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161 Cards in this Set
- Front
- Back
how may carbons are in nucleotides? why?
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5 carbon pentose.
b/c 6 carbon is metabolized. |
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what are the 3 parts of the nucleotide?
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sugar 5C
phosphate group, forms P bond Nitrogen containing Base |
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diff b/w purine & pyrimidine?
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A & G purine (hetracycles)
T & C pyrimidines purines larger w 3 H bonds pyrimidines w 2 H bonds |
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in dna molecule adenine and thymine bases appeared in equal number, & CG too, who discovered this?
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Chargaff.
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how is the double helix oriented?
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antiparallel.
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how many bases per sweep of major groove?
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about 10 bases per sweep - top of the major groove
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distance b/w adjacent bases is how many angstroms?
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about 3.4 angstoms b/w bases. 34 angstroms from the top of the major groove to the bottom of the major groove.. that means 10 bases per sweep of major groove
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what is the function of DNA?
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replication
protein synthesis & regulation |
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what kind of replication goes down?
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semi-conservative
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___ Angrums is the radius of the DNA
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10 angstroms.
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proposals for dna relication?
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dna molecule dissasembled by breaking backbone. Dispersive model. NOT TRUE.
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what did Griffith, Hershey & chase, Roselyn Fraklyn, Chargaff, Messelsyn & stahl, and watson & crick.
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M & S did semi-conservative repro.
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light nitrogen given during to replication in order for what?
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M&S : to prove semi-conservative - heavy nitrogen & light dna nitrogen, not dispersive but semi-conservative. half & half
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what 4 things are unique about prokaryotes?
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1. singular circular DNA molecule
2. specific DNA structure 3. Naked 4. associated plasmids |
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blue green algae (archeabacteria) and bacteria are what?
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prokaryotes
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eukaryotes 3 things unique
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1. more dna (46 chromosomes in humans) it's linear
2. milticellular 3. true organelles 4. nucleus |
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single circular molecule with associated proteins is all together called?
whats in place of nucleus? |
chromosome for prokaryotes. no nucleus.
tethering protein instead, the region is called the nucleoid (b/c no nucleus). |
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free associates are circular, small & outside the nucleoid. separate but can become associated, these are called what?
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plasmids
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Yes / No
can plasmids be used between different prokaryotic individuals? |
YES
can be very useful |
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b/c few assoicated proteins w/ DNA prokarotic chromosome called ...?
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naked
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what is polytene? where are they found?
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found in saliva.
Failure in spindle apparatus pulling dna apart, every time gets wider with each reproduction… b/c wider, you can see it under light magnification |
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where does replication begin for prokaryotes?
what is used - proteins? |
at the at AT rich origin
. they're recognized by dna-a, which recruit helicases & dna-b's, which melt at origin. making 2 forks. replisomes attach at forks & mediated via dna polymerase 3 & ssbp & clamps and other associated proteins help |
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about __ different proteins that make up the replisome of prok. __ for euk. why so many more
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13
30 1. many are part of unwinding of dna off of nucleosomes. 2. Also role in nucleosome formation |
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how do euk make up the slower speed of replication?
1000 base pairs/sec prok 50-100 base paris/sec euk |
they begin replicating at multiple replicating forks. maybe over 1000 origins per chromosome. over 2000 replicating forks... this still takes hours.
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difference of origin b/w prok and euk. both are AT rich, on euk, they're called ____ sites.
annonymous with ____ on prok |
ORC (eukaryotes)
stands for origin recognizing complex proteins. same as dna-a with prok's. |
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after orc, comes ___ protein. this coats the now unwound dna strand.
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ncm proteins
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ncm does what?
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this preps the site for replication by the replisome and enzymatic proteins
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when do you want ncm to work?
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when you want to replicate.
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geminin?
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this protects the newly synthesized strand against re-replication & replisome & enzymatic proteins
inactivates ncm protein. |
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what are the polymerases in proks?
what are polymerases in euks? |
poly 1 & poly 3
poly alpha & poly delta poly gamma (mitochondria) & poly epsilon |
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what does CAF-1 do?
