Voet: Suggested Problems Ch 10: 1, 3, 4, 5, 6, 8, 10, 11, 12, Segel: Chapter 1: 53, 55 2: 1, 2, 13, 30,

1. Voet: Suggested Problems Ch 10: 1, 3, 4, 5, 6, 8, 10, 11, 12, Segel: Chapter 1: 53, 55 2: 1, 2, 13, 30,

2. Suggested problems chapter 13: 3, 4, 5, 7, 8 Chapter 14: 3, 4, 5, 6, 12

3. Table 13-3 Enzyme Classification According to Reaction Type. Page 470

4. Figure 13-1 An enzyme–substrate complex illustrating both the geometric and the physical complementarity between enzymes and substrates. Page 460

5. Figure 13-3 Prochiral differentiation. Page 461

6. Trypsin +inhibitor(VVP Fig 11-28)

7. Common features of enzyme active sites: 1. The active site is a 3-dimensional cleft formed from amino acids at distant sites in the sequence. 2. The active site accounts for a relatively small part of the total volume of the protein. 3. Substrates are generally bound to enzymes by non-covalent interactions. 4. The specificity of S binding depends on the arrangements of atoms in the active site.

8. Number Classification Biochemical Properties 1. Oxidoreductases Act on many chemical groupings to add or remove hydrogen atoms. 2. Transferases Transfer functional groups between donor and acceptor molecules. Kinases are specialized transferases that regulate metabolism by transferring phosphate from ATP to other molecules. 3. Hydrolases Add water across a bond, hydrolyzing it. 4. Lyases Add water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds. 5. Isomerases Carry out many kinds of isomerization: L to D isomerizations, mutase reactions (shifts of chemical groups) and others. 6. Ligases Catalyze reactions in which two chemical groups are joined (or ligated) using ATP.

10. 1.Addition or removal of water a.Hydrolases - these include esterases, carbohydrases, nucleases, deaminases, amidases, and proteases b.Hydrases such as fumarase, enolase, aconitase and carbonic anhydrase 2.Transfer of electrons a.Oxidases b.Dehydrogenases 3.Transfer of a radical a.Transglycosidases - of monosaccharides b.Transphosphorylases and phosphomutases - of a phosphate group c.Transaminases - of amino group d.Transmethylases - of a methyl group e.Transacetylases - of an acetyl group 4.Splitting or forming a C-C bond a.Desmolases 5.Changing geometry or structure of a molecule a.Isomerases 6.Joining two molecules through hydrolysis of pyrophosphate bond in ATP or other triphosphate a.Ligases

11. Oxidoreductases--catalyze redox reactions Usually require a coenzyme Ethanol + NAD+ Acetaldehyde + NADH + H+ Enzymes receive “common” names reflecting their function, either in the forward or reverse direction. The enzyme for this reaction is called Alcohol Dehydrogenase

12. Transferases-transfer functional groups Kinases transfer phosphates from ATP (or GTP) E.g Hexokinase: Glucose + ATP glc-6-P + ADP Hydrolases catalyze hydrolytic cleavages Proteases are hydrolases

13. Lyases catalyze group elimination to form double bonds e.g. Enolase (glycolysis) 2-Phosphoglycerate  H2O + phosphoenolpyruvate Isomerases--duh, interconvert isomers e.g. phosphoglucose isomerase Glucose-6-phosphate  Fructose-6-phosphate

14. Ligases--join to substrates together at the expense of ATP e.g. DNA Ligase Joins Okazaki fragments during DNA replication Some bacterial ligases substitute NAD+ as the energy source.

