Flashcards in DNA Replication, Repair And Recombination II Deck (50):
How often does spontaneous deamination of C to U occur?
What are two additional ways that DNA damage can occur?
From exposure to reactive forms of O2 in the cell or chemicals in the environment.
UV radiation from the sun can produce a covalent linkage between two adjacent pyrimidines.
What happens if DNA is unrepaired when it replicates?
Changes in the DNA lead to either a deletion or a base pair substitution in the daughter strand.
What are the types of repair for damaged DNA?
Base excision repair
Nucleotide excision repair
Transcription-coupled repair (non-homologous end joining and homologous recombination)
What is the function of DNA glycosylases?
They each recognize a specific type of altered base and catalyze its removal.
What happens when DNA glycosylases find an incorrect base?
It cleaves a glycosyl bond connecting base with sugar.
What do AP endonuclease and phosphodiesterase do?
They cute the phosphodiester backbone, which removes the damage and repairs the gap.
What are depurinations diretly repaird with?
What does nucleotide excision repair involve?
The repair of any bulky lesions, such as thymine dimers.
In nucleotide excision repair, what is the function of a multienzyme complex?
It scans DNA for distortion in double helix instead of specific base change.
What does the multienzyme complex in nucleotide excision repair do?
It cleaves phosphodiester backbone on both sides.
A DNA helicase then peels the lesion containing strand away.
In nucleotide excision repair, a large gap left from removing a faulty strand of DNA is repaired by what two enzymes?
DNA polymerase and ligase
True or false: cells can preferentially direct DNA repair to sequences that are being actively transcribed by linking RNA polymerase with DNA repair.
RNA polymerase stalls at lesions and directs repair machinery there.
True or false: repair mechanisms are specific for the strand being transcribed.
What is Cockayne's Syndome?
It is a defect in the transcrption-coupled repair.
It causes growth retardation, skeletal abnormalities and sensitivity to sunglight.
How is the DNA molecule optimally constructed for repair?
It has 2 strands that are backup copies.
The nature of the 4 basese makes distinction between damaged and undamaged DNA obvious, since every deamination event forms an unnatural base.
What is a possible reason that RNA is not the hereditary information?
Because every deamination event does not form an unnatural base.
It is impossible to distinguish between deaminated cytosine and natural uracil.
What problem exists with with methlyated cytosince in vertebrate DNA?
Deamination of methyl-C produces T mismatched with G.
A special DNA glycosylase recognizes and removes the T, but the rEpair is relatively inaffective.
They account for 1/3 of all point mutations associated with inherited human diseases.
What enzyme is used when the cell has sustained extensive damage?
They use less accurate, backup polymerases to reapir damage.
How many different polymerases recognize different types of damage?
They lack exonuclease proofreading ability, and they add only a couple of nucleotides before the replicative polymerase reassociates.
What causese double stranded breaks?
If double stranded breaks are not repaired, what happens?
Chromosomes break into smaller fragments and are lost.
One or more nucleotides would also be lost.
In order to maintain intact and undamaged DNA from one generation to the next, what are additional types of regulation?
Checkpoints - ensure completion of one stage in the cell cycle before the next can begin.
When there is DNA damage, what checkpoints are triggered?
Entery from G1 into S phase is blocked.
Progression through S phase is slowed down.
Transition from G2 to M phase is blocked.
All of these give the cell extra time to repair DNA damage.
What is ATM protein?
A kinase that generates intracellualr signals that alert the cell to DNA damage and upregulate expression of DNA repair genes.
What occurs when there is a mutation in ATM protein?
Ataxia telengiectasia occurs.
Symptoms include neurodegeneration, predisposition to cancer, genonme instability due to unrepaired DNA lesions.
What is homologous recombiation?
Genetic exchange between a pair of homologus DNA sequences.
What three processes are associated with homologus recombination?
Repair of double stranded breaks
Exchange of genetic infomation to create enw combinations of genetic sequences
Mechanical role in assuring accurate chromosome segregation.
Homologous recombination takes place between sequences that are _____
During homologous recombination, what do DNA duplexes do?
They sample each othe rlooking for regions of homology.
What is hybridization?
When the DNA double helix reforms from its separated single strands.
IT is also called reaturation.
When reparing double stranded breaks, the 5' end is degraded by what enzyme?
When repairing doubl stranded breaks, what occurs at the 3' end?
One 3' end invades the homologous template and primes repair for DNA synthesis.
During the repair of double stranded breaks in DNA, the newly synthesized 3' end of the invading strand does what?
It anneals the other original 3' overhand in the damaged chromosome through complementary base pairing.
What does DNA hybridization require?
A single-stranded DNA.
It is freed from pairing with complement so it can pair with the second strand.
DNA synapsis reaction -
Binds cooperatively to a single-stranded DNA and holts it in a unique configuration, with the backbone stretched out.
Singl strand "searches" the duplex 3 nucleotides at a time via an unknown mechanism.
Once a homologous sequence is identified, strand invasion occurs, forming heteroduplex.
HR to repair stalled or broken replication forks - initially, what occurs?
Exchange takes place between similar sequences.
Process requires base pairing but it doesn't have to be a perfect match.
Once a nick in damaged DNA is found, what happens to the replication fork?
5' exonuclease chews back the parental strand to prepare for "strand invasion."
What is strand invasion?
When single-stranded DNA pairs with a complementary strand in different double-stranded helix.
This forms a region of heteroduplex DNA.
How can an accurate repair process still cause problems for a cell?
The use of a non-functioning homolog to repair another homolog causese a loss of heterozygosity.
The process of borken ends in coordinated in the cell cycle. When is it coodianted?
Nucleases for generating 3' invading strand are only active in S and G2 phase.
This ensures a replicated chromosome or sister chromatid will be the most likely template for repair.
What prevents repair in the absence of damage?
Loading of rec A on DNA.
True or false: repair proteins are dispersed throughout the cell.
After damage, repair occurs in "factories" or "foci" at the sites of damage.
True or false: mutations in proteins involved in recombination can cause cancer.
Brca1 and Brca2 lead to increased rates of breast cancer.
What is the function of Brca1?
It regulates the processing of broken ends of chromosomes.
Mutations lead to use of non-homologous end-joining processes.
What is the function of Brca2?
It maintains RecA inactive until it is at the site of damage.
It does not bind to DNA to form invading strand.
What are key features of non-homologus end joining?
No template is required
A mutation is created at the site of repair
Translocations are also created.
What are key features of homologous recombination?
Use of daughter DNA duplex as a template
No loss or alteration of DNA at repair site
Can repair other types of DNA damage.
it is very versatile, and the mechanism and proteins are conserved in all organisms.