Amino acid

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.

Overview

Amino acids are biochemical building blocks. They form long chemical chains called proteins (see below), and shorter chains called polypeptides or peptides.

Twenty amino acids are encoded by the standard genetic code and are called proteinogenic. Rarer, more complicated ones are "made to order" by the body. Proline is the only cyclic proteinogenic amino acid. Other amino acids contained in proteins are usually formed by modification after translation (protein synthesis). These modifications are often essential for the function of the protein. At least two amino acids other than the standard 20 are sometimes incorporated into proteins during translation:

• 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.

Over 500 amino acids have been found in nature. Some of them have also been found in meteoritic material. Microorganisms and plants often produce very uncommon amino acids, which can be found in peptidic antibiotics (for example nisin or alamethicin). Lanthionine is a sulfide bridged alanine dimer which is found together with unsaturated amino acids in lantibiotics (antibiotic peptides from microbial origin). 1-Aminocycloproane-1-carboxylic acid ACC is a small disubstituted cyclic amino acid and a key intermediate in the production of the herbal hormone ethylene.

In addition to amino acids for protein synthesis, there are other biologically important amino acids, such as the neurotransmitters glycine, GABA and glutamate, as well as carnitine (used in lipid transport within a cell), ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine.

Some of the 20 amino acids in the genetic code 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.

Uses of amino acids

Monosodium glutamate is a food additive to enhance flavor.
L-DOPA (L-dihydroxyphenylalanine) is a drug used to treat Parkinsonism.
5-HTP (5-hydroxytryptophan) has been used to treat neurological problems associated with PKU (phenylketonuria).

General structure of an amino acid

The general structure of proteinogenic alpha amino acids is:

   COOH
   |
 H-C-R
   |
   NH2

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. 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 cell walls of bacteria.

Reactions

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

Peptide bond formation

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

List of amino acids

Structures

Following is a chart displaying the structures and symbols of the 20 amino acids represented in the 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 amino acids. The one letter symbol for an undetermined amino acid is X. The three letter symbol asx means the amino acid is either asparagine or aspartic acid.

Abbrev.		Full Name	Side chain type	Mass	pI	pK1(α-COOH)	pK2(α-+NH3)	pKr (R)	Remarks
A	Ala	Alanine	hydrophobic	89.09	6.11	2.35	9.87
C	Cys	Cysteine	hydrophilic	121.16	5.05	1.92	10.70	8.37	Under oxidizing conditions, two cysteines can join together by a disulfide bond to form the amino acid cystine. When cysteines are part of a protein, insulin for example, this enforces tertiary structure.
D	Asp	Aspartic acid	acidic	133.10	2.85	1.99	9.90	3.90
E	Glu	Glutamic acid	acidic	147.13	3.15	2.10	9.47	4.07
F	Phe	Phenylalanine	hydrophobic	165.19	5.49	2.20	9.31
G	Gly	Glycine	hydrophilic	75.07	6.06	2.35	9.78		Because of the two hydrogen atoms at the α carbon, glycine is not optically active.
H	His	Histidine	basic	155.16	7.60	1.80	9.33	6.04
I	Ile	Isoleucine	hydrophobic	131.17	6.05	2.32	9.76
K	Lys	Lysine	basic	146.19	9.60	2.16	9.06	10.54
L	Leu	Leucine	hydrophobic	131.17	6.01	2.33	9.74
M	Met	Methionine	hydrophobic	149.21	5.74	2.13	9.28		Always the first amino acid to be incorporated into a protein; sometimes removed after translation.
N	Asn	Asparagine	hydrophilic	132.12	5.41	2.14	8.72
P	Pro	Proline	hydrophobic	115.13	6.30	1.95	10.64		Can disrupt protein folding structures like α helix or β sheet.
Q	Gln	Glutamine	hydrophilic	146.15	5.65	2.17	9.13
R	Arg	Arginine	basic	174.20	10.76	1.82	8.99	12.48
S	Ser	Serine	hydrophilic	105.09	5.68	2.19	9.21
T	Thr	Threonine	hydrophilic	119.12	5.60	2.09	9.10
V	Val	Valine	hydrophobic	117.15	6.00	2.39	9.74
W	Trp	Tryptophan	hydrophobic	204.23	5.89	2.46	9.41
Y	Tyr	Tyrosine	hydrophilic	181.19	5.64	2.20	9.21	10.46

Amino Acid	hydrophobic	positive	negative	polar	charged	small	tiny	aromatic	aliphatic	van der Waals volume
Ala	X	-	-	-	-	X	X	-	-	67
Cys	X	-	-	-	-	X	-	-	-	86
Asp	-	-	X	X	X	X	-	-	-	91
Glu	-	-	X	X	X	-	-	-	-	109
Phe	X	-	-	-	-	-	-	X	-	135
Gly	X	-	-	-	-	X	X	-	-	48
His	X	X	-	X	X	-	-	X	-	118
Lys	X	X	-	X	X	-	-	-	-	135
Ile	X	-	-	-	-	-	-	-	X	124
Leu	X	-	-	-	-	-	-	-	X	124
Met	X	-	-	-	-	-	-	-	-	124
Asn	-	-	-	X	-	X	-	-	-	96
Pro	-	-	-	-	-	X	-	-	-	90
Gln	-	-	-	X	-	-	-	-	-	114
Arg	-	X	-	X	X	-	-	-	-	148
Ser	-	-	-	X	-	X	X	-	-	73
Thr	X	-	-	X	-	X	-	-	-	93
Val	X	-	-	-	-	X	-	-	X	105
Trp	X	-	-	X	-	-	-	X	-	163
Tyr	X	-	-	X	-	-	-	X	-	141