Lecture 6- Dna Repair

Front 1

protein recognizes mismatch, induces a kink in the DNA, and binds ATP
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Back 1

MutS

Front 2

MutS recruite

Back 2

MutL and MutH

Front 3

MutL activates...

Back 3

MutH

Front 4

In mismatch repair in E. coli, which Mut protein nicks DNA?

Back 4

MutH

Front 5

The E. coli enzyme _________ methylates A residues on both strands of the sequence 5'-GATC-3'.

Back 5

Dam Methylase

Front 6

The ______________ binds the MutH nick and traveles down the DNA until it reaches _____________.

Back 6

Exonuclease, MutS

Front 7

Exonuclease that travels in the 5' to 3' direction, degrading DNA towards MutS

Back 7

Exo VII or RecJ

Front 8

Exonuclease that travels in the 3' to 5' direction, degrading DNA towards MutS

Back 8

Exo I

Front 9

Eukaryotic cells lack a ____________ homolog

Back 9

MutH

Front 10

Then how do the mismatch repair enzymes recognize the newly synthesized strand of DNA in eukaryotic cells?

Back 10

Nicks present in unligated Okazaki fragments may play this role following lagging strand DNA synthesis.
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Front 11

Common types of hydrolytic DNA damage.

Back 11

(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.

Front 12

Which type of damage is worst?
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Back 12

Deamination of 5-mC. Can not tell that thymine was once 5-mC because thymine is normally present in cells.
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Front 13

Why didn’t DNA evolve to use U?
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Back 13

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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Front 14

Deamination of cytosine to uracil and deamination of 5-mc to thymine is an example of _______________ mutations.

Back 14

TRANSITION

Front 15

Describe the Ames test

Back 15

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.

Front 16

In __________, methyl or ethyl groups are transferred to reactive sites on the bases and to phosphates in the DNA backbone

Back 16

alkylation

Front 17

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.

Back 17

Transversion

Front 18

UV light causes adjacent _____________ to covalently bond.
This blocks progression of DNA polymerase.

Back 18

pyrimidines

Front 19

Intercalating agents insert between bases and cause ______________ and ______________ in DNA.

Back 19

insertions, deletions

Front 20

base analog on thymidine

Back 20

5-Bromouracil

Front 21

5-Bromouracile base pairs with _________________ and causes a ___________________ mutation

Back 21

guanine, transition


normal T-->A
mutated 5-bru--->G

transition bc A and G are both purines

Front 22

Enzyme used in the direct DNA repair: Photoreactivation

Back 22

DNA photolyase

Front 23

Enzyme used in direct DNA repair: methyl group removal

Back 23

methyl transferase

Front 24

A ________ on the methyltransferase binds the methyl
group on ___________. Once the methyl group is transferred to the enzyme, the enzyme is _______________.

Back 24

cysteine, guanine, degraded

Front 25

How does uracil usually get in DNA?
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Back 25

deamination of cytosine into uracil (hydrolytic damage)

Front 26

Enzyme used in DNA base excision repair

Back 26

DNA glycosylase

Front 27

What type of site is present after glycosylase action?
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Back 27

an AP site. (abasic site)

Front 28

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 ______________.

Back 28

endonuclease, exonuclease, DNA Pol I.

Front 29

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.

Back 29

glycosylase, A,C

Front 30

Another glycosylase recognizes G:T basepairs and
removes the __ which likely arose from spontaneous
deamination of __________________.

Back 30

T, 5-methylcytosine.

Front 31

Nucleotide excision repair recognizes
__________ in the _____________.

Back 31

distortions, double helix

Front 32

Nucleotide excision repair in E. coli:

UvrA+UvrB scan DNA.
_____ recognizes distortion and leaves.
_____ melts DNA to form single-stranded bubble

Back 32

UvrA, UvrB

Front 33

____ is recruited and cuts DNA __ nucleotides
5’ of the legion and ___ nucleotides 3’ of
the legion.

Back 33

UvrC, 8, 4-5

Front 34

Helicase ____ removes the single strand.
__________________ and _____________ fill the gap.

Back 34

UvrD, DNA polymerase I, DNA ligase

Front 35

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.

Back 35

XPC
XPA AND XPD
RPA

Front 36

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 ____________.

Back 36

ERCC1-XPF, XPG


24-32, polymerase, ligase

Front 37

Xeroderma pigmentosum disease caused by mutations in ________ genes. Patients are susceptiple to cancer from UV light.
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Back 37

XP_ (NER) genes.

Front 38

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.

Back 38

focuses/localizes

Front 39

The TFIIH complex needed for melting DNA for transcription contains ____ and
____. �

Back 39

XPA AND XPD.

Front 40

_______ pathway to repair double stranded
DNA breaks.

Back 40

NHEJ (Mammalian non-homologous end joining)

Front 41

________ heterodimer binds ends of DNA and recruits ______________.

Artemis, an ____________, is phosphorylated by ________ and processes the DNA ends.

_____________ attaches the 2 ends together.

Back 41

Ku70/Ku80, DNA-PKcs

exo/endonuclease, DNA-PKcs

Ligase IV complex

Front 42

Translesion synthesis in E. coli:

used to replicate through ____________.

Back 42

DNA lesions (like thymidine dimer or apurinic site)

Front 43

Translesion polymerases: 1 and 2

Back 43

Polymerase IV and Polymerase V

Front 44

Which translesion polymerase contains UmuC?

Back 44

Polymerase V

Front 45

What happens after the translesion polymerase after it replicates through DNA lesions?

Back 45

Translesion polymerase falls off and DNA
Pol III holocomplex resumes replication.

Front 46

UmuC is part of the ___ family of DNA POLYMERASES.

Back 46

Y

Front 47

Difference between Y family polymerase and normal polymerase?

Back 47

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

Front 48

Adding _____________ to the ____________ at lesion recruits translesion polymerase.
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Back 48

ubiquitin peptide, sliding clamp