Term
|
Definition
catalyze the copying of DNA sequences
promote the formation of the phosphodiester linkages joining the units of the ADNA backbone |
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Term
| the types of DNA polymerases |
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Definition
-polymerase I
-polymerase II
-polymerase III
-polymerase IV
-polymerase V |
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Term
| the better understood DNA polymerases |
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Definition
-polymerase I
-polymerase II |
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Term
| function of DNA polymerase I |
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Definition
| primer removal and DNA repair |
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Term
| function of DNA polymerase II |
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Definition
| repairs attachment of bulky hydrocarbons to bases |
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Term
| function of DNA polymerase III |
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Definition
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Term
| function of DNA polymerase IV |
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Definition
| repairs attachment of bulky hydrocarbons to bases |
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Term
| function of DNA polymerase V |
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Definition
| repairs attachment of bulky hydrocarbons to bases |
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Term
| additional enzyme activities of DNA polymerase I |
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Definition
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Term
| additional enzyme activities of DNA polymerase II |
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Definition
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Term
| additional enzyme activities of DNA polymerase III |
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Definition
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Term
| additional enzyme activities of DNA polymerase IV |
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Definition
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Term
| table of E. coli DNA polymerases |
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Definition
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Term
| DNA polymerases catalyze... |
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Definition
| the step-by-step addition of deoxyribonucleotides to a DNA strand |
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Term
| rxn of the addition of DNA strands, in its simplest form |
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Definition
| (DNA)n + dNTP <--> (DNA)n + 1 PPi |
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Term
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Definition
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Term
|
Definition
| sequence of nucleic acids that determines the sequence of a complementary nucleic acid |
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Term
| depiction of a polymerization rxn catalyzed by DNA polymerases |
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Definition
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Term
| some characteristics of DNA synthesis |
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Definition
| 1: requires all 4 aqctivated precursors -- that is, the deoxynucleoside 5'-triphosphates dATP, dGTP, dCTP, and TTP -- as well as the Mg2+ ion
2: the new DNA strand is assembled directly onto a preexisting DNA template; the DNA polymerase is a template-directed enzyme that synthesizes a complementary product
3: DNA polymerases require a primer to begin synthesis. Elongation proceeds from 5' to 3' direction
4: many DNA polymerases are able to correct mistakes by removing mismatched nucleotides |
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Term
| what is required for DNA synthesis to occur? |
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Definition
| -deoxynucleoside 5'-triphosphates
-Mg+2 ion |
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Term
| the deoxynucleoside 5'-triphosphates |
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Definition
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Term
| how the phosphodiester bond between adjacent nucleotides is formed |
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Definition
| nucleophilic attack by the 3' end of the growing strand on the innermost P atom of the dinucleoside triphosphate (dNTP) |
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Term
|
Definition
| initial segment of of a polymer that is to be extended on which elongation depends |
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Term
| the 3 distinct active sites of DNA polymerase I |
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Definition
-polymerase site
-3' --> 5' exonuclease site
-5' --> 3' exonuclease site |
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Term
| what the 3' --> 5' nuclease activity of DNA polymerase I does |
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Definition
| contributes to the remarkable high fidelity of DNA replication; error rate is less than 10-8 base pair |
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Term
| error rate of DNA replication |
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Definition
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|
Term
| depiction of the strand-elongation rxn |
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Definition
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Term
| depiction of DNA polymerase structure (Klenow fragment) |
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Definition
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Term
| depiction of shape complementarity of bases (in this case, adenosine) |
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Definition
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Term
| one reason DNA polymerase has such a low error rate |
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Definition
| conformational change by induced fit triggered by the binding of a dNTP into the active site such that it forms a tight pocket in which only a properly shaped base will fit |
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Term
| depiction of shape selectivity of DNA polymerase |
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Definition
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Term
| depiction of the helicase mechanism |
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Definition
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Term
|
Definition
|
|
Term
| negative supercoiling arises from... |
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Definition
| the unwinding or underwinding of DNA |
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Term
| negative supercoiling prepares DNA for... |
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Definition
| processes requiring separation of the DNA strands, such as replication |
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Term
