Question

#1. Heparin is a polyanionic polysaccharide that blocks initiation by RNA polymerase by virtue of its binding to double stranded DNA. However, Heparin inhibits only when added before the onset of transcription, and not if added after transcription begins. Explain the difference.

#2. Describe how RNA Polymerase backtracking could function to increase the fidelity of transcription.

Answer 1

1. Heparin is highly negatively charged. It binds to the lysine and Arginine residues of RNA pol which causes it to change its confirmation and prevents its binding to the DNA. However, once bound to the DNA, it no longer has exposed positively charged residues so that heparin could bind to them.

2. RNA pol backtracks and then checks the fidely of the newly synthesized transcript. In backtracked state the wrongly incorporated ribonucleotide is readily cleaved in the presence of elongation factor IIS. Thus, after this the new and correct ribonucleotide is incorporated.