DNA Damage, Repair, and Recombination

Question 1

meiotic recombination allows _

Answer 1

gene diversity

Question 2

mitotic recombination allows _

Answer 2

mutations repair in somatic cells

Question 3

site specific recombinations

Answer 3

used by viruses and transposons to integrate into host, only at specific sites

Question 4

phage recombination is an example of _

Answer 4

site specific recombination

Question 5

transposons

Answer 5

regions of DNA that can duplicate and jump from one position in the genome into another

Question 6

homologous recombination

Answer 6

occurs between two DNA molecules that share sequence homology

Question 7

V(D)J recombination in antibodies is _

Answer 7

site specific recombination

Question 8

damage

Answer 8

affects the structure of DNA molecule (usually chemical)

Question 9

mutation

Answer 9

affects the transmission of information in DNA (usually occurs after replication of damaged DNA)

Question 10

multisite mutations

Answer 10

cause gross chromosome abnormalities and affect large regions of DNA; arise during meiosis

Question 11

types of multisite mutations

Answer 11

inversions, duplications, deletions, insertions, substitutions

Question 12

point mutations

Answer 12

affect only 1 or 2 nucleotides and arise during DNA replication

Question 13

point mutations require _

Answer 13

an error during DNA replication and failure to correct the error

Question 14

types of point mutations

Answer 14

inversions, duplications, deletions, substitutions, insertions

Question 15

types of substitutions

Answer 15

transitions or transversions

Question 16

transitions

Answer 16

purine to purine (A to G) or pyrimidine to pyrimidine (T to C)

Question 17

types of substitutions within coding regions

Answer 17

missense, nonsense, and frameshift

Question 18

What is the first defense against point mutations?

Answer 18

3’ to 5’ exonuclease activity of the DNA polymerases

Question 19

types of damage that cause mutations

Answer 19

base tautomerization, pyrimidine dimer, hydroxylation, deamination, base loss, strand breaks, and methylation/alkylation

Question 20

base tautomerization

Answer 20

an adenine tautomer (double bond at C6) can now bond to cytosine –> will now cause G-C base pair after replication instead of the normal A-T

Question 21

dimerization

Answer 21

thymine dimers caused by UV damage

Question 22

hydroxylation

Answer 22

mediated by free radicals; 8-oxodeoxyguanosine can base pair with A or C

Question 23

spontaneous deamination

Answer 23

adenosine to hypoxanthine, guanine to xanthine, and cytosine to uracil

Question 24

Why is spontaneous deamination possible?

Answer 24

3 of the 4 bases have exocyclic amino groups

Question 25

hypoxanthine

Answer 25

deamination of adenosine; base pairs with cytosine

Question 26

base loss

Answer 26

depurination, depyrimidination; results in abasic site (removes deoxy ribose + phosphate)

Question 27

types of chemical mutagens

Answer 27

chemicals that accelerate deamination reaction, base analogues, alkylation agents, intercalation agents

Question 28

nitrous acid & derivatives

Answer 28

chemicals that accelerate deamination reaction

Question 29

alkylating agents

Answer 29

dimethyl sulfate (DMS methylates guanine) and ethylmethane sulfate (EMS ethylates guanine)

Question 30

base analogues

Answer 30

5-bromouracil will be treated as a thymine (can base pair with A but also G)

Question 31

Ames assay

Answer 31

take mutant E. coli --> plate them without histidine --> add substance of interest --> if it induces growth of the bacteria, it is a mutagen

Question 32

recombination repair/homologous recombination occurs in _

Answer 32

S and G2 phase when there is a spare copy (template strand to correct damage)

Question 33

homologous recombination is used to repair _

Answer 33

double stranded breaks

Question 34

non-homologous end joining happens when _

Answer 34

there is no template available, usually G1 phase

Question 35

non-homologous end joining is used to repair _

Answer 35

double stranded breaks

Question 36

NHEJ process

Answer 36

double stranded breaks are repaired by ligating ends together

Question 37

mismatch repair must be able to _

Answer 37

distinguish parent from daughter strand

Question 38

How does mismatch repair identify the daughter strand?

Answer 38

adenines are methylated during replication so there will be a methylated adenine on the parent strand but no methylation on the daughter strand

Question 39

mismatch repair process

Answer 39

mutH nicks the unmethylated strand --> uvrD (helicase) and exonuclease remove the strand back to mismatch --> pol III fills gap and ligase fixes nick

Question 40

mutH

Answer 40

binds the hemimethylated A

Question 41

mutS

Answer 41

binds the mismatch

Question 42

mutL

Answer 42

brings mutS and mutH together

Question 43

base excision repair is used to correct _

Answer 43

single strand break or single-base damage

Question 44

base excision repair recognizes _

Answer 44

deaminated bases

Question 45

base-excision repair steps

Answer 45

DNA glycosylase removes damaged base --> AP endonuclease cuts the backbone of the abasic site --> DNA polymerase I adds new bases --> DNA ligase seals nick

Question 46

Why do cells use thymine in DNA rather than uracil?

Answer 46

if DNA was U and C rather than C and T, you would not know if the U was supposed to be there or if it was just a deaminated C

Question 47

nucleotide excision repair is used to correct _

Answer 47

bulky lesions and crosslinks

Question 48

nucleotide-excision repair process

Answer 48

enzymes recognize kink --> nick the DNA --> remove damaged strand --> DNA polymerization --> ligation

Question 49

nucleotide excision repair is more active in _

Answer 49

transcribed DNA because repair factors are associated with RNA polymerase

Question 50

SOS response in bacteria

Answer 50

lexA repressor is bound to SOS genes, turning off the repair system --> damage encountered --> recA removes lexA --> SOS genes transcribed

Question 51

translesion DNA synthesis occurs when _

Answer 51

there is damage to both strands and there is no sister strand to copy from

Question 52

translesion DNA synthesis process

Answer 52

damaged bases prevent NHEJ --> allows replication to continue over the damaged base, inserting a random base --> must accept the mutation and just ignore the damaged base

Question 53

TLS is activated by _

Answer 53

SOS response

Question 54

exceptions to mutations in the repair system being lethal

Answer 54

Lynch syndrome, xeroderma pigmentosum, BRCA cancers

Question 55

Lynch syndrome

Answer 55

missing enzymes needed to for the mismatch repair (MutS and MutL)

Question 56

xeroderma pigmentosum

Answer 56

person is unable to repair pyrimidine dimers (no nucleotide excision repair)

Question 57

BRCA1

Answer 57

associates with RNA polymerase to help repair double stranded breaks in DNA, mismatch repair, and recombination repair

Question 58

accelerated aging diseases from deficiencies in DNA repairs

Answer 58

Bloom syndrome, cockayne's syndrome, Fanconi's anemia, Werner syndrome