The 20 different naturally occurring amino acids are the building blocks of peptides and proteins. Amino acids are commonly represented by three-letter abbreviations, but one-letter abbreviations are also sometimes used. Although the human body needs all 20 amino acids, it cannot synthesize some amino acids, known as essential amino acids. Essential amino acids must be obtained from the diet. As the name implies, an amino acid contains an amino group and an acid group in the same molecule. Amino acids have a central carbon atom (a-carbon) to which are attached a carboxyl group, an amino group, a hydrogen atom, and a side chain. Different amino acids differ with respect to the side chain (R) only:
Gly is the simplest amino acid, with no side chain. The side chain of Pro is unique in that it is bonded covalently to the nitrogen atom of the peptide group. The amide forms of Asp and Glu (Asn and Gln, respectively) occur naturally and are incorporated into proteins. Ionizable side chains of amino acids vary from acidic to basic. Aspartic and glutamic acid have a negative charge; lysine and arginine have a positive charge at the physiological pH of 7.4. The imidazole group in histidine carries a partial positive charge at pH 7.4. Serine and threonine have side chains that carry no charge at any pH but are polar in nature. In contrast, tryptophan, phenylalanine, and isoleucine have side chains that are more like hydrocarbon in character. The lipophilicity of amino acids is a property relevant for protein folding,1 as is discussed in Section 2.2.3. All amino acids (except glycine, for which R = H) have a chiral carbon because R, H, COOH, and NH2 are four different groups. Thus, each amino acid (except glycine) exists as two enantiomers: L- and D-amino acids. The proteins in our body are made of only L-amino acids.
Amino acids are zwitterions, both in solution and in solid state. Because amino acids are zwitterions, they are solids with high melting points and have good aqueous solubility. Each functional group has a characteristic dissociation constant K with a negative logarithm that is called the pKa. Because pKa values were measured at fixed ionic strength, they are sometimes called apparent dissociation constants, pKJ. The constant pK1/ usually refers to the most acidic group.2 For example, the dissociation constants for glycine, pK1'(COOH) and pK2'(NH3+), are 2.34 and 9.60, respectively. The pH at which all the molecules are in the zwitterionic form so that there is no charge on the molecule is called the isoelectric point (pi) of the amino acid. Of the 20 amino acids, 15 have a pi near 6.0. The three basic amino acids have a higher pi, and the two acidic ones have lower pi.
The amino acid cysteine exhibits some unique properties that play a crucial role in the stability of proteins. The thiol group of Cys is the most reactive of any amino acid side chain and will be readily oxidized to form a dimer, cystine:
The resulting S-S bond is called a disulfide bridge and serves to hold the protein in its unique conformation, as discussed in Section 2.2.3.
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