Amino acid

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Phenylalanine is one of the standard amino acids.

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In chemistry, an amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.[1] In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine, through a methyl group in alanine, to a large heterocyclic group in tryptophan.

Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. For example, the chelating agents EDTA and nitriloacetic acid are alpha amino acids that are important in the chemical industry.


Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. These twenty amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.

Functions in proteins

See also: Primary structure and Posttranslational modification
A polypeptide is a chain of amino acids.


Non-protein functions

The twenty standard amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.[2] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.[3] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[4]

Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms. Microorganisms and plants can produce uncommon amino acids. In microbes, examples include 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged alanine dimer. Both these amino acids are both found in peptidic lantibiotics such as alamethicin.[5] While in plants, 1-Aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.[6]

In humans, non-protein amino acids also have biologically-important roles. Glycine, gamma-aminobutyric acid and glutamate are neurotransmitters and many amino acids are used to synthesize other molecules, for example:

Also present are hydroxyproline, hydroxylysine, and sarcosine. The thyroid hormones are also alpha-amino acids.

Some amino acids have even been detected in meteorites, especially in a type known as carbonaceous chondrites.[7] This observation has prompted the suggestion that life may have arrived on earth from an extraterrestrial source.

General structure

Further information: List of standard amino acids

In the structure shown to the right, the R represents a side chain specific to each amino acid. The central carbon atom called Cα is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached. Amino acids are usually classified by the properties of the side chain into four groups. The side chain can make them behave like a weak acid, a weak base, a hydrophile if they are polar, and hydrophobe if they are nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are catalogued in the list of standard amino acids.

The phrase "branched-chain amino acids" or BCAA is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear, these are leucine, isoleucine and valine. Proline is the only proteinogenic amino acid whose side group links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed an imino acid, but this is not correct in the current nomenclature.[8]

The two optical isomers of alanine.


Most amino acids can exist in either of two optical isomers, called D and L. The L-amino acids represent the vast majority of amino acids found in proteins. D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails.[9] They are also abundant components of the peptidoglycan cell walls of bacteria.[10]

The L and D conventions for amino acid configuration do not refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde having the same stereochemistry as the amino acid. S-Glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and so S-amino acids are called L- even if they are not levorotary, and R-amino acids are likewise called D- even if they are not dexterorotary.




Peptide bond formation

The condensation of two amino acids to form a peptide bond.
For more details on this topic, see Peptide bond.


However, not all peptide bonds are formed in this way. In a few cases peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.[13] In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.[14]



An amino acid, in its (1) normal (unionized) and (2) zwitterionic forms.


Hydrophilic and hydrophobic amino acids



Table of standard amino acid abbreviations and side chain properties

Amino Acid 3-Letter 1-Letter Side chain polarity Side chain acidity or basicity Hydropathy index[17]
Alanine Ala A nonpolar neutral 1.8
Arginine Arg R polar basic (strongly) -4.5
Asparagine Asn N polar neutral -3.5
Aspartic acid Asp D polar acidic -3.5
Cysteine Cys C polar neutral 2.5
Glutamic acid Glu E polar acidic -3.5
Glutamine Gln Q polar neutral -3.5
Glycine Gly G nonpolar neutral -0.4
Histidine His H polar basic (weakly) -3.2
Isoleucine Ile I nonpolar neutral 4.5
Leucine Leu L nonpolar neutral 3.8
Lysine Lys K polar basic -3.9
Methionine Met M nonpolar neutral 1.9
Phenylalanine Phe F nonpolar neutral 2.8
Proline Pro P nonpolar neutral -1.6
Serine Ser S polar neutral -0.8
Threonine Thr T polar neutral -0.7
Tryptophan Trp W nonpolar neutral -0.9
Tyrosine Tyr Y nonpolar neutral -1.3
Valine Val V nonpolar neutral 4.2

In addition to the normal amino acid codes, placeholders were used historically in cases where chemical or crystallographic analysis of a peptide or protein could not completely establish the identity of a certain residue in a structure. The ones they could not resolve between are these pairs of amino-acids:

Ambiguous Amino Acids 3-Letter 1-Letter
Asparagine or aspartic acid Asx B
Glutamine or glutamic acid Glx Z
Leucine or Isoleucine Xle J
Unspecified or unknown amino acid Xaa X


Nonstandard amino acids

The amino acid selenocysteine.

Aside from the twenty standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.[18] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG.[19]


Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine, [21] while dopamine is synthesized from l-DOPA, and hydroxyproline is made by a posttranslational modification of proline.[22]

Uses in technology

Amino acid derivative Use in industry
L-DOPA (L-dihydroxyphenylalanine) Treatment for Parkinsonism.

