Bio151 WI22-23 Topic 8 Problem Set
Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis Instructions: ✓ Download this problem set, keep the questions in the document and please type your answers in a color other than black so that your answers are easily discernable. ✓ Complete this entire problem set – give robust, detailed responses – this is practice so use it as such. ✓ If you get stuck or need clarification on any of these questions… just ask! ✓ Upload this document with your answers to the appropriate TurnItIn link in our Moodle page in PDF format ✓ Please be advised that TurnItIn is a plagiarism and similarity checking software o You are always welcome to work with other people and/or get help on the problem set, however… o Make sure that you close and put away all sources of information before writing your answers so that you can be sure that your answers are in your own words and to convince yourself that you understand the concept and can explain it yourself. o If your answers are too similar to either someone else’s responses (past or present) or from the internet, points will be deducted as the assumption will be made that the work you’re doing is not your own. Complete the entire problem set. For grading, a problem or two will be randomly chosen for grading of 10 points and will be graded for completeness and originality worth 5 points; 15 points total. Due date: Sunday, January 29th by 11:59pm Question 1: Enzymes A. Give three examples of enzymes that we’ve discussed thus far in this class. For your answer, give a brief explanation of what each enzyme does and what chemical reaction it catalyzes, including describing which covalent bonds the enzyme breaks and/or creates and in what molecules. Bullet point your response for each enzyme. Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis B. Give two examples of proteins we’ve discussed thus far in this class that aren’t enzymes. What do they do and why aren’t they classified as enzymes? Question 2: What do Enzymes Change? Enzymes are catalysts. What does that mean? Which of the following aspects of the chemical reaction do enzymes change? Answer yes or no for each and explain. A. Reaction rate B. Types of products generated Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis C. Activation energy D. Energy of the transition state E. Gibbs free energy Question 3: Enzyme Affinity for Substrate and Product A. You are studying the function of an enzyme and its substrate. You measure the affinity of the enzyme for the substrate and the affinity of the enzyme for the product of the reaction. First describe what we mean by “affinity” in cell biology and then discuss whether the affinity of the enzyme with its substrate would be higher or lower than the affinity of the enzyme with its product? Explain your reasoning and the significance for function of the enzyme. Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis B. A mutation occurs in an enzyme that causes it to have greater affinity for the product of the reaction it catalyzes. What affect would this have on the turnover rate** of the enzyme? Explain your reasoning. **The turnover rate is a measure of the total time it takes for the enzyme to catalyze the chemical reaction and then release the product(s) of the reaction (to then be able to bind another substrate(s) molecule and do the reaction all over again). Question 4: Saturation of Substrate Describe what “saturation of the enzyme” means in the context of enzyme kinetics. What is going on at the molecular level when the enzyme is “saturated” with substrate. What kind of information does a saturating substrate condition give you about that enzyme-substrate pair? Question 5: Parameters of Michaelis-Menten Enzyme Kinetics Define VMAX and KM in the context of a Michaelis-Menton enzyme kinetics graph of reaction rate versus substrate concentration. Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis Question 6: Practicing Michaelis-Menten Rate Kinetics The above graph is showing the Michaelis-Menten kinetics for a particular enzyme and substrate pair (wildtype – black circles in the graph). Two mutations are made in this enzyme – Glu205Lys and Glu206Leu – and the Michaelis-Menten kinetics are shown for those mutants as well. What are the Vmax’s and Km’s for the wildtype enzyme and the two mutants? (Make sure to use appropriate units in your answers; and for the Glu206Leu mutant, which is essentially catalytically dead, do you best to approximate a Km) Enzyme Vmax Km Wildtype (unmutated) Glu205Lys mutant Glu206Leu mutant Question 7: B-gal Kinetics As you learned in Topic 5, the enzyme B-gal, encoded for within the LacZ gene in the lac operon, catalyzes the following reaction: lactose + H20 —–> glucose + galactose To determine Vmax and Km of B-gal with its substrate lactose, the same amount of enzyme was incubated with a series of increasing lactose concentrations. At each lactose concentration, the initial reaction velocity was measured. The following data were obtained: Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis Lactose Concentration (mM) Rate of lactose consumption (umol/min) 1 10.0 2 16.7 4 25.0 8 33.3 16 40.0 32 44.4 A. Plot the rate of the reaction versus lactose concentration. Make sure to label your axes. B. Estimate Km and Vmax from the plot you created. Explain how you found them. Question 8: Enzyme Inhibitor Types and Kinetics A. When an enzyme is treated with a competitive inhibitor, discuss whether Km and Vmax change and how. Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis B. Draw a graph to represent how this might look (so two lines representing with and without inhibitor). Make sure to label your axes and your lines. C. Answer questions A and B but for noncompetitive inhibitors… D. Answer questions A and B but for uncompetitive inhibitors… Question 9: B-gal and Inhibitors Look back at Questions 7 and 8: Imagine that you’re studying B-gal activity and you decide that you want to find an inhibitor of B-gal function. Develop an inhibitor for B-gal using one of the Bio151 WI22-23 Topic 8 Problem Set Answer Key Francis types of inhibitors that we discuss in this unit. Take your graph for B-gal and lactose from Question 7 (keep the data from the situation in which there’s no inhibitor) and draw in some data showing what the graph would look like if you added your inhibitor to the experiment done in Question 7. For the answer to this question, show the resulting graph with the data that includes the data with and without inhibitor and then explain what type of inhibitor you chose and how it’s changing the kinetics of B-gal function.