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Biochemistry and Molecular Biology – Direct Intake
(Coordinated by Department of Chemistry)
Degree Structure
First Year
Faculty Required Course
1. AM 1008 (2C, 30L) Mathematics for Biological Science
Chemistry
Core Courses
1. CH 1008 (2C, 30 L) General & Physical Chemistry
2. CH 1003 (2C, 60 P) Practical Chemistry I
3. CH 1009 (2C, 30 L) Fundamentals of Organic Chemistry I
Available Electives
1. CH 1010 (1C, 15 L) Calculations in Chemistry
2. CH 1004 (1C, 30P) Practical Chemistry II
3. CH 1006 (2C, 30 L) Impact of Chemistry on Society
Biochemistry
Core Courses
1. BC 1001 (1C, 15 L) Chemical Basis of Life
2. BC 1006 (2C, 15 L + 30 P) Techniques in Biochemistry
3. BC 1008 (3C, 30 L + 30 P) Structure and Function of Biomolecules
Electives
None available as yet.
Molecular Biology
Core Courses
1. BT 1002 (1C, 15 L) Cell Biology
2. BT 1003 (1C, 15 L) Genetics
3. BT 1009 (1C, 30 P) Genetics and Cell Biology Practicals
4. ZL 1012 (1C, 15 L) Introduction to Evolution
5. PH 1050 (2C, 30 L) Introduction to Biophysics
Recommended Electives
1. BT 1005 (1C, 15 L) Microbial Life
2. ZL 1007 (1C, 15 L) Biosystematics
Computer Science
Core Courses
1. CS 1002 (3C, 45 L) Introduction to Computing
2. CS 1001 (3C, 30 L + 30 P) Fundamentals of Programming
Second Year
Chemistry
Core Courses
1. CH 2008 (2C, 30 L) Fundamentals of Physical Chemistry
2. CH 2003 (2C, 60 P) Practical Chemistry III
3. CH 2002 (2C, 30 L) Inorganic and Analytical Chemistry
Recommended Electives
1. CH 2009 (1C, 15 L) Intermediate Organic Chemistry
2. CH 2010 (1C, 15 L) Phase Equilibria & Surface Chemistry
3. CH 2004 (1C, 30 P) Practical Chemistry IV
Biochemistry
Core Courses
1. BC 2007 (2C, 30 L) Introduction to Metabolism
2. BC 2008 (1C, 15 L) Metabolism of Nucleic Acids and Proteins
3. BC 2009 (1C, 30 P) Practical Biochemistry
4. BC 2010 (1C, 15 L) Topics in Biochemistry
5. ZL 2008 (1C, 15 L) Human Physiology
Recommended Electives
1. BC 2012 (1C, 15 L) Introduction to Secondary Metabolites
Molecular Biology
Core Courses
1. MB 2004 (1C, 15 L) Principles of Molecular Biology
2. MB 2002 (1C, 15 L) Genome Structure
3. MB 2005 (3C, 30 L + 30 P) Nucleic Acid Technology
4. BT 2006 (1C, 15L) Molecular Biology and Recombinant DNA Technology
Recommended Electives
1. BT 2003 (2C, 15 L + 30 P) Principles of Microbiology
2. BT 2001 (2C, 15 L + 30 P) Biostatistics
3. ZL 2002 (2C, 30 L) Animal Form and Function
Computer Science
Core Courses
1. CS 2001 (3C, 30 L + 30 P) Internet Technologies
2. CS 2002 (3C, 45 L) Fundamentals of Software Engineering
Third Year
Chemistry
Core Courses
1. CH 3001 (2C, 30 L) Topics in Analytical Chemistry I
2. CH 3002 (1C, 30 P) Practical Analytical Chemistry
3. CH 3004 (1C, 15 L) Laboratory Management
Recommended Electives
1. CH 3008 (1C, 15 L) Quality Management
2. CH 3024 (2C, 30 L) Pharmaceutical Chemistry
3. CH 3007 (1C, 15 L) Topics in Analytical Chemistry II
Biochemistry
Core Courses
1. BC 3002 (3C, 30 L + 30 P) Clinical Biochemistry
2. BC 3005 (2C, 15 L + 30 P) Advanced Topics in Biochemistry
3. BC 3006 (1C, 30 P) Biochemistry Seminar
Electives
1. BC 3001 (30L, 2C) Biosynthesis of Macromolecular Precursors
2. BC 3020 (30L, 2C) Enzyme Catalysed Reactions
3. BC 3021 (30L, 2C) Food Chemistry
Molecular Biology
Core Courses
1. BT 3053 (2C, 15 L + 30 P) Introduction to Bioinformatics
2. ZL 3058 (2C, 30 L) Immunology
3. MB 3003 (2C, 30 L) Introduction to Genomics and Proteomics
