The tRNA is referred to a being charged with the amino acid. The amino acid is activated by conversion of the free carboxylic acid to a mixed anhydride. Although stable, the aminoacyl-AMP does not leave the enzyme. Amino acid Aminoacyl-tRNA synthetase discrimination is generally based on the size of the amino acid side chain. Acylation site rejects amino acids that are larger than the correct one because the binding site is too small .
Hydrolytic site destroys activated intermediates that are smaller than the right amino acid.
Acylation and hydrolytic sites can also discriminate based on hydrophobic verses polar interactions. To transcribe the mRNA, the tRNAs must recognize the codon. It is entirely based on the tRNA and on the fact that many tRNAs are capable of binding to several different codons. Recall that the genetic code is degenerate at position 3. Therefore, the base inosine, which can form wobble base pairs to U, C and A, is usually found at position 1 of the anticodon.