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Topic 21 - DNA Repair.docx

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Western University
Biochemistry 2280A
Christopher Brandl

11/20/2012 1:28:00 PM Topic 21 – DNA Repair Topic 21 learning objectives  Describe and differentiate between the different kinds of commonly observed DNA damage  Predict which repair mechanism will be used to repair a particular instance of DNA damage  Predict the consequences of DNA damage that is not repaired before the next round of replication  Describe the role of translesion DNA polymerases as they relate to DNA damage  DNA damage = any unintended physical or chemical change in DNA or its sequence  DNA molecules are huge and are prone to damage  To try to avoid changes in nucleotide sequence, cells have developed mechanisms for repairing DNA damage  Sometimes mutations happen (unintended change)  Mutations are not always bad, occasionally you get beneficial one, but the organism doesn’t know whether or not it will be beneficial  The cell wants to conserve the sequence of DNA Causes of DNA damage 7 1. Copying mistakes: DNA polymerase makes an error about once every 10 nucleotides  Possible outcomes:  mismatched base pair, causing a mutation in one daughter double helix  insertion or deletion of one or more bases, potentially causing a shift in reading frame  Fair number of mutations every time you replicate DNA Result of unrepaired replication error Lets suppose this does not get fixed, in the second round of replication the A will result in a T in the new strand (AT base pair) This looks normal and there is nothing to tell the cell that this used to be GC, you have a new sequence 2. Deamination: spontaneous conversion of amine group to a carbonyl  Most commonly happens to cytosine  Convert amine group on cytosine, into a carbonyl, then we have uracil which is not usually found in DNA  If the cell recognizes that there is a uracil it recognizes some damage  When you have GU you know that U is the problem and you can hopefully fix it with C Question: suppose C in sequence TCGA is deaminated, and the base is only repaired after one round of replication. Which sequence would you expect to find after the repair? Answer: When it is deaminiated it switches to U in the parent strand, and U and T base pair in the same way so then you would get an A opposite the U from the parent strand. It will try to repair is but it will be too late, the repair mechanism uses the strand that is undamaged as a template to fix the damaged strand. So the new UA pair is changed to TA, but this is wrong because it was too late. 3. Depurination: loss of entire guanine or adenine base, promoted by acid  Result: blocks DNA replication (can be overcome by error-prone translesion DNA polymerases)  Also known as an A-basic site, no base (de’purin’ated site)  When DNA replication tries to come along and uses this as a template there is notmuch to go on so it will stop, which is bad news because if cell is trying to divide and split its DNA, we wont have the right number of genomes, probably resulting in the death of the cell  If this site is left, and you have DNA replication happening, when u try and replicate one side will be fine but the other one with missing base wont know what to do and will stop, and then the translesion polymerase will come in and pass over the lesion and just replicate a bit so that the regular polymerase can finish, and it may put the wrong base in the lesion but it has to do something because the DNA needs to be replicated  Why don’t we use the translesion polymerase all the time? because its slower, less accurate because it will make lots of mistakes, so its not worth it (active sites are looser) to use it for all replication 4. Pyrimidine dimers: UV light causes formation of cyclobutane ring be
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