Question

Based on your understanding of translation, explain why it makes sense to limit the structural determinants of specificity (in the ribosome and tRNA synthases) to a few very specific regions of the tRNA (i.e. anticodon loop, acceptor stem, variable arm, etc.)? In some cases, this can be limited to just a couple hydrogen bonds.

Answer 1

tRNA molecular is a clover leaf like structure molecule consisting of 76 nucleotides comprising 4 arms, namely:

• The Acceptor stem
• D loop
• Anticodon loop
• Variable loop

Translation is characterized by the addition of amino acids at the 3'-OH end of the acceptor stem to create a peptide chain based on the information of mRNA read by the anticodon loop.

The amino-acyl tRNA synthetase, is the enzyme that adds an amino acid to the specific tRNA molecule corresponding to the codon. Amino acyl tRNA synthetase binds to the specific amino acid with the use of one ATP molecule. This aa-RS complex so formed then binds to the D loop of specific tRNA. The amino acid is transferred to the 3'-OH end of the acceptor stem, where peptide chain is formed.

The process is highly specific and called as superspecific.

In case the amino-acyl tRNA synthetase binds to a wrong tRNA, this is immediately recognized based on the charge of the different amino acids, and the the bond between the amino-acyl tRNA synthetase and tRNA is hydrolyzed.

It makes sense to limit the structural determinants of specificity to a very few specific regions of tRNA, because

There is a possiblity of repeated occurence of unspecific binding of the amino- acyl tRNA-synthetase to the tRNA, which would lead to a different protein being produced that might be defective. In order to achieve superspecificity the ratio of the concentrationi of amino-acyl tRNA synthetase to the specific tRNA is limited, which further limits the structural determinants of specificity of tRNA synthetase to very few specific regions of tRNA.