Term
| does one molecule often do something by itself? |
|
Definition
| rarely...interactions are pretty much always necessary! |
|
|
Term
| how do you know if something is interacting? |
|
Definition
|
|
Term
| what does it mean to know the topology of proteins pulled down with RNA? |
|
Definition
| is it RNA-X-Y or RNA-Y-X? |
|
|
Term
|
Definition
| take knowledge about how RNA is transcribed (DNA sequences bind proteins which bind other proteins which bind RNA polymerase) & give one protein the DNA binding domain & the other protein the activation domain for RNA polymerase & see if the reporter gene is transcribed; if transcription occurs, those proteins interact! |
|
|
Term
| are DNA binding domains & activation domains transferable? |
|
Definition
| yes! you can take the domain & put it into another protein & that protein will now bind to the DNA (same with activation domains allowing proteins to now bind to other proteins) |
|
|
Term
| 2 hybrid assay: how do you control for if a reporter gene gets transcribed in some other way besides the binding of the two proteins? |
|
Definition
| you have multiple different reporter genes (ex. lacZ, URA3, GFP, etc.) |
|
|
Term
| 2 hybrid assay: how do you control for if just one protein by itself can do the activation? |
|
Definition
| have a yeast where you clone in the proteins separately...if transcription occurs, then you are running into this problem |
|
|
Term
| 2 hybrid assay: how do you control for if the artificial situation of the experiment causes the proteins to interact in a way that they do not normally do in their natural environment? |
|
Definition
| test each protein with other proteins & see if they commonly non-specifically bind |
|
|
Term
| 2 hybrid assay: how do you control for if the addition of the domains prevents protein interactions that normally occur in their physiological conditions |
|
Definition
| cut the protein up into smaller pieces & see if these smaller pieces really do interact with each other |
|
|
Term
| 2 hybrid assay: how do you control for if proteins only normally interact in a very specific scenario (i.e. stress)? |
|
Definition
| you need to test their interactions in a variety of situations |
|
|
Term
| 4 things to be sure of to be sure that a 2 hybrid assay is telling the truth |
|
Definition
1. each fusion protein must fold (function) properly
2. make sure that the two fusion proteins must be able to get into the nucleus
3. make sure that the artificial proteins aren't lethal to the cell!
4. must have enough of each protein |
|
|
Term
| what do you do when you do not have a candidate "friend" for your protein but want to do a 2 hybrid assay? |
|
Definition
| can do a 2 hybrid assay with just one specific protein & have the other "protein" be the rest of the proteome |
|
|
Term
| what would you use to detect protein-protein interactions? |
|
Definition
|
|
Term
| 3 steps for 2 hybrid assay |
|
Definition
1. fuse DNA binding domain to protein A
2. fuse activation domain for RNA polymerase to protein B
3. if DNA gets transcribed, that means A & B are interacting |
|
|
Term
| how could you get a false negative in a 2 hybrid assay (2 ways)? |
|
Definition
1. what if the fusion of the DNA binding domain or the activation domain gets in the way of the protein interaction domains?
