Pre initiation complex of RNA polymerase

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Pre-initiation complex of RNA polymerase in prokaryotes and eukaryotes.

The overall structure and basic biochemistry RNA polymerase in prokaryotes and eukaryotes is conserved[1]. . The difference between them is in size and complexity RNA polymers II in E. coli consists of subunits 2α,β,β’and ω, while in mammals it consists of 12[2]. 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[3]. This metal ion is usually magnesium Mg2+[4].

In order to bind to the correct DNA sequence RNA polymerase requires transcription factors to guide it[5]. 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[6]. 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[7]. A prokaryote can have up to 7 different σ factors[8].

In eukaryotes, more specifically mammals but not only mammals, there are up to six different transcription factors that associate with RNA polymerase[9]. These are TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH[10]. These transcription factors bind in a sequential manner to specific sequences in the DNA and also to the RNA polymerase[11].

The first factor to bind to the DNA is TFIID, it binds to a sequence known as the 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[12]. Next to bind is TFIIE bringing with it TFIIH, this complex binds to the transcription start site[13]. 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 to sDNA at the site of transcription allow the RNA polymerase to read the base[14]. In eukaryotes the TFIIH factor contains the helicase that loops open the DNA[15]. Once this has occurred transcription can take place.

References

  1. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 884
  2. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 884
  3. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 885
  4. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 885
  5. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 889
  6. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890
  7. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890
  8. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. Berg J., Tymoczko J and Stryer L.(2011) Biochemistry, Internation 7th edition, New York: WH Freeman and Company pg 890
  15. 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
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