Module Framework: Biochemistry 344 - 2004

  1. Name and code of the module

    Biochemistry 344 - Advanced Biochemical Topics II
    11053 344

    The module consists of 3 theory sections - Section A: Membrane biochemistry (13 lectures), Section B: Signal transduction (13 lectures), Section C: Immunology (13 lectures) - and the Practical. Various lecturers are responsible for the different sections. All the administrative issues concerning this module will be handled by a module convenor.

  2. Lecturers and contact details

    Module convenor: Membrane biochemistry Signal transduction:
    Prof JM Rohwer Dr A Louw Prof JP Hapgood
    Room A108, JC Smuts Building Room A119, JC Smuts Building Room A123, JC Smuts Building
    Tel.: 021 808-5843 Tel.: 021 808-5873 Tel.: 021 808-5866
    Email: jr@sun.ac.za Email: al@sun.ac.za Email: jhap@sun.ac.za
     
    Immunology: Practical:  
    Prof DU Bellstedt Dr AC Swart Ms RP Louw
    Room A165, JC Smuts Building Room A120, JC Smuts Building Lab A139, JC Smuts Building
    Tel.: 021 808-5840 Tel.: 021 808-5864 Tel.: 021 808-5877
    Email: dub@sun.ac.za Email: acswart@sun.ac.za Email: rpl@sun.ac.za

  3. Objectives of the module

    This module consists of advanced topics all of which are study fields in their own right, but in this module concepts taught in each topic are expanded upon in the next topic. Each topic has its own objectives as listed below:

    Membrane biochemistry
    An overview of membrane structure and characteristics. Comparison of transport systems in terms of type of molecules transported, the mechanism of transport, and the thermodynamics and kinetics of transport. The co-operation of the different transport systems in the context of biology in general and the manipulation of these systems for medical and experimental purposes will be emphasized.
    Signal transduction
    A functional understanding of intracellular signalling pathways: the communication networks that coordinate all cellular processes from membrane to nucleus.
    Immunology
    An overview of the immunology of vertebrates with an emphasis on human immunology. All immunological mechanisms involve cell signalling mechanisms and this section therefore builds on signal transduction course.
    Practical
    Students perform two immunological techniques, ELISA (enzyme-linked immunoassay) and the Western Blot method. The underlying theory of immunological techniques is covered. The acquisition of practical laboratory skills, writing skills, the scientific interpretation and presentation of experimental data form an important component of the practical module.

  4. Outcomes of the module

    Knowledge Based

    The student should, with reference to the text (i.e. open book), be able to:

    Membrane Biochemistry (text includes six review articles)

    1. Explain the molecular basis for self-assembly of membranes and list the characteristics of the fluid-mosaic model of membrane structure.
    2. Compare membrane proteins by discussing the molecular basis of the interactions with the lipid bilayer and the structural motifs involved and explain how lipid composition influences membrane fluidity.
    3. Identify the type and mechanism of transport involved for any given transporter and compare different transporters according to specific criteria.
    4. Identify or predict, quantify, and graphically represent all of the thermodynamic and kinetic forces involved in any transport process across biological membranes.
    5. Define the meaning of each term in the Fick, Michaelis-Menten, Nernst or Goldman equations, determine under which conditions each equation would be used, and apply these equations in calculations.
    6. Defend a prediction of structure-function activity of any given transporter given the primary structure for the ligand binding sites of transporters plus information about highly conserved residues, ligand specificity and affinity (Kd), and inhibitor sensitivity using the basic properties of the amino acids involved.
    7. Assess the effects of specific inhibitors or ionophores on particular transport systems, on the membrane potential, or on transport systems working in concert within the context of physiological systems or design or interpret experiments using these inhibitors or ionophores to dissect physiological systems comprising the interaction of several transport systems or to identify a particular transport system.
    8. Explain how transporters of different types work in concert within the context of physiological systems and in this context evaluate the use of certain medical treatment regimes

    Signal Transduction

    1. Define, describe and summarize, and compare the mechanism of action and role in intracellular signalling of the most important mammalian signalling mechanisms with an emphasis on the role specific protein domains play in these interactions.
    2. Explain, by giving examples, how a coordinated regulatory pathway, involving both kinases and phosphatases, regulates glycogen breakdown.
    3. Compare (similarities and differences) the major types of kinases involved in various pathways, with respect to subunit structure, mechanism of activation, specificity and target proteins, and give examples of responses mediated by the kinase.
    4. Interpret, analyse or design experiments to determine which intracellular signalling pathways, and the key components thereof, are involved in a particular system.
    5. Interpret graphical data, which show the relationship between binding of ligand to a receptor, fractional occupancy of the receptor and physiological response.

