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Flashcards in DNA Damage and Repair Deck (37):

What is a mutation?

* A mutation is a change in the nucleotide sequence that is heritable


What is meant by wild type DNA?

Standard form of gene


What is a forward mutation?

Wild type gene converted to mutant.


What is a reverse mutation?

Mutant form converted back to wild type.


What is a chromosomal aberration?

A missing, extra or irregular portion of chromosome:
eg deletions, insertions, duplications or inversions


What is meant by monosomy and trisomy? How do they occur?

Monosomy- when an individual is missing one in a pair of chromosomes

Trisomy- when an individual has more than two chromosomes instead of a pair.

Usually occur as an error in cell division.


What are transition and transvehrsion mutations?

Transition- purine swapped for purine and vice versa.

Transversion- purine swapped for pyramiding and vice versa.


What is meant by:
-Silent mutation
-Missense mutation
-Non sense mutation
-Read through mutation

-Silent mutation- no affect on aa sequence

-Missense- results in amino acid substitution

-Non-sense- change amino acid to a stop codon

-Read through- changes stop codon to an amino acid


What is an adduct?

Adduct= a segment of DNA that is bound to a mutagen.


Describe three ways in which DNA can be mutated. (Induced mutations).

-Alkylation of bases
-Crosslinking agents
-Intercalated molecules


How do antioxidants, catalase, peroxidase and superoxide dismutases limit damage to DNA?

Antioxidants- mop up reactive oxygen species

Catalase- catalyses reaction of the decomposition of hydrogen peroxide to water

Peroxidase-catalyses the oxidation of a particular substrate by using hydrogen peroxide

Superoxide dismutases- turn super oxidants into hydrogen peroxide (which is less oxidising and can then be converted into water).


Describe three ways in which DNA can be mutated. (Induced mutations).

-Alkylation of bases
-Crosslinking agents
-Intercalated molecules


What are cyclobutane pyrimidine dimers?

Cross links in DNA between two pyrimidines. Covalently fused dimers formed at adjacent pyrimidines which are bulky lesions and distort the double helix and make errors more likely in transcription and replication.


How can radiation damage DNA?

-Produces hydroxyl radicals from damaging water which in turn damage bases
-Production of clustered lesions (two or more lesions (sites of damage) close to each other) leading to chain breaks.


What is DNA intercalation?

The insertion of molecules between the planar bases of DNA. This can cause single nucleotide insertions and deletions (therefore can block DNA replication and transcription).


What is an induced mutation?

Induced mutations occur when an external agent is the cause of the mutation.


What is DNA intercalation?

The insertion of molecules between the planar bases of DNA. This can cause single nucleotide insertions and deletions.


What are the three known examples of direct repair?

-Direct repair of single strand breaks
-Direct repair of methyl groups
-Direct repair of pyrimidine dimers


What is photolyase and what does it do? What are the important features of photolyase?

It is an enzyme that repairs DNA through photo reactivation.

Important features:
-Flavin (source of FAD)
-Folate- harvests light energy and transfers it to flavin.

-It binds to the thymine dimer.
-Folate harvests the list energy and transfers it to flavin (FADH)
-FADH becomes excited when the light energy is transferred
-Electron transferred to pyramiding dimer which breaks the bond and returns it to the original conformation.
-Electron returned to FAD


What is photolyase and what does it do?

It is an enzyme that repairs DNA through photo reactivation


What is ADA (alkyl guanine transferase) protein in E. coli?

Regulates a set of genes involved in repairing methyl group damage to DNA- N terminal.

-Transfers the alkyl group from damaged DNA to internal cysteine residues, inactivating itself (suicide enzyme)


What is ε?

A subunit of DNA polymerase III which is involved in proof reading (3' to 5' activity). dnaQ is what encodes the ε subunit.


Describe mismatch repair.

In E. coli, which enzyme methylates the newly synthesised strand?

