Question

During the elongation phase of protein synthesis, two tRNA binding sites (A and P) orchestrate the elongation of a protein. Describe the recognition of the codon and formation of the peptide bond.

Answer 1

A ribosome binds to the mRNA strand that codes for the initiation codon (AUG). This ribosome (70S) consists of two subunits namely, large subunit (50S) and small subunit (30S), here S signifies the Svedberg unit. On the 70S ribosome, there are three tRNA-binding sites present, which bridge the two subunits of the 70S ribosome. They are called the A-site (aminoacyl), P-site (peptidyl), and E-site (exit). The process of initiation, elongation and termination takes place as given below -

1. Charging of tRNA - At first, the amino acid gets acylated and binds to the tRNA, this process is called the charging of tRNA which prepares amino acid for the further elongation process. In this process, the uncharged tRNA, an ATP molecule and a amino acid are involved. Upon binding of the amino acid with the tRNA, an ATP molecule gets used up and forms an AMP molecule with the release of a phosphate group.
2. Initiation - During initiation the 30S subunit containing the P-site and the A-site bind to the mRNA. This occurs due to the binding of the IF-3 (Initiation Factor )to the 30S subunit and IF-1 and the A-site of the 30S subunit. Further, the charged tRNA (formyl Methionine for the AUG codon) bound to the IF-2 along with a GTP molecule binds at the P-site. At the end of the initiation step, the 50S subunit binds to the mRNA and the IF-1, IF-2 and IF-3 are released. Also, a GDP molecule is released after usage of a phosphate molecule from the GTP.
3. Elongation - The second aminoacyl-tRNA binds at the A-site of the 70S ribosome upon recognition of the codon. Further, the peptide bonding between the -COO^- of the first amino acid and the -NH₃⁺ of the second amino acid takes place. Right after the peptide bonding happens the tRNA at the P-site gets deacylated and the tRNA at the A-site becomes dipeptidyl-tRNA. By the binding of the Elongation Factor - G (EF-G) along with a GTP molecule onto the ribosome the translocation takes place. After the translocation, the EF-G along with the GDP molecule is released upon usage of a phosphate molecule for energy. Also, the dipeptidyl-tRNA moves to the P-site making space for another incoming aminoacyl-tRNA. The steps further repeat causing the elongation of the peptide molecule.??
4. Termination - When the ribosome recognises a stop codon (UAA, UGA, UAG) the release factors (RF) are recruited and the peptide chain is cleaved from the tRNA. This occurs as no aminoacyl-tRNA exists for recognising the stop codons. RF-1 recognises UAA and UAG; RF-2 recognises UAA and UGA.