Chapter 3. Nucleic Acids and Transcription

RNA polymerase adds successive nucleotides to the 3′ end of the transcript.

Once transcriptional initiation takes place, successive ribonucleotides are added to grow the transcript. This step is known as elongation. Transcription takes place in a sort of bubble in which the strands of the DNA duplex are separated and the growing end of the RNA transcript is paired with the template strand, creating an RNA–DNA duplex (Fig. 3.17). In bacteria, the total length of the transcription bubble is about 14 base pairs, and the length of the RNA–DNA duplex in the bubble is about 8 base pairs.

FIG. 3.17 Transcription bubble. Within the polymerase, the two strands of DNA separate and the growing RNA strand forms a duplex with the DNA template.

Details of the polymerization reaction are shown in Fig. 3.18. The incoming ribonucleoside triphosphate, shown at the bottom right, is accepted by the RNA polymerase only if it undergoes proper base pairing with the base in the template DNA strand. In Fig. 3.18, there is a proper match because U pairs with A. At this point, the RNA polymerase orients the oxygen in the hydroxyl group at the 3′ end of the growing strand into a position from which it can attack the innermost phosphate of the triphosphate of the incoming ribonucleoside, competing for the covalent bond. The bond connecting the innermost phosphate to the next is a high-energy phosphate bond, which when cleaved provides the energy to drive the reaction that creates the phosphodiester bond attaching the incoming nucleotide to the 3′ end of the growing chain. The term “high-energy” here refers to the amount of energy released when the phosphate bond is broken that can be used to drive other chemical reactions.

FIG. 3.18 The polymerization reaction that allows the RNA transcript to be elongated.

The polymerization reaction releases a phosphate–phosphate group (pyrophosphate), shown at the lower right in Fig. 3.18, which also has a high-energy phosphate bond that is cleaved by another enzyme. Cleavage of the pyrophosphate molecule makes the polymerization reaction irreversible, and the next ribonucleoside triphosphate that complements the template is brought into line.

Quick Check 3 What is the consequence for a growing RNA transcript if an abnormal nucleotide with a 3′ H is incorporated rather than a 3′ OH? How about a 2′ H rather than a 2′ OH?

Quick Check 3 Answer

The incorporation of a nucleotide with a 3′ H rather than a 3′ OH will stop subsequent elongation because the 3′ OH is necessary to attack the high energy phosphate bond of the incoming nucleoside triphosphate. The incorporation of a nucleotide with a 2′ H rather than a 2′ OH will have no effect on elongation, as this group is not involved in the polymerization reaction.