Procedure of Protein Synthesis

Initiation

Peptide synthesis always starts from methionine (Met). Therefore, the initial aminoacyl-tRNA is Met-tRNA_i^Met, where the subscript "i" specifies "initiation".  In bacteria, the methionine of the initial aminoacyl-tRNA has been modified by the addition of a formyl group (HCO) to its amino group.  The modified methionine is called formylmethionine (fMet), which is unique for bacteria.  Thus, fMet is an obvious foreign substance in eukaryotes.  It can elicit a strong immune response.  In humans, the immune response elicited by the peptide "fMet-Leu-Phe" is about a thousand times greater than "Met-Leu-Phe".

Elongation

A ribosome contains two major tRNA-binding sites: A site and P site.  After the large subunit joins the initiation complex, the initial Met-tRNA_i^Met enters the P site and the newly arrived aminoacyl-tRNA is always placed at the A site ("A" for "aminoacyl").  Then, methionine is transferred to the new aminoacyl-tRNA, forming a "peptidyl-tRNA"   where a peptide is attached to the tRNA.  Subsequently, the empty tRNA at the P site is ejected from the ribosome and the peptidyl-tRNA jumps to the P site ("P" for "peptidyl").  During this translocation step, the ribosome also moves one codon down the mRNA chain.  Similar steps are repeated in the next cycles of elongation.

Termination

Protein synthesis will terminate when the ribosome arrives at one of three stop codons.   The termination process is assisted by special proteins called termination factors which recognize the stop codons.  Their association stimulates the release of the peptidyl-tRNA from the ribosome.  Subsequently, the released peptidyl-tRNA divides into tRNA and a newly synthesized peptide chain.  The ribosome also divides into the large and small subunits, ready for synthesizing another peptide.

Figure 5-C-6. The steps involved in protein synthesis.

(a) In the absence of mRNA, the large and small subunits of a ribosome are separated.   At the beginning of peptide synthesis, initiation factors (IF) first assist the assembly of the small subunit, mRNA and the initial aminoacyl-tRNA.  Then, the large subunit is recruited to join the complex.

(b) In the elongation process, one cycle involves the following steps:

(i) New entry.  A new aminoacyl-tRNA with a correct anticodon is brought to the A site.  This step is catalyzed by  elongation factors Tu and Ts in prokaryotes, and by elongation factors EF₁ and EF_1b in eukaryotes..

(ii) Peptide synthesis.  The peptide attached to the peptidyl-tRNA at the P site is transferred to the new aminoacyl-tRNA at the A site, generating a peptidyl-tRNA with a longer peptide.  This step is catalyzed by peptidyl transferase.

(iii) Translocation.  The empty tRNA at the P site is ejected from the ribosome and the peptidyl-tRNA generated at the A site takes over the vacant P site.  In the mean time, the ribosome moves one codon down the mRNA chain.   The A to P switch is catalyzed by the elongation factor G in bacteria, and by the elongation factor EF₂ in eukaryotes.

Book Section:

Stepwise Formation of Proteins on Ribosomes - From Molecular Cell Biology by Lodish et al.

Review Article:

The social life of ribosomal proteins - FEBS J., 2005.

Internal ribosome entry sites in eukaryotic mRNA molecules - Genes and Development, 2001.