Transfer RNA

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

Quiz:

Which of the two groups corresponds to paired bases? 1 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:

  • D or DHU arm
  • anticodon arm
  • T or TΨC arm
  • amino acid acceptor arm

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.

(you can use the buttons above to show and hide the bases)

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":

along the axis of the acceptor arm (with the 3' end at the front and the 5' end a little farther)

along the axis of the anticodon arm (with the anticodon at the front)


On the spacefilling model let's see some functionally important parts of the molecule.

Quiz:

Identify each part of the molecule and highlight the colour used for its display in the model:
(click on a coloured square to assign that colour to the item at its right)
Backbone
Bases
  5' terminal nucleotide:
Backbone
Base
  3' terminal nucleotide:
Backbone
Base
  Anticodon:
Backbone
Bases

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)