Genetic code, amino acid side chains

The genetic code specifies 20 different amino acid side chains... 

FIGURE 1 The 20 amino acid side chains specified by the genetic code. All except glycine have a / -carbon. Proline is technically an imino acid since it is a secondary amine. 

All of the 20 amino acids have in common a central carbon atom (Co) to which are attached a hydrogen atom, an amino group (NH2), and a carboxyl group (COOH) (Figure 1.2a). What distinguishes one amino acid from another is the side chain attached to the Ca through its fourth valence. There are 20 different side chains specified by the genetic code others occur, in rare cases, as" the products of enzymatic modifications after translation. 

The amino acids that are included in the genetic code (see p.248) are described as proteinogenic. With a few exceptions (see p. 58), only these amino acids can be incorporated into proteins through translation. Only the side chains of the 20 proteinogenic amino acids are shown here. Their classification is based on the chemical structure of the side chains, on the one hand, and on their polarity on the other (see p. 6). The literature includes several slightly different systems for classifying amino acids, and details may differ from those in the system used here. 

Figure 14.2. The biochemistry of protein. Protein is another linear polymer in which each building block is an amino acid. Amino acids have a central ( alpha ) carbon to which an amino group, a carboxyl group, and a variable side chain are joined. Twenty amino acids are encoded within the standard genetic code.

Twenty different amino acids are used for protein synthesis, each of which is encoded by at least one codon (the three-nucleotide genetic code) and differ only in their side-chain group. 

The particular sequence of side chains or amino acids along the polypeptide backbone is known as the primary structure. This structure is determined by a particular sequence of nucleic acids in the gene the relationship between a nucleic acid sequence and an amino acid sequence is known as the genetic code (see section 3.2). 

Although some 300 different amino acids occur in nature, only 20 of these are DNA-encoded a-amino acids (selenocysteine, the twenty-first natural amino acid, is not actually coded for directly in the genetic code). The structures of the 20 natural amino acids can be found in Table 7.1. The amino acids in the table are not listed alphabetically rather, they are tabulated according to properties determined by their side-chain (R) functionality. Interestingly, 19 of the DNA-encoded amino acids have the same stereochemistry and are chiral. The twentieth, Gly, is achiral, because its side-chain R-group is H. The 19 chiral amino acids are all configurationally related to L-glyceraldehyde and, therefore, are still known as L-amino acids, albeit this is an outdated nomenclature. 

Amino acids, the monomeric units of peptides and proteins. From analysis of the vast number of proteins, it follows that 20 proteinogenic or standard amino acids are the building blocks of aU proteins. These amino acids are specified by the genetic code. With selenocysteine and pyrrolysine two additional members have been identified. Besides the imino acid proline, all other building blocks are known as a-amino acids, H2N-CHR-COOH, but the zwitterion form, H3N+-CHR-C00, occurs at physiological pH values. The amino acids can therefore act as either acids or bases. Depending on the side-chain residue R, amino acids can be classified into those with (a) non polar side chains [Gly/G Ala/A Val/V Leu/L Ile/I Met/M Pro/P Phe/F Trp/W] ... 

The substrate specificity of an enzyme and its catalytic activity together result from the three-dimensional interaction of the substrate with the side chains of a few nicely positioned amino acids in the protein. Genetic engineering allows the nucleotide sequences coding for these amino acids to be altered as the DNA is transferred from one organism to another. Thus the amino acids which bind the substrate can be altered to accommodate new ones which are sterically excluded from the natural enzyme. The difficulty with this work is not so much the modification of the enzyme, but rather the purification and crystallization which are necessary to solve the three-dimensional structure in the first place. 

All proteins are synthesized from the 20 a-amino acids specified by the genetic code as shown in Fig. 1. The nature of an amino acid is determined by the side-chain attached to the a-carbon (Table I). All of these amino acids, except for glycine which carries two hydrogens on its a-carbon, have a chiral center located at the a-carbon. Thus the amino acids exist as either the l- or D-isomers. Only the L-stereoisomer is utilized in protein biosynthesis (Fig. 2). This introduces chirality into all protein molecules that is the source of most of the asymmetric features found in protein structures. The use of only one of the two stereoisomers of the amino acids also establishes a structural uniqueness that is essential for biochemical specificity. 

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