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49 Cards in this Set
- Front
- Back
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What are the 3 DNA dependent RNA polymerases? |
RNA Pol I, II, and III |
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What do the polymerases have in common? |
They are big, multimeric proteins with 2 large subunits similar to the beta and beta prime in prokaryotic RNA polymerase. They also all interact with general transcription factors (GTF's) |
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Which polymerase is the most sensitive to alpha amanitin? |
RNA Pol II. |
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What is alpha amanitin and where is it found? |
It is a toxin that blocks elongation, especially of RNA Pol II. It is found in the destroying angel mushroom. |
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How many subunits are found in RNA polymerase II? Which ones are also found in RNA Pol I and III? |
There are 12. RPB5, RPB6, RPB8, RPB10, RPB12 are in all of them. |
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What are the features/purpose of RPB1, 2, 3, and 4? |
RPB1: has special YSPTSPS region on its CTD and is like the beta prime of the prokaryotic one. RPB2: NTP binding and is like the beta of the prokaryotic one. RPB3: Core assembly and is like the alpha of the prokaryotic one. RPB 4: promoter recognition like the sigma unit of the prokaryotic one |
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What does TF stand for? What are they? |
Transcription factors. They are proteins that interact with the RNA polymerases and can affect the rate of transcription. |
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What is the helix-turn-helix motif? |
It is a motif found in DNA binding proteins that helps the protein bind to the DNA. It helps it fit nicely into the major groove and can aid tight binding to a specific sequence. It is found in prokaryotes and eukaryotes. |
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What is a zinc-finger motif? |
It is when you have 2 cys separated by a few aa's, then a long finger, and on the other side, there are 2 his also separated by a few aa's. The Cys and His are linked together by a Zn. These can recognize 5 bases in a major groove, so having multiple ones of these can help proteins identify very specific sequences. |
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What is a basic region-leucine zipper motif (bZIP)? |
These are proteins with 2 major regions: a DNA contact region with 2 alpha helical regions that are very basic, and a leucine zipper region. The leucine zipper region has a leucine every 7 aa's. 2 of these will form a dimer. |
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What is the purpose of a general transcription factor? |
They position RNAP's at transcription initiation sites to form the preinitiation complex (PIC). |
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What is a transcription-initiation complex? |
It is RNAP + general transcription factors bound to promoter region. |
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What are some of the GTF's that associate with RNAP II and initiate transcription from TATA boxes? |
TFIIA, TFIIB, TFIIC, TFIIE, TFIIF, and TFIIH |
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Which is the largest GTF? |
TFIID. It consists of a TATA-box binding protein (TBP) and 8 to 10 TBP associated factors (TAFIIs) |
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What is an example of a universal transcription factor? |
TBP. It associates with promoter of all 3 RNAPs and promoters with and without a TATA box. |
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What are the 2 roles of TFIID? |
Foundation for the transcription PIC complex Prevents nucleosome stabilization in the promoter region (antagonist to H1) |
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True/False: TBP is used by all 3 RNA polymerases, does not always bind to TATA boxes, and may serve as positioning factors for their respective polymerases. |
True. |
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Where does TBP bind in DNA? How does it help stimulate transcription? |
It binds in the minor groove. It bends the DNA and helps bring it closer to the other transcription factors. |
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What is the purpose of RNA Pol I? |
It transcribes genes for the large rRNA precursor. |
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What are the 2 components of RNA Pol I promoters? |
Upstream control element: -156 to -107 Core element: -45 to +20 |
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What is the purpose of RNAP III? What class of promoters does it have? |
It transcribes various small RNAs. It has class III promoters. |
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How are the class III promoters unique? |
The promoter lies entirely in the coding region instead of upstream. |
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Which RNA polymerase II GTF's interact with the carboxy terminal domain (CTD)? |
TFIIH |
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Which RNA polymerase II GTF's have ATP activity? |
TFIIE |
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What are TBP-associated factors? |
TAFs or TAFIIs. They are important for helping TBP to bind to promoters that lack TATA boxes and are different in different cells. |
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In what order do the GTF's bind for eukaryotic RNA pol II transcription? |
TFIID TFIIA TFIIB TFIIF RNA Pol II TFIIE TFIIH |
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What is important about the Carboxyl-Terminal domain? |
It has a stretch of 5 aa's that are repeated multiple times (Tyr-Ser-Pro-Thr-Ser-Pro-Ser). It is critical for viability. They are un-phosphorylated to begin initiation, and become phosphorylated to initiate transcription elongation. |
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What are the 2 parts of RNA Pol II promoters? |
1. Core promoter: TATA box (position about -30) and initiator (on the transcription start site) 2. Proximal promoter elements (can be upstream, downstream, or internal. |
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What is a Hogness box and where is it found? |
It is another name for the TATA box and is usually about 25 bases upstream from transcription start site. |
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True/False: You can have multiple promoter regions for the same element. |
True. |
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True/False: you can have multiple types of promoter regions for the same gene. |
True. |
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How does transcription respond to environmental cues such as heat shock, hormones, etc? |
Through response elements that are binding sites for transacting factors that are activated in response to the environmental cue. Their location is not conserved from gene to gene. |
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What is an example of response element coordinate regulation? |
The metallothionein gene promoter that responds to heavy metals. |
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What are the main regions for hormone/steroid receptors? |
Hormone-binding domain, DNA binding domain, and variable region. |
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How are steroid receptors regulated? |
They are regulated by an inhibitory protein complex on the DNA binding domain. Once a steroid is attached, the inhibitory protein will leave and the DNA binding protein can begin to function. |
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What are some of the ways to activate a transacting factor? |
protein synthesis, ligand binding, protein phosphorylation, addition of second subunit, unmasking, stimulation of nuclear entry, release from membrane. |
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What is a way to differentiate cells? |
Through the expression of Transcription Factors. |
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What is an enhancer? |
A control element that stimulates transcription. |
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What are transcription factors that recognize enhancers? |
Activators or enhancer binding proteins. |
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What is a silencer? |
A negative enhancer. |
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True/False: Activators do not interact with general transcription factors. |
False. |
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Where can you find enhancers? |
Upstream, downstream, in introns or in exons. They are orientation independent, can stimulate expression over long distances, and may be cell-type specific. |
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What is the purpose of insulators/boundary elements? |
They block encroachment of heterochromatin from neighboring loci. They also stop unregulated enhancement or activation of neighboring genes outside of the chromosomal domain. |
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True/False: Methylation is only used to turn genes of. |
False: It can be used to activate or silence a gene. |
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Does histone deacetylation (HDAC) cause activation or silencing? |
Silencing: it makes the histones more positive and cause them to interact more with the DNA. |
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What is the purpose of the histone code? |
It helps control the transcription regulation. |
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What is the purpose of chromatin remodeling? |
It can increase access of replication and transcription factors to DNA, but it does require ATP |
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How do you open up a gene for transcription? |
1. Expose the DNA to a DNA-binding transcription factor 2. HATs (histone acetyl transferases) open up the chromatin by affecting the histones 3. Nucleosome remodelers use ATP to hold DNA off some of the histone to allow other things in. 4. Transcription Factor Coactivators bind and bring in polymerase 5. Once the polymerase is there, the initiation can begin. |
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What does this have to do with cloning? |
By changing the proteins in a cell you can convince an epithelial cell that it is a zygote and clone an animal. |