2. what if A & C don't interact because you don't have protein B present to bring them together? |
|
|
Term
| how could you get a false positive in a 2 hybrid assay? |
|
Definition
| could tell you that A interacts with C when really physiologically B is between them |
|
|
Term
| 5 steps for cross-linking mass spec |
|
Definition
1. treat protein complex with a chemical that has a specific length & had reactive groups at either end
2. if two proteins are interacting with each other the cross-linker will covalently cross link them because they are close enough for both ends to bind
3. digest with trypsin
4. proteins will be cut up into peptides except cross-linked peptides will stick together
5. run peptides through mass spec to see which two proteins you have & will also be left with a read-out that is the molecular weight of peptide of one + peptide of another + cross linker |
|
|
Term
| 2 potential issues with cross-linking mass spec |
|
Definition
1. you could cross-link peptides to each other within the same protein
2. you could distort the dimer & make cross-links that aren't real (need to be very careful about how much to put in & how long to let them incubate) |
|
|
Term
| what was discovered in the eIF2-gamma paper? |
|
Definition
| sequenced genes & compared them from people with ID, people in the family without ID, & a control population --> discovered a mutation in gene for I222T gene in those with ID |
|
|
Term
| how was the I222T gene studied in the eIF2-gamma paper? |
|
Definition
| studied the yeast gene homolog of the human gene mutation |
|
|
Term
| conclusion from the eIF2-gamma paper |
|
Definition
| mutation causes issues with beta + gamma --> beta-gamma dimer |
|
|
Term
| 6 steps for discovery of splicing |
|
Definition
1. people cloned globin mRNA
2. cDNA
3. sequenced it via cutting with restriction enzymes
4. used cDNA as probe on library of lambda clones
5. sequenced what they probed via cutting with restriction enzymes
6. saw HUGE increase in fragment size (despite cutting with same restriction enzymes)! |
|
|
Term
| what is meant by "splicing has to be perfect yet efficient"? |
|
Definition
| sequence must be removed from the mRNA & the right pieces must find each other again to ligate to make the final mRNA |
|
|
Term
| how does exon size/frequency compare to introns? |
|
Definition
| exons are short & not in high numbers compared to introns |
|
|
Term
|
Definition
| no! (last exon must have AAA added at 3' end & first exon must have a cap added at 5' end) |
|
|
Term
| in the beginning, how many classes of introns were there? |
|
Definition
|
|
Term
| why were tRNAs used to study introns? |
|
Definition
| SHORT 100 nt long so sequences were known & could be purified & used as a probe to clone genes |
|
|
Term
| in the middle of genes for tRNAs had ______ |
|
Definition
|
|
Term
| where were introns found in tRNAs? |
|
Definition
| tRNA has secondary structure, anticodon is found in loop & introns were found in anticodon |
|
|
Term
| what do we call RNA that can function as a catalyst (enzyme)? |
|
Definition
|
|
Term
| what was discovered by taking a whole cell extract & adding it to a substrate to see if the extract had an enzyme that removed introns? |
|
Definition
| trans-acting factors for splicing |
|
|
Term
| how do you find an enzyme within an extract? |
|
Definition
|
|
Term
| what is the final step to see if an enzyme from a whole cell extract can perform splicing? |
|
Definition
| leave out the negative control (whole cell extract) --> add in just the enzyme & see if introns are still removed |
|
|
Term
| what catalyzes group 1 type splicing? |
|
Definition
| GTP carries out nucleophile attack on phosphodiester bond (SN2 reaction) (on 5' splicing site) |
|
|
Term
| what is the result of the first reaction in group 1 splicing? |
|
Definition
|
|
Term
| what is the result of the second reaction in group 2 splicing? |
|
Definition
|
|
Term
| what defines group 2 splicing? |
|
Definition
| A is near phosphorylation sister bond & pointed correctly to undergo cleavage reaction (covalent bond) |
|
|
Term
| does group 2 splicing rely on cis or trans acting factors? |
|
Definition
|
|
Term
| does group 1 and/or group 2 splicing require proteins or RNA to be spliced? |
|
Definition
|
|
Term
| can RNA molecules carry out chemical reactions? |
|
Definition
|
|
Term
| what does the fourth class of splicing groups require for splicing? |
|
Definition
| 50-100 proteins (trans-acting, splicing factors & 5 RNA molecules) |
|
|
Term
| which group is the most complicated for splicing: group 1, group 2, or group 4? |
|
Definition
