In biochemistry, this shorter and more general term is frequently used to refer to alpha amino acids, that is, those amino acids in which the amino and carboxylate functionalities are attached to the same carbon. Some molecules like proline don't contain amino group and chamically are not amino acids (technically it is an imino acid), but are also classified as such because of functional similarity to real amino acids in living cells.
The generalized structure of alpha amino acids is:
COOH | H-C-R | NH2
Where "R" represents a side chain specific to each particular amino acid. Amino acids are usually classified by properties of side chain to four groups: acidic, basic, hydrophilic (polar) and hydrophobic (non-polar).
There are two possible optical isomers, called D and L; 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. Proteins are created by polymerization of amino acids by peptide bonds in a process called translation:
1. Amino Acid 2. Zwitterion structure. 3. Two amino acids forming peptide bond.
There are twenty amino acids represented in the genetic code:
The chemical properties of the side chains are as follows:
|Abbrev.||Full Name||Side chain type||Mass||Isoelectric point||Remarks|
|C||Cys||Cysteine||hydrophilic||121.16||5.05||Two cysteines can form a disulfid bond.|
|G||Gly||Glycine||hydrophilic||75.07||6.06||Because of two hydrogen atoms at α carbon, glycine is not optically active.|
|P||Pro||Proline||hydrophobic||115.13||6.30||Can disrupt protein folding structures like α helix or β sheet.|
Selenocysteine, the 21st "natural" amino acid, is not coded for by a single codon. It is known to occur in several dozen proteins; its mRNA codon is UGA, which usually serves as a stop codon. A specific downstream sequence forms a loop, which forces the incorporation of selenocysteine into proteins.
Note that in the case of proline the side chain links to the amino acid's amino group nitrogen atom as well as the central carbon. A few other amino acids are found in nature, including some D and beta forms, and may be produced from the above after they have been incorporated into proteins; these changes are known as post-translational modifications.
Cysteine is often found in excreted proteins due to the ability of two cysteines to form a di-sulfide bond, which enforces tertiary structure. Insulin, for instance, has two disulfide bonds.
Amino acids are bifunctional compounds - they have two functional groups. The COOH group has acidic properties whereas the NH2 acts as a base. These groups actually react with each other, forming zwitterions - molecules with both positive and negatively charged groups. This causes them to be very soluble as they are effectively ionic. Also adding small quantities of acid or alkali to the solution has no effect because the zwitterions neutralise the affect of the addition.
Amino acids and human health
Some amino acids can't be created by organism from simpler compounds and must be taken with food, just like vitamins. They are called exogenous or essential amino acids. For humans these are: arginine, histidine, leucine, isoleucine, methionine, phenylalanine, threonine, tryptophan, valine.