DNA Damage, Repair, and Recombination Flashcards
meiotic recombination allows _
gene diversity
mitotic recombination allows _
mutations repair in somatic cells
site specific recombinations
used by viruses and transposons to integrate into host, only at specific sites
phage recombination is an example of _
site specific recombination
transposons
regions of DNA that can duplicate and jump from one position in the genome into another
homologous recombination
occurs between two DNA molecules that share sequence homology
V(D)J recombination in antibodies is _
site specific recombination
damage
affects the structure of DNA molecule (usually chemical)
mutation
affects the transmission of information in DNA (usually occurs after replication of damaged DNA)
multisite mutations
cause gross chromosome abnormalities and affect large regions of DNA; arise during meiosis
types of multisite mutations
inversions, duplications, deletions, insertions, substitutions
point mutations
affect only 1 or 2 nucleotides and arise during DNA replication
point mutations require _
an error during DNA replication and failure to correct the error
types of point mutations
inversions, duplications, deletions, substitutions, insertions
types of substitutions
transitions or transversions
transitions
purine to purine (A to G) or pyrimidine to pyrimidine (T to C)
types of substitutions within coding regions
missense, nonsense, and frameshift
What is the first defense against point mutations?
3’ to 5’ exonuclease activity of the DNA polymerases
types of damage that cause mutations
base tautomerization, pyrimidine dimer, hydroxylation, deamination, base loss, strand breaks, and methylation/alkylation
base tautomerization
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
dimerization
thymine dimers caused by UV damage
hydroxylation
mediated by free radicals; 8-oxodeoxyguanosine can base pair with A or C
spontaneous deamination
adenosine to hypoxanthine, guanine to xanthine, and cytosine to uracil
Why is spontaneous deamination possible?
3 of the 4 bases have exocyclic amino groups
hypoxanthine
deamination of adenosine; base pairs with cytosine
base loss
depurination, depyrimidination; results in abasic site (removes deoxy ribose + phosphate)
types of chemical mutagens
chemicals that accelerate deamination reaction, base analogues, alkylation agents, intercalation agents
nitrous acid & derivatives
chemicals that accelerate deamination reaction
alkylating agents
dimethyl sulfate (DMS methylates guanine) and ethylmethane sulfate (EMS ethylates guanine)
base analogues
5-bromouracil will be treated as a thymine (can base pair with A but also G)
Ames assay
take mutant E. coli –> plate them without histidine –> add substance of interest –> if it induces growth of the bacteria, it is a mutagen
recombination repair/homologous recombination occurs in _
S and G2 phase when there is a spare copy (template strand to correct damage)
homologous recombination is used to repair _
double stranded breaks
non-homologous end joining happens when _
there is no template available, usually G1 phase
non-homologous end joining is used to repair _
double stranded breaks
NHEJ process
double stranded breaks are repaired by ligating ends together
mismatch repair must be able to _
distinguish parent from daughter strand
How does mismatch repair identify the daughter strand?
adenines are methylated during replication so there will be a methylated adenine on the parent strand but no methylation on the daughter strand
mismatch repair process
mutH nicks the unmethylated strand –> uvrD (helicase) and exonuclease remove the strand back to mismatch –> pol III fills gap and ligase fixes nick
mutH
binds the hemimethylated A
mutS
binds the mismatch
mutL
brings mutS and mutH together
base excision repair is used to correct _
single strand break or single-base damage
base excision repair recognizes _
deaminated bases
base-excision repair steps
DNA glycosylase removes damaged base –> AP endonuclease cuts the backbone of the abasic site –> DNA polymerase I adds new bases –> DNA ligase seals nick
Why do cells use thymine in DNA rather than uracil?
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
nucleotide excision repair is used to correct _
bulky lesions and crosslinks
nucleotide-excision repair process
enzymes recognize kink –> nick the DNA –> remove damaged strand –> DNA polymerization –> ligation
nucleotide excision repair is more active in _
transcribed DNA because repair factors are associated with RNA polymerase
SOS response in bacteria
lexA repressor is bound to SOS genes, turning off the repair system –> damage encountered –> recA removes lexA –> SOS genes transcribed
translesion DNA synthesis occurs when _
there is damage to both strands and there is no sister strand to copy from
translesion DNA synthesis process
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
TLS is activated by _
SOS response
exceptions to mutations in the repair system being lethal
Lynch syndrome, xeroderma pigmentosum, BRCA cancers
Lynch syndrome
missing enzymes needed to for the mismatch repair (MutS and MutL)
xeroderma pigmentosum
person is unable to repair pyrimidine dimers (no nucleotide excision repair)
BRCA1
associates with RNA polymerase to help repair double stranded breaks in DNA, mismatch repair, and recombination repair
accelerated aging diseases from deficiencies in DNA repairs
Bloom syndrome, cockayne’s syndrome, Fanconi’s anemia, Werner syndrome
