Brainscape's Knowledge GenomeTM

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


See full index

Foundations 1 > DNA Replication and Repair > Flashcards

DNA Replication and Repair Flashcards

1
Q

What is euchromatin? What histone modifications promote this structure?

A

Open chromatin = active gene

Permissive histone modifications:

  • lys acetylation
  • some lys methylation
  • arg methylation
  • ser phosphorylation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is heterochromatin? What histone modifications promote this structure?

A

Condensed chromatin = silenced gene

Repressive histone modifications:

  • some lys methylation
  • lys sumoylation
  • lys ubiquitilation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How is the replication fork formed?

A

Loading the origin occurs in G1:

  1. Cdc6 is bound to ORC (origin recognition complex) on the origin
  2. DNA helicase binds and Cdc6 dissociates
  3. Pre-replicative complex formed (pre-RC)

Firing the origin occurs in S:

  1. Helicase is activated via phosphorylation by S-Cdk
  2. Replication machinery (DNA pol) recruited and replication begins
  3. ORC phosphorylated to prevent refiring of origin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Which direction do the replication forks move?

A

Forks travel in opposite directions from the origin and there are multiple origins per chromosome.

Polymerases synthesize in a 5’ -> 3’ direction, traveling along the template in a 3’ -> 5’ direction.

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

How is chromatin remodeling during replication?

A
  • Chromatin is disassembled and histones removed to allow for replication
  • Chromatin reassembled with daughter strands and parental histone modifications are replicated
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How are the leading and lagging strands synthesized?

A

Leading strand: template is 3’ -> 5’ so new strand is continuously synthesized 5’ -> 3’ in the direction of the fork

Lagging strand: template is 5’ -> 3’ so new strand is synthesized in short 5’ -> 3’ Okazaki fragments that will assemble into a 3’ -> 5’ strand

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

How does gene density impact replication timing?

A

Gene rich areas of the chromosome are replicated first because the chromatin is already open.

Condensed heterochromatin is copied last.

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

What are the components of the replisome?

A

DNA:

  • parent strand
  • leading strand synthesized 5’ -> 3’
  • lagging strand synthesized 3’ -> 5’ in 5’ -> 3’ fragments

Protein:

  • DNA polymerase
  • DNA primase: lays down RNA primer
  • DNA polymerase a: synthesizes RNA primer
  • SSBPs: stabilize exposed ssDNA and protect from nucleases
  • DNA helicase: unwinds DNA ahead of fork
  • sliding clamp: prevents polymerase from falling off, enabling high processivity
  • ligase: ligates okazaki fragments
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the functions of DNA pol a, B, g, d, and e?

A 
a = extends RNA primer; no exo activity
B = DNA repair
g = mitochondrial
d = lagging strand; 3' -> 5' exo
e = leading strand; 3' -> 5' exo
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the shared characteristics of all DNA polymerases?

A

Polymerize in the 5’ -> 3’ direction

Require a template

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

How are RNA primers removed in okazaki fragment synthesis?

A
  1. Primase lays down an RNA primer and polymerase extends the fragment until reaching the primer of the previous fragment
  2. RNA primer removed by a polymerase with 5’ -> 3’ exonuclease activity or by an endonuclease
  3. DNA pol replaces sequence with DNA
  4. DNA ligase seals the nicks
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does DNA polymerase proofread?

A
  1. When an incorrect base is added, other proteins can recognize the mismatch due to a distortion in the helix
  2. DNA pol removes the mispaired nucleotide using its endonuclease activity and replaces it with the correct one
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the function of the topoisomerases?

A

To relax the supercoils introduced into DNA ahead of the replication fork due to helicase’s unwinding activity

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

What is the function of topoisomerase I?

A
  • Makes a single stranded nick, relaxes coil, and religates

- Does not require ATP; energy comes from the hydrolysis of the phosphodiester bond in the DNA

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

What is the function of topoisomerase II?

A
  • Makes a double stranded break, untangles concatamers, and then religates
  • Requires ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What drugs target topoisomerases?

A
  • Antitumor agents

- Quinolones (antibacterial)

17
Q

What are cohesin complexes?

A

Protein rings that keep sister chromatids together during mitosis

18
Q

What is the shelterin complex?

A

Protects ssDNA telomeres from being recognized as “DNA damage” by the cell by looping the single stranded region back into the chromosome.

19
Q

Why do the ends of linear chromosomes require special replication?

A
  • As each new okazaki fragment is synthesized, the RNA primer on the previous fragment is degraded and replaced with DNA.
  • For the final fragment synthesized, the primer will be degraded but cannot be replaced by normal DNA synthesis methods
  • Without special replication machinery, the end of the lagging strand would be lost with each replication
20
Q

What cells make telomerase?

