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abasic site (AP site)

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An AP site (apurinic/ apyrimidinic site) is a location in DNA that has neither a purine nor a pyrimidine base usually due to DNA damage. Can also be formed by spontaneous depurination, but also occur as intermediates in base excision repair.

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alkylating agent

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they are classified according to their nucleophilic or eletrophilic character,---nucleophilic deliver the equivalent of an alkyl anion. These compounds typically can add to an electron deficient carbon atom such as at a carbonyl group. --- electrophilic alkylating agents deliver the equivalent of an alkyl cation.

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alkylation

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is the transfer of an alkyl group from one molecule to another. The alkyl group may be transferred as an alkyl carbocation, a free radical a carbanion or a carbene or their equivalents.

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AP endonuclease

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is an enzyme that is involved in the DNA base excision repair pathway. Its main role is the repair of damaged or mismatched nucleotides in DNA is to create a nick in the phosphodiester backbone of the AP site created when DNA glycosylase removes the damaged base.

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carcinogen

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is any substance, radionuclide or radiation that is an agent directly involved in causing cancer. This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes.

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cross-linking

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are bonds that link one polymer chain to another. They can be covalent bonds or ionic bonds.

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pyrmidine dimer

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are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions. UV light induces the formation of covalent linkages by reactions localized on the C=C double bonds.

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dealkylation

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The removal of alkyl groups ?

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deamination

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The removal of an amine group from a molecule. In the human body this primarily takes place in the liver.

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DNA glycosylase

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are a family of enzymes involved in base excision repair. They catalyze the first step in base excision repair, by removing the damaged nitrogenous base while leaving the sugar phosphate backbone intact, creating the AP site.

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DNA glycosylase/lyase

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are a family of enzymes involved in base excision repair. Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced. They catalyze the first step of this process.

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double-strand break

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This is when both strands in the double helix are severed.

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error-prone DNA polymerase

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in cases where DNA damage has escaped the DNA repair system, this allow the lesions to be bypassed during DNA replication

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hydrolytic cleavage

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is a chemical reaction during which molecules of water are split into hydrogen cations, and hydroxide anions, in the process of chemical mechanism. It is used to break down certain polymers.

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LexA

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is a repressor enzyme that represses the SOS response genes coding for DNA polymerases required for repairing DNA damage. It is linked to RecA

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missense mutation

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is a point mutation in which a single nucleotide is changed, resulting in a codon that codes for different amino acid (mutations that change an amino acid to stop condon are considered nonsense mutations, not missense

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mismatch repair

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is a system for recognizing and repairing erroneous insertion, deletion and mis-incorporation of bases that can arise during DNA replication and recombination as well as repairing some forms of DNA damage

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mutagen

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is a physical or chemical agent that changes the genetic material, usually DNA of an organism, and thus increases the frequency of mutation above the natural background level.

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nonsense mutation

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is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete and usually nonfunctional protein product.

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nucleotide excision repair

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is a DNA repair mechanism. It removes the vast majority of UV induced DNa damage, mostly in the form of thymine dimers. This recognizes bulky distortions in the shape of the DNA double helix.

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photolyase

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Are DNA repair enzymes that repair damage caused by exposure to ultraviolet light.

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RecA

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is a protein essential for the repair and maintenance of DNA. In the bacterial SOS response, it functions in the cleavage of the LexA repressor and the lambda repressor. Also holds single and double strands together.

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SOS response

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is a global response to DNA damage in which the cell cycle is arrested and DNA repair and mutagenesis are induced.

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tautomer

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are isomers of readily interconvert by a chemical reaction. It is common that this reaction results in the formal migration of a hydrogen atom or proton accompanied by a switch of a single bond and adjacent double bond.

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transition mutation

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is a point mutation that changes a purine nucleotide to another (A<->G) or a pyrimidine to another (C<->T)

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translesion DNA synthesis

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is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites. It involves switching out regular DNA polymerases for specialized translesion polymerases, often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides.

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transversion mutation

answer

is the substitution of a purine for a pyrimidine. Can be caused by ionizing radiation and alkylating agents.

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UvrABC endonuclease

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Is involved in DNA repair by nucleotide excision repair.
1. They form a dimer
2. The UvrA dimer binds with UvrB and forms a trimer that is able to detect DNA damage.
3. The UvrB part ofthe trimer attaches to the damaged site
4. UvrA is released, UvrC binds to it forming UvrBC dimer
5 This is responsible for cleaving the nucleotides
6. DNA helicase II (sometimes called UvrD then comes in an removes it
7 DNA poly I comes in and fills in the correct nucleotide sequence

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Xeroderma pigmentosum

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is a autosomal recessive genetic disorder of DNA repair in which the ability to repair damage caused by UV light is deficient.

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What are some ways that DNA can be damaged?

answer

Radiation (UV, gamma, x ray)
hydrolytic cleavage
oxidative damage,
alkylation
cross linking

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What are the pathways for DNA repair

answer

-photoreactivation
-base excision repair
-nucleotide excision repair,
-mismatch repair

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What does translesion DNA synthesis do

answer

It allows damaged regions to be bypassed by error prone DNA synthesis without repairing the damage.

