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27 Cards in this Set
- Front
- Back
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in vitro
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this literally means in glass but in our biology class means that the conditions are outside normal cellular condition
- this usually refers without histones |
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in vivo
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literally means in life, but for our purposes it refers to the idea of normal cellular circumstances
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GTF
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general transcription factors
- in vitro, they are all that are required together with pol I, to initiate transcription on a DNA template in eukaryotic cells without histones |
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core promoter
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40 to 60 nucloetides long
it refers to the minimal set of sequence elements required for accurate transcription initiation by the pol 2 machinery |
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draw the core promoter
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from left to right it has to have the flolowing
bre-tata-inr-dce1-dce2-dpe-dce3 tf2b-tbp,tf2d,tf2d,tf2d,tf2d tf2d -30 +1 |
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what ado the general transcription factors do
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1. they polymerase bind to the promoter
2. they help melt the DNA 3. they help polymerase escape from the promoter and embark on the elongation phase |
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preinitiation complex
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the complete set of general transcription factors and polymerase, bound together at the promoter and poised for initiation
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TFIID
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a multisubunit complex that binds to the TATA binding protein called TBP
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the two steps in escaping the promoter
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1. ATP hydrolysis
2. phosphorylation of the polymerase |
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describe how the phosphorylation of the polymerase works
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pol 2 has a CTD which is referred as the tail, and it contains a series of repeats of the heptapeptide sequence. Each repeat contains sites for phosphorylation by kinases
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kinases
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enzymes that add phosphates
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phosphatases
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enzymes that remove phosphates
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how does the TBP bind to the DNA
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it uses it's Beta sheet to recognize the minor groove
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describe the structural distortion that the TBP goes through
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the minor groove is widened almost to a flat conformation and it also bends the DNa by and angle of 80 degree
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where is the specificity of the binding of TBP and DNa
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much of the specificity is imposed by the two pairs of phenylalanine side chains that intercalate between the base pairs at either end of the recognition sequence and drive the strong bend in the DNA
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TFIIH
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transcription factor that has a kinase activity-roles in promoter melting ad escape
- the h stand for helicase, as it also has helicase activities - it controls the ATP-dependent transition of the preinitiation complex to the open complex - it is the largest - it also functions as a ATPase |
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what else is needed for high levels of transcription
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this is of course in vivo and we would need transcription regulatory proteins, the mediator complex, and nucleosome-modifying enzymes
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be able to draw picture the additional proteins
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it is u shaped and has rna pol 2 and activators and mediator complex and HAT and chromatin remodelor
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mediator complex
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this is associated with the CTD tail od the large polymerase subunit, while presenting other surfaces for interaction with dNA-bound activators
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elongation factors in eukaryotes
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these are the factors that stimulate elongation
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enhancer
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promote transcription when the appropriate trans acting (activators) are bound to them
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silencers
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inhibit or prevent transcription when the appropriate trans-acting element (repressors) are bound to them
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why are genes bigger
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because it has more regulatory element
more signal integration more genes to bind |
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draw mediator complex
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include CTD activators, pol 2, and transcription factors
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named some elongation factors
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TFIIS and hSTT5
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TFIIS
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an elongation factor that does not affect initiation, but stimulate elongation
- it limits the length of time that polymerase pauses when it encounters sequences that would otherwise tend to show the enzyme's progress -contributes to proofreading |
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hSPT5
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this helps recruit the 5' caping enzyme to the CTD tail of pol
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