2. The stages of protein synthesis

6.2 The stages of protein synthesis

Figure 6.3 Size comparisons show that the ribosome is large enough to bind tRNAs and mRNA.

Each ribosome subunit has specific roles in protein synthesis. Messenger RNA is associated with the small subunit; ~30 bases of the mRNA are bound at any time. One popular idea is that the mRNA fits between or close to the junction of the subunits. Two tRNA molecules are active in protein synthesis at any moment; so polypeptide elongation involves reactions taking place at just two of the (roughly) 10 codons covered by the ribosome. As evident from Figure 6.3, the two tRNAs are quite large relative to the ribosome; they become inserted into internal sites that stretch across the subunits. A third tRNA may remain present on the ribosome after it has been used in protein synthesis, before being recycled.

Figure 6.4 The ribosome has two sites for binding charged tRNA.

Each tRNA lies in a distinct site on the ribosome. Figure 6.4 shows that the two sites have different features:

• An incoming aminoacyl-tRNA binds to the A site (or acceptor site). Prior to the entry of aminoacyl-tRNA, the site exposes the codon representing the next amino acid due to be added to the chain.
  
• The codon representing the most recent amino acid to have been added to the nascent polypeptide chain lies in the P site (or donor site). This site is occupied by peptidyl-tRNA, a tRNA carrying the nascent polypeptide chain.

The end of the tRNA that carries an amino acid is located on the large subunit, while the anticodon at the other end interacts with the mRNA bound by the small subunit. So the P and A sites each extend across both ribosomal subunits.

For a ribosome to synthesize a peptide bond, it must be in the state shown in step 1 in the figure, when peptidyl-tRNA is in the P site and aminoacyl-tRNA is in the A site. Then peptide bond formation occurs when the polypeptide carried by the peptidyl-tRNA is transferred to the amino acid carried by the aminoacyl-tRNA. This reaction is catalyzed by constituents of the large subunit of the ribosome.

Transfer of the polypeptide generates the ribosome shown in step 2, in which the deacylated tRNA, lacking any amino acid, lies in the P site, while a new peptidyl-tRNA has been created in the A site. This peptidyl-tRNA is one amino acid residue longer than the peptidyl-tRNA that had been in the P site in step 1.

Figure 6.5 Aminoacyl-tRNA enters the A site, receives the polypeptide chain from peptidyl-tRNA, and is transferred into the P site for the enxt cycle of elongation.
Animated figure

Then the ribosome moves one triplet along the messenger. This stage is called translocation, and we discuss it in more detail shortly. The movement transfers the deacylated tRNA out of the P site, and moves the peptidyl-tRNA into the P site (see step 3). The next codon to be translated now lies in the A site, ready for a new aminoacyl-tRNA to enter, when the cycle will be repeated. The animation of Figure 6.5 summarizes the interaction between tRNAs and the ribosome..

Figure 6.6 tRNA and mRNA move through the ribosome in the same direction.

The deacylated tRNA leaves the ribosome via another tRNA-binding site, the E site. This site is transiently occupied by the tRNA en route between leaving the P site and being released from the ribosome into the cytosol. So the flow of tRNA is into the A site, through the P site, and out through the E site. Figure 6.6 compares the movement of tRNA and mRNA, which may be thought of as a sort of ratchet in which the reaction is driven by the codon-anticodon interaction. (We consider this concept in more detail in 7 Using the genetic code.)

Figure 6.7 Protein synthesis falls into three stages.
Multiple figure

Protein synthesis falls into the three stages shown in Figure 6.7:

• Initiation involves the reactions that precede formation of the peptide bond between the first two amino acids of the protein. It requires the ribosome to bind to the mRNA, forming an initiation complex that contains the first aminoacyl-tRNA. This is a relatively slow step in protein synthesis, and usually determines the rate at which an mRNA is translated.
  
• Elongation includes all the reactions from synthesis of the first peptide bond to addition of the last amino acid. Amino acids are added to the chain one at a time; the addition of an amino acid is the most rapid step in protein synthesis.
  
• Termination encompasses the steps that are needed to release the completed polypeptide chain; at the same time, the ribosome dissociates from the mRNA.

Different sets of accessory factors assist the ribosome at each stage. Energy is provided at various stages by the hydrolysis of GTP.

Figure 5.9 A ribosome assembles from its subunits on mRNA, translates the nucleotide triplets into protein, and then dissociates from the mRNA.
Animated figure

The overall process of translation is summarized in the animation of Figure 5.9. In initiation, the small ribosomal subunit binds to mRNA and then is joined by the 50S subunit. In elongation, the mRNA moves through the ribosome and is translated in triplets. (Although we usually talk about the ribosome moving along mRNA, it is more realistic to think in terms of the mRNA being pulled through the ribosome.) At termination, the protein is released, mRNA is released, and the individual ribosomal subunits dissociate in order to be used again.