1. Principles of Biochemistry
Horton • Moran • Scrimgeour • Perry • Rawn
Principles of Biochemistry
Fourth Edition
Chapter 17
Amino Acid Metabolism
Copyright © 2006 Pearson Prentice Hall, Inc.

2. Chapter 17 - Amino Acid Metabolism
Metabolism of the 20 common amino acids is considered from the origins and fates of their: (1) Nitrogen atoms (2) Carbon skeletons
For mammals: Essential amino acids must be obtained from diet Nonessential amino acids - can be synthesized

3. 17.1 The Nitrogen Cycle and Nitrogen Fixation
Nitrogen is needed for amino acids, nucleotides
Atmospheric N2 is the ultimate source of biological nitrogen
Nitrogen fixation: a few bacteria possess nitrogenase which can reduce N2 to ammonia
Nitrogen is recycled in nature through the nitrogen cycle

4. Fig 17.1 The Nitrogen cycle Figure 17.1
Nitrogen cycle. A few free-living or symbiotic microorganisms can convert N2 to ammonia. Ammonia is incorporated into biomolecules such as amino acids and proteins, which later are degraded, re-forming ammonia. Many soil bacteria and plants can carry out the reduction of nitrate to ammonia via nitrite. Several bacteria convert ammonia to nitrite. Others oxidize nitrite to nitrate, and some can reduce nitrate to N2.

5. Nitrogen Fixation
Most green plants and some microorganisms contain nitrate reductase and nitrite reductase, enzymes that together catalyze the reduction of nitrogen oxides to ammonina.

6. Nitrogenase
An enzyme present in Rhizobium bacteria that live in root nodules of leguminous plants
Some free-living soil and aquatic bacteria also possess nitrogenase
Nitrogenase reaction:
N2 + 8 H+ + 8 e ATP
2 NH3 + H ATP + 16 Pi

7. Figure 17.3
Structure of the MoFe7S9N • homocitrate reactive center in Azotobacter vinelandii. (a) Resting state. (b) One possible structure with bound N2. [PDB 2MIN]

8. Figure 17.3
Structure of the MoFe7S9N • homocitrate reactive center in Azotobacter vinelandii. (a) Resting state. (b) One possible structure with bound N2. [PDB 2MIN]

9. Figure 17.3
Structure of the MoFe7S9N • homocitrate reactive center in Azotobacter vinelandii. (a) Resting state. (b) One possible structure with bound N2. [PDB 2MIN]

10. 17.2 Assimilation of Ammonia
Ammonia generated from N2 is assimilated into low molecular weight metabolites such as glutamate or glutamine
At pH 7 ammonium ion predominates (NH4+)
At enzyme reactive centers unprotonated NH3 is the nucleophilic reactive species

11. A. Ammonia Is Incorporated into Glutamate
Reductive amination of a-ketoglutarate by glutamate dehydrogenase occurs in plants, animals and microorganisms
Glutamine is a nitrogen donor in many biosynthetic reactions

12. Fig 17.5 Glutamate synthase catalyze the reductive amination of a-ketoglutarate
Animals do not have glutamate synthase.

13. B. Transamination Reactions
Transfer of an amino group from an a-amino acid to an a-keto acid
In amino acid biosynthesis, the amino group of glutamate is transferred to various a-keto acids generating a-amino acids
In amino acid catabolism, transamination reactions generate glutamate or aspartate

14. Fig 17.6 Transfer of an amino group from an a-amino acid to an a-keto acid

15. Fig 17.7 Pig (Sus scrofa) cytosolic aspartate transaminase
(Space-filling model: the coenzyme pyridoxal phosphate)

16. Fig 17.8 Assimilation of ammonia into amino acids
a. The glutamate dehydrogenase pathway.

17. Fig 17.8 Assimilation of ammonia into amino acids
b. Combined action of glutamine synthetase and glutamate synthase under conditions of low NH4+ concentration.

18. 17.3 Synthesis of Amino Acids
Most bacteria and plants (not mammals) synthesize all 20 common amino acids
Nonessential amino acids for mammals are usually derived from intermediates of glycolysis or the citric acid cycle (11 of the 20 a.a.)
Amino acids with the largest energy requirements are usually essential amino acids

19. Box 17.3 Essential and Nonessential Amino Acids in Animals

20. Fig 17.9 Biosynthesis of Amino Acids

21. A. Asparate and Asparagine
Oxaloacetate is the amino-group acceptor in a transamination reaction that produces asparate.

