1- DNA Damage and Repair Flashcards
What are the types of spontaneous lesions?
Depurination- linkage to deoxyribose hydrolyzes (about 5,000 purine bases cell loses every day)
Deamination- cytosine changed to uracil (100 bases per cell per day)
What is a bulky lesion? And what causes them?
Covalent linkages in DNA
Could be due to reactive oxygen, sunlight or carcinogens between adjacent nucleotides.
What is a mutagen?
Agent which can alter the structure or sequence of DNA.
Chemical or Physical
What are the 4 types of chemical mutagens?
Base analogs- Substitutes for base. Structurally resemble purine and pyrimidines and may be incorporated into DNA during replication (ex. 5-bromo-uracil)
Intercalating agents- insert between double helix (usually flat with many rings.) Causes stretching of double helix and DNA polymerase inserts extra bases opposite of it. (ex. proflabin or acradine orange)
Direct Acting agents- Chemically react with DNA directly (ex. alkylating agents, nitrisoguanine)
Indirect acting agents- Require metabolic conversion before actively altering DNA (usually by a cytochrome p-450 dependent mechanism) (ex. benzopyrene)
What are the types of physical mutagens?
UV radiation- causes excitation or change in energy level of an electron
Ionizing radiation- causes ionization or loss of an electron. (ex X-ray…)
Does shorter or longer wavelengths of radiation have higher energy?
Shorter wavelengths are have higher energy and cause more damage.
What is the wavelength of UV-A radiation?
What does it do to DNA?
Longest wavelength
About 90-95% UV radiation that reaches earth
It induces oxidative damage and double strand breaks.
UV B wavelength
What it does to DNA?
Medium wavelength
about 5-10% of solar radiation
Induces dimers between adjacent pyrimidines
— covalent linkages between two pyrimidine bases on the same strand.
Accounts for more superficial damage to epithelial layers of the skin. SUNBURNS
UV C wavelength
What it does to DNA?
Shortest wavelength
Most is filtered out by ozone.
“Germicidal”
What are the two forms of ionizing radiation?
- electromagnetic– x-rays, gamma rays radiation threapy
- - “Wave” form of ionizing radiation - Particulate– from decaying radioactive material
- - alpha particles(helium nuclei) , Beta particles(high speed electron)
Base Excision Repair (BER)
What are the 4 enzymes and steps for repair?
Repairing spontaneous (small) lesion- one base
- DNA glycosylases(base specific)- scan DNA ‘flip’ out base to check for spontaneously damaged bases. 6+ enzymes that all recognize different damages. Once recognized, base is cut off.
- AP endonuclease- recognizes missing base, cuts out phosphodiester backbone.
- DNA Polymerase- add new nucleotide
- DNA ligase seals the nick
Nucleotide Excision Repair
What are the 4 enzymes and steps?
Repairs bulky lesiosn (large) like pyrimidine dimers.
- Multienzyme complex (excision nuclease)- Scans for distortion of DOUBLE helix. Cleaves phosphodiester backbone on both sides of distortion.
- DNA helicase- remove single strand between the breaks.
- DNA polymerase- Add new nucleotides
- DNA ligase- Stitch it back together.
Mismatch Repair (MMR)
What are the 2 proteins associated with this?
Follows DNA pol during synthesis directly following replications.
- MutS
- MutL
MutS and MutL bind to mismatched base and direct excision of DNA between ss break and the mismatch
DNA polymerase fills in nucleotides
How do they think newly synthesized strand is recognized during MMR?
Nicks that are made to the leading and lagging strand from where they are ‘stitched’ back together.
Replicative repair
During DNA synthesis
3’ to 5’ Nuclease activity. If wrong base DNA shifted to E site for correction.
When DNA polymerase can’t repair it (heavily damaged DNA,) there are 10+ backup DNA Polymerases
- – Backups are less accurate, guess at sequence.
- – Backups have no exonucleolytic activity
Transcription coupled repair (TCR)
- RNA poly II stalls at lesions, directs repair machinery to site of error.
- RNA pol II likely remodeled
- - CSB recognizes stalled RNA pol II and recruits TFIIH
- - TFIIH remodels RNA pol II
- - XPG cuts DNA - Lesion is repaired, RNA pol II restarts
Not as accurate as DNA pol
Actively transcribed genes repaired preferentially
What causes double strand breaks?
What are the two mechanisms to fix these breaks?
Caused by radiation, errors and oxidation
- non homologous end joining
- - less accurate
- - ends brought together and ligated
- - loss of nucleotide occurs - Homologous recombination
- -More accurate
- -Sister chromatid used as template
Non homologous end joining
What are the 3 molecules involved?
- Ku70/80 recognize the end of DNA breaks
- DNA PK recruited –> acts as a kinase to recruit ligase
- DNA ligase- ligates the ends
Homologous Recombination
Double strand break
Ends of break make 3’ ss overhangs
Rad51 pair overhang with homologue on sister chromatid
DNA syn occurs using sister chromatid as template
– holiday junction is formed, resolved, and cleaved from sister chromatid.
When do the 3 checkpoints for DNA damage occur?
What is the main player in the checkpoints?
G1 to S, Slows S and S to M
ATM protein- kinase that sends intracellular signals when damaged DNA is spotted
What is the ATM pathway?++++
What are the targets of ATM?
ATM (sensor of damage) associates with damage, phosphorylates targets which leads to cells arrest.
Target proteins
p53- normally bound to Mdm2 and degraded
– p53 phosphorylated and acts as transcription factor to turn on p21
p21- binds G1/S Cdk or S-Cdk to inhibit them. stops cycle
How does the cell know to stop when telomeres get too short?
Ends of chromosomes are exposed and eventually activate p53 dependent cell cycle arrest.
What are the proteins targeted by ATM to stop M Cdk activation?
Chk1 and Chk2
