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Rules of Transcription

• Start with recognition and a promoter will mark the DNA to show where DNA should be transcribed- protein complex has to combine together before anything can happen

• Eukaryotic Protein Coding Genes- only one region is translated in a monocistronic mRNA (Which starts out as an unprocessed pre-mRNA)

• Eukaryotic Gene Structure- onle one coding region flanked by UTRs but it is broken up into exons

• In the nucleus before translation-Usually in G0 (nondividing cells), G1 or G2(periods when genes coding for cellular organelle proteins are synthesized.

  • gets rid of the introns during this time

  • Transcriton will start at the +1 site and ends in the termination region (3’ UTR) (UTR= untranslated region) - Transcription does NOT start with AUG (start codon)

• Only ertian parts of DNA are stranscribed

• the promoter will have two parts:

  • Core promoter- has a sequence that is common to most genes

  • Proximal promoter- has a sequence that is unique to a gene

• Common Promoter Features

  • The TATA box- seen in core promoters; recoginized by a General TF called TBP

  • GC-rich box- Proximal promoter

  • CAAT box- Proximal promoter

• Transcription Factors- proteins or protein complexes that bind to promoter squences or other regulatory sequences and influene transcription initialtion by ionteracting with RNA polymerase

  • General TFs play a role in transcription for most genes

  • Specific TFs are regulatory and differ among sexes- bind to the proximal promoters

• Core promoter: “on/off” switch a highly conserved sequence which serves conserved sequence which serves as the binding site for General Transcription Factors and RNA Pol II (start site of transcription)

• Proximal Promoter: Contains regulatopry sequences which bind transcriptional activator proteins (Specific Transcription Factors). These stimulate and stabilize activity of the RNA pol II bound at the core promoter

• RNA Polymerase II- requires many general and specific transcription factors to function

Eukaryotic Stages of Transcription

Recognition

The TATA box is recognized and bounded by a general transcription factor

1. First, TBP can bind to the TATA box (TBP= Tata Binding Protein) TBP is a component of the TFIID complex. this allows the complex to recognize and bind to the Tata box in the core promoter

   1. TBP attached by interacting with negatively charged phosphates in the backbone and inserts amino acids side chains betwen the bases- stabilized by hydrogen bonds; it distorts the DNA causing it to bend and “melt”

   2. TFIID complex recruits more transcription factors and mark the promoter

Initiation

1. After the TBP “melts” the DNA, this will be the landing site for other binding complexes- TFIIB recruits RNA Polyermerase II

   1. TFIIH has helicase activity and can phosphorylate RNA polymerase II in order to activate this activity to open the bubble

   2. Need to Know TBP, TFIID, TFIIB, and TFIIH

   3. 

   4. Specific Transcription Factors are bound to distal regulatory regionS in the DNA and to the Proximal Promoter in the DNA

   5. Mediator Complex-part of the complex that bridges specific TFs bound to distal regulatory regions in the DNA and the RNA polymerase II Holoenzymes bound to the core promoter

   6. TFIIH- Open the transcription bubble (helicase activity) and activates the RNA polymerase II

   7. CTD tail is phosphorylated by the TFIIH resulting in active RNA pol II Holoenzyme

      1. CTD tail- Carboxyl-Terminal Domain (this is the end of a protein)

Elongation

1. Some general transcription factors are released

2. RNA poly II- openes the bubble ahead of itself and closes it behind the transcription bibble- remember that eukaryotic DNA contains nucleosomes/ chromatosomes

   1. Rercruits Elongation factors to evict histones anhead of RNA pol II and replace them behind it

   2. EFsmaintian heterduplex RNA:DNA hybrid region

   3. EFs deal with issues

Termination

1. Termination involves cleavage of the RNA at a specific position in the 3’ UTR and this is linked to the dephosphorylation of RNA Pol II (deactivating) and RNA Pol II drops off the DNA

2. By this point we have made the preMRNA ⬇