W15 Final study guide - Final&exam March&16th&8C11&am...

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Bring a calculator AND a RULER Write with pen Prepare ALL labs All lecture material Final exam March 16 th 8C11 am Lecture Halls CS 24 (Last names starJng with A through K) and CS 50 (Last names starJng with L through Z) Designed for 2 hours – you will have 3 hours Jme 40% material unJl midterm exam – 60 % since midterm exam Format comparable to midterm Spectrophotometer 1. schema)c set up 2. What does it measure? 3. Reasoning for 0.1 – 1 range 4. Beer´s law – be able to explain its components and to calculate with it (in all direcJons!) 5. How is using spectrophotometer helpful in the laboratory? 6. Recognize structure of NAD(P)+ and NAD(P)H: where do they differ? With which parts of the molecule do they absorb? CalculaJons 1. Using V1C1 = V2C2 is a basic prerequisite and may have to be used in the exam
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Inducing protein expression 1. What needs to be the composi)on of the plasmid for protein overexpression (inducible or not inducible)? 2. What does it need addi)onally to make it inducible? 3. Why does it make sense to have an inducible system? 4. Review the func)ons of the following plasmid components: selectable marker (here Ampicillin resistance), origin of replica)on, lac I gene, operator, promoter, His6, yqhd? 5. How does induc)on/de[repression work? Inducers? Why do we use one over the other? 6. Is this inducible system found in nature? If so, where and what is it regula)ng? Be able to describe it briefly. 7. What can happen to especially hydrophobic proteins when overexpressed too strong? How can you prevent this to happen? How would you detect this happened? Bradford – or Dye binding assay 1. What is the dye molecule? Recognize its structure 2. How does the dye change in the presence of protein? 3. At which wavelengths does the dye have its absorp)on peak (when protein is bound)? 4. Which part of the protein is being bound by the dye? Anything binding especially well? 5. How do you quan)fy the amount of protein in your unknown sample? 6. Why is it advisable to make a dilu)on series of your unknown protein before measuring it?
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Isobutanol producing bacteria 1. Atsumi 2010 paper describes the engineering of a pathway to over[produce isobutanol in bacteria. Which endogenous bacterial pathway did they use and change? 2. 5 enzymes were overexpressed. Name those. 3. Where do the carbon skeletons come from (metabolic pathway)? 4. What are the intermediates? 5. Two of these enzymes have a very broad substrate specificity and can be used to produce different biofuel molecules. Which are these two enzymes? Alcohol dehydrogenase reacJon 1. What does the enzyme need to func)on? Cofactors? 2. What are possible substrates for alcohol dehydrogenase? Name several. 3. How do we monitor the rate of the reac)on in the laboratory?
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