Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MBIOS 503 Advanced Molecular Biology I > Unit 5 redone b/c last one is too long > Flashcards

Unit 5 redone b/c last one is too long Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

An example of direct repair would be?

A

Photolyase/photoreaction

Uv damage creates a cyclobutane pyrimidine dimer and this is removed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

In most basic terms, what is excision repair?

A

when a damaged region is removed and synthesis of complementary strand replaces damage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Mismatch repair occurs after? And preferentially corrects what?

A

immediately following replication and it can recognize a mismatch in base pairs, deletion/ insertion loops

preferentially corrects newly synthesized strand/daughter strand (biased toward restoration of wild type)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how can mismatch repair recognize parent strand from daughter strand?

A

1) methylation state- daughter strand is usually not methylated and parent strand is methylated (hemimethylated state)
2) G-T mismatch from deamination of methylated cytocine preferentially removes T and replaces with C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the two forms of excision base repair? How do they differ?

A

1) Base Excision - removes a base (deamination/alkylation/uracyl glycosylase)
- short patch (removes 1 base)
- long patch (removes 2-10 bases around damaged site)

2) Nucleotide excision repair (NER) - removes bulky lesions (uv damage = photoreactivation in E.coli but NER in mammals)
- GG-NER
- TC-NER

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the two types of damaged recognize by repair systems?

A

1) Single base change - this type of change affects the sequence only but does not change helix structure not does it affect transcription or replication. It will affect future generations
2) Errors in replication - A instead of C (AG) creates a distortion in the helix (example: methylated bases or depurination)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What kind of errors can distort the helix and affect replication and transcription? How are they repaired?

A

1) methyl group added to base - repaired by dealkylation

2) Depurination - removes purine -repaired by insertion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

In recombination repair what is replaced and how?

A

replaces double stranded regions and gets the undamaged strand via recombination

also corrects DSB of homologous strands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the steps of excision repair in E.coli?

A

1) incision by an endonuclease (12bp on either side)
2) Excision by 5’-3’ exonuclease or a helicase will displace damage strand
3) Synthesis via a polymerase
4) ligase seals the nicks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the steps of the Uvr excision system in bacteria? What patch does this system prefer?

A

1) Uvr AB dimer recognizes bulky lesion
2) Uvr A dissociates from UvrB
3) UvrC joins UvrB to form a dimer
4) UvrCB dimer makes incision on either side of damage
5) Uvr D helicase displaces damaged strand
6) Polymerase I excises damaged strand
* Pol I can also synthesize or Pol II or III
* prefers short patch repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What happens if there is stalled transcription in e.coli? how is Uvr implemented?

A

MFD will recruit Uvr when there is stalled transcription

-transcribed strands are preferentially repaired

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is XP? Xeroderma pigmentosum

A

Xeroderma pigmentosum, mutations in nucleotide excision repair (NER) genes. Patients w/XP cannot excise pyrimidine dimers and this causes skin disorder and susceptibility to cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

In eukaryotes what are the two NER systems?

A

1 GG-NER

2 TC-NER

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What recognizes damage in GG-NER?

A

XPC recognizes damage and initiates repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

GG-NER in eukaryotes recognizes many types of damages, which one does it struggle recognizing?

A

can’t recognize the pyrimidine dimer damage b/c lacks photolyase. A DDB will recruit XPC to the dimer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What recognizes damage in TC-NER in eukaryotes?

A

RNA Polymerase II recognizes damage. This repair system repairs lesions on transcribed parts of active genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

In TC-NER and GG-NER what is the unwinding helicase?

A

TF2H is the unwinding helicase along with XPB and XPD

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

XPF and XPG do what?

A

are exonuclease in the TC/GG NER repair systems

19
Q

In TC/GG NER what seals the nick

A

Ligase III and XRCCI

20
Q

Which enzymes are responsible for base excision repair?

A

Glycolyases and lyases remove bases

21
Q

What is the difference between glyolyases and lyases?

A

Glycolyases use DNA pol delta/epsilon to remove base and does this on long patch path

vs.

Lyases use DNA pol beta and remove bases from short stretch pathways

22
Q

How does glycolyases remove bases?

