A tRNA molecule folds upon itself via complementary base pairing into a general "cloverleaf" shape that is characteristic of tRNAs. Over evolutionary time, a considerable amount of variation on this structure has accumulated, although the basic shape is retained. The sequence at one end of a given type of tRNA determines which amino acid will attach there, and a sequence of three nucleotides at the other end of the (folded) tRNA molecule, called the anticodon, determines its specificity to a particular codon in the assembly of polypeptide (protein) chains.
The genomes of individual organisms contain multiple copies of codon-specific tRNA genes, some of them clustered on their respective chromosomes. Whatever other variation may have occurred, each codon-specific tRNA has a recognition triplet in the proper location (relative to the folded tRNA molecule) and the sequence structure that enables it to carry its specific amino acid. The "same" (amino-acid-specific) tRNA within or among organisms can vary in many details of its sequence, as can be seen by aligning them. Because of the redundancy of the coding system (see below), different recognition triplets that specify the same amino acid can be found in the appropriate positions on their respective tRNA molecules. Thus, within the flexibility of the cloverleaf conformation, there is considerable variation that serves this variation-on-a-theme function (amino acid specificity).
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