RNA, mRNA, rRNA, and tRNA

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. 

The three major types of RNA (mRNA, rRNA, and tRNA) participate directly in the process of protein synthesis. Other less abundant RNAs are involved in replication or in the processing of RNA, that is, in the conversion of RNA precursors to their mature forms. 

RNA, mRNA, rRNA, and tRNA. See Ribonucleic acid Roberts, John D., 928 Robinson, Sir Robert, 4, 402, 724 Robinson annulation, 724, 728 Rotamer, 90. See also Conformation Rotational energy barrier alkenes, 172—173 amides, 779 butane, 94—95 conjugated dienes, 31(r-371 ethane, 93—94... 

Bacteria do not contain nuclei, so transcription and translation occur simultaneously. A single RNA polymerase produces mRNA, rRNA, and tRNA in bacteria. Bacterial transcripts (e.g., those from E. coli) do not contain introns. 

The promoter sequences recognized by mitochondrial RNA polymerases include the transcription start site. These promoter sequences, which are rich in A residues, have been characterized in the mtDNA from yeast, plants, and animals. The circular, human mitochondrial genome contains two related 15-bp promoter sequences, one for the transcription of each strand. Each strand is transcribed in its entirety the long primary transcripts are then processed to yield mitochondrial mRNAs, rRNAs, and tRNAs. A small basic protein called mtTFl, which binds immediately upstream from the two mitochondrial promoters, greatly stimulates transcription. A homologous protein found in yeast mitochondria is required for maintenance of mtDNA and probably performs a similar function. 

Prokaryotic RNA polymerase - A single RNA polymerase catalyzes the synthesis of all three E. coli RNA classes—mRNA, rRNA, and tRNA. This was shown in experiments with rifampicin (Figure 26.4a), an antibiotic that inhibits RNA polymerase in vitro and blocks the synthesis of mRNA, rRNA, and tRNA in vivo. 

Function. In all cells, RNA functions in the transfer of genetic information from DNA to the site of protein biosynthesis (mRNA) and in the translation of this information during protein biosynthesis (mRNA, rRNA and tRNA). In addition, the RNA in . coli and Bacillus subtilis ribonuclease P has been shown to be responsible for the catalytic activity of the ribo-protein [C. Guerrier-Thkada S. Altman Science 223 (1984) 285-286]. The RNA in Small nuclear ribonu-cleoproteins (see) also appears to be catalytically active other examples of catalytically active RNA are known, e.g. the autocatalydc cleavage-ligation of Te-trahymena pre-ribosomal RNA (see Intron). 

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. 

Most eukaryotic mRNA molecules have up to 250 adenine bases at their 3 end. These poly (A) tails can be used in the affinity chromatographic purification of mRNA from a total cellular RNA extract. Under high salt conditions, poly (A) will hybridize to oligo-dT-cellulose or poly(U)-sepharose. These materials are polymers of 10 to 20 deoxythymidine or uridine nucleotides covalently bound to a carbohydrate support. They bind mRNA containing poly (A) tails as short as 20 residues. rRNA and tRNA do not possess poly (A) sequences and will not bind. After washing the mRNA can be eluted with a low salt buffer. 

All RNA found in eukaryotes undergoes major alterations prior to functioning. The cutting out of rRNA and tRNA molecules from larger precursors resembles that in bacteria, but subsequent processing is much more complex, as is that of mRNA. 

The discovery of DNA polymerase and its dependence on a DNA template led to the search for enzymes which could make an RNA molecule complementary to the DNA. RNA synthesis does not require a primer strand it does, however, require a specific initiation signal on the DNA template strand to allow binding and initiation. As the RNA strand is synthesised it forms a temporary helix with the template DNA, but when complete the mRNA breaks off at the stop site on DNA. Once released from DNA, some of the RNA is processed further, for the specific structures of rRNA and tRNA. 

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. 

Most of the DNA sequences which are transcribed give rise to mRNA, which is subsequently translated into protein. However, the most abundant species of RNA are ribosomal RNA (rRNA) and transfer RNA (tRNA), which do not code for protein but function in the process of translation. They are formed by a high level of transcription of a relatively small number of genes (called rRNA and tRNA genes). In bacteria, transcription of all genes is brought about by the enzyme RNA polymerase. 

The genetic information in DNA is converted into the linear sequence of amino acids in polypeptides in a two-phase process. During transcription, RNA molecules are synthesized from a DNA strand through complementary base pairing between the bases in DNA and the bases in free ribonucleoside triphosphate molecules. During the second phase, called translation, mRNA molecules bind to ribosomes that are composed of rRNA and ribosomal proteins. Transfer RNA-aminoacyl complexes position their amino acid cargo in the catalytic site within the ribosome in a process that involves complementary base pairing between the mRNA codons and tRNA anticodons. Once the amino acids are correctly positioned within the catalytic site, a peptide bond is formed. After the mRNA molecule moves relative to the ribosome, a new codon enters the ribosome s catalytic site and base pairs with the appropriate anticodon on another aminoacyl-tRNA complex. After a stop codon in the mRNA enters the catalytic site, the newly formed polypeptide is released from the ribosome. 

Both ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs)are synthesized in the form of larger transcripts (pre-rRNA and pre-tRNA, respectively), which undergo cleavage at both ends of the transcript, en route to becoming mature RNAs. The total amount of DNA encoding these RNAs amounts to less than 1% of the E. coli genome, but because of the instability of mRNA (which is encoded by the remaining 99%), rRNA and tRNA constitute about 98% of the total RNA in a bacterial cell. 

All of the major steps in processing of the pre-mRNA transcripts, which include capping, splicing, 3 -end cleavage, and polyadenylation (Eq. 28-6), are coupled to transcription. This is apparently accomplished, in part, by physical connections of the necessary proteins to the CTD domain of RNA polymerase n, oi,3i2a,b While pre-mRNA usually undergoes all of the steps of Eq. 28-6, rRNA and tRNAs are not capped or poly-adenylated and often are not spliced. 

---