Biochemistry Macromolecules, Proteins, Amino Acids

1. BiochemistryMacromolecules, Proteins, Amino Acids

2. Introduction to Biochemistry • Most biologically important macromolecules are polymers, called biopolymers. • Biopolymers fall into three classes: • proteins, • polysaccharides (carbohydrates), and • nucleic acids.

3. Proteins Amino Acids Proteins are large molecules present in all cells. They are made up of -amino acids. There are two forms of an amino acid: one that is neutral (with -NH2 and -COOH groups) and one that is zwitterionic (with -NH3+ and -COO- groups). A zwitterion has both positive and negative charge in one molecule. There are about 20 amino acids found in most proteins.

4. Amino Acids

5. Fundamentals • While their name implies that amino acids are compounds that contain an —NH2 group and a —CO2H group, these groups are actually present as —NH3+ and —CO2– respectively. • They are classified as a, b, g, etc. amino acids according the carbon that bears the nitrogen.

6. + NH3 – CO2 + – H3NCH2CH2CO2 + – H3NCH2CH2CH2CO2 Amino Acids an a-amino acid that is anintermediate in the biosynthesisof ethylene a a b-amino acid that is one ofthe structural units present incoenzyme A b a g-amino acid involved inthe transmission of nerveimpulses g

7. The 20 (22) Key Amino Acids • More than 700 amino acids occur naturally, but 20 (22?)of them are especially important. • These 22 amino acids are the building blocks of proteins. All are a-amino acids. • They differ in respect to the group attached to the a carbon. • See Handout.

8. O H + – H3N O C C R Amino Acids • The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain). • The properties of the amino acid vary as the structure of R varies.

9. O H + – H3N O C C H Amino Acids • Glycine is the simplest amino acid. It is the only one in the table that is achiral. • In all of the other amino acids in the table the a carbon is a stereogenic center. Glycine (Gly or G)

10. Amino Acids O H + – H3N O C C CH3 Alanine (Ala or A)

11. Amino Acids O H + – H3N O C C CH(CH3)2 Valine (Val or V)

12. Amino Acids O H + – H3N O C C CH2CH(CH3)2 Leucine (Leu or L)

13. Amino Acids O H + – H3N O C C CH3CHCH2CH3 Isoleucine (Ile or I)

14. Amino Acids O H + – H3N O C C CH3SCH2CH2 Methionine (Met or M)

15. O H + – H2N O C C CH2 H2C CH2 Amino Acids Proline (Pro or P)

16. O H + – H3N O C C CH2 Amino Acids Phenylalanine (Phe or F)

17. O H + – H3N O C C CH2 N H Amino Acids Tryptophan (Trp or W)

18. O H + – H3N O C C H2NCCH2 O Amino Acids Asparagine (Asn or N)

19. O H + – H3N O C C H2NCCH2CH2 O Amino Acids Glutamine (Gln or Q)

20. Amino Acids O H + – H3N O C C CH2OH Serine (Ser or S)

21. Amino Acids O H + – H3N O C C CH3CHOH Threonine (Thr or T)

22. O H + – H3N O C C – OCCH2 O Amino Acids Aspartic Acid (Asp or D)

23. O H + – H3N O C C – OCCH2CH2 O Amino Acids Glutamic Acid (Glu or E)

24. O H + – H3N O C C CH2 OH Amino Acids Tyrosine (Tyr or Y)

25. Amino Acids O H + – H3N O C C CH2SH Cysteine (Cys or C)

26. Amino Acids O H + – H3N O C C + CH2CH2CH2CH2NH3 Lysine (Lys or K)

27. Amino Acids O H + – H3N O C C CH2CH2CH2NHCNH2 + NH2 Arginine (Arg or R)

28. CH2 N NH Amino Acids O H + – H3N O C C Histidine (His or H)

29. Amino Acids: #21(2001) Selenocysteine

30. Amino Acids: #22(2002) Pyrrolysine (4 R, 5 R)

31. Amino Acids: #22(2002) Pyrrolysine

32. Acid-Base Behavior of Amino Acids

33. Amino Acids • While their name implies that amino acids are compounds that contain an —NH2 group and a —CO2H group, these groups are actually present as —NH3+ and —CO2– respectively. • How do we know this?

