Lecture 4 - DNA Repair Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

What is a mutation? What is a mutant?

A

Mutation: A heritable change in genetic material; also refers to the process by which the change occurs

Mutant: an organism that exhibits a novel phenotype resulting from a mutation

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

What is a spontaneous mutation?

A
  • A mutation that occurs w/o a known cause, rare
  • Caused by inherent errors in replication or unknown agents in the environment
  • Assuming gene length of 1000 bp => 1 mutation/10,0000 - 10,000,000 genes/generation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is an induced mutation?

A
  • A mutation that results from a known cause
  • Caused by exposure to physical or chemical agents (mutagens)
  • Frequency of mutation depends on agent
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What role does mutation play in evolution?

What is genetic variation?

When do they occur?

What does effect of the mutation on phenotype depend on?

A
  • Mutations are the raw material of evolution and lead to genetic variation
  • Genetic variation: change in genotype that can lead to changes in phenotype, ability to respond to environmental changes (natural selection)
  • Delicate balance is required, otherwise lethal b/c compromise faithful transfer of genetic info from gen to gen
  • Can occur in any cell at any time, but a mutation in one cell type can only affect that cell type
  • Effects of mutation on phenotype depend on cell type, when in life cycle, dominance, and type of mutation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Where do mutations occur in animals?

A
  • Germ-line cells: cells that give rise to gametes
  • Somatic cells: all other cells
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Only mutations that occur in ________ cells will be passed onto progeny

A

Germ-line

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

Example of mutation offering an advantage?

A

Sickle cell anemia: usually problematic, but in Africa, individuals w/ sickle cell are less affected by malaria causing parasite

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

Do mutations result from adaptive or nonadaptive processes? What experiment proved this?

A

Nonadaptive processes; Lederberg experiment of replica plating

Stress simply selects rare pre-existing mutations that result in resistance phenotypes
1. Mutations producing resistance occur
2. Sensitive organisms die
3. Insensitive mutants survive and produce new insensitive populations

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

Mutations are _____

A

Reversible

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

What is a forward mutation?

A

A change from wild-type to mutant phenotype

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

What is a reverse mutation? Two types?

A

Reverse mutation: restoration of wild-type phenotype

Back mutation: second mutation at the same site as the first mutation

Suppressor mutation: second mutation anywhere in genome compensates for effect of first mutation

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

How to differentiate b/t back and suppressor mutation?

A

Use backcross (mutant x wild type)

  • If back mutation, all progeny will be wild type
  • if suppressor, half progeny will be wild type phenotype, half will be recombinant mutant/unknown phenotype
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Mutations that effect phenotype are usually ______ and _______

A

Deleterious and recessive

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

What are the phenotypic effects of mutation? What can they do to pathways? Example

A
  • Mostly result in an AA change that is deleterious to protein function b/c AA sequence is highly adapted to specific environment/function
  • Mutations can disrupt/modulate pathways
  • Example: mutation of phenylalanine hydroxylase leads to PKU and accumulation of a toxic byproduct
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the two molecular mechanisms of the mutation process?

A
  • Point mutation (Transition and Transversion)
  • Frameshift
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are point mutations (transitions and transversions)?

A
  • Point mutation: mutation that alters a single nucleotide w/in a gene
  • Transition: replacement of purine w/ a purine (A to G) or pyrimidine w/ a pyrimidine (T to C)
  • Transversion: substitution of pyrimidine to purine (T to G) or purine to pyrimidine (T to G or A; A to C or T)
17
Q

What are frameshift mutations?

A
  • Base pair addition or deletion in gene => alter reading frame (codons) => result in nonfunctional protein
18
Q

Mutations can be permanently incorporated by replication

True

False

A

True

19
Q

What chemicals act as mutagenic agents?

A
  • Base pair analogs
  • Nitrous Acid
  • Acridine Dyes
  • Alkylating Agents
  • Hydroxylating Agents
20
Q

What are base analogs? What do they do? 5-bromouracil ketone vs enol form; how does this happen, what does it result in?

A
  • Structures similar to normal bases that are incorporated into DNA during replication => increased mispairing => results in transitions
  • Ex: Thymine base analog is 5-Bromouracil, Guanine base analog is 2-Aminopurine

5-BU keto form bps with A
5-BU enol form bps with G
=> transitions

Conversion via tautomeric shift (b/c of Br)

21
Q

What does nitrous acid do?

A
  • Deaminates amino groups => transitions
22
Q

What do acridine dyes do? What structures are formed?

A
  • Intercalate into DNA => increased rigidity/bends/kinks => Addition/deletions (frameshift) during replication => nonfunctional proteins
  • Adenine -> Hypoxanthine which bp w/ cytosine
    -Cytosine -> Uracil which bp w/ adenine
  • Guanine -> Xanthine which bp w/ cytosine
23
Q

What do alkylating agents do?

