Advanced Biochemistry and Chemical Biology CHM4034 Spring 2008

1. Advanced Biochemistry and Chemical BiologyCHM4034 Spring 2008 • Dr. Lyons office hours lyons@chem.ufl.edu 846-3392 • W 10-11 AM • T,R 4:00-5:00 PM Class website http://www.chem.ufl.edu/~lyons/

2. Greek lettering scheme used to identify the atoms in amino acid side chains 2 1 3 4 5 6 7

3. An a-amino acid

4. Non-polar, aliphatic g1 b g2 a a b a a Alanine Valine Glycine

5. Non-polar, aliphatic g1 d g2 d1 g d2 b b a a Leucine Isoleucine

6. Non-polar, aliphatic b g d e g b a d a + 2 Methionine Proline

7. Aromatic h e1 z1 e1 z1 d1 e2 d1 g e2 d2 g b b d2 a a Phenylalanine Tyrosine

8. Aromatic e1 d1 e2 z2 g h b d2 e3 z3 a Tryptophan

9. Polar, uncharged g g2 g b b b g1 a a a Serine Threonine Cysteine

10. Polar, uncharged e1 e1 d1 d1 e2 b d2 d e2 g b d2 g b g a a a Histidine Asparagine Glutamine

11. Positively Charged h2 e e g g b b z d d z a a h1 Lysine Arginine

12. Negatively Charged d1 e1 b g d2 d e2 b g a a Aspartate Glutamate

13. Alanine Ala A Cysteine Cys C Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Methionine Met M Proline Pro P Serine Ser S Threonine Thr T Valine Val V Arginine Arg R Asparagine Asn N Aspartate Asp D Glutamate Glu E Glutamine Gln Q Lysine Lys K Phenylalanine Phe F Tryptophan Trp W Tyrosine Tyr Y

14. Non-standard encoded amino acids Selenocysteine Sec, U a + Pyrrolysine Pyl, O a +

15. Amino acids bear structural similarity to each other Asparate Glutamate d1 e1 b b g a a g d + + d2 e2 Asparagine Glutamine d1 e1 b a g a b g d + d2 + e2

16. Amino acids bear structural similarity to each other Cysteine Selenocysteine b g a a + + Threonine Serine b a a b g g2 + g1

17. Amino acids bear structural similarity to each other Tyrosine d1 e1 b a g z1 h + d2 e2 Phenylalanine e1 d1 b a g z1 d2 e2

18. Amino acids bear structural similarity to each other Histidine Histidine Arginine Asparagine Histidine Histidine Arginine Glutamine

19. Amino acids bear structural similarity to each other Histidine Tryptophan

20. Amino acids bear structural similarity to each other Phenylalanine Tyrosine Phenylalanine Leucine

23. Degeneracy prevents mutation from being deleterious One could argue that this is how RNAP is proofread For Phe UUU or UUC If you mutate almost any position you still end up with a branched chain hydrophobic amino acid. Only U to C or U to G at position 2 result in large changes

24. Degeneracy prevents mutation from being deleterious One could argue that this is how RNAP is proofread For His CAU or CAC You change to Gln, Arg, Asn or Asp Asp is like His functionally in that it binds metal ions….

25. The genetic code can be expanded Stop codons are often reassigned UGA encodes selenocysteine, pyrrolysine

28. These values are the pKa’s of the free amino acids in aqueous solution. As we shall see later an aqueous solution may not represent reality

29. These values are the pKa’s of the free amino acids in aqueous solution. As we shall see later an aqueous solution may not represent reality Hydrophobic pocket

30. Condensation of two a-amino acids to form a dipeptide.

31. Nterm - Histidine-alanine-cysteine-lysine-phenylalanine-leucine-glycine - Cterm Nterm - His-Ala-Cys-Lys-Phe-Leu-Gly - Cterm Nterm - HACKFLG - Cterm

32. Sugars and Polysaccharides 1 2 3 Glyceraldehyde contains one chiral center* at C-2. In general n carbon aldoses contain 2n-2 stereoisomers. 1 2 3 Dihydroxyacetone the simplest ketose, does not contain a chiral center 1 2 3 4 Erythrulose, the second sugar in the ketose series, contains one chiral center at C-3. In general n carbon ketoses contain 2n-3 stereoisomers

33. Nomenclature : - Fischer convention : D sugars have the same absolute configuration at the stereogenic center farthest removed from their carbonyl group as does D-glyceraldehyde. - The L version of the sugars are the mirror image of their D counterparts

35. D-Arabinose D-Xylose

39. L sugars are biologicaly much less abundant than D sugars. Know the structures of the sugars whose names are boxed. • Aldoses to remember are: D-glyceraldehyde, D-erythrose, D-ribose, D-mannose, D-galactose, D-glucose • Ketoses to remember are: Dihydroxyacetone, D-erythrulose, D-ribulose, D-xylulose, D-fructose

40. Epimers

42. Configurations and conformations Sugars can exist in several cyclic conformations, this is a consequence of the intrinsic chemical reactivity of the functional groups in the corresponding sugar Intramolecular reactions The reactions of alcohols with (a) aldehydes to form hemiacetals and (b) ketones to form hemiketals.

46. D-glucose is 33%  and 66%   glucose  glucose

48. -glucose-(1,4)--glucose glucose-(14)-glucose

49. -glucose-(1,4)--glucose glucose-(14)-glucose

50. -glucose-(1,6)--glucose glucose-(1)-glucose