Nutritional importance

Further information: Protein in nutrition

Of the 20 standard proteinogenic amino acids, 8 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.[23] However, the situation is a little more complicated since cysteine, tyrosine, histidine and arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.[24] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

Essential Nonessential
Isoleucine Alanine
Leucine Asparagine
Lysine Aspartate
Methionine Cysteine*
Phenylalanine Glutamate
Threonine Glutamine*
Tryptophan Glycine*
Valine Proline*
Arginine* Serine*
Histidine* Tyrosine*

(*) Essential only in certain cases.[25][26]

Several common mnemonics have evolved for remembering the ten amino acids often described as essential. PVT TIM HALL ("Private Tim Hall") uses the first letter of each of these amino acids.[27] Another mnemonic that frequently occurs in student practice materials beneath "TV TILL Past Midnight", which just includes the 8 essential amino acids, is "These ten valuable amino acids have long preserved life in man".[28]

See also

References and notes

  1. Proline is an exception to this general formula. It lacks the NH2 group because of the cyclization of the side chain.
  2. Sakami W, Harrington H. "Amino acid metabolism". Annu Rev Biochem 32: 355-98. PMID 14144484.
  5. Whitmore L, Wallace B (2004). "Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation.". Eur Biophys J 33 (3): 233-7. PMID 14534753.
  6. Alexander L, Grierson D (2002). "Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening". J Exp Bot 53 (377): 2039-55. PMID 12324528.
  7. Llorca J (2004). "Organic matter in meteorites.". Int Microbiol 7 (4): 239-48. PMID 15666244.
  8. Claude Liebecq (Ed) Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 39-69 ISBN 978-1855780057
  9. Pisarewicz K, Mora D, Pflueger F, Fields G, Marí F (2005). "Polypeptide chains containing D-gamma-hydroxyvaline.". J Am Chem Soc 127 (17): 6207-15. PMID 15853325.
  10. van Heijenoort J (2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan.". Glycobiology 11 (3): 25R-36R. PMID 11320055.
  12. Lengyel P, Söll D (1969). "Mechanism of protein biosynthesis". Bacteriol Rev 33 (2): 264-301. PMID 4896351.
  13. Wu G, Fang Y, Yang S, Lupton J, Turner N (2004). "Glutathione metabolism and its implications for health". J Nutr 134 (3): 489-92. PMID 14988435.
  15. Carpino, L. A. (1992) 1-Hydroxy-7-azabenzotriazole. An efficient Peptide Coupling Additive. J. Am. Chem. Soc. 115, 4397-4398.
  16. Urry, D. W. (2004). "The change in Gibbs free energy for hydrophobic association - Derivation and evaluation by means of inverse temperature transitions". Chemical Physics Letters 399 (1-3): 177-183.
  17. Kyte J & RF Doolittle (1982). "A simple method for displaying the hydropathic character of a protein". J. Mol. Biol. (157): 105-132. PMID 7108955.
  18. Driscoll D, Copeland P. "Mechanism and regulation of selenoprotein synthesis.". Annu Rev Nutr 23: 17-40. PMID 12524431.
  19. Krzycki J (2005). "The direct genetic encoding of pyrrolysine.". Curr Opin Microbiol 8 (6): 706-12. PMID 16256420.
  20. Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N, Bénazeth S, Cynober L (2005). "Almost all about citrulline in mammals". Amino Acids 29 (3): 177-205. PMID 16082501.
  21. Brosnan J, Brosnan M (2006). "The sulfur-containing amino acids: an overview". J Nutr 136 (6 Suppl): 1636S-1640S. PMID 16702333.
  22. Kivirikko K, Pihlajaniemi T. "Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases". Adv Enzymol Relat Areas Mol Biol 72: 325-98. PMID 9559057.
  23. Young VR (1994). "Adult amino acid requirements: the case for a major revision in current recommendations". J. Nutr. 124 (8 Suppl): 1517S–1523S. PMID 8064412.
  24. Imura K, Okada A (1998). "Amino acid metabolism in pediatric patients". Nutrition 14 (1): 143-8. PMID 9437700.
  25. Fürst P, Stehle P (2004). "What are the essential elements needed for the determination of amino acid requirements in humans?". J. Nutr. 134 (6 Suppl): 1558S–1565S. PMID 15173430.
  26. Reeds PJ (2000). "Dispensable and indispensable amino acids for humans". J. Nutr. 130 (7): 1835S–40S. PMID 10867060.
  27. "Chapter 39 PVT TIM HALL". Retrieved 2007-09-29. 
  28. Memory aids for medical biochemistry. Access date 25 February 2006

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