| Code | Faculty |
|---|---|
| 02133173 | Faculty of Natural and Agricultural Sciences |
| Credits | Duration |
|---|---|
| Duration of study: 3 years | Total credits: 428 |
The following persons will be considered for admission: a candidate who is in possession of a certificate that is deemed by the University to be equivalent to the required Grade 12 certificate with university endorsement; a candidate who is a graduate from another tertiary institution or has been granted the status of a graduate of such an institution; and a candidate who is a graduate of another faculty at the University of Pretoria.
Life Orientation is excluded in the calculation of the Admission Point Score (APS).
Grade 11 results are used for the provisional admission of prospective students. Final admission is based on the Grade 12 results.
Minimum requirements | ||||||||||||
Achievement level | ||||||||||||
Afrikaans or English | Mathematics | Physical Science | APS | |||||||||
NSC/IEB | HIGCSE | AS-Level | A-Level | NSC/IEB | HIGCSE | AS-Level | A-Level | NSC/IEB | HIGCSE | AS-Level | A-Level | |
5 | 3 | C | C | 5 | 3 | C | C | 5 | 3 | C | C | 32 |
Candidates who do not comply with the minimum admission requirements for BSc (Chemistry), may be considered for admission to the BSc – Extended programme for the Physical Sciences. The BSc – Extended programme takes place over a period of four years instead of the normal three years.
Admission requirements for BSc Extended programme for Physical Sciences:
Minimum requirements | ||||||||||||
Achievement level | ||||||||||||
Afrikaans or English | Mathematics | Physical Science | APS | |||||||||
NSC/IEB | HIGCSE | AS-Level | A-Level | NSC/IEB | HIGCSE | AS-Level | A-Level | NSC/IEB | HIGCSE | AS-Level | A-Level | |
4 | 3 | D | D | 4 | 3 | D | D | 4 | 3 | D | D | 26 |
A student must pass all the minimum prescribed and elective module credits as set out at the end of each year within a programme as well as the total required credits to comply with the particular degree programme. Please refer to the curricula of the respective programmes. At least 144 credits must be obtained at 300-/400-level, or otherwise as indicated by curriculum. The minimum module credits needed to comply with degree requirements is set out at the end of each study programme. Subject to the programmes as indicated a maximum of 150 credits will be recognised at 100-level. A student may, in consultation with the Head of Department and subject to the permission by the Dean, select or replace prescribed module credits not indicated in BSc three-year study programmes to the equivalent of a maximum of 36 module credits.
It is important that the total number of prescribed module credits is completed during the course of the study programme. The Dean may, on the recommendation of the Head of Department, approve deviations in this regard. Subject to the programmes as indicated in the respective curricula, a student may not register for more than 75 module credits per semester at first-year level subject to permission by the Dean. A student may be permitted to register for up to 80 module credits in a the first semester during the first year provided that he or she obtained a final mark of no less than 70% for grade 12 Mathematics and achieved an APS of 34 or more in the NSC.
Students who are already in possession of a bachelor’s degree, will not receive credit for modules of which the content overlap with modules from the degree that was already conferred. Credits will not be considered for more than half the credits passed previously for an uncompleted degree. No credits at the final-year or 300- and 400-level will be granted.
The Dean may, on the recommendation of the programme manager, approve deviations with regard to the composition of the study programme.
Please note: Where elective modules are not specified, these may be chosen from any modules appearing in the list of modules.
It remains the student’s responsibility to acertain, prior to registration, whether they comply with the prerequisites of the modules they want to register for.
The prerequisites are listed in the Alphabetical list of modules.
General promotion requirements in the faculty
All students whose academic progress is not acceptable can be suspended from further studies.
Minimum credits: 140
Minimum credits:
Fundamental = 12
Core = 96
Electives = 32
Additional information:
Students who do not qualify for AIM 102 must register for AIM 111 and AIM 121.
Module content:
Find, evaluate, process, manage and present information resources for academic purposes using appropriate technology.
Module content:
Apply effective search strategies in different technological environments. Demonstrate the ethical and fair use of information resources. Integrate 21st-century communications into the management of academic information.
Module content:
The module aims to equip students with the ability to cope with the reading and writing demands of scientific disciplines.