4. MB 3004 (1C, 30 P) Advanced Molecular Biology Laboratory
5. MB 3005 (30L, 2C) Industrial Molecular Biotechnology
Recommended Electives
1. BT 3006 (3C, 30 L + 30 P) Plant Tissue Culture Technology
2, BT 3005 (3C, 30 L + 30 P) Advanced Microbiology
3. ZL 3006 (2C, 30 L) Molecular Biological and Immunological Applications
4. ZL 3004 (1C, 15 L) Animal and Human Parasites
Computer Science
Core Courses
1. CS 3001 (3C, 30 L + 30 P) Visual Programming Technologies
2. CS 3002 (3C, 45 L) Management Information Systems
Eighteen (18) students following the General Degree programme (Direct Intake) will be selected at the end of the second year to follow the new Special Degree in Biochemistry and Molecular Biology. Selection for this programme will be according to the criteria specified in page 11 of the Faculty Handbook, and will be based on the marks obtained for the core courses in Chemistry and Biochemistry (Years 1 & 2, minimum GPA 3.00) and Molecular Biology (Year 2 only, minimum GPA 3.00).
Syllabi
The syllabi of the existing courses offered by the respective departments can be found in the web pages of these departments.
AM 1008 : Mathematics for Biological Science (2C, 30 L)
Dependencies : None
Basic Algebra : Numbers and laws of indices, exponential, logarithmic and natural logarithmic functions, solving quadratic and simultaneous linear equations, introduction to complex numbers.
Basic Trigonometry : Trigonometric functions (sine, cos, tan, cot, sec, cosec) and their inverse functions, graphs of sine, cos and tan functions, various identities with trigonometric functions.
Basic Coordinate Geometry: Equations of a straight line, gradient and intercept of a straight line.
Vectors and Matrices: Addition, scalar multiplication and dot product of vectors, addition, scalar multiplication and transpose of matrices, determinants and inverse of square matrices.
Calculus: Limits, differentiation – derivatives of algebraic, trigonometric and inverses of trigonometric functions, introduction to partial differentiation, graphical interpretation of derivatives, maxima and minima, integration – using substitution, by parts and partial functions, linear first order and second order differential equations.
Statistics: Elementary sampling methods, data presentation and simple analyses, elementary probability theory, introduction to simple linear regression.
Assessment: End of semester exam
Suggested Readings:
(i) Mathematics for Chemistry and Biology – Course Guide, Open University of Sri Lanka
(ii) Tebutt, Basic Mathematics for Chemistry
(iii) Arya, Mathematics for Biological Sciences
(iv) Gentry, Introduction to Calculus for Biological and Health Science
(v) Triola, Biostatistics for Biological and Health Science
BC 1001: Chemical Basis of Life (1C, 15 L)
Dependencies: None
Introduction; elements of life; cell structure; properties of water; chemical bonds and non-covalent interactions, including H-bonds; acid-base equilibria and buffers; structures, properties, acid-base behaviour of amino-acids; peptides and the peptide bond; qualitative introduction to thermodynamics: enthalpy, entropy (randomness), free energy; hydrophobic interactions; review of redox reactions, reduction potentials, and the Nernst equation; standard reduction potentials, standard free energies, and equilibrium constants in biochemical systems.
Assessment: End of semester exam
Suggested Readings:
(i) Horton, Moran, Ochs, Rawn & Scrimgeour, Principles of Biochemistry.
