Ribosomes accessibility

As was evident in the previous section, the structural characteristics of the mRNA transcripts play a significant role in translation. An overwhelming majority of the structurally dependent mechanisms of translation control dealt with inhibition or improvement of ribosomal access to the initiation sites or altering the rate at which ribosomes scan across the transcripts. This section aims to complement the previous discussion by considering a more fundamental aspect of translation -codon usage. 

Ultimately, assembly occurs and release of virions from die cell occurs as a result of cell lysis. The features of replication of these simple RNA viruses are themselves fairly simple. The viral RNA itself functions as an mRNA and regulation occurs primarily by way of controlling access of ribosomes to the appropriate start sites on the viral RNA. 

Figure 7.5 Model of ferritin (and erythroid a-aminolaevulinate synthase) translation/ribosome binding regulation by IRP. In (a), with IRP not bound to the IRE (1) binding of the 43S preinitiation complex (consisting of the small ribosomal 40S subunit, GTP and Met-tRNAMet) to the mRNA is assisted by initiation factors associated with this complex, as well as additional eukaryotic initiation factors (elFs) that interact with the mRNA to facilitate 43S association. Subsequently (2), the 43S preinitiation complex moves along the 5 -UTR towards the AUG initiator codon, (3) GTP is hydrolysed, initiation factors are released and assembly of the 80S ribosome occurs. Protein synthesis from the open reading frame (ORF) can now proceed. In (b) With IRP bound to the IRE, access of the 43S preinitiation complex to the mRNA is sterically blocked. From Gray and Hentze, 1994, by permission of Oxford University Press.

Aminoglycosides must traverse the plasma membrane and, in the case of gramnegative bacteria, the outer membrane to gain access to the target ribosomes. Transport across the plasma membrane has been shown to require the proton motive force, and mutants deficient in electron transport chain components fail to transport aminoglycosides and are consequently resistant. ... 

Smjndly, the gold cluster described above was prepared in such a way that it could be bound to accessible -SH groups. Since this cluster is rather bulky, its accessibility was increased by the addition of spacers of various lengths to the cluster and to the free -SH groups on the ribosomal particles. 

The use of a particular mature mRNA for protein biosynthesis is also highly regulated. The regulation can occur via the accessibility of the mRNA for the ribosome or via the initiation of protein biosynthesis on the ribosome. In this manner a given level of mature mRNA can specifically determine when and how much a protein is synthesized on the ribosome. 

Interact with small ribosomal subunits, blocking access of the aminoacyl-tRNA to the mRNA-ribosome complex. 

Once the early code reader had been produced from RNA, which is the active component even in modern ribosomes, the potential information stored in the nucleic acid chains became defined and accessible and the protein products could be recruited as expeditors of the expression of a limitless reservoir of information. The reiteration of complementary strands of nucleic acids never stopped even when all possibilities of every possible protein plus all the failures were produced many times. All structural motifs were exhausted and all of them were potentially available to nascent cells they just had to be there to be collected in a grab-bag fashion. How much nucleic acid material was there Was it enough to buy all the tickets in the lottery ... 

Genetic information is accessed by a process known as transcription, in which the double-stranded DNA splits and the genetic code is transcribed onto a single-strand messenger RNA(mRNA). The mRNA is comprised of the same bases as the DNA, arranged in the same sequence, but in a complementary fashion. The mRNA migrates out of the nucleus and into the cytoplasm, where it attaches to ribosomes. The ribosomes assemble amino acids to form protein molecules through a process known as translation. 

The context of the mRNA sequence around the AUG codon translational start site, where the ribosome initiates translation of protein synthesis, is an important consideration. An appropriate consensus ribosome-binding region for the host organism should be used and potentially inhibitory RNA secondary structure, that may affect the ability of the ribosome to access this translation start site, avoided. Various RNA structure prediction programs such as... 

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