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it is an accessory protein responsible for the remodeling of the histone proteins
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the nucleosome is an _____.
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octomer, consisting of 2 h2a's 2h2b's h3's & ... .
all individual proteins. |
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CAF -1 fxn mainly consists of working with what proteins?
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the nucleosome which is an octomer. it models the octomer and the dna will then wrap around this.
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what is the CLAMP on a eukaryote?
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PCNA is another accessory protein. it's used by polymerizing enzmye making it processive. (proliferating cell nuclear antigen)
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open replicating fork and first on the scene is ___ with euks.
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polymerase alpha
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what's polymerase alpha do?
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it can synthesize 2 diff rxns.
dna strand synthesizing rna strand synthesizing it synthesizes rna primer for replication. |
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the primer with euk's are uinque b/c
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have an rna tag attached to dna section. it's a chimera (part rna, part dna, this is synthesized by polymerase alpha).
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what is the same as primase, but for euks?
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dna polymerase alpha
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distributive
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not clamped
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most dna polymerases are also exonucleases, what does that mean?
is poly alpha an exonuclease? |
it means that it can proof read itself.
no (although poly 1 & 3 are) |
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after primer added w euks, via poly 1, what comes in ...
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pcna. b/c this works as the clamp.
pcna recruits & poly alpha gets kicked off by poly delta and poly delta synthesizing from 5' --> 3' |
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is poly delta an exonucelase?
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yes. it clips out primer, adds appropriate bases where primer set.
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processive
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means clamped. once bases added, it goes until termination signal.
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what are part of the replisome?
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just a few of the 27 proteins, mcm's caf1, pcna's, polymerases, helicases, etc
all pat of replisome. |
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what do MCM's do?
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they are proteins that either activate or inhibit the creation of attachment for replication.
inhibit via protein Geminin. |
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when replicating end of euk, you don't need a primer, you have leading strand. only needed at origin. on lagging strand add primer, go backwards replicating fork opens and go back. problem?
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poly delta fills the pimer gaps, but there's no poly delta addition after the last primer.
these nucleotides therefore are not replicated. |
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telomere
who makes telomeres? |
non-code-ing, highly repetetive, at the end of chromosomes. okay if chopped off every time.
only germ cells can make telomeres |
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how do germ cells add telomeres?
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they are a reverse transcriptase
they have telomerase |
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somatic cells that can't regenerate telomerase, cells therefore have life spans before genetic material is lost. true/false?
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true.
a type of cell programmed death |
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what's the difference b/w rna and dna?
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ribose vs. deoxyribose. C #2 has a hydroxyl group where dna only has H. U replaces T. rna act as ribozymes.
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transcription involves what 3 steps?
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initiation
elongation termination |
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what sites are significant for the promotor in prokaryotes?
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-35 region and -10 region (-10 called pribnow box)
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what protein (peptide) attaches loosely to -35 region?
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the Signma
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what binds to the pribnow box?
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rna polymerase w 2 peptides, the 2a,2b & 2b'.
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what are the 5 types of rna?
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mRNA, tRNA, rRNA, snRNA (euk only) does processing, HnRNA becomes mRNA
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what's the sigma protein do?
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the sigma binds to the pribnow box and melts the dna, unwinding it.
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operons
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s.t coding region is going to be a gene, sometimes multiple genes. (true of proK's) operon is coding sequence that makes mRNA that'll be translated into multiple peptides.
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how many untwisting parts occur per polymerase. why this many?
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the polymerase unwinds about 2 twists or 20 base pairs. no ssb's so we don't want to expose all the nucleotides.
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when does sigma leave
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after 10 - 20 base pairs are paired after polymerase
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what makes up an rna polymerase?
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4 proteins: 2 aplha's, beta and beta prime.
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at start of transcrition, polymerase core attaches another peptide called what?
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sigma peptide
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when sigma attaches to polymerase core, it forms
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functional enzyme that first attaches to 35 region loosely. now sigma attaches to pribnow box and opens dna strand.
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if polymerase core wants to go, but no sigma availible?
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will not melt, can attach, but not melt without sigma.
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no ssbs? so what does replication do?
