module 10

Question 1

1. define Mutation
2. T or F, Mutations are random and usually deleterious (negative impact)
3. Rates are (low/high?) in all genomes, vary among organisms and among
   different genes within a species

Answer 1

1. heritable/permanent change in sequence of genome (i.e. DNA)
2. True
3. Low

Question 2

What causes gene conversion?

Answer 2

When resolution of recombination junctions in meiosis leads to change from original nucleotides?

Question 3

What happens in Transition mutations?

Answer 3

one purine replaces another, or one pyrimidine replaces another

Question 4

Mutation where a pyrimidine is replaced by a purine or vice versa?

Answer 4

Transversion mutations

Question 5

Point mutations in coding regions (3)?

Answer 5

1. Silent (synonymous)
2. Missense
3. Nonsense

Question 6

Determine the type of point mutation
1. no change in amino acid produced
2. change to stop codon
3. change in amino acid produced

Answer 6

1. Silent (synonymous)
2. Nonsense
3. Missense

Question 7

what are Frameshift mutations?

Answer 7

insertion or deletion of nucleotide
changes reading frame

Question 8

what can introduce premature stop codons?

Answer 8

frameshifts

Question 9

Determine the type of REGULATORY point mutation:

1. alter consensus sequence nucleotides of promoters
2. alter ends of introns, can result in retaining introns in mRNA
3. produce new intron splicing sites
4. block addition of poly-A tail

Answer 9

1. promoter mutations
2. splicing mutations
3. cryptic splice sites
4. polyadenylation mutations

Question 10

What happens in a Forward mutation?

Answer 10

converts a wild-type allele to a mutant
allele

Question 11

Which mutation converts mutant alleles to
wild-type or near wild-type allele?

Answer 11

Reverse mutation or reversion

Question 12

Alterations in number of DNA repeats
occur via what?

Answer 12

strand slippage

Question 13

1. _______ mutation: occurs in tissues not associated with reproduction
   ▪ is not passed to sexually produced offspring
2. germ-line mutation: ____________
   ▪ can be passed to offspring

Answer 13

1. somatic
2. occurs in reproductive cells (i.e., sperm
   and egg)

Question 14

Tautomeric shifts are a problem during DNA replication because what?

Answer 14

minor tautomeric forms base pair with
incorrect nucleotide

Question 15

What happens during Depurination?
(leaves apurinic site)

Answer 15

loss of a purine base by breaking the covalent bond linking the nucleotide base to the sugar

Question 16

After depurination, DNA polymerase will usually compensate by doing what?

Answer 16

putting an adenine opposite the apurinic
site during replication

Question 17

Chemical mutagens can be classified by their modes of action on DNA as? (3)

Answer 17

1. Deaminating agents
2. Nucleotide base analogs
3. Intercalating agents

Question 18

what removes amine groups from nitrogenous bases in DNA?

Answer 18

Deaminating agents

Question 19

What removes amine groups from Adenine and Cytosine, causing mispairing?

Answer 19

nitrous acid (HNO2)

Question 20

What is 5-bromodeoxyuridine?

Answer 20

acts as an analog of thymine (but can pair
with guanine instead of adenine)

Question 21

Molecules that fit between DNA
base pairs and distort the duplex?

Answer 21

DNA Intercalating Agents

Question 22

What is Ethidium bromide used for?

Answer 22

to stain DNA in gel electrophoresis
(is an intercalating agent)

Question 23

What are Photoproducts?

What causes them?

Answer 23

aberrant structures with additional bonds involving nucleotide

caused by UV irradiation

Question 24

_________ _______ have additional covalent bonds between adjacent pyrimidines

Answer 24

Pyrimidine dimers

Question 25

In base excision repair what does DNA glycosylases cut out? What does this leave? T/F The pathway is active throughout cell cycle

Answer 25

incorrect or damaged bases apurinic site

Question 26

Mismatch repair is what type of repair mechanism?

