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From Proteopedia

Introduction

RNA Polymerase II is the main workhorse of transcription, and is present in all eukaryotes. It is responsible for transcribing pre-mRNA, some snRNAs, snorRNAs, and some miRNAs. RNA Pol II participates in the initiation, elongation, and termination of transcription.

Structure

The structure of RNA Pol II consists of a wall of amino acids, a pore, a funnel, and a groove. The DNA double helix enters through the groove and unwinds. Due to the angle between the exit and entry points of RNA Pol II, the DNA-RNA hybrid bends and the 3' end of RNA is positioned at the enzyme's active site; thus, new nucleotides can be added to this 3' end.

Function

RNA Pol II and several transcription factors form the basal transcription apparatus, which attaches to the core promoter and initiates conformational changes in the DNA. Then the template strand of DNA binds to the active site of RNA Pol II and forms an open complex. This complex is where two phosphate groups are cleaved off the nucleoside triphosphates and the nucleotides join together to make an RNA molecule.

Termination & Rat1

RNA Pol II does not have a specific termination sequence. Instead, it continues synthesizing RNA past the necessary point. This then requires the exonuclease enzyme Rat1 to degrade the extra nucleotides synthesized by RNA Pol II, after it has been cleaved from the pre-mRNA. Once Rat1 reaches the polymerase, both enzymes detach from the DNA and transcription ends.

Important Regions

RNA Polymerase II has an amphipathic , which means that it has both hydrophobic and hydrophilic regions. The and acidic face assist in creating a transcriptional activation area within the Alpha Helix. This is where the RNA nucleotides are added to the 3' end of the RNA molecule. The in the diagram (acidic = black, basic = red) facilitate the movement of the DNA through RNA Pol II.