Given that DNA and RNA polymerases both carry out template-dependent nucleotide polymerization, it might be expected that the two types of enzymes would be structurally related. However, x-ray crystallographic studies reveal that, other than containing a critical Mg2+ ion at the catalytic site, the two enzymes are quite different. Template-dependent nucleotide-polymerizing enzymes seem to have arisen at least twice during the early evolution of cells. One lineage led to the short region of DNA/RNA helix 5˜5˜ direction of
Figure 6–8 DNA transcription produces a single-stranded RNA molecule that is complementary to one strand of the DNA double helix. Note that the sequence of bases in the RNA molecule produced is the same as the sequence of bases in the non-template DNA strand, except that a U replaces every T base in the DNA.
Figure 6–9 DNA is transcribed by the enzyme RNA polymerase. The RNA polymerase (pale blue) moves stepwise along the DNA, unwinding the DNA helix at its active site indicated by the Mg2+ (red), which is required for catalysis. As it progresses, the polymerase adds nucleotides one by one to the RNA chain at the polymerization site, using an exposed DNA strand as a template. The RNA transcript is thus a complementary copy of one of the two DNA strands. A short region of DNA/RNA helix (approximately nine nucleotide pairs in length) is formed only transiently, and a “window” of DNA/RNA helix therefore moves along the DNA with the polymerase as the DNA double helix reforms behind it. The incoming nucleotides are in the form of ribonucleoside triphosphates (ATP, UTP, CTP, and GTP), and the energy stored in their phosphate– phosphate bonds provides the driving force for the polymerization reaction (see Figure 5–4). The figure, based on an x-ray crystallographic structure, shows a cutaway view of the polymerase: the part facing the viewer has been sliced away to reveal the interior (Movie 6.3). (Adapted from P. Cramer et al., Science 288:640–649, 2000; PDB code: 1HQM.) modern DNA polymerases and reverse transcriptases discussed in Chapter 5, as well as to a few RNA polymerases from viruses. The other lineage formed all of the modern RNA polymerases that we discuss in this chapter.
Cells Produce Different Categories of RNA Molecules