Short Answer Questions Made by yo-cheng

Chapter 5.1 僅供參考 不負責任

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.