Transfer RNA is a type of RNA which acts as the “Intermediary element” which plays a significant role in the loading and transferring of amino acids to the site of protein synthesis, i.e. Ribosome. The t-RNA first decodes the information or the nucleotide sequences carried by the m-RNA. Therefore, t-RNA also plays a major role in the process of “Protein synthesis”, or we can say “Translation of mRNA into a protein”.
To get the idea of this, let us suppose m-RNA carries a code or nucleotide sequences of the DNA and a t-RNA is the key to that code which carries anticodons that decodes the codons of m-RNA. A complementary pairing occurs between the triplet codons of m-RNA with the anticodons of t-RNA.
The codons of m-RNA carry genetic information which decides the type of amino acid that will bind to the amino acid acceptor site of t-RNA. The transfer RNA is named for its key role in transferring the amino acid to the ribosome by reading the information given by m-RNA.
Content: Transfer RNA
Definition of Transfer RNA
Transfer RNA can define as the type of RNA which acts as a carrier molecule which loads the amino acid by decoding the piece of genetic information carried by the codons of m-RNA and converting it into the physical proteins.
Characteristics of Transfer RNA
- Transfer RNA refers to as “Soluble RNA” because it is soluble in the solution of a 1M concentration of NaCl.
- The t-RNA also refers as “Adaptor RNA” because it carries the amino acids to the ribosomes.
- Transfer RNA contributes about 10-15% of the cellular RNA.
- The t-RNA is a highly folded structure due to which the nucleotides come closer to each other and appears to be like double-stranded.
- The sedimentation constant of t-RNA is 3.8 S and molecular weight of 25,000–30,000 Dalton.
- The t-RNA is the smallest form of RNA which is composed of 75-95 nucleotide bases.
- There are twenty types of t-RNA, as there are 20 types of amino acids.
- Transfer RNA is different from the other RNA molecules as it consists of abnormal and modified bases like pseudouracil, inosine, dihydrouridine etc.
- In the structure of t-RNA, there is three looped structure which forms due to abnormal base pairs where no hydrogen bonding occurs. The stems of t-RNA consist of regular base pairs which bind with each other through the hydrogen bond and there is no such formation of a loop.
- The DHU arm of t-RNA consists of di-hydroxy uridine as an abnormal base.
- Anticodon arm of t-RNA consist of Inosine as an abnormal base
- The TΨC arm consists of pseudouracil as an unusual nucleotide.
Structure of Transfer RNA
There are three structural configurations of transfer RNA namely primary, secondary and tertiary structure.
In the primary structure, the t-RNA is having a linear structure and 60-90 nucleotides. The primary structure forms “Post-transcriptionally”. On the 3’-end, CCA sequence is present. The charged t-RNA assembles the amino acids in correct order where the COOH-group attaches above the 3’-OH end.
It is having a large number of modified bases. There are 15 invariant and 8 semi-invariant residues present in the primary structure of t-RNA which position leads to the formation of the secondary and tertiary structure of t-RNA.
The “Clover-Leaf model” is the most popular model to explain the secondary structure of transfer RNA which was given by Robert Holley in 1968. According to the cloverleaf model, there are four arms of the t-RNA, and sometimes one additional arm is also present.
Acceptor, DHU, Anticodon and TΨC are the four common arms found in the structure of transfer RNA and in addition to this, one Variable arm may also present.
It also refers as the site for “Amino acid attachment” and consists of 7 paired nucleotides and 4 unpaired bases. The acceptor arm is a double helical stem which is having both 3’ end and 5’ end. The 3’-end consists of a CCA sequence refers as “Terminal ACC-sequence”. The carboxyl group of amino acid attaches with the 3’–OH end. At the 5’-end, guanine is always present. Therefore, it can define as the site of attachment of activated amino acid.
Here, DHU stands for “Di-hydroxy uridine”. The DHU sometimes refers as “D-arm” which consists of 15-18 total nucleotide bases from which 7-12 are the modified bases and 4 with usual bases. This arm comprises of a 4bp long stem and a loop with 7 unusual pyrimidine bases including dihydroxy uridine.
D-arm is also known as “Aminoacyl synthetase binding site” as it activates the amino acid synthesis by synthesizing an enzyme refers as “Aminoacyl tRNA synthetase”. The enzyme promotes the specific and robust binding of amino acid to the t-RNA with the help of an ATP molecule.
DHU arm plays a very crucial role in the stabilization of the tertiary structure of t-RNA. There are two variable regions which are present on both the sides of guanine residues refers as α and β variable areas.
It also refers as “Codon recognition site”. Anticodon arm also consists of a stem which is 5bp long and a loop consist of 7 unpaired bases. In between the seven unpaired bases of anticodon loops, there are three anticodons. The anticodons recognize the codons of m-RNA and complementarily binds to it.
The anticodons in the loop decide the type of amino acid which will attach to the 3’-end of the t-RNA. Therefore, the anticodon arm is the most essential part of the transfer RNA that recognizes and reads the information carried by m-RNA.
Here, TΨC stands for “Thymine pseudouracil cytosine”. TΨC arm also consists of a stem which is 5bp long and a loop with 7 unpaired bases. Due to the presence of TΨC sequence, it is named as “TΨC arm” in 5’-3’ direction. TΨC arm consists of “Ribosomal recognition site” which plays a vital role in the binding of tRNA with the ribosome.
It is the additional arm which is present between the anticodon and TΨC arms. The variable arm is the shortest arm whose presence differs among species to species. The length of the variable arm recognizes the enzyme translated for the t-RNA. The variable arm helps in the stabilization of the t-RNA. Based on the presence of a variable arm, t-RNA can classify into two types:
- Type-I t-RNA: This type of t-RNA lacks the variable arm.
- Type-II t-RNA: This type of t-RNA consists of the variable arm.
It is the three-dimensional structure which is highly folded and is having an L-shaped structure.
In the tertiary structure of t-RNA, acceptor and TΨC arm form the extended helix downwards. The anticodon and DHU arm form the extended helix upwards. Due to the change in structural configuration, the DHU and TΨC join where both the extended helices align at the angle of 90 degrees. The stabilization of the tertiary structure is through the base pairing and base stacking.
Role of Transfer RNA
The t-RNA first recognizes the codons of mRNA with the help of the anticodon arm. The anticodon arm of t-RNA consists of three anticodons which then complementarily binds with the codons of the m-RNA. This complementary binding then activates the synthesis of an enzyme known as “Aminoacyl tRNA synthetase”. The synthetase enzyme will help in the binding of specific amino acid according to the codons that will code the particular amino acid.
The aminoacyl tRNA synthetase enzyme is different for each amino acids. When both amino acid and the t-RNA molecule attaches with the synthetase enzyme, it will promote the binding of both t-RNA and amino acid with the help of an ATP molecule.
Once the synthetase enzyme charges the t-RNA, it will load the amino acid and transfer it to the ribosome where the amino acid combines for the building up of protein.