Chemistry Reference
In-Depth Information
Initially, the amino acid is activated by an ATP-
dependent process, producing an
aminoacyl-AMP
.
This may be considered to be nucleophilic attack of
the amino acid carboxylate group on to the P
=
O
system of ATP with expulsion of diphosphate as the
leaving group.
phosphate groups are
shown in non-ionized form
O
O
O
P
O
O
O
P
mixed anhydride
Ad
P
P
Ad
P
P
O
O
O
OH
O
O
P
O
O
O
OH
O
O
OH
OH
OH
OH
OH
OH
R
R
C
R
C
O
OAd
O
AT P
O
OH
NH
2
NH
2
carboxylate as
nucleophile
NH
2
diphosphate as
leaving group
aminoacyl-AMP
Carboxylate is not an especially good nucleophile,
but we have seen it used in S
N
2 reactions to
synthesize esters (see Section 6.3.2). Here, attack is
on a reactive anhydride; a similar type of reaction is
seen in fatty acid degradation (see Section 15.4.1).
NH
2
NH
2
O
O
N
N
N
N
O
P
OH
O
P
OH
O
O
P
O
CH
2
N
O
CH
2
N
O
O
P
N
N
O
O
R
R
O
OAd
O
OAd
OH
HO
OH
ester
linkage
O
OH
NH
2
OH
O
NH
2
R
O
aminoacyl-AMP
terminal adenosine of tRNA
NH
2
aminoacyl-tRNA
The intermediate aminoacyl-AMP can also be seen
to be an anhydride, but in this case a mixed anhydride
of carboxylic and phosphoric acids (see Box 7.27).
This can react with a hydroxyl group in ribose, part of
a terminal adenosine group of transfer-RNA (tRNA).
This then binds the amino acid via an ester linkage,
giving an
aminoacyl-tRNA
. The tRNA involved will
be specific for the particular amino acid.
NH
2
NH
2
NH
2
O
O
O
N
N
N
N
N
N
O
P
OH
O
P
OH
O
P
OH
O
CH
2
N
O
CH
2
N
N
N
O
CH
2
N
N
O
O
O
O
OH
O
OH
O
OH
O
NH
R
R
R
R
O
O
O
O
HN
O
NH
2
HN
O
HN
O
aminoacyl-tRNA
R
NH
R
NH
R
NH
R
O
growing peptide chain
attached to tRNA
HN
Peptide bond formation is the result of two
such aminoacyl-tRNA systems interacting, the amino
group in one behaving as a nucleophile and displacing
the
tRNA
from
the
second,
i.e.
simply
amide
