Ribosome shift

The process of elongation will continue in the 5 to 3 direction down the mRNA. Each time the ribosome shifts position by three bases to accept another aminoacyl tRNA, the growing peptide chain will increase in length by one amino acid. Because the carboxyl group of the peptide linked to the tRNA at the P site always forms a covalent bond with the amino group of the amino acid on the tRNA at the A site, peptides are always synthesized from the amino terminus to the carboxyl terminus. 

Protein synthesis begins when the mRNA combines with a ribosome. There, tRNA molecules, which carry amino acids, align with mRNA, and a peptide bond forms between the amino acids. After the first tRNA detaches from the ribosome, the ribosome shifts to the next codon on the mRNA. Each time the ribosome shifts and the next tRNA aligns with the mRNA, a peptide bond joins the new amino acid to the growing polypeptide chain. After all the amino acids for a particular protein have been linked together by peptide bonds, the ribosome encounters a stop codon. Because there are no tRNAs to complement the termination codon, protein synthesis ends and the completed polypeptide chain is released from the ribosome. Then interactions between the amino acids in the chain form the protein into the three-dimensional structure that makes the polypeptide into a biologically active protein (see Figure 18.24). 

Ribosomal shifts can occur over a considerable distance without intermediate steps, a phenomenon known as ribosomal hopping (124). An extreme case of hopping is the skip of 50 nt that separate codon 46 from codon 47 in the mature message of T4 topoisomerase subunit gene 60 (12). The elements contributing to the skip are presumed to be located both at the coding gap which contains a pseudoknot and at the nascent, 46-aa peptide which precedes the interruption. 

What could be the signal for the induction of the cold shock proteins It has been observed that shifting E. coli cells from 37 to 5 °C results in an accumulation of 70S monosomes with a concomitant decrease in the number of polysomes [129]. Further, it has been shown that a cold shock response is induced when ribosomal function is inhibited, e.g. by cold-sensitive ribosomal mutations [121] or by certain antibiotics such as chloramphenicol [94]. These data indicate that the physiological signal for the induction of the cold shock response is inhibition of translation caused by the abrupt shift to lower temperature. Then, the cold shock proteins RbfA, CsdA and IF2 associate with the 70S ribosomes to convert the cold-sensitive nontranslatable ribosomes into cold-resistant translatable ribosomes. This in turn results in an increase in cellular protein synthesis and growth of the cells. 

Hung, M., Patel, P., Davis, S., and Green, S. R. (1998). Importance of ribosomal frame-shifting for human immunodeficiency virus type 1 particle assembly and replication. J. Virol. 72, 4819-4824. 

PMR studies have been performed on a number of other ribosomal proteins isolated by the acetic acid/urea method (Morrison etal., 1977a). The results of these studies have shown that acedc acid/urea-extracted proteins contain little tertiary structure. However, some structure was seen in protein S4 and especially in protein S16 as indicated by the appearance of ring-current shifted resonances in the apolar region of the spectrum (Morrison et al., 1977b). These are due to the interaction of apolar methyl groups with aromatic amino acids in the tertiary structure of the protein. The PMR spectra were recorded either in water or in dilute phosphate buffer at pH 7.0—conditions under which the proteins were soluble. 

If photosynthetic and respiratory changes cannot account for the increases in adenylate concentration, which system is responsible It has been reported that ADP and ATP concentrations of Ehrlich ascites tirnior cells increase in the presence of adenine (15), Whether this wo ild hold true for plant cells is not known, but it seems plausible that equilibrium shifts would initiate similar responses. An increase in adenine concentrations could occur if there was any breakdown of nucleic acids. There is one report that the number of ribosomes in the chloroplast does decrease in response to ozone (16). An increase in synthesis of purines is also possible but there is no evidence to either support or refute this hypothesis. 

The ribosome then translocates to the next codon, with the peptidyl-tRNA shifting from the A site to the P site and the now uncharged tRNA exiting the ribosome from the E site. 

Elongation Step 3 Translocation In the final step of the elongation cycle, translocation, the ribosome moves one codon toward the 3 end of the mRNA (Fig. 27-25a). This movement shifts the anticodon of the dipeptidyl-tRNA, which is still attached to the second codon of the mRNA, from the A site to the P site, and shifts the de-acylated tRNA from the P site to the E site, from where the tRNA is released into the cytosol. The third codon of the mRNA now lies in the A site and the second codon in the P site. Movement of the ribosome along the mRNA requires EF-G (also known as translocase) and the energy provided by hydrolysis of another molecule of GTP. 

It should be mentioned that the ribosomes of chloroplasts and mitochondria synthesize only a comparatively small part of the proteins required for the formation and function of these organelles. This may be due to the fact that the process of symbiosis occurred in a very distant epoch and many genes have shifted from autonomous genomes into nuclei since that time. 

In translocation, the peptidyl-tRNA is shifted from the A site to the P site on the ribosome. What happens to the peptidyl-tRNA anticodon-codon interaction ... 

---