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Codons that encode the same amino acid often differ only by their third base, which is why they tend to be together in the same column when the code is presented as in Table 2.2. This pattern of redundancy in the code is due to less stringent pairing, or wobble, between the last (3′) base in the codon on the mRNA and the first (5′) base in the anticodon on the tRNA (remember that RNA sequences are always given 5′ to 3′ and that the pairing of strands of RNA, like that of DNA, is antiparallel [Figure 2.25]). As a consequence of wobble, the same tRNA can pair with more than one of the codons for a particular amino acid, so there can be fewer types of tRNA than there are codons. For example, even though there are two codons for lysine, AAA and AAG, E. coli has only one tRNA for lysine, which, because of wobble, can pair with both lysine codons.

While the term “wobble” may suggest that the process is random or that there is a lack of stringency inherent in the system, this is not really the whole story. As indicated earlier in the chapter, base pairing in RNA is different than in DNA, and modification of the anticodon itself contributes to alternative base-pairing rules, resulting in a process in which fewer tRNAs can be utilized to accurately recognize more codons (Figure 2.33). For example, wobble allows a G in the first position of the anticodon to pair with either a C or a U in the third position of the codon but not with an A or a G; this explains why UAU and UAC, but not UAA or UAG, are codons for tyrosine and can be recognized by a single tRNA with a GUA anticodon sequence. Similarly, a U in the first position of the anticodon can pair with either an A or a G in the third position of the codon (corresponding to the fact that both CAA and CAG are glutamine codons and can be recognized by a single tRNA with a UUG anticodon sequence). The rules for wobble are complicated by the fact that the bases in tRNA are sometimes modifed, and a modified base in the first position of an anticodon can have altered pairing properties. Inosine, which is a purine base found only in tRNA, can pair with any residue, so a single tRNA with inosine at the first position of the anticodon can recognize multiple codons (UCU, UCA, and UCC in Figure 2.33C, all of which encode serine). In other cases, an organism may use multiple tRNAs to recognize different codons that specify the same amino acid.

Figure 2.33 Wobble pairing between the anticodon on the tRNA and the codon in the mRNA. Non-Watson-Crick pairing interactions are possible in the third position of the codon. Alternative pairings for the anticodon base are shown: (A) guanine to cytosine or uracil; (B) uracil to adenine or guanine; and (C) inosine (a purine base found only in tRNAs) to adenine, cytosine, or uracil. This allows a single tRNA to recognize multiple codons.