Other Classes of RNA

Many of regulatory RNAs referred to as small nonmessenger RNAs (snmRNA) or noncoding RNAs (ncRNA) act to regulate gene expression pathways in one of two basic mechanisms  

pair-pairing interactions with other nucleic acids such as antisense RNA and miRNA and 

acting as aptamers to bind and modify the activity of a protein or protein complex such E. coli 6S (184nt) RNA, humau SRA (steroid receptor RNA activator) RNA that modulate transcription (Storz et al, 2005). 

Databases of ncRNA can be found at http //www.sanger.ac.uk/Software/Rfam and http //jsm-research.imb.uq.au/madb. 

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Genes encoding other classes of RNA are also expressed. The RNA products are not translated to produce proteins, but rather serve different roles in the process of translation. 

Two other classes of RNA molecules are also involved in protein synthesis. These are ribosomal RNA (rRNA), a major component of the ribosomes, the organelles responsible for protein synthesis and transfer RNA (tRNA), which plays a key role in the mechanism of protein synthesis. Unlike mRNA, rRNA and tRNA are much more stable and account for about 80% and 15% respectively of the total RNA in a bacterial cell. 

Detailed analysis of t-RNA molecules (similar results have been obtained with other classes of RNA and with DNA) has shown that although A, G, C, U (or T) are the major nucleotides a variety of other nucleotides are present. Some such as inosine (I) and pseudo-uridylic acid (IP) may be scattered within the molecules whereas others are limited to specific sites. Isopentenylaminopurine (IPA) appears to be located at a specific position near to the anticodon in certain t-RNAs (Fig. 5.15) and may play a part in the control of t-RNA activity through affecting the conformation of the anticodon loop or even the whole secondary structure of the molecule. Much remains to be learned about the potentially important functions of these uncommon nucleotides and considerable research effort is presently being directed to this end (see p. 298). 

Other classes of low-molecular-weight TLR7-selective compounds such as loxoribine, 20 [67], a prodrug of isatoribine, ANA-975, 21 [68], oxopurine analogs such as 22 [69], and stabilized immunomodulatory RNAs are in development [70]. 

The counterpart of DNA polymerases in replication is RNA polymerases in transcription. Just as there are several DNA polymerases in vertebrate cells, so there are several RNA polymerases. To be precise, there are three of them. The different RNA polymerases are associated with three of the classes of RNA molecules found in vertebrate cells. Specifically, RNA polymerase I is responsible for the synthesis of the precursors of most rRNAs. RNA polymerase II plays the same role for the precursors of mRNA. Finally, RNA polymerase III is responsible for the synthesis of the precursors to the tRNAs as well as a few other small RNA molecules. Note here that I have specifically referred to precursors of these classes of RNA molecules. The initial products of the action of the RNA polymerases undergo further metabolism to yield the mature, functional products. 

Linezohd (Zyvox) is an oxazolidinone, a tive-membered heterocychc ring that forms the core of the hnezohd structure. The approval of hnezohd by the FDA in 2000 marked the first new structural class of antibacterial introduced into medical practice in the United States in 40 years. It is notable for its activity against methicillin-resistant Staph aureus, MRSA, and vancomycin-resistant Enterococcus faecium, VRE. It is bacteriostatic rather than bactericidal but finds significant use in patients with an intact immune system. Like several other classes of antibacterials, linezolid is an inhibitor of protein synthesis. It interacts specifically with the RNA component of a bacterial ribosome subunit to prevent initiation of protein synthesis. 

Eukaryotes also have transposons, structurally similar to bacterial transposons, and some use similar transposition mechanisms. In other cases, however, the mechanism of transposition appears to involve an RNA intermediate. Evolution of these transposons is intertwined with the evolution of certain classes of RNA viruses. Both are described in the next chapter. 

There are three distinct classes of RNA polymerase in the nucleus of eukaryotic cells. RNA polymerase I synthesizes the precursor of large rRNAs in the nucleolus. RNA polymerase II synthesizes the precursors for mRNAs, and RNA polymerase III produces the precursors of tRNAs and some other small RNAs in the nucleoplasm. 

