Term
| Semiconservative DNA replication |
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Definition
| Describes the mechanism by which DNA is replicated in all known cells. The deciphering of the structure of DNA by Watson and Crick in 1953 suggested that each strand of the double helix would serve as a template for synthesis of a new strand; one strand was to be synthesized continuously and the other discontinuously. |
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Term
| In which direction is DNA synthesized? Why? |
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Definition
| DNA is synthesized in the 5' to 3' direction. This is because DNA polymerase enzymes are only able to join the phosphate group at the 5' carbon of a new nucleotide to the hydroxyl (OH) group of the 3' carbon of a nucleotide already in the chain. |
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Term
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Definition
| The one with a terminal hydroxyl (OH) group on the deoxyribose of the 3' carbon of the deoxyribose. |
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Term
| Which end of the DNA is 5'? |
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Definition
| The one with the terminal phosphate group on the 5' carbon of the deoxyribose. |
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Term
| What are the three theoretical models of DNA replication? |
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Definition
1) Semiconservative - produce two copies that each contained one of the original strands and one new strand.
2) Conservative - leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs.
3) Dispersive - would produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands. |
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Term
| Which experiment elucidated the semiconservative nature of DNA replication? |
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Definition
| The Meselson-Stahl experiment in 1958. |
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Term
| Describe the Meselson-Stahl experiment. |
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Definition
E. coli were grown for several generations in a medium with 15N. When DNA is extracted from these cells and centrifuged on a salt density gradient, the DNA separates out at the point at which its density equals that of the salt solution. The DNA of the cells grown in 15N medium had a higher density than cells grown in normal 14N medium. After that, E. coli cells with only 15N in their DNA were transferred to a 14N medium and were allowed to divide; the progress of cell division was monitored by measuring the optical density of the cell suspension.
DNA was extracted periodically and was compared to pure 14N DNA and 15N DNA. After one replication, the DNA was found to have close to the intermediate density. Since conservative replication would result in equal amounts of DNA of the higher and lower densities (but no DNA of an intermediate density), conservative replication was excluded. However, this result was consistent with both semiconservative and dispersive replication. Semiconservative replication would result in double-stranded DNA with one strand of 15N DNA, and one of 14N DNA, while dispersive replication would result in double-stranded DNA with both strands having mixtures of 15N and 14N DNA, either of which would have appeared as DNA of an intermediate density.
The authors continued to sample cells as replication continued. DNA from cells after two replications had been completed was found to consist of equal amounts of DNA with two different densities, one corresponding to the intermediate density of DNA of cells grown for only one division in 14N medium, the other corresponding to DNA from cells grown exclusively in 14N medium. This was inconsistent with dispersive replication, which would have resulted in a single density, lower than the intermediate density of the one-generation cells, but still higher than cells grown only in 14N DNA medium, as the original 15N DNA would have been split evenly among all DNA strands. The result was consistent with the semiconservative replication hypothesis. |
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Term
| What did the results of the Meselson-Stahl experiment indicate (image)? |
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Definition
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Term
| What would have been the results of the Meselson-Stahl experiment if DNA replication was conservative (image)? |
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Definition
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Term
| What would have been the results of the Meselson-Stahl experiment if DNA replication was dispersive? |
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Definition
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Term
| When does DNA replication occur? |
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Definition
| During S (synthesis) phase of the cell cycle. |
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Term
| How many times does DNA replication occur per cell cycle? Why? |
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Definition
| Only once, because of the activity of cyclin dependent kinase. (Elucidate.) |
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Term
| From where does DNA replication begin? In what direction does it move? |
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Definition
| DNA replication begins at multiple origins of replication and moves bidirectionally. |
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Term
| How big is the average human chromosome? |
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Definition
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Term
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Definition
| A particular sequence in a genome at which replication is initiated. |
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Term
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Definition
| When replication begins, each of these origins becomes a site where the two sides of the DNA "melt" and replication begins. This forms a configuration called a replication bubble. |