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only exposes ~20 bases at a time.
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what is the name of the -35 and -10 regions
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consensus sequences. these are the binding sites for the polymerases.
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how do you get different regions transcribed?
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all cores are the same, but not all sigmas are not equal. the sigma factor attached to polymerase decides which is transcribed
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in transcription, name the region that is the first translated part of the strand.
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the 5' end. it takes about 10 bases before the first translation occurs, this is called the 5' UTR (un-translated region)
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do rna polymerases have exonuclease activity
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no rna polymerases do not have proof reading exonuclease activity
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in what state are the nucleotides coming in?
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coming in as triphosphates to help form phosphodiester bonds
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what causes speed to be checked during transcription?
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AT rich regions slow down the polymerase to help stabilize.
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how fast can rna polymerases work?
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30-50 bases/second
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there are 2 strands, sense and nonsense. what region is read?
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the sense region is read. the nonsence strand is a template only.
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what are the 2 possible mechanisms for termination?
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RHO independent and dependent
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at the end of the rho independent what is found?
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40 base pairs that are AT rich followed by AAAA's . it would go slow here making UUUU's.
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what helps pinch off the end at termination?
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a hairpin loop caused by CG's. a hairpin loop is formed and when polymerase looks back it's kicked off. although cant proof read, it can survey.
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what finally kicks the polymerase?
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it becomes distributive and when surveying the look kicks it off.
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rho independent AKA
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intrinsic mechanism
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rho independent region terminates how?
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the CG base pairs form a loop and polyerase drops after stalling
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the rho dependent region terminates how?
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40 to 50 GGG's make CCC's and afterwards comes a region: "rut site". this "rut site" binds RHO. conformational change causes the popping off of the polymerase
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RHO binds to What?
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RUT. by acting rho to rut (rut is on rna strand) it pulls polymerase off
rho is an independent protein |
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what're rna poly's in eukaryotes? jobs of each?
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poly I - makes rRNA (ss)
poly II - hmRNA (pre mRNA's), sometimes makes snRNA (rhomozymes) poly III - tRNA, 5s rRNA, snRNA's |
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what allows for fast, slow or medium rate of transcription in euK's?
these are analogus to what in the prok? |
the GTF's (general transcrition factors). there's GTF II, IIa, IIb, etc. these are ACCESSORY PROTEINS, or similar b/c they're like prok's sigma
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an _______ increases the binding affinity for polymerase, speeds it up
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enhancer
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what part do we need to cut out of a gene
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cut out introns, need to use exxons.
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what's the general regulation of proK's
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operon control. on or off.
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what's general regulation of euK's
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on/off high rate/slow rate ... this is seen b/c of the GTF's (Transcription Factors)
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GTF's play a role in removing DNA from protein so it can be transcribed. T/F
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True. helps get off of histones some TF's help find right start code
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in proK's what helps find pribnow box?
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sigma.
series of GTF's do a similar fxn in euK's |
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what's a major difference b/w proK & euK & transcription
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location. translation in nucleus. transcription outside nucleus. separated by Time & Space
- in proK's happen simultaneously |
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at ~ - 30 is a consensus sequence called ____. this site is significant for what?
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TATA
this is promotor region of the gene. polymerase attaches here |
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for TATA to work. we take a TF (transcription factor) called ____ and this protein binds to TATA box.
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TF is called the 2 TF II D.
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After TF II D bound. what happens?
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other TGF's called to promotor. IIA, IIF ... others come in and act as enhancers (better binding for polymerase) NOW CALLED PRE INitiation COMPLEX
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what's included in pre initiation complex?
function? |
the sense strand of dna. GTF's IIA & IID, other regulatory proteins. this calls polymerase to site
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After pre complex ready, what happens?
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polymerase attaches and elongation occurs. in the 5' to 3' direction
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is rna polymerase an exonuclease?
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no. not even in euK's
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the initiation coplex is there, and starts what are the options now?
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to be re-copied, or to be disposed of. depends on what signals it receives.
signaling usually to phosphorylate or dephosphorylate via kinases. |
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what happens if signalling is messed up?
