Term
|
Definition
| a side product that is produced when lactose is present in E.coli. It is an inducer which binds to the lac repressor and thereby greatly reduces the repressor’s affinity for operator. |
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Term
| IPTG (isopropylthiogalactoside) |
|
Definition
| a potent inducer of ß-galactosidase expression. Very useful in lab settings used for inducing the expression of cloned genes. |
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Term
|
Definition
| Enzyme which is expressed when glucose is scarce (E.coli). This enzyme breaks lactose through hydrolysis converting lactose into: glucose + galactose. (enzyme number increases when lactose is present >100 molecules) |
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Term
| Three proteins that are INDUCED by Lactose |
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Definition
| i. ß-galactosidase ii. galactoside permease iii. thiogalactoside transacetylase |
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Term
| Gene expression proteins block access to ______________ to their promoters. |
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Definition
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Term
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Definition
| motif capable of binding DNA. It consists of 2 helixes. Helix 1: this helix is the one that makes contact with the DNA backbone. Helix 2: lies in the major groove of DNA and serves as the recognition motif. |
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Term
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Definition
| DNA binding site of the lac repressor. Binds between the Arginine residue and a G-C base pair in the binding site. |
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Term
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Definition
| represses the expression of lactose-processing gene |
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Term
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Definition
| a hydrophobic and easily permeable molecule able to pass through the membrane. It is a highly specific molecule that binds to soluble receptor proteins. |
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Term
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Definition
| part of the ERE's (estrogen binding sites) on DNA. Binds by zinc to the major groove of DNA. |
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Term
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Definition
| modifies the expression of specific genes by binding to control element in the DNA. Ligand binding does NOT affect binding & specificity. However, it does change the conformation in the ligand-binding domain which gives it highly favorable sites for coActivator binding. |
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Term
| CoActivator Recruitement Mechanism (5-steps) |
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Definition
| alpha-helix --[ligand]-> alpha-helix w/ ligand binded --[coActivator]-> alpha-helix with ligang and coActivator binded |
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Term
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Definition
| molecule that acts to losen up the histone complex from the DNA. The result is exposure of DNA regions to the transcriptional machinery. (essentially meaning that it catalyzes rxn so that chromatin structure can be modified). |
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Term
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Definition
| binds to the signal triggering pathway |
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Term
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Definition
| receptor ligand that does NOT provoke a biological response itself upon binding to a receptor antagonist but does not trigger signaling pathways. Bind to hormone receptors |
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Term
| Histone acetyltransferase |
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Definition
| modify the histone residues. It recruites acetyl-groups onto lysine in histone residues. It takes the histone from a positively charged amine group to a uncharged amine-group. |
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Term
| How do coActivators modulate transcription activity? |
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Definition
| coActivators act to loosen up the histone complex from the DNA. Exposing additional DNA regions to transcriptional machinery. |
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Term
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Definition
| protein domain that recognizes acetylated protein residues (important for Chromatin remodeling) |
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Term
| Chromatin-Remodeling complexes |
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Definition
| uses the free energy of ATP hydrolysis to shift position of nucleosomes. |
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Term
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Definition
| transfer protein that carries iron in the serum |
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Term
|
Definition
| membrane protein that binds iron loaded transferrin & initiates entry into cell. |
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Term
|
Definition
| iron-storage protein found in the liver and kidneys. |
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Term
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Definition
| has a stem-loop termed (IRE) in it's 5'-untranslated region |
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Term
| Four characteristics of Activator Domains |
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Definition
They help recruit (promote) transcription and interaction w/ RNA polymerase.They are:
1. REDUNDANT - one part can be deleted w/o loss of function
2. SYNERGISTIC - if paired, it has twice as strong effect than when alone
3. MODULAR - can activate transcription when paird with DNA binding domains (domains that bind by zinc w/ major groove of DNA)
4. LESS CONSERVED - can be acidic, hydrophobic, glutamine rich or proline rich. |
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Term
| What is one issue with methylation on the 5' carbon on cystein? |
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Definition
| This interferes with the major groove on binding of proteins which stimulates transcription. |
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Term
| Catabolite Activator Protein (CAP) |
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Definition
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Term
| lambda-repressor (lambda-cI protein) |