Module content:
Find, evaluate, process, manage and present information resources for academic purposes using appropriate technology. Apply effective search strategies in different technological environments. Demonstrate the ethical and fair use of information resources. Integrate 21st-century communications into the management of academic information.
Module content:
General introduction to inorganic, analytical and physical chemistry. Atomic structure and periodicity. Molecular structure and chemical bonding using the VSEOR model. Nomenclature of inorganic ions and compounds. Classification of reactions: precipitation, acid-base, redox reactions and gas-forming reactions. Mole concept and stoichiometric calculations concerning chemical formulas and chemical reactions. Principles of reactivity: energy and chemical reactions. Physical behaviour gases, liquids, solids and solutions and the role of intermolecular forces. Rate of reactions: Introduction to chemical kinetics.
Module content:
Theory: General physical-analytical chemistry: Chemical equilibrium, acids and bases, buffers, solubility equilibrium, entropy and free energy, electrochemistry. Organic chemistry: Structure (bonding), nomenclature, isomerism, introductory stereochemistry, introduction to chemical reactions and chemical properties of organic compounds and biological compounds, i.e. carbohydrates and aminoacids. Practical: Molecular structure (model building), synthesis and properties of simple organic compounds.
Module content:
*This module serves as preparation for students majoring in Mathematics (including all students who intend to enrol for WTW 218 and WTW 220). Students will not be credited for more than one of the following modules for their degree: WTW 114, WTW 158, WTW 134, WTW 165.
Functions, limits and continuity. Differential calculus of single variable functions, rate of change, graph sketching, applications. The mean value theorem, the rule of L'Hospital. Definite and indefinite integrals, evaluating definite integrals using anti-derivatives, the substitution rule.
Module content:
SI-units. Significant figures. Waves: intensity, superposition, interference, standing waves, resonance, beats, Doppler. Geometrical optics: Reflection, refraction, mirrors, thin lenses, instruments. Physical optics: Young-interference, coherence, diffraction, polarisation. Hydrostatics and dynamics: density, pressure, Archimedes’ principle, continuity, Bernoulli. Heat: temperature, specific heat, expansion, heat transfer. Vectors. Kinematics of a point: Relative, projectile, and circular motion. Dynamics: Newton’s laws, friction. Work: point masses, gasses (ideal gas law), gravitation, spring, power. Kinetic energy: Conservative forces, gravitation, spring. Conservation of energy. Conservation of momentum. Impulse and collisions. System of particles: Centre of mass, Newton’s laws. Rotation: torque, conservation of angular momentum, equilibrium, centre of gravity.
Module content:
Simple harmonic motion and pendulums. Coulomb’s law. Electric field: dipoles, Gauss’ law.Electric potential. Capacitance. Electric currents: resistance, resistivity, Ohm’s law, energy, power, emf, RC-circuits. Magnetic Field: Hall-effect, Bio-Savart. Faraday’s and Lenz’s laws. Oscillations: LR-circuits. Alternating current: RLC-circuits, power, transformers. Introductory concepts to modern physics. Nuclear physics: Radioactivity.
Module content:
*Students will not be credited for more than one of the following modules for their degree:
WTW 124, WTW 146, WTW 148 and WTW 164. This module serves as preparation for students majoring in Mathematics (including all students who intend to enrol for WTW 218, WTW 211 and WTW 220).
The vector space Rn, vector algebra with applications to lines and planes, matrix algebra, systems of linear equations, determinants. Complex numbers and factorisation of polynomials. Integration techniques and applications of integration. The formal definition of a limit. The fundamental theorem of Calculus and applications. Vector functions, polar curves and quadratic curves.
Module content:
Simple statistical analysis: Data collection and analysis: Samples, tabulation, graphical representation, describing location, spread and skewness. Introductory probability and distribution theory. Sampling distributions and the central limit theorem. Statistical inference: Basic principles, estimation and testing in the one- and two-sample cases (parametric and non-parametric). Introduction to experimental design. One- and twoway designs, randomised blocks. Multiple statistical analysis: Bivariate data sets: Curve fitting (linear and non-linear), growth curves. Statistical inference in the simple regression case. Categorical analysis: Testing goodness of fit and contingency tables. Multiple regression and correlation: Fitting and testing of models. Residual analysis. Computer literacy: Use of computer packages in data analysis and report writing.
