BMB400Test_2 - BMB 400 Dr. Keith Hutchison 12/18/07 Exam 2...

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BMB 400 Dr. Keith Hutchison 12/18/07 Exam 2 1) Here is my sequence and the binding sites within it:
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My promoter region was missing the TBF, INR, BRE, MRE, GC BOX binding sites.
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The following image shows the steps of transcription initiation:
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1) This image shows approximately where the major binding domains are. The black z in DNA strand indicates a large distance. The enhancer region is 800 to 1000bp upstream (although it can be downstream) from the start of transcription. GC box is a proximal control element that Sp1 binds to. Sp1 has a zinc finger protein motif that allows for DNA binding. This protein enhances the transcription of a gene. 2) TFIID, which is made of TATA- Binding protein (TBF) and several TBP- associated factors (TAF’s), binds to the TATA box upstream of the start of transcription. TFIID then binds to the DNA strand and bends it (not shown in image to reduce complexity of image) by binding to the minor grove. TFIID acts like a platform for the assemblage of the rest of preinitiation complex. The binding of TFIID is the rate limiting set in the initiation of transcription since at this point all other enhancers/ silencers can control transcription. 3) TFIIB and TFIIA then bind. TFIIA binds to the TBP subunit of TFIID and helps to stabilize the protein by blocking other proteins that inhibit binding or knock TBP off from the TATA box. TFIIB binds to the BRE (TFIIB recognition element) sequence (which is next to the TATA box) and indicates which strand of DNA will act as a template for transcription. TFIIB also has a zinc ribbon domain that is used in the next step to bind to RNA polymerase II (RNA polII) and guide it into the initiation site. 4) TFIIF binds to RNA polII and helps to bind it the TFIIB complex. RNA polII then moves onto the initiation sequence and binds to it. It also is bound to the TFIIB
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complex by the zinc ribbon motif mentioned before. The RNA polII is also bound to a protein complex referred to as the mediator. This complex allows for the binding of enhancers and activators that are long distances from the initiation site. 5) TFIIH and TFIIE then bind to the initiation complex. TFIIH has both helicase and kinase activity. TFIIE is needed to facilitate the binding of TFIIH into the complex and TFIIE also regulates the helicase and kinase activity of TFIIH. TFIIH is a multisubunit protein that melts the promoter DNA strands so RNA polII can move into the elongation phase. 6) This image simply shows how an enhancer region can bind to the mediator protein complex as well as some transcription factors to enhance the rate of transcription. 7) The “tail” of RNA polII is phosphorylated by the kinase function of TFIIH when ATP (or CTP, etc) binds. TFIIH also unwinds the DNA when it hydrolyses ATP allowing for RNA polII to bind to the DNA template strand and begin transcription. 8) In this image the RNA polII is bound to the template strand and the elongation
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BMB400Test_2 - BMB 400 Dr. Keith Hutchison 12/18/07 Exam 2...

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