DNA repair Flashcards
What are mutagens
Chemical agents that alter dna bases
How can dna bases be altered
Oxidation
Deamination
Alkylation
UV radiation
X ray exposure
How is guanine altered via oxidation
A hydroxyl radical reacts with guanine a makes 8-oxoguanine
The H on the imidzole is replaced with c=o
This is bad because 8-oxoguanine pairs with adenine instead of cytosine
During replication this makes it so that one strand has a ga pair and the other has a AT base pair
What is cytosine deamination
The amino NH2 group is removed by hydrolysis (water coming in)
Replaced with c=o and makes nh3
Cytosine turns into uracil instead of cg it UA
What is adenine demaination
Changed adenine to hypoxanthine
Pairs with cytosine not thymine
What is 5 methyl cytosine demaination
5 methyl cytosine is where cytosine had methyl group on c5 (next to c=O)
It regulated gene transcription
If demaination it turns into thymine and pairs with A
What base is deamination most unlikely for
Thymine
What is guanine alkylation
Adding a hydrocarbon to the base
First alfatoxin b1 reaction with cytochrome p450 to make aflatoxin B epoxied
aflatoxin B epoxide is reactive and reaction with the guanine in dna
It alkylates N7 of guanine and makes gc. To TA
What is a thymine dimer
When Uv light covalenty links adjacent (next to each other) pyrimidines along the dna strand
This causes a pyrimidines dimer where a bulge is formed and alters the DNA structure, causes a kink
What are approximate repairs and apoptosis
When it’s not possible to fix the error completely and restore the original information
The cell does approximate repairs or programmed cell death
What are the steps for repair
Recognizing the damage
Removing the damaged section
Repair (filling in where you removed with the proper thing)
What is mismatch repair
A base is match wrong during replication
This mismatch is recognized by MutS
This causes MutL to bind and recruits MutH
MutH endonuclease cleaves around the mismatch
exonuclease cuts out the incorrect base and backbone with it
DNA pol 111 fill the gap
How the the mismatch repair machinery know which strand on the dna has the incorrect base
The adenines in the template strand of the dna is methylated but the newly synthesized stand isn’t
The methylated strand is then seen as the correct sequence and it cleave off the opposite strand
What is direct repair
It was discovered in ecoli, mammals don’t use this
It repairs the site of pyrimidines dimers without removing dna fragments from it
It does this by DNA photo Lyase doing photochemical cleavage of the dimers
The energy of the visible light breaks the dimers cyclobutane ring and keeps the bases separated
What is nucleotide excision repair
It was discovered in E. coli
This is how mammals repair thymine dimers
Protiens detect the distorined in the helix due to the dimer
The uvrABC excinuclease (cut out) cuts out the dna and two sites across the distortion
DNA pol 1 fill in the gap, and DNA ligase repairs the resulting small nick in the backbone
What is base excision repair
Occurs in modified bases
The defective base is flipped and faces out of the helix into a enzyme glycosylases active site (if cyctosine is deaminated its uracil, so a uracil glycosylase comes in)
The glycosidic bond between the base and backbone is cleaved . This forms an AP site where a base is missing
An ap endonuclease come in and nicks the back bone next to the missing base
Deoxyribophosphodiesterase removes the depxyribose phosphate back bone unit
DNA pol 1 inserts the correct nucleotide, ligase seals the strand
Slide 24/25
Mechanism
Why does dna use thymine instead of uracil which is in rna
Cytosine delaminates to uracil
Uracil base pairs with adenine
If uracil is already in the dna as a normal base, actual mutations to uracil won’t be detected as good
By using thymine instead of uracil, the cell can detect the product of cytosine deaminations
