Lecture 4 Flashcards
Mutations doe not only occure because of mistakes in replication
spontaneous DNA damage
What needs to be repaired in DNA
replications errors
accidental lesions
What is the spontaneous reaction to which 5000 purines are lost every day?
depurination
hydrolysis of the N-glycosyl linkage
What spontaneously occurs with 100 C to U bases/ day?
damination
What is caused by UV readation from the sun, or chemicals in the environment?
Produce a covalent linakge btw two adjacent pyrimidines (T-T) or (C-T)
purimidine dimers
What if DNA goes unrepaired?
deletion or base pair substitution in the duaghter strand
Base excision repair
Takes out the base, small repair
BER, six different types
- each recognizes a specific type of altered base and catalyzes its removal
DNA glycosylases
BER… Enzyme probes for damage by…
flipping out of base from helix to check if it is correct
BER, What happens if DNA glycosylases find an incorrect base?
cleaves glycosyl bond connecting base w sugar
BER What cuts the phosphodiester backbone to remove and repair gap?
AP endonuclease and phosphodiesterase
BER what are directly reapired begging w AP endonuclease?
depurinations
BER What adds new nucleotides/
DNA polymerase
What seals nick in DNA
DNA ligase
nucleotide excision repair…
repairs any bulky lesion like those chemically induced and thymine dimers
How does NER work?
a multienzyme complex scans DNA for distortion in double helix instead of specific base change
What does NER cleave?
phosphodiester backbone on both sides; DNA helicase peels lesion containg strand away
With NER what is the large gap repaired by?
DNA polymerase and ligase
Transcription coupled repair
cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair
- sequences that urgentyl need repair
TCR repairs by?
RNA plymerase stalls at lesions and directs repair machinery there
How does TCR work with BER, NER and others to repair genes?
Repairs genes that are being expressed when the damage occurs
What is TCR specific too?
the strand being transcribed
TCR
Non- transcribed strand repaired at the same rate as DNA not being trnascribed
- defect in transcritipon coupled repair
- growth retardation, skeletal abnormalitites, sensitivty to light
- RNA polymerase is permanetely stalled at sites of damage in importnat genes
Cockayne’s syndrome
Damage detection
optimal for constructed remair
two strands=backup copy
all 4 bases are distinct so damage is obvious
RNA is not primary bc C and U would not be able to tell defect
special problem with methylated cytosines in vertebrate DNA
occurs at CpG sequences
associtated with inactive genes
deamination of methyl-C produces
T mismatched with G
what recognizes and removes the T
special DNA glycosylase
- repairs ineffectvie
- only 3% of C nucleotides in human genome are methylated, but it counts for 1/3 of all point mutaionts associated with inherited hjman diseases
Causes of double stranded breaks
ionizing, radiation, replication errors, oxidizing agents and other metabolites
if double stranded break is left un repaired
chromosomes would break into smaller fragments and be lost
how does DSB repair work?
non hologous end joining brings broken ends together and rejoins by DNA ligation; one or more nucleotides will be lost
-predominates in humnas and is genreally ok since so little of genome is protein coding
Damage delays the cell cycle
very importnat to maintian intact and undamaged DNA from one gnereation to the next
ensure the completion of one stage in the cell cycle before the next can begin
checkpoints
Presnend of DNA damage triggers various checkpoints
- blocks entry from G1 into S phase
- Slows down progression through S phase
- blocks transition from G2 to M phase
- goves the cell extra time to repair DNA damage
homologous recombination
genetic exchange btw a pair of homolgous DNA sequences
Repair of double stnrad breaks
homologous recombination
-especially at stalled or broked replicaiton forks
exhange of genetic informaiton to create new combinations of gnetic sequences
homologous recombination
-crossing over and gene converstion in meiosis
homologous recombination mechanical role
assuring accurate chromosome segregation
HR to repair stalled or broken replication fork
- exchange takes place btw similar sequences … process requries base pairing but it doesnt have to be a perfect match
- replication fork will collapse and break when nick is encountered
- 5’ exonucleauses chews back parental strand to prepare for strand invation
pairs single standed DNA with complementary strand in different double standed helix
-forms a region of heteroduplex DNA
strand invasion
What happens in stand invasion
- strands break/dissociates
- dAN synthessi continues as replication fork restarts
What guides homolougus recombination?
base-pariing
HR
must be sequences that are similar
DNA dboule helix reforming from its spearated single strands
hybridizatino also called renaturation
once a region of homology is found,
the single strands rapidly pair up
creates a double helix from strands that orginate from different moclecules
heteroduplex DNA
What allows single stranded DNA pairing with homologous double helix
Rec A
What requires a single stranded DNA
DNA hybridization
-freed from pariing with complement so it can pair with the 2nd strand
How is the singld stranded invading strand directed?
RecA(Rad51 in eukaryotes) and other proteins
What happeds after the strand is guided to the SS
DNA synapsis reaction
- beinds cooperatively to SS DNA and holds it together with the double helix until homologous seqence is foudn
- SS searches via an unaknown mechanism
once homologous sequnce is identified…
strand invasion occurs, fomring heteroduplex
Once strand invations occurs, the point of exchang can move through?
Branch migration
Branch migration
unpaired region of one single strand displaces a paired region on the other
-happens spontaneously in both directions or can be catalyzed by special helicase to move in one direction
non-homologous end joinging
- no template requried
- creates a mutation at the site of repair
- can also create translocation
homologous recombination repair
- uses daught DNA duplex as template
- no loss or alteratioon of DNA at repair site
- can repair other tiypes of DNA damage
- very versatile
- mechanism and proteins conserved in all organisms
Repairing double stranded breaks by HR not at a replicaiton fork
- 5’ ends degraded by exonucleases
- one 3’ end invades homologous template and primes repair DNA synthesis
- gaps are filled in and ligated
- the newly synthesized 3’ end of the inading strand is then able to anneal to the other orgiinal 3; overhang in the dmaged chromsome through complementary base pairing
homologous recombination in meiosis is slightly different
has many portine and sturcurual compononets in common
Regulation of homologous recombination
- accurate repair process can still casue problmes for a cell
- use of a non functioning homolog to repair the other homolog
What is a danger of homologous recombination?
loss of heterozygosity
- critcal first step in cancer development
- rare occurance
prevention of repair in the absnece of damage
repair proteins dispersed thoughout the cell
-after damage, repair occurs in factories or foci at the sites of damage
Regulation of homologous recombination of absence of damage
Brca2 maintains Rad51(recA) inactive
-mutations in BRAC2 leads to increase of breast cancer
localization of repair proteins to DNA damage
fibroblasts Xrayed to produce double strand breaks
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