| what's mismatch repair (MMR) ? | A type of repair that corrects mispaired bases, typically immediately following replication.
-The process preferentially corrects the sequence of the daughter strand by distinguishing the daughter strand and parental strand, sometimes on the basis of their states of methylation. |
| what's photoreactivation (Direct Repair) ? | A repair mechanism that uses a white light-dependent enzyme to split cyclobutane pyrimidine dimers formed by ultraviolet light. |
| what's excision repair ? | A type of repair system in which one strand of DNA is directly excised and then replaced by resynthesis using the complementary strand as template. |
| what's base excision repair (BER) ? | A pathway of excision repair that recognizes damage to single bases, such as deaminiation or alkylation, and either repairs the base alone (short-patch repair) or replaces 2–10 nucleotides (long-patch repair). |
| what's nucleotide excision repair (NER) ? | An excision repair pathway that recognizes bulky lesions in DNA (such as UV-induced pyrimidine dimers).
-NER is divided into two major subpathways: transcription-coupled repair (TC-NER), which repairs damaged in the transcribed strand of active genes; and global genome repair (GG-NER), which repairs damage anywhere in the genome. |
| how does the DNA repair system correct damaged DNA? | -Repair systems recognize DNA sequences that do not conform to standard base pairs.
-Excision systems remove one strand of DNA at the site of damage and then replace it. |
| what are the Types of damages that trigger repair system ? | -Single base changes.
-Structural distortions/bulky lesions.
-Strand breaks. |
| what happens in single base changes? | corrected by either replacing U with C or corrected by removing A or G. |
| what happens in Structural distortions? | -Introduction of covalent links between bases on one strand of DNA or between bases of opposite strands.
-Photoreactivation is a nonmutagenic repair system that acts specifically on pyrimidine dimers. |
| what happens when a DNA strand breaks? | -Can occur in one or both strands.
-A single –stranded break, or nick, can be directly ligated.
-DSBs are major damage, if unrepaired, can result in extensive loss of DNA. |
| what's the Excision Repair Systems in E. coli? | -The Uvr system makes incisions ~12 bases apart on both sides of damaged DNA, removes the DNA between them (excision), and resynthesizes new DNA.
-Transcribed genes are preferentially repaired when DNA damage occurs. |
| what's Xeroderma pigmentosum (XP) ? | it is a human disease caused by mutations in any one of several nucleotide excision repair genes.
-Numerous proteins, including XP products and the transcription factor TFIIH, are involved in eukaryotic nucleotide excision repair. |
| what are Eukaryotic Nucleotide Excision Repair Pathways? | -Global genome repair recognizes damage anywhere in the genome.
-Transcriptionally active genes are preferentially repaired via transcription-coupled repair.
-Global genome repair and transcription-coupled repair differ in their mechanisms of damage recognition (XPC vs. RNA polymerase II). |
| what's the Eukaryotic Nucleotide Excision Repair Pathways link to a complex of repair enzymes and what's the mutation that occurs? | TFIIH provides the link to a complex of repair enzymes.
Mutations in the XPD component of TFIIH cause three types of human diseases. |
| what's Base Excision Repair Systems Require Glycosylases? | -Base excision repair is triggered by directly removing a damaged base from DNA.
-Base removal triggers the removal and replacement of a stretch of polynucleotides.
-The nature of the base removal reaction determines which of two pathways for excision repair is activated.
-The polδ/ε pathway replaces a long polynucleotide stretch; the polβ pathway replaces a short stretch. |
| Uracil and alkylated bases are recognized by what enzyme?what does this enzyme do? | -bases are recognized by glycosylases and removed directly from DNA.
-Glycosylases and photolyase (a lyase) act by flipping the base out of the double helix, where, depending on the reaction, it is either removed or modified and returned to the helix. |
| what are Error-Prone Repair and Translesion Synthesis? | -Damaged DNA that has not been repaired causes DNA polymerase III to stall during replication.
-DNA polymerase V (coded by umuCD) or DNA polymerase IV (coded by dinB) can synthesize a complement to the damaged strand.
-The DNA synthesized by repair DNA polymerases often has errors in its sequence (error-prone synthesis). |
| what's a mutator? what gene encodes for that? | -A mutation or a mutated gene that increases the basal level of mutation.
Such genes often code for proteins that are involved in repairing damaged DNA.
-The mut genes code for a mismatch repair system that deals with mismatched base pairs. |
| how is the Direction of Mismatch Repair Controlled? | -There is a bias in the selection of which strand to replace at mismatches.
-The strand lacking methylation at a hemimethylated GATCCTAG is usually replaced.
-The mismatch repair system is used to remove errors in a newly synthesized strand of DNA. At G-T and C-T mismatches, the T is preferentially removed. |
| how is The mismatch repair system is used ? | Eukaryotic MutS/L systems repair mismatches and insertion/deletion loops |
| what's The recombination-repair system? | -The rec genes of E. coli code for the principal recombination-repair system.
-The recombination-repair system functions when replication leaves a gap in a newly synthesized strand that is opposite a damaged sequence. |
| how does Recombination-Repair Systems in E. coli happen? | -The single strand of another duplex is used to replace the gap (single-strand exchange).
-The damaged sequence is then removed and resynthesized. |
| how does Recombination occur to Recover from Replication Errors? | A replication fork may stall when it encounters a damaged site or a nick in DNA.
A stalled fork may reverse by pairing between the two newly synthesized strands. |
| how is Recombination-Repair used for Double-Strand Breaks in Eukaryotes? | -The yeast RAD mutations, identified by radiation-sensitive phenotypes, are in genes that code for repair systems.
-The RAD52 group of genes is required for recombination repair.
-The MRX (yeast) or MRN (mammals) complex is required to form a single-stranded region at each DNA end. |
| how does a nucleoprotein filament on the single-stranded region formed? | by the The RecA homolog Rad51 assisted by Rad52 and Rad55/57 (involved in homology search and strand invasion). |
| how are Nonhomologous End-Joining and how do they Repair Double-Strand Breaks? | -Repair of double-strand breaks when homologous sequence is not available occurs through a nonhomologous end-joining (NHEJ) reaction.
-The NHEJ pathway can ligate blunt ends of duplex DNA.
-Mutations in double-strand break repair pathways cause human diseases. |
| how does DNA Repair in Eukaryotes Occur in the Context of Chromatin? | -Both histone modification and chromatin remodeling are essential for repair of DNA damage in chromatin.
-H2A phosphorylation (y-H2AX) is a conserved double-strand break-dependent modification that recruits chromatin modifying activities and facilitates assembly of repair factors. |
| what does different patterns of histones distinguish, and what is required to reset chromatin? | -Different patterns of histone modifications may distinguish stages of repair or different pathways of repair.
-Remodelers and chaperones are required to reset chromatin structure after completion of repair. |
| how does RecA Trigger the SOS System? | -Damage to DNA causes RecA to trigger the SOS response, which consists of genes coding for many repair enzymes.
-RecA activates the autocleavage activity of LexA.
-LexA represses the SOS system; its autocleavage activates those genes. |
