1. Organic Chemistry 6th Edition Paula Yurkanis Bruice Chapter 23 The Organic Chemistry of Amino Acids, Peptides, and Proteins

2. Peptides and proteins are polymers of amino acids linked together by amide bonds:

3. Classification of Amino Acids • Hydrophobic: water-fearing, nonpolar side chains • Alkyl side chain • Hydrophilic: water-loving side chains • Polar, neutral side chains • Anionic • Cationic

4. Nonpolar Side Chains

5. Polar, Neutral Side Chains

6. Polar, Acidic Side Chains

7. Basic, Polar Side Chains

9. Configuration of Amino Acids

10. Acid–Base Properties of Amino Acids An amino acid can never exist as an uncharged compound

12. Some amino acids have ionizable hydrogens on their side chains:

13. The isoelectric point (pI) of an amino acid is the pH at which it has no net charge:

14. The pI of an amino acid that has an ionizable side chain is the average of the pKa values of ionized groups of the same charge:

15. A mixture of amino acids can be separated by electrophoresis on the basis of their pI values: Ninhydrin is used to detect the individual amino acids

17. A mixture of amino acids can also be separated on the basis of polarity:

18. Ion-exchange chromatography can be used to perform preparative separation of amino acids: Negatively charged resin binds selectively to positively charged amino acids

19. Ion-Exchange Chromatography • Cations bind most strongly to cation-exchange • resins. • Anions bind most strongly to anion-exchange • resins. • An amino acid analyzer is an instrument that automates • ion-exchange chromatography.

20. Synthesis of Amino Acids HVZ reaction followed by reaction with ammonia: Reductive amination:

21. A more efficient way of synthesizing amino acids:

22. The Strecker Synthesis

23. Resolution of Racemic Mixtures of Amino Acids

24. Formation of a Peptide

25. A peptide bond has 40% double-bond character:

26. Formation of Disulfide Bonds Disulfides can be reduced to thiols

27. The disulfide bridge in proteins contributes to the overall shape of a protein:

29. Peptide Examples ENKEPHALINS Natural ligands for opioid receptors Tyr-Gly-Gly-Phe-Leu Tyr-Gly-Gly-Phe-Met NUTRASWEET Peptide-based sweetener GLUTATHIONE Antioxidant and electrophile trap

30. Because amino acids have two functional groups, amide bond formation with a mixture of two amino acids affords four products:

31. Strategy for Making a Specific Peptide Bond

32. t-BOC protection of an amine group: The t-BOC protecting group is stable during amide bond formation but is removed under acidic conditions

33. Carboxylic acid activation by DCC:

34. Amide bond formation:

35. Amino acids can be added to the growing C-terminal end by repeating these two steps:

36. When the desired number of amino acids has been added to the chain, the protecting group can be removed:

37. C-terminal amino acid An Improved Peptide Synthesis Strategy Attachment of N-protected amino acid to resin

38. Removal of t-BOC protecting group Carboxylic acid activation of second amino acid

39. Amide bond formation Removal of t-BOC protecting group

40. Carboxylic acid activation of N-terminal amino acid Amide bond formation Removal of t-BOC protecting group

41. Release of tripeptide from Merrifield resin

42. N-terminal amino acid? C-terminal amino acid? What is in between? Sequencing Proteins

43. The first step in determining the sequence of amino acids in a peptide or protein is to cleave the disulfide bridges:

44. The next step is to determine the number and kinds of amino acids in the peptide or protein by hydrolysis and then analysis of the mixture:

45. The N-terminal amino acid of a peptide or a protein can be determined by Edman degradation:

46. The particular PTH–amino acid can be identified by chromatography using known standards

47. The C-terminal amino acid can be identified by treating the protein with carboxypeptidase: • Carboxypeptidase B: ONLY Arg and Lys • Carboxypeptidase A: ALL amino acids EXCEPT Arg and Lys

48. The peptide or protein can be partially hydrolyzed using endopeptidases: • Trypsin: C-side of Arg and Lys • Chymotrypsin: C-side of Phe, Tyr, Trp • Elastase: C-side of Gly and Ala • No cleavage for any endopeptidase if Pro on either side Example of trypsin hydrolysis:

50. Cyanogen bromide causes the hydrolysis of the amide bond on the C-side of a methionine residue: