Classification of AAs by Chemical Structure

Various systems have been proposed to classify AAs by their chemical structures according to similar components in their R groups, net electrical charges in solution, and polarity in water at physiological pH. An example of amino classification used by Garrett et al.1 based on polarity and electrical charge is illustrated in Figure 15.2 through Figure 15.5.

Nonpolar AAs (Figure 15.2) include those with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline, methionine, and two aromatic AAs (phenylalanine and tryptophan). Nonpolar AAs are generally considered hydrophobic.

FIGURE 15.1 Anatomy of an AA. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure. Illustration, Irving Geis; Garrett RH, Grisham CM, Biochemistry, 3rd ed, Belmont, CA: Thomson Brooks/Cole, 2005. Rights owned by Howard Hughes Medical Institute. Not to be reproduced without permission.

FIGURE 15.1 Anatomy of an AA. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure. Illustration, Irving Geis; Garrett RH, Grisham CM, Biochemistry, 3rd ed, Belmont, CA: Thomson Brooks/Cole, 2005. Rights owned by Howard Hughes Medical Institute. Not to be reproduced without permission.

Polar, uncharged AAs (Figure 15.3) except for glycine contain R groups that can form hydrogen bonds with water, making these generally more soluble in water than the nonpolar AAs.1

In the two acidic AAs (Figure 15.4), the R groups each contain a carboxyl group. Such negatively charged AAs play a unique role in proteins requiring metal binding sites for structural and functional purposes.

The two basic AAs (Figure 15.5) have R groups with a net positive charge and a neutral pH. ARG and lysine side chains participate in electrostatic interactions in proteins.

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