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27 Cards in this Set
- Front
- Back
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Describe HIV TAT |
its a "Trans-Activator of Transcription" and works without even binding DNA, it binds tar mRNA |
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what are examples of acidic activators that recruit TFIIB? |
gal4p and vp16 (herpes simplex) recruit TFIIB after TFIID is bound |
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how can transcription factors contact basal apparatus indirectly? |
by using coactivator intermediates |
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how do the follow affect basal apparatus assembly: transcription activators, transcription repressors |
activators: assemble basal transcription apparatus repressors: blocks basal apparatus assembly |
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whats an example of a transcription repressor and how does it effect basal apparatus assembly? |
DR1 prevents TFIIB from joining TFIID complex thus assembly is blocked, and transcription initiation is also blocked |
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what are response elements? what are two examples? |
elements bound by inducible transcription factors that respond to signals, often found in promoter/enhancer regions 1)HSE: heath shock response element 2)GRE: glucocorticoid response element |
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what gene has several response elements in it? |
metallothionein gene |
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how can you identify transcription factor binding sites? |
by using ChIP (chromatin immunoprecipitation), using an antibody against the specific TF, ChIP can determine where within a gene of interest the TF binds |
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how can you do a genome wide analysis of transcription factor binding sites? describe how it works |
using ChIp-chip or ChIP-seq, first isolate chromatine, sonicate, immunoprecipitate with antibody, reverse crosslink, isolate dna, amplify samples and label with fluorescent dyes |
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what are the 3 transcription-activation domains? and give an example of each |
acidic domains: Gal4 glutamine-rich domains: Sp1 Proline-rich domains: CTF |
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what are the 4 DNA-binding domains? |
zinc fingers, helix turn helix (homeodomains (HDs), helix-loop-helix (HLHs), leucine zippers |
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Describe the Zinc fingers motif's structure |
30 resiudes w/ 2 cys (beta sheets) and 2 his (alpha helix) 12 amino acids apart, coordinated to a zinc ion (Cys2-His2) anti-parallel beta sheet followed by an alpha helix occurs in tandem with short linker in between |
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where does recognition between zinc finger and target dna occur? |
recognition between finger and target dna occurs in major groove |
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what kind of receptors are found in zinc fingers? |
nuclear receptors: bind steroids and other hormones |
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describe a steroid receptor |
it has two zinc fingers, the first recognizes DNA and the 2nd is involved in receptor dimerization |
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what repressors of transcription are helix-turn-helix motifis? |
cl and cro |
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describe the helix-turn-helix motifs, what interacts with the minor groove? |
each homeodomain contains three alpha helicies, HTH formed by 2 and 3; 3-recognition helix, N-terminal interacts with minor groove |
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describe helix-loop-helix motif structure, how does it interact with the DNA target, whats an example? |
40-50 aa that comprises two HLH amphipathic helices seperated by a loop, involved in dimerization, interacts with DNA target via major groove, comprises of a family of transcription facotrs called HLH proteins, example is MyoD |
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describe leucine zipper motifs structure, how does it interact with target DNA, whats an example? |
dimerization motif, alpha helices with leucines every 7 positions in dimerization domain, interacts DNA target sites like a pair of tons, example is Myc |
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what are the 2 hypotheses for the mechanism of insulator function? |
a) sliding and b) looping |
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what are the packaging steps for dna to be packaged into a mitotic chromosome? |
double helix -> beads on a string -> 30nm chromatine fiber packed nucleosomes -> section of chromosome in extended form -> condensed section of chromosome -> mitotic chromosome |
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how would you release a nucleosome core particle from "beads-on-a-string"? |
use a micrococcal endonuclease that cuts naked DNA between nucleosomes and digests away linker dna or you can use high salt |
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describe the assembly of a nucleosome |
H3-H4 tetramer formation initiates and binds to dsDNA, then recruits two copes of H2A-H2B dimer to complete assembly of nucleosome |
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whats the structure of the core histones? |
histone fold- 3 alpha helices linked by 2 loops, H4 basic tail is exposed on both sides of the core, interacts with H2A and H2B acidic regions of neighboring particle (mediates nucleosome linking) |
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what does addition of H1 to the linker DNA and to the middle of the 147bp DNA wrapped around the core histone do? |
addition of H1 leads to more compact nucleosomal DNA because it induces tighter DNA wrapping around the nucleosome |
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what are the two forms that the 30-nm fiber exists in? |
inactive chromatin that favours solenoid folding and interacts with H1 and active chromatin and folds zigzag |
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how did researchers figure out that histone H1 is a nucleosome stabilizer? |
they reconstructed chromatin with DNA containing two enhancer-promoter constructs, then added core histones and H1, then transcribed the reconstituted chromain in vitro when they increased the amounts of H1 it caused a progressive loss of template activity, until transcription was barely detectible. at moderate h1 levels, activators could prevent much of the repression |
