Brainscape's Knowledge GenomeTM

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


See full index

Biochem > Lecture 13: DNA Repair > Flashcards

Lecture 13: DNA Repair Flashcards

1
Q

Biological scale:
How many feet of DNA in each cell?
Humans receive how many base pairs from each parents?
Human genome is how many chromosomes?

A

3 feet of DNA in each cell
>3 billion base pairs from each parent
46 chromosomes

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

What is an absolute requirement of DNA?

A

High-fidelity of DNA replication is an absolute requirement. Have to replicate accurately and precisely, otherwise genome instability would occur.

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

DNA Damage

A

Occurs spontaneously or through chemical & environmental means. Normal metabolic processes in the body can also produced DNA-damaging by products.

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

If the damage is passed on to subsequent generations, then…

A

Permanent changes are left in the DNA –> mutations. If not corrected, mutations can be passed on to successive generations of cells and organisms if the mutation occurs
in the germline of multicellular organisms.

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

Mutations occur if

A

nucleotides are added incorrectly or if nucleotides base pair
incorrectly due to damage to the template DNA.

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

Mutations can have many effects, including

A
  1. Most will lead to no obvious phenotypes (neutral mutations)
  2. Some will have mild effects, such as altered pigmentation
  3. Some will have serious consequences
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Mutations in germ (sex) cells can result in

A

an inherited disease

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

Mutations in somatic cells can result in

A

cancer

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

Mutations occur where a what residue is methylated?

A

Guanine residue. Methylated guanine is considered damaged.

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

During replication, the methylated guanine pairs with?

A

Thymine rather than cytosine; the other parental strand is unaffected.

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

When DNA polymerases synthesize new daughter strands, these mutations will become?

A

Fixed in the genome - half of all new daughter cells will now contain the mutation.

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

Sickle cell anemia mutation

A

Glutamic acid –> Valine

Single base change substitution causing disease

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

DNA polymerases actively incorporate bases that are correctly base paired through

A

conformational changes in the polymerase.

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

DNA polymerase selectively gives an error rate of about

A

one incorrect nucleotide in very 104 – 105 nucleotides.

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

tautomeric shifts

A

Misincorporation of bases can still occur. There is a spontaneous redistribution of protons and electrons in the bases that lead them to form isomers. These shifts are temporary.

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

Tautomeric shift example

A

Keto –> enol (for guanine and thymine)

Amino –> imino (for adenine and cytosine)

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

Tautomeric shifts causes which mis-matches?

A

C-A and T-G

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

In a tautomeric shift, cytosine can become what form? Matches with what?

A

Can become imino form and base pairs with adenine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

In tautomeric shift, guanine can become what form? Base pair with what?

A

Guanine can become enol form and base pair with thymine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

In tautomeric shift, adenine can become what form? Base pair with what?

A

Adenine can become imino form and base pair with cytosine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

In tautomeric shift, thymine can become what form and base pair with what?

A

Thymine can become enol form and base pair with guanine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

As the DNA polymerase (DNApol) proceeds along the template, it uses

A

correct base pairing to incorporate the next nucleotide in the chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

If the template base has shifted to its rare
tautomeric form, an

A

incorrect base will be added since the hydrogen bonding appears correct.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

The rare tautomeric form will shift back to the

A

common isomer, and the bases will be a mismatch.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

DNApol check the? If there is a mismatch, the polymerease?

A

DNApol checks the last base added. If there is a mismatch, the polymerase will remove the wrong nucleotide using their 3’ to 5’ exonuclease activity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Polymerase will hydrolyze DNA in the

A

3’ to 5’ direction (analogous to a backspace key) then, the polymerase will insert the correct nucleotide and synthesis continues. This is referred to as proofreading.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

3 to 5 Exonuclease activity increases the accuracy of DNA replication by

A

100 to 1000 fold

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Some lesions in DNA cannot be copied by ___________. An example is:

A

the replicative DNA polymerase, ex: thymine dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

The replication fork ______ at these locations, and if DNA synthesis cannot continue the cell will…. (translesion DNA synthesis)

A

stalls, die

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Special DNA polymerases replace the normal polymerases at these lesions. These polymerases have a

A

larger activity site to accommodate “base pairing” across from lesions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

These special DNA polymerases (ex: eta - poly n) are

A

error-prone having low fidelity and no 3’ to 5’ exonuclease activity (no proofreading). However, making a few mistakes in the replicated strand is a better alternative for survival.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

DNA polymerase eta (Pol η)

A

specialized polymerase that replicates UV-damaged DNA. When thymine dimers are present, Pol η inserts adenine nucleotides in the newly synthesized DNA, bypassing the lesion and preventing mutation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Pol η inserts

A

adenine nucleotides in the newly synthesized DNA,

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

With selectivity and proofreading, the fidelity of replication is approximately

A

1 mismatch in every 10^7 to 10^8 nucleotides

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

. The human genome is made up of how many nucleotides?