15. Coenzymes • Enzymes often require the participation of other small molecules to carry out a particular reaction. • These small molecules, called coenzymes, are metabolic derivatives of vitamins. • Vitamins are nutrients required in small amounts by organisms. Vitamin deficiencies usually present as metabolic disorders, e.g. scurvy

16. Table 13-1 The Common Coenzymes.

17. Table 13-2 Vitamins That Are Coenzyme Precursors. Page 464

18. Figure 13-2 The structures and reaction of nicotinamide-adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). Page 461

19. Figure 13-4 Structures of nicotinamide and nicotinic acid. Page 464

20. Enzyme Activities Are Regulated at Various Levels • Transcription • Processing • Translation • Post-translational modification • Transient modification (e.g. phosphorylation) • Allosteric Effectors

21. Figure 13-5 The rate of the reaction catalyzed by ATCase as a function of aspartate concentration. Page 465

22. Figure 13-6 Schematic representation of the pyrimidine biosynthesis pathway. Page 466

23. Figure 13-7a X-Ray structure of ATCase. (a) (left) T-state ATCase along the protein’s molecular threefold axis of symmetry; (right) R-state ATCase along the protein’s molecular threefold axis of symmetry. Page 467

24. Figure 13-7b X-Ray structure of ATCase. (b) (left) T-state ATCase along the protein’s molecular twofold axis of symmetry; (right) R-state ATCase along the protein’s molecular twofold axis of symmetry. Page 467

25. Figure 13-8 Comparison of the polypeptide backbones of the ATCase catalytic subunit in the T state (orange) and the R state (blue). Page 468

26. Figure 13-9 Schematic diagram indicating the tertiary and quaternary conformational changes in two vertically interacting catalytic ATCase subunits. Page 469

29. Styer p.277

30. Stryer p. 278

32. Figure 18-12 A bicyclic enzyme cascade. Page 638

33. Figure 18-13 Control of glycogen metabolism in muscle. Page 639

34. Stryer Fig. 10.37

35. Ch 14 Kinetics!

36. Stryer Fig. 8.11

37. Stryer Fig. 8.12 Determining initial velocity

38. What other factors can affect enzyme activity? Is the product stable or transformed into something else? [E] pH Temperature Salt concentration

39. After the first few milliseconds of a reaction, a steady state is attained. Stryer Fig. 8.13

40. Figure 14-1 Plot of ln[A] versus time for a first-order reaction. Page 474

41. Figure 14-4b Transition state diagrams. (b) For a spontaneous reaction, that is, one in which the free energy decreases. Page 475

42. Figure 14-5 Transition state diagram for the two-step overall reaction A ® I ® P. Page 477

43. Figure 14-6 The effect of a catalyst on the transition state diagram of a reaction. Page 477

44. Figure 14-7 Progress curves for the components of a simple Michaelis–Menten reaction. Page 478

45. Figure 14-8 Plot of the initial velocity vo of a simple Michaelis–Menten reaction versus the substrate concentration [S]. Page 479

46. k2 k1 E + S ESE+P k-1 (k-2 is negligible until products start to build up) Steady state conditions--[ES] remains relatively constant over the course of the rxn until S starts runing out. Vo = k2[ES] [k1[E][S] = k-1[ES] + k2[ES] = (k-1 + k2)[ES] Define a new constant: [E][S]/[ES] = (k-1 + k2)/ k1= KM Km[ES] = [S][E] Km[ES] = [ET][S]-[ES][S] [E] = [E]T -[ES]

47. [ES](KM + [S]) = [E]T[S] ([E]T[S] And [ES] = v/k2 [ES] = ------------------- KM + [S] k2[E]T[S] Define Vmax=k2[E]T v = ------------------ KM + [S] vmax[S] Michaelis-Menton equation v = ----------------- KM + [S]

48. Figure 14-1 Plot of ln[A] versus time for a first-order reaction. Page 474

49. Figure 14-8 Plot of the initial velocity vo of a simple Michaelis–Menten reaction versus the substrate concentration [S]. Page 479

50. An enzyme obeys Michaelis-Menten kinetics with: Vmax = 1.8 umol ml-1 s-1 at an enzyme concentration of 15 umol ml-1. Calculate kcat and KM for the enzyme. Is the value you obtain for KM what you would expect given your data? Why or why not? [S] uM vo (umol ml-1 s-1) 1600 1.39 800 1.13 400 0.83 200 0.54 100 0.32