Berg J.M., Tymoczko J.L., Stryer L. Biochemistry

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10.

Valium target. γ-Aminobutyric acid (GABA) opens channels that are specific for chloride ions. The GABA

receptor channel is pharmacologically important because it is the target of Valium, which is used to diminish

anxiety.

(a) The extracellular concentration of Cl

is 123 mM and the intracellular concentration is 4 mM. In which direction

does Cl

flow through an open channel when the membrane potential is in the -60 mV to +30 mV range?

(b) What is the effect of chloride-channel opening on the excitability of a neuron?

receptor resembles that of the acetylcholine receptor. Predict the number

of subunits in this chloride channel.

See answer

11.

The price of extrusion. What is the free-energy cost of pumping Ca

out of a cell when the cytosolic concentration

is 0.4 µM, the extracellular concentration is 1.5 mM, and the membrane potential is -60 mV?

See answer

12.

Rapid transit. A channel exhibits current increments of 5 pA at a membrane potential of -50 mV. The mean open

time is 1 ms.

(a) What is the conductance of this channel?

(b) How many univalent ions flow through the channel during its mean open time?

See answer

13.

Pumping protons. Design an experiment to show that lactose permease can be reversed in vitro to pump protons.

See answer

Chapter Integration Problem

14.

Speed and efficiency matter. Acetylcholine is rapidly destroyed by the enzyme acetylcholinesterase. This enzyme,

which has a turnover number of 25,000 per second, has attained catalytic perfection with a k

cat

of 2 × 10

-1

. Why is it physiologically crucial that this enzyme be so efficient?

See answer

Mechanism Problem

15.

Remembrance of mechanisms past. Acetylcholinesterase converts acetylcholine into acetate and choline. Show the

reaction as chemical structures :

Like serine proteases, acetylcholinesterase is inhibited by DIPF. Propose a catalytic mechanism for acetylcholine

digestion by acetylcholinesterase.

See answer

Data Interpretation Problem

16.

Tarantula toxin. Acid sensing is associated with pain, tasting, and other biological activities (Chapter 32). Acid

sensing is carried out by a ligand-gated channel that permits sodium influx in response to H

. This family of acid-

sensitive ion channels (ASICs) comprises a number of members. Psalmotoxin 1 (PcTX1), a venom from the

tarantula, inhibits some members of this family. Below are electrophysiological recordings of cells containing one

of several members of the ASIC family made in the presence of the toxin at a concentration of 10 nM. The channels

were opened by changing the pH from 7.4 to the indicated values. The PcTX1 was present for a short time

(indicated by the black bar above the recordings) after which time it was rapidly washed from the system.

(a) Which of the ASIC family members

ASIC1a, ASIC1b, ASIC2a, or ASIC3 is most sensitive to the toxin?

(b) Is the effect of the toxin reversible? Explain.

See answer

17.

Channel problems 1. A number of pathological conditions result from mutations in the acetylcholine receptor

channel. One such mutation in the β subunit, βV266M, causes muscle weakness and rapid fatigue. An investigation

of the acetylcholine-generated currents through the acetylcholine receptor channel for both a control and a patient

yielded the following results. What is the effect of the mutation on channel function? Suggest some possible

biochemical explanations for the effect.

See answer

18.

Channel problems 2. The acetylcholine receptor channel can also undergo mutation leading to fast channel

syndrome (FCS), with clinical manifestations similar to those of slow channel syndrome (SCS). What would the

recordings of ion movement look like in this syndrome? Again, suggest a biochemical explanation.

See answer

19.

Transport differences. The rate of transport of two molecules, indole and glucose, across a cell membrane is shown

in the right column. What are the differences between the transport mechanisms of the two molecules? Suppose that

ouabain inhibited the transport of glucose. What would this inhibition suggest about the mechanism of transport?

See answer

Media Problem

20.

