We saw earlier in this chapter that RNA molecules can fold into precise three-dimensional structures, and the tRNA molecules provide a striking example. Four short segments of the folded tRNA are double-helical, producing a molecule that looks like a cloverleaf when drawn schematically (Figure 6–50). For example, a 5ʹ-GCUC-3ʹ sequence in one part of a polynucleotide chain can form a relatively strong association with a 5ʹ-GAGC-3ʹ sequence in another region of the same molecule. The cloverleaf undergoes further folding to form a compact L-shaped structure that is held together by additional hydrogen bonds between different regions of the molecule (see Figure 6–50B and C).
Two regions of unpaired nucleotides situated at either end of the L-shaped molecule are crucial to the function of tRNA in protein synthesis. One of these regions forms the anticodon, a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule. The other is a short single-stranded region at the 3ʹend of the molecule; this is the site where the amino acid that matches the codon is attached to the tRNA.
We saw above that the genetic code is redundant; that is, several different codons can specify a single amino acid. This redundancy implies either that there is more than one tRNA for many of the amino acids or that some tRNA molecules can base-pair with more than one codon. In fact, both situations occur. Some amino acids have more than one tRNA and some tRNAs are constructed so that they require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position (Figure 6–51). This wobble base-pairing explains why so many of the alternative codons for an amino acid differ only in their third nucleotide (see Figure 6–48). In bacteria, wobble base-pairings make it possible to fit the 20 amino acids to their 61 codons with as
Figure 6–51 Wobble base-pairing between codons and anticodons. If the nucleotide listed in the first column is present at the third, or wobble, position of the codon, it can base-pair with any of the nucleotides listed in the second column. Thus, for example, when inosine (I) is present in the wobble position of the tRNA anticodon, the tRNA can recognize any one of three different codons in bacteria and either of two codons in eukaryotes. The inosine in tRNAs is formed from the deamination of adenosine (see Figure 6–53), a chemical modification that takes place after the tRNA has been synthesized. The nonstandard base pairs, including those made with inosine, are generally weaker than conventional base pairs. Codon–anticodon base-pairing is more stringent at positions 1 and 2 of the codon, where only conventional base pairs are permitted. The differences in wobble base-pairing interactions between bacteria and eukaryotes presumably result from subtle structural differences between bacterial and eukaryotic ribosomes, the molecular machines that perform protein synthesis. (Adapted from C. Guthrie and
J. Abelson, in The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression, pp. 487–528. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1982.) few as 31 kinds of tRNA molecules. The exact number of different kinds of tRNAs, however, differs from one species to the next. For example, humans have nearly 500 tRNA genes, and among them 48 different anticodons are represented.
tRNAs Are Covalently Modified Before They Exit from the Nucleus