Asymmetry: Right-Handed and Left- Handed Molecules.

The left hand looks much like the right hand, but they are different. One is the mirror image of the other. A practical difference is that your right hand will not fit into a left-handed glove. Despite our daily acquaintance with “handedness” it may seem difficult to explain in words how a right and a left hand differ. However, since most biochemical compounds are asymmetric, it is important to be able to visualize these molecules in three dimensions and to draw their structures on paper. One of the best ways of learning to do this is to study molecular models. You may learn the most by making your own models (see
Appendix).
Whenever four different groups are bonded to a central carbon atom, the molecule is asymmetric and the four groups can be arranged in two different configurations. Consider alanine, one of the alpha (α)-amino acids from which proteins are built.



It is called an α-amino acid because the amino group is attached to the α carbon atom. To indicate its three-dimensional structure on a flat piece of paper, the bonds that project out of the plane of the paper and up toward the reader are often drawn as elongated triangles, while bonds that lie behind the plane of the paper are shown as dashed lines. The isomer of alanine having the configuration about the α-carbon atom shown in the following structural formulas is called S-alanine or L-alanine. The isomer
which is a mirror image of S-alanine is R-alanine or D-alanine. Pairs of R and S compounds (see Section B for definitions) are known as enantiomorphic forms or enantiomers.


Notice that in the foregoing drawings, the carboxyl
group, abbreviated –COOH-, is shown as havinglost a proton to form the carboxylate ion –COO–. Likewise, the amino group (–NH2) has gained a proton to form the –NH3 + ion. The resulting dipolar ionic or zwitterionic structure is the one that actually exists for amino acids both in solution and in crystals.