(ii) Zumdahl, Chemistry.
BC 1006 : Techniques in Biochemistry (2C, 15 L + 30P)
Dependencies: None
General principles of analytical biochemistry, electrochemical techniques, spectroscopy; absorption & emission, luminescence, separation methods; chromatography & electrophoresis; column chromatography, thin layer chromatography, affinity chromatography & HPLC, preparative centrifugation, electrophoresis of proteins and nucleic acids, capillary electrophoresis & iso-electric focusing.
Practicals
Laboratory safety and basic laboratory techniques, buffers solutions, spectroscopy, chromatography, isolation, purification and identification of nucleic acids, PAGE
Assessment: End of semester theory exam (50 %) and practical exam/ assessment (50%)
Suggested Readings:
(i) Holme & Peck, Analytical Biochemistry
(ii) Day & Underwood, Quantitative Analysis
(iii) Bates, Determination of pH-theory & Practice
(iv) Dick, Analytical Chemistry
BC 1008: Structure and Function of Biomolecules (3C, 30 L + 30 P)
Dependencies: CH 1008
Nucleotides and nucleic acids; information storage and retrieval; the genetic code; introduction to proteins; primary, secondary, tertiary, and quaternary structure; fibrous proteins; myoglobin and haemoglobin; immunoglobulins; introduction to enzymes; enzyme kinetics and inhibition; modes of enzyme catalysis; serine proteases; introduction to lipids; steroids and eicosanoids; phospholipids and membranes; transport across membranes; introduction to carbohydrates; stereochemistry and Fischer projections; linear and cyclic structures; Haworth projections; glycoside bonds; disaccharides; complex carbohydrates and polysaccharides (energy storage and structural).
Practicals
Qualitative and simple quantitative methods in biochemistry; characterization of biomolecules.
Assessment: End of semester exam (theory), practical exam and continuous assessments (practicals).
Suggested Readings:
(i) Horton, Moran, Ochs, Rawn & Scrimgeour, Principles of Biochemistry.
(ii) Voet, Voet, & Pratt, Principles of Biochemistry.
BT 1009: Genetics and Cell Biology Practicals (1C, 30 P)
Dependencies: Co-enrollment in BT 1002 and BT 1003.
Laboratory practicals in Cell Biology and Genetics.
Assessment: Practical examination at the end of the semester and / or continuous assessments.
ZL 1012: Introduction to Evolution (1C, 15 L)
Dependencies: None.
Nucleosynthesis; pre-biotic synthesis of biomolecules; evolution of genetic systems; Darwinian selection; neo-Darwinism; units of selection; units of evolution; modes of selection; genetic drift; founder effect.
Assessment: End of semester exam
Suggested Readings:
(i) Stephen Mason, Chemical Evolution.
(ii) Mark Ridley, Evolution
(iii) Richard Dawkins, The Selfish Gene.
PH 1050: Introduction to Biophysics (2C, 30 L)
Dependencies: None
Linear and angular motion: forces and torques at elbow joint, knee, hip and neck; effects of lifting and bending on the spinal column; Physics of walking, running, jumping, swimming and flying, friction; centrifugation; diffusion; Hydrostatics and hydrodynamics: viscosity, blood flow, measurement of blood pressure, pressure transducers, surface tension, Physics of respiration; Geometrical optics: the eye, iris, retina, rods and cones, resolution power of the eye, quantum efficiency of the eye, Eye pressure, defects of the eye; Electrostatics: current electricity, motion of charged particles, electrocardiography, nerve conduction; Quality of sound: pitch, loudness, intensity levels, Physics of the ear; ear canal as a resonance tube; Radioactivity: non ionizing radiation, endoscopy, lasers and its uses, thermography, ultrasonic imaging, Doppler scanning, ionizing radiation; X – rays and gamma rays and their uses, radioactive isotopes and tracers, CAT, PET and MRI scanning; Quantum tunneling: scanning tunneling and atomic force microscopes, nano–science; biological nano- machines
Assessment: End of semester exam
Suggested Readings:
(i) Carl Gans, Biomechanics – An Approach to Vertebrate Biology
(ii) Steven Vogel, Life’s Devices – the Physical World of Animals and Plants
BC 2007: Introduction to Metabolism (2C, 30 L)
Dependencies: BC 1008, CH 1009
Overview of metabolism: energetics and control mechanisms; glycolysis and pyruvate metabolism; citric acid cycle and pentose phosphate pathway; electron transport and oxidative phosphorylation; photosynthesis and photophosphorylation; gluconeogenesis; glycogen metabolism; fatty acid oxidation; biosynthesis of fats, phospholipids, eicosanoids and steroids; nitrogen metabolism: nitrogen fixation, transamination, the urea cycle; amino-acid degradation; haem metabolism; regulation of metabolic pathways.
