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31 Cards in this Set
- Front
- Back
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#11 A) describe the structure of and function of the CTD of RNA poly II.
B)do any other RNA ploys process a CTD |
A)CTD(Carboxyl terminal Domain) the largest subunit of the RNA ployII contains a carboxyl end of the stretch of 7 amino acids (trp-ser-pro-thr-ser-pro-ser) that is repeated multiply, domain is critical cell viability
B)RNA Poly II is the only RNA with CTD |
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#7. what is mean by epigenetic control of transcription ? provide examples
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epigenetic a process that affects the expression of specific gene and its inherited by daughter cell, but does not involve a change in dna sequence. examples of epigenetic regulate of transcription histone modification dna methylation |
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i added explain the step of Attenuation involving the Trp operon |
Attenuation mechanism (inhibits transcription elongation) high TRPlots of tRNAtrp so ribosome translate through region 1 into region 2 , this prevents region 3 from base pairing with region 2. this causes region 3 and 4 to form an RNA hairpin which is followed by a string of U’s (termination signal) low TRPfew tRNAtrp, so ribosome stalls at region 1, this causes region 2 to basepair with region 3, a hair pin does NOT form , and RNA poly counts to transcribe the trip operon |
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#9 Differentiate between promoter- proximal elements and enhances |
promotor-proximal enhancers-long bp(50-200bp) -located 50kbp upstream or downstream of start of transcription within a intron or down stream from the final exon Promotor - proximal elements -short bp(6-10bp) -located with the first 200bp upstream or downstream of the start of transcription. |
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#10 a) what do TATA boxes,initiators sequence and CpG islands have in common? b) which was the first to be identified and why ? |
a.they all DNA sequences that function as promoter regions for RNA poly II to bind b. the TATA box was the first to be identified |
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#12 Describe the similarities and differences between prokaryotic and eukaryotic RNA polymerases. |
eukaryotes have 3 RNA poly while prokaryotes have 1eukaryotic poly II is simular to prokaryotic RNA poly in structure with simular subunits -eurkartoic RNA Poly II has CTD and recognizes TATA box domain prokaryotic RNA poly II used Sigma factor 70 to recognize DNA |
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#13 there are a number of conserved sequences found in an mRNA which dictate where the splicing occurs. what are these sequences and where are they found relative tot he exon/ intron junctions ? |
-most convcerved intron (remove) sequence arre the 5' GU ,3'AG and branch point -splicng is carried out by snRNA(U1,U2,U3,U4,U5,U6) -5'end of U1 bp with 5'end of splice site -U2 bp with branch point -U4 +U5+U6 bp and form complex -U6 dissocates with U4 and bp with 5' splice site and U5 bp with exon -rearrangement of splicespome catayles 2 transferesterfications -rxn,results in intro removal and exon ligation snRNA disscoate |
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#14 function of 5’ cap and poly A tail |
protect against digration from RNA digesting enzymes in nucleus and cyctosole marks RNA as mRNA medediates the export out of the nucleus |
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#15mRNA stability is a key regulator of protein levels in the cell . briefly describe the 3 mRNA degradation pathways |
Deadenalyation -dependent path way ploy A tail is shortened by deadenylase unit 20 A’s -intercation withPABPI with mRNA destablized
-results in weak interaction between 5’ cap and ELF’s 2 fates 1 exposed cap is decapped by enzyme and mRNA is degraded 5’ to 3’ by endonuclease 2 degrade by 3’ to 5’ by endonuclease deadenalyation - independent path way-certain sequence at 5’ end of the mRNA make the cap sensitive to the decapping enzyme -mRNA is decapeed and then degraded endonucleolytic pathway -does not involve decaping or deadenylation -endonucelases medaite interal cleavge and the fragemetns are degraded by exonuclease |
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#16in aniamal cell nearly all cytoplasmic mRNAs have a 3’ poly A tail which is added to the pre mRNA before splicing. Describe the mechanism |
1.CPSF binds to the AAUAAA ploy A signal 2. 3 additional proteins bind, one of interacts with GU sequence, forming a loop in mRNA 3.binding of PAP(poly A ploymerase. stimulates cleaving of the pre-mRNA at the ploy A site by the cleaving factor 4.release of proteins and RNA cleavage product 5.PAP adds 12 A residues at a slow rate to the 3’ OH end 6. binding of PABPII to the short tai causes: 1.PAP to polymerase at a faster rate 2.signals PAP to terminate after the addition of 200 A’s 3.PABPII is needed for the export out of the nucleus |
