Question

What is the role of the hairpin in an intrinsic terminator?

A. It alters the conformation of the active site of RNA polymerase causing the synthesis reaction to run backwards.

B. The hairpin produces DNA scrunching of the non-template strand resulting in a misalignment of the RNA:DNA hybrid portion of the transcription bubble.

C. It causes the RNA polymerase to pause so that the stretch of U:As are positioned in the RNA:DNA region of the transcription bubble.

D. It causes the polymerase to stall, which requires either processing of the 3-end or termination to occur.

Answer 1

Option (B), The hairpin in an intrinsic terminator functions to stall RNA polymerase by forming a stable structure, which, when followed by weak U-A interactions, prompts the dissociation of the RNA polymerase and the newly synthesized mRNA.

Step-by-step explanation:

The role of the hairpin loop in an intrinsic terminator is to cause the RNA polymerase to pause, aligning the U:As in the RNA:DNA region of the transcription bubble. During rho-independent termination, the hairpin is formed when the mRNA folds back on itself because of a C-G rich region in the DNA template, which results in a stable structure.

This stalling is intensified as the polymerase transcribes a region rich in A-T nucleotides, leading to the weak interaction between the U-A nucleotides in the mRNA transcript and the DNA template. Ultimately, this instability, along with the hairpin-caused stalling, induces the RNA polymerase to dissociate from the DNA template, releasing the new mRNA transcript.