Term
| Why is RNA less stable than DNA? |
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Definition
| The 2' hydroxyl group can act as a nucleophile to attack the phosphate (a "juicy target") of the phosphodiester backbone, causing hydrolysis. Also, RNA can't make a B-form when in helical structure, and so it makes the more squished A-form. |
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Term
| Typically, what types of RNA are long-lived? |
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Definition
| rRNA and tRNA. mRNAs are usually meant to "destroy after reading" (very James Bond style...) |
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Term
| What recently discovered types of RNA are used to regulate stability or expression of mRNAs? |
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Definition
| Micro RNAs (miRNAs) and short interfering RNAs (siRNAs) |
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Term
| Imagine the DNA helix. Which strand (the coding or template strand) will have the same sequence as the RNA that is being made? |
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Definition
| the Coding strand! (which is displaced). NOT the template strand. |
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Term
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Definition
| Where Prokaryotic RNA polymerase jumps on the DNA promoter region and makes a stable, inert closed complex. |
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Term
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Definition
| Only Prokaryotic RNA Polymerase it sensitive to it, so it can be used as an antibiotic. |
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Term
| What region of the histones (H3 and H4) are acetylated or methylated? |
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Definition
| The "histone tails" of the N-terminal tails of histones. These areas don't contribute to the formation of the nucleosome core, and don't alter stability of the histone-DNA interactions. |
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Term
| What 4 enzymes add or remove acetyl and methyl groups from the histones? |
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Definition
| HATs, HDACs, HMTases, histone demethylases. |
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Term
| Zolinza (vorinostat) is an HDAC inhibitor that is FDA approved for treatment of cutaneous T-cell lymphoma. How does it work? |
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Definition
| Inhibiting HDAC results in hyperacetylation, and is somehow worse for tumor cells than it is for normal cells. Maybe the result is hyperacetylation of tumor suppressor gene that reduces cell growth more specifically in cancer cells. |
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Term
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Definition
| They recognize acetylation on the H teminal H4 tail and "bring friends" (the remodeling complex). |
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Term
| What is the "histone code"? |
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Definition
| It is the pattern of modifications. How many Acs do you have? How many Mes? How many Ps? These combinations interact to mean different things. |
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Term
| What happens if you have a mutation in the MeCP2 gene? |
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Definition
| Leads to Rett's Syndrome. Normally, MeCP2 binds to methylated (inactive) DNA and calls in HDAC (which un-acetylates and inactivates even more!). If you don't have MeCP2, you don't silence areas that are supposed to be totally inactive. |
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Term
| Decitabine completed a Phase I trial for inhibiting growth of certain tumor types. How does it work? |
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Definition
| When tumor suppressor genes are methylated, they are silenced and growth goes crazy! Decitabine looks like a cytosine, but doesn't have a carbon at the 5' position (it has a nitrogen instead). This nitrogen can't get methylated! |
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Term
| What is the difference between "cis" and "trans" elements? |
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Definition
| "Cis" elements (like promoters) only affect the expression of the DNA they are embedded in. "Trans" elements (like binding proteins) are encoded in one place, but affect any DNA molecule in the cell that has their recognition site. |
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Term
| RNA polymerase cannot recognize a Eukaryotic promoter sequence. How does it know where to go? |
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Definition
| It recognizes the combination of DNA binding proteins, general transcription factors, TBP, mediator. (Order differs from promoter to promoter) |
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Term
| What do General Transcription Factors (GTFs) do? |
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Definition
| They make a landing zone for the RNA polymerase. If they don't create a "suitable platform," RNA Polymerase will keep cruising around. They do this by calling in TBP to the TATA box and mediator to the promoter. |
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Term
| Prokaryotic promoters are all very similar. What does this tell us about one promotor? |
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Definition
| It can control multiple genes in an operon. Also, in prokaryktes, the strength of a promoter is mostly controlled only by how well it matches the sigma factor binding site. |
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Term
| What does it mean to act "in cis"? |
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Definition
| A change in the promoter sequence will affect how often the gene on the DNA molecule that is altered is transcribed. How most promoter mutation act. |
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Term
| What does it mean to act "in trans"? |
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Definition
| The factor will affect aLL DNA molecules in the cell (not just the one that encodes it). How most DNA binding proteins that recognize promoter elements act. |
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Term
| In prokaryotes, what do operators do? |
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Definition
| They modulate promoter activity, and are usually very close to the promoter (or can overlap). |
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Term
| p53 is usually very unstable and gets degraded soon after it is made. If DNA in a cell is damaged, what happens to the signal to degrade p53? |
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Definition
| It gets interrupted. The protein builds up, and gets transported to the nucleus where is acts as a transcriptional activator. bad news! cancer! |
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Term
| In eukaryotes, transcription factors are often regulated how? |
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Definition
| By altering their stability or subcellular location. |
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Term
| Why do we use Northern Blots? |
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Definition
| To look at size/structure/abundance/tissue distribution of mRNA. |
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Term
| Why do we use a microarray? |
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Definition
| To detect chromosomal changes. A microarray can see changes in gene expression patterns. It uses LOTS of messages at the same time. |
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Term
| What does Drosha do? How does this relate to Dicer? |
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Definition
| It is an endonuclease that digests dsRNA hairpins in the nucleus. These small fragments are transported to the cytoplasm where they are digested even more by Dicer. End product is miRNAs. |
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Term
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Definition
| It uses the miRNA as a guide to stop translation of mRNAs with the same sequence. |
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Term
| What must be on the 3' end of all tRNAs? |
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Definition
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Term
| What does poly-A polymerase do? |
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Definition
| It is an RNA polymerase that adds a poly-A tail to the 3' end of mRNAs. It works without a template. |
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Term
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Definition
| Convert specific adenosines to inosines. Inosine pairs with cytosine. This is an example of how bases within the RNA can be modified. |
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Term
| ApoB48 is shorter than ApoB-100 due to a point mutation. What causes this? |
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Definition
| Cytosine deamination. The mRNA for ApoB-48 is processed to change the CAA codon to UAA, resulting in premature termination of translation. |
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