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#17 Descirbe 2 ways in which post- transciptsional control of protien coding genes could be accomplished in the cytoplasm |
1.control the stability of the functional mRNAthe concentration of a mRNA int he cytoplasm is dependent on both its rate of synthesis and it rate of degration if 2 genes have the same rate of transcription the one that has the more stable mRNA will be producing protein for the longer time 2.Inhibit translation of a specific mRNA inhinited translation of mRNA by miRNAinhibition can also be accomplished by the actin of RNA binding proteins that recognize sequences in the 5’ UTR of a mRNA -this inhibits the ribosome lability to scan for the first initaion codon for translation (AUG) so translation initaition is blocked |
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#18 Signaling by soluble extracellular molecules can be classified as endocrine, autocrine or paracine. describe how theses cellular signals differ
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endocrine signalling produces chemicals into the blood stream acts on a receptor of the target cell. ex insulin Paracine signalling - chemicals only diffuse a short distance to reach the target cellAutocrine signalling - chemcials is introduced by cell and affect the same cell |
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#19 explain how FRET could be used to monitor the association of GalphaS and adenylyl cyclase following activation of the epinephrine receptor |
when cAMP is not bound to receptor : -CFP- Gα close to YFP-Gβγ -CFP is able the fluorescence energy transfer to YFP -this allows YFP to fluorescence yellow (amount of yellow telling us that cAMP -when cAMP is bound - CFP -Gα moves away from YFP-Gβγ -Fluorescence energy transfer is unable to occur and on cyan light is fluoresced |
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#20 A) what are some examples of the second messages?B) what are the the advantages of these molecules ? |
A)Ca+ ions , cAMP, cGMP B) -they diffuse through the cytosol faster than proteins -this makes them more useful at transmitting signals to targets that are distant from the plasma memberane -they facility amplification of the extrcellualr signals |
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#21what is the purpose of A-kinase association protein (AKAPs) |
AKAPs act as scaffold for proteins interaction to occur, isolating PKA to regions of the cell where a specific ligand is locatedwhen cAMP levels increase and PKA is activated it will phosporlate this substrates different cells with different AKAPs result in PKA being near different substrate in the cell |
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\#22 summarize the steps in the cycling of GTPase switch proteins from active to inactive states |
switch protein can turn downstream proteins on or off depending on their conformation G proteins -bing to GDP and GTP 1. activate (on) - GTPase has GTP bind 2. inactivator protein GAP removes Pi inactivating GTPase 3. inactive (off) - GTPase with GDP bind 4. Activator protein GEP removes GDP 5. Allows GTP to bind to GTPase and re activate it in active state, the GTPase switch protein can bind a protein ,thus transducing a signal |
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#24 Even though GRB2 lacks intrinsic enzymatic activity, it is essential component of the epidermal growth factor (EDF) signalling pathway that actives MAP kinase. what is the function of GRB2 ? |
-Two cytosolic adaptor protein GRB2 and Sos are recruited to link Ras with the receptor -binding of Sos-GRB2 to Ras-GDP leads to a conformational change of Ras switch 1 and 2 segments so that GDP is releases -GTP binds and Ras dissocaties from Sos -GRB2 complex -Ras-GTP is now active state ( has its switch segments in a conformation to activate the next protein in the pathway-Ras wiill active Raf , which will activate MEK, which will activate MAP kinase |
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#25 how can multiple MAP kinase pathways be segregated when they share a common component? |
the pathways are activated by different extracellular signals that activate different MAP kinasases, that phosphorlate different transcription factors, that act on different genes to cause different physiological changes (in cell division, cell differentitoaion or function ) |
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#26 Many kinases, including MAP kinase and receptors tyrosine kinase posses activation lips. what is an activation lip?what modification of the activation lip is required for activation of theses kinases ? |
activation lip- is a flexable domain thats confromation depends on the phosphorlation statustyrosine kinases activated by phodphorlationMAP kinases - MEK phosphorlates MAP kinases acttiving it |
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#29 what are p bodies ? |