22. B. Lysine, Methionine, and Threonine
Aspartate is the precursor of lysine, methionine, and threonine.

23. C. Alanine, Valine, Leucine, and Isoleucine
Pyruvate is the amino group acceptor in the synthesis of alanine by a transamination reaction.

24. C. Alanine, Valine, Leucine, and Isoleucine
Pyruvate is also a precursor in the synthesis of the branched-chain amino acids valine, leucine, and isoleucine.

25. D. Glutamate, Glutamine, Arginine, and Proline
Fig Conversion of glutamate to proline and arginine

26. E. Serine, Glycine, and Cysteine
Serine, glycine, and cysteine- are derived from the glycolytic/gluconeogenic intermediate 3-phosphoglycerate.
Fig Biosynthesis of serine.

27. E. Serine, Glycine, and Cysteine
Serine, glycine, and cysteine- are derived from the glycolytic/gluconeogenic intermediate 3-phosphoglycerate.
Fig Biosynthesis of glycine.

28. E. Serine, Glycine, and Cysteine
Serine, glycine, and cysteine- are derived from the glycolytic/gluconeogenic intermediate 3-phosphoglycerate.
Fig Biosynthesis of cysteine from serine in many bactera and plants.

29. Fig 17.17 Biosynthesis of cysteine in mammals
Animals do not have the normal cysteine biosynthesis pathway shown in fig

30. F. Phenylalanine, Tyrosine, and Tryptophan
Chorismate, a derivative of shikimate, is a key branch-point intermediate in aromatic amino acid synthesis.
Animals can not synthesize chorismate.

31. Fig 17.19 Biosynthesis of phenylalanine and tyrosine from chorismate in E. coli

32. Indole glycerol phosphate for Trp biosynthesis
Anthranilate is produced from chorismate
Anthranilate is then converted into indole glycerol phosphate for Trp synthesis

33. Fig 17.21 Reactions catalyzed by tryptophan synthase

34. G. Histidine

35. 17.4 Amino Acids as Metabolic Precursors
The primary role of amino acids is to serve as substances for protein synthesis.
Some amino acids are essential precursors in other biosynthesis pathways.
Glutamate, glutamine, and asparate
Required in the urea cycle
Involved in many transamination
Purine and pyrimidine biosynthesis
Serine and glycine (Fig 17.23)
Arginine (Fig 17.24)

36. Fig 17.23 Compounds formed from serine and glycine

37. Synthesis of Nitric Oxide (NO) from Arginine
Nitric oxide (.N=O) is a gas which can diffuse rapidly into cells, and is a messenger that activates guanylyl cyclase (GMP synthesis)
NO relaxes blood vessels, lowers blood pressure, and is a neurotransmitter in the brain (high levels of NO during a stroke kill neurons)
Nitroglycerin is converted to NO and dilates coronary arteries in treating angina pectoris

38. Fig 17.24 Conversion of arginine to nitric oxide and citrulline

39. Sidenafil citrate is the active ingredient in Viagra®

40. 17.5 Protein Turnover
Proteins are continuously synthesized and degraded (turnover) (half-lives minutes to weeks)
Lysosomal hydrolysis degrades some proteins
Some proteins are targeted for degradation by a covalent attachment (through lysine residues) of ubiquitin (C terminus)
Proteasome hydrolyzes ubiquitinated proteins

41. Fig 17.25 Ubiquitination and hydrolysis of a protein
Ubiquination enzymes attach multiple ubiquitins
Proteasome hydrolyzes uniquinated proteins

42. 17.6 Amino Acid Catabolism
Amino acids from degraded proteins or from diet can be used for the biosynthesis of new proteins
During starvation proteins are degraded to amino acids to support glucose formation
First step is often removal of the a-amino group
Carbon chains are altered for entry into central pathways of carbon metabolism

43. Catabolism of the Carbon Chains of Amino Acids
After removal of amino groups, carbon chains of the 20 amino acids can be degraded
Degradation products:
Citric acid cycle intermediates
Pyruvate
Acetyl CoA or acetoacetate

44. Catabolism of Carbon Skeletons
Fig (next slide)
Conversion of the carbon skeletons of amino acids to:
Pyruvate
Acetoacetate
Acetyl CoA
Citric acid cycle intermediates

