In vivo Peptide Bond formation & growth of the polypeptide chain
The
amino
acids in the ribosome are
attached
to
their respective tRNAs by
an
ester bond (R - O - R) between the carboxyl terminus and
the amino acceptor stem
(left). During formation of a peptide bond, the ester bond of the amino
acid in the (P)eptidyl site is cleaved, and Peptidyl Transferase catalyzes a reaction (see Note)
between its carboxyl terminus and the amino
terminus of the amino acid in the (A)mino site. This
transfers the P-site
amino
acid to the A-site
amino acid, and the
original amino terminus remains unmodified.
The
polypeptide thus "grows" from the amino terminus to the
carboxyl terminus.
Note: In vitro formation of the peptide bond is often described as a dehydration reaction that involves the splitting out of an H20. However, the in vivo reaction does not.
Note first that the C terminus of the amino acid in the P site participates in the ester bond as a carbonyl radical (-C=O), without a separate -OH group. The peptide bond is formed by a nucleophilic attack of the N of the A site amino terminus on this carbonyl C. The -O- of the ester bond remains attached to the 3'-C of the tRNA. The proton on the 2'-C then shifts to the 3'-C to restore the -OH terminus of the uncharged tRNA, and a proton from the amino terminus of the incoming amino acid the shifts to the 2'-C. The in vivo reaction balances, without production of an H20 molecule.
Note: In vitro formation of the peptide bond is often described as a dehydration reaction that involves the splitting out of an H20. However, the in vivo reaction does not.
Note first that the C terminus of the amino acid in the P site participates in the ester bond as a carbonyl radical (-C=O), without a separate -OH group. The peptide bond is formed by a nucleophilic attack of the N of the A site amino terminus on this carbonyl C. The -O- of the ester bond remains attached to the 3'-C of the tRNA. The proton on the 2'-C then shifts to the 3'-C to restore the -OH terminus of the uncharged tRNA, and a proton from the amino terminus of the incoming amino acid the shifts to the 2'-C. The in vivo reaction balances, without production of an H20 molecule.
Figure after ©2008 by Watson et al.; All text material ©2012 by Steven M. Carr