Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the glutamic acid tRNA molecules, as well as all of the glutamine tRNA molecules. Then, a second enzyme chemically modifies the glutamic acid into glutamine on the latter tRNA molecules, thus forming the proper pair.

The equal importance of tRNA and aminoacyl-tRNA synthetase was established by a series of experiments in which one amino acid was chemically converted into a different amino acid after being attached to its paired tRNA. In an in vitro protein synthesis experiment, these "hybrid" aminoacyl-tRNA molecules inserted the incorrect amino acid at every point in the peptide chain where that tRNA was used. The results showed that both the tRNA and the enzyme are equally required for proper translation of the amino acid sequence encoded by the mRNA.

In cells, aminoacyl-tRNA synthetases use structural and chemical complementarity to identify the correct tRNA that must be coupled to the amino acid bound at its active site. Most tRNA synthetases contain three adjacent nucleotide-binding pockets, each of which is complementary in shape and charge to a nucleotide in the anticodon. While these pockets recognize the specific nucleotides in the anticodon loop of the tRNA, additional amino acids interact with the amino acid-accepting arm, thus allowing the correct tRNA to fit into the synthesis site of the enzyme.