tRNAs, or transfer RNAs, are single-stranded molecules that adopt a characteristic folding or three-dimensional structure, in the shape of an L. (The secondary structure that produces this folding or tertiary structure is called the clover leaf)
You can note that there are regions where the molecule forms an intra-chain double strand. This happens thanks to hydrogen bonding between complementary bases located in two regions of the same chain:
Display/hide base group nº 1 base group nº 2
These bonds drive the three-dimensional folding, giving the molecule its characteristic three-dimensional structure.
The paired zones define four arms in the structure of tRNA; in sequence from 5' to 3', they are:
colour the arms this way
Each arm (except the amino acid acceptor) has a paired region, the stem, and an unpaired one on its end, the loop.
In addition to the 4 arms, there is another region, of variable length, which may or not pair its bases: the variable arm .
End views along the two arms of the "L":
On the spacefilling model let's see some functionally important parts of the molecule.
When you finish, click on
Let's go back to the simplified rendering. The former example corresponds to yeast tRNA specific for phenylalanine (tRNAPhe). Let's see now another example, where the variable arm (thicker trace) is longer: (tRNASer from yeast). (on this molecule the buttons for displaying/hiding bases will not work correctly)