Amino Acids, Peptides, and Proteins

1. Amino Acids, Peptides, and Proteins

2. Objectives • Draw a general amino acid and identify the two functional groupscommon to all. • Classify each amino acid according to the chemical nature of its R group. • Define the meaning of an essential amino acid. • Draw the reaction that joins two amino acids to form a peptide bond. • Describe and differentiate primary, secondary, tertiary, and quaternary protein structures. • Describe and differentiate co-enzymes and prosthetic groups. • List and discuss four forces that stabilize globular protein structure. • List important structural similarities and differences between myoglobin and hemoglobin. • Describe the mutation present in hemoglobin giving rise to sickle cell disease.

3. What is an amino acid? Twenty different kinds of amino acids are used by living organisms to produce proteins An amino acid is a molecule containing an amine (-NH2) an acid (-COOH) and a third chemical group (-R) that defines the amino acid. In glycine, the simplest amino acid, R is –H, or a hydrogen atom. In alanine, R = -CH3. The R groups give specific properties to each amino acid, and to the proteins composed of amino acids. R | Structure of an amino acid: H2N – C – COOH H

4. 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 , , , etc. amino acids according the carbon that bears the nitrogen.

5. The 20 Key Amino Acids • More than 700 amino acids occur naturally, but 20 of them are especially important. • These 20 amino acids are the building blocks of proteins. All are -amino acids. • They differ in respect to the group attached to the  carbon. • These 20 are listed in Table 27.1.

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

7. Classification of Amino Acids

8. O H + – H3N O C C R • 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 R • The major differences among the side chains concern: • Size and shape Electronic characteristics

10. General categories of a-amino acids • nonpolar side chainspolar but nonionized side chains acidic side chains basic side chains

11. Amino Acid R-groups Non-Polar Hydrophobic Tryptophan Phenylalanine Isoleucine Tyrosine Leucine Valine Methionine Polar Charged Arginine (+) Glutamic acid (-) Aspartic Acid (-) Lysine (+) Histidine (+) Uncharged Cysteine Proline Serine Glutamine Asparagine Ambivalent Glycine Threonine Alanine

12. 1. Hydrophobic (non-polar) residues • Usually interior of proteins away from water. • Hydrocarbon: do not contain polar atoms.

13. Arginine [Arg] Glutamate [Glu] Aspartate [Asp] Lysine [Lys] Charged Amino Acids + + - - + Histidine [His]

14. Arginine Arg [R] -11.2 Glutamic Acid Glu [E] -9.9 Aspartic Acid Asp [D] -7.4 Lysine Lys [K] -4.2 Histidine His [H] -3.3 Cysteine Cys [C] -2.8 Proline Pro [P] -0.5 Serine Ser [S] -0.3 Glutamine Gln [Q] -0.3 Asparagine Asn [N] -0.2 Glycine Gly [G] 0 Threonine Thr [T] 0.4 Alanine Ala [A] 0.5 Methionine Met [M] 1.3 Valine Val [V] 1.5 Leucine Leu [L] 1.8 Tyrosine Tyr [Y] 2.3 Isoleucine Ile [I] 2.5 Phenylalanine Phe [F] 2.5 Tryptophan Trp [W] 3.4 Hydrophobic Indexes

15. Essential amino acids • Definition - Those amino acids that cannot be synthesized in the body in sufficient quantities for anabolic needs. • In humans, • Isoleucine Leucine Valine • Tryptophan Methionine Lysine • Phenylalanine Threonine Histidine

16. 20 Amino acids Leucine (L) Isoleucine (I) Valine (V) Alanine (A) Glycine (G) Proline (P) Asparagine (N) Methionine (M) Tryptophan (W) Phenylalanine (F) Tyrosine (Y) Threonine (T) Serine (S) Cysteine (C) Glutamine (Q) Histidine (H) Glutamic acid (E) Arginine (R) Asparatic acid (D) Lysine (K) White: Hydrophobic,Green: Hydrophilic,Red: Acidic,Blue: Basic

17. O H + – H3N O C C H • 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  carbon is a chirality center. Glycine (Gly or G)

