KEY CONCEPTS:
- 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.