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Only l amino acids are constituents of proteins. For almost all amino acids, the l isomer has S (rather than R) absolute
configuration (Figure 3.5). Although considerable effort has gone into understanding why amino acids in proteins have
this absolute configuration, no satisfactory explanation has been arrived at. It seems plausible that the selection of l over
d was arbitrary but, once made, was fixed early in evolutionary history.
Amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions). In the dipolar form,
the amino group is protonated (-NH3
+) and the carboxyl group is deprotonated (-COO-). The ionization state of an
amino acid varies with pH (Figure 3.6). In acid solution (e.g., pH 1), the amino group is protonated (-NH3
+) and the
carboxyl group is not dissociated (-COOH). As the pH is raised, the carboxylic acid is the first group to give up a proton,
inasmuch as its pK a is near 2. The dipolar form persists until the pH approaches 9, when the protonated amino group
loses a proton. For a review of acid-base concepts and pH, see the appendix to this chapter.
Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and
chemical reactivity are commonly found in proteins. Indeed, all proteins in all species bacterial, archaeal, and
eukaryotic are constructed from the same set of 20 amino acids. This fundamental alphabet of proteins is several
billion years old. The remarkable range of functions mediated by proteins results from the diversity and versatility of
these 20 building blocks. Understanding how this alphabet is used to create the intricate three-dimensional structures that
enable proteins to carry out so many biological processes is an exciting area of biochemistry and one that we will return
to in Section 3.6.
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Let us look at this set of amino acids. The simplest one is glycine, which has just a hydrogen atom as its side chain. With
two hydrogen atoms bonded to the a-carbon atom, glycine is unique in being achiral. Alanine, the next simplest amino
acid, has a methyl group (-CH3) as its side chain (Figure 3.7).
Larger hydrocarbon side chains are found in valine, leucine, and isoleucine (Figure 3.8). Methionine contains a largely
aliphatic side chain that includes a thioether (-S-) group. The side chain of isoleucine includes an additional chiral
center; only the isomer shown in Figure 3.8 is found in proteins. The larger aliphatic side chains are hydrophobic that
is, they tend to cluster together rather than contact water. The three-dimensional structures of water-soluble proteins are
stabilized by this tendency of hydrophobic groups to come together, called the hydrophobic effect (see Section 1.3.4).
The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures
with few holes. Proline also has an aliphatic side chain, but it differs from other members of the set of 20 in that its side
chain is bonded to both the nitrogen and the a-carbon atoms (Figure 3.9). Proline markedly influences protein
architecture because its ring structure makes it more conformationally restricted than the other amino acids.
Three amino acids with relatively simple aromatic side chains are part of the fundamental repertoire (Figure 3.10).
Phenylalanine, as its name indicates, contains a phenyl ring attached in place of one of the hydrogens of alanine. The
aromatic ring of tyrosine contains a hydroxyl group. This hydroxyl group is reactive, in contrast with the rather inert side
chains of the other amino acids discussed thus far. Tryptophan has an indole ring joined to a methylene (-CH2-) group;
the indole group comprises two fused rings and an NH group. Phenylalanine is purely hydrophobic, whereas tyrosine and
tryptophan are less so because of their hydroxyl and NH groups. The aromatic rings of tryptophan and tyrosine contain
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