Question

From a chemical view, how is an amino acid is being recognized by its specific aminoacyl tRNA synthetase?

Answer 1

During translation, rRNA and tRNA read mRNA in 5´ to 3´ direction. According to the codons being readen, tRNA transfers the correct amino acids to build the polypeptide chain. A codon is a short sequence of three nucleotides that store the genetic information for the aminoacids´ assembly.

Each tRNA has two important sites. One of them that couples with the codon of the mRNA molecule, named anticodon. The other site couples with an amino acid through the action of the aminoacyl-tRNA synthase enzyme. The whole complex, amino acid + enzyme + tRNA is named aminoacyl-tRNA.        

Each tRNA is recognized by a specific aminoacyl-tRNA synthase enzyme. The enzyme is also capable of recognizing a specific amino acid. Let us say, for instance, that tRNA is specific for phenylalanine. The molecule is attached to the enzyme that is specific for that tRNA(Phe). Then, when the enzyme and tRNA(Phe) are together, they get to find phenylalanine. The enzyme links the aminoacid to the RNA. Once the whole complex is formed, the tRNA gets to pair its anticodon with the mRNA codon. This is,

1. Recognition of enzyme and the specific tRNA(aa) ⇒ aa being aminoacid
2. Recognition of enzyme and the specific aminoacid
3. Linkage of the aminoacid to RNA by the enzyme action
4. Pairing of tRNA anticodon to mRNA codon.

Considering that there are twenty amino acids available, there are also twenty complexes of aminoacyl-tRNA, one for each amino acid. Each of the mRNA codons represents one of the 20 amino acids used to build the protein. Each amino acid can be codified by more than one codon. Of the total 64 codons, 61 codify amino acids, and one is a start codon. The left three codons are stopping translation points.

tRNA decodes genetic information from the nucleotidic sequence in the mRNA molecule and allows amino acids to align composing the new protein.  

Once the new peptidic link joins, placing together the new amino acid to the growing peptidic chain, the binding between the amino acid and the tRNA molecule breaks. The tRNA is now free to join another amino acid and repeat the cycle.

In conclusion, a specific aminoacyl-tRNA synthase enzyme recognizes a tRNA, which is also specific for a certain amino acid. When together, the enzyme recognizes the amino acid and links it to the RNA. The whole complex is known as aminoacyl-tRNA. Once the tRNA is joined to its amino acid, it gets to pair a codon of mRNA to add that amino acid to the new synthesizing protein.