Alanine which is present in proteins has? (a) Both D and R-configuration (b) Both \(\mathrm{L}\) and \(\mathrm{S}\) -configuration (c) Both D and S-configuration (d) Both \(\mathrm{L}\) and \(\mathrm{R}\) -configuration

In the study of molecular structures, particularly amino acids, the D/L and R/S configuration systems are essential concepts that help us understand their spatial arrangements. Alanine, for example, an important component in protein synthesis, demonstrates these configurations prominently.

The D/L nomenclature is rooted in the historical classification related to the optical rotation of glyceraldehyde, a simple sugar molecule. 'D' stands for 'dexter', meaning right, and 'L' stands for 'laevus', meaning left. This designation is specifically related to the orientation of the molecule in relation to glyceraldehyde, indicating how it deflects light: to the right, D, or to the left, L.

In contrast, the R/S configuration is a notation that comes from the Latin words 'rectus' for right, and 'sinister' for left. These terms refer to the actual spatial arrangement of atoms around a chiral center—the central carbon in an amino acid. The R/S system uses a set of priority rules, known as the Cahn-Ingold-Prelog (CIP) priority rules, to determine the three-dimensional layout of molecules.

Chirality is a geometric property of some molecules where a molecule and its mirror image are not superimposable on one another, much like left and right hands. This is a common feature of amino acids, which are the building blocks of proteins. Alanine is one such chiral amino acid.

In proteins, the amino acids used are almost exclusively of the L-configuration, which means they are related to the L-form of glyceraldehyde. This is an important concept for students, as it emphasizes that while a laboratory may synthesize both D- and L-alanine, in nature – particularly in human biology – only L-amino acids are incorporated into proteins. The chiral center in alanine is the central carbon atom, known as the alpha carbon, to which four different groups are attached: an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and an R-group, which in the case of alanine is a methyl group (CH3).

When discussing chirality and molecular structure, one cannot overlook the Cahn-Ingold-Prelog (CIP) priority rules. These rules are a set of guidelines that determine the 'priority' of the groups attached to a chiral center. They are critical for assigning the R/S notation to chiral centers.

The basic principle is to rank the substituents attached to the chiral center based on their atomic number; the higher the atomic number, the higher the priority. In the case of alanine, the NH2 group has a higher priority than the COOH group because nitrogen has a higher atomic number than carbon.

After prioritizing the groups, one views the molecule from the side opposite the lowest priority group. If the remaining groups decrease in priority in a clockwise direction, the configuration is R. If they decrease in a counterclockwise direction, it's designated as S. As such, in the context of alanine—because the highest priority group (NH2) is on the left side and the priorities decrease counterclockwise—the L form of alanine corresponds to the S configuration.