Population density. How many phospholipid molecules are there in a 1-μm² region of a phospholipid bilayer membrane? Assume that a phospholipid molecule occupies 70 Ų of the surface area.

Through the looking-glass. Phospholipids form lipid bilayers in water. What structure might form if phospholipids were placed in an organic solvent?

Lipid diffusion. What is the average distance traversed by a membrane lipid in 1 μs, 1 ms, and 1 s? Assume a diffusion coefficient of 10⁻⁸ cm² s⁻¹.

Protein diffusion. The diffusion coefficient, D, of a rigid spherical molecule is given by

D = kT/6πηr

in which η is the viscosity of the solvent, r is the radius of the sphere, k is the Boltzman constant (1.38 × 10⁻¹⁶ erg degree⁻¹), and T is the absolute temperature. What is the diffusion coefficient at 37° C of a 100-kDa protein in a membrane that has an effective viscosity of 1 poise (1 poise = 1 erg s⁻¹ cm⁻³)? What is the average distance traversed by this protein in 1 μs, 1 ms, and 1 s? Assume that this protein is an unhydrated, rigid sphere of density 1.35 g cm⁻³.

Cold sensitivity. Some antibiotics act as carriers that bind an ion on one side of a membrane, diffuse through the membrane, and release the ion on the other side. The conductance of a lipid-bilayer membrane containing a carrier antibiotic decreased abruptly when the temperature was lowered from 40°C to 36°C. In contrast, there was little change in conductance of the same bilayer membrane when it contained a channel-forming antibiotic. Why?

Melting point 1. Explain why oleic acid (18 carbons, one cis bond) has a lower melting point than stearic acid, which has the same number of carbon atoms but is saturated. How would you expect the melting point of trans-oleic acid to compare with that of cis -oleic acid? Why might most unsaturated fatty acids in phospholipids be in the cis rather than the trans conformation?

Melting point 2. Explain why the melting point of palmitic acid (C₁₆) is 6.5 degrees lower than that of stearic acid (C₁₈).

A sound diet. Small mammalian hibernators can withstand body temperatures of 0° to 5°C without injury. However, the body fats of most mammals have melting temperatures of approximately 25°C. Predict how the composition of the body fat of hibernators might differ from that of their nonhibernating cousins.

Flip-flop 1. The transverse diffusion of phospholipids in a bilayer membrane was investigated by using a fluorescently labeled analog of phosphatidylserine called NBD-PS. The fluorescence signal of NBD-PS is quenched when exposed to sodium dithionite, a reducing agent that is not membrane permeable.

Lipid vesicles containing phosphatidylserine (98%) and NBD-PS (2%) were prepared by sonication and purified. Within a few minutes of the addition of sodium dithionite, the fluorescence signal of these vesicles decreased to ˜45% of its initial value. Immediately adding a second addition of sodium dithionite yielded no change in the fluorescence signal. However, if the vesicles were allowed to incubate for 6.5 hours, a third addition of sodium dithionite decreased the remaining fluorescence signal by 50%. How would you interpret the fluorescence changes at each addition of sodium dithionite?

Flip-flop 2. Although proteins rarely if ever flip-flop across a membrane, the distribution of membrane lipids between the membrane leaflets is not absolute except for glycolipids. Why are glycosylated lipids less likely to flip-flop?

Linkages. Platelet-activating factor (PAF) is a phospholipid that plays a role in allergic and inflammatory responses, as well as in toxic shock syndrome. The structure of PAF is shown here. How does it differ from the structures of the phospholipids discussed in this chapter?

A question of competition. Would a homopolymer of alanine be more likely to form an α helix in water or in a hydrophobic medium? Explain.

A false positive. Hydropathy plot analysis of your protein of interest reveals a single, prominent hydrophobic peak. However, you later discover that this protein is soluble and not membrane associated. Explain how the hydropathy plot may have been misleading.

Maintaining fluidity. A culture of bacteria growing at 37° C was shifted to 25° C. How would you expect this shift to alter the fatty acid composition of the membrane phospholipids? Explain.

Let me count the ways. Each intracellular fusion of a vesicle with a membrane requires a SNARE protein on the vesicle (called the v-SNARE) and a SNARE protein on the target membrane (called the t-SNARE). Assume that a genome encodes 21 members of the v-SNARE family and 7 members of the t-SNARE family. With the assumption of no specificity, how many potential v-SNARE–t-SNARE interactions could take place?

Cholesterol effects. The red curve on the following graph shows the fluidity of the fatty acids of a phospholipid bilayer as a function of temperature. The blue curve shows the fluidity in the presence of cholesterol.

Hydropathy plots. On the basis of the following hydropathy plots for three proteins (A–C), predict which would be membrane proteins. What are the ambiguities with respect to using such plots to determine if a protein is a membrane protein?

Not all inhibitors are equal. Ibuprofen and indomethacin are clinically important inhibitors of prostaglandin H₂ synthase-1. Cells expressing this enzyme were incubated under the following conditions, after which the activity of the enzyme was measured by adding radiola-beled arachidonic acid and detecting newly-produced prostaglandin H₂:

The proper environment. An understanding of the structure and function of membrane proteins has lagged behind that of other proteins. The primary reason is that membrane proteins are more difficult to purify and crystallize. Why might this be the case?