Assessment: End of semester exam
Suggested Readings:
(i) Mathews, Van Holde, & Ahern, Biochemistry.
(ii) Voet & Voet, Biochemistry.
BC 2008: Metabolism of Nucleic Acids and Proteins (1C, 15 L)
Dependencies: BC 1008, CH 1009
Amino-acid biosynthesis; nucleotide metabolism; overview of translation; mechanism of protein synthesis; protein folding and post-translational modifications; regulation of protein synthesis.
Assessment: End of semester exam
Suggested Readings:
(i) Mathews, Van Holde, & Ahern, Biochemistry.
(ii) Voet & Voet, Biochemistry.
BC 2009: Practical Biochemistry (1C, 30 P)
Dependencies: BC 1006.
Intermediate biochemistry practicals in quantitative and spectroscopic methods, reaction rates, centrifugation, and electrophoresis.
Assessment: Practical examination at the end of the semester and / or continuous assessments.
BC 2010: Topics in Biochemistry (1C, 15 L)
Dependencies : None
The cell cycle and its regulation
Overview of the cell cycle; biochemical studies of cell cycles; oocytes and early embryos; steps of the cell cycle; cell cycle controls in yeast and multi-cellular organisms; check points in cell cycle regulation; genes involved in the control of the cell cycle.
Overview of extracellular signaling; G-protein couple receptors and their effectors; enzyme linked receptors and their effectors; second messengers / map kinase pathways .
Assessment: End of semester exam
Suggested Readings:
(i) Stryer, Biochemistry.
(ii) Lodish et al., Molecular Cell Biology.
ZL 2008: Human Physiology (1C, 15 L)
Dependencies: None.
Excitable cells - nerves and muscles, impulse generation and propagation, communication between excitable cells, muscle contraction; role of hormones in development, growth and homeostatic regulation of physiological processes; human nutrition - nutritional requirements of man, secretion and its regulation, digestion and absorption; elimination of metabolic by products - urine formation and its regulation, gaseous exchange and its regulation; transport within the body - functioning and regulation of cardiovascular system; chemistry of blood; human fertility - functioning and regulation of the human reproductive system, infertility and contraception.
Assessment: End of term assessment (80%) and class assignments (20%)
Suggested readings:
(i) Guyton & Hall, Textbook of Medical Physiology.
(ii) Ganong, Review of Medical Physiology.
MB 2004: Principles of Molecular Biology (1C, 15 L)
Dependencies: BT 1003, BC 1008.
DNA replication – enzymology, replication errors; proof reading, and mutations, and DNA repair; DNA in flux; recombination, transposons
Assessment: End of semester exam
Suggested Readings:
(i) Weaver, Molecular Biology.
(ii) Lodish et al., Molecular Cell Biology.
(iii) Watson et al., Recombinant DNA.
MB 2002 Genome Structure (1C, 15 L)
Dependencies: MB 2001
Overview and complexity of genome; prokaryotic genomes; organization of bacterial chromosome, prokaryotic operons , E.coli genome organisation; archaeal genomes organization; eukaryotic nuclear genomes; eukaryote chromosome structure and organisation; centromers , telomers and karyotype of human metaphase chromosomes; single copy DNA, moderately repeated/intermediate-repeat DNA, highly-repeated/simple-sequence/satellite DNA; eukaryotic gene organization, alternative splicing, mobile genetic elements , genome of Saccharomyces cerevisiae; human genome and mitochondrial genome.
