| Initiation of transcription
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| Initiation involves the interaction of the RNA polymerase with DNA in a site-specific fashion, so that the correct sequence of DNA can be used as a template for synthesis of an RNA molecule (Fig. 31.5). The focus on specific sequences of DNA for transcription is an important consideration, because most of the DNA in a cell does not encode proteins. This problem is solved through the interaction of RNA polymerase with specific sites on the DNA, known as promoters. Promoters are characteristic sequences of DNA, usually located in front (upstream) of the gene that is to be transcribed.
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| Figure 31.5 Prokaryotic promoters. Prokaryotic transcription promoters are located upstream of the gene. DNA sequences that act as transcription promoters are indicated at their respective positions relative to the gene. Position +1 indicates the first nucleotide that will be transcribed into RNA. The TATA box is a common A-T-rich promoter element. |
| The simplest promoters are found in prokaryotic cells, in which two general types of sequence elements are found in front of most genes: one sequence element is believed to promote initial binding of the RNA polymerase, and the other element usually has a high content of adenine (A) and thymine (T). Because hydrogen bonding is weaker between A-T base pairs than between guanine-cytosine (G-C) base pairs, the increased A-T content helps in the dissociation of the two DNA strands, enabling transcription to begin. These promoter sequences, 6-8 nt in length, are generally located about 35 and 10 bp upstream from the start of transcription of prokaryotic genes. Because these sequence elements are required for any level of transcription to occur, they are called basal promoters. The promoter located at -10 base pair, i.e. 10 bp before the transcription starting site (Fig. 31.5), is known commonly as the TATA or Pribnow box (Chapter 33, Fig. 33.1).
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| Promoters found in eukaryotic cells are more complicated. In addition to the sequence elements required for basal expression, they have additional sequences that are responsible for regulating the rate of initiation of transcription. These sequence elements are known as either enhancers or silencers, depending on the effect they have on transcription. They can be located at great distances either upstream or downstream of the start of transcription. Promoters with these types of sequence elements exert their effect on transcription by acting as the binding site for a variety of proteins known as trans-acting factors. The type of trans-acting factor that binds to these sequence elements will determine whether the rate of transcription is increased or decreased.
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