Remembering something about the structures of the amino acids is
just one to those basic language things that must be dealt with since it
crops up over and over again—not only in protein structure but later in
metabolism. You need to get to the point that when you see Asp you
don’t think snake but see a negative charge. Don’t memorize the amino
acids down to the last atom, and don’t spend too much time worrying
about whether glycine is polar or nonpolar. Methylene groups (–CH
may be important, but keeping track of them on an individual basis is
just too much to ask. Organize the amino acids based on the functional
group of the side chain. Having an idea about functional groups of amino
acids will also help when you get to the biosynthesis and catabolism of
amino acids. Might as well bite the bullet early.
• CHARGED POLAR
) amino acid
side chains have a charge at neutral pH and strongly “prefer” to be on
the exterior, exposed to water, rather than in the interior of the protein.
for residues may seem a little strange. Asp
and Glu are called acidic amino acids, although at neutral pH in most
proteins, Asp and Glu are not present in the acidic form (–COOH) but
are present in the basic form (–COO
). So the acidic amino acids, Asp
and Glu, are really bases (proton acceptors). The reason that Asp and Glu
are called acidic residues is that they are such strong acids (proton
donors) they have already lost their protons. Lys, Arg, and His are con-
sidered basic amino acids, even though they have a proton at neutral pH.
The same argument applies: Lys, Arg, and His are such good bases (pro-
ton acceptors) that they have already picked up a proton at neutral pH.
Lys, Arg, His
Ser, Thr, Tyr
Ala, Val, Leu, Ile, Met
Phe, Trp, Tyr