Classes of RNA

In all prokaryotic and eukaryotic organisms, three main classes of RNA molecules exist messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA... 

All eukaryotic cells have four major classes of RNA ri-bosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). The first three are involved in protein synthesis, and snRNA is involved in mRNA splicing. As shown in Table 37-1, these various classes of RNA are different in their diversity, stability, and abundance in cells. 

The genetic information within the nucleotide sequence of DNA is transcribed in the nucleus into the specific nucleotide sequence of an RNA molecule. The sequence of nucleotides in the RNA transcript is complementary to the nucleotide sequence of the template strand of its gene in accordance with the base-pairing rules. Several different classes of RNA combine to direct the synthesis of proteins. 

The second dogma had to undergo drastic correction about ten years after the correction of the first Sidney Altman from Yale University and Thomas Cech from the University of Colorado at Boulder independently discovered enzymatically active ribonucleic acids in different RNA species. This new class of RNA was called ri-bozyme (from n/wnuclease and enzyme). It was now necessary to modify the second dogma as follows ... 

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. 

In protein synthesis, there are three classes of RNA to worry about ribosomal RNA, rRNA messenger RNA, mRNA and transfer RNA, tRNA. All three classes of RNA play key roles in the final stage of the process the biosynthesis of proteins. However, we are going to take this one step at a time. We turn attention first to the... 

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. 

Each of these enzymes is found in the cell nucleus, as one would expect. DNA is localized in the nucleus and does not leave it. DNA is the template for the synthesis of all classes of RNA molecules. The base sequence in one of the strands of the DNA... 

There are three classes of RNA ribosomal RNA, messenger RNA, and transfer RNA. It is messenger RNA that codes for the structure of proteins. 

In eukaryotic cells, there are three classes of RNA polymerases (I, II and III) which synthesise different classes of RNA, as follows ... 

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. All are large enzymes with multiple subunits. Each class of RNA polymerase recognizes particular types of genes. 

Unlike prokaryotes, in which all major types of RNA are synthesized by one RNA polymerase, eukaryotic cells contain three nuclear DNA-dependent RNA polymerases, each responsible for synthesizing a different class of RNAs. 

In this chapter we described the synthesis, transcription, and posttranscriptional reactions undergone by the three major classes of RNA. The main points we covered are as follows ... 

The major classes of RNA in both prokaryotes and eukaryotes are messenger RNA, ribosomal RNA, and... 

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,... 

Jarmolowski, A., Boelens, W.C., Izaurralde, E. and Mattaj, I.W. (1994) Nuclear export of different classes of RNA is mediated by specific factors. J. Cell Biol, 124, 627-635. 

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. 

Cells contain three major classes of RNA (mRNA, rRNA, and tRNA), all of which are synthesized from DNA templates by DNA-dependent RNA polymerase (Moldave, 1981), which binds to the promoters (typically 40-bp region upstream of the transcription start site containing a hexameric TATA box). Prokaryotic and eukaryotic RNA transriptions show strong parallels, though there are several important differences. 

Only one RNA polymerase catalyzes the synthesis of all three classes of RNA in prokaryotes. While three RNA polymerases mediate the synthesis of eukaryotic RNA, namely, RNA polymerase I for major rRNA, RNA polymerase II for mRNA, and RNA polymerase III for tRNA (Palmer and Folk, 1990 Woychik and Young, 1990). 

Reverse transcription (which occurs in both prokaryotes and eukaryotes) is the synthesis of DNA from an RNA template. A class of RNA viruses, called retroviruses, are characterized by the presence of an RNA-dependent DNA polymerase (reverse transcriptase). The vims that causes AIDS, Human Immunodeficiency Virus (HIV), is a retro-vims. Because nuclear cell division doesn t use reverse transcriptase, the most effective anti-HIV drugs target reverse transcriptase, either its synthesis or its activity. Telomerase, discussed in the previous section, is a specialized reverse transcriptase enzyme. See Figure 12-5. 

All classes of RNA transcripts must be processed into mature species. The reactions include several types Nucleolytic cleavage, as in the separation of the mature rRNA species from the primary transcript of RNA polymerase I action Chain extension (non-template-directed), as in the synthesis or regeneration of the common CCA sequence at the 3 end of transfer RNAs or of PolyA at the 3 end of mRNAs and Nucleotide modification, for example, the synthesis of methylated nucleotides in tRNA or rRNA. These reactions are a feature of both prokaryotic and eukaryotic gene expression, and the biological consequences are diverse. For example, modified nucleotides can affect the way in which a tRNA recognizes different codons. 

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