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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.

Amino acid residue is what is left of an amino acid once a water molecule has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond .

Contents

Overview

Amino acids are biochemical building blocks. 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. Rarer, more complicated ones are produced by the body and are called nonstandard. 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. 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. At least two amino acids other than the standard 20 are sometimes incorporated into proteins during translation:

Although only 20 amino acids are genetically coded, over 100 have been found in nature. Some of those were found in meteoritic material. 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 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 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.

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

List of standard 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 standard 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 hydrophobic (Nagano, 1999) 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 In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome.
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 hydrophobic 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 - - - - 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

Uses of substances derived from 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).


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