Term
| What is a cis element, a trans element? |
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Definition
| a CIS element is actually part of the DNA. A trans element is not |
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Term
| What are some examples of Cis elements? |
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Definition
| Core promoters (eg TATA..-25 to -30), Promoter proximal elements (-50 to -100), Enhancer sequences (-10,000 to +10,000). |
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Term
| What are some examples of trans elements, and where do they bind? |
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Definition
| TBP subunit of TFIID binds the TATA core promoter element. Constitutive TF's bind promoter proximal elements. Regulated TFs bind enhancer squences. |
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Term
| What is a transcription activator protein? |
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Definition
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Term
| What are the three domains of TF's, and what do they do? |
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Definition
| 1. DNA binding domain--binds to inverted repeats. 2. Activating domain 3. Dimerization domain (forms dimers with other TF's--heterodimers vs homodimers. |
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Term
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Definition
| It is when the enhancer interacts with the TF by looping around. This can greatly enhance TXN. |
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Term
| What do TF activation domains interact with? |
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Definition
| 1. mediator protein complex. 2. Co-activators such as HAT (acetylation loosens nucleosomes) 3. enhancers through DNA looping |
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Term
| What are some ways TF activity can be regulated? |
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Definition
| 1. increase/decrease cellular concentration either by regulating degradation of TFs or producing more/less of them. 2. TF modification such as phosphorylation 3. bind co-activators 4. Location--allow TF into the nucleus 5. Use repressor proteins to do the opposite of TF's |
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Term
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Definition
| acetylates histones to make them less +. -DNA unwinds |
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Term
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Definition
| HDAC is histone deacetylase. This removes the acetyl group and makes the histone more + so it more tightly winds DNA |
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Term
| Besides HAT and HDAC, is there another way chromatin can be made more or less accessible? |
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Definition
| Chromatin remodeling complexes |
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Term
| What is DNA methylation and what does it do? |
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Definition
| DNA methylation adds methyl grops to deoxyctosine (C) by DNA methyl transferase. DNA methylation physically prevents some TF's and stuff from binding, but also attracts MECP2 protein, which attracts HDAC's--resulting in non-acetylated and thus tightly bound DNA. |
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Term
| What permanently shuts off gene expression and is responsible for keeping cells differentiated? |
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Definition
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Term
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Definition
| This is where a phosphodiester bond occurs between a cytosine and a guanine in a linear DNA sequence. This is usually not common, and these sequences are often methylated. Unmethylated CpG sequences are detected by the immune system because they could be viral. Somtimes CpGs arent supposed to be methylated, and when they are silence a tumor suppressor gene--causing oncogenesis. |
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