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Definition
| the protein that blocks directly or indirectly the transcription of almost all genes encoded by a virus in the lysogenic state and even encodes itself (lambda virus itself). |
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Term
| Where does the lambda repressor have highest affinity on the gene? |
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Definition
| Or1 site! But it also binds on Or2 site but not on Or3 (unless there is a high amount of lambda repressors present, blocking access to the promoter and hence RNA polymerase) |
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Term
| How does the binding of the Lambda-repressor at the Or1 site affect transcription? |
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Definition
| blocks access to the promoter on the right side of the operator sites repressing transcription on the adjacent gene which encodes for a protein called Cro. |
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Term
| Interaction between Cro and Lambda-repressor? (How it works) |
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Definition
| Cro binds favorable to Or3 which blocks the production of the lambda-repressor, but the lambda repressor blocks the production of Cro by binding most favorable to Or1. This forms a switch which determines whether is follows lysogenic or lytic pathway. |
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Term
| What state does a virus enter when Cro is present & why? |
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Definition
| It enters the lytic pathway. Since lambda-repressor protein is repressed due to the binding of Cro on Or3 preventing the binding of repressor to Or1, this causes the virus to enter and become active in the cell. |
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Term
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Definition
| a prokaryotic mechanism for regulating transcription through the modulation of nascent RNA secondary structure. Attenuation provides sensing supply of tryptophan required for protein synthesis (in bacteria). |
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Term
| High Levels of Tryptophan cause what? |
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Definition
| High levels causes translation to end faster, hence there is a smaller set of nucleotide sequence (in the hundreds) |
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Term
| Low levels of Tryptophan causes what? |
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Definition
| low levels causes translation to stall, hence, it takes longer to reach a stop codon, and the nucleotide sequence is longer (in the thousands). |
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Term
| Leader region of nucleotide mRNA |
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Definition
| The nucleotide sequence of the 5'-end of a nucleotide mRNA includes a short open reading that is before the attenuation portion (which eventually forms stem-loops) |
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Term
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Definition
| DNA-binding protein which controls genes that digest lactose (to make energy). When lactose is is present, it is converted to 1,6-allolactose which inhibits the lac repressor's DNA binding ability. [Note: binds as a DIMER on DNA and is able to recognize symmetry sequence] |
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Term
|
Definition
| consumation of glucose (preferred method of energy in prokaryotes, however, it can use lactose when glucose is scarce or grown on lactose culture). |
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Term
|
Definition
| the DNA strand that is replicated continuously |
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Term
|
Definition
| an RNA enzyme that serves as the the primer for DNA synthesis. |
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Term
| How is DNA polymerase III able to correct it's mistakes in replication? |
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Definition
| Because it has a 3'->5' activity which allows it to proofread. |
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Term
| Thymine dimers are formed when? |
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Definition
| DNA is exposed to UV light. This causes alteration of the DNA which causes blocking of DNA replication and transcription. |
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Term
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Definition
| the human skin disease caused by mutations in the human nucleotide-excision-repair pathway. |
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Term
|
Definition
| intermediates in recombination pathways composed of FOUR polynucleotides chains in a cross-like structure. |
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Term
| What is the linking number formula? |
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Definition
|
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Term
|
Definition
| the enzyme that relaxes DNA. It attacks the OH on tyr-723 and attacks the phosphate group on one DNA strand. As the backbone one one strand is cleaved, the DNA rotates. |
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Term
| Which direction does REPLICATION move in? |
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Definition
|
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Term
| What causes Huntingtons Disease? |
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Definition
|
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Term
|
Definition
| a compound that is converted to a reactive epoxide by cytochrome P450 and causes a G-C to T-A transaversion |
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Term
| What is the function of photylase? |
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Definition
| repairs pyrimidine dimers |
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Term
|
Definition
| enzymes that have a repeating sequence that bind to the ends of replicated DNA strands (daughter and parent). They prevent DNA degradation over generations. Also serve as antagonistic enzymes, meaning that high amounts may increase life-span, but also include a high-risk of cancer if there is a low amount. |
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Term
|
Definition
| removes the primer pieces |
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Term
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Definition
| member of the AAA ATPase family, promotes the formation of the displacement loop, D-loop. This process is often called strand invasion. Rec A helps the invading strand find the complementary sequence in the duplex DNA. |
