• Miller-Urey Experiment: Amino Acids & The Origins of Life on Earth
  

The general structure of an α-amino acid molecule, with the amine group on the left and the carboxyl group on the right. The R group is dependent on the amino acid.

In chemistry, an amino acid is any molecule that contains both amine and carboxyl functional groups. In biochemistry, this shorter and more general term is frequently used to refer to alpha amino acids: those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, the so-called α–carbon. These amino acids are used as the basic components of proteins. There are twenty "standard" amino acids used by cells in protein biosynthesis that are specified by the general genetic code. A list of standard amino acids describes their chemical structures and basic physical and chemical properties.

An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H⁺ from the nitrogenous side and an OH^- from the carboxylic side) in the formation of a peptide bond, the chemical bond that links the amino acid monomers in a protein chain. Each protein has its own unique amino acid sequence that is known as its primary structure. Just as the letters of the alphabet can be combined in different ways to form an almost endless variety of words, amino acids can be linked together in varying sequences to form a huge variety of proteins. The unique shape of each protein determines its function in the body.

Overview

Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or polypeptides which in turn form structures called proteins. The process of such formation from an mRNA template is known as translation, which is part of protein synthesis.

Phenylalanine is one of the standard amino acids.

Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. The mean mass of the standard amino acids, weighted by abundance in proteins, is roughly 111 Daltons (Senko 1995). Combinations of these amino acids produce every single essential protein for the homeostasis of the human body. At least two others are also coded by DNA in a non-standard manner as follows:

• Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
• Pyrrolysine is used by some methanogenic bacteria in enzymes that they use to produce methane. It is coded for with the codon UAG.

Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function of the protein.

Proline is the only proteinogenic amino acid whose side group cyclizes onto the backbone: it 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 by current nomenclature rules.

Hundreds of non-proteinogenic alpha-amino acids have been found in nature. Some of these have even been detected in meteorites, especially in a type known as carbonaceous chondrites. Microorganisms and plants can produce uncommon amino acids, which can be found in peptidic antibiotics (e.g., nisin or alamethicin). Lanthionine is a sulfide-bridged alanine dimer which is found together with unsaturated amino acids in lantibiotics (antibiotic peptides of microbial origin). 1-Aminocyclopropane-1-carboxylic acid (ACC) is a small disubstituted cyclic amino acid and a key intermediate in the production of the plant hormone ethylene. The Thyroid hormones are also alpha-amino acids.

In addition to protein synthesis, amino acids have other biologically-important roles. Glycine and glutamate are neurotransmitters as well as standard amino acids in proteins. Many amino acids are used to synthesize other molecules, for example:

• Tryptophan is a precursor of the neurotransmitter serotonin
• Glycine is one of the reactants in the synthesis of porphyrins such as heme
• Arginine is used to synthesize the hormone nitric oxide

Numerous non-standard amino acids are also biologically-important: Gamma-aminobutyric acid is another neurotransmitter, carnitine is used in lipid transport within a cell, ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine.

General structure

Further information: List of standard amino acids

The general structure of proteinogenic alpha amino acids at a physiologically relevant pH:

     R
     |
+H3N-Cα-COO-
     |
     H

Where R represents a side chain specific to each amino acid, and C_α the chiral central carbon atom 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 cataloged in the list of standard amino acids.

The phrase "branched-chain amino acids" is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear: leucine, isoleucine and valine.

Isomerism

Most amino acids occur in two possible 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. They are also abundant components of the proteoglycan cell walls of bacteria. The D-isomer of aspartic acid is found in some proteins as the result of a spontaneous post-translational modification associated with protein aging or as the by-product of enzymatic modification catalyzed by protein L-isoaspartyl methyltransferase.

The L and D conventions for amino acid do not refer to their own optical activity, but rather to the optical activity of glyceraldehyde as an analogue of the amino acids. 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.

