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Genetics Block 1 > Lecture 2 Dr. Filleur > Flashcards

Lecture 2 Dr. Filleur Flashcards

DNA Replication, Repair, and Recombination

1
Q

What is the sugar of RNA?

A

Ribose

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2
Q

What is the sugar of DNA

A

Deoxyribose

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3
Q

Difference between RNA and DNA

A

Uracil instead of Thymine,
hydroxyl instead of hydrogen on the sugar’s 2’ carbon,
RNA is circular and single where DNA is linear and double-stranded

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4
Q

Define: Nucleotide

A

A molecule of DNA or RNA

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5
Q

What is DNA’s overall direction?

A

5’ to 3’

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6
Q

How do the nucleotides bond?

A

A-T, and C-G

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7
Q

How many hydrogen bonds are found between Thymine and Adenine?

A

2

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8
Q

Which two nitrogenous bases are pyrimidines?

A

Thymine and Cytosine

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9
Q

Which two nitrogenous bases are purines?

A

Adenine and Guanine

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10
Q

How many hydrogen bonds are found between Guanine and Cytosine?

A

3

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11
Q

What structure does the antiparallel DNA form?

A

Right Hand Double-Helix (B-DNA)

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12
Q

What are the grooves formed by the double helix called?

A

Major and Minor Grooves

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13
Q

What is the diameter of each turn?

A

20 Angstroms

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14
Q

What is the distance between each nucleotide?

A

3.4 Angstroms

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15
Q

What is the distance of a complete turn?

A

34 Angstroms

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16
Q

How many nucleotides are in one turn of the double-helix?

A

10

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17
Q

What is the function of the Major Groove?

A

The location where proteins interact and bind to the DNA for Transcription or Replication

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18
Q

What type of bonds and interactions stabilizes the double-helix?

A

Hydrogen Bonds and Hydrophobic Interactions

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19
Q

What is a right-handed double-helix called?

A

B-DNA

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20
Q

What is a left-handed double-helix called?

A

Z-DNA (The sugar backbone has a zigzag pattern)

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21
Q

What is Semi-Conservative Replication?

A

Where one half of the parent strand of DNA is kept in each subsequent daughter cell. One strand is “old” the other is “new”

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22
Q

Describe the four steps of the Watson and Crick model of DNA Replication

A
  1. Original Double-Helix
  2. Strands separate
  3. Complementary bases align on opposite template
  4. Enzymes link sugar-phosphate elements of aligned nucleotides into a continuous new strand
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23
Q

Define: DNA Replication

A

The process of copying a double-stranded DNA molecule to form two double-stranded molecules

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24
Q

What is the function of DNA Polymerase?

A

Assemble incoming deoxynucleotide triphosphates (one at a time) on a single-stranded DNA template such that the grow strand is elongated in its 5’ to 3’ direction

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25
Q

What direction is DNA synthesized in?

A

DNA is synthesized by extending the 3’ end of the primer

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26
Q

What is DNA Polymerases’ self correcting behavior called?

A

Proofreading Activity

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27
Q

What is Proofreading Activity?

A

DNA Polymerase is capable of noticing and correcting any incorrectly inserted nucleotides

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28
Q

Where is DNA replication initiated?

A

Origin of Replication, specific cis-acting DNA sequences

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29
Q

What binds to the origin of replication to initiate replication?

A

Initiator Protein binds to the Origin or replication

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30
Q

What does the Initiator Protein recruit?

A

DNA Helicase, which catalyzes the unwinding of the double-helix, and is powered by ATP hydrolysis

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31
Q

What is the replication bubble?

A

The opening formed by the separation of DNA strands

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32
Q

What is the direction of replication?

A

Bidirectional, replication forks move outwards from the bubble

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33
Q

What is the function of Primase?

A

Primase is an enzyme that synthesizes the RNA primer at the replication fork

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34
Q

What stabilizes the single strand prior to replication?

A

Single-Strand DNA Binding Proteins, these rest on the unpaired nucleotides and prevent them from reannealing to the opposite strand

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35
Q

Why must primase first synthesize an RNA primer before replication can begin?

