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CHM376 Biochemistry I Fall 2023 Problem Set #8: Protein Function and Oxygen Transport Note : throughout the PowerPoint you will see K a and K A ; K d and K D . Note that the capitalization of the subscript is a matter of style and does not change the meaning of these terms. However, if the K is not capitalized, it carries a different meaning. K a is the same as K A but different from k a or k A . We will introduce the use of the lowercase k in the following lecture. Also note that K a (or K A ) used here is distinct from the K a (or K A ) of acid base chemistry. Although they are both equilibrium constants, they describe different phenomena. 1. What is a ligand? What is a receptor? 2. Can a ligand bind anywhere on a receptor or is there a specific part of the receptor that the ligand binds to? 3. What is association? What is dissociation? 4. Write an equilibrium expression for the binding of a ligand to a receptor. Write the equilibrium constant for this reaction. 5. If the equilibrium constant for a ligand binding to a receptor is small, is it correct to say that the receptor will never bind to the ligand? Explain why or why not? 6. What is the role of LCP is determining how much of a free ligand vs. bound ligand is present in a mixture of ligand and receptor. 7. Define affinity and specificity. In what way are these two terms similar and in what way are they different? 8. Dexedrine and Benzedrine are both stimulant class drugs that are prescribed for Attention Deficit Hyperactivity Disorder (ADHD). The chemical and physical properties of the two drugs (elemental analysis, melting point, solubility, NMR, and IR spectra) of the two drugs are identical . The structure of both drugs is shown below; the figure does not , however indicate anything about the actual stereochemistry of either drug. The recommended oral dosage of Dexedrine is 5 mg/day while that of Benzedrine, which has been discontinued, is 10 mg/day. Based on the information provided, give the most plausible explanation as to the differing required dosages of the two drugs.

8. What is the lock-in-key model and what is the induced fit model? Do most biological receptor – ligand interactions resemble lock-in-key or induced fit? 9. If we are comparing the interaction of a receptor with two ligands, L 1 and L 2 , if K A of L 1 is greater the K A of L 2 , which ligand is more likely to be found bound to its receptor? 10. If we are comparing the interaction of a receptor with two ligands, L 1 and L 2 , if K D of L 1 is greater the K D of L 2 , which ligand is more likely to be found bound to its receptor? 11. Why do we express receptor affinities in terms of K D instead of K A ? Write the equilibrium expression for K D . 12. What is meaning of the term fractional saturation? How is fractional saturation defined mathematically? How would we measure the fractional saturation of a receptor binding to a ligand? 13. Show that when [L] = K D , =0.5. 14. Three different proteins can all bind to the organic molecule 2-(4- isobutylphenyl)propanoic acid (ibuprofen). Based on the data in the table below, (a) What is the K D for Protein 2 binding to ibuprofen (include appropriate units)? (b) Which of these proteins binds most “tightly” to ibuprofen (highest affinity)? Ibuprofen (nM)  -Protein 1  -Protein 2  -Protein 3 0.2 0.048 0.29 0.17 0.5 0.11 0.5 0.33 1 0.2 0.67 0.5 4 0.5 0.89 0.8 10 0.71 0.95 0.91 20 0.83 0.97 0.95 50 0.93 0.99 0.98 15. Why is the fractional saturation curve (binding curve) generally hyperbolic ? How can you obtain the K D from a fractional saturation curve? 16. If K D = 20 nM and [L] = 6 nM, calculate the fractional saturation (  ). 17. What type of interactions are responsible for ligands binding to receptors? What is the role of “molecular shape” in determining if a ligand binds to a receptor?

18. What is the role of chirality in determining the specificity of ligand-receptor binding? 19. If K A for the reaction A+B  is small, is most of A found free or as part of a complex? 20. What is the relationship between K A and K D ? Since K A is far more intuitive, why do we measure receptor – ligand interactions using K D ? ( This is a repeat of a question presented earlier; make sure you understand this concept ). 21. Using the fractional saturation curve on the slide titled “Sample Binding Curve”, estimate (do not calculate) the K D . 22. What general class of ligand – receptor interactions is the highest affinity? What general class of ligand-receptor interactions is the lowest affinity? 23. What is allostery? 24. What is cooperativity? Can one have allostery without cooperativity? Can one have cooperativity without allostery? 25. Explain the following terms: heterotropic, homotropic, negative cooperativity, positive cooperativity. 26. What is avidity? How can a high avidity compensate for a low affinity? What are the requirements for a ligand-receptor interaction to have avidity? 27. What are some of the major roles for oxygen in biology? 28. What was the “Great Oxygenation Event” and how did it shape the evolution of life on earth? 29. Why is oxygen required to have mechanically stable organ tissues? 30. Why is a specialized form of gas transport required by multicellular organisms? 31. Describe the gas transport system used by insects. Why is this mechanism potentially insufficient to explain the gas transport system of insects that lived during the Carboniferous? 32. What is the evolutionary origin of lungs? 33. What is unique about the respiratory mechanism of the loach fish? 34. What is Henry’s Law? Why is Henry’s law useful in the study of oxygen binding proteins?

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