to refine energies of systems (Monte Carlo and molecular dynamics simulations, simulated annealing, energy minimization); Computational docking and drug designing
Assessment: End of semester written examination
Suggested Readings: Molecular Modelling (A. R. Leach), High Throughput Techniques in Post Genomic Era (R.S. Dassanayake & Y.I.N. Silva Gunawardene), Computer Simulation of Liquids (M.P. Allen & D.J. Tildsley), Bioinformatics and Drug Discovery (R. S. Larson), Web Resources
BC 4001: Biochemistry and Molecular Biology Research Project (8C)
Dependencies: None
Syllabus: Research project supervised by internal or external examiner/s
Assessment: By interview and dissertation
Suggested Readings: Literature published on the topic given
BC 4002: Biochemistry and Molecular Biology Seminar and Essay (3C)
Dependencies: None
Syllabus: Seminar and an essay on a current topic in Biochemistry/Molecular Biology
Assessment: End of semester examination, presentation and interview
Suggested Readings: Will be announced during the course
BC 4003: General Paper (3C)
Dependencies: First and second year Chemistry and Biochemistry core units
Syllabus: Problem solving in Chemistry and Biochemistry
Assessment: End of semester theory examination
Suggested Readings: Books recommended for first and second year core Chemistry and Biochemistry units
BC 4004: Optional Topics in Biochemistry and Molecular Biology (60L, 4C)
Dependencies: None
Syllabus: Selected topics in Chemistry/Biochemistry/Molecular Biology. Will be announced at the beginning of the academic year
Assessment: End of semester theory examination
Suggested Readings: Will be announced during the course
BC 4005: Advanced Topics in Biochemistry and Molecular Biology (30L, 2C)
Dependencies: None
Syllabus: Principles and applications of gene therapy; Cancer: The development and causes of cancer, Oncogenes, Tumor suppressor genes, Application of molecular biology to cancer prevention and treatment; RNA interference; Cell signaling and signal transduction; Protein engineering
Assessment: End of semester theory examination
Suggested
Readings:
Human Molecular Genetics
(T. Strachan & A.P. Read),
Molecular Cell Biology (H. Lodish, M.P. Scott, P. Matsudaira & J. Darnell),
Molecular Biotechnology: Principles and Applications of Recombinant DNA
(B.R. Glick & J.J. Pasternak)
ZL 4060: Molecular Immunology (15L, 1C)
Dependencies: ZL 3058
Syllabus: Molecular interactions involved with immune responses, cells, tissues and organs of the immune system; Integration of innate and adaptive immune mechanisms; Cell and Cytokine Regulatory mechanisms of immunity; Molecular and genetic mechanisms for generating antibody diversity and antigen expression: Maturation of B and T lymphocytes and expression mechanisms of immunoglobulin genes; Molecular aspects of Antigen processing, presentation and recognition mechanisms; Molecular involvements of major histocompatibility complex (MHC) and its genetic variation and expression of HLA antigens; Molecular aspects of Host pathogen interactions: Immune evasion mechanisms, Immunosuppression, Tolerance and autoimmunity; Cytokines and their molecular roles in immunity and immunopathogenesis; Molecular basis of Immune responses to tissue transplants, Immunity to tumors, Innate and acquired immunodeficiencies; Hybridoma technology and Monoclonal antibody production and its applications, Molecular biological methodologies involved in vaccine production.
Assessment: End of semester theory examination
Suggested Readings: Roitt's Essential Immunology (I. Roitt), Immunology (I. Roitt et al.), Immunobiology: The Immune System in Health and Disease (J. Way & C. B. Travers), Cellular and Molecular Immunology (A. K. Abbas, A. H. Lichtman & J. S. Pober), Practical Immunology (L. Hudson & F. C. Hay), Immunology (R. A. Goldsby, T. J. Kindt, B. A. Osborne & J. Kuby)
Department of Chemistry, Faculty of Science, University of Colombo,
P.O. Box 1490, Colombo 03, Sri Lanka.
Tel : (9411) 2583105-7, Ext.225 Fax : (9411) 2503148, (9411) 2587239
This website designed and maintained by Prof. K. M. Nalin de Silva.
Last Updated September2007