-Dam is the enzyme which methylates newly synthesised GATC sites

-Uses the fact that the newly synthesised strand is not methylated yet to distinguish between strands
-MutS scans the DNA for mismatches
-MutL binds to MutS forming a complex which binds to MutH further away in the DNA which causes the DNA to fold over in a loop.
-MutH cleaves the un-methylated strand
-An exonuclease digests the DNA from MutH to just beyond the mismatch site
-DNA polymerase III adds nucleotides correctly to repair the mismatch
-Ligation occurs


In mismatch repair, what do these enzymes do?

-MutS- binds to DNA mismatch
-MutL-activates MutS and MutH
-MutH-cleaves the un-methylated strand
-Dam- methylates the new strand
-MutU- unwinds the strands


Describe base excision repair.

DNA glycosylase
cuts out the
damaged base

AP endonuclease
cuts on either the
3’ or 5’ side of
abasic site
the backbone is
processed to leave
a single nucleotide
gap that is filled by
DNA polymerase
and the nick
sealed by DNA


How can uracil end up in DNA?

-Deamination of Cytosine to Uracil
-Mis-incorporation of uracil by DNA polymerase.


What is an AP endonuclease?

An apurinic/ apyrimidinic endonuclease which is involved in base excision repair.

It cleaves either there 3' or 5' AP (no base/ no purine or pyrimidine) site


What are the functions of:
-DNA polymerase I
-DNA polymerase II
-DNA polymerase III
-DNA polymerase IV
-DNA polymerase V

DNA polymerase I
-DNA replication

DNA polymerase II
-Repair of DNA damaged by UV radiation

DNA polymerase III
-Primary enzyme involved in prokaryotic DNA replication

DNA polymerase IV
-Involved in non targeted mutagenesis
-No 3'-5' exonuclease proofreading activity

DNA polymerase V
-Repair mechanisms
-Adds nucleotides to damaged DNA (normal III polymerase stalls).

I, II and III all have 3'-5' exonuclease activity


Describe nucleotide excision repair.

-Removal of damage as a short oligonucleotide
-Introduce nicks on either side and unwind the strand which is 12 or 13 bases long
-DNA strand removed by a helicase and rebuilt using a polymerase

-UvrA and UvrB complex moves along strand scanning for damage (e.g. thymine dimer)
-When damage reached, UvrC joins complex and cuts the strand with the damage on it
-UvrD comes in and removes this piece of DNA strand
-Gap filled by polymerase and ligated.


How does UvrB ensure that the DNA stays in place?

UvrB creates a beta hairpin bend to lock the DNA in place.


How can DNA lesions kill a cell?

- Interfering with DNA replication
-Blocking transcription (depriving cell of essential proteins)


What is transcription coupled repair?

-When DNA that is actively transcribed is preferentially repaired over DNA that is less transcribed


What is Mfd (enzyme)?

-Mutation Frequency Decline (otherwise known as transcription repair coupling factor).
-An enzyme that recognises when RNA polymerase has stalled at a lesion in the DNA


Describe the Mutation Frequency Decline phenomenon in bacteria

Fewer mutations on bacteria grown on poor mediums as they replicated fewer times so there was more time to repair the mutations.


Describe transcription coupled repair in bacteria.

-RNA polymerase stops at lesion as it knows it will wrongly transcribe if it continues.
-Mfd recognises the stalled polymerase
-RNA polymerase and RNA are released
-UvrA attaches to the lesion and recruits UvrB to form a complex
-UvrC cuts the strand either side of the damage
-UvrD unwinds the broken part of the strand
-Gap filling and ligation by DNA Pol I and ligase


Describe how inter strand cross links are repaired.

-Nucleotide excision repair of one strand
-Crosslinked bases still attached to one strand
-Homologous recombinaison of DNA in gap
-Nucleotide excision repair of the other side of the strand with the cross linkage still attached
-Gap filled by polymerase and sealed by ligase.


What is a translesion bypass and why is this sometimes useful?

-Some DNA polymerases in E. coli can bypass lesions by inserting any old nucleotide
-This is useful when cells are
so damaged that managing to replicate
and transcribe takes precedence over
the risk of generating lots of mutations