Nucleophilic substitution at a carbonyl group Nucleophilic substitution at a carbonyl group (A) If the carbonyl subjected to a nucleophilic attack has a good leaving group, then nucleophilic substitution is possible. The substitution reaction proceeds via an obligatory tetrahedral species. (B) Three nucleophilic substitution reactions are important in the formation of an amide bond between two amino acids. The first reaction involves nucleophilic substitution at a phosphate group and the second nucleophilic reactions involve substitution at a carbonyl. In the first reaction, the carboxylate group attacks a phosphate of ATP releasing pyrophosphate – two phosphate groups connected together via a bridging oxygen atom – and attaching AMP to the carboxylate group. This step is energetically favourable and converts one of the oxygen atoms of the carboxylate group of the amino acid into a good leaving group. In the second reaction, the amino acid is loaded on to the tRNA ready for protein formation. In the third reaction, the enzyme ensures that the amino group of the attacking amino acid is not protonated, and this group then carries out a nucleophilic attack on another tRNA–conjugated amino acid. Amanda L. Jonsson et al. Essays Biochem. 2017;61:401-427 ©2017 by Portland Press Ltd