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Associate Professor of Biochemistry & Head of Department
CG Whiteley, PhD(Natal), MRSC, CChem
Professor of Biotechnology
PD Rose, BSc (Hons)(Cape Town), PhD(Rhodes)
Professor of Biochemistry and Dean of Research
JR Duncan, PhD(Natal), FRSSAf
Professor of Microbiology
R Kirby, Pr. Nat. Sci., MA(Cantab), PhD(East Anglia)
Associate Professor & Head of Biochemistry
GL Blatch, BSc(Hons)(Natal), PhD(Cape Town),
Wellcome Trust Seniot Fellow
Associate Professor of Microbiology
DA Hendry, MSc(Stell), PhD(CapeTown)
Associate Professor & Head of Microbiology
RA Dorrington, BSc Agric (Stell), PhD(Cape Town)
Senior Lecturer in Biotechnology
W Leukes, PhD(Rhodes)
Senior Lecturer in Biochemistry
G Bradley, PhD(UPE)
Lecturer in Biochemistry
B Pletschke, PhD(UPE)
Lecturer in Environmental Biotechnology
K Whittington-Jones, PhD(Rhodes)
Mellon Foundation Programme Lecturer (Biotechnology)
J.Limson, PhD(Rhodes).
Research Fellows
R van der Merwe, BSc(Rhodes), BSc(Hons) (UNISA), PhD(Rhodes)
OO Hart, MSc(Potchefstroom), DSc(Pretoria)
Research Associate in Biochemistry A.Boshoff, PhD (Rhodes)
The Department offers courses in Biochemistry, Microbiology and Biotechnology.
See the Departmental Web Page http://www.ru.ac.za/academic/departments/biochem/ for further details, particularly on the contents of courses.
Introductory Molecular Biology (IMB) is a two-semester subject offered at the second year level to students not majoring in either Biochemistry or Microbiology who require a basic understanding in biochemistry and molecular biology for application in other biological sciences, law, journalism, pharmacy, computer science and education. The subject is comprised of two semester courses offered in Biochemistry and Microbiology, namely IMB 201 (same as BCH 201) and IMB 202 (same as MIC 202). Credit may be obtained in each course separately and, in addition, an aggregate mark of at least 50% will be deemed to be equivalent to a two-credit course IMB 2, provided that a candidate obtains the required subminimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, essays and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Chemistry (CHE 1) is required before a student may register for IMB 2. A subminimum of 40% in IMB 201 is required for registration in IMB 202. Students unable to complete IMB 201 and IMB 202 in the same calendar year will be required to pass both courses to obtain a credit in IMB 2. Credit in IMB 2 will not enable registration for either BCH 3 or MIC 3.
Biochemistry (BCH) is a four-semester subject which may be taken as a major subject for the degrees of BSc, BCom and BJourn.
To major in Biochemistry, a candidate is required to obtain credit in the following courses: CHE 1; BCH 2; BCH 3: See Rule S.23. In addition, students wishing to major in Biochemistry are strongly encouraged to obtain credit for MIC 202.
Students who aim to major in Biochemistry and progress to postgraduate studies in computational biology, genomics, protein structure and function and biotechnology are encouraged to register for advanced courses in one or more of Microbiology, Computer Science, Chemistry and Mathematics.
Second-year level courses in Biochemistry
There are two second-year courses in Biochemistry. BCH 201 is held in the first semester and BCH 202 in the second semester. Credit may be obtained in each course separately and, in addition, an aggregate mark of at least 50% will be deemed to be equivalent to a two-credit course BCH 2, provided that a candidate obtains the required subminimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, essays and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Chemistry (CHE 1) is required before a student may register for BCH 201 or BCH 202. Adequate performance in BCH 201 is required before a student may register for BCH 202. In addition, a credit in MIC 202 is strongly encouraged for students wishing to major in Biochemistry.
BCH 201
(One theory paper and a practical examination in June)
Introductory Biochemistry: Aqueous biochemistry & buffers; building blocks in biochemistry; amino acids & proteins; nucleotides, DNA & RNA; carbohydrates; lipids & membranes; vitamins, coenzymes & enzymes.
Bioenergetics & metabolism: Enzyme kinetics, specificity & regulation; bioenergetics & thermodynamics; catabolism & catabolic pathways; oxidative phosphorylation & substrative phosphorylation; anabolism and anabolic pathways.