| group 4 (looks like groups 1 & 2 but is more complicated in requirements in terms of trans-acting factors) |
|
|
Term
| what does groups 1 & 2 rely on for splicing? |
|
Definition
| tertiary structure of introns (position reactive residues near the splice sites) |
|
|
Term
| how do exons 1 & 2 stay together during splicing? |
|
Definition
| no matter how carry out pathway --> keep together from start |
|
|
Term
| yeast experiment to figure out which molecules carry out splicing reactions |
|
Definition
| take yeast & grow, spin down, resuspend in buffer & pipette into liquid nitrogen & make "dots" of yeast floating in nitrogen --> then put in mortary & pestle --> in cold & now you have yeast extract --> molecules that can carry out splicing reaction & keeps cold & then add to substrate that has intron --> ask if exons 1 & 2 will be ligated |
|
|
Term
| how did they label the RNA to know whether splicing had happened in the yeast splicing experiment? |
|
Definition
| take one mRNA with intro & add to RNAP in test tube so you can make synthetic RNA & since added only one gene --> only RNA made & then feed P32 (CTP or UTP) so every 4th nt is "hot" |
|
|
Term
| why do you want to label introns in yeast splicing experiment? |
|
Definition
| hot band on left in pre-spliced RNA & see if spliced when add to extract from yeast cell, at different times run this on gel & see if RNA is made shorter |
|
|
Term
| what was weird that they discovered about the pathway in yeast splicing experiment? |
|
Definition
| precursor went to product --> but there was intermediate before product was made that hints about pathway to product |
|
|
Term
| what is the shape of the intron intermediate? |
|
Definition
| lariat (intron product did not go from linear to degraded) |
|
|
Term
| which nucleotide is important to make sure splicing occurs correctly? |
|
Definition
|
|
Term
| why did intron intermediate products migrate more slowly on the gel? |
|
Definition
| circular RNA migrate more slowly --> because bonds with adenosine |
|
|
Term
| when running a splicing experiment how do you know when you have reached the end? |
|
Definition
| you have a product & a band for the lariat intron |
|
|
Term
| 3 things linear RNA becomes during splicing |
|
Definition
1. lariat intron
2. 3' exon
3. 5' exon |
|
|
Term
| originally, people found ______ classes of introns |
|
Definition
| 4 (does not mean there are only 4 though!) |
|
|
Term
| 2 things that work to cleave mRNA so that product can be shorter than original mRNA |
|
Definition
1. endonucleases
2. exonucleases |
|
|
Term
| does splicing happen to RNA or DNA? |
|
Definition
|
|
Term
| how do you find necessary & sufficient cis elements for splicing? |
|
Definition
| look to see what is conserved across all RNA or within a given group of RNA |
|
|
Term
| 2 things that could be trans-acting factors for splicing |
|
Definition
|
|
Term
| how do you find the cis element substrate for splicing? |
|
Definition
| set of consensus sequences arose that almost all introns have in common |
|
|
Term
|
Definition
|
|
Term
| discovery of different RNAs (besides mRNA, tRNA, or rRNA) |
|
Definition
| did a gel where anything >1000 nt would get caught in top of gel & only the small nuclear RNAs would run through the gel to search for the most abundant small nuclear RNAs |
|
|
Term
| what was discovered with the small nuclear RNA gel test? |
|
Definition
| U-rich snRNAs (sn = "small nuclear") |
|
|
Term
| what makes splicing flexible? |
|
Definition
| alternative splice site choice |
|
|
Term
| how do you learn what cis elements are necessary/sufficient for a process? |
|
Definition
|
|
Term
| bio chem or genetics: gives you more general trans-acting factors |
|
Definition
|
|
Term
| bio chem or genetics: gives you more specific trans-acting factors |
|
Definition
|
|
Term
| ______ snRNA has potential to base pair to 5' splice site in RNA |
|
Definition
|
|
Term
| how did they test if U1 snRNA is present with pre-mRNA & bound to 5' splice site? |
|
Definition
| biotinylate parts of mRNA & pull down & see if they co-purify |
|
|
Term
| how would you cross link U1 snRNA to 5' splice site in vivo? |
|
Definition
|
|
Term
| is there an antibody you can use to co-IP snRNPs? |
|
Definition
|
|
Term
| what happened when scientists weakened the interaction between splice site & U1? |
|
Definition
| U1 doesn't stick as well, U1 there less of the time |
|
|
Term
| how do you test whether it is a specific sequence or just the ability to bind that is important? |
|
Definition
1. mutate just one sequence so it is the same as the other (binding will not occur)
2. mutate the other one to be complementary to the mutation (can bind)
