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49 Cards in this Set
- Front
- Back
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What is the start codon?
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it codes for the aa methionine
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what is considered part of the open reading frame?
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it means its open for translation.
the start codon, all coding codons, but NOT the stop codon |
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what are the 4 classification schemes for mutations?
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1)location
2)phenotypic behaviour 3)type of alteration in dna seq 4)creation of mutation |
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describe some of the location based scheme of classification of mutations.
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WITHIN OPEN READING FRAMES:
silent - change does not affect the amino acid missense - changes single letter that changes the amino acid nonsense - changes the amino acid to a stop codon (premature) frameshift - shifts the bases (changes the whole meaning) |
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definitions for mutation, mutagen, and carcinogen
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mutation: a permanent permissible change in DNA (usually one gene)
mutagen: a substance that increases the rate at which mutations can occur carcinogen: substance that causes cancer, (>90%=mutagens) |
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what is a transition mutation & what is a transversion mutation
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transition: a purine base is replaced by another purine or a pyrimidine base is replaced by another pyrimidine base
transversion: purine replaced by a pyrimidine or vice versa |
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what is more common, transition mutation or transversion mutation?
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transition is much more common
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what is the usual reason for transition mutations?
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tautomeric shifts.
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GC->TA, AT->CG are both transition mutations. T or F
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False, their both transversion
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what are the two base analogues?
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pyramidine - 5-bromouracil
purine - 2-aminopurine |
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CTCA --> ATCA is what type of mutation?
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transversion
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how is 5-bromouracil able to exist in tautomeric equilibrium / what does this mean?
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because the electronegative Br allows for tautomeric eq bw keto and enrol form
Keto form pairs with adenine enol form pairs with guanine TRANSITION RXN |
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WHAT CAN 2-aminopurine pair with?
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thymine or cytosine (thymine favoured)
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what is the worst chemical for DNA damage?
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water! because it can hydrolyze the n-gycosidic bond
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what are the 3 types of DNA damage?
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1) polymerase errors
-unusual due to 3'-5'exonuclease proofreading action -> but additions /deletions possible - could be due to incorrect dNTPs like dUTP or 8-oxo-dGTP 2) chemical reactions - hydrolysis (purines), deamination (dC,dA,dG) -alkylation -oxidation 3) radiation uv/xray |
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describe chemical damage to DNA (depurination)
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via water, the n-glycosyl bond bw the base(purine) and pentose undergoes hydrolysis = base removed and an AP site created
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describe chemical damage to DNA (base demamination) -> which bases can it only happen to?
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it can ONLY happen to cytosine (bc it has the free amine group.
spont loss of exocyclic amino group and converted to another group cytosine--> into uracil amine -> double bond O |
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what is an AP site?
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abasic
apurinic/apyrimidinic |
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what are the 3 types of polymerase errors?
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mispairs
incorporation of dUTP or 8-oxo-dGTP insertions/deletions |
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replacing guanine the 8-oxo-dGTP is what kind of mutation?
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transversion. bc having Oxygen at the 8th position changes the config from anti to syn, and this forces guanine to pair with Adenine
--> BUT depending on polymerase, dATP or dCTP may be inserted opposite 8-oxo-dGTP |
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describe oxidative damage:
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occurs when ROS (reactive oxygen species) are introd'd = OH*, h2o2,o2-
create mispairs |
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what does alkylation damage do?
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it induces tautomerization which changes the hydrogen bonding interface for the watson crick model
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what is the best atom for alkylation
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7th atom of guanine = most nucleophilic -> need strong nuc for alkylation (most heteratoms = good nuc)
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what happens when you alkylate the O6 of guanine?
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the entire yield of hydrogen bonds changes. = result is a mispair. you get repelling by the lone pairs on N bw g and c
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what is EMS and what does it do?
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ethyl methanesulfonate - an alkylating agent
transfers ethyl group onto O-6 of guanine causes disruption in H-bonding and causes G to bond with T instead of C = a transition mutation (can only form 2 bonds instead of 3 now) |
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what happens with bulky adducts benzo(a)pyrene?
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in attempt to solubilize it the liver oxidizes inert BaP into an epoxide in attempt to make it hydrophilic for excretion.
epoxide BaP = electrophile, then reacts with nucleophiles in DNA bases like guanine via covalent bonds BaP = mutagen and carcinogenic |
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Describe problems with UV rad.