Module content:
Basic plant structure and function; introductory plant taxonomy and plant systematics; principles of plant molecular biology and biotechnology; adaptation of plants to stress; medicinal compounds from plants; basic principles of plant ecology and their application in natural resource management.
Module content:
This module begins by fostering an understanding of human geography. Then follows with the political ordering of space; cultural diversity as well as ethnic geography globally and locally; population geography of the world and South Africa: and four economic levels of development. The purpose is to place South Africa in a world setting and to understand the future of the country.
Module content:
Investigating southern African landscapes and placing them in a theoretical and global context. The geomorphological evolution of southern Africa. Introduction to the concepts of Geomorphology and its relationships with other physical sciences (e.g. meteorology, climatology, geology, hydrology and biology). The processes and controls of landform and landscape evolution. Tutorial exercises cover basic techniques of geomorphological analysis, and topical issues in Geomorphology.
Module content:
Chromosomes and cell division. Principles of Mendelian inheritance: locus and alleles, dominance interactions and epistasis. Probability studies. Sex determination and sex linked traits. Pedigree analysis. Extranuclear inheritance. Genetic linkage and chromosome mapping. Chromosome variation.
Module content:
The module will introduce the student to the field of Microbiology. Basic Microbiological aspects that will be covered include introduction into the diversity of the microbial world (bacteria, archaea, eukaryotic microorganisms and viruses), basic principles of cell structure and function, microbial nutrition and microbial growth and growth control. Applications in Microbiology will be illustrated by specific examples i.e. bioremediation, animal-microbial symbiosis, plant-microbial symbiosis and the use of microorganisms in industrial microbiology. Wastewater treatment, microbial diseases and food will be introduced using specific examples.
Module content:
Introductory study of the ultra structure, function and composition of representative cells and cell components. General principles of cell metabolism, molecular genetics, cell growth, cell division and differentiation.
Module content:
An introduction to the climate and general seasonal climatic circulation patterns of Southern Africa. Basic weather types and weather processes within the Southern African context. Interpretation of synoptic maps and synoptic station reports. Impacts of climate change and extreme climate events on society.
*BSc (Geography) and BSc (Environmental Sciences) students may register for WKD 155. Students are not allowed to earn credits for both WKD 155 and WKD 164.
Module content:
Propositional logic: truth tables, logical equivalence, implication, arguments. Mathematical induction and well-ordering principle. Introduction to set theory. Counting techniques: elementary probability, multiplication and addition rules, permutations and combinations, binomial theorem, inclusion-exclusion rule.
Module content:
*Students will not be credited for more than one of the following modules for their degree: WTW 162 and WTW 264.
Introduction to the modelling of dynamical processes using elementary differential equations. Solution methods for first order differential equations and analysis of properties of solutions (graphs). Applications to real life situations.
Module content:
Animal classification, phylogeny, organization and terminology. Evolution of the various animal phyla, morphological characteristics and life cycles of parasitic and non-parasitic animals. Structure and function of reproductive, respiratory, excretory, circulatory and digestive systems.
Module content:
*Students are not allowed to earn credits for WKD 155 and WKD 164
Introduction to weather and climate. Climate of South Africa. Urban and rural climate. Meteorological instruments. Motion of the earth. Atmospheric mass and pressure. Energy and heat budget. Moisture in the atmosphere. Cloud development. Climate change. ENSO. Electromagnetic spectrum and remote sensing in meteorology. Synoptic weather systems of South Africa.
Minimum credits: 144
Minimum credits:
Core = 48
Elective = 96
Additional information:
Electives in the second year of study can be chosen from modules in the following departments: Geography, Geoinformatics and Meteorology, Geology, Zoology and Entomology, Physics, Plant Science, Computer Science, Mathematics and Applied Mathematics.
Module content:
Theory: Classical chemical thermodynamics, gases, first and second law and applications, physical changes of pure materials and simple compounds. Phase rule: Chemical reactions, chemical kinetics, rates of reactions.
