Chemistry Reference
In-Depth Information
ionic form at pH 7
Amino acids with ionizable side-chains
p
K
a
1.96
p
K
a
10.29
CO
2
CO
2
H
Cysteine
HS
HS
NH
3
NH
2
p
K
a
8.18
p
K
a
2.2
Tyrosine
CO
2
H
CO
2
p
K
a
10.06
NH
2
NH
3
p
K
a
9.11
HO
HO
The ionization properties of side-chain substituents
will usually carry through into the peptide or protein
and influence the behaviour of the polymer. However,
the actual p
K
a
values of the amino acid side-chains
in the protein are modified somewhat by the position
of the amino acid in the chain, and the environment
created by other substituents. Typical p
K
a
values are
shown in Table 13.2.
Note that the side-chains of glutamine and
asparagine are not basic; these side-chains contain
amide functions, which do not have basic properties
(see Section 4.5.4). The heterocyclic ring in trypto-
phan can also be considered as non-basic, since the
nitrogen lone pair electrons form part of the aromatic
π
A frequently encountered modification is the
conversion of the
C
-terminal carboxyl into an amide.
This is represented as Phe-NH
2
, for example, which
must be considered carefully, and not be interpreted
as an indication of the
N
-terminus (see Section 13.2).
CO
2
H
CO
2
H
NHMe
NHMe
HO
Tyr(Me)
Leu(Me)
CO
2
H
CONH
2
NHMe
NH
2
Sar
(Sarcosine;
N
-methylglycine)
Phe
−
NH
2
electrons and are unavailable for bonding to a pro-
ton (see Section 11.8.2).
In addition to the 20 amino acids described,
there are also a few amino acids quite frequently
encountered that are not encoded by DNA. These are
mainly found in peptides, and are typically slightly
modified versions of the common amino acids, such
as
N
-methyl amino acids. These components are
represented by an appropriate variation of the normal
abbreviation,
Some other variants are shown below, with their
abbreviations. Pyroglutamic acid may be found where
a terminal glutamic acid residue, linked to the chain
through its carboxyl, forms a cyclic amide (lactam)
(see Section 7.10).
e.g.
N
-methyl
amino
acids
such
as
Some common amino acids not encoded by DNA
Tyr(Me)
or
Leu(Me),
though
N
-methylglycine
is
Pyroglutamic acid
(5-oxoproline)
CO
2
H
Glp
oxoPro
<Glu
often referred to as sarcosine (Sar).
H
NH
O
Table 13.2
p
K
a
values for free and protein-bound amino
acids
Hydroxyproline
CO
2
H
HPro
H
HO
NH
Amino acid
p
K
a
Free amino acid
In proteins
Hydroxyleucine
CO
2
H
HLeu
Aspartic acid
3.65
3.5 - 4.5
HO
NH
2
Glutamic acid
4.25
3.5 - 4.5
Lysine
10.52
9.5 - 10.5
Ornithine
CO
2
H
Orn
Arginine
12.48
12 - 13
H
2
N
Histidine
6.00
6 - 7
NH
2
