DNA to RNA: RNA Polymerase

RNA polymerase in Prokaryotes

• Have 1 type

• holoenzyme - does all the RNA processing for the organism

• Multi-Subunit enzyme consists of:

  • sigma units

  • alpha units

  • beta units

  • omega units

• aaBB are the core enzymes which remain for the elongation of RNA strand

  • Sigma unit removed once RNA Polymerase binds to DNA strand

Prokaryotic RNA Polymerase: Sigma Unit

• Helps RNA polymerase find promoter by scanning DNA to look for/recognise specific sequence

  • ensures RNA Pol has the correct orientation and direction

• Once RNA polymerase attached to DNA strand, unit is lost

• to allow for transcription

Prokaryotic RNA Polymerase: Alpha Unit

• 2 units

• Activates RNA Polymerase

  • interacts with DNA and proteins that tether to DNA

Prokaryotic RNA Polymerase: Beta Unit

• 2 units

• Catalyses transcription of DNA to produce and RNA copy

• Termination

Prokaryotic RNA Polymerase:: Omega Unit

• Disposable

• Required for some genes for assembly and folding

Eukaryotic RNA Polymerase I

• Transcribes RNA to make ribosomes rRNA genes

Eukaryotic RNA Polymerase II

• Transcribes mRNA and other RNA species that don’t code for proteins e.g snRNA

Eukaryotic RNA Polymerase III

• Transcribes lots of RNA types and is used in protein synthesis

Features of Genes Coding for RNA:

• Different architecture

• Different core promoter sequences and structures

• Use different RNA polymerases

• Each RNA polymerase needs a distinct set of accessory factors - general transcription facts

RNA Polymerase II Complex Part 1

• Large Enzyme can’t bind to specific DNA sequence

  • Needs transcription factors to recognise the promoter

• TFIID recognises TATA sequence in promoter and acts as a saddle for other proteins→TBP associated factors

  • TATA sequence allows RNA polymerase to bind to DNA

    • Only specific DNA-protein interaction

• TFIIA helps TFIID bind to promoter and activated transcription

• TFIIB measures distance from TATA element to start codon

TBP-DNA Complex

• Sits on the side of DNA

• TBP protein binds to minor groove of DNA

  • Saddle like strucutre

TBP-TFIIB DNA Complex

• Hangs off one side of DNA

TBP-TFIIA DNA Complex

• Saddle and sheet like structure interact with DNA

  • TBP organises and binds to other required proteins

RNA Polymerase II Complex Part 2

• Made up of 10 subunits

  • TFII E,F,H,J,K

• Interact with D.A.B complex and recruitment of polymerase II

• Blocks non-specific binding RNA polymerase II to DNA

• Has promoter clearance

  • polymerase makes a short transcript to check sequence is correct

• Has Helicase Activity - unwinds DNA to make RNA

• Processivity (RNA’s ability to stick to a substance

• Elongation - RNA’s abitlity to make RNA chain

• Transcription-Coupled DNA repair using TFIIH

  • If a gene is being transcribed a lot, it is kept in good condition by checking for errors to ensure they are not passed on

RNA Polymerase I:

• Transcribes genes making RNA

  • Not highly regulates

  • Uses different transcription factors

• Binds to complex and initiates transcription

SL1

• Multi-protein complex in RNA Pol I

• Species specific

• Made up of TBP and Pol I TAF’s

  • TBP organisational function for polypeptides and makes RNA Pol II

Upstream Binding Factor

• Binds to UCE and core elements in DNA

• They interact with the core sequence and themself

• Attract SL1

RNA Polymerase III-tRNA genes

• Promoter infront of transcription start site at 3’

• TFIIIC binds to box B

• This recruits TFIIIB which then transcribes a gene

  • TFIIIB consists of TBP AND 2 Pol III TAFs

• Once TFIIIB is recruited TFIIIC is dispensable - can be removed

• RNA Polymerase III is recruited and initiates transcription

Other RNA Polymerase III Genes

• 5S rRNA genes are similar to tRNA genes

  • Use extra factor TFIIIA to recruit TFIIIC

• snRNA genes have a similar structure to pol II GENES

  • Have an upstream promoter

  • TATA box present

    • recognised by TBP