A

3 billion (3x10^9)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

To preserve the DNA sequence in subsequent generations, cells have

A

DNA repair mechanisms to remove any mismatches that are not removed by DNA polymerase proofreading, resulting in less than 1 error in 109 nucleotides.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Error replication image

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Okazaki fragments are numbered in the order in which they were

A

synthesized on each lagging strand (i.e., ‘1’ is
the oldest, ‘5’ is the newest).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

The replication bubble is

A

bidirectional

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Mismatches that are missed by the proofreading of the DNA polymerase are repaired by the

A

DNA mismatch repair (MMR) system.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

MMR proteins detect

A

distortions in the DNA helix that result from a misfit between non-complimentary base pairs. MMR proteins will replace the incorrect base in the newly replicated strand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

The MMR system can discriminate between
the mother strand and the daughter strand
based on the presence of

A

“nicks” (single strand breaks) in the DNA strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

In eukaryotes, ‘nicks’ in newly replicated DNA appears to

A

specify the strand to be repaired.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

The newly-synthesized lagging strand could be identified by nicks at either end
of Okazaki fragments, whereas the leading strand might be identified by

A

its growing 3’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

MSH
MLH

A

MSH: Sits on mismatch
MLH: Looks for Nick

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

In humans, the MSH2 proteins finds?

A

slide along the DNA until they find mismatched bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

MSH2 binds at the site of a mismatch in the double-stranded DNA. MSH recruits the

A

MLH protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

The MLH protein then scans for the

A

closest nick in the lagging strand or the 3’ end of the leading strand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Once a nick is found, MLH introduces

A

nicks in the daughter strand between the strand break and the mismatch.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

MLH recruits

A

exonuclease 1 (EXO1). EXO1
excises the DNA between the nicks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

The gap is then filled in by

A

DNA polymerase and sealed by DNA ligase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

This repair mechanism takes place as

A

DNA replication is occurring, before replication is completed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Mutations in MMR genes can result in

A

hereditary non-polyposis colorectal
(HNPCC) cancer, also known as Lynch syndrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

Lynch syndrome

A

the most common cause of inherited colorectal cancer.

55
Q

Non-polyposis means that

A

colorectal cancer can occur when only a small number of polyps are present (or polyps are not present at all).

56
Q

~1/300 individuals in the US have a

A

genetic variant associated with NHPCC

57
Q

HNPCC is due to mutations in

A

MSH2 and MLH1 genes (MSH2, 60% of cases and MLH1, 30% cases).

58
Q

Individuals who inherit on mutant copy of an MMR gene have an increased risk of developing colorectal cancer

A

as well as other cancers because it is likely they will acquire a mutation in the second copy of the MMR gene during their lifetime.

59
Q

Cancer is not inherited. What is inherited is a

A

predisposition (an
increased risk) to develop cancer. Not all individuals with a variant will develop
cancer.

60
Q

DNA repair becomes

A

compromised, resulting in the accumulation of mutations in
cells. This will eventually lead to mutations in genes required to maintain control of
cell division

61
Q

Progression from an adenoma to a carcinoma takes place in only

A

2-3 years compared to the usual 8-10 years seen in non-HNPCC patients.

62
Q

Cells have several DNA repair
mechanisms that can function at times other than

A

during DNA replication. However,
only so much DNA damage can be repaired. If the damage is so severe that it overwhelms the repair pathways, the cell will die.

63
Q

Repair pathways depends on the type of

A

damage

64
Q

Single-strand damages can be repaired by

A
  1. Base Excision Repair (BER)
  2. Nucleotide Excision Repair (NER)
65
Q

Double stranded breaks are due to

A

chemical, chemotherapeutics, radiation, etc

66
Q

Double stranded breaks

A
  1. Non-homologous end joining (NHEJ)
  2. Homologous recombination repair (HR)
67
Q

BER is used to replace

A

single bases in DNA that are incorrect, damaged, or missing

68
Q

A missing base is called

A

abasic (a=without, without a base)

69
Q

Abasic sites are called

A

AP sites, can occur spontaneously

70
Q

Depurination

A

the glycosidic bond between the purine base and sugar in a nucleotide can spontaneously hydrolyze, creating an apurinic site (sugar without a base)

71
Q

Depyrimidination

A

occurs in cells but less frequently

72
Q

Under physiological conditions, how many apurinic and apyrimidinic sites are generated in a cell each day?

A

10,000 apurinic sites
500 apyrimidinic sites

73
Q

AP sites can be made by

A

enzymes

74
Q

Glycosylases

A

used to remove damaged or incorrect bases generating an AP site (ex: in the case of spontaneous deamination of cytosine in DNA)

75
Q

Glycosylases are lesion specific: how many types in humans?