Module content:
Theory: Statistical evaluation of data, gravimetric analysis, aqueous solution chemistry, chemical equilibrium, precipitation-, neutralisation- and complex formation titrations, redox titrations, potentiometric methods, introduction to electrochemistry.Module content:
Theory: Resonance, conjugation and aromaticity. Acidity and basicity. Introduction to 13C NMR spectroscopy. Electrophilic addition: alkenes. Nucleophilic substitution, elimination, addition: alkyl halides, alcohols, ethers, epoxides, carbonyl compounds: ketones, aldehydes, carboxylic acids and their derivatives.
Module content:
Theory: Atomic structure, structure of solids (ionic model). Coordination chemistry of transition metals: Oxidation states of transition metals, ligands, stereochemistry, crystal field theory, consequences of d-orbital splitting, chemistry of the main group elements, electrochemical properties of transition metals in aqueous solution, industrial applications of transition metals.Fundamentals of spectroscopy and introduction to IR spectroscopy.
Module content:
Structural and ionic properties of amino acids. Peptides, the peptide bond, primary, secondary, tertiary and quaternary structure of proteins. Interactions that stabilise protein structure, denaturation and renaturation of proteins. Introduction to methods for the purification of proteins, amino acid composition, and sequence determinations. Introduction to enzyme kinetics and enzyme inhibition. Allosteric enzymes, regulation of enzyme activity, active centres and mechanisms of enzyme catalysis. Examples of industrial applications of enzymes. Practical training in laboratory techniques and Good Laboratory Practice. Techniques for the quantitative and qualitative analysis of biological molecules. Processing and presentation of scientific data.
Module content:
Biochemistry of carbohydrates. Thermodynamics and bioenergetics. Glycolysis, citric acid cycle and electron transport. Glycogen metabolism, pentose-phosphate pathway, gluconeogenesis and photosynthesis. Practical training in study and analysis of metabolic pathways and enzymes. Scientific method and design: Hypothesis design and testing, method design and scientific controls.
Module content:
Biochemistry of lipids, membrane structure, anabolism and catabolism of lipids. Nitrogen metabolism, amino acid biosynthesis and catabolism. Biosynthesis of neurotransmitters, pigments, hormones and nucleotides from amino acids. Catabolism of pureness and pyrimidines. Therapeutic agents directed against nucleotide metabolism. Examples of inborn errors of metabolism of nitrogen containing compounds. The urea cycle, nitrogen excretion. Practical training in scientific writing skills: evaluation of a scientific report. Techniques for separation and analysis of biological molecules
Module content:
Biochemistry of nutrition and toxicology. Proximate analysis of nutrients. Review of energy requirements and expenditure. Respiratory quotient. Requirements and function of water, vitamins and minerals. Interpretation and modification of RDA values for specific diets, eg growth, exercise, pregnancy and lactation, aging and starvation. Interactions between nutrients. Comparison of monogastric and ruminant metabolism. Cholesterol, polyunsaturated, essential fatty acids and dietary anti-oxidants. Oxidation of fats. Biochemical mechanisms of water- and fat-soluble vitamins and assessment of vitamin status. Mineral requirements, biochemical mechanisms, imbalances and diarrhoea. Biochemistry of xenobiotics: absorption, distribution, metabolism and excretion (ADME); detoxification reactions: oxidation/reduction (Phase I), conjugations (Phase II), export from cells (Phase III); factors affecting metabolism and disposition. Toxic responses: tissue damage and physiological effects, teratogenesis, immunotoxicity, mutagenesis and carcinogenesis. Examples of toxins: biochemical mechanisms of common toxins and their antidotes. Antibiotics and resistance. Natural toxins from fungi, plants and animals: goitrogens, cyanogens, cholineesterase inhibitors, ergotoxin, aflatoxins Practical training in analyses of nutrients, fatty acids separations, antioxidant determination, and enzyme activity measurements, PO ratio of mitochondria, electrophoresis, extraction, solubility and gel permeation techniques.
Module content:
Origin and affinity of South African flora and vegetation types; principles of plant geography; plant diversity in southern Africa; characteristics, environments and vegetation of South African biomes and associated key ecological processes; centra of plant endemism; rare and threatened plant species; biodiversity conservation and ecosystem management; invasion biology; conservation status of South African vegetation types.
