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48 Cards in this Set
- Front
- Back
protein recognizes mismatch, induces a kink in the DNA, and binds ATP
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MutS
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MutS recruite
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MutL and MutH
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MutL activates...
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MutH
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In mismatch repair in E. coli, which Mut protein nicks DNA?
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MutH
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The E. coli enzyme _________ methylates A residues on both strands of the sequence 5'-GATC-3'.
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Dam Methylase
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The ______________ binds the MutH nick and traveles down the DNA until it reaches _____________.
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Exonuclease, MutS
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Exonuclease that travels in the 5' to 3' direction, degrading DNA towards MutS
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Exo VII or RecJ
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Exonuclease that travels in the 3' to 5' direction, degrading DNA towards MutS
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Exo I
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Eukaryotic cells lack a ____________ homolog
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MutH
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Then how do the mismatch repair enzymes recognize the newly synthesized strand of DNA in eukaryotic cells?
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Nicks present in unligated Okazaki fragments may play this role following lagging strand DNA synthesis.
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Common types of hydrolytic DNA damage.
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(a) Deamination of cytosine creates uracil.
(b) Depurination of guanine by hydrolysis creates apurinic deoxyribose. (c) Deamination of 5-methylcytosine generates a natural base in DNA, thymine. |
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Which type of damage is worst?
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Deamination of 5-mC. Can not tell that thymine was once 5-mC because thymine is normally present in cells.
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Why didn’t DNA evolve to use U?
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Because high frequency deamination occurs in cytosine to uracil. If uracil was naturally present in DNA, you can not tell if a cytosine was deaminated to uracil or if the uracil is naturally present.
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Deamination of cytosine to uracil and deamination of 5-mc to thymine is an example of _______________ mutations.
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TRANSITION
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Describe the Ames test
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Used to detect mutagens.
A base substitution or frameshift mutation is introduced in a gene used to make the amino acid histidine of a bacteria culture. Plated on plates with suspected mutagen. if cells grow then the mutagen induced a revertant mutation that rescues the cell. Reverses the initial base sub or frameshift mutation. THE MUTAGEN INDUCES MUTATIONS THAT RESTORECELL GROWTH. |
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In __________, methyl or ethyl groups are transferred to reactive sites on the bases and to phosphates in the DNA backbone
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alkylation
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One of the most vulnerable sites of alkylation is the keto group at carbon atom 6 of guanine (Fig. 10-8). The product of this methylation, O6-methylguanine, often mispairs with thymine, resulting in the change of a G:C base pair into an A:T base pair when the damaged DNA is replicated. This is an example of a _________________ mutation.
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Transversion
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UV light causes adjacent _____________ to covalently bond.
This blocks progression of DNA polymerase. |
pyrimidines
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Intercalating agents insert between bases and cause ______________ and ______________ in DNA.
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insertions, deletions
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base analog on thymidine
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5-Bromouracil
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5-Bromouracile base pairs with _________________ and causes a ___________________ mutation
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guanine, transition
normal T-->A mutated 5-bru--->G transition bc A and G are both purines |
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Enzyme used in the direct DNA repair: Photoreactivation
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DNA photolyase
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Enzyme used in direct DNA repair: methyl group removal
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methyl transferase
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A ________ on the methyltransferase binds the methyl
group on ___________. Once the methyl group is transferred to the enzyme, the enzyme is _______________. |
cysteine, guanine, degraded
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How does uracil usually get in DNA?
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deamination of cytosine into uracil (hydrolytic damage)
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Enzyme used in DNA base excision repair
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DNA glycosylase
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What type of site is present after glycosylase action?
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an AP site. (abasic site)
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AP __________ cuts the DNA backbone at the 5' position of the AP site, leaving a 3' OH.
AP _____________ cuts at the 3' position of the AP site, leaving a 5' -phosphate. The resulting gap is filled in by ______________. |
endonuclease, exonuclease, DNA Pol I.
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It’s not always too late to repair DNA after replication.
A ___________recognizes oxo-G:A and removes the ___. It is then replaced with C. |
glycosylase, A,C
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Another glycosylase recognizes G:T basepairs and
removes the __ which likely arose from spontaneous deamination of __________________. |
T, 5-methylcytosine.
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Nucleotide excision repair recognizes
__________ in the _____________. |
distortions, double helix
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Nucleotide excision repair in E. coli:
UvrA+UvrB scan DNA. _____ recognizes distortion and leaves. _____ melts DNA to form single-stranded bubble |
UvrA, UvrB
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____ is recruited and cuts DNA __ nucleotides
5’ of the legion and ___ nucleotides 3’ of the legion. |
UvrC, 8, 4-5
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Helicase ____ removes the single strand.
__________________ and _____________ fill the gap. |
UvrD, DNA polymerase I, DNA ligase
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Nucleotide excision repair in humans:
____ recognizes distortions (like UvrA in E. coli). ____ and ____ helicases melt DNA (like UvrB in E. coli). Single stranded binding protein ___ binds DNA. |
XPC
XPA AND XPD RPA |
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5’-cleavage site cut by _________ nuclease and 3’-cleavage site cut by _____ nuclease (similar to UvrC in E. coli)
____ nucleotide long DNA strand is released that is filled in by a _______________ and sealed by DNA ____________. |
ERCC1-XPF, XPG
24-32, polymerase, ligase |
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Xeroderma pigmentosum disease caused by mutations in ________ genes. Patients are susceptiple to cancer from UV light.
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XP_ (NER) genes.
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The significance of transcription-coupled repair is that it _________ repair enzymes on DNA (genes) being actively transcribed. In effect, RNA polymerase serves as another damage-sensing protein in the cell.
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focuses/localizes
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The TFIIH complex needed for melting DNA for transcription contains ____ and
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XPA AND XPD.
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_______ pathway to repair double stranded
DNA breaks. |
NHEJ (Mammalian non-homologous end joining)
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________ heterodimer binds ends of DNA and recruits ______________.
Artemis, an ____________, is phosphorylated by ________ and processes the DNA ends. _____________ attaches the 2 ends together. |
Ku70/Ku80, DNA-PKcs
exo/endonuclease, DNA-PKcs Ligase IV complex |
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Translesion synthesis in E. coli:
used to replicate through ____________. |
DNA lesions (like thymidine dimer or apurinic site)
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Translesion polymerases: 1 and 2
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Polymerase IV and Polymerase V
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Which translesion polymerase contains UmuC?
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Polymerase V
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What happens after the translesion polymerase after it replicates through DNA lesions?
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Translesion polymerase falls off and DNA
Pol III holocomplex resumes replication. |
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UmuC is part of the ___ family of DNA POLYMERASES.
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Y
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Difference between Y family polymerase and normal polymerase?
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The active site in the Y family is less constrained/more open than the normal. Also, the Y family has an absence of the protein region that closes the channel
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Adding _____________ to the ____________ at lesion recruits translesion polymerase.
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ubiquitin peptide, sliding clamp
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