Exceptions

Two exceptions exist:

• In glycine, where R = H, and there is no isomerism, because two groups on the central carbon atom are identical

• In cysteine, the L = S and D = R assignment is reversed to L = R and D = S. Cysteine is structured similarly (with respect to glyceraldehyde) to the other amino acids but the sulfur atom alters the interpretation of the Cahn-Ingold-Prelog priority rule.

Reactions

Summary of a peptide bond forming.

Proteins are created by polymerization of amino acids. This condensation reaction yields the newly formed peptide bond and a molecule of water.

Hydrophilic and hydrophobic amino acids

Depending on the polarity of the side chain, aminoacids can be hydrophilic or hydrophobic to various degrees. This influences their interaction with other structures, both within the protein itself and within other proteins. The distribution of hydrophilic and hydrophobic aminoacids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. For example, soluble proteins have surfaces rich with polar aminoacids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic aminoacids that anchors them to the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged aminoacids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine.

Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of aminoacids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophilic glycoproteins.

Table of standard amino acid abbreviations and basic properties

A star (*) indicates that either can be chosen.

Nonstandard amino acids

Aside from the twenty standard amino acids and the two special amino acids, selenocysteine and pyrrolysine, already mentioned above, there are a vast number of "nonstandard amino acids" which are not incorporated into protein. Examples of nonstandard amino acids include the sulfur-containing taurine and the neurotransmitters GABA and dopamine. Other examples are lanthionine, 2-Aminoisobutyric acid, and dehydroalanine. Nonstandard amino acids often occur in the metabolic pathways for standard amino acids - for example ornithine and citrulline occur in the urea cycle, part of amino acid breakdown.

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, taurine can be formed by the decarboxylation of cysteine, while dopamine is synthesized from tyrosine and hydroxyproline is made by a posttranslational modification of proline (common in collagen).

Over 79 amino acids were found in the primitive Murchison meteorite.

Uses of substances derived from amino acids

• Aspartame (aspartyl-phenylalanine-1-methyl ester) is an artificial sweetener.
• 5-HTP (5-hydroxytryptophan) has been used to treat neurological problems associated with PKU (phenylketonuria), as well as depression (as an alternative to L-Tryptophan).
• L-DOPA (L-dihydroxyphenylalanine) is a drug used to treat Parkinsonism.
• Monosodium glutamate is a food additive to enhance flavor.

Nutritional importance

Some of the 20 standard proteinogenic amino acids are called essential amino acids because the human body cannot synthesize them from other compounds through chemical reactions, and they therefore must be obtained from food. Histidine and arginine are generally only considered essential in children, because the metabolic pathways that synthesize these amino acids are not fully developed in children.

(*) Essential only in certain cases

A helpful mnemonic for remembering essential amino acids is "Private Tim Hall" (PVT TIM HALL). Arginine, although not required in normal adults is required for infants. Another, that lists them in alphabetical order, is "ILL MPs Take To Valium." Kreb's trick to remember the essential amino acids: Archibald Vivian HILL Member of Parliament Tee Totalist.

See also

• Beta amino acid
• Strecker amino acid synthesis
• List of standard amino acids
• Murchison meteorite, an extraterrestrial source of amino acids.

References

• Senko, Michael W.; Beu, Steven C.; McLafferty, Fred W.: "Determination of Monoisotopic Masses and Ion Populations for Large Biomolecules from Resolved Isotopic Distributions", Journal of the American Society for Mass Spectrometry, 1995, 6:229-233
• Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp. 599-623
• David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6
• On the hydrophobic nature of cysteine.

External links

• Molecular Expressions: The Amino Acid Collection - Has detailed information and microscopy photographs of each amino acid.
• 22nd amino acid - Press release from Ohio State claiming discovery of a 22nd amino acid.
• Amino acid properties - Properties of the amino acids (a tool aimed mostly at molecular geneticists trying to understand the meaning of mutations)
• Synthesis of Amino Acids and Derivatives
• Right-handed amino acids were left behind