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| translesion DNA polymerase |
-A widely opened nucleotide binding pocket in the Y-family DNA polymerases allows the enzyme positioning the incoming nucleotide at active site without Watson-Crick base pair with template DNA |
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| Y-family (error-prone) DNA polymerase |
synthesizes DNA with template DNA but it is also able to incorporate nucleotide without DNA base-paring (SOS-response)
-Pol IV or Pol V in E. coli |
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| Nonhomologous End Joining (NHEJ) pathway (Fig. 9-18) |
does not use a sister chromosome for repair. This repair pathway introduces mutation at the junction.
The NHEJ pathway is ubiquitous in eukaryotes, but less frequently in bacteria |
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| Double-strand break (DSB) repair pathway |
uses an homologous recombination with undamaged DNA for repair the double-stranded DNA break without introducing any mutation. (discussed in Chap. 10) |
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| Transcription-coupled repair |
The system forces repair enzymes on DNA being actively transcribed. In bacteria, DNA mutation on a template strand for making RNA is repaired more efficient than mutation on a non-template strand. |
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| nucleotide excision repair |
-recognize distortions in shape (unlike base excision)
-removes patch
-ssDNA gap
-DNA pol fills in |
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mcs5109 Thu, 25 Sep 2008 06:58:59 GMT |
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| How do DNA glycosylase detect damaged bases if it is buried in the double helix? |
Flipped out damaged DNA base from double helix (Fig. 9-14) |
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| base excision repair |
-glycocyase recognizes/removes damaged base by hydrolyzing gylcosidic bond
-abasic sugar removed from backbone
-AP endonuclease cuts DNA backbone |
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| 2 principle repair systems |
-base excision repair
-nucleotide excision repair |
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| Methyl group removal (Fig. 9-12): |
Methyl transferase (e.g., Ada) is a protein for removing mehylgroup from base; it is also a transcription factor (methylated form of Ada) to expressing genes for DNA repairs (Coupling between DNA repair and transcription) |
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mcs5109 Thu, 25 Sep 2008 06:37:43 GMT |
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| Photoreactivation (Fig. 9-11) |
: pyrimidine dimer is made by an energy of light. The repair enzyme (DNA photolyase) also uses an energy of light for repair it. |
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| Gamma radiation and X-ray (ionizing radiation): |
double-strand DNA breaks (which is difficult to repair) |
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| Ultraviolet light: |
thymine dimmer, unable of base paring and stop DNA polymerase and also RNA polymerase |
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| Alkylation: |
Methyl or ethyl groups are transferred to bases |
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| Hydrolytic damage: |
spontaneously deamination of cytosine, adenine and guanine |
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| Dam methylase |
methylates A residues of GATC sequence
-only parental strand methylated for a while
-until Dam catches up, only template methylated |
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mcs5109 Thu, 25 Sep 2008 06:34:14 GMT |
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| mismatch repair system corrects the mismatch only in the newly synthesized DNA? |
Solution: using DNA methylation as a marker to identify an newly synthesized DNA strand (e.g. Dam methylase)
-MutH makes incision in unmyethylated daughter strand |
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mcs5109 Thu, 25 Sep 2008 06:34:14 GMT |
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| MutS/MutL/MutH system in E. coli |
-system scans whole genome to fine mismatch
-The MutS recognizes unusual DNA structure (DNA bending) because of the mismatch base pairing instead of directly monitor the DNA mismatch. The MutS uses ATP as a cofactor. |
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mcs5109 Thu, 25 Sep 2008 06:24:58 GMT |
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| Mismatch repair increases accuracy of DNA synthesis by an additional x100~1000 |
Q. What is an error rate of the replicative DNA polymerase? |
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| DNA mutation |
produces mismatch in first round of replication and permanently incorporates in second round replication |
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mcs5109 Thu, 25 Sep 2008 06:24:58 GMT |
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| DNA microsatellites: |
mutation-prone sequence, di-, tri- or tetranucleotide sequenes
e.g. CA repeats in human genome, it causes DNA synthesis slippage to increase number of copies of repeated sequences |
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mcs5109 Thu, 25 Sep 2008 06:22:23 GMT |
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| “Hot spot”: |
mutation arise at high frequency |
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| Transversions: |
pyrimidine-to-purine and purine-to-pyrimidine |
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| Transitions: |
pyrimidine-to-pyrimidine and purine-to-purine |
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mcs5109 Thu, 25 Sep 2008 06:22:23 GMT |
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