Aging & DNA Repair Flashcards
(23 cards)
What is the DNA damage theory of aging?
It suggests that aging is a consequence of unrepaired accumulation of naturally occurring DNA damage
What is the difference between DNA damage and DNA mutation?
DNA damage is the alteration in the chemical structure of DNA, while DNA mutation is an alteration in the DNA sequence, DNA damage can be repaired by the DNA repair system however if it fails it might lead to DNA mutation
What are the Purine bases?
1) Adenine
2) Guanine
What are the pyrimidine bases?
1) Thymine
2) Cytosine
3) Uracil
What are the types of Genomic DNA damage?
1) Single-base alteration
2) Two-base alteration
3) Chain breaks
4) Cross links
What are the different types of DNA damage that are caused by Single-base alteration?
1) Depurination
2) Deamination
3) Interaction with reactive metabolites
4) Base analog incorporation
What is Depurination?
It is the spontaneous hydrolysis of a purine base (Adenine & guanine), leaving an empty space AP site (Apurinic/Apyrimidinic)
- Affects 5000 bases per cell per day
What is Deamination?
A type of DNA damage via the spontaneous hydrolysis of the amine group (it is the removal of the amine group), converting
- cytosine to uracil
- Adenine to Hypoxanthine (can base pair with cytosine)
- Guanine to xanthine (can base pair with cytosine)
- Affects 100 Uracil per cell
What is meant by interaction with reactive metabolite?
- Oxidative Damage by the ROS produced by the metabolic pathway which can interact with the nucleotide
- Alkylation of a base (Addition of an alkyl group “-CH3” affecting guanine most often, converting it to Adenine which will paint with thymine instead of cytosine, with aging it can be permanent
What is meant by base analog incorporation?
It is the incorporation of 5-Bromouracil into the DNA sequence which is regarded as thymine and will bind to adenine, causing the adenine to be read as guanine where the tautomeric shift will come and substitute it for guanine and bind a cytosine to it resulting in a base substitutions and, as a result, mutations.
What is an example of DNA damage caused by Two-base alteration?
UV light-induced thymine-thymine dimer
Explain UV light-induced thymine-thymine dimer
It is when the exposure of DNA to UV light causes the thymine to stick together forming a dimer
What is meant by the process (Chain break) which causes DNA damage?
It is both single and double-stranded DNA mutation caused by ionizing radiation and free radicals
What are the two points that make repairing DNA damage possible?
1) A damaged base causes a mismatch between the bases which causes a defect in the double helix & can be detected by enzymes
2) The undamaged complementary DNA strand provides the needed information to repair the damaged strand
- Undamaged complementary chain usually has more methylated groups
Describe the mechanism of cross-link mutation
- It is between bases in the same (Intrastrand cross link) or opposite (interstrand cross link) strand or DNA & protein molecules
- Cross-linking stops DNA polymerase from continuing the addition of nucleotides.
- The proteins formed will be smaller and mutations may occur if DNA doesn’t get repaired.
What are the “common” steps in DNA repair? (the doctor will ask about this she said)
1) Excision (removal of the damaged site by endo (cuts before the damage site) /exonucleases (Cuts after the damage site))
2) Resynthesis (replacing the missing nucleotide base using DNA polymerase)
3) Ligation (Seals the nick in sugar-phosphate backbone using “DNA ligase”)
What are the different mechanisms of DNA repair?
1) At the same time as DNA replication
- Proofread repair (during DNA replication DNA polymerase checks its work with each base)
2) Right after DNA replication
A) Mismatch repair
B) Base excision repair
C) Nucleotide excision repair (Mostly occurs with significant DNA error)
D) Double-strand break repair (a spare chromosome is used)
What is a nick?
It is a discontinuity in a double-stranded DNA, where there is no phosphodiester bond between adjacent nucleotides
Describe the process of mismatch repair
- Complementary strand is recognized as it is highly methylated
1) Endo and Exo nucleases remove the damaged site
2) The DNA polymerase adds the correct base for resynthesis
3) DNA ligase seals the site
Describe the process of Base excision repair
It corrects spontaneous chemical or radiation damage to a single base by removing the incorrect base created in an AP (Apurinic, Apyrimidinic) site and then proceeds like mismatch repair
Describe the process of Deamination repair
The damage started by deamination (Cytosine to Uracil)
1) Uracil N-glycosylase excises the base creating an AP site
2) AP endonuclease creates a nick before the AP site
3) Exonucleases create a nick after the AP site
4) DNA polymerase re-synthesizes the complementary start again
5) DNA ligase seals the nicks
What is nucleotide excision repair? (Very important is the fact that it can correct up to 30 bases)
- Corrects spontaneous chemical/radiation damage to a DNA segment (up to 30 bases in length)
- Corrects (UV-causing pyrimidine-pyrimidine dimers, smoking-causing adducts, strand breaks, & cross linkages
- It is a complex process involving complex damage
Describe the process of nucleotide excision repair
for example, let’s imagine that UV radiation produced a thymine dimer
1) Once thymine is detected, the surrounding DNA is opened to form a bubble via helicase enzyme (DNA-opening enzyme)
2) Nucleases chop out the damaged part of the DNA
3) DNA polymerase (replaces the missing DNA)
4) DNA ligase seals the gap in the backbone
