Chemistry of amino acids

Structure, properties and reactions of amino acids for undergraduate medical and biochemistry students

1. Chemistry of Amino Acids R.C . Gupta M.D. (Biochemistry) Jaipur , India

2. A mino acids are the building blocks of proteins Living cells produce a vast array of proteins Proteins are among the most important biomolecules Proteins perform a variety of biological functions

3. RCG

4. Carboxylic acids having one or more amino groups Carbon atoms are numbered 1, 2, 3 etc starting from the carboxyl group Also named a, b, g etc starting from carbon atom next to the carboxyl group Amino acids RCG

5. R — CH 2 — CH 2 — CH 2 — COOH The amino group may be attached to any of the carbon atoms next to the carboxyl group The amino acid is accordingly known as a - amino acid (2-amino acid), b -amino acid (3- amino acid), g -amino acid (4-amino acid) etc RCG 4  3 2 1 g b a

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7. Proteins are made up of only a -amino acids The amino acid can exist as a D-isomer and an L-isomer Therefore, they exhibit stereo-isomerism and optical isomerism The a -amino acids contain at least one asymmetric carbon atom RCG

8. R R | R | H — C* — NH 2 | COOH D-Amino acid L-Amino acid H 2 N— C * — H | COOH D- and L- Isomers A mino group is present on right hand side of a -carbon * in D-amino acids, and on left hand side in L-amino acids RCG

9. Glycine is the only amino acid that has no asymmetric carbon atom and, hence, no stereoisomers Threonine, isoleucine, hydroxylysine and hydroxyproline have two asymmetric carbon atoms, and hence four stereoisomers each RCG

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11. Classification RCG

12. The side chain of the amino acid may be polar or non-polar Accordingly, the amino acids may be polar or non-polar amino acids Classification according to polarity RCG

13. P olar and non-polar amino acids Non-p olar amino acids Have no ionizable groups in side chain Include alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan and proline P olar amino acids Have ionizable groups in side chain Include glycine, serine, threonine, cysteine, aspartate, glutamate, asparagine, glutamine, tyrosine, lysine, arginine and histidine RCG

14. They are less polar and less soluble in polar solvents than the polar amino acids However, non-polar amino acids are not absolutely non-polar RCG

15. In trans-membrane proteins: The polar amino acids are present outside or inside the membrane Non-polar amino acids are generally embedded in the lipid bilayer RCG

16. Polar amino acids Non-polar amino acids

17. The side chains of amino acids may differ in chemical nature T he amino acids may be divided into several groups on this basis Classification according to nature of side chain RCG

18. 1 . Amino acids with aliphatic side chains CH—CH—COOH NH 2 CH 3 CH 3 Valine (Val or V) CH — CH — COOH | NH 2 CH 2 CH 3 Isoleucine (Ile or I) CH 3 CH —CH 2 — CH —COOH | NH 2 CH 3 CH 3 Leucine (Leu or L) | RCG

19. 2. Amino acids with side chains having hydroxyl group RCG

20. 3. Amino acids with side chains containing sulphur RCG

21. 4. Amino acids with side chains having acidic groups or their amides CH 2 CH COOH COOH NH 2 Aspartate (Asp or D) CH 2 CH COOH CONH 2 NH 2 Asparagine ( Asn or N) CH 2 CH 2 CH COOH COOH NH 2 Glutamate ( Glu or E) CH 2 CH 2 CH COOH CONH 2 NH 2 Glutamine ( Gln or Q) RCG

22. 5. Amino acids with side chains having basic groups — CH — CH — COOH 2 | NH 2 Histidine (His or H) N HN RCG

23. 6. Amino acids with side chains containing aromatic rings —CH 2 —CH—COOH | NH 2 Tyrosine (Tyr or Y) HO ‒ — CH 2 —CH—COOH | NH 2 Tryptophan ( Trp or W) N H — CH 2 —CH—COOH | Phenylalanine ( Phe or F) NH 2 RCG

24. 7 . Imino acids RCG

25. Lysine and proline can be hydroxylated after their incorporation into proteins N H COOH HO CH 2 — CH — CH 2 — CH 2 — CH — COOH | NH 2 | NH 2 | OH Hydroxylysine ( Hyl ) Hydroxyproline ( Hyp ) They are converted into hydroxylysine and hydroxyproline respectively RCG

