Amino acids

In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid 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 &alpha;–carbon.

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.

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.



Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. 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 methanogens in enzymes that they use to produce methane. It is coded for similarly to selenocysteine but with the codon UAG instead.

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

Proline is the only proteinogenic amino acid whose side group is cyclic and links to the a-amino group, forming a secondary amino group. Formerly, proline was misleadingly called an imino acid.

Over one hundred amino acids have been found in nature. Some of these have been detected in meteorites, especially in a type known as carbonaceous chondrites. Microorganisms and plants often produce very 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.

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.

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

Some of the 20 standard amino acids are called essential amino acids because they cannot be synthesized by the body from other compounds through chemical reactions, but instead must be taken in with food. In humans, the essential amino acids are lysine, leucine, isoleucine, methionine, phenylalanine, threonine, tryptophan, valine, and (in children) histidine and arginine.

The phrase "branched-chain amino acids" is sometimes used to refer to the aliphatic amino acids: leucine, isoleucine and valine.

General structure
The general structure of proteinogenic alpha amino acids is:

R | H2N-C-COOH |     H Where R represents a side chain specific to each amino acid. Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).

Isomerism
Except for glycine, where R = H, amino acids occur in two possible optical isomers, called D and L. Using the newer Cahn Ingold Prelog priority rules for designating the configuration of optical isomers, the L isomer would assigned the letter S and the D isomer would be assigned the letter R.  The L (or S) amino acids represent the vast majority of amino acids found in proteins. D (or R) amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the cell walls of bacteria.

Reactions
Proteins are created by polymerization of amino acids by peptide bonds in a process called translation.

''Peptide bond formation 1. Amino acid; 2, zwitterion structure;  3, two amino acids forming a peptide bond. (See also bond.)''

Structures
Structures and symbols of the 20 amino acids present in genetic code.

Chemical properties
Following is a table listing the one letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The mass listed is the weighted average of all common isotopes, and includes the mass of H2O. The one-letter symbol for an undetermined amino acid is X. The three-letter symbol Asx or one-letter symbol B means the amino acid is either asparagine or aspartic acid, whereas Glx or Z means either glutamic acid or glutamine. The three-letter symbol Sec or one-letter symbol U refers to selenocysteine. The letters J and O are not used.

Hydrophilic and hydrophobic amino acids
Depending on how polar the side chain, aminoacids can be hydrophilic or hydrophobic to various degree. 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 positive-charged molecules have surfaces rich with negatively charged aminoacids like glutamate and aspartate, while proteins binding to negative-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 aminoacids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophylic glycoproteins.

Nonstandard amino acids
Aside from the twenty standard amino acids and the two special amino acids, selenocysteine and pyrrolysine, already mentioned above, there is a vast number of "nonstandard amino acids" which are not used in the body's regular manufacturing of proteins. Examples of nonstandard amino acids include the sulfur-containing taurine and the neurotransmitters GABA and dopamine. Other examples are lanthionine, 1-amino isobutyric acid, dehydroalanine, dehydro-amino-butyric acid,

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 from proline.

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.