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Term
| Importance of Shape Complimentarity in DNA replication |
|
Definition
pairing with the right shape is important because it allows correct base pairing by hydrogen bonding. DNA polymerases close down around the incoming dNTP. This binding triggers a
conformation change such that only a properly shaped base pair will fit. |
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Term
| Aminoacyl-tRNA synthetases contain? (2) |
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Definition
| Activation and Editing site. |
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Term
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Definition
| In E. coli, the signal sequence that properly aligns the initiation codon in the P site. |
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Term
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Definition
| The first amino acid in bacterial proteins. |
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Term
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Definition
| transcribes a single precursor that encodes for the 18S rRNA, the 28S rRNA, and the 5.8S rRNA. |
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Term
|
Definition
| cleaves only 1 strand of DNA. The mechanism of topoisomerase I involves NO energy. It merely isomerizes. |
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Term
|
Definition
| Cleaves 2 strands of DNA. Utilizes free enrgy from ATP hydrolysis to add NEGATIVE supercoils to DNA. |
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Term
| What is meant by processitivity of an Enzyme? |
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Definition
| this means that an enzyme can catalyze many reactions without release of it's substrate. |
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Term
| Lagging vs Leading strand synthesis |
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Definition
| Lagging strand is synthesized continuously. Leading strand is synthesized in fragments. |
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Term
| What are the 2 domains of the lambda-repressor? |
|
Definition
| amino-terminal and carboxy terminal |
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Term
|
Definition
| inhibits peptidyl transferase activity in the 50S subunit. |
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Term
|
Definition
| inhibits protein synthesis by causing a misreading of mRNA |
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Term
|
Definition
| inhibits translocation (in EUKARYOTES) |
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Term
|
Definition
| causes premature chain termination by acting as an analog of aminoacyl-tRNA |
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Term
|
Definition
| binds the 30S subunit & inhibits the binding of aminoacyl-tRNA's |
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Term
|
Definition
| binds to the 50S subunit and inhibits translocation. |
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Term
|
Definition
| enzyme responsible for exchanging GTP for bound GDP on eIF2. |
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Term
| vanishing white matter disease |
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Definition
| caused by a mutation in eIF2B |
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Term
|
Definition
| prevents reassociation of ribosomal subunit in the absense of initiation complex. |
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Term
|
Definition
|
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Term
|
Definition
| elongation factor-2; mediates GTP-driven translocation. |
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Term
|
Definition
| catalyzes the exchange of GTP for bound GDP |
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Term
|
Definition
| delivers aminoacyl-tRNA to the A-site. |
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Term
|
Definition
| a nucleotide sequence that allows for translocation initiation in the middle of mRNA. |
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Term
|
Definition
| an operon required for the transport and metabolism of lactose in E.coli (consists of lac(z), lac(y) and lac(a)) |
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Term
|
Definition
| binds DNA specifically only when bound to a small molecule (corepressor). Its behavior is opposite of lac repressor |
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Term
| What are the 3 proteins induced by lactose? |
|
Definition
| b-galactosidase, thiogalactoside transacetylase, galactoside permease. |
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Term
| Francis Jacob, Lwoff, and Monod won the Nobel prize for? |
|
Definition
| discovering the genetic control of enzyme and virus synthesis. |
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Term
|
Definition
| used to test for the presence of beta-galactosidase (both in vivo and in vitro). Undergoes spontaneous dimerization w/ itself. |
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Term
|
Definition
| prokaryotic mechanism for regulating transcription. It depends on the 5'-end of mRNA product. If there is a low concentration of a tryptophan = longer nucleotide (b/c it stalls transcription). But if there's a high concentration, then the process is fast and the chain becomes small. |
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Term
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Definition
| a type of mechanism used by bacteria and some social insects which is used to coordinate gene expression. |
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Term
|
Definition
| chemical signaling molecules produced in bacteria and partake in quorum sensing. Allow communication both w/in and with different species. |
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Term
| Helix 1 and Helix 2 (helix-turn-helix) |
|
Definition
helix 1 = contacts the DNA backbone
helix 2 = recognition helix that lies in the major-groove and contacts the edges of the base pairs. |
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Term
| How does the lac repressor bind to operator? |
|
Definition
|
|
Term
| What is an adavantage of DNA condesing into chromatin? |
|
Definition
| to prevent cleavage from DNase I. |
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Term
|
Definition
| transcription factors that can bind to regulatory sites that are considerable distance from the promoter. (the distant regulatory sites are the enhancers) |
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Term
|
Definition
transcription factors that can initiate transcription by recruiting other proteins that promote transcription.
