Problems

http://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c07/dm9ld...

1. Estimate K from the following data describing ligand binding to a protein.
[Ligand] (mM) Y

0.25 0.50 0.80 1.4 2.2 3.0 4.5 6.0 Answer:

0.30 0.45 0.56 0.66 0.80 0.83 0.86 0.93

2. Which set of binding data is likely to represent cooperative ligand binding to an oligomeric protein? (a)
[Ligand] (mM) Y

0.1 0.2 0.4 0.7 (b)
[Ligand] (mM)

0.3 0.5 0.7 0.9
Y

0.2 0.3

0.1 0.3

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Problems

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[Ligand] (mM)

Y

0.4 0.6 Answer:

0.6 0.8

Set b describes sigmoidal binding to an oligomeric protein and hence represents cooperative binding.

3. In active muscles, the pO2 may be 10 torr at the cell surface and 1 torr at the mitochondria (the organelles where oxidative metabolism occurs). Use Eq. 7-6 to show how myoglobin (p50 = 2.8 torr) facilitates the diffusion of O2 through these cells. Answer: According to Eq. 7-6,

When pO2 = 10 torr,

When pO2 = 1 torr,

The difference in values is 0.78 – 0.26 = 0.52. Therefore, in active muscle cells, myoglobin can transport a significant amount of O2 by diffusion from the cell surface to the mitochondria. 4. In humans, the urge to breathe results from high concentrations of CO2 in the blood; there are no direct physiological sensors of blood pO2. Skindivers often hyperventilate (breathe rapidly and deeply for several minutes) just before making a dive in the belief that this will increase the O2 content of their blood. (a) Does it do so? (b) Use your knowledge of hemoglobin function to evaluate whether this practice is useful. Answer: (a) Hyperventilation eliminates CO2, but it does not significantly affect the O2 concentration, since the hemoglobin in arterial blood is already essentially saturated with oxygen.

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(b) The removal of CO2 also removes protons, according to the reaction The resulting increase in blood pH would increase the O2 affinity of hemoglobin through the Bohr effect. The net result would be that less oxygen could be delivered to the tissues until the CO2 balance was restored. Thus, hyperventilation has the opposite of the intended effect (note that since hyperventilation suppresses the urge to breathe, doing so may cause the diver to lose consciousness due to lack of O2 and hence drown). 5. Drinking a few drops of a commercial preparation called “vitamin O,” which consists of oxygen and sodium chloride dissolved in water, is claimed to increase the concentration of oxygen in the body. (a) Use your knowledge of oxygen transport to evaluate this claim. (b) Would vitamin O be more or less effective if it were infused directly into the bloodstream? Answer: (a) Vitamin O is useless because the body's capacity to absorb oxygen is not limited by the amount of oxygen available but by the ability of hemoglobin to bind and transport O2. Furthermore, oxygen is normally introduced into the body via the lungs, so it is unlikely that the gastrointestinal tract would have an efficient mechanism for extracting oxygen. (b) The fact that oxygen delivery in vertebrates requires a dedicated O2-binding protein (hemoglobin) indicates that dissolved oxygen by itself cannot attain the high concentrations required. Moreover, a few drops of vitamin O would make an insignificant contribution to the amount of oxygen already present in a much larger volume of blood. 6. Is the p50 higher or lower than normal in (a) hemoglobin Yakima and (b) hemoglobin Kansas? Explain. Answer: (a) Lower; (b) higher. The Asp 99β → His mutation of hemoglobin Yakima disrupts a hydrogen bond at R equilibrium to shift toward R state the α1–β2 interface of the T state (Fig. 7-9a), causing the T (lower p50). The Asn 102β → Thr of hemoglobin Kansas causes the opposite shift in the T R equilibrium by abolishing an R-state hydrogen bond (Fig. 7-9b). 7. Hemoglobin S homozygotes who are severely anemic often have elevated levels of BPG in their erythrocytes. Is this a beneficial effect? Answer: The increased BPG helps the remaining erythrocytes deliver O2 to tissues. However, BPG stabilizes the T conformation of hemoglobin, so it promotes sickling and therefore aggravates the disease. 8. In hemoglobin Rainier, Tyr 145β is replaced by Cys, which forms a disulfide bond with another Cys residue in the same subunit. This prevents the formation of ion pairs that normally stabilize the T state. How does hemoglobin Rainier differ from normal hemoglobin with respect to (a) oxygen affinity, (b) the Bohr effect, and (c) the Hill coefficient? Answer: (a) Because the mutation destabilizes the T conformation of hemoglobin Rainier, the R (oxy) conformation is more stable. Therefore, the oxygen affinity of hemoglobin Rainier is greater than normal.

