Transfer RNA (t RNA) : its Two-dimensional Structure

Transfer RNA (t RNA)

Introduction t RNA

tRNA also known as soluble RNA (sRNA), makes another small fraction (10-15%) or RNA. These are the smallest molecules of RNA and work as adapter smallest molecules of RNA and work as adapter molecules for carrying amino acid molecules to the site of protein synthesis. Being the smallest in size, these molecules have been intensively investigated.

Two-dimensional Structure of tRNA (Clover Leaf Model)

Clover-leaf model of tRNA - Structures of different tRNAS for almost all amino acids are now available and fit the clover leaf model. It has the following four or more double helical regions, each having a loop.

(i)  An 'anticodon' is usually present in the loop on the second helical region (often described as anticodon arm), and recognizes its corresponding 'codon' in mRNA. However, the number of tRNAs is not necessarily the same as the number of codons, with the result that a tRNA species may recognize multiple synonymous codons for the same amino acid. Similarly, there can be more than one tRNA species for the same amino acid. They are described as isoaccepting tRNAs.

(ii)  The 3' acceptor end of the tRNA, which is recognized by the base sequence, is represented by a single-stranded region on the acceptor arm, which is composed of a double helix arm. 5'CCA3', to which an amino acid is attached.

(iii)  The TψC arm (or T arm) is so named due to this triplet sequence in the loop carried in this arm.

(iv)  The DHU (or D) arm is characterized by the presence of dihydrouridine in the loop attached to this arm. There is also a highly variable region, called the variable loop, which varies greatly among different tRNAs. This variable loop, sometimes described as an extra arm, is located between the TψC arm and the anticodon arm.

Class I and Class II tRNAs - On the basis of the size divided into two classes -

(i) Class I tRNAs have a small variable loop, consisting of only 3-5 bases; 75% of tRNAs belong to this class.

(ii) Class II tRNAs have a large variable loop with 13-21 bases along with 5 base pairs in the variable stem. The bases in this loop are numbered as 47:1 to 47:18 (since these bases are not counted in the total number of bases in a tRNA).

Read more - Nucleic Acids

Three Dimensional Structure of tRNA

In order to understand the structure-function relationship of tRNA, its three-dimensional structure (TDS) should be known. When tRNA became crystalline in 1968, X-ray crystallography could be used to study tRNA's TDS, just like it was done for DNA's double helix.

A Kluge from the MRC Laboratory, Cambridge, who was awarded the 1982 Nobel Prize in Chemistry, contributed greatly to the study of TDS of tRNA. There were initially over a dozen models for TDS, but S.H. Kim's model from 1973 was the most recent and widely accepted. 

The TDS of tRNA, according to his hypothesis, has a thickness of 20 A and is shaped like the letter L. An easy way to get this is from a two-dimensional clover-leaf model. This L-shaped structure is obtained by condensing the four arms of the clover-leaf into following two major domains -

1. Acceptor arm-TyC mini-helix.
2. Arm-DHU (or D) arm-biloop is an anticodone. Without changing the TDS shape, the additional arm, which differs among the different tRNA molecules, can be lengthened. The CCA stem extends and can be oriented in various ways. The protrusions of individual bases or variations in the angle between the two arms of the L-shaped structure can also be used to identify between different tRNAs.