View source for Pre initiation complex of RNA polymerase

Pre-initiation complex of [[RNA polymerase|RNA polymerase]] in [[Prokaryotes|prokaryotes]] and [[Eukaryotes|eukaryotes]]. 

The overall structure and basic biochemistry RNA polymerase in prokaryotes and eukaryotes is conserved<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 884</ref>. . The difference between them is in size and complexity RNA polymers II in ''[[Escherichia coli|E. coli]]'' consists of subunits 2α,β,β’and ω, while in mammals it consists of 12<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 884</ref>. The active site of the of both have a central metal ions, one is bound to the active and the other comes in with the NTP and leave with the PPi<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 885</ref>. This [[Metal ion|metal ion]] is usually [[Magnesium|magnesium]] Mg<sup>2+</sup><ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 885</ref>. 

In order to bind to the correct [[DNA|DNA]] sequence RNA polymerase requires transcription factors to guide it<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 889</ref>. In prokaryotes, the transcription factor responsible for this is the sigma factor(σ). It recognises promoter sequences -35 and -10 bases from the start site<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890</ref>. A bacterial cell can have many different sigma factor to recognise different promoter sequences for example sigma 70 σ70 which recognises the consensus sequences TTGACA and TATAAT at -35 and -10 respectively<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890</ref>. A prokaryote can have up to 7 different σ factors<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890</ref>. 

In eukaryotes, more specifically mammals but not only mammals, there are up to six different transcription factors that associate with RNA polymerase<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 297</ref>. These are [[TFIIA|TFIIA]], [[TFIIB|TFIIB]], [[TFIID|TFIID]], [[TFIIE|TFIIE]], [[TFIIF|TFIIF]] and [[TFIIH|TFIIH]]<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 297- 298</ref>. These transcription factors bind in a sequential manner to specific sequences in the DNA and also to the RNA polymerase<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 297</ref>. 

The first factor to bind to the DNA is [[TFIID|TFIID]], it binds to a sequence known as the [[TATA box|TATA box]]. TFIIA follows binding to TFIID, once this complex has been formed the RNA polymerase bound to TFIIF can then bind to the start site<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 297-298</ref>. Next to bind is TFIIE bringing with it TFIIH, this complex binds to the transcription start site<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 298</ref>. The complex is then ready to start transcription. 

In order for transcription to take place there must be helicase activity in both prokaryotes and eukaryotes, this melts the [[DsDNA|dsDNA]] to [[SDNA|sDNA]] at the site of transcription allow the RNA polymerase to read the base<ref>Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890</ref>. In eukaryotes the TFIIH factor contains the helicase that loops open the DNA<ref>Lodish H, Berk A, Kaiser C, Krieger M, Scott M, Bretscher A, Ploegh H, Matsudaira P,.(2008) Molecular Cell Biology, 6th edition, New York: WH Freeman and Company pg 298</ref>. Once this has occurred transcription can take place. 

=== References  ===

<references />