DNA Repair Mechanisms PDF

DNA repair Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-038 DNA repair Because many mutations are harmful, DNA repair systems are vital to the survival of all organisms In most cases, DNA repair is a multi-step process 1. Irre...

DNA repair Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-038 DNA repair Because many mutations are harmful, DNA repair systems are vital to the survival of all organisms In most cases, DNA repair is a multi-step process 1. Irregularity in DNA structure is detected 2. Abnormal DNA is removed 3. Normal DNA is synthesized Review – thymine dimers UV light can cause the formation of cross-linked thymine dimers Thymine dimers may cause mutations when that DNA strand is replicated Direct repair of damaged bases in DNA In a few cases, the modifications of a nucleotide can be reversed by specific enzymes Photolyase can repair thymine dimers The base does not needs to be removed and can be modified while still in the DNA strand Review - deamination of cytosine Removal of an amino group from the cytosine base DNA repair enzymes can recognize uracil as an inappropriate base in DNA and remove it Base excision repair removes a damaged base Base excision repair involves removing one damaged or abnormal base Base excision repair involves a category of enzymes known as DNA N-glycosylases These enzymes recognize an abnormal base and cleave the bond between it and the sugar in the DNA Nucleotide excision repair removes damaged DNA segments In nucleotide excision repair the DNA is fixed by removal (excision) and replacement of a damaged region of DNA. This type of system can repair many types of DNA damage, including thymine dimers, chemically modified bases, missing bases, and more! Talk to a neighbor: What is the difference between base excision and nucleotide excision? Nucleotide excision repair removes damaged DNA segments In E. coli, the nucleotide excision repair system requires four proteins UvrA, UvrB, UvrC and UvrD. Named because they are involved in Ultraviolet light repair (but also important in repairing chemically damaged DNA) Nucleotide excision repair removes damaged DNA segments Talk to a neighbor: Several human diseases have been shown to involve inherited defects in genes involved in nucleotide excision repair. e.g. xeroderma pigmentosum (XP) and Cockayne syndrome (CS) A common characteristic of all three syndromes is an increased sensitivity to sunlight Why might sunlight sensitivity be increased by defects in nucleotide excision repair? Mismatch repair systems recognize and correct a base pair mismatch DNA polymerases have a 3’ to 5’ proofreading ability (using an exonuclease) that can detect base mismatches and fix them If proofreading fails, the mismatch repair system comes to the rescue An important aspect of these systems is that they are specific to the newly made strand  Review - DNA methylation Unmethylated Hemimethylated Prior to replication, both strands are methylated. Immediately after replication, the parental strand is methylated and the newly made daughter strand is not Fully methylated Mismatch repair in E. coli Three proteins, MutL, MutH and MutS detect the mismatch and direct its removal from the newly made strand The proteins are named Mut because their absence leads to a much higher mutation rate than normal  Talk to a neighbor: How does methylation ensure the sequence of bases remains the same as what was present in the parental strands? It’s better to replicate DNA poorly than not at all Replicative DNA polymerases, such as DNA pol III in E. coli, are sensitive to shape distortions in DNA In E. coli, DNA polymerase V, IV and II can replicate through DNA mismatches and other distortions. Their mutation rate is typically higher in the range of 1 in 100 to 1,000 compared to 1 in 108 for DNA polymerase III Double-strand breaks in DNA can be repaired by recombination DNA double-strand breaks are very dangerous and can cause breakage of chromosomes into pieces They may be repaired by two systems known as homologous recombination repair and nonhomologous end joining Talk to a neighbor What kinds of chromosome variations that we previously discussed can arise from double-stranded DNA breaks? Homologous recombination Homologous recombination is found in all species The cells of any given species may have more than one molecular mechanism for homologous recombination The enzymology of homologous recombination is best understood in E. coli and involves RecA, B, C, and D and single-strand binding proteins Rec indicates that the proteins function in recombination Generally enzymes involved in recombination are called recombinases Repair of a double-strand break by homologous recombination Talk to a neighbor What other applications of homologous recombination have we discussed in class so far? Repair of a double-strand break in DNA via nonhomologous end joining Broken ends are recognized by end-binding proteins Processing may result in deletion of a small region of DNA