Amino Acids Are Three-Dimensional

Among all the possible amino acids, only 20 are usually found in proteins. The general structure of amino acids includes an amino group and a carboxyl group, both of which are bonded to the ­-carbon (the one next to the carboxyl group).

The ­-carbon is also bonded to a hydrogen and to the side chain group, which is represented by the letter R. The R group determines the identity of the particular amino acid (Figure).

The general formula of amino acids showing the ionic forms that predominate at pH 7

The two-dimensional formula shown here can only partially convey the common structure of amino acids because one of the most important properties of these compounds is their threedimensional shape or stereochemistry.

Every object has a mirror image. Many pairs of objects that are mirror images can be superimposed on each other; two identical solid-colored coffee mugs are an example.

In other cases, the mirror-image objects cannot be superimposed on one another but are related to each other as the right hand is to the left. Such non-superimposable mirror images are said to be chiral (from the Greek cheir, “hand”); many important biomolecules are chiral.

A frequently encountered chiral center in biomolecules is a carbon atom with four different groups bonded to it (Figure 3.1). Such a center occurs in all amino acids except glycine. Glycine has two hydrogen atoms bonded to the ­-carbon; in other words, the side chain (R group) of glycine is hydrogen.

Glycine is not chiral (or, alternatively, is achiral) because of this symmetry. In all the other commonly occurring amino acids, the ­-carbon has four different groups bonded to it, giving rise to two non-superimposable mirror-image forms.

See Figure shows perspective drawings of these two possibilities, or stereoisomers, for alanine, where the R group is }CH3. The dashed wedges represent bonds directed away from the observer, and the solid triangles represent bonds directed out of the plane of the paper in the direction of the observer.

The two possible stereoisomers of another chiral compound, l- and d- glyceraldehyde, are shown for comparison with the corresponding forms of alanine. These two forms of glyceraldehyde are the basis of the classification of amino acids into l and d forms.

The terminology comes from the Latin words laevus and dexter, meaning “left” and “right,” respectively, which comes from the ability of optically active compounds to rotate polarized light to the left or the right.

The two stereoisomers of each amino acid are designated as l- and d-amino acids on the basis of their similarity to the glyceraldehyde standard. When drawn in a certain orientation, the l form of glyceraldehyde has the hydroxyl group on the left side of the molecule, and the d form has it on the right side, as shown in perspective in Figure (a Fischer projection).

To determine the l or d designation for an amino acid, it is drawn as shown. The position of the amino group on the left or right side of the ­-carbon determines the l or d designation. The amino acids that occur in proteins are all of the l form.

Although d-amino acids occur in nature, most often in bacterial cell walls and in some antibiotics, they are not found in proteins. The concept of chirality will be seen many times as we continue our study of biochemistry.

Although it may not be obvious, whether a molecule is L- or d- is extremely important to its characteristics and function. A sugar molecule with the d- orientation may be sweet, whereas its L-isomer is bitter.

A drug that is helpful in one orientation may be poisonous in the other orientation. We will see more of this in the chapters on proteins and enzymes, where specific orientations about a chiral carbon are critical to a molecule’s function.

● The amino acids that are the monomer units of proteins have a general structure in common, with an amino group and a carboxyl group bonded to the same carbon atom.

● The nature of the side chains, which are referred to as R groups, is the basis of the differences among amino acids.

● Except for glycine, amino acids can exist in two forms, designated l and d. These two stereoisomers are nonsuperimposable mirror images of each other.

● The amino acids found in proteins are of the l form, but some d-amino acids occur in nature.