| what unwinding of part of a strand does to adjacent DNA |
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Definition
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Term
| why DNA must be locally unwound |
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Definition
| to expose single-stranded templates for replication |
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Term
| depiction of the consequences of strand separation |
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Definition
|
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Term
|
Definition
| to move in a circle or spiral or to revolve, usually about a fixed point or on an axis |
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Term
|
Definition
| introduce or eliminate supercoils by temporarily cleaving DNA |
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Term
|
Definition
| catalyze the relaxation of supercoiled DNA, which is thermodynamically favorable |
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Term
|
Definition
| utilize free energy from hydrolysis to add negative supercoils to DNA |
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Term
|
Definition
| type II topoisomerases in bacteria |
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Term
| function of the exonuclease on DNA polymerase I |
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Definition
| removes mismatched nucleotides from the 3' end of DNA by hydrolysis |
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Term
| why it's easy for mismatched nucleotides to be removed |
|
Definition
weaker H bonding due to mismatch of nucleotides makes the malformed product flop around and be hot held as tightly in the polymerase active site
it finds itself in the exonuclease active site, where the trespassing nucleotide is removed |
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Term
| depiction of proofreading of DNA |
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Definition
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Term
| what happens if an incorrect base is incorporated into the DNA strand? |
|
Definition
enzyme stalls due to structural disruption caused by the mismatch
the pause gives it time to wander into te exonuclease active site |
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Term
| cost of exonuclease activity |
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Definition
| DNA polymerase I removes about 1 correct nucleotide in 20; slight wasteful energetically |
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Term
| origin of replication (oriC locus) |
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Definition
| unique site within the genome where replication begins |
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Term
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Definition
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Term
| what the origin of replication is in E. coli |
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Definition
| a 245-bp region that has several unusual features |
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Term
| composition of the oriC locus in E. coli |
|
Definition
-binding sites for DnaA protein
-tandem array of 13-bp sequences (AT rich) |
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Term
|
Definition
| structure in the E. coli chromosome where replication begins |
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Term
| how the prepriming complex is formed |
|
Definition
1: oriC locus wraps around DnaA protein
2: DnaB (a helicase) unwinds strand, including AT rich regions
3: single-strand-binding proteins (SSB) bind to newly generated single strands, preventing re-forming of 2bl helix |
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Term
| depiction of the origin of replication in E. coli and formation of the prepriming complex |
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Definition
|
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Term
| depiction of the oriC locus in E. coli |
|
Definition
| refer to p. 634 (figure 34.11 A) |
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Term
| DNA polymerases can add nucleotides only to... |
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Definition
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Term
| why a primer is required for DNA synthesis |
|
Definition
| because DNA polymerases can't start a strand de novo |
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Term
| what primes the synthesis of DNA? |
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Definition
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Term
|
Definition
| specialized RNA polymerase that joins the prepriming complex in a multisubunit assembly called the primosome |
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Term
|
Definition
| multisubunit assembly that primase joins the prepriming complex in |
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Term
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Definition
| synthesizes a stretch of about 10 RNA nucleotides that is complementary to one of the template DNA strands |
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Term
| what removes the RNA primer? |
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Definition
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Term
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Definition
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Term
| depiction of DNA replication at low resolution |
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Definition
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Term
| how Okazaki fragments are joined |
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Definition
| covalently by way of DNA ligase, which uses ATP hydrolysis to power the joining of DNA fragments |
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Term
|
Definition
| strand formed from Okazaki fragments |
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Term
|
Definition
| strand synthesized continuously 5' --> 3' |
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Term
| depiction of Okazaki fragments |
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Definition
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Term
| the enzyme responsible for the rapid and accurate synthesis of DNA in E. coli |
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Definition
| the holoenzyme DNA polymerase III |
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Term
| hallmarks of the holoenzyme DNA polymerase III |
|
Definition
-its fidelity
-its very high catalytic potency
-its processitivity |
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Term
|
Definition
| the ability of an enzyme to catalyze many consecutive rxns without releasing its substrate |
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Term
| the amount of phosphodiester linkages formed by the holoenzyme DNA polymerase III before releasing its template |
|
Definition
| many thousands, compared with only 20 for DNA polymerase I |
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Term
| catalytic potency of the holoenzyme DNA polymerase III |
|
Definition
| adds 1000 nucleotides per second compared to only 10 per second by DNA polymerase I |