Module content:
Nitrogen metabolism in plants; nitrogen fixation in Agriculture; plant secondary metabolism and natural products; photosynthesis and carbohydrate metabolism in plants; applications in solar energy; plant growth regulation and the Green Revolution; plant responses to the environment; developing drought tolerant and disease resistant plants.
Module content:
Orientation in physiology, homeostasis, cells and tissue, muscle and neurophysiology, cerebrospinal fluid and the special senses.
Practical work: Practical exercises to complement the theory.
Module content:
Body fluids; haematology; cardiovascular physiology and the lymphatic system. Practical work: Practical exercises to complement the theory.
Module content:
Structure, gas exchange and non-respiratory functions of the lungs; structure, excretory and non-urinary functions of the kidneys, acid-base balance, as well as the skin and body temperature control.
Practical work: Practical exercises to complement the theory.
Module content:
Nutrition, digestion and metabolism; hormonal control of the body functions and the reproductive systems. Practical work: Practical exercises to complement the theory.
Module content:
The nature of geographical data and measurement.Application of statistics in the geographical domain. Probability, probability distributions and densities, expected values and variances, Central Limit theorem. Sampling techniques. Exploratory data analysis, descriptive statistics, statistical estimation, hypothesis testing, correlation analysis and regression analysis.
Module content:
Origin and development of soil, weathering and soil formation processes. Profile differentiation and morphology. Physical characteristics: texture, structure, soil water, atmosphere and temperature. Chemical characteristics: clay minerals, ion exchange, pH, buffer action, soil acidification and salinisation of soil. Soil fertility and fertilisation. Soil classification. Practical work: Laboratory evaluation of simple soil characteristics. Field practicals on soil formation in the Pretoria area.
Module content:
Chemical nature of DNA. Replication transcription, RNA processing and translation. Control of gene expression in prokaryotes and eukaryotes. Recombinant DNA technology and its applications in gene analysis and manipulation.
Module content:
Chromosome structure and transposable elements. Mutation and DNA repair. Genomics and proteomics. Organelle genomes. Introduction to genetic analysis of populations: allele and genotypic frequencies, Hardy Weinberg Law, its extensions and implications for different mating systems. Introduction to quantitative and evolutionary genetics.
Module content:
Growth, replication and survival of bacteria, Energy sources, harvesting from light versus oxidation, regulation of catabolic pathways, chemotaxis. Nitrogen metabolism, iron-scavenging. Alternative electron acceptors: denitrification, sulphate reduction, methanogenesis. Bacterial evolution, systematic and genomics. Biodiversity; bacteria occurring in the natural environment (soil, water and air), associated with humans, animals, plants, and those of importance in foods and in the water industry.
Module content:
Organisation and molecular architecture of fungal thalli, chemistry of the fungal cell. Chemical and physiological requirements for growth and nutrient acquisition. Mating and meiosis; spore development; spore dormancy, dispersal and germination. Fungi as saprobes in soil, air, plant, aquatic and marine ecosystems; role of fungi as decomposers and in the deterioration of materials; fungi as predators and parasites; mycoses, mycetisms and mycotoxicoses; fungi as symbionts of plants, insects and animals. Applications of fungi in biotechnology.
Module content:
This is an introduction to linear algebra on Rn. Matrices and linear equations, linear combinations and spans, linear independence, subspaces, basis and dimension, eigenvalues, eigenvectors, similarity and diagonalisation of matrices, linear transformations.
Module content:
Calculus of multivariable functions, directional derivatives. Extrema and Lagrange multipliers. Multiple integrals, polar, cylindrical and spherical coordinates.
Module content:
Properties of real numbers. Analysis of sequences and series of real numbers. Power series and theorems of convergence. The Bolzano-Weierstrass theorem. The intermediate value theorem and analysis of real-valued functions on an interval. The Riemann integral: Existence and properties of the interval.
Module content:
Abstract vector spaces, change of basis, matrix representation of linear transformations, orthogonality, diagonalisability of symmetric matrices, some applications.Module content:
Setting up and solving recurrence relations. Equivalence and partial order relations. Graphs: paths, cycles, trees, isomorphism. Graph algorithms: Kruskal, Prim, Fleury. Finite state automata.
