Chem 27 - Exam 1 Review Wednesday Feb. 22, 2006 Science Center Hall D

1. Chem 27 - Exam 1 ReviewWednesday Feb. 22, 2006Science Center Hall D K.C. O’Brien Carol Fang Walter Kowtoniuk

2. Outline of Topics • 1) Conformational Analysis of amino acids • 2) Protein Folding • 3) Edman Degradation(-like) chemistry • 4) Cyanogen bromide(-like) chemistry • 5) Peptide Coupling/Synthesis • 6) Biosynthesis of Proteins

3. Conformational Analysis K.C. O’Brien

4. Amino Acid Structure • Amino acids are chiral molecules • Stereochemistry at a-carbon always as shown (R group coming out) • All natural amino acids have S configuration, except cysteine • pKa’s: NH3+ is about 9 • COO- is about 2.2 • Hydrophobic, polar and charged side chains

5. Staggered vs. Eclipsed Conformation • Hyperconjugation sC-H-> s*C-H • Newman projections help visualize interactions

6. Gauche interactions

7. Cyclohexane Chair Conformations • Ring flip changes groups from axial to equatorial • Lower energy conformation has large groups equatorial • A values are used to quantify the energy difference between the axial and equatorial positions

8. Syn-pentane Interaction • Syn-pentane > 3.7 kcal /mol • 1,3-diaxial groups generate a syn pentane interaction

9. A1,3 Strain • H is in the same plane as double bond • If R=R’=R”=Me, A1,3=3.5 kcal/mol • Minimize A1,3 in amide bonds

10. Template Projection of Amino Acids • Amino acid template projection is based on cyclohexane chair structure • Add up gauche and syn-pentane interactions to find the lowest energy conformation • R1>R2>R3 is a good place to start, but consider other conformations • Make sure you don’t invert the stereochemistry of the amino acid or its side chain!!!!

11. Protein Folding: Hydrogen Bonds • 1-4 kcal/mol • Directionality is important • N-H-----O=C • Stabilize a-helices, b-sheets and turns

12. Protein Folding: a-helix • stabilized by hydrogen bonding • 3.6 amino acids per turn

13. Protein Folding: b-sheet • NH’s of one strand H-bond to C=O of next strand • R groups alternate on opposite sides of the plane

14. Protein Folding: b-turn • C=O and N-H are 10 atoms apart • Changes the direction of the main chain

15. Protein Folding: Electrostatic Interactions • Between oppositely charged amino acids • Most important in the interior of the protein • Neutralizes charges

16. Hydrophobic Interactions: Hydrophobic amino acids pack into the interior of the protein Folding increases the disorder of the solvent Positive DH is overcome by positive DS Disulfide Bonds: Dihedral angle 90o ns donates into s*S-R Two Cys oxidized to form a disulfide bond Protein Folding:

17. Edman Degradation Carol Fang

18. Nucleophilic Amine (primary and secondary) E and Nu are 5 atoms apart Rotatable bond Thiazolinone Derivative Kinetic product New N-terminal

19. Enol Formation Pre-note Potential racemization PTH, to be detected by HPLC Thermodynamic Product

20. Frame of Reaction When racemization is taken care of

21. Brain teasers: • a peptide is not reactive to Edman Degradation • After a round of Edman degradation, only one fragment is obtained c) After a round of Edman degradation, two PTH products are obtained • Bicyclic PTH product from Edman Degradation c) Special case: Lysine D05 Cyclic peptide No nucleophilic amine Breaking the peptide bond does not break the molecule D10, D12 Presence of Nu amine; Cyclic 2 Nu amines at both ends / 1 PTH end and 1 Nu amine end D10, D12 A ring before Edman degradation D02, D04 A more protonated amine D09

22. Cyanogen Bromide Cleavage

23. Nucleophilic S Nu and E 5 atoms apart Rotatable bond Met (C) N cleaved

24. Brain teasers: A peptide gives only one fragment after CNBr cleavage A cyclic peptide C-terminal Methionine 2) It is known that a peptide has n Met. It gives n pieces of fragments 3) How about (n+1) fragments?

25. How this reacts with CNBr? (2004 Exam 1)

26. Why S / C=O combo can be so different in these two reactions? CNBr Cleavage Edman Degradation 3 C-S bond, S has an extra Covalent bond; adjacent C is ready for SN2 C=S bond, S is Nucleophilic

27. Peptide Syntheses Walter Kowtoniuk

28. Amide Bond Synthesis • Synthesis of an amide bond using the corresponding carboxylic acid and amine. • - Use DCC to both activate the acid and serve as a dehydrating agent

29. Amide Bond Synthesis

30. Amide Bond Synthesis

31. Protecting GroupsWhy do we need them?

32. Protecting Groups Lecture Notes pg33

33. Protecting Groups • t-Boc Synthesis • t-Boc Deprotection

34. Protecting Groups • Cbz follows the same mechanism as shown for t-Boc

35. Protecting Groups • Ts synthesis • Ts Deprotection

36. Protecting Groups • DNP synthesis • DNP deprotection

37. C to N Directionalitywhy not N to C?

38. Solid Phase Peptide Synthesis

39. Solid Phase Peptide Synthesis

40. Peptide Fragment Coupling • Thioester • True coupling

41. Determining Yield • Synthesizing a 100mer requires 99rxns, thus n=99 • If we factor in the initial coupling to the solid phase, the 100mer requires 100rxns, thus n=100 • For convergent synthesis we are concerned with the longest linear sequence of steps. In this case the yield of each individual reaction is multiplied

42. Translation

43. Biological Carbonyl Activation

44. Biological Carbonyl Activation

45. Biological Carbonyl Activation

46. Ribosome

47. Role of A2486