A

11

76
Q

Uracil-DNA glycosylase removes

A

uracil in DNA

77
Q

Thymine DNA glycosylase

A

removes pyrimidine mismatches

78
Q

8-oxoG DNA glycosylase

A

removes oxidative base damage

79
Q

A spontaneous deamination of

A

cytosine to uracil in DNA occurs at a rate of about 100 bases per cell per day

80
Q

Unnatural DNA bases (uracil, 8-oxoG, etc.) incorporated in DNA results in

A

structural distortion

81
Q

DNA glycosylases travel along the DNA helix to

A

probe all faces of the nucleotide for damage and remove all unnatural DNA bases.

82
Q

BER Steps

A
  1. A specific ‘damaged’ base is recognized
  2. Glycosylase cleaves the bond between the damaged base and the sugar, leaving behind an AP site (an apurinic or apyrimidinic; “a”=without)
  3. AP endonucleases cut the sugar-phosphate backbone, and exonuclease removes the abasic residue. (‘endo-’ cuts the phosphodiester bonds; ‘exo-’ removes the nucleotides). There is a single-base gap now.
  4. DNA polymerase adds new nucleotides, and DNA ligase seals the nick.
83
Q

NER detects

A

structural distortions in the double helix due to either pyrimidine dimers (where two adjacent thymine or
cytosine residues are covalently linked on the SAME strand) or bulky lesions added to bases due to exposure to carcinogens.

84
Q

NER system removes a segment of

A

contiguous nucleotides (“oligonucleotide”) to either side of the damaged base(s).

85
Q

General Steps of NER

A
  1. A multi-enzyme XP complex recognizes the DNA for distortion of the double helix
  2. A nuclease cleaves the phosphodiester backbone on both sides of the distortion
  3. A DNA helicase separates the damaged DNA from the undamaged, complimentary DNA. (Depending on the size of the complex and types of damage, the excised base length differs)
  4. The gap is then repaired by DNA
    polymerase using the undamaged strand as a template and DNA ligase
86
Q

Common/shared mechanisms between BER and NER

A
  1. Enzyme complexes recognize distortion in structure and excise damages (specific enzymes for specific mistakes)
  2. DNA polymerase adds correct nucleotides
  3. DNA ligase joins new, correct fragment with the existing polymer

Net result: repaired DNA

87
Q

Double-strand DNA (dsDNA) breaks can occur due to problems with

A

DNA replication (when polymerase encounters a nick in the template strand), exposure to certain chemicals, ROS, or by ionizing radiation.

88
Q

NHEJ mechanism, speed, timing, and accuracy

A

Simple process of ‘gluing” the ends together. Fast process. Does not require a template, so it can happen anytime (mostly in G1 phase of the cell cycle). Error prone.

89
Q

HRR mechanism, timing, and accuracy

A

Requires a duplicate chromosome, occurs after DNA replication before separation of chromosomes (S, G2, and M). Accurate.

90
Q

A classic NHEJ process can be used to glue the

A

DNA strands back together upon a double-stranded break

91
Q

When does NHEJ typically happen?

A

happens in G1 phase of the cell cycle when there is no copy of the chromosome to use as a template.

92
Q

The Ku70–Ku80 heterodimer binds to the

A

damage sites and recruits the polymerase, nuclease and ligase complexes

93
Q

The processing of the ends creates

A

microhomology between the two DNA ends for the polymerases to work from

94
Q

This mutagenic and error-prone can result in

A

Diverse DNA sequences at the repair junction. Repaired DNA generally suffer a deletion of nucleotides

95
Q

Double-strand break repair - HRR

A
  1. Double stranded DNA break
  2. Resection of the damaged strand
  3. Undamaged, homologous DNA
  4. Strand invasion
  5. Repair synthesis: the homologous DNA provides an undamaged template for DNA synthesis
  6. Fully restored, undamaged strands (error-free)
96
Q

Normal functions of BRCA1 and BRCA2 proteins involve repairing

A

double-strand DNA breaks; mutations in these genes lead to the failed repair of other genes.

97
Q

Mutations in the BRCA1 and BRCA2 genes
are major contributors to

A

to inherited (familial) breast cancer. ~1/3 of all breast cancers are due to mutations in one of these genes. The type of cancer is inherited in an autosomal dominant manner.

98
Q

Cancer is not inherited. What is
inherited is a

A

a predisposition (an increased
risk) to develop cancer. Not all individuals
with a variant will develop cancer.

99
Q

Individuals who inherit one mutant copy of a
BRCA gene have an increased risk of

A

developing cancer, because it is likely they will acquire a mutation in the second copy of
the BRCA gene during their lifetime.