i. less conserved than DNA-binding domain
ii. often are redundant
iii. they are modular
iv. can act synergistically. |
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Term
|
Definition
| comprises of tandem sets of small domains each of which binds a zinc ion thru conserved sets of 2 cystein and 2 histidine residues. |
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Term
|
Definition
consists of long helices. Has TWO units:
1. basic region - in major groove of DNA
2. coiled-coil that pairs w/ partners |
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Term
|
Definition
| homeodomain is part of DNA-binding unit. it recognizes asymmetric DNA sequences. It has a heterodimer formed from 2 different binding domains. |
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Term
| Histones are _________ which means they're (positively charged) |
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Definition
|
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Term
|
Definition
| iron-response element. This is a short stem-loop bound by IRP's found in untranslated regions of various mRNA. |
|
|
Term
| Craig Mellow & Andrew Fiire |
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Definition
| won nobel prize for discovering gene-interfering (small regulatory RNA - snRNA) |
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Term
| Low Concentration of IRE's means? |
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Definition
| this means that it blocks the initiation of translation |
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Term
| High concentration of IRE's mean? |
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Definition
| this means that IRP binds as a 4Fe-4S cluster, IRP bound to iron CANNOT bind RNA making excess iron. |
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Term
| What does acetylation of Histone tails provide? |
|
Definition
| acetylation of the tails on histones allows a mechanism for recruiting other components of the transcriptional machinery. |
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Term
|
Definition
| transport protein that carries iron in serum |
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Term
| Chromatin-Remodeling complexes |
|
Definition
| use the energy of free ATP hydrolysis to shift position of nucleosome. |
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Term
|
Definition
| membrane protein that binds iron-loaded transferrin and initiates entry into cells. |
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Term
|
Definition
| efficient iron-storage protein found in the liver and kidneys. |
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Term
| TATA-box-binding Protein Associated Factors |
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Definition
| acetylation of histone tails provide a mechanism for recruiting other components of transcriptional machinery. |
|
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Term
|
Definition
| comprises of about 110 amino acids that form a 4-helical bundle. Contains proteins that are essential for transcription |
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Term
| Consequence of histone acetylation? |
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Definition
| since the lysine bears a (+) charge, the acetylation by histone acetytransferase changing the affinity of the tail for DNA. Therefore, the entire histone complex loosens the histone from DNA. |
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Term
| Histone acetyltransferases |
|
Definition
i. loosens up the histone complex from the DNA
ii. acetylated histone residue interacts w/ acetylysine binding domain present in many proteins that regulate transcription |
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Term
|
Definition
| binds in the pocket normally occupied by estrogen. It extends the pocket so the 12-helix can't pack in the position blocking coactivator binding site. |
|
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Term
| Selective Estrogen Receptor Modulators (SERM's) |
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Definition
| compounds that have distinct effects on different forms of estrogen receptors |
|
|
Term
| What are TWO antagonists of estrogen receptors (for breast cancer)? |
|
Definition
| tamoxifen and raloxifene. they both inhibit estrogen mediated pathways for growth |
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Term
|
Definition
| molecules that bind to nuclear hormone receptors but DON'T effect the trigger signaling pathways. |
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Term
|
Definition
| molecules that bind to receptor and trigger signaling pathways. |
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Term
| AHL (acyl-homoserine lactone) |
|
Definition
| triggers development of flouresence in squid. |
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Term
|
Definition
a genetic switch. When there are high concentrations = lytic stage
low concentrations of Cro = lysogenic state. |
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Term
| Lambda repressor functions |
|
Definition
i. blocks genes encoded by virus.
