BIOINORGANIC CHEMISTRY A Short Course Second Edition

32 BIOCHEMISTRY FUNDAMENTALS

amino acids are shown in their zwitterion form at pH 7 in which they have
their COOH group (p Ka = 2.35) in the COO − form and their NH 2 group
(pKa = 9.69) in the NH 3 + form.^2 Side - chain R groups will be protonated or
deprotonated at physiological pH ( ∼ 7.4) based on the p K values of the side
chain. All amino acids found in proteins are called α - amino acids because the
amine group is bonded to theα carbon. All amino acids found in proteins are
l - stereoisomers with respect to the α carbon (except glycine whose R group
is H), although d - stereoisomers are found in bacterial cell walls and some
peptide antibiotics.
In nomenclature for amino acids as ligands, the R group atoms are labeled
with Greek letters starting withβ for the fi rst atom attached to the α carbon,
followed byγ and δ and ε. The common bioinorganic ligands from amino acid
side chains have their atoms labeled in this manner in Figure 2.5. The labeling
becomes important in identifying the ligand atom that may be the metal
binding site in metalloproteins. In histidine, metals bind at either the δ or ε
positions. In superoxide dismutase, one his ligand bridges two metal ions with
Zn(II) coordinated at theδ nitrogen and Cu(II) at the ε nitrogen. For carbox-
ylic acid side chains, metals may bind in monodentate mode (Asp - M), in
bidentate chelate mode, or with the carboxylic acid oxygens bonding to two

Figure 2.3 Zwitterions of acidic amino acids at physiological pH.

glutamic acid, glutamate,

Glu, E

aspartic acid, aspartate,

Asp, D

+H 3 NC

H

H 2 C

C

O - O

COO- +H 3 NCCOO-

H

CH 2

C

O O

HC 2

tyrosine, Tyr, Y

OH

+H 3 NC

H

CH 2

COO-

Figure 2.4 Zwitterions of basic amino acids at physiological pH.

histidine, His, H arginine, Arg, R lysine, Lys, K

+H 3 NC

H

H 2 C

CH 2

H 2 C

NH

C

H 2 N + NH 2

COO- +H 3 NC

H

H 2 C

CH 2

H 2 C

CH 2

H+ 3 N

+H 3 NC COO-

H

H 2 C

NH

N

COO-