What is the basic enzymology of RNA synthesis; i.e., making the primary transcript?
Figure 10.6 shows the basic polymerization reaction catalyzed by RNA polymerases. With the template DNA strand getting read in the 3′-5′ direction, the RNA gets synthesized 5′-3′, using nucleoside triphosphates that get incorporated (as monophosphates) into the growing RNA chain. Figure 10.7 shows the structure of a bacterial RNA polymerase, a large protein consisting of six distinct polypeptide chains. Eukaryotic RNA polymerases are even larger, and moreover there are three types, each responsible for making different classes of transcripts (described on page 406). The one we will consider most is RNA polymerase II, which synthesizes all the primary transcripts that eventually become mRNAs. The other two RNA polymerases, I and III, synthesize the rRNAs and tRNAs. 2. What makes transcription start and stop at the correct places, to result in RNA copies of complete genes, rather than copies of fragments of genes? For prokaryotes, Figure 10.8 shows eight “promoters”, short (20 to 200 bp)