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UV light induces damage and causes damage in what?

answer

B DNA

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DNA lesions can lead to what

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Deletions, duplications, inversions, and translocations

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_____ of N glycosyl bonds and bonds linking amine groups are significant forms of of DNA damage.

answer

Hydrolytic cleavage

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N glycosyl bond cleavage leads to what

answer

formation of an abasic or AP site

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What does an Ap site do

answer

Its formation sensitizes the neighboring phosphodiester bond to cleave.

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Hydrolytic deamination converts cytosine, guanine, and adenine to ______, ________. and _________ respectively

answer

Uracil, xanthine, and hypoxanthine

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What is the Ames test? What is it useful for?

answer

It is used to detect mutagens. in this test, the potential mutagenic agent is tested for its ability to cause the reversion of a histidine requiring bacterium back to the His+ phenotype

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Alkylating agents are highly reactive electrophiles that transfer what

answer

methyl ethyl or large alkyl groups to DNA

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Pyrimidine dimers can be reversed by what

answer

photoreactivation

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Some alkylation damage can be directly reversed by what?

answer

dealkylation

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What is the main pathway for repair of DNA damage caused by deamination oxidation and alkylation

answer

Base excision repair

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Nucleotide excision repair involves what

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-Damage recognition
-incision in the DNA on both sides of the damage,
-excision of the damaged DNA
-synthesis of a new strand,
-ligation of the nick

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Bacterial nucleotide excision repair involves what

answer

-UvrABC endonuclease,
-UvrD
-DNA polymerase I
-Ligase

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What does the DNA mismatch repair system do

answer

it corrects rare base pair mismatches and short deletions or insertions introduced during DNA replication

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What are responsible for recognition of the mismatch and incision of the nearest unmethylated GATC sequence

answer

MutS, MutL, and MutH

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Translesion synthesis does not repair the lesion, but instead does what

answer

Allows the cell to survive DNA damage that has not been repaired.

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The SOS response is what?

answer

A multigene response to DNA damage in E coli after UV irradiation or a chemically induced chromosomal change.

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Humans have at least how many template dependent DNA polymerases. Their main function is what?

answer

14, DNA repair.

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UV induced DNA damage is mainly in the form of what?

answer

dimer formation between adjacent pyrimidine bases on the same DNA strand

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Water mediated deamination converts cytosine to ____

answer

uracil

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Ionizing radiation and cellular respiration both produce ____

answer

reactive oxygen species

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Some nitrogens and oxygens in DNA are targets of alkylating agents because they are

answer

electron rich

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The ames test is based upon the idea that a mutagen will

answer

revert a percentage of histidine mutants to wild type

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Photolyases use light energy to repair___

answer

pyrimidine dimers

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Damage to DNA bases caused by deamination, oxidation and alkylation is mainly repaired by

answer

nucleotide excision repair

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In nucleotide excision repair, damaged DNA is detected by

answer

recognition of helical disortion

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Which of the is required for mismatch repair in E.coli

answer

helicase activity
SSB protein
DNA ligase

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The SOS response signal is

answer

a nucleoprotein filament composed of single stranded DNA and RecA

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What mechanisms would an E. Coli cell use to repair pyrimidine dimers?

answer

Nucleotide excision repair and photoreactivation

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DNA damage is caused by _____ cleavage reactions

answer

hydrolytic

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_____ can be detected based on their ability to restore mutant gene activity.

answer

Mutagens

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T or F- reactive oxygen species damage DNA

answer

True

question

How does E. coli mismatch repair machinery know which strand to repair?

answer

The unmethylated strand is always repaired

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____ reverses damage done to DNA caused by pyrimidine dimer formation

answer

Photolyase

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Error prone DNA polymerases catalyze ______ DNA synthesis

answer

translesion

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____ and LexA regulate the E. coli SOS response

answer

RecA

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The ____ repair pathway remove and replaces damaged bases.

answer

Base excision

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The ____ repair pathway removes bulky adduct from DNA by excising an oligonucleotide bearing the lesion and replacing it with new DNA

answer

nucleotide excision

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T or F- Many environmental agents must be modified by cell metabolism before they can alkylate DNA

answer

True

question

DNA has three kinds of bonds with the potential for hydrolytic damage, namely: ______, n-glycosyl bonds, and bonds linking amine groups to bases.

answer

phosphodiester bonds

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DNA has electron rich atoms that are readily attacked by electron-seeking chemicals called

answer

electrophiles

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____ is the repair of UV-damaged DNA by a light dependent enzymatic reaction.

answer

Photoreactivation.

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_____ is a genetic disorder of DNA repair in which the ability to repair damage caused by UV light is deficient

answer

Xeroderma pigmentosum

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T or F- There are a variety of DNA repair mechanisms, but all of them depend on the existence of two copies of the genetic information, one in each chromosome of a diploid organism

answer

False-Repair depends on the two copies of genetic information contained in the two strands of the DNA double helix. Bacteria are haploid and repair works great

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T or F-Spontaneous depurination and the removal of a deaminated C by uracil DNA glycosylase both leave an identical intermediate, which is the substrate recognized by AP endonuclease.

answer

True

question

T or F -The principle function of the SOS response in the E coli is to increase cell survivial by introducing compensating mutations near the site of the original DNA damage.

answer

False. Its job is to relax the fidelity of DNA synt. so that it can proceed past a block. (cell dies if not synt occurs, hence it survives with a mutation)

question

T or F- All the spontaneous deamination products of the usual four DNA bases are recognizable as unnatural when they occur in DNA

answer

True

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