Chemical Structures and Nomenclature

Amino acids are small organic molecules with the general formula shown in Figure 1.

The central carbon atom in this structure is called the a-carbon, and the amino and carboxyl groups attached to it are known as the a-amino group and the a-carboxyl group, respectively. The R groups of the 20 amino acids that can be incorporated into proteins are shown in Table 1; these R groups give the different amino acids their specific chemical and physical properties.

The a-amino group acts as a weak base and is always protonated at physiological pH; similarly, the a-carboxyl group acts as weak acid and at physiological pH is always ionized. Thus, free amino acids in biological material exist as zwitterions, as shown in Figure 2.

R-C-CO2H

Figure 1 Amino acid structure.

Table 1 Amino acid characteristics

Name (3 letter code; 1 letter code) Structure

Molecular weight pKa

Small neutral amino acids Glycine (Gly; G)

h-c-co2h nh2

Branched-chain amino acids Valine (Val; V)

Isoleucine (Ile; I)

NH2 H

Aromatic amino acids Tryptophan (Trp; W)

2.43

9.44

Tyrosine (Tyr; Y)

CH2-C-CO2H

CH2-C-CO2H

Phenylalanine (Phe; F)

CH2-C-CO2H

CH2-C-CO2H

Hydroxyl-containing amino acids Serine (Ser; S)

Threonine (Thr; T)

Sulfur-containing amino acids Cysteine (Cys; C)

Methionine (Met; M)

2.09

9.10

Table 1 Continued

Name (3 letter code; 1 letter code) Structure

Molecular weight pKa

Imino acid Proline (Pro; P)

CH2-CH

CH2 CrH Y CO2H H

1.95 10.64

Acidic side chains Aspartic acid (Asp; D)

Glutamic acid (Glu; E)

2 I NH2

Amides

Asparagine (Asn; N)

Glutamine (Gln; Q)

Basic side chains Histidine (His; H)

conh2h

ch2-ch2-c-co2h nh2

Arginine (Arg; R)

HN nh2

Nonprotein amino acids Ornithine

Citrulline

CONH2 H

Not determined

7-Aminobutyric acid (GABA)

CH2-CO2H

4.03 10.56

Homocysteine

Figure 2 Zwitterionic structure of an amino acid.

acids, and creatine; it acts as a neurotransmitter and as a conjugating substance that aids the excretion of xenobiotics by making them more water-soluble. Alanine is the transamination product of pyruvic acid and is thus closely associated with the metabolism of carbohydrates, acting as a major precursor for gluconeogenesis.

The a-carbon atom is asymmetric so that amino acids show stereoisomerism; the exception to this is glycine, in which the R group is a second hydrogen atom. Most of the amino acids found in nature are in the l form, and only l-amino acids can be used for protein synthesis in higher organisms. However, d-amino acids may be ingested from bacterial sources, and if high concentrations accumulate they may be toxic. The human body has a d-amino acid oxidase enzyme, found in the liver and the kidney, that disposes of these molecules by oxidative deamination.

The most important common chemical property of the amino acids is their ability to form peptide bonds with one another. The a-amino group of one amino acid reacts with the a-carboxyl group of another to form a peptide bond with the elimination of water (Figure 3). The results of this process are conventionally known as peptides or oligopeptides if they contain 2-20 amino acid residues or as polypeptides, which may contain 21 to several thousand amino acid residues. The polypeptides may undergo further processing, including chemical modification, before taking up their final conformation as proteins.

Each amino acid also has specific chemical properties that depend on the nature of the R group. This affects the behavior of the free amino acids and the corresponding amino acid residues in peptides and polypeptides. For convenience, the amino acids may be considered in groups according to some common properties.

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