A

DNA polymerase cannot bind and begin synthesizing DNA without a primer

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36
Q

What does DNA Polymerase III do?

A

It binds to the RNA primer and begins adding nucleotides along the template strand, beginning at the 3’ hydroxyl end of the RNA primer

37
Q

What is the lagging strand?

A

The new strand of DNA that due to the template strand being 5’ to ‘3 must undergo repeated additions of primers

38
Q

What are Okazaki fragments?

A

DNA fragments formed on the lagging strand, as a result of the orientation of the strand

39
Q

What is the function of DNA Polymerase I?

A

DNA Polymerase I, with other enzymes, replaces the RNA primers with DNA

40
Q

What joins the successive Okazaki fragments into a continuous strand of DNA?

A

DNA Ligase

41
Q

E.coli Pol I

A

RNA Primer Removal and DNA Repair, 1 subunit

42
Q

E.coli Pol II

A

DNA Repair, 1 subunit

43
Q

E.coli Pol III

A

Chromosome Replication, 3 subunits

44
Q

Euk. Pol Alpha

A

Primer Synthesis during DNA Replication, 4 subunits

45
Q

Euk. Pol Delta

A

Lagging-strand DNA synthesis; Nucleotide and Base Excision repair, 2-3 subunits

46
Q

Euk. Pol Epsilon

A

Leading-strand DNA synthesis; Nucleotide and Base Excision repair, 4 subunits

47
Q

Name 2 important E.coli Origin of Replication sites

A

Tandem Array of Consensus Sequence and Binding site for dnaA protein

48
Q

What does the E.coli Binding sites for dnaA protein do?

A

Recruitment of dnaA protein causes DNA to structurally modify and then recruit a helicase that will bind to the AT rich consensus sequence

49
Q

What is the significance of the Consensus sequence being AT rich?

A

A-T are bound by 2 hydrogen bonds, whereas G-C are bound by 3. The 2 hydrogen bonds require less energy to break and thus helicase will have an easier job of separating the double-helix

50
Q

What is the function of Topoisomerase?

A

When helicase begins to unwind and separate the double helix, supercoil structures form ahead of the replication forks. To combat tension, Topoisomerase will routinely nick the DNA strands ahead of the fork to unwind the supercoil structure

51
Q

What is “The End Replication Problem”?

A

Gaps at the end of the DNA strands when the primers are removed. If the gaps are not filled, every subsequent daughter cell will have shorter and shorter chromosomes

52
Q

How is “The End Replication Problem” resolved?

A

Telomerase, a protein that lengthens the ends of the chromosome ensuring that coding DNA is not lost in the replication process.

53
Q

What is the telomeric sequence?

A

AAUCCCAAU

54
Q

1st type of DNA damage

A

Substitution where nucleotides are replaced. 2 types.

55
Q

Substitution Transition

A

Purine is replaced with Purine, and Pyrimidine for Pyrimidine

56
Q

Substitution Transversion

A

Purine for Pyrimidine or Pyrimidine for Purine

57
Q

2nd Type of DNA Damage

A

Deletion, where following double-stranded breaks, whole segments are lost

58
Q

3rd Type of DNA Damage

A

Insertion, where double stranded segments are inserted into the genome

59
Q

4th Type of DNA Damage

A

Inversion, where segments of the DNA is cut, flipped, and reinserted into the chromosome

60
Q

5th Type of DNA Damage

A

Reciprocal Translocation, where multiple chromosomes swap segments of DNA

61
Q

Causes of DNA Damages (3)

A
  1. Replication Errors
  2. Stall of Replication Fork
  3. Mutagens
62
Q

Chemical Causes of DNA Damage (3)

A
  1. Depurination - loss of a purine
  2. Deamination - modification of Cytosine to Uracil. When replicated, a Thymine is inserted rather than the original cytosine.
  3. Oxidation - Guanine interacts with an active oxygen species and becomes 8-oxo-dg(GO)
63
Q

Causes of DNA Damage: Mutagens (2)

A
  1. X-rays cause double stranded deletions

2. UV Rays produce thymine dimers

64
Q

Mismatch Repair (MMR) Step 1 of 5

A

Designed to correct errors made during the process of replication. Parental groups are marked with methyl groups.

