tRNA Activation

To decode an mRNA into a protein sequence, each tRNA molecule carrying an amino acid, recognizes the three-nucleotide codon sequence on the mRNA, that corresponds to the amino acid.

There are 61 distinct codon sequences that encode 20 amino acids present in a cell. A single amino acid is coded for by several different codons, with one tRNA carrying one amino acid.

During the pairing of the tRNA anticodon with the mRNA codon, once the first two positions are paired, the third base can pair to either of the purines or either of the pyrimidines. This “wobble base”, allows 20 tRNAs to decode 61 mRNA codons.

An amino acid is covalently attached to the 3’ end of its partner tRNA by a group of enzymes called aminoacyl tRNA synthetases. There are 20 different aminoacyl tRNA synthetases corresponding to 20 amino acids.

The catalytic reaction proceeds in two steps.

The first step is amino acid activation, where within the enzyme pocket, the amino acid reacts with an ATP to form an aminoacyl AMP synthetase intermediate. 

In the second step of esterification, the activated amino acid is joined to a hydroxyl group at the 3’ terminus of the tRNA, forming the final aminoacyl-tRNA molecule.

If the enzyme binds the wrong amino acid, it can correct the mistake through a proofreading mechanism.

The correct amino acid has high affinity for the active site of the enzyme. Larger amino acids are rejected from the active site.

If an amino acid is similar in size to the correct one, before getting coupled to a tRNA, the incorrect aminoacyl AMPs are forced into a second editing pocket within the enzyme. 

Because the dimensions of this editing site precisely fit the correct amino acid, incorrect amino acyl AMPs are hydrolyzed rather than being joined to the tRNA.