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Term
| why the holoenzyme DNA polymerase III is able to add 1000 nucleotides per second |
|
Definition
| largely because of its processitivity |
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Term
| the source of the holoenzyme DNA polymerase III's processitivity |
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Definition
| the β2 subunit, which has the form of a star shaped ring that can readily accommodate the DNA strand, encircle it, and spin around it to add nucleotides |
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Term
| function of the β2 subunit in the holoenzyme DNA polymerase III |
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Definition
| functions as a sliding clamp that spins around the molecule and adds nucleotides as it spins |
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Term
| depiction of the structure of a sliding DNA clamp (the β2 subunit in the holoenzyme DNA polymerase III) |
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Definition
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Term
| how DNA gets into the β2 subunit in the holoenzyme DNA polymerase III |
|
Definition
| by way of sliding clamp loaders |
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Term
|
Definition
| unwinds the DNA duplex ahead of the DNA polymerase |
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Term
| single-strand-binding proteins |
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Definition
| they bind to unwound strands to keep the strands separated so that both strands can serve as templates |
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Term
|
Definition
| introduces negative supercoils ahead of the replication fork to avoid a topological crisis |
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Term
| depiction of the replication fork |
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Definition
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|
Term
| depiction of the DNA polymerase holoenzyme |
|
Definition
|
|
Term
| the DNA polymerase holoenzyme consists of... |
|
Definition
-2 copies of the polymerase core enzyme linked to a central structure
-the central structure includes the clamp-loader complex, which binds to the hexameric helicase Dnab |
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Term
| what fills the gaps between fragments of the nascent lagging strand in the trombone model? |
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Definition
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|
Term
| what removes the RNA primers in the lagging strand? |
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Definition
| the 5' --> 3' exonuclease activity in DNA polymerase I |
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Term
| why DNA polymerase III can't erase the RNA primers |
|
Definition
| because it doesn't have 5' --> 3' editing capacity |
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Term
| how DNA ligase joins fragments of DNA |
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Definition
| catalyzes the formation of a phosphodiester linkage between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of the other |
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Term
| depiction of the trombone model |
|
Definition
|
|
Term
| depiction of the DNA ligase rxn |
|
Definition
refer to p. 638
this is how it occurs in archaea and eukaryotes |
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Term
| why DNA synthesis is more complex in eukaryotes than in bacteria |
|
Definition
-size of genome
-eukaryotes have pairs of chromosomes that must be replicated
-eukaryotes have linear instead of circular chromosomes
-the nature of DNA synthesis on the lagging strand; linear chromosomes subject to shporteninbg on each round of replication unless countermeasures are taken |
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Term
| how the challenges of size of genome and number of chromosomes are dealt with |
|
Definition
| multiple origins of replication |
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|
Term
| how far apart are the different origins of replication? |
|
Definition
| 30-300 kilobase pairs (kbp) apart |
|
|
Term
| how many origins of replication are in humans? |
|
Definition
| about 30,000, with each chromosome having several hundred |
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Term
|
Definition
|
|
Term
|
Definition
proteins that bind to the origin of replication and permit (license) the DNA synthesis initiation complex
they ensure that each each replicon is replicated only once in each round of DNA synthesis |
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|
Term
| how replicons are controlled such that each replicon is replicated only once in each cell division |
|
Definition
licensing factors bind to the origin of replication and get destroyed after the initiation of the initiation complex
license expires after 1 use |
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|
Term
| the 2 distinct polymerases needed to copy a eukaryotic replicon |
|
Definition
-DNA polymerase α
-DNA polymerase δ |
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Term
|
Definition
begins the copying of a replicon
includes primase subunit to synthesize RNA primer as well as an active DNA polymerase
adds about 20 deoxynucleotides to the primer |
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Term
|
Definition
replaces DNA polymerase α
more processive than DNA polymerase α and is the principal replicative polymerase in eukaryotes |
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Term
|
Definition
| DNA polymerase α being replaced by DNA polymerase δ |
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|
Term
| complications introduced by having linear chromosomes |
|
Definition
-unprotected termini at the ends of chromosomes more vulnerable to digestion by exonuclease if left to dangle at the end of the chromosome during replication
-complete replication of DNA ends is difficult because polymerases act in 5' --> 3' direction and the lagging strand would have an incomplete 5' end after the removal of the RNA primer; each round of replication would shorten the chromosome |
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|
Term
| depiction of telomere shortening |
|
Definition
|
|
Term
|
Definition
| the DNA at the end of a chromosome; consists of hundreds of repeats of a hexanucleotide sequence characteristic of the organism |
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|
Term
| the most notable feature of telomeric DNA |
|
Definition
| it contains hundreds of tandem repeats of a hexanucleotide sequence |
|
|
Term
| how the telomere is structured in humans |
|
Definition
one of the strands is G rich at the 3' end and is slightly longer than the other
it is proporsed to loop back to form a DNA duplex with another part of the repeating sequence, displacing part of the original telomeric duplex |
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|
Term
| the G rich repeating strand in human telomeres |
|
Definition
|
|
Term
| depiction of a proposed model for telomeres |
|
Definition
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