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cancer maybe
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what's the role & name of the polymerase tail?
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the tail is called the CDT (carboxyl tail domain) tail
helps to break from initiation complex and helps to break away at termination |
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if signal required dephosphorylation then not a kinase, but a ....
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phosphatase
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post transcriptional processsing, what happens?
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introns removed. after transcription. before termination however.
happens during elongation |
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post transcriptional processing requires a ______. this is put in the wrong orientation, why?
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the 5' CAP is a 7 methyl guanosine. ints in incorrect orientation. reason is to protect from degredation and to find the right orientation on ribosome
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what are enzymes that help attach/splice the exons?
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splice-o-zymes
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what's the major difference in transcription b/w prok's & euk's?
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the structure, ie. histones.
also, multiple polymerases in eukaryotes (we study poly 2 mostly) also, transcript must be processed |
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where's the initiaion in prok's vs. euks?
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think about it, look it up
what one is -30 tata box? the tata box binds proteins to TBP & is part of the TF II D |
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what is TF II D?
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it's a general transcription factor. these proteins locate, assist with binding, recuriting and regulating transcrition. some bind, some melt, some recruit others regulate
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other promotor sites besides TaTa box?
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yes, try the CaaT box. this one is big on regulation.
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what's the fxn of the pre-initiation complex?
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for recruitment of poly & opens dna (uses sense strand) from 3' to 5'. poly goes, complex stays
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what's with the poly's tail?
CTD is name of tail. means what? |
this is 5-7 AA's long & can be phosphorylated or dephosphorlated. this action allows attachment of poly. called CTD or carboxyl tail domain
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what causes the termination of euk?
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a terminator sequence. AAUAAA or AUUAAA. it ends ~ 20 bases furhter down stream. the 5' end is given CAP, a modified guanosine
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how does splicing occur? where does it cut exactly?
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from a splice-o-zome.
cuts at the GU and AG. includes the GU and AG |
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What's trans splicing?
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the exon is spliced out and tagged onto the 5' end of a new strand. when transcribed a whole new protein is made
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what was discovered with splicing and the human genome project?
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thought some 100 k genes, but discovered only ~30K. b/c trans splicing.
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why 1.7 million bases, 1.7 megabases long but widdled to only 10K?
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b/c they believe lots of transposons left around.
some are thought to be evolutionary past, grandmas closet. |
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when reacing termination sequence like _ _ _ _ _ _ go 20 and cut. the following AAA's are considered what/why?
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are the poly A tail. they are registers for the # of times used and tells cell machinery how many times this has been used.
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that are the 4 phases of a polypeptide chain?
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1' (straight)
2' (beta sheet, alpha helix) 3' (folded & often fxnal) 4' (multiple 3's, ie. hemoglobin) |
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when is a gene considered "on"?
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when the info is made into a FUNCTIONAL protein
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are "-ogens" on?
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no, not until a part is clipped off
ie. pepsinogen --> pepsin pepsin would be an active protease |
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where does AA bind on the tRNA?
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on the 3' end
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what enzyme holds the AA on the tRNA?
how many enzymes are there? |
aminoacetyl-t-RNA-synthase
like 20 of these. look @ proline, think proline-aminoacetyl-trna-synthase |
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what 's with the 3 loops on tRNA?
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the 2 sides play regulatory and placement roles
the 3rd middle one has the anti-codon that's read 3' to 5' |
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what's with the subunits of ribosomes of euk's vs prok's?
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2 subunits. ProK have 50 s & 30 s to make 70 s ribosome.
euK's made up of 60 s & 40 s to make 80 S ribosome. S - svedburg units (centrifuge) |
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what's with the "rosetta stone" of coding AA's?
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its degenerate.
the 3rd base is the wobble base so it's a wobble code. |
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what're the stop codons?
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UAA & UAG
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what're the stop codons?
codes for what? |
UAG is the major one.
codes for MET. when at beginning, called the N-Formyl MET (i). met often cut out when folded |
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what's significant about the 5' UTR?
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this is the "un-translated region"
5-10 bases up from this is location of the Shine delgarno region. |
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what's shine delgarno do?