A
  • Transfer alkyl group to base at N or O’s => alter bp potential => induce transitions, transversions, or frameshifts
24
Q

What do hydroxylating agents do?

A
  • Hydroxylamine (NH2OH) hydroxylates amino group of cytosine => bps with adenine => G/C -> A/T bp
25
Q

What non-chemical mutagenic agents exist?

A
  • UV radiation
  • Ionizing radiation
  • Transposons
26
Q

What does UV radiation do?

A

It excites bases => pyrimidine dimers and pyrimidine hydrates => interferes w/ DNA replication

27
Q

What does ionizing radiation do?

A

X-rays, gamma rays, and cosmic rays

Cause increased reactivity of bases

28
Q

What are transposons? What do they do?

A

Transposon: DNA fragments that can move from one site in a genome to another site

  • Insertion of transposon into an expressed gene will often render gene non-functional
29
Q

What kinds of DNA repair mechanisms exist in prokaryotes in nature?

A
  1. Light-dependent repair
  2. Excision repair (base, nucleotide)
  3. Mismatch repair
  4. Error-prone repair system (SOS)
  5. Post-replication repair (w/ homologous recombination)
30
Q

What kinds of DNA repair mechanisms exist in eukaryotes in nature?

A
  1. Excision repair (base, nucleotide)
  2. Mismatch repair
  3. Error-prone repair system (SOS)
  4. Post-replication repair (w/ homologous recombination)
31
Q

What is light dependent repair by DNA photolyase?

A
  • Prokaryotes only
  • Photolyase binds thymine dimers
  • Use visible light for energy to cleave crosslink
32
Q

What is base excision repair? What are glycosylases? What is the general outline?

A
  • Prokaryotes and eukaryotes
  • Removes abnormal or chemically modified bases

Glycosylases: enzymes that recognize specific base alterations

Outline:
1. Glycosylases mediate base removal => AP site (A-purine or A-pyrimidine)
2. AP endonuclease removes backbone
3. DNA polymerase I/delta adds new base
4. DNA ligase reforms phosphodiester bond

33
Q

What is nucleotide excision repair? What is exinuclease? Role of helicase (ATP or no)? What fills in the base gap and missing phosphodiester bond?Difference in bacteria and humans?

A
  • Prokaryotes and eukaryotes
  • Unique mechanism that removes large base defects (thymine dimers, large alkylated bases, etc.)

Exinuclease: enzyme that cuts on either side of defect and excises large piece

-Helicase mediates release of nucleotide ssDNA from site of damage (localized unwinding, no ATP)

  • Bacteria release 12 nucleotide, human release 29 nucleotide
  • Bacteria fill base gap w/ DNA polymerase I and missing phosphodiester bond w/ DNA ligase
  • Human fill base gap w/ DNA polymerase delta and missing phosphodiester bond w/ DNA ligase
34
Q

What is mismatch repair? What removes mismatch? What fills gap? What reforms phosphodiester bonds? Directionality?

A
  • Prokaryotes and eukaryotes
  • Checks newly synthesized strand mismatches in addition to 3’-5’ exonuclease proofreading activity of polymerases

Strand detection:
- Bacteria: more methylated A’s => older => template | less methylated => younger => new strand
-Humans: detects nicks prior to DNA ligase sealing of Okazaki fragments

  • Bacteria fill base gap w/ DNA polymerase I and missing phosphodiester bond w/ DNA ligase
  • Human fill base gap w/ DNA polymerase delta and missing phosphodiester bond w/ DNA ligase
  • There is directionality in mismatch repair
35
Q

What is SOS response: translesion synthesis?

A
  • Prokaryotes and eukaryotes
  • Last resort
  • Allows replication to proceed across damaged template strands even though accurate replication is not possible
  • Increased replication errors, desperate/risky attempt to escape lethal effects of heavily damaged DNA
36
Q

What is postreplication repair?

A
  • Prokaryotes and eukaryotes
  • Doesn’t repair w/ TT dimer, but replicates around dimer => template strand still has dimer
  • Restarts replication downstream of dimer
  • Gap is filled by homologous recombination from sister chromatid, using recombinase A
37
Q

What is mechanism of DNA recombination? What is the Holliday model?

A

Homologous chromosome recombination: crossing over b/t nonsister chromatids during prophase of first meiotic division

Holliday model: a model for homologous recombination - looks like a cross

38
Q

What is xeroderma pigmentosum? (XP) What is the phenotype?

A

A defect in DNA repair that is autosomal recessive resulting from defects in 9 different genes (6 involved in nucleotide excision repair/exinuclease activity)

Phenotype: extreme sensitivity to sunlight, intense freckling, skin cancer