9 Mutation and DNA repair The functional consequences of mutations The types of repair mechanisms The state the definition of mutation and define and give an example of the different types of mutations To describe the Ames test and its utility. To describe each of the following repair systems in terms of the damage repaired and the mechanism by which the damage is repaired Mismatch repair And how strand discrimination occurs What the signal for nicking is What nicking results in How repair proceeds Base excision repair What is initially cleaved What the product of cleavage is Which DNA polymerase is involved? Nucleotide excision repair The distinction with base excision repair The common DNA mutations involved To describe the potential effect on human health of defects in DNA repair and give at least one example To identify the mechanism by which uv mediated damage is repaired without splitting phosphodiester bonds To describe a mechanism by which 6 methylguanine is directly restored To understand the effect of methylation on methyltransferase gene expression To describe the mechanism of recombinational repair To describe in general terms the mechanism of error prone repair
+ See chapter 8 Tortora
Quizzish What is a mutation? What three types of DNA alterations responsible for mutations? What is a silent mutation? Where might a silent mutation occur? What does the Ames test measure? What gene is mutated in the Ames test? What sort of mutation must occur in order for the Ames test to score a positive result? What is meant by mismatch repair? What system is mismatch repair a part of? How does mismatch repair discriminate between old and new strands of DNA? Following discrimination, how does mismatch repair proceed? What binds the mismatched bases? How is the mismatched base excised? How is it replaced? What enzyme replaces it? Mutations in the human homolog of mut proteins can result in what disease? What enzymes carry out base excision repair? Which excises a damaged base? How is it excised? What results from base excision? What is the first cut made to restore an apurinic or apyrimidinic site? What catalytic process follows? What enzyme restores the DNA duplex? What seals the final phosphodiester break? Describe the complete process of nucleotide excision repair The type of damage most commonly restored. The genes in E. coli involved The function of the uvr genes. The amount of DNA removed The restoration of the double helix What human disease is a reslt of a failure of nucleotide excision repair? What is meant by direct repair? What activates a photolyase? What is the target and the product of photolyase activity? What type of damage does methyl transferase restore? What happens to methyltransferase following restoration of a methylated nucleotide base? How does recombinational repair proceed? Why is error prone repair error prone? When does it happen?
10 Recombination Mechanisms and effect The Holliday structure The enzymatic processes Transposition and transposons Correlation with Meiosis and visible cytological structures Sister chromatid exchange And the genetic map Utility Lola meditates on your objectives Describe three types of recombination in terms of their mechanism Describe four results of recombination Describe the circumstances under which recombinational repair occurs Describe two mechanisms of recombinational repair Describe the point at which recombination occurs during meiosis Define tetrad, chiasmata Describe the result of recombination in eukaryotes in terms of the effect on homologous chromosomes Understand the nature of a genetic map Describe the mechanism of homologous recombination Draw a Holliday structure Show how a Holliday structure can be resolved Understand how mismatches in recombined sequences are resolved into two non-identical homologs Describe the combined functions of the Rec BCD complex Describe the function of Rec A Describe the mechanism of site specific recombination Describe the tow possible outcomes of site specific recombination within one molecule Describe how a dimeric genome may come about and how it can be resolved Distinguish between site specific recombination and transposition Describe the structure of an insertion sequence Distinguish between an insertion sequence and a complex transposon In terms of structure In terms of function Distinguish between direct and replicative transposition in terms of mechanism Describe how repeated host sequences are produced at the site of transposition Compare the resolution of a dimeric genome with that of a replicative transposon Compare the structure of a bacterial transposon with that of a retrovirus
Quizzish What are three forms of recombination? How do the three forms differ? What specific functions does recombination perform? What form of repair restores a stalled replication fork? Recombination creates a duplex between which two pairs of strands during recombinational repair? What occurs following recombination between the stalled extending strand and the other extending strand? Once the stalled extending strand has replicated beyond the point of damage, what happens? Which strand then serves as template at the stalled fork? When the fork stalls due to a break, which strands serve as template strands over the region of the break? What does meiosis accomplish? What is the maximum amount of DNA in a meiotic cell? How many cell divisions occur during meiosis? What is the final number of chromosomes in the products of meiosis? What are the final products of meiosis? When does recombination occur during meiosis? What are the recombining structures called? What are the points of recombination within the tetrads called? What is the effect of recombination on the homologous chromosomes? How does homologous recombination initiate? What is branch migration? What is a Holliday structure? How can a Holliday structure be resolved? Are the two strands of a single DNA double helix identical following homologous recombination? What process makes them identical? Since the homologous chromosomes each have two non-identical strands making up their duplexes following homologous recombination, why do two different sequences result following error correction? What does the Rec BCD complex do during homologous recombination in bacteria? What structure does Rec A bind to? What does Rec A do? What specific structures are required for site specific recombination to proceed? How does a recombinase link two DNA strands? What are two possible results of site specific recombination within a single molecule? How can a dimeric genome come about? How are dimeric genomes resolved? What are transposons? Are transposons site specific? What enzyme is necessary for transposition? What is the minimal structure of an insertion sequence? What does a complex transposon contain? What happens to the DNA sequence of a chromosome when direct transposition occurs? What is the template strand for the synthesis of direct repeats at the site of transposon integration? What is the functional difference between replicative and direct transposition? What resolves the intermediate of replicative transposition? What is the genome of a retrovirus? Through what process is a DNA genome made? What is the fate of the DNA genome? How are retroviral genes expressed? How are retroviral genomes made? What are the repeated sequences at the end of a retroviral genome called? What is a retrotransposon?
The repair systems <ul><li>Mainly, the undamaged complementary strand acts as a template for the DNA polymerases involved in repair </li></ul><ul><ul><li>Mismatch repair </li></ul></ul><ul><ul><li>Base excision repair </li></ul></ul><ul><ul><li>Nucleotide excision repair </li></ul></ul><ul><ul><li>Direct repair </li></ul></ul><ul><ul><li>Recombinational repair </li></ul></ul><ul><ul><li>Error-prone repair </li></ul></ul>