Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MCDB 131 > Lecture 7 - DNA repair and recombination > Flashcards

Lecture 7 - DNA repair and recombination Flashcards

1
Q

Mutation

A

Heritable change in the DNA

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

Different types of mutations

A

Point mutation, insertion/deletion, inversion, reversion

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

Types of point mutations

A

Transition and transversion

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

Transition mutation

A

Purine –> purine or pyrimidine –> pyrimidine (less traumatic for the cell)

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

Transversion

A

Purine <–> pyrimidine

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

Do mutations always change the protein sequence?

A

No, but they can give rise to new phenotypes
- depends on where the mutation is and what it is

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

Information classes of mutations

A

Silent, missense, nonsense, and frame-shift

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

Silent mutation

A

Doesn’t change the aa sequence

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

Missense mutation

A

Changes an amino acid sequence to another
- doesn’t always have deleterious effects
- if the change is to the wobble position of a codon, the cell generally can compensate for it

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

Nonsense mutation

A

Changes the amino acid sequence to a stop codon (almost always deleterious)

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

Frame-shift mutation

A

Changes the open reading frame of the gene

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

Relationship between the protein sequence and the function of the protein

A

Proteins are tolerant to certain small changes
- many proteins that have the same function across species will have slightly different sequences
- wobble position changes will either result in no change to the aa placed or a change to an aa with similar properties

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

Chemical reactions that can induce spontaneous mutations

A
  1. tautomeric shifts that alter base-pairing properties (changes the pairing)
  2. oxidative deamination of bases (can change the identify of a base, most often C to U)
  3. formation of apurinic sites (no nucleotide present)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Sources of spontaneous mutations in bacteria

A
  1. chemical reactions
  2. DNA replication
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How does the tautomeric shift of thymine result in a mutation?

A

TA pair to TG pair during DNA replication
1. thymine changes to the enol form
2. during replication, enol form of thymine pairs with guanine
3. enol thymine reverts to normal thymine –> TG pairing

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

Other examples of tautomeric shifts that result in mutations?

A
  • AT –> AC due to rare imino form of adenine
  • CG –> CA due to imino form of cytosine
  • GC –> GT due to enol form of guanine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is spontaneous deamination?

A

Water attacks amine groups on C and converts them to uracil
- result: accumulation of U in the DNA

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

How does depurination occur?

A

Water attacks purine and removes the base
- result: abasic site

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

Purines

A

Adenine and Guanine

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

Pyrimidines

A

Thymine and Cytosine

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

Chemical mutagens

A
  • base analogs (ex: 2-aminopurine)
  • base modifiers and alkylating agents
  • intercalators
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Electromagnetic mutagens

A
  • ionization radiation (x-rays and gamma rays)
  • UV radiation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How does ionization radiation cause mutations?

A

X-rays and gamma rays can interact with water to form free radical oxygen species
- free radicals cleave the phosphodiester backbone of DNA

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

How does UV radiation cause mutations?