Assessment: End of semester exam
Suggested Readings:
(i) Lewin, Genes VI.
MB 2005: Nucleic Acid Technology (3C, 30 L + 30 P)
Dependencies: MB 2001
DNA modifying enzymes; vector systems; cloning; construction of DNA and cDNA libraries; recombinant and gene analysis methods: gel electrophoresis methods, identification using oligonucleotide probes, antibody probes, southern and northern hybridization, DNA sequencing, chromosome walking, PCR, DNA finger printing, DNA and protein micro array; molecular evolution; basic molecular phylogenetics; genes and society – applications of molecular biology to society with regard to medicine, agriculture, forensics, & environmental issues; discoveries in molecular biology
Practicals
Introduction of DNA into cell; isolation of plasmid and chromosomal DNA; protein isolation; DNA cloning, restriction mapping; screening of recombinant clones; Southern hybridization, Western blotting, PCR.
Assessment: End of semester exam (theory), continuous assessment (practicals).
Suggested Readings:
(i) Glick & Pasternak, Molecular Biotechnology.
(ii) Watson et al., Recombinant DNA.
(iii) Drlica, Understanding DNA and Gene Cloning.
BC 3002 : Clinical Biochemistry (3C, 30 L + 30 P)
Dependencies: BC 1007, BC 2005
Disorders of metabolism and nutrition deficiency, biochemical basis of common human diseases (diabetes, atherosclerosis, cancer, cardiovascular disorders etc.), hematology, immunological diseases, biochemical tools for clinical diagnosis.
Practicals
Clinical Chemistry in Diagnosis and Treatment
Assessment: End of semester theory exam (65 %) and practical exam/ assessment (35%)
Suggested Readings:
(i) Kaplan, Pesce & Kazmierezak, Clinical Chemistry: Theory, analysis, correlation.
BC 3005 : Advanced Topics in Biochemistry (2C, 15 L + 30 P)
Dependencies: BC 1006, BC 2005
Practicals
Assessment: End of semester theory exam (50 %) and practical exam/ assessment (50%)
BC 3006 : Biochemistry Seminar (1C, 30 P)
Dependencies: None
Topics will be given by academic staff members
Assessment: Based on presentations
MB 3003: Genomics and Proteomics (2C, 30 L)
Dependencies: MB 2001
Proteomics
Overview of proteomics, methods used in proteome analyses, 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, protein sequencing by Edman degradation, and protein sequence analyses; protein arrays, types of protein arrays, data analysis, applications of protein microarrays.
Genomics
Assessment: End of semester exam
Suggested Readings:
Internet and primary literature
MB 3004: Advanced Molecular Biology Laboratory (1C, 30 P)
Dependencies: MB 2003.
Advanced techniques in the molecular biology laboratory: isolation of DNA, restriction digestion of DNA, DNA hybridisation, cloning, and screening, isolation of RNA, PCR, expression of target genes, ELISA, and computer analysis of DNA and protein sequences.
Assessment: Continuous assessment.
MB 3005: Industrial Molecular Biotechnology (30L, 2C)
Dependencies: None
Syllabus: Microbial biotechnology: Commercial production of microorganisms; Products from microorganisms: Metabolites, Enzymes, Antibiotics, Fuels, Plastics; Bioremediation: Oil spills, Water treatment, Chemical degradation; Plant and animal biotechnology: Genetically modified organisms, Transgenic animals, Crop improvements, Herbicide resistance, Plants as bioreactors, Genetically engineered food; Medical applications: Gene therapy, Commercialization of gene therapy, Vaccines, Synthetic DNAs, Therapeutic ribozymes, Antibody engineering, Protein engineering, Pharmaceutics; Ethics: Regulations, Patents and society.
Assessment: End of semester
Suggested Readings: Biotechnology: An introduction (S. R. Barnum), Molecular Biotechnology (B. R. Glick & J. J. Pasternak)
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 July 2009