Term
| the simplest source of damage in the DNA double helix |
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Definition
| errors introduced in the replication process |
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Term
| how mismatching DNA bases causes damage |
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Definition
| distorts double helix, which can become mutagenic |
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Term
| how a mismatch of bases is mutagenic |
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Definition
| results in daughter helices with different sequences |
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Term
| some types of errors in DNA |
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Definition
-mismatches
-insertions
-deletions
-breaks in one or both strands |
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Term
| how errors in DNA can inhibit replication |
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Definition
| replicative polymerases can stall or fall off the damaged template entirely, making replication of the genome halt before it's complete |
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Term
| one way to repair damage in DNA |
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Definition
| translesion or error-prone polymerases |
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Term
| function of translesion or error-prone polymerases |
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Definition
| allow for the completion of a draft sequence of the damaged area of the genome that can be at least partly repaired by DNA-repair processes |
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Term
| drawback to the use of translesion or error-prone polymerases |
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Definition
| substantially more error prone than other polymerases when replicating DNA |
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Term
| depiction of triplet-repeat expansion |
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Definition
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Term
| bases in DNA can be damaged by... |
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Definition
-oxidizing agents
-alkylating agents
-light |
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Term
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Definition
| chemical agents that alter specific bases within DNA after replication is complete |
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Term
| how hydroxyl radical (a reactive oxygen species) is mutagenic |
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Definition
| converts guanine to 8-oxoguanine, which is mutagenic because it pairs with adenine instead of cytosine |
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Term
| depiction of guanine oxidation |
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Definition
refer to p. 645
this is mutagenic |
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Term
| how deamination causes mutations |
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Definition
| example: deaminates adenine to form hypoxanthine, which pairs with cytosine instead of thymine |
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Term
| depiction of adenine deamination |
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Definition
refer to p. 645
this causes mutations |
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Term
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Definition
| aflatoxin B1, which is produced by molds that grow on peanuts and other foods |
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Term
| how aflatoxin B1 causes mutations |
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Definition
| cytochrome P450 enzyme converts it into a highly reactive epoxide, which reacts with the N-7 atom of guanine to form a mutagenic adduct that binds with adenine instead of cystine |
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Term
| depiction of aflatoxin B1 activation |
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Definition
refer to p. 646
causes mutations |
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Term
| the most pertvasive DNA-damaging agent |
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Definition
| the UV light from sunlight |
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Term
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Definition
| by covalently linking adjacent pyrimidine residues along the DNA strand |
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Term
| depiction of a cross-linked dimer of 2 thymine bases |
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Definition
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Term
| how high energy em radiation, such as X-rays, damages DNA |
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Definition
by producing high concentrations of reactive chemicals
also causes sinbgle- and double-stranded breaks |
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Term
| many systems repair DNA by... |
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Definition
| using sequence information from the uncompromised strand |
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Term
| mechanistic outline followed by many single-strand replication systems |
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Definition
1: recognize the offending base(s)
2: remove the offending base(s)
3: repair the resulting gap with a DNA polymerase ad a DNA ligase |
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Term
| a mechanism in essentially all cells that corrects errors not corrected by proofreading |
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Definition
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Term
| how mismatch repair works in E. coli |
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Definition
1: detecting mismatch
2: removing part of the strand containing the mismatch
3: replace it with correct sequence |
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Term
| the mismatch repair proteins in E. coli |
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Definition
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Term
| the endonuclease in E. coli |
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Definition
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Term
| depiction of mismatch repair |
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Definition
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Term
| how mismatch repair machinery determines incorrect base in E. coli |
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Definition
| some adenine bases in the parent strand are methylated, whereas the newly synthesized daughter strand is not yet methylated. thus, the machinery recognizes that the methylated base is correct and the unmethylated mismatch is incorrect |
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Term
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Definition
| repairing damage to DNA without having to remove any fragments of the DNA |
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Term
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Definition
| a photoreactivating enzyme that direct repairs DNA by photochemical cleavage of pyrimidine dimers |
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Term
| how photochemical cleavage works |
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Definition
| photolytic enzyme binds to distorted region and absorbs photon to form an excited state that cleaves the dimer into its component bases |
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Term
| what happens to damaged bases in E. coli? |
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Definition
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Term
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Definition
| replacing damaged bases with undamaged bases |
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Term
| depiction of base-excision repair |
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Definition
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Term
|
Definition
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Term
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Definition
| site in DNA strand devoid of base |
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Term
|
Definition
| knicks the backbone adjacent to the missing base |
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Term
| deoxyribose phosphodiesterase |
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Definition
| excites residual phosphate unit |
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Term
| role of DNA polymerase I in base-excision repair |
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Definition
| inserts undamaged nucleotide |
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Term
| how the base-excision-repair system know to remove T in the T-G pair |
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Definition
| because the C-->T mutation is so common |
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Term
| depiction of the deamination of 5-methylcytosine forms thymine. |
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Definition
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Term
| what mechanism recognizes improper nucleotide pairs that escape the base-excision-repair system? |
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Definition
| nucleotide-excision repair |
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Term
| what the nucleotide-excision repair system does |
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Definition
| recognizes distortions in the DNA double-helix caused by the presence of a damaged base |
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Term
| depiction of nucleotide-excision repair |
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Definition
|
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Term
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Definition
| in nucleotide-excision repair, this cuts out DNA sequence that contains the defective base |
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Term
| why DNA uses thymine instead of uracil |
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Definition
-cytosine spontaneously deaminates to form uracil
-thymine contains methyl group, but uravil instead contains an H in that place
-thus, the methyl group is a tag that distinguishes thymine from deaminated cytosine, which is uracil; this mechanism enhances the fidelity of the genetic message |
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Term
| depiction of uracil repair |
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Definition
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Term
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Definition
| hydrolyzes the glycosidic bond between the uracil and deoxyribose moieties, but does not attack thymine-containing nucleotides |
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Term
| double-strand breaks arise when... |
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Definition
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Term
| one thing that can cause replication to stall |
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Definition
| when the polymerase encounters an unrepaired nick in one of the template strands at the replication fork |
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Term
| depiction of generation of a double-strand break |
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Definition
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Term
| things that can cause double-strand breaks |
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Definition
-unrepaired nicks
-ionizing radiation, such as gamma rays and X-rays |
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Term
| what happens when the replication machinery encounters a nick in the DNA? |
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Definition
| the replication fork collapses, leaving a double-stranded break on one of the daughter helices |
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Term
| types of ionizing radiation that can cause double-stranded breaks |
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Definition
-x-rays
-gamma rays
they are powerful enough to break the DNA backbone |
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Term
| where recombination is most efficient |
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Definition
| between stretches of DNA that are similar in sequence |
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Term
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Definition
| parent DNA duplexes align at regions of sequence similarity, and new DNA molecules are formed by the breaking and joining of homologous segments |
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Term
| one key protein in recombination in humans |
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Definition
| RAD 51, which is an ATPase that binds single-stranded DNA |
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Term
| depiction of repair of double-strand break by using recombination |
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Definition
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Term
| something recombination between alleles can be used for |
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Definition
| generation of new DNA sequences and molecular diversity |
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Term
| a biochemical tool recombination is the foundation for |
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Definition
-gene knock-out
-gene knock-in |
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Term
|
Definition
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Term
|
Definition
| specific gene is inserted |
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