Chemistry Reference
In-Depth Information
13
Amino acids, peptides and proteins
13.1 Amino acids
not necessarily capable of synthesizing all of these.
Some amino acids are obtained from the diet. The
amino acids are combined in a sequence that is
defined by the genetic code, the sequence of bases
in DNA (see Section 14.2.4). Table 13.1 gives the
structures of these 20 amino acids together with
the standard three-letter and one-letter abbreviations
used to represent them. Proline is strictly an imino
acid rather than an amino acid, but it is normally
included as one of the 20 amino acids. The amino
acids are also subclassified according to the chemical
and physical characteristics of their R substituent.
Since the polypeptide structure combines both the
amino and carboxylic acid functions of an amino
acid into amide linkages, the overall properties of the
polypeptide are going to be defined predominantly by
the characteristics of these R substituents.
The amino acid components of proteins have
the
L
configuration (see Section 3.4.10), but many
peptides are known that contain one or more
D
-amino acids
in their structures.
D
-Amino acids
are not encoded by DNA, and peptides containing
them are produced by what is termed 'non-ribosomal
peptide biosynthesis' (see Section 13.5.2).
D
-Amino
acids generally arise by epimerization of
L
-amino
acids (see Box 10.10). All the protein
L
-amino
acids have the
S
configuration, except for glycine,
which is not chiral, and
L
-methionine which is
R
,
a consequence of the priority rules for systematic
descriptors of configuration (see Section 3.4.10).
Numerous amino acids are found in nature, but in
this chapter we are concerned primarily with those
that make up the structures known as peptides and
proteins. Peptides and proteins are both
polyamides
(see Section 7.10) composed predominantly of
α-
amino acids
linked through their carboxyl and
α
-
amino functions.
R
4
R
2
HN
CO
2
H
H
2
N
H
2
N
CO
2
H
H
2
N
CO
2
H
CO
2
H
R
1
R
3
α
-amino acids
R
2
R
4
O
O
N
N
H
H
R
1
R
3
O
O
peptide
O
peptide bond
=
amide bond
H
In biochemistry, the amide linkage is traditionally
referred to as a
peptide bond
. Whether the resultant
polymer is classified as a
peptide
or a
protein
is not
clearly defined; generally, a chain length of more than
40 residues confers protein status, whereas the term
polypeptide
can be used to cover all chain lengths.
Proteins in all organisms are made up from the
same set of 20
R
CO
2
H
R
CO
2
H
NH
2
L-amino acid
H
H
NH
2
D-amino acid
α
-amino acids, though the organism is
