Biochemistry

Reginald H. Garrett, Charles M. Grisham

Chapter 9 Membranes and Membrane Transport - all with Video Answers

Educators

Chapter Questions

03:28

Problem 1

In problem 1 (b) in Chapter 8 (page 257), you were asked to draw all the possible phosphatidylserine isomers that can be formed from palmitic and linolenic acids. Which of the PS isomers are not likely to be found in biological membranes?

Freddie Montague

Numerade Educator

02:13

Problem 2

The purple patches of the Halobacterium halobium membrane, which contain the protein bacteriorhodopsin, are approximately $75 \%$ protein and $25 \%$ lipid. If the protein molecular weight is 26,000 and an average phospholipid has a molecular weight of 800 , calculate the phospholipid-to-protein mole ratio.

Lottie Adams

Numerade Educator

01:12

Problem 3

Sucrose gradients for separation of membrane proteins must be able to separate proteins and protein-lipid complexes having a wide range of densities, typically 1.00 to $1.35 \mathrm{g} / \mathrm{mL}$
a. Consult reference books (such as the $C R C$ Handbook of Biochemistry $)$ and plot the density of sucrose solutions versus percent sucrose by weight (g sucrose per $100 \mathrm{g}$ solution), and versus percent by volume (g sucrose per 100 mL solution). Why is one plot linear and the other plot curved?
b. What would be a suitable range of sucrose concentrations for separation of three membrane-derived protein-lipid complexes with densities of $1.03,1.07,$ and $1.08 \mathrm{g} / \mathrm{mL} ?$

David Collins

Numerade Educator

01:42

Problem 4

Phospholipid lateral motion in membranes is characterized by a diffusion coefficient of about $1 \times 10^{-8} \mathrm{cm}^{2} / \mathrm{sec} .$ The distance traveled in two dimensions (across the membrane) in a given time is $r=(4 D t)^{1 / 2},$ where $r$ is the distance traveled in centimeters, $D$ is the diffusion coefficient, and $t$ is the time during which diffusion occurs. Calculate the distance traveled by a phospholipid across a bilayer in 10 msec (milliseconds).

Niamat Khuda

Numerade Educator

00:30

Problem 5

Protein lateral motion is much slower than that of lipids because proteins are larger than lipids. Also, some membrane proteins can diffuse freely through the membrane, whereas others are bound or anchored to other protein structures in the membrane. The diffusion constant for the membrane protein fibronectin is approximately $0.7 \times 10^{-12} \mathrm{cm}^{2} / \mathrm{sec},$ whereas that for rhodopsin is about $3 \times 10^{-9} \mathrm{cm}^{2} / \mathrm{sec}$
a. Calculate the distance traversed by each of these proteins in 10 msec.
b. What could you surmise about the interactions of these proteins with other membrane components?

Rabeya Zahid

Numerade Educator

01:49

Problem 6

Discuss the effects on the lipid phase transition of pure dimyristoyl phosphatidylcholine vesicles of added (a) divalent cations, (b) cholesterol, (c) distearoyl phosphatidylserine, (d) dioleoyl phosphatidylcholine, and (e) integral membrane proteins.

Lottie Adams

Numerade Educator

04:46

Problem 7

Calculate the free energy difference at $25^{\circ} \mathrm{C}$ due to a galactose gradient across a membrane, if the concentration on side 1 is $2 \mathrm{m} M$ and the concentration on side 2 is $10 \mathrm{m} M$.

Nicholas Sacco

Numerade Educator

01:56

Problem 8

Consider a phospholipid vesicle containing $10 \mathrm{m} M \mathrm{Na}^{+}$ ions. The vesicle is bathed in a solution that contains $52 \mathrm{mM} \mathrm{Na}^{+}$ ions, and the electrical potential difference across the vesicle membrane $\Delta \psi=\psi_{\text {outside }}-\psi_{\text {inside }}=-30 \mathrm{mV} .$ What is the electrochemical potential at $25^{\circ} \mathrm{C}$ for $\mathrm{Na}^{+}$ ions?

Narayan Hari

Numerade Educator

03:52

Problem 9

Transport of histidine across a cell membrane was measured at several histidine concentrations:
$$\begin{array}{cc}
\text { [Histidine], } \mu M & \text { Transport, } \mu \text { mol/min } \\
2.5 & 42.5 \\
7 & 119 \\
16 & 272 \\
31 & 527 \\
72 & 1220
\end{array}$$
Does this transport operate by passive diffusion or by facilitated diffusion?

Arwen Xu

Numerade Educator

View

Problem 10

(Integrates with Chapter $3 .$ ) Fructose is present outside a cell at $1 \mu M$ concentration. An active transport system in the plasma membrane transports fructose into this cell, using the free energy of ATP hydrolysis to drive fructose uptake. What is the highest intracellular concentration of fructose that this transport system can generate? Assume that one fructose is transported per ATP hydrolyzed; that ATP is hydrolyzed on the intracellular surface of the membrane; and that the concentrations of ATP, ADP, and Pi are $3 \mathrm{m} M, 1 \mathrm{m} M,$ and $0.5 \mathrm{m} M,$ respectively. $T=298 \mathrm{K} .$ (Hint: Refer to Chapter 3 to recall the effects of concentration on free energy of ATP hydrolysis.)

Susan Hallstrom

Numerade Educator

03:08

Problem 11

In this chapter, we have examined coupled transport systems that rely on ATP hydrolysis or on primary gradients of $\mathrm{Na}^{+}$ or $\mathrm{H}^{+}$. Suppose you have just discovered an unusual strain of bacteria that transports rhamnose across its plasma membrane. Suggest experiments that would test whether it was linked to any of these other transport systems.