26. Two cysteine residues in a protein may be linked through their –SH groups to form a cystine residue CH 2 — CH — COOH | S | NH 2 CH 2 — CH — COOH | NH 2 | | S Cystine RCG

27. Some enzymes contain an unusual amino acid, selenocysteine , at their catalytic site Selenocysteine SeH CH 2 — CH — COOH | | NH 2 RCG

28. Classification according to nutritional importance RCG

29. Proteins are synthesized from 20 standard amino acids However, some of these amino acids can be synthesized in our body Essential amino acids All the standard amino acids are equally important for protein synthesis RCG

30. Some of the standard amino acids cannot be synthesized by human beings These amino acids are known as essential amino acids If these are not provided in diet, protein synthesis will be impaired RCG

31. Thus, the essential amino acids are nutritionally indispensable V aline , leucine, isoleucine, threonine, methionine , lysine, phenylalanine and tryptophan are essential amino acids RCG Animal proteins generally contain all the the essential amino acids

32. Synthesis of semi-essential amino acids is below their requirement in childhood Hence, t hey must be provided in the diet of children Arginine and histidine are semi-essential amino acids Semi-essential amino acids RCG

33. Endogenous synthesis of non-essential amino acids can meet our requirement Hence, t heir presence in the diet is not essential Glycine, alanine, serine, cysteine, aspartate, glutamate, asparagine, glutamine, tyrosine and proline are non-essential amino acids Non-essential amino acids RCG

34. Besides the 20 standard amino acids, some other L- a -amino acids are also found in human beings These are either intermediates or products of various metabolic pathways Non-standard amino acids RCG

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36. ‒CH 2 ‒CH‒COOH NH 2 I HO D ihydroxyphenylalanine (DOPA) HO ‒ ‒CH 2 ‒CH‒COOH NH 2 I I Mono- iodo -tyrosine (MIT) HO ‒ ‒CH 2 ‒CH‒COOH NH 2 I I I Di- iodo -tyrosine (DIT) HO ‒ RCG

37. ‒O‒ ‒CH 2 ‒CH‒COOH NH 2 I I I I I Tetra- iodo - thyronine (T 4 ) HO ‒ ‒O‒ ‒CH 2 ‒CH‒COOH NH 2 I I I I Tri- iodo - thyronine (T 3 ) HO ‒ RCG

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39. CH 2 — CH 2 — COOH | NH 2 b -Alanine CH 2 — CH— COOH | NH 2 | CH 3 b - Aminoisobutyric acid CH 2 —CH 2 — CH 2 — COOH | NH 2 g -Aminobutyric acid CH 2 — CH 2 — SO 3 H | NH 2 Taurine Some non- a -amino acids are also present in human beings Examples are b -alanine , taurine, b -amino- isobutyric acid, g -aminobutyric acid etc

40. b -Alanine is a constituent of pantothenic acid, acyl carrier protein and coenzyme A g -Aminobutyric acid (GABA) is a neuro-transmitter b - Aminoisobutyric acid is a metabolite of some pyrimidines Taurine is a neurotransmitter, and is a constituent of bile acids and bile salts

41. Physical properties Amino acids are crystalline solids All amino acids have high melting points Aromatic amino acids absorb ultraviolet light They are soluble in polar solvents

42. All amino acids have at least one carboxyl and one amino group Amphoteric nature Both these groups are ionizable R ‒COOH R ‒COO ‒ + H + R ‒NH 2 + H + R ‒NH 3 + RCG

43. R–COOH and R–NH 3 + are acidic forms as they can donate hydrogen ions (protons ) Thus, amino acids can act as acids (proton donors) as well as bases (proton acceptors) R–COO – and R–NH 2 are conjugate bases as they can accept hydrogen ions RCG

44. Therefore , amino acids are said to be amphoteric in nature They can behave as acids as well as bases depending upon the pH of the medium in which they are present RCG

45. The amino acid, therefore, behaves as an acid in an alkaline medium In an alkaline medium, the carboxyl group is dissociated while ionization of amino group is suppressed R ‒CH‒COOH R ‒CH‒COO ‒ + H + I I NH 2 NH 2 RCG

