During transcription of DNA, one DNA strand acts as a template, determining the order in which ribonucleoside triphosphate (rNTP) monomers are polymerized to form a complementary RNA chain. Bases in the template DNA strand base-pair with complementary incoming rNTPs, which then are joined in a polymerization reaction catalyzed by RNA polymerase. Polymerization involves a nucleophilic attack by the 3' oxygen in the growing RNA chain on the a phosphate of the next nucleotide precursor to be added, resulting in formation of a phosphodiester bond and release of pyrophosphate (PPi). As a consequence of this mechanism, RNA molecules are always synthesized in the 5'n3' direction (Figure 4-9).
The energetics of the polymerization reaction strongly favors addition of ribonucleotides to the growing RNA chain because the high-energy bond between the a and p phosphate of rNTP monomers is replaced by the lower-energy phosphodiester bond between nucleotides. The equilibrium for the reaction is driven further toward chain elongation by pyrophosphatase, an enzyme that catalyzes cleavage of the released PP( into two molecules of inorganic phosphate. Like the two strands in DNA, the template DNA strand and the growing RNA strand that is base-paired to it have opposite 5'n3' directionality.
By convention, the site at which RNA polymerase begins transcription is numbered +1. Downstream denotes the direction in which a template DNA strand is transcribed (or mRNA translated); thus a downstream sequence is toward the 3' end relative to the start site, considering the DNA strand with the same polarity as the transcribed RNA. Upstream denotes the opposite direction. Nucleotide positions in the DNA sequence downstream from a start site are indicated by a positive (+) sign; those upstream, by a negative (-) sign.
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