A

Forms pyrimidine dimers that put strain on the DNA and prevent progress of the replisome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
How does 2-aminopurine (a base analog) cause mutations?
Structure is an intermediate between adenine and guanine, so it can pair with either C or T
26
How does nitrous acid (HNO2) result in mutations?
Promotes deamination of C and A (accelerates normal oxidative deamination)
27
How does alkylation (addition of methyl or ethyl groups specifically) induce mutations?
Alkylation stabilizes the enol form of G and T --> conversion of G and T to forms that pair erroneously
28
How do pyrimidine dimers form?
1. Pyrimidine bases absorb UV light 2. Electrons are excited and react with adjacent base 3. Formation of covalent bonds
29
Where are pyrimidine dimers most common?
At sites of adjacent pyrimidine bases, mostly at T-T sequences
30
Outcome of pyrimidine dimer formation
- strain introduced to the double helix - DNA replication is blocked because replisome can't move past the dimer
31
What is the Ames test?
Test that identifies if a material is a chemical mutagen
32
What does the Ames test use?
Relies on a mutant bacterial strain that is defective in hisG (can't grow on a medium without histidine)
33
How do you perform an Ames test?
1. Plate histidine-deficient bacteria on agar plate without histidine 2. Place a potential mutagen-soaked paper disk on the plate 3. If bacteria grow near the suspected mutagen, its mutagenicity is confirmed
34
Why does bacterial growth signify the presence of a mutagen in the Ames test?
Mutagen causes reversion mutations that repair the defect in hisG
35
Pattern of colony growth to identify mutagen in the Ames test
High concentration of colonies near the mutagen, no colonies (or very few) far away and very close to the mutagen - far away, mutagen hasn't diffused; no reversion mutations - very close: too much mutation --> death
36
Examples of error-proof DNA repair
- methyl mismatch repair - photoreactivation - nucleotide excision repair - base excision repair - recombinational repair
37
When is error-prone repair used?
Only when DNA damage is so severe that it is potentially lethal - risk of introducing mutations in order to save the cell from death
38
Methyl mismatch repair
Uses methylation of the parental strand to discriminate from newly replicated DNA - new DNA doesn't have time to be methylated
39
When does methyl mismatch repair occur?
Occurs right after DNA replication
40
Steps of methyl mismatch repair
1. Mismatch detected by MutS which binds to the site 2. MutS recruits other Mut proteins which scan the adjacent DNA for methylation to determine old vs new strand 3. DNA is looped and unmethylated strand is cleaved 4. Damaged strand removed and replaced with DNA pol I
41
Methods of pyrimidine dimer repair
Photoreactivation, nucleotide excision repair
42
Photoreactivation
Photolyase binds to pyrimidine dimer and cleaves the cyclobutane ring using energy from blue light; not present in placental mammals
43
Nucleotide excision repair
Endonuclease removes a patch of ssDNA containing damage
44
What proteins are responsible for nucleotide excision repair
Uvr proteins (ultraviolet radiation)
45
Steps of nucleotide excision repair
1. UvrAB binds damaged DNA and bends it 2. UvrC cleaves phosphodiester backbone around the area of damage 3. damaged ssDNA is removed and replaced by DNA pol I
46
What causes xeroderma pigmentosum?
Defective nucleotide excision repair --> inability to repair UV damage
47
What damage does base excision pair correct?
Apurinic sites and cytosine deamination (C-->U)
48
Steps of base excision repair
1. Either an abasic site is already present, or uracil is recognized and cut off to make an abasic site 2. Abasic site recovnized and cleaved by a DNA endonuclease 3. DNA pol I synthesizes replacement
49
What does recombinational repair fix?
Pyrimidine dimers
50
Where does recombinational repair take place?
At the replication fork, binds ssDNA
51
Steps of recombinational repair
1. DNA pol skips over region with dimer 2. RecA binds ssDNA of the sister strand to the dimer and scans neighboring daughter DNA for homology 3. RecA catalyzes recombination (uses ssDNA from other daughter DNA to fill gap on damaged strand 4. Gap in undamaged strand is repaired by DNA pol
52
What kinds of damage is SOS repair generally used for?
Extensive DNA damage, usually from excessive UV damage
53
Why does excessive UV damage trigger SOS repair?
Lots of pyrimidine dimers cause extensive stalling of replication forks
54
What is LexA?
Transcriptional repressor bound to the promoter regions of specific DNA repair protein sequences
55
How is SOS repair triggered?
1. ssDNA accumulates in the cell due to DNA damage 2. RecA binds ssDNA --> activates its coprotease activity 3. RecA binds LexA and stimulates LexA to cleave itself 4. Cleaved LexA has a low affinity for DNA anad falls off --> de-represses synthesis of SOS repair proteins
56
DinB
"Damage inducible" - error prone DNA polymerase involved in SOS system - aka DNA Pol IV
57
UmuCD
"UV mutation repair" - error prone DNA polymerase involved in SOS system
58
What are error-prone DNA polymerases?
Polymerases that lack proofreading ability but can perform translesion synthesis
59
What proteins are upregulated during the SOS response?
SulA, UmuDC, UvrA, LexA, RecA
60
SulA
Inhibits cytokinesis by inhibiting FtsZ - important for preventing cell division before DNA is replicated
61
Why is UvrA upregulated in the SOS response?
UvrA is involved in nucleotide excision repair, another method of fixing damage from pyrimidine dimers

MCDB 131 (15 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions