Internal ribosomal structure

See also Internal Ribosomal Structure, Translation. Initiation of Translation, Elongation of Translation, Termination of Translation, Antibiotic Inhibition of Translation, Genetic Code, Codons... 

S. Bonnal, C. Schaeffer, L. Creancier, S. Clamens, H. Moinc, A.C. Prats, and S. Vagner, A single internal ribosome entry site containing a G quartet ENA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons, J Biol Chem 278, 39330-39336 (2003). 

The eukaryotic protein-synthesizing machinery begins translation of most cellular mRNAs within about 100 nucleotides of the 5 capped end as just described. However, some cellular mRNAs contain an internal ribosome entry site (IRES) located far downstream of the 5 end. In addition, translation of some viral mRNAs, which lack a 5 cap, is initiated at IRESs by the host-cell machinery of infected eukaryotic cells. Some of the same translation initiation factors that assist in ribosome scanning from a 5 cap are required for locating an internal AUG start codon, but exactly how an IRES is recognized is less clear. Recent results indicate that some IRESs fold into an RNA structure that binds to a third site on the ribosome, the E site, thereby positioning a nearby internal AUG start codon in the P site. 

Figure 5.5. The generic structure of a eukaryotic niRNA. illustrating some post-transcriptional regulatory elements that affect gene expression. Abbreviations (from 5 to 3 ) UTR. untranslated region inVG, 7-inelhyl-guanosinc cap Hairpin, hairpin-like secondary structures uORF, upstream open reading frame IRES, internal ribosome entry site CPE. cytoplasmic poiyadenylation element AAUAAA. polyadenyla-...

In a special class of internal initiations, the ribosomes bind at a specific internal AUG codon to start translation. The internal AUG may be located as far as 800 bases from the 5 end as in picornaviruses with uncapped, (+)-sense genomic RNAs. According to the model of cap-independent translation or internal ribosome entry (55), the internal RBS or ribosome landing pad is a 5 UTR sequence that forms a stable stem-loop structure. Hepatitis B virus (HBV) and some retroviruses also use an internal AUG codon, rather than ribosomal frameshifting, to express their reverse transcriptase genes (56,57). 

The cytosol is the fluid compartment of the cell and contains the enzymes responsible for cellular metabolism together with free ribosomes concerned with local protein synthesis. In addition to these structures which are common to all cell types, the neuron also contains specific organelles which are unique to the nervous system. For example, the neuronal skeleton is responsible for monitoring the shape of the neuron. This is composed of several fibrous proteins that strengthen the axonal process and provide a structure for the location of specific membrane proteins. The axonal cytoskeleton has been divided into the internal cytoskeleton, which consists of microtubules linked to filaments along the length of the axon, which provides a track for the movement of vesicular material by fast axonal transport, and the cortical cytoskeleton. 

The known catalytic repertoire of ribozymes continues to expand. Some virusoids, small RNAs associated with plant RNA viruses, include a structure that promotes a self-cleavage reaction the hammerhead ribozyme illustrated in Figure 26-25 is in this class, catalyzing the hydrolysis of an internal phosphodiester bond. The splicing reaction that occurs in a spliceosome seems to rely on a catalytic center formed by the U2, U5, and U6 snRNAs (Fig. 26-16). And perhaps most important, an RNA component of ribosomes catalyzes the synthesis of proteins (Chapter 27). 

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