Lecture 2 Dr. Filleur Flashcards
DNA Replication, Repair, and Recombination (88 cards)
1
Q
What is the sugar of RNA?
A
Ribose
2
Q
What is the sugar of DNA
A
Deoxyribose
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
4
Q
Define: Nucleotide
A
A molecule of DNA or RNA
5
Q
What is DNA’s overall direction?
A
5’ to 3’
6
Q
How do the nucleotides bond?
A
A-T, and C-G
7
Q
How many hydrogen bonds are found between Thymine and Adenine?
A
2
8
Q
Which two nitrogenous bases are pyrimidines?
A
Thymine and Cytosine
9
Q
Which two nitrogenous bases are purines?
A
Adenine and Guanine
10
Q
How many hydrogen bonds are found between Guanine and Cytosine?
A
3
11
Q
What structure does the antiparallel DNA form?
A
Right Hand Double-Helix (B-DNA)
12
Q
What are the grooves formed by the double helix called?
A
Major and Minor Grooves
13
Q
What is the diameter of each turn?
A
20 Angstroms
14
Q
What is the distance between each nucleotide?
A
3.4 Angstroms
15
Q
What is the distance of a complete turn?
A
34 Angstroms
16
Q
How many nucleotides are in one turn of the double-helix?
A
10
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
18
Q
What type of bonds and interactions stabilizes the double-helix?
A
Hydrogen Bonds and Hydrophobic Interactions
19
Q
What is a right-handed double-helix called?
A
B-DNA
20
Q
What is a left-handed double-helix called?
A
Z-DNA (The sugar backbone has a zigzag pattern)
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”
22
Q
Describe the four steps of the Watson and Crick model of DNA Replication
A
- Original Double-Helix
- Strands separate
- Complementary bases align on opposite template
- Enzymes link sugar-phosphate elements of aligned nucleotides into a continuous new strand
23
Q
Define: DNA Replication
A
The process of copying a double-stranded DNA molecule to form two double-stranded molecules
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
25
What direction is DNA synthesized in?
DNA is synthesized by extending the 3' end of the primer
26
What is DNA Polymerases' self correcting behavior called?
Proofreading Activity
27
What is Proofreading Activity?
DNA Polymerase is capable of noticing and correcting any incorrectly inserted nucleotides
28
Where is DNA replication initiated?
Origin of Replication, specific cis-acting DNA sequences
29
What binds to the origin of replication to initiate replication?
Initiator Protein binds to the Origin or replication
30
What does the Initiator Protein recruit?
DNA Helicase, which catalyzes the unwinding of the double-helix, and is powered by ATP hydrolysis
31
What is the replication bubble?
The opening formed by the separation of DNA strands
32
What is the direction of replication?
Bidirectional, replication forks move outwards from the bubble
33
What is the function of Primase?
Primase is an enzyme that synthesizes the RNA primer at the replication fork
34
What stabilizes the single strand prior to replication?
Single-Strand DNA Binding Proteins, these rest on the unpaired nucleotides and prevent them from reannealing to the opposite strand
35
Why must primase first synthesize an RNA primer before replication can begin?
DNA polymerase cannot bind and begin synthesizing DNA without a primer
36
What does DNA Polymerase III do?
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
What is the lagging strand?
The new strand of DNA that due to the template strand being 5' to '3 must undergo repeated additions of primers
38
What are Okazaki fragments?
DNA fragments formed on the lagging strand, as a result of the orientation of the strand
39
What is the function of DNA Polymerase I?
DNA Polymerase I, with other enzymes, replaces the RNA primers with DNA
40
What joins the successive Okazaki fragments into a continuous strand of DNA?
DNA Ligase
41
E.coli Pol I
RNA Primer Removal and DNA Repair, 1 subunit
42
E.coli Pol II
DNA Repair, 1 subunit
43
E.coli Pol III
Chromosome Replication, 3 subunits
44
Euk. Pol Alpha
Primer Synthesis during DNA Replication, 4 subunits
45
Euk. Pol Delta
Lagging-strand DNA synthesis; Nucleotide and Base Excision repair, 2-3 subunits
46
Euk. Pol Epsilon
Leading-strand DNA synthesis; Nucleotide and Base Excision repair, 4 subunits
47
Name 2 important E.coli Origin of Replication sites
Tandem Array of Consensus Sequence and Binding site for dnaA protein
48
What does the E.coli Binding sites for dnaA protein do?
