Information on the amino acid sequences of proteins is written down as nucleotide sequences of the messenger RNA. The template triplet (codon) should determine unambiguously the position of a corresponding amino acid. However, there is no apparent steric fit between the structure of amino acids and their respective codons. In other words, codons cannot serve as direct template surfaces for amino acids. In order to solve this problem, in 1955 Francis Crick put forward his "adaptor hypothesis" in which he proposed the existence of special small adaptor RNA species and of specialized enzymes covalently attaching the amino acid residues to these RNAs (see Hoagland, 1960). According to this hypothesis each of the amino acids has its own species of adaptor RNA, and the corresponding enzyme attaches this amino acid only to a given adaptor. On the other hand, the adaptor RNA possesses a nucleotide triplet (subsequently termed the anticodon) that is complementary to the appropriate codon of the template RNA. Hence, the recognition of a codon by the amino acid is indirect and is mediated through a system consisting of the adaptor RNA and the enzyme: a specific enzyme concomitantly recognizes an amino acid and the corresponding adaptor molecule, so that they become ligated to each other; in its turn, the adaptor recognizes an mRNA codon, and thus the amino acid attached becomes assigned specifically to this codon. In addition, this mechanism implied the energy supply for amino acid polymerization at the expense of chemical bond energy between the amino acid residues and the adaptor molecules.

This model was soon fully confirmed experimentally. In 1957 Hoagland, Zamecnik, and Stephenson, and simultaneously Ogata and Nohara, reported the discovery of a relatively low-molecular-weight RNA ("soluble RNA") and a special enzyme fraction ("pH 5 enzyme") that attached amino acids to this RNA. It was demonstrated that the aminoacyl-tRNA formed was indeed an intermediate in the transfer of amino acids into a polypeptide chain. Subsequently, this RNA was termed transfer RNA (tRNA); the enzymes were called aminoacyl-tRNA synthetases (ARSases).

The cell contains a specific aminoacyl-tRNA synthetase for each of the 20 amino acids participating in protein synthesis (the individual aminoacid-specific ARSases will be designated below as AlaRS, ArgRS, AspRS, etc.). Therefore, prokaryotic cells contain 20 different ARSases.. The situation with eukaryotic cells is more complex, particularly because, in addition to the main cytoplasmic synthetases, there are special sets of ARSases for chloroplasts and mitochondria.

The number of different tRNA species is always greater than the number of amino acids and aminoacyl-tRNA synthetases. For example, in E. coli 49 tRNA species encoded by different genes have been discovered (some tRNA species are encoded by multiple genes, so that the total number of tRNA genes approaches 80). This implies that several different tRNAs may be recognized by the same ARSase and, correspondingly, can be ligated to the same amino acid; such tRNAs are called isoacceptor tRNAs. Some isoacceptor tRNAs differ only in a few nucleotides and possess the same anticodon (thus recognizing the same codons), but in most cases different isoacceptor tRNA species have different anticodons and therefore recognize different codons for a given amino acid. In E. coli there are about 40 tRNA species carrying different anticodons including tRNA for selenocysteine (recognizing UGA) and a special initiator tRNA (having the same anticodon as methionine tRNA). An example of isoacceptor tRNAs is 5 different leucine tRNA species in E. coli, with anticodons CAG, GAG, U*AG (U* is modified uridine), CAA, and U*AA, recognizing 6 leucine codons; among them, tRNAiLeu recognizes the leucine codon CUG (anticodon CAG), and tRNA5Leu recognizes the leucine codons UUA and UUG (anticodon U*AA). The situation is similar in the cytoplasm of eukaryotic cells.

Cellular organelles (mitochondria and chloroplasts) of eukaryotic cells contain their own sets of tRNA species which are simpler than those of the cytoplasm, and also, as a rule, they have their own ARSases. Only 22 to 23 tRNA species encoded by the organelle genome can be found in animal mitochondria, and they are sufficient to recognize all 62 sense codons of mitochondrial mRNA. Thus, there usually exists just a single species of tRNA which corresponds to each amino acid and to all codons of a given amino acid. The exceptions are tRNALeu and tRNASer where two species correspond to two different codon boxes.

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