BIOL 211 Exam # 2 Study Guide Lectures: 12 - 20Lecture 12 (September 24)Replication Errors and the Mismatch Repair SystemsArticle: "Corrupt DNA Might Be Good For You"What is the difference between the results of translational errors, transcriptional errors, and mutations?Translational errors affect only one protein. Transcriptional errors affect one subset of proteins. Mutations are permanent DNA changes that alter all proteins encoded by a given gene and all proteins of cell descendents.Transitions and Transverions are both types of replication errors. What is the difference?Transitions switch a pyrimidine for a pyrimidene or a purine for a purine. Transversions switch a pyrimidine for a purine and vice versa. Note that the pyrimidines are Thymine and Cytosine and the purines are Guanine and Adenine.What are the other two main types of replication errors? Describe them.Insertions and deletions are the other types of replication errors. In insertion, DNA polymerase slips and adds one or more nucleotides, looping the new DNA strand. In deletion, DNA polymerase slips and removes one or more nucleotides, looping the template DNA strand.Where are replication errors the most common?Replication errors are the most common at repetitive sequences.Huntington's Disease is the result of a genetic mutation. What are the symptoms of Huntington's disease, and what causes the symptoms?The symptoms of Huntington's Disease include cognitive decline over time and gradual loss of physical control. The mutation, which is the result of too many trinucleotide (CAG) repeats on a certain gene, causes the excess production of glutamine. The excess glutamine causes the symptoms.Describe the mismatch repair system in E. Coli, emphasizing the unique roles of MutS, MutH.In E. Coli, the mismatch repair system begins with a MutS dimer, which seeks and finds distortions in DNA and changes conformation to attach to DNA once it finds them. After attaching to DNA, MutS uses energy to attract MutL and MutH. MutH nicks the newly synthesized DNA (discriminating between the template strand and the newly synthesized strand). Helicase (UvrD) then unwinds the problem stretch. An exonuclease is then able to comeand remove the incorrect DNA. DNA polymerase and DNA ligase can then close and repair the gap.What is the purpose of Dam Methylation?Dam methylation allows MutH to distinguish between the template strand and the new strand. The new strand is not methylated.How is the mismatch repair system different in Eukaryotes?Eukaryotes have no MutH. Thus, MutL becomes responsible for nicking the erred strand. Additionally, the new strand is recognized by the gaps between Okazaki fragments (as opposed to dam methylation).Lecture 13 (September 26) Chemical and Environmental Mutagens and Cellular Damage MechanismsWhat are the two types of mutagens?Chemical and EnvironmentalWhat is the resulting nucleotide when water deaminates cytosine?UracilWhat causes guanine to pair with adenine instead of cytosine?OxidationDescribe the Base Excision Repair mechanism.Glycosylase enzymes recognize specific damaged bases where they shouldn't be. Glycosylase breaks the glycosidic bond, flipping the damaged base out and away from the double helix, to remove the damaged base. An AP site (apyrimidinic or apurinic) site is formed out of a phosphate and a sugar. Exonucleases and endonucleases find the AP site and make single stranded breaks. DNA polymerase replaces the base (with the correct base). Repair is complete by DNA ligase, which reforms the phosphodiester bond.What are the backups for the Base Excision Repair mechanism?Fail-safe glycosylases, which find errant bases missed by base excision repair. They cut out the incorrect pair on the new strand and insert the proper pair, but to not fix the issue in the original strand. This process allows the cell another chance to catch the problem.What is the purpose of nucleotide excision repair (as opposed to base excision repair)?Nucleotide excision repair removes thymine dimers (which are formed by UV radiation).Describe the process of Nucleotide Excision Repair.A UvrA and UvrB (such named because the errors they seek are caused by UV light) tetramer complex scans DNA, looking for the distortions caused by dimers. Once a distortion is found, UvrA is no longer necessary, and departs. UvrB remains and bubbles around the distortion, creating a stretch of ssDNA that allows proteins to access the thymine dimers. UvrC then comes and makes single stranded nicks on either side of the distortion by UvrB. UvrD (helicase)unwinds the single-strand fragment, which causes it to float away. DNA polymerase and ligase then fill in and close the gap.What does the cell do if nucleotide excision repair fails?If nucleotide excision repair fails, RNA polymerase will stall during transcription at the distortion site, and nucleotide excision repair proteins will be recruited.What are Error Prone Polymerases and what do they do?When DNA polymerase stalls at a thymine dimer during replication, DNA polymerase is replacedby error-prone polymerase for a stretch. Unfortunately, error-prone polymerase is error-prone and likely to cause mutations. The advantage is that the chromosome is replicated and repair pathways can come back and repair the error later.What is DNA photolyase?DNA photolyase is an enzyme that reverses the formation of thymine dimers by physically separating them.What is the purpose of methyltransferase?Methyltransferase removes methylated groups, which is beneficial because when guanine is methylated, it acts like adenine, which causes the incorrect pairing with thymine as a result. Methyl groups are small and hard to recognize by other repair systems, so methyltransferase is necessary.Lecture 14 (September 29)Double-Stranded Breaks, Non-Homologous End Joining, and Homologous RecombinationArticle: "DNA May have Had Humble Beginnings as Nutrient Carrier"Why are double stranded breaks so dangerous?DSBs are dangerous because they break the phosphodiester bond, which can result in deletions.Phosphodiester bonds are what keep strands together.What are some common causes of DSBs?Radiation, Physical Constraints, and Reactive Oxygen SpeciesWhat are reactive oxygen species?Reactive oxygen species are chemically reactive molecules with oxygen in them.What is superoxide?Superoxide reacts with and damages all macromolecules with which it interacts, especially DNA,where it modifies bases and/or produces double