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Term
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Definition
| A structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. |
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Term
| T or F: The lagging strand is made continuously. |
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Definition
| False: The leading strand is made continuously and the lagging strand is made discontinuously. |
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Term
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Definition
| A complex molecular machine that carry out replication of DNA. It is made up of a number of subcomponents that each provide a specific function during the process of replication. |
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Term
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Definition
| Motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis. |
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Term
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Definition
| Enzyme that catalyzes the synthesis of a short RNA segment (called a primer) complementary to a ssDNA template. Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation). |
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Term
| Single-strand binding proteins (SSB) |
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Definition
| Binds to single stranded regions of DNA to prevent premature annealing. The strands have a natural tendency to revert to the duplex form, but SSB binds to the single strands, keeping them separate and allowing the DNA replication machinery to perform its function. |
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Term
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Definition
| An enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best-known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand. This process copies a piece of DNA. DNA polymerase can add free nucleotides to only the 3' end of the newly-forming strand. This results in elongation of the new strand in a 5'-3' direction. No known DNA polymerase is able to begin a new chain (de novo). DNA polymerase can add a nucleotide onto only a preexisting 3'-OH group, and, therefore, needs a primer at which it can add the first nucleotide. |
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Term
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Definition
| A protein fold that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because the rate-limiting step in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase. |
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Term
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Definition
| A non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. In DNA replication, RNase H is responsible for removing the RNA primer, allowing completion of the newly synthesized DNA. |
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Term
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Definition
| The protein encoded by this gene removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. Direct physical interaction between this protein and AP endonuclease 1 during long-patch base excision repair provides coordinated loading of the proteins onto the substrate, thus passing the substrate from one enzyme to another. |
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Term
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Definition
| A specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules. The mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide, ("acceptor") with the 5' phosphate end of another ("donor"). ATP is required for the ligase reaction. |
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Term
| How long are RNA primers? |
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Definition
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Term
| How does DNA ligase join Okazaki fragments? |
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Definition
| The mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide, ("acceptor") with the 5' phosphate end of another ("donor"). ATP is required for the ligase reaction, which proceeds in three steps: (1) adenylation (addition of AMP) of a residue in the active center of the enzyme, pyrophosphate is released; (2) transfer of the AMP to the 5' phosphate of the so-called donor, formation of a pyrophosphate bond; (3) formation of a phosphodiester bond between the 5' phosphate of the donor and the 3' hydroxyl of the acceptor. |
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Term
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Definition
| Short molecules of single-stranded DNA that are formed on the lagging strand during DNA replication. They are between 100 to 200 nucleotides long in eukaryotes. |
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Term
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Definition
| Enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. In order to help overcome these types of topological problems caused by the double helix, topoisomerases bind to either single-stranded or double-stranded DNA and cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again. |
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Term
| Error correction by DNA polymerase |
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Definition
| Error correction is a property of some, but not all, DNA polymerases. This process corrects mistakes in newly-synthesized DNA. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue. |
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Term
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Definition
| Enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs. |
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Term
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Definition
| Enzymes that cleave the phosphodiester bond within a polynucleotide chain. |
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Term
| What is the difference between exonucleases and endonucleases? |
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Definition
Exonucleases cleave phosphodiester bonds at the end of a polynucleotide chain.