34. O O •• •• •• •• + – •• •• •• H3NCH2C O H2NCH2C OH •• •• •• Properties of Glycine • The properties of glycine: • high melting point (when heated to 233°C it decomposes before it melts)solubility: soluble in water; not soluble in nonpolar solvent more consistent with this than this

35. O •• •• + – •• H3NCH2C O •• •• Properties of Glycine • The properties of glycine: • high melting point (when heated to 233°C it decomposes before it melts)solubility: soluble in water; not soluble in nonpolar solvent more consistent with this called a zwitterion or dipolar ion

36. Acid-Base Properties of Glycine • The zwitterionic structure of glycine also follows from considering its acid-base properties. • A good way to think about this is to start with the structure of glycine in strongly acidic solution, say pH = 1. • At pH = 1, glycine exists in its protonated form (a monocation).

37. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The zwitterionic structure of glycine also follows from considering its acid-base properties. • A good way to think about this is to start with the structure of glycine in strongly acidic solution, say pH = 1. • At pH = 1, glycine exists in its protonated form (a monocation).

38. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • Now ask yourself "As the pH is raised, which is the first proton to be removed? Is it the proton attached to the positively charged nitrogen, or is it the proton of the carboxyl group?" • You can choose between them by estimating their respective pKas.

39. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • Now ask yourself "As the pH is raised, which is the first proton to be removed? Is it the proton attached to the positively charged nitrogen, or is it the proton of the carboxyl group?" • You can choose between them by estimating their respective pKas. typical ammonium ion: pKa ~9 typical carboxylic acid: pKa ~5

40. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The more acidic proton belongs to the CO2H group. It is the first one removed as the pH is raised. typical carboxylic acid: pKa ~5

41. O •• •• + – •• H3NCH2C O •• •• O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • Therefore, the more stable neutral form of glycine is the zwitterion. typical carboxylic acid: pKa ~5

42. O •• •• + •• H3NCH2C OH •• Acid-Base Properties of Glycine • The measured pKa of glycine is 2.34. • Glycine is stronger than a typical carboxylic acid because the positively charged N acts as an electron-withdrawing, acid-strengthening substituent on the a carbon. typical carboxylic acid: pKa ~5

43. O O •• •• •• •• – + HO – – •• •• •• H3NCH2C O H2NCH2C O •• •• •• •• Acid-Base Properties of Glycine A proton attached to N in the zwitterionic form of nitrogen can be removed as the pH is increased further. • The pKa for removal of this proton is 9.60.This value is about the same as that for NH4+

44. O •• •• + •• H3NCH2C OH •• O •• •• + – •• H3NCH2C O •• •• O •• •• – •• •• H2NCH2C O •• •• Isoelectric Point pI • The pH at which the concentration of the zwitterion is a maximum is called the isoelectric point. Its numerical value is the average of the two pKas. • The pI of glycine is 5.97. pKa = 2.34 pKa = 9.60

45. Acid-Base Properties of Amino Acids • One way in which amino acids differ is in respect to their acid-base properties. This is the basis for certain experimental methods for separating and identifying them. • Just as important, the difference in acid-base properties among various side chains affects the properties of the proteins that contain them.

46. O H + – H3N O C C H Amino Acids with Neutral Side Chains pKa1 = 2.34pKa2 = 9.60pI = 5.97 Glycine

47. O H + – H3N O C C CH3 Amino Acids with Neutral Side Chains pKa1 = 2.34pKa2 = 9.69pI = 6.00 Alanine

48. O H + – H3N O C C CH(CH3)2 Amino Acids with Neutral Side Chains pKa1 = 2.32pKa2 = 9.62pI = 5.96 Valine

49. O H + – H3N O C C CH2CH(CH3)2 Amino Acids with Neutral Side Chains pKa1 = 2.36pKa2 = 9.60pI = 5.98 Leucine

50. Amino Acids with Neutral Side Chains O H pKa1 = 2.36pKa2 = 9.60pI = 5.98 + – H3N O C C Isoleucine CH3CHCH2CH3