The acceptor stem and anticodon are at ends of the tertiary structure

  • The clover-leaf forms an L-shaped tertiary structure with the acceptor arm at one end and the anticodon arm at the other end.
The secondary structure of each tRNA folds into a compact L-shaped tertiary structure in which the 3 end that binds the amino acid is distant from the anticodon that binds the mRNA. All tRNAs have the same general tertiary structure, although they are distinguished by individual variations.

The base paired double-helical stems of the secondary structure are maintained in the tertiary structure, but their arrangement in three dimensions essentially creates two double helices at right angles to each other, as illustrated in Figure 5.6. The acceptor stem and the TψC stem form one continuous double helix with a single gap; the D stem and anticodon stem form another continuous double helix, also with a gap. The region between the double helices, where the turn in the L-shape is made, contains the TψC loop and the D loop. So the amino acid resides at the extremity of one arm of the L-shape, and the anticodon loop forms the other end.
The tertiary structure is created by hydrogen bonding, mostly involving bases that are unpaired in the secondary structure. Many of the invariant and semiinvariant bases are involved in these H-bonds, which explains their conservation. Not every one of these interactions is universal, but probably they identify the general pattern for establishing tRNA structure.

A molecular model of the structure of yeast tRNAPhe is shown in Figure 5.7. The left view corresponds with the bottom panel in Figure 5.6. Differences in the structure are found in other tRNAs, thus accommodating the dilemma that all tRNAs must have a similar shape, yet it must be possible to recognize differences between them. For example, in tRNAAsp, the angle between the two axes is slightly greater, so the molecule has a slightly more open conformation.
The structure suggests a general conclusion about the function of tRNA. Its sites for exercising particular functions are maximally separated. The amino acid is as far distant from the anticodon as possible, which is consistent with their roles in protein synthesis.