A

will cleave bond between base and sugar sometimes it can use amino acids to open up sugar ring

23
Q

Uracil and alkylated bases are recognized by what enzyme? And how are these repaired?

A

Through glycolyases

glycolyases uses a base flipping mechanism in which the base are flipped out of double helix, excised or modified, and returned to helx

24
Q

What is error prone synthesis in e.coli

A

When DNA polymerase inserts nucleotides at random when it can’t find the complementary base

  • DNA pol V (umuCD) - repairs UV damage
  • DNA pol IV
25
Q

What is a mut gene?

A

a gene that codes for a mismatch repair system that deals w/mismatch base pairs

mut genes also have a mutator phenotype in that they increase the spontaneous mutations

26
Q

Mismatch repair system is biased toward restoration of what?

A

wil-type

27
Q

In eukaryotes what is the MutS/L repair system

A

muts/l fixes errors caused by replication slippage

slippage creates a single stranded loop and mut S/L bind to mismatch

exonuclease, helicase, DNA pol, and ligase are involved in mismatch repair in muts/l

28
Q

Recombination repair systems in e.coli are coded by what genes?

A

coded by rec genes.

after replication, there are gaps that are produced due to the opposite sequence having to be repair

29
Q

Explain recombination repair

A

1) damage on one strand of DNA
2) when replication occurs the two daughter duplexes will be different
- one daughter will have intact parent and intact complementary
- the other daughter. will have a gap on parent
3) single strand from intact duplex is used to replace gap but this leaves a gap in duplex
4) gap is repaired by repair synthesis

30
Q

In recombination repair system, what happens when replication fork stalls? what can resolve this issue?

A

Resolvase - targets holliday junction created between two duplex DNA

helicase will also help roll the fork and restore replication

31
Q

How can resolvase create a DSB?

A

if it cuts either side of complementary strand. if damage is a nick it can also lead to DSB

32
Q

What causes DSB in eukaryotes? What repairs it?

A

radiation and free radicals. Recombination is preferred in homologous but if stands are non homologous then NHEJ repair comes into play

33
Q

what are the repair genes involved in repairing DSB?

A

Rad - named this way b/c of their sensitivity to radiation

Rad52 is required for recombination repair of DSB

34
Q

What is non-homologous end joining NHEJ repair

A

in absence of homologous sequence, NHEJ repairs DSB by ligating blunt ends of duplex DNA

35
Q

What are the steps involved in NHEJ repair?

A

1) recognition of broken ends by Ku 70 + 80
2) Ku binds to ends of DNA and forms a bridge between two ends of DNA
3) DNA strands are ligated by ligase V and XRCC

36
Q

Failure to repair DSB can lead to what?

A

chromosome instability and increase chance of cancer

37
Q

Why must chromatin and histones be considered in DNA repair of eukaryotes?

A

b/c chromatin impedes replication and transcription b/c nucleosome must be diplaced and DNA unwound

thus, histone modification and chromatin remodeling are essential for repair of DNA damage in chromatin

38
Q

How are histones modified and chromatin remodeled?

A

by phosphorylation of H2A at DSB, phosphorylation stabilizes assembly of repair factors and modifying activities

39
Q

Explain the steps of chromatin remodeling

A

1) damage occurs at chromatin

2) REMODELING - allows access to lesion
3) REPAIR - lesion is repaired
4) RESTORE - chromatin assembly restores original structure (remodelers and chaperones are needed to restore chromatin structure)

40
Q

What is SOS and what triggers this system?

A

SOS is the global repair response in bacteria and it is triggered by RecA

41
Q

RecA cleaves what?

A

LexA which is a repressor of operons and SOS

42
Q

Inactivated LexA causes what?

A

operons and SOS to be expressed

43
Q

Explain how RecA interacts with LexA and affects SOS

A

Inducing Signal > causes RecA to increase and this cleaves LexA, LexA no longer suppresses operons and SOS is activated

No inducing signal = equals no RecA = no LexA cleavage = repressor for operons = SOS shuts off

MBIOS 503 Advanced Molecular Biology I (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions