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32 Cards in this Set
- Front
- Back
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What are housekeeping genes?
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Part of gene regulation, always on. Includes metabolism proteins and DNA polymerases.
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What are specialized genes?
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Can be either on or off, expressed in specialized cells- Hb in red blood cells.
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What are finely tuned genes?
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Most genes, can change in response to external signals. e.g. changes in liver enzymes under starvation conditions.
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What are the 6 levels of gene regulation?
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1. Transcriptional
2. RNA processing 3. RNA transport and localization 4. translation control 5. mRNA degradation 6. protein activity |
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What are examples of transcriptional regulation?
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RNA polymerase II requiring transcription factors to assemble at the promoter. DNA packed into chromatin and coiled around histone proteins.
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What is a genetic switch?
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A variety of signals that turn on and off genes. Include specific DNA sequences and the proteins that bind to them. e.g. tryptophan operon
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What is the importance of the major and minor grooves?
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Proteins tend to bind to the major groove because can 'see' more active sites because more exposed. Can see 4 active sites instead of three on minor groove. Active sites include H-bond acceptor, H-bond donor, hydrogen atom and methyl group between paired bases.
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What is a gene regulatory protein?
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A protein that contain structural motifs that can 'read' DNA sequences. Can suppress or activate transcription. e.g. helix-turn-helix proteins.
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What are some examples of gene regulatory proteins and protein dimers?
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helix-turn-helix proteins, Zinc-finger proteins, p53 DNA binding protein (a repressor often mutated in cancer). Dimers include leucine sipper proteins (can be homo or heteromer) and proteins with any ligand.
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What is positive and negative regulation?
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When a regulatory protein binds to DNA and gene turns on, called positive control and activator proteins.
When a regulatory protein binds and gene turns off, called negative control with a repressor protein. |
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What is an operator?
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A DNA sequence within the promotor.
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Describe the tryptophan Operon.
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Tryptophan acts as a ligand with the repressor. When tryptophan is present, it binds with the repressor and repressor binds to the operator, blocking transcription. When to tryptophan, repressor can't bind, transcription begins. Example of negative control.
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What is the function of ligands with regulation proteins?
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Ligands can bind to remove a regulatory protein from DNA- if protein is a repressor, transcription begins, if protein is a activator, transcription stops. Ligands can also bind to allow regulator to bind to DNA, then opposite effects occur.
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Describe the Lac operon.
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Example of both negative and positive control. Repressor binds in absence of lactose, CAP promotor binds in the absence of glucose. So most active in presence of lactose and absence of glucose.
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Can regulatory proteins can regulate expression of different genes?
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yes
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What are enhancers?
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Regulatory sequences can be a distance from the gene and can be up or down stream. They tether the complex close to the promoter.
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What are the 4 mechanisms of action for activator proteins?
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1. recruit transcription factors to the promoter.
2. position transcription factors at the promoter. 3. increase affinity of RNA pol II for the promoter. 4. alter chromatin structure a) recruit ATP-driven chromatin remodeling complexes b)recruit histone modification enzymes. e.g. acetylation of histone N-terminal by histone acetyl transferase (HAT) |
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What are the known modifications of the histone core proteins?
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addition of
1. acetyl group 2. methyl group 3. phosphate 4. ubiquitin |
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What are the 5 mechanisms of action for gene repressors.
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1. Competitive DNA binding
2. Masking the activation surface 3. Direct interaction with the general transcription factors 4. Recruitment of repressive chromatin remodeling complexes 5. Recruitment of histone deacetyleases. |
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What are the 7 ways regulatory proteins can be regulated?
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1. Protein is synthesized only when needed and broken down quickly.
2. Activation by ligand 3. Activation by covalent modification 4. Formation of complex between DNA binding protein and a protein with a transcription activating domain. 5. Unmasking of an activating domain by phosphorylation of an inhibitor protein. 6. Removal of inhibitory protein that keeps protein in the cytocol. 7. release from a membrane bilayer by proteolysis. |
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What is combinatorial gene regulation?
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When different cell types are created because of the different combination f gene regulatory proteins.
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What are the five forms of post-transcriptional regulation?
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1. Attenuation
2. Alternative splicing 3. mRNA stability and degradation 4. RNA transport 5. mRNA localization |
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What is attenuation?
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The premature termination of transcription used by constantly transcribed genes. Sometimes the RNA chain can interact with the RNA polymerase that aborts the transcription. When protein needed, a regulatory protein can bind to RNA chain.
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What are two examples of alternative splicing?
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1. exon skipping- one or more exons are omitted from the spliced RNA.
2. Cryptic splice site- a site that resembles an authentic splice site and might be selected instead of the authentic site, leads to disease. Splicing can be controlled by activator and repressor proteins also. |
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What is the mechanism of RNA Interference (RNAi) that causes mRNA to degrade post-transcription?
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Long dsRNA strands are cleaved by Dicer in ATP-dependent reaction creating short interfering RNA (siRNA). The siRNAs are incorporated into the RISC complex which cleaves the sense strand of the siRNA and activates the complex. The antisense strand then guides the RISC complex to its homologous mRNA strand and cleaves it.
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How does RNA transport regulation work?
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Only correctly processed mRNAs, with a 3' poly A and 5' cap 7mG, will be transported to the cytosol.
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What is mRNA localization regulation?
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Happens when mRNA is associated with the ribosomes in the cytosol or the ER, involves 3' UTR, mechanism unknown.
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What are the three types of translational control?
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1. mRNA stability and degradation
2. Translational Initiation 3. Efficiency of Translation Initiation |
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How does mRNA degradation work to control translation?
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Its a competition between mRNA translation and mRNA decay with 5'cap and 3'poly A site used in both translation and deadenylation dependent mRNA decay. An enzyme called DAN shortens he poly-A tail in the 3'-5' direction. miRNA may also be involved.
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Describe translational initiation regulation.
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The Kozak sequence is the first AUG sequence from the 5' cap. This can be blocked by a represser. miRNA may also be involved here.
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How can the efficiency of translation be controlled for regulation?
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eIF2 and eIF4 and other ribosomal factors that initiate translation can be controlled by phosphorylation or with ligands (eIF2 can need eIF-2B to become active). Elongation factors can enhance translation (EF-1 and EF-2 in eukaryotes) and includes hydrolysis of GTP to GDP.
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What are the three mechanisms of post-translational control?
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1. Control of protein activity- proteins can be modified to be made active e.g. protein folding, processing, phosphorylation-dephosphorylation
2. Compartmentalization- 3. Protein degradation |