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DNA photoproducts will occur bw adjacent pyrimidines
1)they can form cyclobutane's linking the rings together = cyclobutane dimer (adjacent T's) double bonds reactive = carbons 5 and 6 bond to each other 2)adjacent T to C = a 6,4 photoproduct (C6 of T and C4 of cytosine) |
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why do mutational hotspots often contain 5-methylcytosine
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bc it results in base deamination which gives you thymine
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an euk cells, a triphosphate cleaves deoxy-8-oxyguanisine (oxo-GTP) into oxo-GMP & PPi. what is the advantage of this?
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the advantage is now the oxo-GMP cannot be incorporated into DNA. DNA only accepts dNTPs, not dNMPs. so even tho this rxn costs 2ATP it means that the oxo-GTP won't be incorported into the DNA.
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describe the mismatch repair system for e.coli:
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have a palindromic 4 base repeat that occurs throughout the chromosome (GATC). an enzyme exists that goes thru the sequence and methylates every adenine on within this 4 repeat sequence.
be4 rep, both strands methylated. after rep, only old strand methylated and new strand completely unmethylated bc methylation system hasn't begun = DNA is hemimethylated --> at this point the mismatch repair system targets new (unmethylated) strand for mismatches |
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how often is a strand methylated? If we have a mismatch bw this distance what is the ATP cost?
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1kb (every 1000 bases) (500 bases down) = 1000ATP total
(excluding binding of MUTh/s/l) |
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what is DAM?
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DNA Adenine Methylation (after a few minutes, new strand is also methylated so the two can't be distinguished)
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describe the mismatch repair system process
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1)Mut L/S proteins bind the mismatch
2)Mut H binds this complex (ATP dependent) and scans to the nearest GATC, and cuts the strand with the nonmethylated GATC 3)after the slice, a helicase and an exonuc degrades the strand up to the mismatch 4)Repair syn by DNA pol III |
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what is MutH
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an ATP dependent translocator w/ endonuclease activity
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detailed review of mismatch DNA repair
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1) MutS/L bind to the mismatch using ATP
2) MutH recruited to the scene for dual action: a) find nerest methylated GATC b) preform its endonuclease activity on non-methylated GATC and do incision using ATP 3) |
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what are the players in dna mismatch repair?
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Mut S/L/H
helicase SSB DNAp exonuclease activity |
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what is the substrate for DNAp I & III
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I = nick
III = 3'-OH |
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what does DNA ligase do
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seal the nick
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what removes modified or dmg'd bases? describe them.
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DNA glycosylases.
ex. if a cytosine deaminated into uracil, it'll fix it - catalyze the glycosidic linkage bw the deoxyribose and the nucleobase - are very specific for the type of BASE it removes |
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what is uracil gycosylase?
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it is specific to removing the uracil moiety resulting from deamination of cytosine
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describe the base excision repair system:
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1) hydrolysis of N-glycosidic bond gives AP site (done by DNA glycosylases)
2) empty base site = substrate for AP endonuclease = cleave DNA at point near the lesion 3) DNA pol1 can catalyze repair syn and goes a few bps down (bc has low processivity) where new nick is made sealed by DNA ligase |
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what are the dif repair systems?
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-mismatch repair system (methylation/mutSLH)
-Base excision(glycosylases/APendonuc's/ligase) -nucleotide excision (DNA excinuclease) -direct repair (photolyase, |
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describe the general process of the nucleotide excision repair system
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lesions made in dna struc (like pyrimidine dimers formed by UV rad
1) DNA excinuclease recognizes distortion and cuts DNA be4 and after the lesion 2)helicase removes lesion containing fragment 3)gap repaired by DNAp1 and nick sealed by ligase |
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which of the 3 repair systems use ssb's?
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mismatch repair system
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whats different about direct repair?
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fixes problems without removing bases or nucleotides
-converts mishaps back into original form |
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describe photolyase (a type of direct repair)
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uses light to fixed what caused pyrimidine dimers to form
- use chromophores (molecs that can absorb light) MTHFpolyGlu absorbs light and is energetically excited. it passes e- to e- carrior (FADH-) to created excited electron carrier excited electron carrier dumped onto pyrimidine dimer which breaks them up into monomeric pyrimidines |
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how much ATP does photolyase use? where do e'- from photolysae end up/
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none, its energetically favourable
back on cofactors (e- carriers) |
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describe the direct repair system when the O-6 of guanine is methylated.
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O6-methylguanine-DNA methyl transferase
aids in transferring the O6 methyl of G onto a cys residue on this enzyme = protein becomes inactivated |
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what type of enzyme is O6-methylguanine DNA methyltransferase?
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a suicide enzyme! after taking the methyl group it is inactivated and has no more use. in inactive form it serves as a tc factor.
very costly rxn |