3. see if interaction/reaction still happens (this says that binding is important not the sequence) |
|
|
Term
| U1 leaves & is replaced by _______ |
|
Definition
|
|
Term
|
Definition
| tells cell this is 5' splice site & holds place until U6 comes (place holder or identifier --> commitment step player) |
|
|
Term
| bulge carries out nucleophilic attack on 5' splice site --> mediated by binding of ______ |
|
Definition
|
|
Term
| ______ binds to 5' splice site only after U1 leaves |
|
Definition
|
|
Term
| ______ base pairs with U2 & forms bridge |
|
Definition
|
|
Term
| 2 snRNPs that make the branch point bridge |
|
Definition
|
|
Term
| why is it important for U6 & U2 to form a bridge? |
|
Definition
| allows branch point & 5' splice site to be close to each other --> proteins bind RNAs that strengthen brdiges |
|
|
Term
| what is one way to regulate splice sites? |
|
Definition
| mutate proteins that interact to form the snRNPs |
|
|
Term
| _______ is best friends with U4 |
|
Definition
| U6 (base pairs to U4, U4 U6 bisnRNP) |
|
|
Term
| ______ is by itself & base pairs with itself --> helix |
|
Definition
|
|
Term
| nucleotides of U2 are base paired with ______ |
|
Definition
|
|
Term
| nucleotides of U6 are base paired with ______ |
|
Definition
|
|
Term
| nucleotides of the U2 helix & the U6-U4 binding are now bound together --> ? |
|
Definition
|
|
Term
| 2 things that must happen for U6 & U2 bridge to form |
|
Definition
1. 6 is peeled off 4
2. 2 is unbound from itself |
|
|
Term
| must be a ______ that unwinds RNAs |
|
Definition
|
|
Term
| once done binding introns the snRNPs go inert --> ? |
|
Definition
| 6 & 2 are pulled off each other & introns, 4 & 6 then bind back & U2 folds back |
|
|
Term
| how do proteins maintain a splicing equilibrium? |
|
Definition
| series of proteins that shift snRNPs & base pairs back & forth |
|
|
Term
| 4 cis elements of splicing |
|
Definition
1. 5' splice site
2. branch site sequence
3. (pyr)n sequence
4. 3' splice site |
|
|
Term
| 2 trans acting factors of splicing |
|
Definition
1. U1 - U6 snRNAs
2. about 100 - 300 proteins |
|
|
Term
| what were discovered to be involved in splicing because the sequence matches up with the U1 snRNA? |
|
Definition
|
|
Term
| scientists tried to fractionate the steps of splicing in vitro using _______ |
|
Definition
| whole cell extract (cultured mammalian cells or yeast) |
|
|
Term
| what was learned via in vitro splicing experiments where scientists tried to reconstitute splicing? |
|
Definition
| identification of complexes of protein & RNA necessary for steps |
|
|
Term
| how did yeast genetics help understand trans-acting splicing factors? |
|
Definition
| do a screen for mutants defective in splicing & see what was different in those colonies |
|
|
Term
| what does it mean if a yeast colony is temperature sensitive for growth? |
|
Definition
| could only grow at certain temperatures & not others |
|
|
Term
| are all prp genes essential? |
|
Definition
| yes; all conserved from yeast to humans |
|
|
Term
| what lead to the discovery that there are around 70 splicing factors in yeast? |
|
Definition
| looking for genes that were lethal in a prp- background or could suppress prp mutants |
|
|
Term
| why would humans have more splicing factors? |
|
Definition
| we have alternative splicing! we need to be able to get more complicated with our splicing |
|
|
Term
| ______ is necessary for step that takes exon---intron---exon --> 5' exon + lariat structure---3' exon |
|
Definition
|
|
Term
| how do you figure out a function of a specific splicing factor? |
|
Definition
| epitope tag your SF --> co-IP --> see which step of the RNA gets pulled down with it --> Northern blot |
|
|
Term
| how to look for RNA friends of splicing factors |
|
Definition
| epitope tag your SF --> co-IP --> see which UsnRNAs get pulled down with it |
|
|
Term
| how to look for protein friends of splicing factors |
|
Definition
| epitope tag your SF --> co-IP --> Western blot/mass spec |
|
|
Term
| how do you figure out protein "close friends" of your splicing factor? |
|
Definition
| 2 hybrid screen for proteins/splicing factors that can exhibit interaction with your splicing factor |
|
|
Term
| how do you tell if any RNAs are directly working with your splicing factor? |
|
Definition
|
|
Term
| what would you learn from mutating specific codons for specific amino acids once you have your splicing factor sequence? |
|
Definition
| see which ones are necessary for it to function |
|
|
Term
| do all UsnRNPs have the same proteins that are bound to/associated with them? |
|
Definition
| no (they each have some individual unique ones too) |
|
|
Term
