Characteristics of Amino Acids

Line drawings of the amino acids. The amino acids are roughly divided into three groups: amino acids with dissociable protons (A), other amino acids with polar side chains (A), and nonpolar amino acids (B). These groupings are designed to facilitate an understanding of enzymology and the thermodynamics of protein folding.

In this representation, hydrogens are omitted except in showing ionization or stereochemistry. In the case of arginine the delocalized positive charge is indicated by dashed double bonds. At stereocenters, bold lines indicate a group is coming out of the page toward the viewer, while hashed lines indicate that the group goes into the page away from the viewer.

Amino acids with dissociable protons are generally intimately involved in the chemistry of enzymes. Acidic and basic groups can form salt bridges to substrates or to each other. They can also act as proton donors/acceptors in mechanisms that rely on acid/base catalysis. The polar side chains of some of these amino acids (notably cysteine, serine, and histidine) can act as nucleophiles. The pK_a values for the free amino acids are shown, but these values can markedly change when these groups are buried in proteins. The pK_as of the -amino groups range from 8.7 to 10.7, while the pK_as of the -carboxylates range from 1.8 to 2.4.

Amino acids with polar side chains (A) can form hydrogen bonds to substrates or to each other. Cysteine, serine, and tyrosine could also be included in this group, since the ionized forms of these amino acids do not generally perform structural roles in proteins. In general, these amino acids (and the amino acids with dissociable protons) will be found on the surfaces of proteins. Cysteine is an exception, since it is slightly hydrophobic and can often be buried as a disulfide bond.

The nonpolar amino acids (B) are often found in the interiors of proteins or in hydrophobic substrate-binding pockets. They interact with one another like jigsaw pieces, forming tight-fitting associations that have a density similar to that of an amino acid crystal. Proline is buried less frequently than might be expected because of its predominance in turns, which are often found on the periphery of a protein.

Space-filling representations of the amino acids. The amino acids are arranged in order of size. The conformations shown maximize the two-dimensional area but are not necessarily the most stable geometries.