Amino acids

[Brooke]

_{Phenylalanine is one of the standard amino acids.}

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. 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 are also important. The chelating agents EDTA and nitriloacetic acid are alpha amino acids that are industrially synthesized (sometimes from naturally occurring amino acids).

[Brooke]

The two optical isomers of alanine.

[Brooke]

Alpha-amino acids are the building blocks of proteins. A protein forms via the condensation of amino acids to form a chain of amino acid "residues" linked by peptide bonds. Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins.

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.

[Brooke]

A polypeptide is a chain of amino acids.

Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or longer chains either called polypeptides or proteins. The process of such formation from an mRNA template is known as translation which is part of protein biosynthesis. Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. 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 or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues and responding to oxygen starvation. Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.

[Brooke]

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.

[Brooke]

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.

[Brooke]

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. They are also abundant components of the peptidoglycan cell walls of bacteria.

The L and D conventions for amino acid configuration do not refer to the optical activity, 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.

There are two exceptions to these general rules of amino acid isomerism. Firstly, glycine, where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Secondly, 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.

[Brooke]

As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group. The multiple side chains of amino acids can also undergo chemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in the articles dealing with each specific type of amino acid.

[Brooke]

The condensation of two amino acids to form a peptide bond.

[Brooke]

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly, instead the amino acid is activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond. As a result of this mechanism, all proteins are synthesized starting at their N-terminus and moving towards their C-terminus.

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. 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.

In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.

[Brooke]

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