46. Glucogenic vs Ketogenic Amino Acids
Glucogenic amino acids can supply gluconeogenesis pathway via pyruvate or citric acid cycle intermediates
Ketogenic amino acids can contribute to synthesis of fatty acids or ketone bodies
Some amino acids are both glucogenic and ketogenic

47. A. Alanine, Asparagine, Aspartate, Glutamate, and Glutamine
Reentry into pathways from which carbon skeletons arose by reverse transamination Alanine pyruvate Aspartate oxaloacetate Glutamate a-ketoglutarate
Glutamine and asparagine are first hydrolyzed to glutamate and aspartate

48. B. Arginine, Histidine, and Proline
Fig

49. C. Glycine and Serine

50. Alternate routes for the degradation of threonine to glycine
D. Threonine
Alternate routes for the degradation of threonine to glycine
Figure (next slide)

51. Fig 17.29 Alternate routes for the degradation of threonine

52. E. The Branched-Chain Amino Acids
Leucine, valine and isoleucine are degraded by related pathways
The same three enzymes catalyze the first three steps in all pathways
A branched-chain amino acid transaminase catalyzes the first step

53. Fig 17.30 Catabolism of branched-chain amino acids

54. F. Methionine
Fig 17.31
(X represents any of a number of methyl-group acceptors)

55. F. Methionine
Fig 17.31
(X represents any of a number of methyl-group acceptors)

56. Fig (cont)

57. Fig (cont)

58. G. Cysteine
Fig Conversion of cysteine to pyruvate

59. H. Phenylalanine, Tryptophan, and Tyrosine
Fig 17.33

60. Fig 17.34 Conversion of tryptophan to alanine and acetyl CoA

61. I. Lysine
Fig 17.35

62. I. Lysine
Fig 17.35

63. Fig (cont)

64. 17.7 The Urea Cycle Converts Ammonia into Urea
Waste nitrogen must be removed (ammonia is toxic to plants and animals)
Terrestrial vertebrates synthesize urea (excreted by the kidneys)
Birds, reptiles synthesize uric acid

65. Fig 17.37 A. Synthesis of Carbamoyl Phosphate
Synthesis of carbamoyl phosphate (removal of NH3)
Catalyzed by carbamoyl phosphate synthetase I (CPS I)

66. Fig Synthesis of carbamoyl phosphate (removal of NH3) catalyzed by carbamoyl phosphate synthetase I (CPS I)

67. Fig (cont)

68. B. The Reactions of the Urea Cycle
Urea cycle (Fig & 39 next four slides) Rxn 1 (mitochondria), Rxns 2,3,4 (cytosol)
Two transport proteins are required: Citrulline-ornithine exchanger Glutamate-aspartate exchanger
Overall reaction for urea synthesis is:
NH3 + HCO3- + Aspartate + 3 ADP
Urea + Fumarate + 2 ADP + 2 Pi + AMP + PPi

69. The Urea Cycle

73. C. Ancillary Reactions of the Urea Cycle
Supply of nitrogen for the urea cycle can be balanced by supply of NH3 and amino acids
Glutamate dehydrogenase and aspartate transaminase catalyze near equilibrium reactions
Flux through these enzymes depends upon relative amounts of ammonia and amino acids
Two cases (next slides): (a) NH3 in excess, (b) aspartate in excess

74. Fig 17.40 Balancing the supply of nitrogen for the urea cycle

75. NH3 in extreme excess

76. Aspartate in extreme excess

77. Glucose-alanine cycle
Some amino acids are deaminated in muscle
Exchange of glucose and alanine between muscle and liver
Provides an indirect means for muscle to eliminate nitrogen and replenish its energy supply

78. Fig 17.41 Glucose-alanine cycle

79. 17.8 Renal Glutamine Metabolism Produces Bicarbonate
Bicarbonate can be lost by buffering H+ in blood
Bicarbonate can be replenished by glutamine catabolism in the kidneys
a-Ketoglutarate (formed from glutamine oxidation) can be further metabolized to yield bicarbonate
Glutamine a-ketoglutarate NH4+

80. Glutamine → → a-ketoglutarate2- + 2 NH4+
2 a-ketoglutarate2- → → glucose + 4 HCO3-
2C5H10N2O3 + 3O2 + 6H2O → C6H12O6 + 4HCO3- + 4NH4+

81. Fig 17.42 Loss of bicarbonate as a buffer