    Immunology

    1. Explain how the innate immune mechanisms as opposed to the specific acquired immune mechanisms fight off pathogens and their limitations.
    2. Explain specific acquired immune mechanisms of pathogen attack and how these systems overcome the limitations of innate immunity.
    3. With regard to antibodies explain their structure and their function as specific recognition molecules and activators of innate immune mechanisms.
    4. With regard to T-cells explain how they serve as specific recognition cells and how they can attack pathogens.
    5. Explain that immune memory (both antibody and T-cell) is built up and forms the basis of vaccination procedures.
    6. Explain how B-cells and T-cells are activated through extra- and intracellular signalling.
    7. Describe various immunodeficiencies with specific emphasis on the role played by HIV in AIDS and the role of immediate type hypersensitivity reactions in allergic reactions.

    Practical

    1. Explain the practical applications of antibodies in selected immunological techniques (enzyme-linked immunoassay and Western blotting).
    2. Execute the above immunological techniques.
    3. Plan the execution of an experiment, calculate dilutions, process and interpret data, present experimental data in a written report.

    Generic

    After completing this module, the student should be able to:

    1. Take responsibility for own learning.
    2. Learn to focus on and understand the "big picture" and concepts, and know where to find the details.
    3. Integrate, apply and synthesise information, including placing the material in the broader context of this module, other modules (Physiology, Genetics, Microbiology), medicine and science.
    4. Appreciate and understand the nature of the experimental based scientific process of discovery.
    5. Access information on the web and CD rom.
    6. Solve problems
    7. Use textbooks.
    8. Have gained writing skills.

  5. Language specification

    T

  6. Compulsory study material

    • Compendium of Study Material provided by Content Solutions.
    • Roitt, I. & Rabson, A. (2000) Really Essential Medical Immunology, Blackwell Scientific Publishers, 1st edition.
    • Wilson, K. & Walker, J. (2000) Principles and Techniques of Practical Biochemistry, Cambridge University Press, 5th edition.
    • Optional text book: Lodish, H. et al. (2000) Molecular and Cell Biology, W.H. Freeman & Co., 4th edition.
    • Optional text book: Voet, D. & Voet, J.G. (1995) Biochemistry, 2nd Edition, John Wiley & Sons Inc.
           OR
      Voet, D. & Voet, J.G. (2004) Biochemistry. Volume 1, Biomolecules, Mechanism Of Enzyme Action And Metabolism, 3rd Edition. John Wiley & Sons, Inc.

  7. Learning opportunities

    Lectures: all lectures are in lecture hall A203, JC Smuts Building
      Monday 10:00-10:50 (3rd period)
      Tuesday 08:00-08:50 (1st period)
      Friday 11:00-11:50 (4th period)
     
    Practicals: Wednesday afternoon 14:00-17:00
      Timetable and group allocation will be handed out by Dr AC Swart.
     
    Tutorials: Timetable will be announced later.

  8. Assessment

    Assessment in this course is sub-divided into self-assessment and formal assessment.

    Formal assessment

    Continuous assessment is used in this course as opposed to a course mark and an examination. Every assessment opportunity counts a percentage towards the final mark.

    1. Means of assessment

      Assessment of the theoretical sections in two open book tests in which the emphasis is on application of the subject knowledge in solving problems, and not merely on the knowledge itself.

      • Written test in the mid-semester test series (on Membrane Biochemistry and Signal Transduction)
      • Written test during November exam-time (on Signal Transduction and Immunology)

      Assessment of practical

      • Flow chart and reports on ELISA and Western blot experiments
      • Written test on practical towards the end of the semester

    2. Place and time of assessment opportunities

      Theory

      • Mid-semester test on 01/09/2004 at 19h00 in the First-Year Chemistry Building (lower and upper lecture halls)
      • Test during exam time on 16/11/2004 at 19h00 in the First-Year Chemistry Building

      Practial

      • Written test on practical on 27/10/2004 at 14h00 in the First-Year Chemistry Building

    3. Turnaround time and format of feedback

      Where at all possible, assignments and tests will be marked within 3 weeks and handed back to the students.

    4. Calculation of final mark

      The theory counts 70% and the practical counts 30% towards the final mark. There is a pass subminimum for both the theory and the practical components of the module. This means that if you obtain less than 50% for either the theory or the practical, you will fail Biochemistry 344 in its entirety!

      The theory mark (in total 70% of the final mark) is comprised as follows:

      • Mid-semester test (23.3% Membrane Biochemistry and 11.7% Signal Transduction)
      • Test during exam time (11.7% Signal Transduction and 23.3% Immunology)

      The practical component accounts for 30% of the final mark:

      • Flow chart and practical reports (15%)
      • Written test on practical (15%)

    Self assessment

    • Two tutorials on membrane biochemistry with self-assessment by means of a memorandum.
    • Two tutorials on signal transduction with self-assessment by means of a memorandum.
    • Tutorial on immunology with self-assessment by means of a memorandum.

  9. Other special requirements

    If you have missed an assessment opportunity as a result of illness, you have to hand in a doctor's certificate to the module convenor within 7 days, in order to be admitted to a supplementary test.

    Supplementary (“siekte”) test

    There will only be one supplementary test for the theory section. This will be on all the work and will be written on Monday 22 November 2004 from 14h00–17h00. Everyone who has missed one assessment opportunity will be required to write this supplementary test. Students who have missed two assessment opportunities, will additionally have to take an oral examination on the work.