Recognition of the codon or codons specifying a given amino acid by a particular tRNA is actually the second step in decoding the genetic message. The first step, attachment of the appropriate amino acid to a tRNA, is catalyzed by a specific aminoacyl-tRNA synthetase. Each of the 20 different synthetases recognizes one amino acid and all its compatible, or cognate, tRNAs. These coupling enzymes link an amino acid to the free 2′ or 3′ hydroxyl of the adenosine at the 3′ terminus of the tRNA molecule by an ATP-requiring reaction. In this reaction, the amino acid is linked to the tRNA by a high-energy bond and is thus said to be activated. The energy of this bond subsequently drives the formation of the peptide bonds linking adjacent amino acids in a growing polypeptide chain. The equilibrium of the aminoacylation reaction is driven further toward activation of the amino acid by hydrolysis of the high-energy phosphoanhydride bond in the released pyrophosphate (see Figure 5-19).

Aminoacyl-tRNA synthetases recognize their cognate tRNAs primarily by interacting with the anticodon loop and acceptor stem, although interactions with other regions of a tRNA also contribute to recognition in some cases. Furthermore, specific bases in incorrect tRNAs that are structurally similar to a cognate tRNA will inhibit charging of the incorrect tRNA. Thus recognition of the correct tRNA depends on both positive interactions and the absence of negative interactions. Still, because some amino acids are so similar structurally, aminoacyl-tRNA synthetases sometimes make mistakes. These mistakes are corrected, however, by the enzymes themselves, which have a proofreading activity that checks the fit in their amino acid–binding pocket. If the wrong amino acid becomes attached to a tRNA, the bound synthetase catalyzes removal of the amino acid from the tRNA. This crucial function helps guarantee that a tRNA delivers the correct amino acid to the protein-synthesizing machinery. The overall error rate for translation in E. coli is very low, approximately 1 per 50,000 codons, evidence of both the fidelity of tRNA recognition and the importance of proofreading by aminoacyl-tRNA synthetases.