Lecture 32 Flashcards
What are the two categories of DNA repair mechanisms?
- repair of damaged bases
- repair of incorrectly base- paired bases during replication
What type of damage does X-ray and cancer drug do? What type of repair does it need?
double strand break; double strand repair
What type of damage does UV light do? What type of repair does it need?
Thymine dimer, bulky adduct; nucleotide excision repair
What type of damage does replication errors do? What type of repair does it need?
Base mismatch; mismatch repair
What type of damage does radiation, ROS, spontaneous hydrolysis? What type of repair does it need?
Depurination, cytosine deamination, single strand break, and base alkylation; base excision repair and direct reversal
What do environmental mutagens do?
- depurination
- deamination
- oxidation
- non-enzymatic methylation
What happens during long UV radiation?
It causes for DNA to form thymine dimers
How does a thymine dimer happen?
the result between two adjacent thymine residues forming two bonds (dimer) with each other
What is photolyase?
Repair the thymine dimers via direct repair or nucleotide excision repair by splitting the dimer and restoring the DNA
What is true about thymine dimer formation? Who forms it?
Lower eukaryotes not so much mammals
How can thymine dimers be repaired?
Direct repair mechanism by using photolyase. Also, nucleotide excision repair(NER)
How does photolyase work?
The photolyase enzyme binds to the DNA at the site of the thymine dimers in the dark. When visible light is present the enzyme breaks the bonds linking the pyrimidine rings, then the enzyme dissociates from the DNA in the dark.
What is NER?
A DNA repair mechanism also able to repair thymine dimers caused by UV light
What does NER apply to? What eukaryote uses it?
mammals
How does NER work?
The three-subunit UVrABC enzyme recognizes the thymine dimer as damaged DNA and with the help of ATP hydrolysis forces the DNA to bend. There is cleavage surrounding the damaged DNA on either side and the damaged DNA is removed. Polymerase and ligase replaces the damaged DNA with new DNA using the other strand (undamaged DNA) as a template
What happens if the NER pathway is deficient?
Can result in a rare genetic disease called Xeroderma Pigmentosa (XP)
What happens when nitrogenous bases are altered?
It can base pair with an incorrect base and result in a mis-pairing.
What is an example of a nitrogenous base getting altered? What happens?
If guanine gets altered by ionizing radiation or nitrosamines this will result in the guanine being changed to an oxidation of guanine (oxoG) or O6-methylguanine (O6-methylG).
What is found in food preservatives?
nitrosamines
What happens when oxoG or O6-methyl-G is formed? What does it bind to?
An oxoG can be mis-paired to an adenine, this DNA damage can be repaired via base excision repair. An O6-methylG can be mis-paired to a thymine, this DNA damage can be repaired via direct repair or base excision repair.
How can you fix O6-methylG?
Specific methyltransferase(direct repair). It recognizes methylG and cuts it away
What happens when O6-methyguanine is formed and forms residue?
It can lead to mutagenesis
How does AP site and base excision repair?
These enzymes can recognize a single damaged base and cleave the bond between it and the sugar in the DNA.
How does AP site and base excision repair work? How does it function?
Removes one base, excises
several around it, and replaces with several new bases using Pol adding
to 3’ ends then ligase
attaching to 5’ end
What happens if a purine or pyrimidine is present during base excision and AP site?
creates an a purinic or an a pyrimidinic site
What is true about base excision repair?
Base Excision Repair relies on specific DNA glycosylases
that remove abnormal bases. We have 11 in humans and can fix abasic sites.
What do replicative DNA polymerases do?
They have proofreading exonucleases where if there is a mistake, it cuts aways and fixes.
What does Pol 1 do in corrections and mistakes?
If it makes a mistake, it just continues
How does the proofreading exonuclease work?
removes the terminal 3’ base, thus restoring the correct geometry of the primer-template junction, which can move back to the polymerase site.
What happens when mismatches pass through the polymerase system?
makes bulges
What does MutS do?
recognizes mismatch
What does MutL do?
It links to MutS
What does MutH do?
It binds with GATC and indentifies unmethylated strand
What does Pol3 do?
It adds bases or synthesizes new strand
What does Exonuclease, helicase II, and SSB do?
It removes DNA
How does double strand damage happen?
caused by Ionizing Radiation (IR) and also occur normally during meiosis
What are the ways in which DBS damage can be repaired?
NHEJ, Alt-EJ, HR
What is NHEJ?
Non-homologous end-joining which is fast but error-prone. Uses G1
What is Alt-EJ?
A rare backup plan that is slow and error prone
What is HR?
A super slow but error-free approach. Uses S/G2
How does HR work?
It works by using the same gene but difference sequence where damages chromosomes use undamaged chromosomes for replication, causes heteroduplex DNA
What is HR mechanism? How does it work? How does it bind?
- resection of 5’ ends
- strand invasion on top of damage
- DNA interacts and exchanges while Pol adds bases
- branch migration to cover DNA
- HJ resolution to remove HJ enzyme and restore DNA
What is the holiday junction?
It is the HJ and it where a cross-shaped structure that forms during the process of homologous
recombination, when two double-stranded DNA
molecules become separated into four strands in order to exchange regions of genetic
information
What can happen during a HJ crossover?
It can lead to different DNA sequences
What are the proteins involved in HR in eukaryotes?
Rad51, DNA polymerase,
What does rad51 do?
pairs the 3’ end with the sister chromatid
What happens if the proteins in HR are damaged?
Cancer
What is gene conversion?
The process by which one DNA sequence replaces a homologous sequence such that the sequences become identical
What can happen if there is a mismatch repair of heteroduplex DNA?
gene conversion and LOH
What happens if there is damage to non-coding regions?
It can result in more energy being used and leads to trans-lesions DNA and tolerance. Checkpoint in euk and SOS in prok.