18. O H • Alanine, valine, leucine, and isoleucine have alkyl groups as side chains, which are nonpolar and hydrophobic. + – H3N O C C CH3 Alanine (Ala or A)

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

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

21. O H + – H3N O C C CH3CHCH2CH3 Isoleucine (Ile or I)

22. O H • The side chain in methionine is nonpolar, but the presence of sulfur makes it somewhat polarizable. + – H3N O C C CH3SCH2CH2 Methionine (Met or M)

23. O H + – H2N O C C CH2 H2C CH2 • Proline is the only amino acid that contains a secondary amine function. Its side chain is nonpolar and cyclic. Proline (Pro or P)

24. O H + – H3N O C C CH2 • The side chain in phenylalanine (a nonpolar amino acid) is a benzyl group. Phenylalanine (Phe or F)

25. O H + – H3N O C C CH2 Tryptophan (Trp or W) N H • The side chain in tryptophan (a nonpolar amino acid) is larger and more polarizable than the benzyl group of phenylalanine.

26. O H • The —CH2OH side chain in serine can be involved in hydrogen bonding. + – H3N O C C CH2OH Serine (Ser or S)

27. O H • The side chain in threonine can be involved in hydrogen bonding, but is somewhat more crowded than in serine. + – H3N O C C CH3CHOH Threonine (Thr or T)

28. O H • The side chains of two remote cysteines can be joined by forming a covalent S—S bond. + – H3N O C C CH2SH Cysteine (Cys or C)

29. O H + – H3N O C C CH2 OH • The side chain of tyrosine is similar to that of phenylalanine but can participate in hydrogen bonding. Tyrosine (Tyr or Y)

30. O H + – H3N O C C H2NCCH2 O • The side chains of asparagine and glutamine (next slide) terminate in amide functions that are polar and can engage in hydrogen bonding. Asparagine (Asn or N)

31. O H + – H3N O C C H2NCCH2CH2 O Glutamine (Gln or Q)

32. O H + – H3N O C C – OCCH2 O • Aspartic acid and glutamic acid (next slide) exist as their conjugate bases at biological pH. They are negatively charged and can form ionic bonds with positively charged species. Aspartic Acid (Asp or D)

33. O H + – H3N O C C – OCCH2CH2 O Glutamic Acid (Glu or E)

34. O H • Lysine and arginine (next slide) exist as their conjugate acids at biological pH. They are positively charged and can form ionic bonds with negatively charged species. + – H3N O C C Lysine + (Lys or K) CH2CH2CH2CH2NH3

35. O H + – Arginine H3N O C C (Arg or R) CH2CH2CH2NHCNH2 + NH2

36. CH2 N NH O H • Histidine is a basic amino acid, but less basic than lysine and arginine. Histidine can interact with metal ions and can help move protons from one site to another. + – H3N O C C Histidine (His or H)

37. Stereochemistry of Amino Acids

38. – CO2 + H3N H R Configuration of -Amino Acids • Glycine is achiral. All of the other amino acids in proteins have the L-configuration at their carbon.

39. Amino Acids All DNA encoded aa are All are chiral, except Glycine R = H All DNA encoded aa are usually L-

40. Acid-Base Behavior of Amino Acids

41. Recall • 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?

42. aa are high melting point solids! Why? Answer = aa are ionic compounds under normal conditions Isoelectric Point = concentration of zwitterion is at a maximum and the concentration of cations and anions is equal For aa with basic R-groups, we require higher pHs, and for aa with acidic R-groups, we require lower pHs to reach the Isoelectric Point

43. Isoelectric Pointis the pH at which an aa or peptide carries no net charge. i.e. [RCOO-] = [RNH3+] So, for basic R-groups, we require higher pHs, and for acidic R-groups we require lower pHs e.g. Isoelectric point for gly pH = 6.0 Asp pH = 3.0 Lys pH = 9.8 Arg pH = 10.8

47. more consistent with this than this 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

48. 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

49. 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).

50. typical ammonium ion: pKa ~9 typical carboxylic acid: pKa ~5 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.