65
Q

Mismatch Repair (MMR) Step 2 of 5

A

MutS and MutL recognize mismatch in replicated DNA.

66
Q

Mismatch Repair (MMR) Step 3 of 5

A

MutL recruits MutH(endonuclease) to GATC; where they will cut the strand of DNA with the mutation

67
Q

Mismatch Repair (MMR) Step 4 of 5

A

Exonuclease are then recruited and they excise a segment of the unmethylated new strand.

68
Q

Mismatch Repair (MMR) Step 5 of 5

A

DNA Polymerase is recruited to replace the missing nucleotides, Ligase will seal the nicks

69
Q

Exonuclease

A

an enzyme that removes successive nucleotides from the end of a polynucleotide molecule

70
Q

Inherited mutation os MSH2, MLH1, PMS1, PMS2 and MSH6 are linked to what?

A

increased risk of malignancy (HNPCC). Genetic inactivation of MMR genes, particularly MLH1, is a frequent event in sporadic colon carcinoma and has been implicated in prostate and bladder carcinoma

71
Q

Base Excision Repair (BER)

A

repairs damage caused by deamination of bases, radiation, oxidative stress, alkylating agents, or oxidative lesions caused by ROS (reactive oxygen species)

72
Q

Base Excision Repair (BER) Step 2 of 6

A

Glycosylase removes uracil, leaving an AP (apurinic/apyrimidinic) site

73
Q

Base Excision Repair (BER) Step 3 of 6

A

AP endonuclease cuts backbone to make a nick at the AP site

74
Q

Base Excision Repair (BER) Step 4 of 6

A

DNA Exonuclease removes nucleotides near the nick creating a gap

75
Q

Base Excision Repair (BER) Step 5 of 6

A

DNA polymerase synthesizes new DNA to fill in the gap

76
Q

Base Excision Repair (BER) Step 6 of 6

A

DNA ligase seals the nicks

77
Q

Nucleotide Excision Repair (NER)

A

The major defense against DNA damage caused by ultraviolet radiation and chemical exposure

78
Q

Nucleotide Excision Repair (NER) Step 1 of 6

A

Exposure to UV light

79
Q

Nucleotide Excision Repair (NER)

A

Recognize distortions in the DNA helix, excising the damaged DNA, replacing it with the correct sequence. The major defense against DNA damage caused by ultraviolet radiation and chemical exposure

80
Q

Nucleotide Excision Repair (NER) Step 3 of 6

A

Uvr B and C endonucleases nick strand containing dimer

81
Q

Nucleotide Excision Repair (NER) Step 4 of 6

A

Damaged segment is released from DNA

82
Q

Nucleotide Excision Repair (NER) Step 5 of 6

A

DNA polymerase fills in gap with new DNA

83
Q

Nucleotide Excision Repair (NER) Step 6 of 6

A

DNA ligase seals the nicked strand

84
Q

Nucleotide Excision Repair (NER) requires how many enzymes in humans?

A

6: RPA, XPA, XPC, TFIIH, XPG, and XPF

85
Q

What is the risk of skin cancer for patients with xeroderma pigmentosum by age 20?

A

100%

86
Q

Double-Stranded Break Repair (DSBR)

A

Arise from ionizing radiation or x-rays, free radicals, chemicals, and during replication of a single-strand break
IS THE MOST DISRUPTIVE FORM OF DNA DAMAGE
If not repaired, the cell will likely undergo apoptosis.

87
Q

Double-Stranded Break Repair (DSBR) Non-homologous End-Joining

A

When double stranded break is neatened and rejoined without replacement of lost gene region. Has region with altered segment due to missing nucleotides

88
Q

Double-Stranded Break Repair (DSBR) Homologous End-Joining

A

Complete sequence restored by copying from second chromosome

Genetics Block 1 (6 decks)

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