Prokaryotes rRNA structure

Other antibiotics inhibit protein synthesis on all ribosomes (puromycin) or only on those of eukaryotic cells (cycloheximide). Puromycin (Figure 38—11) is a structural analog of tyrosinyl-tRNA. Puromycin is incorporated via the A site on the ribosome into the carboxyl terminal position of a peptide but causes the premature release of the polypeptide. Puromycin, as a tyrosinyl-tRNA analog, effectively inhibits protein synthesis in both prokaryotes and eukaryotes. Cycloheximide inhibits peptidyltransferase in the 60S ribosomal subunit in eukaryotes, presumably by binding to an rRNA component. 

The small ribosomal subunit binds to the mRNA. In prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgamo sequence in the 5 untranslated region of the niRNA. In eukaryotes, the small subunit binds to the 5 cap structure and slides down the message to the first AUG. 

Ribosomal RNAs (rRNAs) are found in association with several proteins as components of the ribosomes—the complex structures that serve as the sites for protein synthesis (see p. 433). There are three distinct size species of rRNA (23S, 16S, and 5S) in prokaryotic cells (Figure 30.2). In the eukaryotic cytosol, there are four rRNA size species (28S, 18S, 5.8S, and 5S). [Note "S" is the Svedberg unit, which is related to the jnolecular weight and shape of the compound.] Together, rRNAs make up eighty percent of the total RNA in the cell. 

Ribosomes are large complexes of protein and rRNA (Figure 31.8). They consist of two subunits—one large and one small—whose relative sizes are generally given in terms of their sedimentation coefficients, or S (Svedberg) values. [Note Because the S values are determined both by shape as well as molecular mass, their numeric values are not strictly additive. For example, the prokaryotic 50S and 30S ribosomal subunits together form a ribosome with an S value of 70. The eukaryotic 60S and 40S subunits form an 80S ribosome.] Prokaryotic and eukaryotic ribosomes are similar in structure, and serve the same function, namely, as the "factories" in which the synthesis of proteins occurs. 

Ribosomal RNA (rRNA) As discussed on p. 414, prokaryotic ribosomes contain three molecules of rRNA, whereas eukaryotic ribosomes contain four molecules of rRNA (see Figure 31.8). The rRNAs have extensive regions of secondary structure arising from the base-pairing of complementary sequences of nucleotides in different portions of the molecule. The formation of intramolecular, double-stranded regions is comparable to that found in tRNA. 

Initiation The components of the translation system are assembled, and mRNA associates with the small ribosomal subunit. The process requires initiation factors. In prokaryotes,a purine-rich region (the Shine-Dalgarno sequence) of the mRNA base-pairs with a complementary sequence on 16S rRNA, resulting in the positioning of the mRNA so that translation can begin. The 5 -cap on eukaryotic mRNA is used to position that structure on the ribosome. The initiation codon is 5 -AUG-3. ... 

Ribosomes, the intracellular particles on which proteins are assembled, are highly complex and dynamic entities. The structural framework of ribosomes is provided by ribosomal RNA (rRNA) molecules with which many proteins are associated (summarized in Capowski and Tracy, 2003). Homologous rRNA genes occur in all prokaryotes and eukaryotes. The mitochondrial and chloroplast rRNA genes in eukaryotes clearly have prokaryote affinities (Pace et ai, 1986). The genomic DNA from which ribosomal genes are transcribed, along with any associated spacers, is collectively termed ribosomal DNA (rDNA). Sequences and other data from rDNA and its products,... 

The cap protects the 5 end of the primary transcript against attack by ribonu-cleases that have specificity for 3 5 phosphodiester bonds and so cannot hydrolyze the 5 5 bond in the cap structure. In addition, the cap plays a role in the initiation step of protein synthesis in eukaryotes. Only RNA transcripts from eukaryotic protein-coding genes become capped prokaryotic mRNA and eukaryotic rRNA and tRNAs are uncapped. 

The rRNA transcription units in E. coli contain some tRNA genes that are transcribed and processed at the time of rRNA transcription (Topic G9). Other tRNA genes occur in clusters of up to seven tRNA sequences separated by spacer regions. Following transcription by the single prokaryotic RNA polymerase, the primary RNA transcript folds up into the characteristic stem-loop structures (Fig. 2) and is then processed in an ordered series of cleavages... 

Hybrid reconstitution assays using archaeal and bacterial ribosomal constituents [103] suggest that the large ribosomal subunits from the two prokaryotic domains possess a structurally conserved common core . This is inferred from the fact that the proteins involved in the early assembly of Sulfolobus SOS subunit (including all of the primary RNA-binding proteins) are also able to specifically and cooperatively interact with 23S rRNAs from H. mediterranei and E. co/i [103], and to generate a discrete particle sedimentally similar (40S) to the Sulfolobus low-temperature reconstitution intermediate (see section 2.7.1). 

Ribosomal RNA (rRNA) is the major component of ribosomes (Chapter 30). In prokaryotes there are three kinds of rRNA, called 23S, I6S, and 5S RNA because of their sedimentation behavior. One molecule of each of these species of rRNA is present in each ribosome. Ribosomal RNA was once believed to play only a structural role in ribosomes. We now know that rRNA is the actual catalyst for protein synthesis. 

As described, ribosomes are cytoplasmic structures that synthesize proteins. (Because they are composed of both protein and rRNA, the ribosomes are sometimes described as ribonucleoprotein bodies.) The ribosomes of prokaryotes and eukary-... 

A FIGURE 4-24 The general structure of ribosomes in prokaryotes and eukaryotes. In all cells, each ribosome consists of a large and a small subunit. The two subunits contain rRNAs (red) of different lengths, as well as a different set of proteins. All ribosomes contain two major rRNA molecules... 

The processing of rRNAs is primarily a matter of methylation and of trimming to the proper size. In prokaryotes, there are three rRNAs in an intact ribosome, which has a sedimentation coefficient of 70S. (Sedimentation coefficients and some aspects of ribosomal structure are reviewed in the discussion of ribosomal RNA in Section 9.5.) In the smaller subunit, which has a sedimentation coefficient of SOS, one RNA molecule has a sedimentation coefficient of 16S. The BOS subunit contains two kinds of RNA, with sedimentation coefficients of 5S and 23S. The ribosomes of eukaryotes have a sedimentation coefficient of SOS, with 40S and 60S subunits. The 40S subunit contains an 18S RNA, and the 60S subunit contains a 5S RNA, a 5.8S RNA, and a 28S RNA. Base modifications in both prokaryotic and eukaryotic rRNA are accomplished primarily by methylation. 

The binding site of aminoglycosides was ultimately discovered to be the 16S rRNA aminoacyl site (A-site) of the small ribosomal subunit (30S) in prokaryotic bacteria.Studies in the 1980s largely relied on enzymatic footprinting, but advances in NMR and crystallographic techniques have vastly widened the views. As a result of structural elucidations of the complexes, both in solution and in crystal form, there is a much clearer picture of the aminoglycoside-RNA interaction. 

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