Organic Chemistry

1. Organic Chemistry William H. Brown & Christopher S. Foote

2. Amino Acids & Proteins Chapter 27

3. Amino Acids • Amino acid: a compound that contains both an amino group and a carboxyl group • -Amino acid: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group • although -amino acids are commonly written in the unionized form, they are more properly written in the zwitterion (internal salt) form

4. Chirality of Amino Acids • With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral • the vast majority have the L-configuration at their -carbon

5. Nonpolar side chains

6. Polar side chains

7. Acidic & basic side chains

8. Other Amino Acids

9. Acid- Base Proper- ties

10. Acid-Base Properties

11. Acidity: -CO2H Groups • The average pKa of an -carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa 4.76) • the greater acidity is accounted for by the electron-withdrawing inductive effect of the adjacent -NH3+ group

12. Acidity: side chain -COOH • Due to the electron-withdrawing inductive effect of the -NH3+ group, side chain -COOH groups are also stronger than acetic acid • the effect decreases with distance from the -NH3+ group. Compare: -COOH group of alanine (pKa 2.35) -COOH group of aspartic acid (pKa 3.86) -COOH group of glutamic acid (pKa 4.07)

13. Acidity: -NH3+ groups • The average value of pKa for an -NH3+ group is 9.47, compared with a value of 10.76 for a 1° alkylammonium ion

14. Basicity-Guanidine Group • basicity of the guanidine group is attributed to the large resonance stabilization of the protonated form relative to the neutral form

15. Basicity- Imidazole Group • the imidazole group is a heterocyclic aromatic amine

16. Ionization vs pH • Given the value of pKa of each functional group, we can calculate the ratio of each acid to its conjugate base as a function of pH • consider the ionization of an -COOH • writing the acid ionization constant and rearranging terms gives

17. Ionization vs pH • substituting the value of pKa (2.00) for the hydrogen ion concentration at pH 7.0 (1.0 x 10-7) gives • at pH 7.0, the -carboxyl group is virtually 100% in the ionized form and has a net charge of -1 • we can repeat this calculation at any pH and determine the ratio of [-COO-] to [-COOH] and the net charge on the -carboxyl at that pH

18. Ionization vs pH • We can also calculate the ratios of acid to conjugate base for an -NH3+ group; for this calculation, assume a value 10.0 for pKa • writing the acid ionization constant and rearranging gives

19. Ionization vs pH • substituting values for pKa of an -NH3+ group and the hydrogen ion concentration at pH 7.0 gives • thus at pH 7.0, the ratio of -NH3+ to -NH2 is approximately 1 to 1000 • at this pH, an -amino group is 99.9% in the protonated form and has a charge of +1

20. Henderson-Hasselbalch • for the ionization of any weak acid HA • taking the log and rearranging gives • substitution pH and pKa gives the Henderson-Hasselbalch equation

21. Henderson-Hasselbalch • using the Henderson-Hasselbalch equation we see that • when pH = pKa, the concentrations of weak acid and its conjugate base are equal • when pH < pKa, the weak acid predominates • when pH > pKa, the conjugate base predominates

22. Isoelectric Point • Isoelectric point, pI, of an amino acid: the pH at which the majority of its molecules in solution have no net charge • the pH for glycine, for example, falls between the pKa values for the carboxyl and amino groups

25. Electrophoresis • Electrophoresis: the process of separating compounds on the basis of their electric charge • electrophoresis of amino acids can be carried out using paper, starch, agar, certain plastics, and cellulose acetate as solid supports • In paper electrophoresis • a paper strip saturated with an aqueous buffer of predetermined pH serves as a bridge between two electrode vessels

26. Electrophoresis • a sample of amino acids is applied as a spot on the paper strip • an electric potential is applied to the electrode vessels and amino acids migrate toward the electrode with charge opposite their own • molecules with a high charge density move faster than those with low charge density • molecules at their isoelectric point remain at the origin • after separation is complete, the strip is dried and developed to make the separated amino acids visible

27. Electrophoresis • a reagent commonly used to detect amino acid is ninhydrin

28. Polypeptides & Proteins • In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds to which he gave the name peptide bonds • Peptide bond:the special name given to the amide bond between the -carboxyl group of one amino acid and the -amino group of another

29. Serylalanine (Ser-Ala)

30. Peptides • peptide:the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain • dipeptide: a molecule containing two amino acids joined by a peptide bond • tripeptide: a molecule containing three amino acids joined by peptide bonds • polypeptide: a macromolecule containing many amino acids joined by peptide bonds • protein: a biological macromolecule of molecular weight 5000 g/mol of greater, consisting of one or more polypeptide chains

31. Writing Peptides • by convention, peptides are written from the left, beginning with the free -NH3+ group and ending with the free -COO- group on the right

32. Primary Structure • Primary structure: the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid • Amino acid analysis • hydrolysis of the polypeptide, most commonly carried out using 6M HCl at elevated temperature • quantitative analysis of the hydrolysate by ion-exchange chromatography

33. Cyanogen Bromide, BrCN • cleavage of peptide bonds formed by the carboxyl group of methionine

34. Cyanogen Bromide, BrCN

35. Cyanogen Bromide, BrCN • Step 1: nucleophilic displacement of bromine

36. Cyanogen Bromide, BrCN • Step 2: internal nucleophilic displacement

37. Cyanogen Bromide, BrCN • Step 3: hydrolysis of the imino group

38. Enzyme Catalysis • A group of protein-cleaving enzymes can be used to catalyze the hydrolysis of specific peptide bonds

39. Edman Degradation • Edman degradation: cleaves the N-terminal amino acid of a polypeptide chain

40. Edman Degradation • Step 1: nucleophilic addition to the C=N group of phenylisothiocyanate

41. Edman Degradation • Step 2: nucleophilic addition of sulfur to the C=O of the adjacent amide group

42. Edman Degradation • Step 3: isomerization of the thiazolinone ring

43. Primary Structure Example 27.8 Deduce the 1° structure of this pentapeptide

44. Polypeptide Synthesis • The problem is join the -carboxyl group of aa-1 by an amide bond to the -amino group of aa-2, and not vice versa

45. Polypeptide Synthesis • protect the -amino group of aa-1 • activate the -carboxyl group of aa-1 • protect the -carboxyl group of aa-2

46. Amino-Protecting Groups • the most common strategy for protecting amino groups and reducing their nucleophilicity is to convert them to amides

47. Amino-Protecting Groups • treatment of an amino group with either of these reagents gives a carbamate (an ester of the monoamide of carbonic acid)

48. Amino-Protecting Groups • a carbamate is stable to dilute base but can be removed by treatment with HBr in acetic acid

49. Amino-Protecting Groups • The benzyloxycarbonyl group is removed by hydrogenolysis (Section 20.6C) • the intermediate carbamic acid loses carbon dioxide to give the unprotected amino group

50. Carboxyl-Protecting Grps • Carboxyl groups are most often protected as methyl, ethyl, or benzyl esters • methyl and ethyl esters are prepared by Fischer esterification, and removed by hydrolysis in aqueous base under mild conditions • benzyl esters are removed by hydrogenolysis (Sect. 20.6C); they are also removed by treatment with HBr in acetic acid