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Much like DNA polymerase (see chapter 1), RNA polymerase makes a complementary copy of a DNA template, building a chain of RNA by attaching the 5′ phosphate of a ribonucleotide to the 3′ hydroxyl of the one preceding it in the growing chain (Figure 2.5A). However, in contrast to DNA polymerases, RNA polymerases do not need a preexisting primer to initiate the synthesis of a new chain of RNA. To begin transcription, the RNA polymerase holoenzyme binds to the promoter sequence and separates the strands of the DNA, exposing the bases. Unlike DNA polymerases, which require helicases to separate the strands, the RNA polymerase can complete this step by itself. Then, an rNTP complementary to the nucleotide at the transcription start site enters the complex through a channel in the RNA polymerase and pairs with the template; this first rNTP is usually ATP or GTP. The second rNTP comes in, and if it is complementary to the next base in the DNA template, it is retained, but if it is not complementary, it is rejected. RNA polymerase then catalyzes the reaction in which the α phosphate of the second nucleotide joins with the 3′ hydroxyl of the first nucleotide. Then, the third nucleotide comes in and pairs with the next nucleotide in the template, and so forth. In this way, RNA polymerase makes a complementary copy, i.e., transcribes the sequence of one strand of DNA into RNA. As shown in Figure 2.5B, the strands of DNA in a region that is transcribed are named to reflect the sequence of the RNA made from that region. The template strand of DNA that is copied is also called the transcribed strand. The other strand of the DNA, which has the same sequence as the RNA copy, is called the nontemplate strand or coding strand, since it has the same sequence as the mRNA that encodes the protein (even if the RNA that is made does not actually encode a protein). The sequence of a gene is usually written as the sequence of the nontemplate, or coding, strand.

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Figure 2.5 RNA transcription. (A) The polymerization reaction, in which incoming nucleoside triphosphates (NTPs) pair with the template strand of DNA during transcription and are joined to generate the RNA chain. The β and γ phosphates of each incoming NTP (other than the initiator NTP) are removed as pyrophosphate (PP_i). (B) The coding strand (or nontemplate strand) of the DNA has the same sequence as the mRNA (with T residues in the DNA replaced with U residues in the RNA). The template strand is the DNA strand to which the mRNA is complementary.