Endonucleasese cleave the phosphodiester bond within a polynucleotide chain. |
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Term
| What is the replication error rate in DNA polymerase? |
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Definition
| 1 in 10^7 BPs (1 in 10^5 without the proofreading mechanism). |
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Term
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Definition
| A range of antiviral products used to prevent viral replication in infected cells. These agents can be used against hepatitis B virus, hepatitis C virus, herpes simplex, and HIV. Once they are phosphorylated, they work as antimetabolites by being similar enough to nucleotides to be incorporated into growing DNA strands; but they act as chain terminators and stop viral DNA Polymerase. They are not specific to viral DNA and also affect mitochondrial DNA. Because of this they have side effects such as bone marrow suppression. |
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Term
| What are the five main types of endogenous DNA damage? |
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Definition
1) Oxidation of bases
2) Alkylation of bases
3) Hydrolysis of bases
4) Bulky adduct formation |
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Term
| What are some examples of exogenous DNA damage? |
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Definition
1) UV light damage
2) Ionizing radiation damage
3) Thermal disruption
4) Exposure to environmental mutagens |
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Term
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Definition
| A type of DNA damage. DNA oxidation is the process of oxidative damage on Deoxyribonucleic Acid. It occurs most readily at guanine residues due to the high oxidation potential of this base relative to cytosine, thymine, and adenine. It is widely believed to be linked to certain disease and cancers. |
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Term
| DNA methylation (alkylation) DIFFERENCE? |
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Definition
| DNA methylation in vertebrates typically occurs at CpG sites (cytosine-phosphate-guanine sites, that is, where a cytosine is directly followed by a guanine in the DNA sequence). This methylation results in the conversion of the cytosine to 5-methylcytosine. |
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Term
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Definition
| The hydrolysis reaction of cytosine into uracil, releasing ammonia in the process. In DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. The resulting abasic site is then recognised by enzymes(AP endonucleases) that break a phosphodiester bond in the DNA, permitting the repair of the resulting lesion by replacement with another cytosine. A DNA Polymerase may perform this replacement via nick translation, a terminal excision reaction by its 3'-->5' exonuclease activity, followed by a fill-in reaction by its polymerase activity. DNA ligase then forms a phosphodiester bond to seal the resulting nicked duplex product, which now includes a new, correct cytosine. |
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Term
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Definition
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Term
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Definition
| An alteration of DNA in which the purine base (adenine or guanine) is removed from the deoxyribose sugar by hydrolysis of the beta-N-glycosidic link between them. After depurination, an apurinic site is formed where the sugar phosphate backbone remains and the sugar ring has a hydroxyl (-OH) group in the place of the purine. |
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Term
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Definition
| Molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions. Ultraviolet light induces the formation of covalent linkages by reactions localized on the C=C double bonds. Two common UV products are cyclobutane pyrimidine dimers (CPDs, including thymine dimers) and 6,4 photoproducts. These premutagenic lesions alter the structure of DNA and consequently inhibit polymerases and arrest replication. Dimers may be repaired by photoreactivation or nucleotide excision repair, but unrepaired dimers are mutagenic. In humans they are the primary cause of melanomas. |
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Term
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Definition
| When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. |
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Term
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Definition
| Both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements. |
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Term
| How does the cell repair single-strand DNA damage? |
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Definition
1) Base excision repair
2) Nucleotide excision repair
3) Mismatch repair |
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Term
| How does the cell repair double-strand DNA damage? |
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Definition
1) Homologous recombination
2) Non-homologous end joining |
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Term
| How does the cell repair cell damage from pyrimidine dimers? |
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Definition
Through photoreactivation by photolyase. Photolyases are enzymes that repair damage caused by exposure to ultraviolet light. This enzyme mechanism requires visible light, preferentially from the violet/blue end of the spectrum, and is known as photoreactivation.
