Rna Synthesis Is A Cyclical Process Involves Initiation Elongation Termination

The process of RNA synthesis in bacteria—depicted in Figure 37-3—involves first the binding of the RNA holopolymerase molecule to the template at the promoter site to form a PIC. Binding is followed by a con-formational change of the RNAP, and the first nu-cleotide (almost always a purine) then associates with the initiation site on the P subunit of the enzyme. In the presence of the appropriate nucleotide, the RNAP catalyzes the formation of a phosphodiester bond, and the nascent chain is now attached to the polymerization site on the P subunit of RNAP. (The analogy to the A and P sites on the ribosome should be noted; see Figure

Initiation of formation of the RNA molecule at its 5' end then follows, while elongation of the RNA mole cule from the 5' to its 3' end continues cyclically, antiparallel to its template. The enzyme polymerizes the ribonucleotides in a specific sequence dictated by the template strand and interpreted by Watson-Crick base-pairing rules. Pyrophosphate is released in the polymerization reaction. This pyrophosphate (PP;) is rapidly degraded to 2 mol of inorganic phosphate (P;) by ubiquitous pyrophosphatases, thereby providing irreversibility on the overall synthetic reaction. In both prokary-otes and eukaryotes, a purine ribonucleotide is usually the first to be polymerized into the RNA molecule. As with eukaryotes, 5' triphosphate of this first nucleotide is maintained in prokaryotic mRNA.

As the elongation complex containing the core RNA polymerase progresses along the DNA molecule, DNA unwinding must occur in order to provide access for the appropriate base pairing to the nucleotides of the coding strand. The extent of this transcription bubble (ie, DNA unwinding) is constant throughout transcription and has been estimated to be about 20 base pairs per polymerase molecule. Thus, it appears that the size of the unwound DNA region is dictated by the polymerase and is independent of the DNA sequence in the complex. This suggests that RNA polymerase has associated with it an "unwindase" activity that opens the DNA helix. The fact that the DNA double helix must unwind and the strands part at least transiently for transcription implies some disruption of the nucleo-some structure of eukaryotic cells. Topoisomerase both precedes and follows the progressing RNAP to prevent the formation of superhelical complexes.

Termination of the synthesis of the RNA molecule in bacteria is signaled by a sequence in the template strand of the DNA molecule—a signal that is recognized by a termination protein, the rho (p) factor. Rho is an ATP-dependent RNA-stimulated helicase that disrupts the nascent RNA-DNA complex. After termination of synthesis of the RNA molecule, the enzyme separates from the DNA template and probably dissociates to free core enzyme and free 0 factor. With the assistance of another 0 factor, the core enzyme then recognizes a promoter at which the synthesis of a new RNA molecule commences. In eukaryotic cells, termination is less well defined. It appears to be somehow linked both to initiation and to addition of the 3' polyA tail of mRNA and could involve destabilization of the RNA-DNA complex at a region of A-U base pairs. More than one RNA polymerase molecule may transcribe the same template strand of a gene simultaneously, but the process is phased and spaced in such a way that at any one moment each is transcribing a different portion of the DNA sequence. An electron micrograph of extremely active RNA synthesis is shown in Figure 37-4.

Figure 37-4. Electron photomicrograph of multiple copies of amphibian ribosomal RNA genes in the process of being transcribed. The magnification is about 6000 x. Note that the length of the transcripts increases as the RNA polymerase molecules progress along the individual ribosomal RNA genes; transcription start sites (filled circles) to transcription termination sites (open circles). RNA polymerase I (not visualized here) is at the base of the nascent rRNA transcripts. Thus, the proximal end of the transcribed gene has short transcripts attached to it, while much longer transcripts are attached to the distal end of the gene. The arrows indicate the direction (5' to 3') of transcription. (Reproduced with permission, from Miller OL Jr, Beatty BR: Portrait of a gene. J Cell Physiol 1969;74[Suppl 1]:225.)

Figure 37-4. Electron photomicrograph of multiple copies of amphibian ribosomal RNA genes in the process of being transcribed. The magnification is about 6000 x. Note that the length of the transcripts increases as the RNA polymerase molecules progress along the individual ribosomal RNA genes; transcription start sites (filled circles) to transcription termination sites (open circles). RNA polymerase I (not visualized here) is at the base of the nascent rRNA transcripts. Thus, the proximal end of the transcribed gene has short transcripts attached to it, while much longer transcripts are attached to the distal end of the gene. The arrows indicate the direction (5' to 3') of transcription. (Reproduced with permission, from Miller OL Jr, Beatty BR: Portrait of a gene. J Cell Physiol 1969;74[Suppl 1]:225.)

THE FIDELITY & FREQUENCY OF TRANSCRIPTION IS CONTROLLED BY PROTEINS BOUND TO CERTAIN DNA SEQUENCES

The DNA sequence analysis of specific genes has allowed the recognition of a number of sequences important in gene transcription. From the large number of bacterial genes studied it is possible to construct consensus models of transcription initiation and termination signals.

The question, "How does RNAP find the correct site to initiate transcription?" is not trivial when the complexity of the genome is considered. E coli has 4 X 103 transcription initiation sites in 4 X 106 base pairs (bp) of DNA. The situation is even more complex in humans, where perhaps 105 transcription initiation sites are distributed throughout in 3 X 109 bp of DNA. RNAP can bind to many regions of DNA, but it scans the DNA sequence—at a rate of > 103 bp/s—until it recognizes certain specific regions of DNA to which it binds with higher affinity. This region is called the promoter, and it is the association of RNAP with the promoter that ensures accurate initiation of transcription. The promoter recognition-utilization process is the target for regulation in both bacteria and humans.

Diabetes 2

Diabetes 2

Diabetes is a disease that affects the way your body uses food. Normally, your body converts sugars, starches and other foods into a form of sugar called glucose. Your body uses glucose for fuel. The cells receive the glucose through the bloodstream. They then use insulin a hormone made by the pancreas to absorb the glucose, convert it into energy, and either use it or store it for later use. Learn more...

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