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pairs w/ initation complex, so initation codon put in correct location relative to complex forming. on the P site.
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where/how does shine delgarno attach?
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5-10 bases up from utr. it attaches in the 30s subunit plasing P site just right.
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what do IF factors 1,2 & 3 do?
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1 & 2 do alignment
3 plays a role in keeping 30 S and 50S apart |
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First real step w/ translation is what?
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the IF3, IF1 & 30S unit all come together binding to mRNA by the shine delgardo region.
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who comes first with initation, trna w AA, or the large subunit?
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the initaiton, AUG, with IF 2 help in alignment.
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how fast does the average molecule move?
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3200 ft/sec
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what are the 3 sites on the ribosome?
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the E (exit)
P (peptidyl) & A (amino) sites |
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T/F
the sine delgarno was attached to 30S unit so it would align with P |
T
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what direction is peptide synthesized
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in the 5' to 3' direction
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what's the name for the shift in the RNA when reading an mRNA?
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translocation
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what's the name of the enzyme that helps with translocation?
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peptidyl transferase
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where does the 30 S subunit initially bind with prok's?
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10 bases upstream in the shine delgarno region. this region is in the 5' UTR.
the 16 S ribosomal unit has compliment bases to shin delgarno region |
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what else bids during prok initiation of translation? what do they do?
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you have IF3 & IF1 binding here too. they basically work to ensure alignment. they make sure that 30S fits just right so E & I sites are aligned.
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what site is availible after the 50 S sits down?
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the P site is open, the E & A are covered.
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anything unique about the first tRNA?
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yes. the first tRNA is i tRNA. It carries the AA : met.
it binds to AUG. |
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IF 2 is helpful relative to the initation complex because why?
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b/c the IF2 is a gtp-ase. there is energy required to recruit the 50S subunit.
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how doe's IF 1 and others get kicked off?
what's the last IF factor kicked? |
when initiation complex attached at P site the anticodon - codon makes a conformational change on the 30S ribosome. happens before 50S binds.
last kicked is IF2 (b'c it's a gtpase) |
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elongation. what's a charged tRNA?
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one that has an AA on the 3' end.
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what protein helps with the binding of the complimentary anti-codon?
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EF-TU
this EF-TU is also a GTP-ase. |
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what 2 rxn's must occur after the tRNA bring in the 2nd AA?
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first hydrolysis and then formation of Peptide bond (met w/ 2nd AA)
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what enzymes help prok's with this rxn?
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ribozyme and peptidyltransferase.
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to put it into steps. with elongation what is step 1?
(is a gtp-ase that helps match up the anticodon) |
the EF-TU protein
it's |
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what is located in the 23S region of 50S?
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the peptidyl transferase
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what would step 2 be?
(related to last question) |
the formation of a peptide bond
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step 3
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translocation. everything shifted 1 reading frame.
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what protein aids in reading frame shifting?
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elongation factor G
EFG (an associated protein) |
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step 4
(final step) |
termination.
occurs when termination codon falls in the A site. |
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w/ termination, we don't bind the tRNA anticodon, instead we bind what?
|
we bind 1 of 2 releasing factors.
either RF1 or RF2 |
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RF 1 is called in with ____ or ____
RF 2 is called in with ____ |
RF 1 with UAA or UAG
RF 2 with UGA |
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so, what exactly happens when an RF factor binds?
|
hydrolysis of ester bond. breaks las AA from tRNA.
1. RF binds A site. 2. bond breaks, untethers peptide. 3. exits via E site (tunnel) |
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who get s the RF off?
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RF1 & RF 2 released from RF 3
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polysomes
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multiple ribosomes re transcribing at the same time. they are at least 100 bp's apart.
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polycistronic
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systron is a more specific name for a gene. you can have 3 cistrons lined up with 1 promotor
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when would you want to make a polycistronic line-up?
|
usually with metabolism, or some kind of pathway
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true/false
operons are polycistronic. |
true. 1 promotor
ie. lac operon or trp operon again operons only in prok's |
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what's the poly A tail have to do with any function?
|
just basically tells how many times a transcript has been read.
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