Module content:
*Students will not be credited for more than one of the modules for their degree: WTW 264, WTW 286
Theory and solution methods for ordinary differential equations and initial value problems: separable and linear first-order equations, linear equations of higher order, systems of linear equations. Application to mathematical models. Numerical methods applied to nonlinear systems.Qualitative analysis of linear systems.
Module content:
An urbanising world. Urban structure and land use. Urban processes. The urban environment. Social structure and change in cities. Living in the city. Economy, society and politics in the city. Third-world cities and South African cities. Urban futures.
Module content:
Vectors and geometry. Calculus of vector functions with applications to differential geometry, kinematics and dynamics. Vector analysis, including vector fields, line integrals of scalar and vector fields, conservative vector fields, surfaces and surface integrals, the Theorems of Green, Gauss and Stokes with applications.
Minimum credits: 144
Minimum credits:
Core = 72
Elective = 72
Module content:
Theory: Molecular quantum mechanics. Introduction: Shortcomings of classical physics, dynamics of microscopic systems, quantum mechanical principles, translational, vibrational and rotational movement. Atomic structure and spectra: Atomic hydrogen, multiple electron systems, spectra of complex atoms, molecular structure, the hydrogen molecule ion, diatomic and polyatomic molecules, structure and properties of molecules. Molecules in motion: Viscosity, diffusion, mobility. Surface chemistry: Physisorption and chemisorption, adsorption isotherms, surface tension, heterogeneous catalytic rate reactions, capillarity.
Module content:
Theory: Separation methods: Extraction, multiple extraction, chromatographic systems. Spectroscopy: Construction of instruments, atomic absorption and atomic emission spectrometry, surface analysis techniques. Mass spectrometry. Instrumental electrochemistry.
Module content:
Theory: NMR spectroscopy: applications. Aromatic chemistry, Synthetic methodology in organic chemistry. Carbon-carbon bond formation: alkylation at nucleophilic carbon sites, aldol and related condensations, Wittig and related reactions, acylation of carbanions (Claisen condensation).
Module content:
Theory: Structure and bonding in inorganic chemistry. Molecular orbital approach, diatomic and polyatomic molecules, three-centre bonds, metal-metal bonds, transition metal complexes, magnetic properties, electronic spectra, reactivity and reaction mechanisms, reaction types, acid-base concepts, non-aqueous solvents, special topics.
Module content:
*Note: The content of this module is the same as GGY 361 and students are not allowed to earn credits for both GGY 361 and GGY 363.
Interactions of geomorphic processes within the physical and built environments; themes such as geomorphology and environmental change, slope processes and the environment, geomorphic risks and hazards, soil erosion and conservation, geomorphology in environmental management, applied weathering.
Module content:
Advanced theory and practice of Geographic Information Systems; GIS applications; design and implementation of GIS applications.
Module content:
Construction of Raster Geovisualisations, spatial model construction and use, multi-criteria decision analysis. Factor analysis: Principle component analysis. Geostatistics: Spatial dependence modelling, ordinary kriging. Markov chains and cellular Automata, combined models.A project or assignments of at least 64 notional hours.
Module content:
Direct methods for the numerical solution of systems of linear equations, pivoting strategies. Iterative methods for solving systems of linear equations and eigenvalue problems. Iterative methods for solving systems of nonlinear equations. Introduction to optimization. Algorithms for the considered numerical methods are derived and implemented in computer programmes. Complexity of computation is investigated. Error estimates and convergence results are proved.
Module content:
Axiomatic development of neutral, Euclidean and hyperbolic geometry. Using models of geometries to show that the parallel postulate is independent of the other postulates of Euclid.
Module content:
The module conceptually integrates environmental, economic, and social components of sustainable development. Other topics covered include changing perceptions on development and environment, development paradigms, challenges of sustainable development, actors and actions in sustainable development, rural and urban livelihoods, and a Third World assessment of sustainable development in the developing world.
Module content:
Classic development frameworks. Spatial development history and legacy in South Africa. Overview of contemporary environmental legislation in South Africa. Rural development strategy. Rural and agricultural reconstruction. Land reform. Urban development and strategy. Urban spatial reconstruction. National spatial development frameworks.
