chapter 11 part 2 Flashcards
mutagens
agents that cause DNA damage
induced mutations
produced by mutagens in an experimental setting to study types of damage caused, mutation process, or repair responses
chemical mutagens can be classified by their modes of action on DNA as:
- nucleotide base analogs
- deaminating agents
- alkylating agents
- oxidizing agents
- hydroxylating agents
- intercalating agents
intercalating agents
molecules that fit between DNA base pairs and distort the DNA duplex
what does distortion from intercalating agents lead to
DNA nicking that is no efficiently repaired
- results in added or lost nucleotides
DNA stains that are intercalating agents
- ethidium bromide
- acridine orange
photoproducts
aberrant structures with additional bonds involving nucleotides
what are photoproducts caused by
UV irradiation
pyrimidine dimers
produced by formation of one or two additional covalent bonds between adjacent pyrimidine nucleotides
2 common types of photoproducts
- thymine dimer
- 6-4 photoproduct
thymine dimer
formed between 5 and 6 carbons of adjacent thymines
6-4 photoproduct
formed by bond between carbon 6 on one thymine and carbon 4 on other
types of radiation higher than UV
X-rays, gamma rays, radioactive materials
most serious damage from radiation
single-stranded or double-stranded breaks in DNA
what can ss or ds breaks block
DNA replication
how do organisms preserve the fidelity of DNA
using multiple repair systems
how to multiple repair systems fix problems
directly repair DNA or allow organism to circumvent the problems
most direct way to repair DNA
proofreading activity of DNA polymerase
- 3’ to 5’ exonuclease activity
do humans have photo reactive repair?
no
is photo reactive repair direct?
yes
direct repair of UV-induced photoproducts
- photo reactive reapir
enzyme photolyase uses energy from visible light to break bonds between pyrimidine dimers
what is photolyase encoded by
E. coli phr (photo reactive repair) gene
how is DNA damage by alkylating agents repaired
by enzymes that remove the added chemical groups to restore the nucleotide to its normal form
what is the direct repair of damage by alkylating agents performed by
class of enzymes called alkyltransferases
alkyltransferases
- remove alkyl groups (methyl/ethyl)
- can reverse effects of EMS and NG
ex. of alkyltransferases
- O6-methylguanine is converted back to guanine by enzyme O6-methylguanine methyltransferase
- enzyme permanently inactivated after one such reaction
nucleotide base excision repair (BER)
multistep process that may repair damage to a nitrogenous base or replace an incorrect base
DNA glycosylases
series of enzymes that recognize specifically modified/incorrect bases and remove modified purine bases
- leaves an AP site
AP site
apurinic/apyrimidic site - no base
nucleotide base excision repair
- DNA glycosylases recognize incorrect base, remove it, and leave AP site
- AP endonuclease creates single-stranded nick near AP site
- nick translation - DNA polymerases initiate removal/replacement of nucleotides including AP site
- DNA ligase seals sugar-phosphate backbone
nucleotide excision repair (NER)
used to repair UV-induced damage to DNA
what is nucleotide excision repair also known as
ultraviolet repair
nucleotide excision repair basic process
- enzymes recognize and bind to damaged region
- segment of nucleotides is removed from the damaged strand
- DNA polymerase fills in gap
- DNA ligase seals the sugar-phosphate backbone
UV repair (NER)
- UVR A and B proteins bind to DNA strand opposite photoproduct
- UVR C joins UVR B to form UVR BC complex
- UVR C cleaves damaged DNA strand about 4-5 nucleotides to 3’ and 5’ sides of the photoproduct
- UVR D (a helicase) helps remove DNA fragment containing photoproduct
- DNA polymerase fills gap and DNA ligase seals backbone
xeroderma pigmentosa
human hereditary cancer-prone condition that is caused by the mutation of any seven different genes involved in NER
symptoms of xeroderma pigmentosa
- extreme UV sensitivity
- develop UV-induced pre-cancerous and cancerous lesions
mismatch repair
detects and repairs mismatched nucleotides that escape DNA polymerase
how do repair enzymes distinguish between the original, correct nucleotide and the new, mismatched nucleotide
using presence of methylation on original strand
- E. coli: methylation common on adenine of 5’GATC3’
mismatch repair process
- MuhH binds to hemimethylated DNA region
- MutS locates/binds to DNA mismatch and then forms a complex with MutL
- MutS/MutL complex binds to MutH
- MutH protein breaks phosphodiester bond on 5’ side of guanine on unmethylated daughter strand
- exonuclease enzymes digest nucleotides from nick
- DNA polymerase fills gap on daughter strand
- DNA ligase completes the repair
- Dam methylate methylates the adenine of the GATC sequence on the daughter strand
what do DNA damage signaling systems to
- recognize presence of
DNA lesions - initiate repair response
ATM
plays pivotal role in communicating DNA damage to activate transcription of p53 gene
what does ATM activate
p53 repair pathway
p53 repair pathway
controls cell responses to mutation
how does p53 repair pathway control cell responses to mutation
- pauses cell cycle at G1-to-S transition to allow time for repair
- initiates apoptosis
p53 levels are ______ in healthy cells
low
p53 levels ________ as ATM levels __________
increase, increase
how does p53 initiate G1 arrest
by inducing synthesis of p21
p21
inhibits formation of cyclin-CDK complexes
what do completed repairs do to the p53 levels
- reduce them
- allows cell cycle to proceed
what does the synthesis of p21 allow
time to repair damaged DNA
p53 activates transcription of the ______ gene
BAX
BAX gene
encodes a slowly acting inhibitor of BCL2
what does BCL2 repress
apoptosis
activity of BCL2 protein in healthy cells
mains repression of apoptosis
activity of BCL2 protein in damaged cells
if p53-induced pause is too long, then apoptotic pathway is induced when BCL2 inhibited
SOS repair system is activated in response to what?
heavily damaged DNA in E. coli cells
how is SOS repair accomplished
by activation of translesion DNA polymerases
another name for translesion DNA polymerases
bypass polymerases (Pol V)
translesion polymerases
error-prone polymerases that have no proofreading ability and can replicate across lesions that would stall DNA pol III
SOS repair in E. coli
- when pol III stalls at damaged DNA, RecA proteins coat the template strand ahead of the lesion (already bound by SSB protein) to form a DNA-RecA-SSB complex
- RecA also activates transcription of pol V
- Pol V displaces pol III, synthesizes short stretch of new DNA across lesion, and is then replaced by pol III which resumes normal replication
what happens when both strands of DNA are broken
neither can act as a template for repair
how can double-stranded breaks happen
exposure to X-rays and certain types of oxygen radicals
what can double-stranded breaks cause
- chromosome instability
- incomplete replication
- cell death
- increase risk of cancer
- chromosome structure mutations
2 mechanisms for carrying out double-stranded break repair
- non-homologous end joining
- synthesis-dependent strand annealing