BCH 202
(One theory paper and a practical examination in November)
Biochemical techniques: This course is taught in the context of protein purification and analysis and includes: protein purification strategies; cell disruption & centrifugation; chromatography; spectroscopy; electrophoresis; radioactivity in biochemistry.
Biological chemistry & computational biochemistry: Non-covalent interactions and molecular recognition in biological systems; theory and application of computational methods and tools for the visualization and modelling of biomacromolecules; organic reaction mechanisms in biological systems; stereochemistry and stereospecificity of biological systems.
Third-year level courses in Biochemistry
There are two third-year courses in Biochemistry. BCH 301 is held in the first semester and BCH 302 in the second semester. Credit may be obtained in each course separately and, in addition, an aggregate mark of at least 50% will be deemed to be equivalent to a two-credit course BCH 3, provided that a candidate obtains the required subminimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, essays and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Biochemistry (BCH 2) is required before a student may register for BCH 301 or BCH 302. Adequate performance in BCH 301 is required before a student may register for BCH 302. In addition, a credit in MIC 202 is strongly encouraged for students wishing to major in Biochemistry.
BCH 301
(Two theory papers and a practical examination in June)
Biochemistry of Information Flow: The structure of chromosomes and plasmids; DNA replication and repair; transcription and regulation of gene expression; protein synthesis, transport and degradation.
Advanced Techniques in Biochemistry & Molecular Biology: Recombinant DNA technology; sequencing and analysis of genes and genomes; immunochemistry; differential & analytical centrifugation; advanced chromatography; advanced spectroscopy.
BCH 302
(Two theory papers and a practical examination in November)
Physiological & Medical Biochemistry: Signal transduction in the context of hormones and neurotransmission; blood protein chemistry; biosynthesis of biomolecules; inborn errors of metabolism.
Enzymology & Molecular Modelling: Enzyme mechanisms; advanced enzyme kinetics; advanced theory and application of computational methods and tools for the visualization and modelling of enzymes.
Biochemistry Honours
The course consists of course-work modules and lectures on selected advanced topics such as drug metabolism, drug discovery, antibiotics, biomedical biochemistry, receptors, hormones, structure & function of biomacromolecules, protein folding, protein engineering, advanced enzymology, applied enzymology & immobilized enzymes, food chemistry & brewing; a seminar including a literature review on a general biochemical topic, essays and a research project.
Microbiology (MIC) is a four-semester subject which may be taken as a major subject for the degrees of BSc, BCom and BJourn.
To major in Microbiology, a candidate is required to obtain credit in the following courses: CHE 1; ZOO 1 or BOT 1 or BIO 1; MIC 2; MIC 3. See Rule S.23. In addition, students wishing to major in Microbiology are strongly encouraged to obtain credit for BCH 201.
Students who aim to major in Microbiology and progress to postgraduate studies in computational biology, genomics, cell biology and biotechnology are encouraged to register for advanced courses in one or more of Biochemistry, Computer Science, Chemistry, Mathematics and Environmental Science.
Second-year level courses in Microbiology
There are two second-year courses in Microbiology. MIC 201 is normally held in the first semester and MIC 202 in the second semester. Credit may be obtained in each course separately and, in addition, an aggregate mark of at least 50% will be deemed to be equivalent to a two-credit course MIC 2, provided that a candidate obtains the required subminimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, essays and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Chemistry (CHE 1) and a credit in either Botany (BOT 1) or Zoology (ZOO 1) or Biology (BIO 1) is required before a student may register for MIC 201. A subminimum of 40% in MIC 201 is required for registration in MIC 202. In addition, a credit in BCH 201 is strongly recommended for students wishing to major in Microbiology.
The courses are comprised of the following modules, not necessarily in the given position, each module lasting about three weeks.
MIC 201
(One paper and a practical examination in June).
Microbes and their environment: Introductory Microbiology (classification, growth, assay and control of microorganisms). Organization and replication of microbes (microbial structure; cellular organization and modes of replication of fungi, bacteria and viruses). Microbial interactions (microorganisms of soil and water, medical and agricultural pathogens; their interrelationships, activity and impact; nutrient cycling). The course includes practical experience in the isolation and culture of microbes, their identification and interaction with each other and the environment and a two day field trip.
MIC 202
(One paper and a practical examination in November).
