Enzymes: Basic Principles

1. Enzymes: Basic Principles SBS017 Basic Biochemistry Dr John Puddefoot J.R.Puddefoot@qmul.ac.uk

2. Objectives: • To introduce the basic concepts and definitions of enzymology • You should be able to able to define the terms Enzyme, Specificity and Co-factor • You will understand the concept of Gibbs Free Energy and its relation to reaction equilibrium • You will be able to describe how enzymes effect the rate of biological reactions and be able to define • the term Activation energy in the context of Transition state theory .

3. Enzymes • Biological catalysts • Almost all enzymes are proteins (but RNA can have enzymic activity too, “ribozymes”) • Function by stabilizing transition states in reactions • Enzymes are highly specific

4. Enzymes accelerate biologicalreactions • e.g. Carbonic Anhydrase • CO2 + H2O H2CO3 • Each molecule of enzyme can hydrate 1,000,000 molecules of CO2 per second, 10,000,000 times faster than uncatalysed reaction

5. Catalase 2H2O2 2H2O + O2

6. Rate enhancement by enzymes • Kcat- maximum number of enzymatic reactions catalyzed per second.

7. Enzymes are highly specificProteolytic enzymes

8. Hydrolysis of esters

9. Proteolytic Enzymes differ in degree of substrate specificity e.g Peptide bond hydrolysis (proteolysis) A. Trypsin cleaves only after arginine and lysine residues. B. Thrombin cleaves between arginine and glycine only in particular sequences. But Papain cleaves all peptide bonds irrespective of sequence

10. Specificity is important e.g. DNA polymerase I • Adds nucleotides in sequence determined by template strand. • Error rate of < 1 in 1,000,000 • Due to precise 3D interaction of enzyme with substrate

11. Major classes of enzymes

12. Many enzymes require cofactors • Cofactors are small molecules essential for enzyme catalysis Can be: • Coenzymes (small organic molecules) • Metal ions

13. Holoenzymes • Enzyme without its cofactor “apoenzyme” • With its cofactor “holoenzyme” • Cofactors are essential for activity e.g. many vitamins are cofactors, many diseases associated with vitamin deficiency due to lack of specific enzyme activity

14. Enzyme cofactors

15. Energy transformation • Many enzymes transform energy into different forms • Adenosine Triphosphate (ATP) is universal currency Light ATP Photosynthesis Food ATP Respiration ATP work

16. ATP is an energy carriere.g. • ATP provides energy to pump Ca2+ acrossmembranes

17. Free energy • The free energy of a reaction is the difference in free energy between its reactants and its products This called the ΔG • If ΔG is negative, the reaction will occur spontaneously “exergonic” • If ΔG is positive, energy input is required “endogonic”:

18. Endergonic reactions ………………… ΔG is positive ……………………………………………………………………..

19. Exergonic reactions …………………………………………………………………….. !G negative • ΔG is negative …………………

20. Exergonic reactions H2O2 ΔG is negative 2H2O2 + O2

21. ΔG is independent of reactionpath

22. A system is at equilibrium and no net change • can occur if ΔG is zero

24. Calculating ΔG • The free energy of a reaction is given by: Where: ∆G° is the standard free energy change (i.e. change at 1M concentrations), R is the universal gas constant T the absolute temperature

25. Calculating ΔG at pH7 (ΔG’) • At equilibrium and standard pH 7 And so

26. Calculating ΔG at pH7 (ΔG’) • Rearrange and substitute K’eq • or in log 10 • Rearranges

29. Example • Calculate ΔG and ΔG°’ • At equilibrium GAP to DHAP is 0.0475 + 7.53 kJ mol-1

30. If DHAP is 2 x10-4 M and GAP is 3 x 10-6 M -2.89