46. Thus, the amino acid acts as a proton acceptor (base) in an acidic medium In an acidic medium, the amino group is ionized while ionization of carboxyl group is suppressed NH 3 + R ‒CH‒COOH + H + R ‒CH‒COOH I I NH 2 RCG

47. T here is a certain pH at which both carboxyl and amino groups are ionized NH 3 + R – CH – COO‾ This form of amino acid is known as a zwitterion The carboxyl group is un-protonated and the amino group is protonated RCG

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49. Isoelectric pH is constant for every amino acid Solubility of the amino acid is the least at its isoelectric pH Completely un-dissociated form of amino acids is shown frequently for the sake of simplicity It does not exist in solution at any pH

50. S trength of an acid depends on the degree to which it dissociates and liberates protons Strength of acids is generally expressed in terms of their dissociation constants Since amino acids are very weak acids, their strength is expressed in terms of pK RCG

51. RCG

52. One of the most important reactions of amino acids The bond by which amino acids are linked with each other in peptides and proteins Formed between carboxyl group of one amino acid and amino group of another amino acid Formation of peptide bonds RCG

53. H 2 N ‒CH‒C‒ N ‒CH‒COOH R 1 R 2 O H H 2 O Amino acid 1 Amino acid 2 Dipeptide Peptide bond ► ► RCG R 1 H 2 N ‒CH‒COOH R 2 H 2 N ‒CH‒COOH

54. F ormation of peptide bonds in living cells is a complex process The reaction occurs in stages, and requires the presence of enzymes, coenzymes and other factors RCG

55. RCG ↑ Amino end ↑ Carboxyl end -COOH H 2 N- AA AA AA AA AA AA AA AA

56. RCG ↑ N-Terminus ↑ C-Terminus -COOH H 2 N- AA AA AA AA AA AA AA AA

57. Reactions of carboxyl and amino groups RCG

58. The sulphydryl ( ‒ SH) group of cysteine can undergo reversible oxidation and reduction Disulphide bonds can be formed between the ‒ SH groups of two cysteine residues The ‒ SH groups are essential for the biological activity of many proteins Reactions of sulphydryl groups RCG

59. ‒ N ‒ CH ‒ C ‒ | S | | H | | S Cysteine residue CH 2 CH 2 | ‒ N ‒ CH ‒ C ‒ | H | | | | O O Cysteine residue Disulphide bond RCG

60. Reactions for determining amino acid sequence of proteins RCG

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63. Sanger’s reaction RCG

64. HF 1-Fluro-2,4-dinitro benzene N-Terminal amino acid residue N-Terminal amino acid residue tagged with 2,4-dinitrobenzene O 2 N— NO 2 — HN—CH—C— R O O 2 N— NO 2 —F H 2 N—CH—C— R O   RCG

65. Edman’s reaction RCG

66. S || —NH—C—NH—CH—C— R | O || Phenyliso thiocyanate N-Terminal amino acid residue Phenylthiohydantoic acid residue H 2 O Acid, nitromethane Phenylthiohydantoin Phenylthiohydantoic acid RCG S || C CH | R C || O —NH NH OH S || C CH | R C || O —N NH  — N=C=S H 2 N—CH—C— R O ►

67. Reactions for identification of specific amino acids

68. Ninhydrin reaction

69. O ‒ NH 4 + | || O — N = O | | | | O Coloured complex O || || O OH OH Ninhydrin a -Amino acid R—CH—COOH | NH 2 R—CHO + CO 2 + NH 3 O || || O OH H Reduced ninhydrin O || || O OH OH Ninhydrin 2 NH 3 RCG

70. Xanthoproteic reaction

71. This reaction is given by the 3,5-unsubs-tituted hydroxyphenyl group of tyrosine Mercuric sulphate and nitrous acid cause mercuration and nitration or nitrosation of the hydroxyphenyl group of tyrosine This produces a red colour Millon-Nasse reaction

72. Aldehyde reaction

73. Hopkins-Cole reaction

74. This reaction is given by the guanidino group of arginine In a basic medium, a - naphthol reacts with the guanidino group forming a complex On adding sodium hypobromite / hypochlorite, the complex is oxidized to a red coloured product Sakaguchi’s reaction

75. Lead sulphide reaction

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