| why do you find unique splicing factors the higher up the evolutionary chain you go? |
|
Definition
| splicing becomes more complicated |
|
|
Term
| 3 ways to find "friends" of splicing factors |
|
Definition
1. co-IP --> RNA-protein
2. 2 hybrid assay --> "close friends"
3. cross linking --> "close friends" |
|
|
Term
| how do you figure out the function of a splicing factor? |
|
Definition
| mutations --> assay the effects of the mutations on the various steps of splicing and/or integrity of various complexes in the process |
|
|
Term
|
Definition
| a cold-sensitive yeast mutant; name = "bad response to refrigeration" |
|
|
Term
| what comes along when you co-IP Brr2? |
|
Definition
| U4/U6 snRNA & U4/U6 snRNP proteins & pre-mRNA |
|
|
Term
|
Definition
| mutant prevents unwinding of U4 & U6 |
|
|
Term
| Brr2 mutant strains accumulate ______ |
|
Definition
|
|
Term
| 2 roles RNA can have in splicing |
|
Definition
|
|
Term
| 5 roles proteins can have in splicing |
|
Definition
1. scaffold (non-enzymatic protein)
2. chaperone (non-enzymatic protein)
3. adapter/recruiter
4. enzyme
5. do PTMs |
|
|
Term
| what role can "friends" have in splicing? |
|
Definition
| regulate protein activity |
|
|
Term
| why must splicing be precise? |
|
Definition
| if you are off by just one nucleotide, the entire reading frame will be shifted & may result in a completely different protein being made (or no protein at all!) |
|
|
Term
| what is the bonus for splicing being flexible? |
|
Definition
|
|
Term
| 2 SN2 transesterification reactions required in splicing |
|
Definition
1. "A" residue attacks phosphodiester bond between intron & first exon (makes exon + lariat---exon structures)
2. remove the lariat from the second exon (makes ligated final product + intron structure) |
|
|
Term
| what does it mean that splicing must be coupled with transcription? |
|
Definition
| not just splicing whatever becomes available to you, but it must splice at the right place at the right time (waiting for the right "A" residue) |
|
|
Term
| splicing can only happen in the ______ |
|
Definition
|
|
Term
| how do ribosomes in the cytoplasm know if an incorrect product is transported out of the nucleus? |
|
Definition
| splicing machinery gives it information to know that the mRNA must be turned over instead of translated |
|
|
Term
| why must splicing machinery be able to communicate with turnover machinery? |
|
Definition
| somehow the cell must know if a mistake has been made & to turn over that mRNA |
|
|
Term
| 4 cis elements of splicing |
|
Definition
1. 5' splice site
2. BPS
3. (pyr)n
4. 3' splice site |
|
|
Term
| 2 types of cis elements of splicing |
|
Definition
1. strong sites
2. weak sites |
|
|
Term
| the enhancer & silencer sequences may always be present --> whether they are used in splicing or not can depend on _______ |
|
Definition
| the existence of the enhancer or silencer protein to bind it |
|
|
Term
| 5' splice site & 3' splice site must come together & be lined up properly for _______ |
|
Definition
| the lariat formation to occur |
|
|
Term
| U2-U6 base pairing can't occur until _______ |
|
Definition
| U2 unwinds from itself & U6 unwinds from U4 |
|
|
Term
| what does it mean that U6-U4 base paired, U2 paired with itself vs U6-U2 are mutually exclusive isoforms |
|
Definition
| can be in one form or the other but cannot be in both at the same time |
|
|
Term
| 6 base pairs involved in U1 snRNA & 5' splice site |
|
Definition
1. C-G
2. A-U
3. G-A
4. U-U
5. C-G
6. A-U |
|
|
Term
| what does it mean that U1 is never "naked" |
|
Definition
| covered in proteins, but its bases are exposed so that it can base pair with the 5' splice site |
|
|
Term
| what is the name of the ribonucleoprotein complex that forms at the 5' splice site? |
|
Definition
|
|
Term
| what is the implication that U2 forms 7 base pairs with UACUAC sequence? |
|
Definition
| a lot of U-A base pairs --> weaker than C-G |
|
|
Term
| the way that U2 & UACUAC sequence bind, there is an _______ that gets bulged out |
|
Definition
|
|
Term
| does U2 also base pair with itself in addition to UACUAC sequence? |
|
Definition
|
|
Term
| U6 will eventually bind with ______ |
|
Definition
|
|
Term
| when U6 unwinds from U4 & part of it binds with U2, what does the other part of U6 bind to? |
|
Definition
|
|
Term
| U4-U6 complex is called a ______ |
|
Definition
|
|
Term
| U1 is kicked out of 5' splice site so that ______ can bind to it |
|
Definition
|
|
Term
| when U6 base pairs with U2, is part of U2 still base paired with the UACUAC sequence? |
|
Definition
|
|
Term
| ______ is the snRNA that will catalyze the splicing reaction at the 5' splice site! |
|
Definition