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(b) The ion pairs that normally form in deoxyhemoglobin absorb protons. The absence of these ion pairs in hemoglobin Rainier decreases the Bohr effect (in fact, the Bohr effect in hemoglobin Rainier is about half that of normal hemoglobin). (c) Because the R conformation of hemoglobin Rainier is more stable than the T conformation, even when the molecule is not oxygenated, O2-binding cooperativity is reduced. The Hill coefficient of hemoglobin Rainier is therefore less than that for normal hemoglobin. 9. The crocodile, which can remain under water without breathing for up to 1 h, drowns its air-breathing prey and then dines at its leisure. An adaptation that aids the crocodile in doing so is that it can utilize virtually 100% of the O2 in its blood whereas humans, for example, can extract only ~65% of the O2 in their blood. Crocodile Hb does not bind BPG. However, crocodile deoxyHb preferentially binds . How does this help the crocodile obtain its dinner? Answer: As the crocodile remains under water without breathing, its metabolism generates CO2 and hence the content of its blood increases. The preferentially binds to the crocodile's deoxyhemoglobin, which allosterically prompts the hemoglobin to assume the deoxy conformation and thus release its O2. This helps the crocodile stay under water long enough to drown its prey. 10. Some primitive animals have a hemoglobin that consists of two identical subunits. (a) Sketch an oxygen-binding curve for this protein. (b) What is the likely range of the Hill coefficient for this hemoglobin? Answer: (a)

(b) The Hill coefficient most likely has a value between 1 (no cooperativity) and 2 (perfect cooperativity between the two subunits). 11. Is myosin a fibrous protein or a globular protein? Explain. Answer: Myosin is both fibrous and globular. Its two heads are globular, with several layers of secondary structure. Its tail, however, consists of a lengthy, fibrous coiled coil. 12. A myosin head can undergo five ATP hydrolysis cycles per second, each of which moves an actin monomer by ~100 Å. How is it possible for an entire sarcomere to shorten by 1000 Å in this same period?

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Answer: Because many myosin heads bind along a thin filament where it overlaps a thick filament, and because the myosin molecules do not execute their power strokes simultaneously, the thick and thin filaments can move past each other by more than 100 Å in the interval between power strokes of an individual myosin molecule. 13. Rigor mortis, the stiffening of muscles after death, is caused by depletion of cellular ATP. Describe the molecular basis of rigor. Answer: In the absence of ATP, each myosin head adopts a conformation that does not allow it to release its bound actin molecule. Consequently, thick and thin filaments form a rigid cross-linked array. 14. Explain why a microfilament is polar whereas a filament of keratin is not. Answer: Microfilaments consist entirely of actin subunits that are assembled in a head-to-tail fashion so that the polarity of the subunits is preserved in the fully assembled fiber. In keratin filaments, however, successive heterodimers align in an antiparallel fashion, so that in a fully assembled intermediate filament, half the molecules are oriented in one direction and half are oriented in the opposite direction (Fig. 6-16). 15. Give the approximate molecular masses of an immunoglobulin G molecule analyzed by (a) gel filtration chromatography, (b) SDS-PAGE, and (c) SDS-PAGE in the presence of 2-mercaptoethanol. Answer: (a) 150–200 kD; (b) 150–200 kD; (c) ≈23 kD and 53–75 kD. 16. Explain why the variation in VL and VH domains of immunoglobulins is largely confined to the hypervariable loops. Answer: The loops are on the surface of the domain, so they can tolerate more amino acid substitutions. Amino acid changes in the β sheets would be more likely to destabilize the domain. 17. Why do antibodies raised against a native protein sometimes fail to bind to the corresponding denatured protein? Answer: The antigenic site in the native protein usually consists of several peptide segments that are no longer contiguous when the tertiary structure of the protein is disrupted. 18. Antibodies raised against a macromolecular antigen usually produce an antigen–antibody precipitate when mixed with that antigen. Explain why no precipitate forms when (a) Fab fragments from those antibodies are mixed with the antigen; (b) antibodies raised against a small antigen are mixed with that small antigen; and (c) the antibody is in great excess over the antigen and vice versa. Answer: (a) Fab fragments are monovalent and therefore cannot cross-link antigens to produce a precipitate. (b)

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Problems

http://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c07/dm9ld...

A small antigen has only one antigenic site and therefore cannot bind more than one antibody to produce a precipitate. (c) When antibody is in great excess, most antibodies that are bound to antigen bind only one per immunoglobulin molecule. When antigen is in excess, most immunoglobulins bind to two independent antigens.

Copyright © 2009 John Wiley & Sons, Inc. All rights reserved.

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