Photolyases bind complementary DNA strands and break certain types of pyrimidine dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA become covalently linked. These dimers result in a 'bulge' of the DNA structure, referred to as a lesion. The more common covalent linkage involves the formation of a cyclobutane bridge. Photolyases have a high affinity for these lesions and reversibly bind and convert them back to the original bases. |
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Term
| METHYLATED GUANINE: MGMT (PG 12)??? |
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Definition
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Term
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Definition
| A cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky helix-distorting lesions. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication. |
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Term
| Nucleotide excision repair |
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Definition
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Term
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Definition
| A cellular mechanism that removes mispaired nucleotides by 3'-->5' proofreading and inserts correct nucleotide to allow continuation of synthesis. Mismatch repair reduces the replication error rate from 1 in 10^7 to 1 in 10^9. |
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Term
| What causes double strand breaks? |
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Definition
| Double strand breaks can arise from scheduled events (e.g. meiotic chromosome breaks), ionizing radiation, or DNA replication errors or replication fork stress (e.g. collapsed forks). |
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Term
| Which method of repair of double strand breaks do human cells prefer? |
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Definition
| Non-homologous end joining. |
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Term
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Definition
| A type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks. |
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Term
| Non-homologous end joining |
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Definition
| A pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template. NHEJ typically utilizes short homologous DNA sequences called microhomologies to guide repair. These microhomologies are often present in single-stranded overhangs on the ends of double-strand breaks. When the overhangs are perfectly compatible, NHEJ usually repairs the break accurately. Imprecise repair leading to loss of nucleotides can also occur, but is much more common when the overhangs are not compatible. Inappropriate NHEJ can lead to translocations and telomere fusion, hallmarks of tumor cells. |
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Term
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Definition
| Ataxia-telangiectasia is rare childhood disease that affects the brain and other parts of the body. Ataxia refers to uncoordinated movements, such as walking. Telangiectasias are enlarged blood vessels (capillaries) just below the surface of the skin. Telangiectasias appear as tiny, red, spider-like veins. Ataxia-telangiectasia is inherited, which means it is passed down through families. It is an autosomal recessive trait. This means that both parents must provide a defective gene for the child to have symptoms of the disorder. The disease results from defects in the ataxia telangiectasia mutated (ATM) gene which encodes a kinase essential for p53 activity, being responsible for recognizing and correcting errors in duplicating DNA when cells divide, and in destroying the cells when the errors can't be corrected. The protein normally repairs double-stranded DNA breaks. Defects in this gene can lead to abnormal cell death in various places of the body, including the part of the brain that helps coordinate movement. |
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Term
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Definition
| A rare autosomal recessive chromosomal disorder characterized by a high frequency of breaks (defect in the replication stress response) and rearrangements in an affected person's chromosomes. The BLM protein is important in maintaining the stability of the DNA during the replication process. The mutations in the BLM gene associated with Bloom's syndrome inactivate the BLM protein's DNA helicase activity or nullify protein expression (the protein is not made). Lack of BLM protein or protein activity leads to an increase in mutations. Persons with Bloom's syndrome have an enormous increase in exchange events between homologous chromosomes or sister chromatids (the two DNA molecules that are produced by the DNA replication process); and there are increases in chromosome breakage and rearrangements compared to persons who do not have Bloom's syndrome. |
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Term
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Definition
| a rare autosomal recessive congenital disorder characterized by growth failure, impaired development of the nervous system, abnormal sensitivity to sunlight (photosensitivity), and premature aging. Hearing loss and eye abnormalities (pigmentary retinopathy) are other common features, but problems with any or all of the internal organs are possible. It is associated with a group of disorders called leukodystrophies. The underlying disorder is a defect in the nucleotide excision repaire mechanism. |
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Term
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Definition
| The result of a genetic defect in a cluster of proteins responsible for DNA repair. As a result, the majority of FA patients develop cancer, most often acute myelogenous leukemia, and 90% develop bone marrow failure (the inability to produce blood cells) by age 40. About 60-75% of FA patients have congenital defects, commonly short stature, abnormalities of the skin, arms, head, eyes, kidneys, and ears, and developmental disabilities. Around 75% of FA patients have some form of endocrine problem, with varying degrees of severity. FA results from a defect in the replication stress response. |
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Term
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Definition
| An autosomal recessive genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet (UV) light is deficient. In extreme cases all exposure to sunlight must be forbidden, no matter how small. The most common defect in xeroderma pigmentosum is an autosomal recessive genetic defect in which nucleotide excision repair (NER) enzymes are mutated, leading to a reduction in or elimination of Nucleotide Excision Repair. If left unchecked, damage caused by UV light can cause mutations in individual cell's DNA. If tumor suppressor genes (e.g. p53) or proto oncogenes are affected, the result may be cancer. Patients with XP are at a high risk for developing skin cancers, such as basal cell carcinoma, for this reason. |
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Term
| Hereditary nonpolyposis colorectal cancer |
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Definition
| n autosomal dominant genetic condition which has a high risk of colon cancer[1] as well as other cancers including endometrium, ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, and skin. The increased risk for these cancers is due to inherited mutations that impair DNA mismatch repair. |
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