P bodies - are cytoplasmic domains that contain proteins involved in diverse posttranscriptional processes, such as mRNA degradation, , translational repression, and RNA-mediated gene silencing. |
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#1 major difference in the synthesis of mRNA in prokaryotes and Eurkaryotes |
Prokaryote -transcription occurs in cytoplasm -mrna does not need further processing after synthesis -has operons -no introns Eukaryotes -transcription occurs in nucleus -Translation in cytoplasm -primary transcript is initial made -transcript is processe to produce mature funcation mRNA -has introns -no operons |
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#2compare and contrast Prokaryotic and Eukaryotic Transcription initiation |
both: gene expression is primary controlled at he level of transcription initiation Pro: RNA poly requires assocatie with sigma factor -sigma 70 binds to both RNA poly anf the promoter -sigma 70 reconizes -35 and -10bp sequence to bring the RNA poly to sit, also unwinds stands Eur:-RNA poly II requires GTF to bind to the promter regions (tata box) -have CpG islands upsteam as promoter -CTD gets phosphorylated |
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#3 promoter region of prokaryotes and eukaryotes |
Pro: -promoter region includes -35 bp up to and including +1 -promoter region only contain 3 diff promoter elements -10,-35 promter and upstream elements Eur: - promoters are :TATA box, Intionator and CpG islands - contain several proomoter elements |
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#4 compare and contrast prokaryotic and Eukaryotic gene expression. |
Both: - primary control of gene expression by using mechanism that regulate transcription initiation and elongation -used DNA binding proteins -environmental changes induces changes in gene expression Pro: - gene control is mainly to a single cell to adjust to environmental changes -activation and rescission of genes are reversible Eur: -gene control is mainly for embryological development -interaction with other proteins determines whether or not it will function as a repressor protein or activator -TF's bind to control element further aways from promoter they regulate -developmental steps are not reversible - |
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#5 differentiate between positive and negative regulation |
Positive regulation: the presence of a activator protein is required for transcription( bind to activator binding site) negative regulation: the absence of a repressor protein is required for transcription (bind to operator site) |
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#6 describe the molecular events that occur at he Lac operon when E.coli cells are shifted to a glucose medium to a lactose medium |
-glucose regulates cAMP in cell -cAMP allosertic effector in the system cell CAP -when cAMP is bound to CAP the complex can bind to the CAP site on the Lac operon high glucose -no lactose so repressor binds to Lac operon both -lactose binds to repressor -slow transcription only lactose -lactose binds ot repressor -cAMP binds CAP which binds to operon speeding up transcription( activator protein) |
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#27 Differentaite between GPCr and RTK |
GPCr -7 trans-membrane domain -4 cytosolic domains -4 extra cellular domains -associates with G proteins RTKs -1 trans-membrane domain -no cytosolic domain -no extracellular domain -activation lip -binding of ligand casues dimerization |
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#28 reasons which may account for different cells giving a different response to the same ligand to the same receptor |
Binding of ligand to receptors with GPCr with different Gα subunits -these Gα subunits influence effector protiens differently -causing different effects on the cell type |
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#8 transcription in bacteria can be regulated by controlling transcriptional elongation in the promoter-proximal region. explain how this occurs in the case of the Trp operon. discuss the role of the Trp repressor protein in the regulation of the Trp operon.
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High Trp -Trp binds to the repressor protein and causes the repressor protein to bind to the operator. -this inhibits RNA ploy from transcribing the Trp operon Low Trp -no Trp to bind to repressor protein -operator is not effected -RNA ploy transcribes Operon |
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#23 how does the body respond to decrease blood glucose ? |
-Alpha cells in pancreas release glucagon -cause liver to break down glycogen into glucose -raises blood glucose level |
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#23 b) mechanism of down regulate signalling pathways |
1.) once GDP is replaces in G-alpha, the affinyt for the receptor tot the ligand decreases -limits 3of G-alpha activated 2.)cAMP phosphodiesterase hydrolyese cAMP TO 5'-AMP (cant act as ligand ) |