Rabeya Zahid

Numerade Educator

01:45

Problem 12

Which of the following peptides would be the most likely to acquire an N-terminal myristoyl lipid anchor?
a. VLIHGLEQN
b. THISISIT
c. RIGHTHERE
d. MEMEME
e. GETREAL

Ramesh Singh

Numerade Educator

00:57

Problem 13

Which of the following peptides would be the most likely to acquire a prenyl anchor?
a. RIGHTCALL
b. PICKME
c. ICANTICANT
d. AINTMEPICKA
e. None of the above

Emily Himsel

Numerade Educator

02:43

Problem 14

What would the hydropathy plot of a soluble protein look like, compared to those in Figure $9.14 ?$ Find out by creating a hydropathy plot at $w w$ w. expasy $c h .$ In the search box at the top of the page, type in "bovine pancreatic ribonuclease" and click "Go." The search engine should yield UniProtKB/Swiss-Prot entry P61823. Scroll to the bottom of the page and click "ProtScale" under Sequence Analysis Tools. On the next page, select the radio button for "Hphob. / Kyte and Doolittle," then scroll to the bottom of the page, and click "Submit." On the next page, scroll to the bottom of the page and click "Submit" again. At the bottom of the next page, after a few seconds, you should see a hydropathy plot. How does the plot for ribonuclease compare to those in Figure $9.14 ?$ You should see a large positive peak at the left side of the plot. This is the signal sequence portion of the polypeptide. You can read about signal sequences on page 1095.

Maja Ratkovic

Numerade Educator

00:55

Problem 15

Proline residues are almost never found in short $\alpha$ -helices; nearly all transmembrane $\alpha$ -helices that contain proline are long ones (about $20 \text { residues }) .$ Suggest a reason for this observation.

Dalton Hilovsky

Numerade Educator

01:45

Problem 16

As described in this chapter, proline introduces kinks in transmembrane $\alpha$ -helices. What are the molecular details of the kink, and why does it form? A good reference for this question is von Heijne, G., 1991 Proline kinks in transmembrane $\alpha$ -helices. Journal of Molecular Biology $218: 499-503$. Another is Barlow, D. J., and Thornton,
J. M., 1988. Helix geometry in proteins. Journal of Molecular Biology $201: 601-619$.

Ma Ednelyn Lim

Numerade Educator

01:01

Problem 17

Compare the porin proteins, which have transmembrane pores constructed from $\beta$ -barrels, with the Wza protein, which has a transmembrane pore constructed from a ring of $\alpha$ -helices. How many amino acids are required to form the $\beta$ -barrel of a porin? How many would be required to form the same-sized pore from $\alpha$ -helices?

Rabeya Zahid

Numerade Educator

04:50

Problem 18

The hop-diffusion model of Akihiro Kusumi suggests that lipid molecules in natural membranes diffuse within "fenced" areas before hopping the molecular fence to an adjacent area. Study Figure 9.29 and estimate the number of phospholipid molecules that would be found in a typical fenced area of local diffusion. For the purpose of calculations, you can assume that the surface area of a typical phospholipid is about $60 \AA^{2}$.

Niamat Khuda

Numerade Educator

02:38

Problem 19

What are the energetic consequences of snorkeling for a charged amino acid? Consider the lysine residue shown in Figure $9.16 .$ If the lysine side chain was reoriented to extend into the center of the membrane, how far from the center would the positive charge of the lysine be? The total height of the peak for the lysine plot in Figure 9.15 is about $4 k T$, where $k$ is Boltzmann's constant. If the lysine side chain in Figure 9.16 was reoriented to face the membrane center, how much would its energy increase? How does this value compare with the classical value for the average translational kinetic energy of a molecule in an ideal gas $(3 / 2 k T) ?$

Salamat Ali

Numerade Educator

03:12

Problem 20

As described in the text, the $\mathrm{p} K_{\mathrm{a}}$ values of $\mathrm{Asp}^{85}$ and $\mathrm{Asp}^{96}$ of bacteriorhodopsin are shifted to high values (more than
11) because of the hydrophobic environment surrounding these residues. Why is this so? What would you expect the dissociation behavior of aspartate carboxyl groups to be in a hydrophobic environment?

Henry R

Numerade Educator

02:15

Problem 21

Extending the discussion from problem $20,$ how would a hydrophobic environment affect the dissociation behavior of the side chains of lysine and arginine residues in a protein? Why?

Christy Bales, Ph.D.

Numerade Educator

01:32

Problem 22

In the description of the mechanism of proton transport by bacteriorhodopsin, we find that light-driven conformation changes promote transmembrane proton transport. Suggest at least one reason for this behavior. In molecular terms, how could a conformation change facilitate proton transport?

Vivek Singh

Numerade Educator

03:35

Problem 23

Singer and Nicolson's fluid mosaic model of membrane structure presumed all of the following statements to be true EXCEPT:
a. The phospholipid bilayer is a fluid matrix.
b. Proteins can be anchored to the membrane by covalently linked lipid chains.
c. Proteins can move laterally across a membrane.
d. Membranes should be about 5 nm thick.
e. Transverse motion of lipid molecules can occur occasionally.

Kendrick Buford

Numerade Educator

00:26

Problem 24

Examine the ActiveModel for the KesA potassium channel and explain the concept of a selectivity filter. Explain how the structural features of the KcsA selectivity filter enable its function.

Sam Limsuwannarot

Numerade Educator

01:24

Problem 25

Study the ActiveModel for aquaporin 1 and propose a reason for the different water transport rates for AQP0 and AQP1.

Manik Pulyani

Numerade Educator

03:21

Problem 26

Consider the ActiveModel for the P-glycoprotein and describe how the primary structure of the Walker A region of this protein facilitates ATP binding.

Rabeya Zahid

Numerade Educator