|
|
Term
| part of U2 that was originally bound to itself eventually binds to ______ |
|
Definition
|
|
Term
| part of U6 that is originally bound to U4 eventually binds to ______ |
|
Definition
| U2 and itself (parts of it bind to U2 & parts of it bind to itself) |
|
|
Term
| when U6 binds to U2, ______ gets kicked out! |
|
Definition
|
|
Term
| which snRNA makes sure the two exons find each other after the large intron in between them is cut out? |
|
Definition
|
|
Term
| what is the implication that splicing requires many helices to be pulled apart & new ones formed? |
|
Definition
| all of the energy required to do this must mean that there are enzymes involved! |
|
|
Term
| _______ proteins have to arrive at the splicing scene just at the right time or become activated just at the right time |
|
Definition
|
|
Term
| why is timing of splicing important? |
|
Definition
| there are so many trans-acting factors |
|
|
Term
| 3 proteins bind to the _______ (before the U2 snRNP gets there!) & the _______ (don't think they are binding them together though in a loop...more like a line) |
|
Definition
| branch point sequence & 3' splice site (line from UACUAC sequence to the 3' splice site) |
|
|
Term
| are the branch point sequence & 3' splice site usually close or far from each other in the cis sequence? |
|
Definition
|
|
Term
| When SF1 factor leaves, _______ replaces it & brings in the U2 snRNP |
|
Definition
|
|
Term
| 4 RNA cis elements for splicing (complex E) |
|
Definition
1. 5' splice site
2. BPS
3. (pyr)n
4. 3' splice site |
|
|
Term
| 5 ways to find trans-acting factors of splicing |
|
Definition
1. do antibodies vs any of them & then co-IP
2. cross link SF1 with BPS via UV light
3. knock down/mutate any of them --> block step one of splicing (exon---exon --> exon + lariat---exon)
4. 2 hybrid assays --> protein-protein interactions
5. look at predicted amino acid sequence of the proteins |
|
|
Term
| SF1 leaves & SF3 + U2snRNP come in to the _______ |
|
Definition
|
|
Term
| proteins make a kind of bridge with their _______ interactions |
|
Definition
|
|
Term
| does the protein interaction bridge form around the exon or the intron |
|
Definition
|
|
Term
| how does exon definition work for the exons at the end? |
|
Definition
| the 5' end exon uses the cap-binding protein for the formation of its bridge; the 3' end exon uses the poly-A binding protein for the formation of its bridge |
|
|
Term
| what experiment revealed exon definition occurs before intron definition? |
|
Definition
| mutated the 5' splice site (***) for the middle exon (exon---exon***---exon) so that it was inactive; this resulted in exon 1 ligated to exon 3! (meant that mutating exon 2's downstream splice site, it is somehow inhibiting the splice site directly to the left of exon 2...cell can only do the splicing from right of exon 1 to left of exon 3) |
|
|
Term
| 2 things that can happen to make the cell use the weak site for splicing (instead of the strong splice site) |
|
Definition
1. weakening the strong site
2. strengthening the weak site |
|
|
Term
| can a strong site have an enhancer? can a weak site have a silencer? |
|
Definition
|
|
Term
| is the conservation of silencer/enhancer sequence evolutionarily conserved? |
|
Definition
|
|
Term
| cassette alternative exon |
|
Definition
out of exon 1---exon 2---exon 3---exon 4---exon 5 cell can make:
exon1-exon2-exon3-exon4-exon5 all ligated
exon1-exon2-exon4-exon5 |
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Term
| what is the result of alternative 5' or 3' splice sites? |
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Definition
| splice out something that is normally part of an exon in 1 setting & part of the intron in the other |
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Term
| can changing which exon you start transcription with greatly affect how the splicing works? |
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Definition
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Term
| can alternative transcription initiation work with alternative splicing? |
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Definition
| yes; helps you make different proteins from one gene |
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Term
| can changing where you end transcription greatly affect how splicing works? |
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Definition
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Term
| is last exon where STOP codon is? is first exon where START codon is? |
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Definition
| not necessarily; alternative UTRs can affect how translation occurs! |
