The enzymes that perform transcription are called RNA polymerases. Like the DNA polymerase that catalyzes DNA replication (discussed in Chapter 5), RNA polymerases catalyze the formation of the phosphodiester bonds that link the nucleotides together to form a linear chain. The RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead of the active site for polymerization to expose a new region of the template strand for complementary
Figure 6–7 RNA can fold into specific structures. RNA is largely single-stranded, but it often contains short stretches of nucleotides that can form conventional base pairs with complementary sequences found elsewhere on the same molecule. These interactions, along with additional “nonconventional” base-pair interactions, allow an RNA molecule to fold into a three-dimensional structure that is determined by its sequence of nucleotides (Movie 6.1).
Diagram of a folded RNA structure showing only conventional base-pair interactions. (B) Structure with both conventional (red) and nonconventional (green) base-pair interactions.
Structure of an actual RNA, one that catalyzes its own splicing (see p. 324). Each conventional base-pair interaction is indicated by a “rung” in the double helix. Bases in other configurations are indicated by broken rungs.
base-pairing. In this way, the growing RNA chain is extended by one nucleotide at a time in the 5ʹ-to-3ʹdirection (Figure 6–9). The substrates are ribonucleoside triphosphates (ATP, CTP, UTP, and GTP); as in DNA replication, the hydrolysis of high-energy bonds provides the energy needed to drive the reaction forward (see Figure 5–4 and Movie 6.2).
The almost immediate release of the RNA strand from the DNA as it is synthesized means that many RNA copies can be made from the same gene in a relatively short time, with the synthesis of additional RNA molecules being started before the previous RNA molecules are completed (Figure 6–10). When RNA polymerase molecules follow hard on each other’s heels in this way, each moving at about 50 nucleotides per second, over a thousand transcripts can be synthesized in an hour from a single gene.
Although RNA polymerase catalyzes essentially the same chemical reaction as DNA polymerase, there are some important differences between the activities of the two enzymes. First, and most obviously, RNA polymerase catalyzes the linkage of ribonucleotides, not deoxyribonucleotides. Second, unlike the DNA polymerases involved in DNA replication, RNA polymerases can start an RNA chain without a primer. This difference is thought possible because transcription need not be as accurate as DNA replication (see Table 5–1, p. 244). RNA polymerases make about one mistake for every 104 nucleotides copied into RNA (compared with an error rate for direct copying by DNA polymerase of about one in 107 nucleotides); and the consequences of an error in RNA transcription are much less significant as RNA does not permanently store genetic information in cells. Finally, unlike DNA polymerases, which make their products in segments that are later stitched together, RNA polymerases are absolutely processive; that is, the same RNA polymerase that begins an RNA molecule must finish it without dissociating from the DNA template.
Although not nearly as accurate as the DNA polymerases that replicate DNA, RNA polymerases nonetheless have a modest proofreading mechanism. If an incorrect ribonucleotide is added to the growing RNA chain, the polymerase can back up, and the active site of the enzyme can perform an excision reaction that resembles the reverse of the polymerization reaction, except that a water molecule replaces the pyrophosphate and a nucleoside monophosphate is released.