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Transcription
Question | Answer |
---|---|
What bind on basal promoter sequences? | transcription factors |
Where is the TATA sequence located? | Upstream binding region |
What binds to TATA? | TBP |
Where is the function of the INR region and what binds to it | initiating sequence and TF2D |
What binds to BRE and what is its function | TF2B binds to it, and positions the RNA pol II |
What binds to DPE and what is its function | TFIID can bind to it, and it is a downstream promoter |
What starts first in the assembly of the general transcription machinery? _____ carries _____ to ______ | TF2D carries TBP to TATA sequence |
What happens after the TF2D and TBP bind to TATA? _______ recognizes __________ and binds in order to __________ | TF2B recognizes BRE element and binds in order to position RNA Pol II |
What happens after TF2B and TF2D and TBP is bound? ________ brings in _______ to _________ site | TF2F brings in RNA pol II to TF2B site |
Finally, _______ recruits ______ to bind to DNA. What does the latter do? (3 things) | Finally, TFIIE recruits TFIIH. TFIIH unwinds DNA the the start point, phosphorylates the C-term of rna Pol II, and releases RNA pol II from the promoter |
What is usually present in DNA binding domains? | DNA binding motifs and a dimerization motif |
What are activation domains? | Protein-protein interacting domains |
What can activate activation domains? | Mediators and co-activators |
What are types of things would a repressor domain recruit? | A silencing complex or a co-repressor |
What do gel shift assays do, in short? | The isolate DNA binding proteins in solution to identify which fractions have a certain protein |
What are gel shift assays also known as? | Electromobility shift assays (EMSA) |
What do chromatin immunoprecipitations do? | They detect proteins attached to chromatin |
What is the process of immunoprecipitations, in short? | Binding proteins attach to DNA sequences in a cell. They are crosslinked with formaldehyde and the DNA is broken into small fragments. Then the protein-DNA complex can be precipitated with antibodies and amplified. |
What does the mediator do | Binds to activators, repressors and DNA pol II to create one big signal. |
What does the chromatin remodeling complex do? (3 things) | Remodels nuceosomes in terms of distance Removes histones Replaces histones |
What does the histone modifying enzyme do? | Methylates, phosphorylates, ubiquitinates, and acetylates histones...and can do it reversely as well |
How does combinatorial regulation work? Is it more like 0 to 100% or on/off? | It's more like 0 to 100% |
Help with the ordering of events leading to transcription initiation. 1. _______________ activates chromosome 2. _________________ and ______________ modify respective sites 3. __________ and __________ all bind together to the _____________ | 1. Gene activation protein 2. chromatin remodeling complexes and histone modification enzymes 3. Transcription factors and RNA pol II bind together to the mediator |
What can repressors do? (6 things) | 1. interfere with binding site of receptors 2. binds with activator and prevents binding 3. prevents an activator from binding to pre-initiation complex 4. recruit chromatin remodeling complex 5. methylate promoter region 6. histone methyll transfera |