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Term
| cis elements involved in transcription |
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Definition
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Term
| trans-acting factors involved in transcription |
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Definition
| proteins that bind to the cis element DNA sequences that also bind the RNA polymerase |
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Term
| _______ must know which nucleotides should go opposite of the DNA codes |
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Definition
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Term
| how can a promoter sequence for transcription be involved in trans-acting factors? |
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Definition
| can bind a protein which binds the polymerase |
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Term
| promoter sequences were discovered via _______ |
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Definition
| deletion analysis (deletion --> no transcription of the downstream gene) |
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Term
| how were promoter sequences discovered to be sufficient for transcription? |
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Definition
| moved it to a different gene & causing that gene to be transcribed |
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Term
| what lead to the discover of enhancers for transcription? |
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Definition
| deleting cis elements further upstream from gene (compared to promoter) --> less efficient transcription |
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Term
| how far away can enhancers be from the gene for transcription? |
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Definition
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Term
| enhancer right before the promoter is called _______ |
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Definition
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Term
| how does a distal enhancer affect gene transcription? |
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Definition
| a loop in the strand can bring the distal enhancer close to the proximal enhancer --> they together bind a protein that helps recruit RNA polymerase |
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Term
| can there be loops within the loops of the enhancer looping model? |
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Definition
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Term
| what allows genes to be regulated together by same enhancers? |
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Definition
| TAD (domains of the genome that have insulators at their edges within which there may be a group of genes that share enhancers that can act on them) |
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Term
| pools of polymerase & transcription factors that come together to make one pool & turn a gene on are called ______ |
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Definition
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Term
| transcription factories come together via _______ |
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Definition
| liquid-liquid phase separation |
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Term
| can the position of a gene within a nucleus affect its transcription? |
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Definition
| yes (ex. chromosomes on the nuclear membrane might not get transcribed so genes can move back & forth depending on whether they need to be transcribed or not) |
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Term
| can cis elements also down-regulate transcription? |
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Definition
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Term
| must trans acting factors be DNA binding for transcription? |
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Definition
| not necessarily (ex. a protein can bind a protein that binds DNA) |
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Term
| 5 kinds of trans acting factor enzymes that can be involved in transcription |
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Definition
1. readers
2. writers
3. erasers
4. chromatin remodelers/markers
5. carry out post-transcriptional modifications |
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Term
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Definition
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