Short Answer Questions Chapter 5.

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1. Reversible binding of a protein to a ligand: oxygen-binding proteins Page: 158 Describe the concept of “induced fit” in ligand-protein binding. The binding of a protein and ligand is often coupled to a conformational change in protein that makes the binding site more complementary to lighad , permitting tighter bindin. 2. Reversible binding of a protein to a ligand: oxygen-binding proteins Page: 158 Explain why most multi-cellular organisms use an iron-containing protein for oxygen binding rather than free Fe2+. Your answer should include an explanation of (a) the role of heme and (b) the role of the protein itself. (a)Free ion promotes the formation of highly reactive oxygen species that can damage DNA and other macro molecules, so ion is incorporated into a protein bound-prosthetic group called heme to make it less reactive ; (b)Oxygen is poorly soluble in aqueous solution, so larger, multi-cellular animals depend on the evolution of protein that could transport and storage oxygen. 3. Reversible binding of a protein to a ligand: oxygen-binding proteins Pages: 160.161 Describe how you would determine the Ka (association constant) for a ligand and a protein.

4. Reversible binding of a protein to a ligand: oxygen-binding proteins Page: 160 For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?

5. Reversible binding of a protein to a ligand: oxygen-binding proteins Page: 162 Explain briefly why the relative affinity of heme for oxygen and carbon monoxide is changed by the presence of the myoglobin protein. Carbon monoxide binds to free heme with the CO axis perpendicular to the plane of the porphyrin ring. When binding to the heme in myoglobin, CO is forced to adopt a slight angle because the perpendicular arrangement is sterically blocked by His E7, the distal His. This effect weakens the binding of CO to myoglobin. 6. Reversible binding of a protein to a ligand: oxygen-binding proteins Pages: 161, 166 Explain why the structure of myoglobin makes it function well as an oxygen-storage protein whereas the structure of hemoglobin makes it function well as an oxygen-transport protein. Myoglobin with its hyperbolic binding curve for oxygen, is relatively insensitive to small changes in the concentration of dissolved oxygen and so functions well as an oxygen-storage protein. (eight α-helix segments ) Hemoglobin, with its multiple subunits and O2-binding sites, is better suited to oxygen transport. (four α and β segments) 7. Reversible binding of a protein to a ligand: oxygen-binding proteins (a) What are the characteristics of an allosteric protein? (b) How can cooperative ligand binding be described quantitatively? (a)An allosteric protein is one in which the binding of a ligand to one site affects the binding properties of another site on the same protein. (b)

8. Reversible binding of a protein to a ligand: oxygen-binding proteins Pages: 167.170 Describe briefly the two principal models for the cooperative binding of ligands to proteins with multiple binding sites 1. MWC(concerted): all the subunit are the same. 2. Sequential model: individual subunit conformation, can gradually change.

9. Reversible binding of a protein to a ligand: oxygen-binding proteins Pages: 171.172 How does BPG binding to hemoglobin decrease its affinity for oxygen? BPG lowers hemoglobin’s affinity for oxygen by stabilizing the T state. 10. Reversible binding of a protein to a ligand: oxygen-binding proteins Page: 170 (a) What is the effect of pH on the binding of oxygen to hemoglobin (the Bohr Effect)? (b) Briefly describe the mechanism of this effect.

At the relatively low pH and high CO2 concentration of peripheral tissues, the affinity of hemoglobin for oxygen decreases as H+ and CO2 are bound, and O2 is released to the tissues. Conversely, in the capillaries of the lung, as CO2 is excreted and the blood pH consequently rises, the affinity of hemoglobin for oxygen increases and the protein binds more O2 for transport to the peripheral tissues. This effect of pH and CO2concentration on the binding and release of oxygen by hemoglobin is called the Bohr effect.

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