R

FIGURE 3-2 General structure of an amino acid. This structure is common to all but one of the a-amino acids. (Proline, a cyclic amino acid, is the exception.) The R group or side chain (red) attached to the a carbon (blue) is different in each amino acid.

symbols (Table 3-1), which are used as shorthand to indicate the composition and sequence of amino acids polymerized in proteins.

TWo conventions are used to identify the carbons in an amino acid—a practice that can be confusing. The additional carbons in an R group are commonly designated 3, y, 8, e, and so forth, proceeding out from the a carbon. For most other organic molecules, carbon atoms are simply numbered from one end, giving highest priority (C-1) to the carbon with the substituent containing the atom of highest atomic number. Within this latter convention, the carboxyl carbon of an amino acid would be C-1 and the a carbon would be C-2. In some cases, such as amino acids with heterocyclic R groups, the Greek lettering system is ambiguous and the numbering convention is therefore used.

fNHf>

fNHf>

Lysine

For all the common amino acids except glycine, the a carbon is bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom (Fig. 3-2; in glycine, the R group is another hydrogen atom). The a-carbon atom is thus a chiral center (p. 17). Because of the tetrahedral arrangement of the bonding orbitals around the a-carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers. Since they are nonsuperimposable mirror images of each other (Fig. 3-3), the two forms represent a class of stereoisomers called enantiomers (see Fig. 1-19). All molecules with a chiral center are also optically active—that is, they rotate plane-polarized light (see Box 1-2).

Special nomenclature has been developed to specify the absolute configuration of the four substituents of asymmetric carbon atoms. The absolute configurations of simple sugars and amino acids are specified by the d, l system (Fig. 3-4), based on the absolute configuration of the three-carbon sugar glyceraldehyde, a convention proposed by Emil Fischer in 1891. (Fischer knew what groups surrounded the asymmetric carbon of glyceraldehyde but had to guess at their absolute configuration; his guess was later confirmed by x-ray diffraction analysis.) For all chiral compounds, stereo-isomers having a configuration related to that of L-glyceraldehyde are designated l, and stereoisomers related to D-glyceraldehyde are designated d. The functional groups of L-alanine are matched with those of L-glyceraldehyde by aligning those that can be intercon-verted by simple, one-step chemical reactions. Thus the carboxyl group of L-alanine occupies the same position about the chiral carbon as does the aldehyde group of L-glyceraldehyde, because an aldehyde is readily converted to a carboxyl group via a one-step oxidation. Historically, the similar l and d designations were used for levorotatory (rotating light to the left) and dextrorotatory (rotating light to the right). However, not all

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