Different classes of RNAs, including mRNAs, tRNAs, and U snRNAs, are transcribed and processed within the nucleus and then exported to the cytoplasm by multiple pathways. Competition experiments with microinjected Xenopus oocytes have revealed that tRNA, mRNA, U snRNA and ribosomal subunits all use saturable pathways, but none of them saturated the export of others (Jarmolowski et al, 1994). For instance,... 

There are three major classes of RNA in cells messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Of these, the latter two are termed stable RNAs, as they have a longer half-life than that of mRNA [1], Ribosomal RNA is the most abundant class of RNA in a cell. In a typical eukaryotic cell (yeast, plant, and animal), there are other RNAs, such as organelle RNA and small RNAs in nuclei (snRNAs) or in the cytoplasm (7S RNA). In eukaryotic cells, most RNAs are synthesized as larger precursor molecules and are then processed into smaller mature RNAs. Total RNA in a human cell may range from 10 to 30 pg, with most of it in the cytoplasm (about 85%), while the rest is in the nucleus. 

Enzymes are biological catalysts, all of which are proteins, except for a class of RNA-modifying catalysts known as ribozymes ribozymes are molecules of ribonucleic acid that catalyse reactions on the phosphodiester bond of other RNAs. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers each enzyme is described by a sequence of one of four numbers preceded by EC . The first number broadly classifies the enzyme based on its mechanism. 

Genes specify the kinds of proteins that are made by cells, but DNA is not the direct template for protein synthesis. Rather, the templates for protein synthesis are RNA (ribonucleic acid) molecules. In particular, a class of RNA molecules called messenger RNA (mRNA) are the information-carrying intermediates in protein synthesis. Other RNA... 

RNA (ribonucleic acid). A chemical found in the nucleus and cytoplasm of cells it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose. 

Mupirocin inhibits bacterial protein synthesis by reversible binding and inhibition of isoleucyl transfer-RNA synthetase. There is no cross-resistance with other classes of antibiotics. Low-level resistance, which is not clinically significant, is due to mutations of the host gene encoding isoleucyl transfer-RNA synthetase or an extra chromosomal copy of a gene encoding a modified isoleucyl transfer-RNA synthetase. High-level resistance (MIC > 1 mg/ml) is mediated by a plasmid or chromosomal copy of mupA, which encodes a bypass synthetase that binds mupirocin poorly. 

Important differences between DNA and RNA appear in their secondary and tertiary structures, and so we shall describe these structural features separately for DNA and for RNA. Even though nothing in nucleic acid structure is directly analogous to the quaternary structure of proteins, the interaction of nucleic acids with other classes of macromolecules (for example, proteins) to form complexes is similar to the interactions of the subunits in an oligomeric protein. One well-known example is the association of RNA and proteins in ribosomes (the polypeptide-generating machinery of the cell) another is the self-assembly of tobacco mosaic virus, in which the nucleic acid strand winds through a cylinder of coat-protein subunits. 

Ribonucleic Acid Ribonucleic acid (RNA) is a polymer consisting of nucleotides containing ribose and four different nucleotides adenine, guanine, cytosine, and uracil. Three main classes of RNA molecules are transcribed from DNA by three different types of RNA polymerases mRNA, tRNA and rRNA. Other RNA types are found in very small amounts including snRNAs, double-stranded RNA (dsRNA) and other non-coding RNAs such as the SRP RNAs. All RNA classes present in cells serve different functions. 

Selections and affinity-based methods have also been used to expand the scope of RNA-catalyzed reactions to other classes of reactions including isomerization, carbon-carbon bond forming, metalation, and alkylation reactions. For example, by exploiting the same notions of transition state theory that were used in the initial generation of catalytic antibodies, an RNA was isolated that catalyzes the isomerization of a bridged biphenyl substrate to its diastereomer Fig. 12) [89], In this case a library of 10 random RNA mole-... 

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