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23 Cards in this Set
- Front
- Back
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What is a chromosome territory.
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A domain occupied by chromosomes in the interphase nucleus. Allows chromosomes to stay separate from other chromosomes.
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What are interchromosomal domains?
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Channels between chromosomes. Contain little to no DNA.
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What are transcription factories?
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Specific nuclear sites at which most RNA plymerase Ii transcription occurs.
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What is chromatin remodeling?
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Chromatin modifications. Important step in gene regulation.
2 ways it can happen: . 1. involves changes to nucleosomes 2. involves modifications to DNA |
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What does the presence of nucleosomes on DNA and compaction of chromatin into higher order structures do to gene expression?
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Inhibits gene expression.
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How can nucleosomal chromatin be remodeled?
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3 ways
1. altering nucelosome composition 2. adding or removing covalent modifications to or from histones 3. repositioning the nucleosome on a gene region |
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How is nucelosoomal chromatin remodeling done?
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By specific chromatin remodeling complexes, all of which require ATP hydrolysis.
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How is histone modification (chromatin alteration mechanism) accomplished?
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Acetylation: catalyzed by HATS. Acetate group is added to histone tails, causes ithe interaction between histone and DNA to decrease. Allows promoter regions to be available for binding to TF that initation gene transcription.
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What do HDACs do?
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Remove acetate groups from histone tails.
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What is Dna methylation and how does it work?
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Added methyl group to cytosine.
High levels of methylation = low levels of gene expression. Occurs in cytosine of CG doublets in DNA: usually in both strands. |
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How can you tell if DNA is methylated?
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Using HpaII and MspI. HpaII won't cut methylated C, but MSPI will. Can compare the restriction pattern of bands to see if match up. If not, DNA is methylated.
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Where is transcription regualted?
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At specific cis-acting sites.
Promoters and Enhancers are involved. |
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What are promoters?
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Recognition sites for trascription machienry. Initiate transcription. Located right next to the genes they regulate.
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What elements do promoters contain?
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TATA box (-25) [upstream] =initiation point of transcriptions
CAAT (-70): increases rate of transcription. GC box (-110): binds TF |
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What are enhancers?
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Can be upstream, downstream, or within the gene
Increases expression and has maximum level of transcription Interacts with regulatory proteins and TF for expression at right time and with right amounts. Cis-regulators because function when adjacent to gene they regulate. |
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What are silencers?
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Decrease expression
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What is deletion analysis?
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Where there are dots there is no expression therefore these bases are really importat for trans and different for each promoter.
-decreased levels of trans in mutated regions of TATA, CAAT, and GC boxes |
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What are enhancer motifs?
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Conserved sequences in different promoters so that certain genes can be turned off at the same time.
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Example of regulation by transcription factors.
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hMTIIA: in humans matallothionen gene: creates a product that binds to heavy metals that can have toxic effects if in excess.
Contains promoter elemtns of TATA box |
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What are the different enhancers on hMTIIA.
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GC binds SP1 factor
BLE: binds to AP1 and 4, and ARE( AP factor response element): bind to AP2 MRE(metal response element): binds to MTF-1 TF that responds to metal conc. |
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How do TF bind to DNA?
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DNA binding domain: binds to DNA sequences in cis-acting reg. site
DNA activation/repression domain: activates or represses DNA through protein interactions. Helix-turn-helix domain: #3 helix fits in DNA major groove and interacts with specific base pairs. (1 and 2 are perpendicular and interact with backbone for stable interaction) Zinc-finger motif: regulates cell growth, differentiation, development Leucine zipper: binds to DNA as a dimer with 2 alpha helices joined by leucine and specific bases in DNA : orients DNA to bind to DNA |
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How does the pre-initiation complex (PIC) form?
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TFIID: made of TATA binding protein (TBP) and TAF's. TFIID binds to TATA box. Then binds additional factors such as TF2B, TF2A TF2F TF2H and TF2J
RNA pol recruited to complex with TF2F. Once all TF have assembled at a promoter, RNA pol II is in contact with start site of transcription and DNA helix is unwound and transcription begins. |
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Explance the enhanceosome.
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A complex that interacts with general transcription factors in PIC, causes DNA to bend or loop between promoter and enhancer.
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