Transcription begins when RNA polymerase recognizes a sequence of nucleotides on the DNA called a promoter. The promoter identifies the region of the DNA molecule that will be transcribed into RNA. In addition, the promoter orients the RNA polymerase in one of the two possible directions. This dictates which of the two DNA strands is used as a template (figure 7.8). Like DNA polymerase, RNA polymerase can only synthesize nucleic acid in the 5' to 3' direction and must "read'' the template in the 3' to 5' direction. Unlike DNA polymerase, however, RNA polymerase can begin to synthesize a new chain without a primer.
The transcribed RNA molecule can be used as a reference point to describe direction on the analogous DNA. Upstream implies the direction toward the 5' end of the transcribed region, whereas downstream implies the direction toward the 3' end. Thus, a promoter is upstream of a gene.
Transcription begins when RNA polymerase recognizes and binds to a promoter region on the double-stranded DNA molecule. The binding melts a short stretch of DNA, creating a region of exposed nucleotides that serves as a template for RNA synthesis.
A particular subunit of RNA polymerase recognizes the promoter region prior to the initiation of transcription. This subunit, sigma (a) factor, is only a loose component of the enzyme. After transcription is initiated, the a factor dissociates from the enzyme, leaving the remaining portion of RNA polymerase, called the core enzyme, to complete transcription. A cell may have different types of a factors that recognize different promot ers. These may be expressed at different stages of cell growth, enabling the cell to transcribe specialized sets of genes as needed.
In the elongation phase, the RNA polymerase moves along the template strand of the DNA, synthesizing the complementary single-stranded RNA molecule. The RNA molecule is synthesized in the 5' to 3' direction as the enzyme adds nucleotides to the 3'OH group at the end of the growing chain. The core RNA polymerase advances along the DNA, melting a new stretch and allowing the previous stretch to close (figure 7.9). This exposes a new region of the template, permitting the elongation process to continue. The rate of polymerization is about 30 nucleotides per second.
Once elongation has proceeded far enough for RNA poly-merase to clear the promoter, another molecule of RNA poly-merase can bind to that promoter, initiating a new round of transcription. Thus, a single gene can be transcribed multiple times in a very short time interval.
Just as an initiation of transcription occurs at a distinct site on the DNA, so does termination. When RNA polymerase encounters a terminator, it falls off the DNA template and releases the newly synthesized RNA. The terminator is a sequence of nucleotides in the DNA that, when transcribed, permits two complementary regions of the resulting RNA to base-pair, forming a hairpin loop structure. For reasons that are not yet understood, this causes the RNA polymerase to stall, resulting in its dissociation from the DNA template and release of the
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