Recruitment of dnaA protein causes DNA to structurally modify and then recruit a helicase that will bind to the AT rich consensus sequence
49
What is the significance of the Consensus sequence being AT rich?
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
What is the function of Topoisomerase?
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
What is "The End Replication Problem"?
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
How is "The End Replication Problem" resolved?
Telomerase, a protein that lengthens the ends of the chromosome ensuring that coding DNA is not lost in the replication process.
53
What is the telomeric sequence?
AAUCCCAAU
54
1st type of DNA damage
Substitution where nucleotides are replaced. 2 types.
55
Substitution Transition
Purine is replaced with Purine, and Pyrimidine for Pyrimidine
56
Substitution Transversion
Purine for Pyrimidine or Pyrimidine for Purine
57
2nd Type of DNA Damage
Deletion, where following double-stranded breaks, whole segments are lost
58
3rd Type of DNA Damage
Insertion, where double stranded segments are inserted into the genome
59
4th Type of DNA Damage
Inversion, where segments of the DNA is cut, flipped, and reinserted into the chromosome
60
5th Type of DNA Damage
Reciprocal Translocation, where multiple chromosomes swap segments of DNA
61
Causes of DNA Damages (3)
1. Replication Errors
2. Stall of Replication Fork
3. Mutagens
62
Chemical Causes of DNA Damage (3)
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
Causes of DNA Damage: Mutagens (2)
1. X-rays cause double stranded deletions
| 2. UV Rays produce thymine dimers
64
Mismatch Repair (MMR) Step 1 of 5
Designed to correct errors made during the process of replication. Parental groups are marked with methyl groups.
65
Mismatch Repair (MMR) Step 2 of 5
MutS and MutL recognize mismatch in replicated DNA.
66
Mismatch Repair (MMR) Step 3 of 5
MutL recruits MutH(endonuclease) to GATC; where they will cut the strand of DNA with the mutation
67
Mismatch Repair (MMR) Step 4 of 5
Exonuclease are then recruited and they excise a segment of the unmethylated new strand.
68
Mismatch Repair (MMR) Step 5 of 5
DNA Polymerase is recruited to replace the missing nucleotides, Ligase will seal the nicks
69
Exonuclease
an enzyme that removes successive nucleotides from the end of a polynucleotide molecule
70
Inherited mutation os MSH2, MLH1, PMS1, PMS2 and MSH6 are linked to what?
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
Base Excision Repair (BER)
repairs damage caused by deamination of bases, radiation, oxidative stress, alkylating agents, or oxidative lesions caused by ROS (reactive oxygen species)
72
Base Excision Repair (BER) Step 2 of 6
Glycosylase removes uracil, leaving an AP (apurinic/apyrimidinic) site
73
Base Excision Repair (BER) Step 3 of 6
AP endonuclease cuts backbone to make a nick at the AP site
74
Base Excision Repair (BER) Step 4 of 6
DNA Exonuclease removes nucleotides near the nick creating a gap
75
Base Excision Repair (BER) Step 5 of 6
DNA polymerase synthesizes new DNA to fill in the gap
76
Base Excision Repair (BER) Step 6 of 6
DNA ligase seals the nicks
77
Nucleotide Excision Repair (NER)
The major defense against DNA damage caused by ultraviolet radiation and chemical exposure
78
Nucleotide Excision Repair (NER) Step 1 of 6
Exposure to UV light
79
Nucleotide Excision Repair (NER)
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
Nucleotide Excision Repair (NER) Step 3 of 6
Uvr B and C endonucleases nick strand containing dimer
81
Nucleotide Excision Repair (NER) Step 4 of 6
Damaged segment is released from DNA
82
Nucleotide Excision Repair (NER) Step 5 of 6
DNA polymerase fills in gap with new DNA
83
Nucleotide Excision Repair (NER) Step 6 of 6
DNA ligase seals the nicked strand
84
Nucleotide Excision Repair (NER) requires how many enzymes in humans?
6: RPA, XPA, XPC, TFIIH, XPG, and XPF
85
What is the risk of skin cancer for patients with xeroderma pigmentosum by age 20?
100%
86
Double-Stranded Break Repair (DSBR)
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
Double-Stranded Break Repair (DSBR) Non-homologous End-Joining
When double stranded break is neatened and rejoined without replacement of lost gene region. Has region with altered segment due to missing nucleotides
88
Double-Stranded Break Repair (DSBR) Homologous End-Joining
Complete sequence restored by copying from second chromosome
