BMB 462 Lecture 26 Outline of Last Lecture I Mutations and Carcinogens II DNA Repair Mechanisms Overview III Mismatch Repair IV Base Excision Repair V Nucleotide Excision Repair Outline of Current Lecture I II III IV Review of Nucleotide Excision Repair Direct Repair Recombinational Repair Error Prone Repair Mechanisms a Nonhomologous End Joining NHEJ b SOS repair V DNA Recombination a Homologous Recombination b Site Specific Recombination Current Lecture Concepts to remembers from previous courses lectures I Review of Nucleotide Excision Repair a In humans you cleave a larger section of DNA which is more costly for the cell because it has to polymerize it all again b This underlines how important it is for the cell to conserve the information in its DNA c d There are multiple ways to repair the same error e Nucleotide excision results in major structural change f In humans nucleotide excision is the only way to fix a pyrimidine dimer These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute g There are certain mutations in the NER enzymes that predispose the individual to cancer because the pyrimidine dimers are introduced by UV light h xeroderimer pigmentosis is one such disorder individuals with this disorder have mutations in the NER enzymes that make them sensitive to UV light They cannot go out into direct sunlight because they are predisposed to developing skin cancer i II Direct Repair a Repair with Photolyase b Bacteria have another mechanism for repairing pyrimidine dimers the enzyme photolyase Mammals do not have this enzyme which is why the rely on NER c Photolyase is an example of direct repair d e In direct repair the bases are fixed in place when they are repaired f Dimer repair mechanism g The dimer forms between two adjacent thymines The thymines can actually form a covalent bonds to create a cyclobutane structure h The dimer formation creates a kink in the DNA even one kink can be fatal for E coli i The enzyme uses 2 cofactors both are chromophores MTHFpolyglutamate and FADH along with the energy of light to repair the cyclobutane j Light is used to repair a light induced damage k 1 Light activates the MTHFpolyglutamate l 2 The light energy is then transferred to FADH which activates it and excites an electron m 3 the electron is transferred to the cyclobutane pyrimidine dimer for the repair a 4 After the pyrimidines are repaired the electron is transferred back to the FADH so that it can be recycled b Repair with O6 methylguanine DNA methyltransferase c Specific enzymes are used to repair specific damage the enzyme that fixes O6methylguanine is O6 methylguanine DNA methyltransferase d It removes the methyl group from the O6 methylguanine allowing the guanine to be regenerated e The methyltransferase can t be regenerated because it creates a covalent bond with the methyl and has to be degraded a again it s a costly way for the cell to ensure the information in DNA is preserved b Repair with AlkB c The last form of direct repair d AlkB repairs alkylation damage e It uses the cofactor alpha ketoglutarate to repair the methylated residue f In the process the base gets oxidized and formaldehyde is release this regenerates the base g The cofactor is also oxidized from alpha ketoglutarate to succinate h The enzymes are called mixed function oxidases or dioxygenases because they oxidize two substrates in the repair process a This process can repair two substrates 1 methyladenine and 3 Methylcytosine it is a very specific enzyme for 2 types of damage b These are all the mechanisms that use one strand of the double helix to repair the other III Recombinational Repair a Recombination repair uses the second duplex to repair the first b This repair occurs when the replication fork comes across an unrepaired lesion or an unrepaired break c When the cell comes across this kind of damage it can either use the recombinational repair or error prone repair which requires error prone polymerases polymerases IV and V in E coli d These polymerases don t have a proofreading mechanism so they essentially read through the error and then fall off so that regular replication resume e If there is an unrepaired break in the DNA the replication fork again stalls and the cell can undergo recombinational repair or Non homologous end joining the latter mechanism is also error prone f When the replication fork encounters an unrepaired lesion or break it stalls and normal replication can t proceed so it has to resort to one of the aforementioned mechanisms IV Error Prone Repair Mechanisms a These error prone repairs are used when it is better to continue through with normal replication at any rate than have nothing produced at all b Nonhomologous End Joining NHEJ c SOS repair V DNA Recombination a Homologous Recombination b Site Specific Recombination
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