BCHM2071/2971

Protein Biochemistry

Course Information

These course outlines are a guide only. They are provided for the information of prospective students. Although every effort is made to ensure the most up to date information is provided, timetables often change each semester due to the availability of rooms and resources. Content (including lecture/practical topics, assessment and textbooks) is also regularly reviewed to ensure relevance and effective learning.

BCHM2071 extends the basic concepts of protein science introduced at the beginning of MBLG1001. It provides a firm foundation for students wishing to continue in biochemistry, molecular biology and biotechnology as well as for those students who intend to apply protein techniques in solving other biological or medical problems. BCHM2971 is the advanced option of the course.

BCHM2971 is the advanced course and covers all the lecture material in the normal (BCHM2071) course but is extended by four extra topics. The advanced practical course contains a number of modified laboratory experiments designed to cover some of the material in more depth.

A/Prof Charles Collyer

Room 671, Biochemistry & Microbiology Building,

Telephone: 9351 2794

E-mail: C.Collyer@mmb.usyd.edu.au

MBLG1001 (D+ required for BCHM2971) and 12credit points of Junior Chemistry

1st Lecture: Monday 10:00am Carslaw Lecture Theatre 375
2nd Lecture: Wednesday 10:00am Carslaw Lecture Theatre 375
For BCHM 2971: Monday 10:00am for weeks 4, 5, 12 and Wednesday 10:00am for weeks 4, 11, 12 only in Eastern Avenue Seminar Room 116

Practicals: Monday or Wednesday 1:00pm-6:00pm fortnightly in Room 380

Pratt, CW & Cornely, K. Essential Biochemistry. John Wiley & Sons. 2004.

The Resource Manual for Biochemistry 2 Practical Sessions, Sem 1

Lecture Theme 1: Introduction to proteins (10 lectures + 2 revision)

1. Proteins: their place in the dogma of molecular biology; diversity of roles; structure-function relationships; as biopolymers of amino acids, the peptide bond, diversity of amino acids.
2. Primary structure defines a protein. Determining the sequence of a peptide. Evolutionary relationships in protein sequences.
3. Protein synthesis, folding and degradation. Folding as a balance of forces - thermodyanimcs. The generation of 'regular' structure - α-helices and β-pleated sheets. Defining the shape of a protein - 'Ramachandran plot'.
4. Globular proteins: evolutionary relationships of domains and families. Post-translational modifications.
5. Protein purification. Chromatography, electrophoresis; dialysis.
6. Fibrous proteins: the major structural subclasses including, keratin, collagen, silk fibroin.
7. Membrane proteins. Structure of the lipid bilayer. Communication and transport across membranes. Intrinsic and peripheral membrane proteins.
8. Protein assemblies. Quaternary structure and protein oligomers. Protein interactions and interfaces.
9. Myoglobin and haemoglobin: an 'in depth' study of structure and function. Dioxygen binding; carbon dioxide transport; carbon monoxide poisoning; the Bohr effect; foetal haemoglobin.
10. Motor proteins: ATPsynthase as a model for a rotary motor; kinesin and cargo transport; myosin and muscles.

Lecture Theme 2: Enzymology (10 lectures + 2 revision)

1. Catalytic mechanism of serine proteases: The transition state in enzymatic catalysis and the lowering of the free energy of activation; oxyanion hole and the Transition state
2. How do we measure enzyme function? Developing the Michaelis-Menten relationship.
3. Analysis of enzyme kinetics and measuring the strength of the binding of inhibitors.
4. Preorganisation; substrate selectivity, proximity and orientation in serine proteases. Enzymatic catalysis and destabilising the Michaelis complex, the induced fit hypothesis; lysozyme.
5. Acid base catalysis - triose phosphate isomerase
6. Chirality and enzymes; prochiral substrates (aconitase), D-form of HIV protease.
7. The pKa's of side chains of amino acids in folded proteins (aspartate proteases); HIV protease vs pepsin.
8. Selecting a reaction pathway and stable intermediates; chymotrypsin vs pepsin, aconitase vs triose phosphate isomerase
9. Regulation of enzymes, zymogens (chymotrypsinogen), competitive inhibitors (BPTI)
10. Protein conformation and regulation, intrasteric control (PKA). Allosteric regulation and the MWC (symmetric) model (PFK). Effector molecules, feedback and metabolic control

Advanced lectures : (4 lectures)

1. GFP and friends: from jellyfish to fluorescent mice
2. Conotoxins: feeding frenzies to the clinic. Highly constrained structures and modified amino acids, probing ion channel function, pain relief.
3. Inteins: protein splicing
4. Antibodies: generating diversity, binding targets, catalytic antibodies, therapeutic antibodies

P1 - Methods of Protein Determination
P2 - Protein Modelling and Structure
P3A - Protein Fractionation I
P3B - Protein Fractionation II
P4 - Enzyme Kinetics & Analysis.
P5 - Enzyme mechanism of action.

Marks breakdown: 50% theory, 35% practical, 15% theory of practical

Tasks: One 2 hour theory and theory of practical exam, 2 in-semester theory quizzes, 2 in-semester hand-in laboratory assignments, continuous assessment during practical classes and laboratory book hand-in for final assessment.