100
Q

When mutated/deficient BRCA1 and
BRCA2 genes are inherited, affected
women are

A

40-80% more likely to develop breast and ovarian cancer.

101
Q

Many sources of DNA damage can alter the

A

DNA before or after replication,
creating chemically altered bases or segments of DNA that are eventually replicated with the incorrect bases.

102
Q

Endogenous sources of DNA damage

A

-DNA replication error
-Spontaneous base deamination
-Base hydrolysis
-Oxidation of bases

103
Q

Exogenous sources

A

-Radiation
-Carcinogens
-Chemotherapeutics

104
Q

Deamination is the removal of an

A

amine group

105
Q

Example of deamination

A

Cytosine to uracil.

Solution: Uracil-DNA glycosylase removes uracil bases in DNA

106
Q

Demination of 5-methylcytosine (5mC) to

A

thymine

107
Q

5mC is a naturally occurring

A

methylated cytosine. It is involved in gene regulation.

108
Q

If the mutation is not corrected, the altered base will

A

pair with different partners during DNA replication

109
Q

repair mechanism utilized for DNA damage by spontaneous deamination

A

base excision repair

110
Q

Base hydrolysis results in

A

de-purination, removal of a purine base from the DNA strand.

111
Q

The glycosidic bond between the purine
base and sugar in a nucleotide can
spontaneously

A

hydrolyze, creating an Depurination apurinic site (AP site).

112
Q

Replication without a
base

A

If not repaired, the loss of a base can result in a deletion mutation.

113
Q

DNA damage by base hydrolysis repair mechanism utilized

A

base excision repair

114
Q

DNA damage by oxidation of bases

A

Many of the metabolic reactions in the mitochondria generate Reactive
Oxygen Species (ROS: O2, H2O2, OH_ that can damage DNA.

115
Q

ROS can

A

-damage the bases of DNA to cause mis-pairing
-cause the complete loss of a base from a ribose residue
-induce single and double stranded breaks

116
Q

example of oxidation of bases

A

deoxyguanosine oxidized to 8-oxo-deoxyguanosine

guanine oxidized to 8-oxo-guanine

117
Q

DNA damage by oxidation of bases repair mechanism

A

base excision repair

118
Q

DNA damage by UV irradiation

A

Exposure to UV light can induce pyrimidine dimer formation in
DNA.

119
Q

Two adjacent pyrimidine bases on the what? Becomes linked to?

A

On the same strand, become linked to create a cyclobutane ring by exposure to UV light.

120
Q

DNA damage by UV irradiation repair mechanism

A

Nucleotide excision repair (NER). The covalent bond between adjacent bases requires that NER be used rather than base excision repair mechanism.

121
Q

Defective NER mechanism

A

results in inability to repair DNA damage that results from UV radiation. Accumulation of un-repaired DNA damage leads to the development of cancerous tumors.

122
Q

Mutations in NER genes can result in

A

Xeroderma pigmentosum (XP). XP is caused by mutations in genes that are involved in repairing damaged DNA.

123
Q

XP is a

A

are genetic disorder that affects ~1/250,000 people. It is inherited in an
autosomal recessive manner.

124
Q

Since NER will not function, pyrimidine dimers will

A

form in the presence of UV light and not be repaired. They bulky
dimers are not replicated properly, and translesion synthesis is used to bypass the damage. This results in the accumulation of mutations in the cells, which will eventually lead to mutations in genes required to maintain control of cell division, which can result in cancer.

125
Q

Carcinogens (cancer-causing agents) include

A

natural and synthetic chemicals

126
Q

Many carcinogens can react with

A

DNA bases, often adding bulky adducts to DNA

127
Q

benzopyrene

A

a ubiquitous compound that comes from wood burning; also
found in coal tar, automobile exhaust, in smoke resulting from burning organic
material, and in charbroiled food (found in coal tar)

128
Q

chemical carcinogen repair mechanism

A

nucleotide excision repair

129
Q

topoisomerase inhibitors

A

intercalate into the DNA (i.e., stack with bases) or bind the topoisomerase-DNA complexes. They inhibit the re-ligation of the DNA by the topoisomerase

130
Q

Antibacterial chemotherapeutics

A

Fluoroquinolones

131
Q

Fluoroquinolones

A

broad-spectrum antibacterial agents that inhibit bacterial Type II
topoisomerases and not mammalian topoisomerases. Used in human and
veterinary medicine.

Example: ciprofloxacin (“cipro”)

132
Q

Anticancer drugs

A

include Type 1 and Type II topoisomerase inhibitors, generating
single- and double-strand breaks, leading to apoptosis (programmed cell death).

133
Q

Examples of topoisomerase I inhibitors

A

irinotecan and camptothecin

134
Q

Examples of topoisomerase II inhibitors

A

etoposide and doxorubicin

Biochem (7 decks)

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