ii. binding is cooperative. |
|
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Term
|
Definition
i. modification of histones
ii. methylation of 5'carbon on cystein in DNA. |
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|
Term
| catabolite activator protein |
|
Definition
| stimulates expression of catabolic enzymes. |
|
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Term
|
Definition
| this sequence is determined by an alignment of DNA base sequences used to deduce a recurring pattern or motif |
|
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Term
|
Definition
| this subunit of RNA polymerase recognizes promoters during heat-shock conditions. |
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Term
| Rho Protein does what in transcription? |
|
Definition
| It terminates transcription by acting as a helicase. |
|
|
Term
| How many bases can RNA polymerase unwind? |
|
Definition
| 17 bases or 1.6 turns of B-DNA. |
|
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Term
| Class I Amynoacyl-tRNA Synthetase |
|
Definition
| this enzyme acylates the 2'-hydroxyl group of the terminal adenosine of tRNA. |
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Term
|
Definition
| the intermediate formed in the activation of tRNA. |
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Term
| g-protein is a family that is required for? |
|
Definition
| initiation, elongation, and termination. |
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Term
| What are some function of RNA polymerase? |
|
Definition
1.searching for promoter sites
2. unwinding short stretches of DNA
3. detecting termination signals. |
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Term
|
Definition
| a technique that allows one to determine where proteins bind to DNA. |
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Term
|
Definition
| antibiotic that interferes with transcription by binding to the DNA helix and preventing its use as an RNA template. |
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Term
| The key in Eukaryotic transcriptional activation is? |
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Definition
| binding of the TATA-box-binding protein to the TATA box. |
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|
Term
| What modifications are made to eukaryotic tRNA transcripts? |
|
Definition
1. modification of base and ribose moieties
2. removal of 3' trailer
3. cleavage of 5' leader by RNase P
4. CCA is added |
|
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Term
|
Definition
| a domain that is part of RNA polymerase II that is involved in coordinating post-transcriptional processing events. |
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Term
|
Definition
| proteins that posses alternative splicing products. |
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|
Term
| What is the role of GTP in self-splicing? |
|
Definition
|
|
Term
| Requirements for initiation of protein synthesis in prokaryotes |
|
Definition
1. mRNA
2. 30S subunit
3. fmet-tRNA
4. GTP |
|
|
Term
| mRNA contains signals that define? |
|
Definition
| the beginnign and end of protein synthesis. |
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Term
|
Definition
| responsble for translocation of mRNA as a result of conformation change due to hydrolysis of GTP. |
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|
Term
| IF1, IF2 and IF3 are necessary for what on mRNA AND tRNA? |
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Definition
| They are necessary for correct placement of mRNA and initiating tRNA on the ribosome. |
|
|
Term
| ACceptor Stem and Anticodon Loop |
|
Definition
| components on the tRNA that are important for the binding specificity of tRNA synthetase. |
|
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Term
| How do class I and class II aminoacyl-tRNA synthetases differ? |
|
Definition
| They bind to ATP differently. Class 1 enzymes are monomeric. Class 2 = dimeric. Class 1 acylate the 2'-OH group while class II acylates the 3'-OH group at the terminal A at the CCA and of tRNA. |
|
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Term
|
Definition
| these are found in eukaryotes anre are cleaved from initial transcripts produced by RNA polymerase II and sometimes RNA polymerase II. The 20-23 nucleotide long single stranded RNA's bind proteins involved in controlling gene expression. They either trigger mRNA degradation and or inhibition of translation. |
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Term
|
Definition
| a mechanism for maintining the fidelity of tRNA aminoacylation. The synthetase has an acylation site (activation site) and an editing site (hydrolytic site). The acylation excludes amino acids that are larger than the correct amiino acid from being attached to the tRNA. The editing site will bind all the amino acids that are smaller than the correct amino acid and remover them from the tRNA. By using this double sieve mechanism, only the correct amino acid is attached to the tRNA which improves the fidelity of aminacylation. |
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|
Term
| What are the major steps in pre-mRNA splicing? |
|
Definition
1. recognition of the 5'splice site by U1 snRNP
2. U2 snRNP binds to the branch site in the intron
3. preassmbled U4-5 tri snRNP joins the complex to formthe spliceosome.
4. U5 snRNP interacts with the xon sequences in the 5' splice site and 3' exon.
5. U snRNA disengages from U4 and rearranges to base pair with U2 snRNP
6. U1 and U4 dissociate
7. first transesterification reaction occurs resulting in the cleavage at the 5'splice site.
8. U5 snRNP aligns the 5' exon with the 3' exon such that the second transesterification occurs so that the 3'OH group of the 5' exon attacks the 3' splice site to generate a spliced product. |
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