A

Fetal cells, stem cells, tumor cells

21
Q

How does telomerase help preserve the chromosome end?

A
  1. Telomerase binds to the 3’ end of the lagging strand template strand
  2. Using its attached RNA template, telomerase adds additional telomere repeats to the end of the lagging strand template, extending it in the 3’ direction
  3. DNA polymerase completes synthesis of the lagging strand by synthesizing another okazaki fragment complementary to the newly extended template
22
Q

What kind of polymerase is telomerase?

A

RNA-templated DNA synthesis

23
Q

What are some causes of DNA replication stress that may collapse the replication fork or cause double stranded breaks?

A
  • DNA damage
  • fork barriers
  • DNA secondary structure
  • Transcription machinery
  • Heterochromatin
  • DNA-binding proteins
  • Replisome malfunction
  • dNTP depletion
24
Q

What are some biochemical causes of DNA damage?

A
  • Depurination: hydroxyl group replaces purine base
  • Deamination: amine replaced by carbonyl
  • Oxidation: by ROS (guanine => 8-oxoguanine)
25
Q

What are main pathways for and the basic steps in single stranded DNA damage repair?

A

Pathways: Base excision repair, nucleotide excision repair, mismatch repair

Steps:

  1. Identify
  2. Remove
  3. Replace
  4. Ligate
26
Q

What are the main pathways for and the basic steps in repairing double stranded breaks?

A

Pathways: Nonhomologous end joining, microhomology-mediated end joining, homology directed repair

Steps:

  1. Identify
  2. Rejoin
  3. Ligate
27
Q

Base excision repair

A

Repairs damage to a single base by oxidation, alkylation, hydrolysis, or deamination.

  1. Specific enzyme removes mismatched base from DNA helix
  2. AP endonuclease and phosphodiesterase remove sugar phosphate
  3. DNA pol adds new nucleotide
  4. DNA ligase seals nick
28
Q

Nucleotide excision repair

A

Resolves helix-distorting lesions such as thymine dimers and 6,4 photoproducts.

  1. Excision nuclease cleaves a chunk of DNA surrounding the problematic bases
  2. DNA helicase separates the cleaved fragment from the rest of the helix
  3. DNA polymerase and DNA ligase refill and religate the gap
29
Q

Mismatch repair

A

Corrects errors in DNA replication and recombination missed by proofreading (on daughter strand)

  1. proteins that coat DNA recognize the mismatch
  2. signaling and recruitment of repair proteins
  3. nicking and excision
  4. ssDNA stabilized by SSPBs during resynthesis and ligaiton
30
Q

Non-homologous end joining

A

Rapid but low fidelity repair system for double stranded breaks in G1

  1. Nuclease chews back from the ends of the break to blunt ends
  2. Blunt end joining by ligase
  3. Break is repaired with deletion of nucleotides at repair site
31
Q

What are some causes of double stranded DNA breaks?

A

Ionizing radiation, drugs, collapsed replication forks

32
Q

Microhomology-mediated end joining

A

Similar to NHEJ but occurs in S; also error prone

33
Q

Homology directed repair

A

High fidelity repair during and after DNA replication (S/G2: occurs only when sister chromatids are together)

  1. Nuclease digests 5’ ends of broken strands
  2. Strand inversion by complementary base pairing: broken strand aligns with complementary undamaged strand from sister chromosome
  3. Repair polymerase extends broken strand using undamaged sister strand as template
  4. Invading strand released and broken double helix reformed
  5. DNA synthesis continues using complementary strands from damaged DNA as template
  6. Ligation
34
Q

What happens when DNA repair is defective?

A
  • Point mutations, frameshift mutations, nonsense mutations: can change protein structure, modification sites, or stability
  • Deletion of gene regions affecting splicing or polyadenylation
  • Alteration of promoter region increasing or decreasing transcription
  • Removal of enhancers
  • Gene fusions
  • Chromosome loss
35
Q

What are the components of and function of the Genome Surveillance Complex (BASC)

A

Complex of factors for damage sensing and repair:

  • ATR/ATM kinases sense damage
  • Phosphorylate BRCA1
  • BRCA1 stops replication and recruits appropriate repair machinery (NHEJ, mismatch repair, HDR, BER)
  • if damage can’t be fixed, BRCA1 induces pRB and p53, leading to apoptosis and cell-cycle arrest
36
Q

What are some diseases associated with DNA repair defects?

A
  • Xeroderma pigmentosum: no NER means patients can’t excise thymine dimers caused by UV irradiation
  • Bloom’s syndrome: DNA helicase defect
  • Werner syndrome: repair helicase defect
  • Hereditary nonpolyposis colorectal cancer: DNA mismatch repair defect

Foundations 1 (26 decks)

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