Answer 26

post-replication

Question 27

Repair enzymes distinguish between the original, correct nucleotide and the new, mismatched nucleotide using what?

Answer 27

Methylation on the original strand

Question 28

In E. Coli, the unmethylated strand is cut where?

Answer 28

GATC methylation site

Question 29

Nucleotide Excision Repair recognizes and removes what 2 things caused by UV light damage, that do what to DNA?

Answer 29

Bulky chemical adducts covalent modifications distorts DNA

Question 30

How can pyrimidine dimers be directly repaired?

Answer 30

photoreactive repair

Question 31

What does photolyase use for energy to break bonds?

Answer 31

energy from visible light to break the bonds between pyrimidine dimers

Question 32

The _______ repair mechanism is a ________ mechanism, distinguishing between parent and daughter DNA strands by __________ of the parent strand. a) mismatch; post-replication; methylation b) base excision; pre-replication; acetylation c) photoreactive; post-replication; double-strand breaks d) mismatch; pre-replication; methylation e) nucleotide excision; post-replication; acetylation

Question 33

Two repair mechanisms for double-strand break

Answer 33

Nonhomologous end joining (NHEJ) Synthesis-dependent strand annealing (SDSA

Question 34

Double-strand breaks can be repaired by an error-free process called what and is this before or after replication?

Answer 34

Synthesis-Dependent Strand Annealing, AFTER

Question 35

ORDER THESE STEPS OF Synthesis-Dependent Strand Annealing Sister chromatids re-form, resulting in replacement of the excised DNA with duplex identical to the sister chromatid Trims (excision) one broken strand, Rad51 attaches to resulting 3ʹ overhangs Replication fork at D-loop synthesizes new DNA from the intact template strands Intact sister chromatid has strand invasion by end of broken strand, forms a displacement (D) loop

Answer 35

1. Trims (excision) one broken strand, Rad51 attaches to resulting 3ʹ overhangs 2. Intact sister chromatid has strand invasion by end of broken strand, forms a displacement (D) loop 3. Replication fork at D-loop synthesizes new DNA from the intact template strands 4. Sister chromatids re-form, resulting in replacement of the excised DNA with duplex identical to the sister chromatid

Question 36

What does the p53 repair pathway control? How (2 things)?

Answer 36

cell responses to mutation 1. Pause the cell cycle 2. Direct the cell to undergo programmed cell death

Question 37

In synthesis-dependent strand annealing, why does the repair mechanism result in ‘perfect’ repairs? a) use of a homologous chromosome as template guarantees DNA repair without any sequence changes b) any damaged nucleotides are removed without replacement c) use of a sister chromatid as template guarantees DNA repair without any sequence changes d) any long section with damaged DNA is entirely removed without replacement e) SDSA typically does not result in perfect repairs, instead it usually introduces mutations

Question 38

What initiates homologous recombination?

Answer 38

DNA double strand breaks

Question 39

The exchange of genetic material between homologous DNA molecules

Answer 39

Homologous recombination

Question 40

In eukaryotes when does homologous recombination occur?

Answer 40

Prohphase I of meiosis

Question 41

In holiday junction resolution, when must connection between homologs be resolved?

Answer 41

before metaphase I

Question 42

two ‘north-south’ (NS) resolution or two ‘east west’ (EW) resolution cuts are defined as

Answer 42

Same sense resolution

Question 43

____________ sense resolution is much more common: a resolution in which one Holliday junction is resolved by a NS cut and the other by an EW cut

Answer 43

Opposite sense resolution

Question 44

A simple test with Salmonella typhimurium tests what? two mutant forms of S. typhimurium are used, that cannot synthesize _________, due to ?

Answer 44

the mutagenicity of compounds histidine single base substitution single base frameshift

Question 45

Which of the following is true of the Ames test? (select all that apply) a) used to scan for forward mutations b) reverse mutations indicate a compound is mutagenic c) can detect substitution mutations d) can detect frameshift mutations e) uses mutant strains of E. col