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Professor of Microbiology & Head of Department
RA Dorrington, BSc Agric(Stell), PhD(UCT)
Professor of Biotechnology
& Director Environmental Biotechnology Research Unit
PD Rose, BSc(Hons)(UCT), PhD(Rhodes)
Professor of Biochemistry & Dean of Research
JR Duncan, PhD(Natal), FRSSA
Professor, Biochemistry
GL Blatch, BSc(Hons)(Natal), PhD(UCT)
Associate Professor, Biochemistry
CG Whiteley, PhD(Natal), MRSC, CChem
Senior Lecturer & Head of Biochemistry
BI Pletschke, PhD(UPE)
Lecturers, Biochemistry
BS Wilhelmi, B.Tech:Ed(TWR), PhD(Rhodes)
A Boshoff, PhD(Rhodes)
Lecturer & Head of Microbiology
J Dames, PhD(Wits)
Lecturer, Microbiology
C Knox, PhD(Wits)
Senior Lecturer & Head of Biotechnology
JE Burgess, PhD(Cranfield)
Senior Lecturer, Biotechnology
J Limson, PhD(Rhodes)
Research Associates
J Brand, PhD(Natal), DSc(Natal)
Emeritus Associate Professor
DA Hendry, PhD(UCT)
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 sub-minimum (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 sub-minimum 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 or 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 sub-minimum (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. A sub-minimum of 40% 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)
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)
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 normally held in the first semester and BCH 302 in the second semester but the department reserves the right to offer them in either semester subject to timetable constraints. 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 sub-minimum (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. A sub-minimum of 40% in the first semester is required before a student may register for the second semester. 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)
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; differential & analytical centrifugation; advanced chromatography; advanced spectroscopy.
BCH 302
(Two theory papers and a practical examination)
Physiological & Medical Biochemistry: Signal transduction in the context of hormones and neurotransmission; 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 identification, antibiotics, biomedical biochemistry, receptors, hormones, structure & function of biomacromolecules, protein folding, protein engineering, advanced enzymology, applied enzymology & immobilized enzymes; bioinformatics, protein purification and biotechnology, proteomics, plant biochemistry, seminars, a literature review, 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; CEL 101 (or an aggregate pass in ZOO 1 or BOT 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 or 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 sub-minimum (40%) in each component. No supplementary examinations will be offered for either course. Practical reports, tutorials and class tests collectively comprise the class mark, which forms part of the final mark.
Credit in Chemistry (CHE 1) and in Cell Biology (CEL 101) (or an aggregated credit in either Botany (BOT 1) or Zoology (ZOO 1)) is required before a student may register for MIC 201. A sub-minimum 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).
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 yeast, bacteria, fungi and viruses). Microbial interactions (microorganisms of soil and water; their interrelationships, activity and impact; nutrient cycling). Metabolism (energy generation; biosynthetic pathways; enzyme regulation). The course includes practical experience in the isolation and culture of microbes, their identification and interaction with each other and the environment and a field trip.
MIC 202
(One paper and a practical examination).
Molecular Biology and Genetics: Introductory molecular biology (the structure of nucleic acids and proteins; the flow of genetic information). Basic bacterial genetics (bacterial conjugation, transformation and transduction; plasmids; bacteriophages). Procaryote gene regulation (plasmid replication and host range; transposable elements; regulation of gene expression). Genetic engineering. 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 sub-minimum (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. A sub-minimum of 40% 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).
Eukaryote Molecular Biology and Advanced Virology: Eukaryote cell biology (structure and function of the cellular organelles; cellular sorting and trafficking). Eukaryote molecular genetics (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 recombinant 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). A field trip to local laboratories is included.
MIC 302
(Two papers and a practical examination).
Industrial and applied microbiology: Exploiting microorganisms for industrial and commercial purposes. Topics covered include biological control, 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. Gene therapy (implications and applications of recombinant DNA research). The course includes practical experience in isolating microorganisms from specific environments and molecular techniques used for identification of microbes and the fermentation of alcoholic beverages. A field trip to local industries is included.
Microbiology Honours
The course consists of practical modules on general recombinant DNA techniques, genomics and mammalian cell culture techniques and specialized topics on agriculturally important fungi and emerging infectious diseases. The course is assessed through essays, tutorials and seminars with three written examinations. Each candidate is required to submit a report on practical work done on a specific project in the areas of virology, mycology, mycorrhizal fungi, molecular biology and microbial genetics during the course, and this together with all assessment marks 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 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, biosensor technology, enzyme engineering, industrial bioprocess design and strategy, advanced topics in environmental biotechnology and management. The course also includes modules in bio-entrepreneurship, intellectual property management and current trend analysis. Practical work will consist of a course concentrating on small projects offering exposure to methods and techniques essential to the subject. This will be followed by a research project of original investigation. All seminars, essays, practical reports and examinations will contribute to the final mark.
MSc in Environmental Biotechnology
An MSc in Environmental Biotechnology was offered in recent years, but will not be offered in 2008.
Higher Diploma in Environmental Biotechnology
A Higher Diploma in Environmental Biotechnology was offered in recent years, but will not be offered in 2008.
CHE 1 CSC 1 MAT 1 STA 1 CEL 101 BCH 2 CSC 2 MAT 2 or MST 2 BCH 3 CSC 3 or MAT 3 or MST 3 MIC 202
This curriculum will prepare students for careers in the bioinformatics sector, and be the entrance route to the MSc(Bioinformatics and Computational Molecular Biology) in the future.
CEL 101 and MIC 202 are strongly recommended as additional credits (giving 19 or 20 credits overall). MIC 202 can be taken without MIC 201, as long as BCH 201 has been taken.
MSc in Bioinformatics and Computational Molecular Biology
[Suspended in 2008].
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 incorporates 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:
The course work consists of modules and lectures on introductory and advanced topics covering computer operating systems and programming (e.g. Linux/Unix, BioPerl, Java and MatLab), genomics (genome sequencing, biological database management, genome annotation, assembly and analysis, gene discovery and drug target identification, structural and functional prediction, neural networks), and molecular modelling and protein engineering (e.g. Ligandfit, Whatif and SWISS-MODEL). Students may also be required to attend courses offered through the National Bioinformatics Network from time to time.
Assessment:
The course work modules will be assessed by internal grading of tutorials and practicals, and by internal and external grading of work assignments, mini-projects and 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 sub-minimum (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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