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.

Unit of Study Overview

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 intending to apply protein techniques to other biological or medical problems. The lectures and laboratory classes undertaken in Protein Biochemistry will enhance the understanding of many concepts taught in subjects such Immunology, Pharmacology, Cell Biology and Physiology.

BCHM2971 is the advanced course and covers all the lecture material in the normal (BCHM2071) course but is extended by extra topics. It is also designed to cover some of the material in more depth.

Course Coordinator Contact Details

Dr Sandro Ataide

Room 672, Molecular Bioscience Building,

Telephone: 9351 7817

E-mail: sandro.ataide@sydney.edu.au

Prerequisites

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

Timetable

1st Lecture: Wednesday 10:00am Pharmacy Lecture Theatre (Room N342)
2nd Lecture: Friday 10:00am Eastern Avenue Lecture Theatre

Practicals: Practical sessions & tutorials on one of Tue, Wed, Thu, Fri 1:00pm-5:00pm in Room 302

Lecture Outlines

Lecture Theme 1: Introduction to proteins (17 lectures)

  1. Introduction lecture.Proteins: their place in central dogma; introduction to structure and function
  2. Introduction to globular and fibrous proteins; determining the sequence of a peptide, evolutionary relationships from protein sequences
  3. Protein synthesis, folding and degradation. Folding as a balance of forces - thermodynamics. The generation of 'regular' structure - α-helices and β-pleated sheets. Defining the shape of a protein - 'Ramachandran plot'. Protein assemblies. Quaternary structure and protein oligomers. Protein interactions and interfaces.
  4. Protein purification methods: chromatography, electrophoresis and dialysis.
  5. Globular proteins: closer look at structure and function relationships of protein using haemoglobin and myoglobin as examples- dioxygen binding, carbon dioxide transport, carbon monoxide poisoning, Bohr effect, foetal haemoglobin, diseases relating to changes in Hb structure(also advanced).. Post-translational modifications.
  6. Fibrous proteins: structure and functions, major structural subclasses including keratin, collagen, silk fibroin. Disease relating to the structural changes of these proteins (also advanced).
  7. Fibrous proteins: the major structural subclasses including, keratin, collagen, silk fibroin (also advanced).
  8. Role of proteins in biological membranes: membrane composition and properties; interaction with lipids, fatty acids, carbohydrates Structure of the lipid bilayer. Intrinsic and peripheral membrane proteins (also advanced).
  9. Membrane proteins: folding and structure, intrinsic peripheral and anchored proteins Communication and transport across membranes. (also advanced)
  10. Role of proteins in communication and transport across membranes: energetics; carriers and channels; carriers and pumps (also advanced).
  11. Signaling across membranes. G-protein coupled receptors and receptor tyrosine kinases, integrins. Focus on the structural features of the receptors and signaling proteins (also advanced).
  12. Motor proteins: ATPsynthase as a model for a rotary motor; kinesin and cargo transport. Myosin and muscles.
  13. GFP and friends: from jellyfish to fluorescent mice. Conotoxins: feeding frenzies to the clinic.Inteins: protein splicing. Antibodies: generating diversity, binding targets, catalytic antibodies, therapeutic antibodies.
  14. Glycosylation of proteins (outline TBA)
  15. Glycosylation of proteins
  16. Glycosylation of proteins
  17. Glycosylation of proteins

Lecture Theme 2: Enzymology (8 lectures)

  1. Properties of enzymes: active site, specificity, proximity effect, orbital steering, free-energy profile for reaction, activation energy, thermodynamics, rate enhancement versus chemical reaction.
  2. Catalytic mechanisms of serine proteases, HIV aspartyl protease, carboxypeptidase A, ribonuclease A, β-lactamase and dihydroorotase.
  3. Transition-state theory: thermodynamics, transition state analogues, oxyanion hole in serine proteases, induced conformational changes
  4. Acid-base catalysis, pH-activity profiles, zinc enzymes
  5. Enzyme inhibitors as drugs, mechanisms of drug resistance.
  6. Assays for kinetic analysis of enzymes, measurement of initial reaction velocities
  7. Enzyme kinetics: the Michaelis-Menten equation, Lineweaver-Burk plot, positive and negative cooperativity, the steady-state assumption, derivation of velocity equations from models, fitting of data by non-linear regression.
  8. Enzyme kinetics: kinetic analysis of enzyme inhibitors, dissociation constants of substrates and inhibitors, inhibition patterns, competitive, non-competitive and uncompetitive inhibition, tight-binding inhibitors, slow tight-binding inhibitors. Chirality and enzymes; prochiral substrates (aconitase), D-form of HIV protease. Regulation of enzymes, zymogens (chymotrypsinogen), competitive inhibitors (BPTI). Protein conformation and regulation, intrasteric control (PKA). Allosteric regulation glycogen phosphorylase, feedback and metabolic control

Practical Course

P1A: Spectrophotometry for Proteins
P1B: Methods of Protein Determination
P3: Protein Modelling and Structure (tutorial session)
P4A: Protein Fractionation I
P4B: Protein Fractionation II
P5A: Enzyme Kinetics & Analysis I
P6 - Enzyme mechanism of action.

Assessment

Marks breakdown: 60% theory, 20% practical, 20% theory of practical

Tasks: One 2.5 hour theory and theory of practical exam, 2 in-semester one hour quizzes, In-semester electronically submitted laboratory assignments, continuous assessment during practical classes.