Module content:
Perspectives on the flow of information from nucleic acids to proteins, the structure and functions of nucleic acids and proteins and their organisation into hierarchical, interdependent systems. Nucleic acid structure as observed in fibres and crystals as well as global DNA and RNA analyses (methods and bioinformatic analyses). Biochemical analyses of nucleotides. DNA-DNA recognition: non-standard and higher order DNA structures. The RNA structural world, RNAi, miRNA and ribosomes. Cellular functions of coding and non-coding nucleic acids. Principles of small molecule-DNA recognition. Principles of protein-DNA recognition and interactions. Bioinformatics predictions of protein and small molecule DNA interactions. Chemical reactivity of amino acids. Domain structures of proteins and Ramachandran plots. Protein folding, sequence motifs and domains, higher order and supramolecular structure, self-assembly, conjugated proteins, post-translational modifications, conjugated proteins and bioinformatics predictions. Principles of protein function and protein structure relationships. Protein-ligand and protein-protein interactions. Protein aggregation in disease. Examples of the diverse functions of proteins and peptides, including enzymes, hormones, neurotransmitters, antibodies, receptors, transport and membrane proteins. Global analysis of proteins through proteomics. Basic principles of nuclear magnetic resonance, mass spectrometry and X-ray crystallography. Protein purification and characterization including, pI, molecular mass, amino acid composition and sequence. Practical training will include interactive computer-guided demonstrations of protein analysis, hands-on practical sessions for nucleic acid purification and chemical structure characterisation, protein expression and purification (including SDS-PAGE), protein sequence analysis including mass spectrometry, protein structure analysis by 3D protein modelling and protein folding (Bioinformatics).
Module content:
Nomenclature: enzyme nomenclature and classification. Specificity and mechanisms: the active site, mechanisms of catalysis and examples of specific enzyme mechanisms, e.g. lysozyme and carboxypeptidase A. Advanced enzyme kinetics, Cleland nomenclature and multi-substrate reactions. Allosteric enzymes: models by Koshland, Hill and Monod. Ligands binding to proteins. Problems and answers: tutorials of problems and answers based on above concepts. Integration of metabolism; hormones and second messengers; cell signalling; a case study in connectivity among metabolic pathways and their regulation, in for example diabetes and starvation. Inhibitors of angiotensin converting enzyme (ACE). RNA as enzymes. Applications of enzymes in food and cosmetics industries and in clinical pathology assays as biomarkers of diseases and toxic responses. Elucidation of metabolic pathways.
Practical sessions cover tutorials on calculations, isolation of an enzyme, determination of pH and temperature optimum, determination of Km and Vmax, enzyme activation, enzyme inhibition, purification table and final report, oral defense of report.
Module content:
Visualising cell structure and localising proteins within cells. Cell ultrastructure. Purification of subcellular organelles. Culturing of cells. Diversity and commonality of cells. Biomembrane structure. Transmembrane transport of ions and small molecules. Moving proteins into membranes and organelles. Vesicular traffic, secretion, exocytosis and endocytosis. Cell organisation and movement. Cell-cell and cell-matrix adhesion. Practical training includes tutorials on cytometry and mircoscopy, mini-research projects where students are introduced and guided through aspects of research methodology, experimental planning as well as techniques associated with cellular assays. Active transport studies in yeast cells.
Module content:
Normal and abnormal regulation of the cell cycle: The biochemistry of proliferation, quiescence, senescence, differentiation and apoptosis, illustrated by cancer. Host-Pathogen co-evolution: How adaptive immunity emerged from innate immunity. Infection: Molecular and cellular immunobiochemistry of protection against viral, bacterial and parasitic pathogens. Auto-immunity: Molecular mechanisms of the maintenance and failure of the recognition of foreign in the context of self in the mammalian body. Practical training includes debate on ethics of research on animal and human diseases, experimental design and execution of an immunoassay to test for a biomarker antibody of an infectious disease, tutorials to determine the performance of a diagnostic test for disease, including the principle of ROC curve analysis, positive and negative predictiveness, sensitivity, specificity and accuracy, applications of polyclonal and monoclonal antibodies for characterisation of disease with fluorescence, confocal and electron microscopy, flow cytometry and biosensors.
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