Molecular Biology and Genetics: Introductory molecular biology (the flow of genetic information, the genetic material, proteins, DNA replication, transcription and translation). Microbial genetics (The flow of genetic information between microbes, cconjugation, transformation and transduction; plasmids; bacteriophages). Gene regulation with emphasis on prokaryotes (plasmid replication and host range; transposable elements; regulation of gene expression); immunology (nature of the immune response; structure of antigens and immunoglobulins; cellular immunology; serology; introduction to genetic engineering (DNA cloning, PCR, genetically modified organisms). The course will include a practical introduction to basic molecular techniques (DNA isolation and characterization, bacterial transformation gene regulation studies).
Third-year level courses in Microbiology
There are two third-year courses in Microbiology. MIC 301 is normally held in the first semester and MIC 302 in the second semester. Credit may be obtained in each course separately and, in addition, an aggregate mark of at least 50% will be deemed to be equivalent to a two-credit course MIC 3, provided that a candidate obtains the required subminimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, essays and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Microbiology (MIC 2) is required before a student may register for MIC 301 or MIC 302. Adequate performance in the first semester is required before a student may register for the second semester. In addition, a credit in BCH 201 is strongly recommended for students wishing to major in Microbiology.
The courses are comprised of the following modules, not necessarily in the given position, each module lasting about three weeks:
MIC 301
(Two papers and a practical examination in June).
Eukaryote Molecular Biology and Advanced Virology: Eucaryote cell biology (structure and function of the cellular organelles; cellular sorting and trafficking). Eucaryote molecular genetices (genome structure and organisation, the eukaryotic gene, the flow of information, transcriptional and translational regulation of gene expression; the cell cycle and apoptosis). Virology (families of plant and animal viruses; molecular biology of representative DNA and RNA viruses; stages and strategies of viral replication; vaccines). The practical component of this course focuses on recombiant DNA techniques (DNA cloning, genetic manipulation of bacterial and yeast cells, PCR, purification of viruses and immunological techniques such as Elisa and Western blot analysis of proteins).
MIC 302
(Two papers, a comprehension and a practical examination in November).
Molecular and Industrial Biotechnology: Process Biotechnology; metabolic engineering; microbial growth kinetics; batch and continuous culture; downstream processing; primary and secondary metabolism; antibiotic production; amino acid production; beer brewing. Gene manipulation (gene identification and isolation; cloning strategies; expression of recombinant genes). Environmental Biotechnology: industrial ecology, bioremediation, waste treatment technology. Molecular Biotechnology (implications and applications of recombinant DNA research). The course includes practical experience in molecular techniques used for identification of microbes andfermentation of alcoholic beverages as well as a field trip to local industries and laboratories.
Microbiology Honours
The course consists of practical modules, essays, tutorials and seminars on advanced aspects of Microbiology including virology, immunology, serology, molecular biology, microbial biochemistry and microbial genetics. Each candidate is required to submit two copies (one to be returned) of a report on practical work done on a specific project during the course, and these together with all seminars, essays and practical reports will be considered part of the final examination.
Biotechnology is offered at the postgraduate level.
Biotechnology Honours
This course is offered as a professional qualification for students interested in careers in the biotechnology sector.
Candidates must normally have either Microbiology or Biochemistry as major BSc subjects, but candidates with other majors will be considered. The course consists of lectures, seminars and essays covering a series of topics in Biotechnology such as process biotechnology, genetic manipulation, applied immunology, enzyme engineering, industrial bioprocess design and strategy, advanced topics in environmental biotechnology and management. The course also includes topics in bio-entrepreneurship, intellectual property management and market trend analysis.
Practical work will consist of an 18 week course concentrating on small projects offering exposure to methods and techniques essential to the subject. This will be followed by a second 18 week project of original investigation. All seminars, essays and practical reports will be considered part of the final examination.
MSc in Environmental Biotechnology
Environmental Biotechnology involves the use of biological systems, mainly micro-organisms and their derivatives and processes, in both environmental protection and restoration. It is a knowledge-intensive, research-driven field which addresses a broad spectrum of Environmental Sector needs in the major areas of water, air, soil and waste disposal. The MSc course emphasises a Bioprocess approach within the context of Environmental Management.
The course is open to candidates holding the BSc(Hons) degree, or its equivalent. In exceptional cases only, applications may be considered from candidates who hold a BSc degree and have at least 3 years relevant experience.
