Topic list - Amino Acids, Proteins, Enzymology

  1. Neutral amino acids: Optical activity (enantiomers, diastereomers). Grouping principles (aliphatic and aromatic side chains, branched chain amino acids, sulfur containing amino acids). Acid-base character of neutral amino acids (protonic equilibria, isoelectric point, titration curve of alanine).
  2. Neutral amino acids: polar side chains. Hydrogen bonds between side chains (examples!). Aromatic side chains in amino acids: their hydrophobic or hydrophilic character. Biologically important derivatives of tyrosine (thyroxine, dopamine, noradrenaline, adrenaline). Biogen amines.
  3. Acidic amino acids. Calculation of isoelectric point. Titration curve of aspartic acid. Comparison of acidity of different side chains and the a-carboxyl group. Amides of aspartic and glutamic acid.
  4. Basic amino acids. Calculation of isoelectric point. Comparison of basicity of amine and imine groups in amino acids. Titration curve of arginine. Which of common amino acids has buffering capacity at neutral pH?
  5. Peptides. Formation and properties of the peptide bond (cis and trans configuration of a peptide bond). Ionic side chains, possible charges on a peptide, dependence of the net charge on pH. Isoelectric point of peptides and proteins. The structure of glutathione.
  6. Proteins: conformation. Definition of primary, secondary, tertiary and quaternary structure, types of bonds and interactions at each level. Ramanchandran plot. α-helix, parallel and antiparallel ß-sheets.
  7. Fibrous proteins. α-keratin, silk fibroin and collagen. The collagen helix. Post-translational modification (hydroxylation). Defective hydroxylation in scurvy. Procollagen, tropocollagen, collagen fiber (nature of Lys cross-links).
  8. Myoglobin. Structural features of the globin chain. Formula of heme, oxidation state of iron. Function of proximal and distal histidine.
  9. Haemoglobin as an allosteric protein. Oxygen saturation curves for myoglobin and haemoglobin: a comparison. Function of BPG. The Bohr-effect and its molecular mechanism. Conformational changes during oxygenation.
  10. Effect of altered amino acid sequence on protein function. Normal human haemoglobin chains, comparison of foetal form to adult forms. Abnormal human haemoglobins: neutral and harmful mutation. HgM. HbS and the sickle cell anaemia.
  11. pH and temperature dependence of enzyme activity. Definition of enzyme activity, specific enzyme activity and turnover number. Clinical importance of enzyme assays.
  12. Effect of the enzyme on the equilibrium and on the activation energy. Transition states. The active centre of the enzymes (lock and key model, induced fit model). Acid/base and covalent catalysis.
  13. Serine proteases. Proteolytic activation of zymogens. Reaction mechanism: tetrahedral transition states. Specificity of proteases (chymotrypsin, trypsin, elastase). Specific inhibitor of Ser proteases (DIPF).
  14. The Michaelis Menten model of enzyme kinetics. Initial rate. The Michaelis constant. Maximal velocity. Graphic evaluation of Vmax and KM.
  15. Isoenzymes. Definition, examples (glucokinase - hexokinase, lactate dehydrogenases).
  16. Reversible inhibition of enzymes. Competitive and non-competitive inhibition.
  17. Control of enzyme activity by allosteric activation/inactivation. Homotrope and heterotrope cooperativity (e.g. aspartate transcarbamoylase).
  18. Control of enzyme activity by reversible covalent modification. Post-translational modification of proteins (phosphorylation). Protein kinases and protein phosphatases. Complex regulation (e.g. phosphorylase kinase).