The course covers theoretical and practical aspects of Environmental Biotechnology. Instruction is through the medium of lectures, seminars, directed reading, assignments and practical work led by staff of the Department, and supported by input from experts drawn from industry and other universities. ?
Requirements for award of the degree include completion of any six of the following modules offered, and presentation of a research project, based on original work on a topic selected in consultation with the Department. The research project may be undertaken off campus under approved supervision.
Candidates may complete all requirements for the degree in one year of full-time study, or enrol on a part-time basis over a longer period not exceeding three years. Assessment of candidates is based on written and oral presentations covering all aspects of the course.
Higher Diploma in Environmental Biotechnology
The Higher Diploma in Environmental Biotechnology is intended as an exit qualification from the MSc in Environmental Biotechnology. The regulations and syllabus for this Diploma are the same as those for the MSc in Environmental Biotechnology, save that a project is not required. On application to the Dean, students who have registered for, and passed the coursework component of the MSc, may be awarded the Higher Diploma.
MSc in Bioinformatics and Computational Molecular Biology
General background:
Bioinformatics and computational molecular biology is the systematic development and application of information technologies and data mining techniques for analysing biological data obtained by experiments, modelling, database searching and instrumentation to make novel observations and predictions about biological function. This course will be taught in an interdisciplinary manner and focussing on the interface between the computational sciences and the biological, physical and chemical sciences. Graduates who complete this course will be skilled in the assimilation of biological information through the use and development of computational tools for a range of applications including simple pattern recognition, molecular modelling for the prediction of structure and function, gene discovery and drug target discovery, the analysis of phylogenetic relationships, whole genome analysis and the comparison of genetic organization.
Eligibility:
The course is open to candidates who hold a BSc Honours degree with subjects from the life sciences (especially biochemistry and microbiology) and physical and chemical sciences (especially chemistry), and who have basic computer literacy.
Course structure:
The Masters programme will be offered over 12 months and incorporate a number of course work modules and a research project running concurrently throughout the programme. The course work modules will involve an integration of formal lectures, self-learning computer-based tutorials and practicals. In addition, problem solving tutorials would be designed to guide the student through current information-based problems and involve the assimilation and reduction of biological information. A number of the tutorials and practical components will be assessed and contribute towards a course work year mark. The examination of the course work component would be through oral and open-book theory examinations. The course work component will be externally examined.
The research projects will involve a significant computer based component, but will be supported by data obtained from independently conducted experimental laboratory work. The extent of experimental laboratory work will need to be flexibly applied and may require that certain practical components are built into the course work modules. The projects will be assessed by seminar presentations of the proposed and final work, and as a written project research report. Each project report will be examined by an external examiner.
Course work modules:
Mathematical Modelling and Technical Computing
Revision of discrete mathematics, limits, linear algebra, differentiation and integration; differential equations; revision of essential statistics and statistical tools; mathematical modelling of biochemical and biotechnological systems using the MATLAB scientific computing environment.
Computer Programming and Software Engineering
The design of algorithms to solve general and biological problems, and their implementation using object-based JAVA programming language.
Computational Chemistry and Molecular Modelling
Structure and energy of organic molecules; computational methods; molecular mechanics; experimental techniques for accessing geometrical parameters.
Structure & Function of Biomacromolecules, Molecular Modelling and Protein Engineering
Analysis and display of protein structures; ligand (drug) and protein contact analysis; homology modelling; enzyme active site analysis; building a functional peptide loop from a monomer; developing electron density maps; structural superimposition; Ramachandran plots; analysis of structural folds of proteins; mechanisms of enzyme action; rational and arational protein/enzyme engineering; oligonucleotide-based mutagenesis.
DNA Sequencing & Analysis, the Genome and Genomics
The storage, transmission and expression of genetic information; gene and genome sequencing and analysis; gene discovery and gene target identification; genome profiling and fingerprinting; molecular population genetics; forensic science.
Assessment:
The course work modules will be assessed by internal grading of tutorials, work assignments and practicals, and by internal and external grading of examinations. The project report will be graded internally and externally. The overall course work mark and the research report mark will each contribute equally to the final mark. Successful completion of the course will be subject to a final mark of at least 50%, provided that a candidate obtains at least a subminimum (40%) for the course work and at least 50% for the project report.
Suitably qualified students are encouraged to proceed to the research degrees of MSc and PhD under the direction of the staff of the Department. Requirements for the MSc and PhD degrees are given in the General Rules.
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