The merits of inflexibility. The selectivity filter of potassium channels restricts passage of sodium ions even

though sodium ions are smaller than potassium ions. Mutation of the tyrosine that is part of this filter to

leucine has been shown to reduce selectivity against sodium in a channel homologous to the one whose structure

has been determined [Chapman, M. L., Krovetz, H. S., and VanDongen, A. M. J., 2001. GYGD pore motifs in

neighboring potassium channel subunits interact to determine ion selectivity. J. Physiol. 530:21 33]. Look at the

three-dimensional structure in the Potassium Channel Structural Insights module and propose, in general terms,

an explanation for the role of this tyrosine in the wild-type protein and the effect of its mutation to leucine.

I. The Molecular Design of Life 13. Membrane Channels and Pumps Problems

Phyllobates terribilis. [Tom McHugh, Photo Researchers.]

I. The Molecular Design of Life 13. Membrane Channels and Pumps Problems

(A) Electrophysiological recordings of cells exposed to tarantula toxin. (B) Plot of peak current of a cell containing the

ASIC1a protein versus the toxin concentration. [from P. Escoubas, et al., 2000, J. Biol. Chem. 275:25116-215121.]

I. The Molecular Design of Life 13. Membrane Channels and Pumps

Selected Readings

Where to start

M.J. Welsh and A.E. Smith. 1995. Cystic fibrosis Sci. Am. 273: (6) 52-59. (PubMed)

N. Unwin. 1993. Neurotransmitter action: Opening of ligand-gated ion channels Cell 72: 31-41. (PubMed)

G.E. Lienhard, J.W. Slot, D.E. James, and M.M. Mueckler. 1992. How cells absorb glucose Sci. Am. 266: (1) 86-91.

(PubMed)

E. Neher and B. Sakmann. 1992. The patch clamp technique Sci. Am. 266: (3) 28-35.

B. Sakmann. 1992. Elementary steps in synaptic transmission revealed by currents through single ion channels Science

256: 503-512. (PubMed)

Books

Ashcroft, F. M., 2000. Ion Channels and Disease. Academic Press.

Conn, P. M. (Ed.), 1998. Ion Channels, vol. 293, Methods in Enzymology. Academic Press.

Aidley, D. J., and Stanfield, P. R., 1996. Ion Channels: Molecules in Action. Cambridge University Press.

Hille, B., 1992. Ionic Channels of Excitable Membranes (2d ed.). Sinauer.

Läuger, P., 1991. Electrogenic Ion Pumps. Sinauer.

Stein, W. D., 1990. Channels, Carriers, and Pumps: An Introduction to Membrane Transport. Academic Press.

Hodgkin, A., 1992. Chance and Design: Reminiscences of Science in Peace and War. Cambridge University Press.

Voltage-gated ion channels

F. Bezanilla. 2000. The voltage sensor in voltage-dependent ion channels Physiol. Rev. 80: 555-592. (PubMed)

P.C. Biggin, T. Roosild, and S. Choe. 2000. Potassium channel structure: Domain by domain Curr. Opin. Struct. Biol.

10: 456-461. (PubMed)

M.S.P. Sansom. 2000. Potassium channels: Watching a voltagesensor tilt and twist Curr. Biol. 10: R206-R209.

(PubMed)

C.-C. Shieh, M. Coghlan, J.P. Sullivan, and M. Gopalakrishnan. 2000. Potassium channels: Molecular defects, diseases,

and therapeutic opportunities Pharmacol. Rev. 52: 557-594. (PubMed)

R. Horn. 2000. Conversation between voltage sensors and gates of ion channels Biochemistry 39: 15653-15658.

(PubMed)

E. Perozo, D.M. Cortes, and L.G. Cuello. 1999. Structural rearrangements underlying K

-channel activation gating

Science 285: 73-78. (PubMed)

D.A. Doyle, J. Morais Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998.

The structure of the potassium channel: Molecular basis of K

conduction and selectivity Science 280: 69-77. (PubMed)

E. Marban, T. Yamagishi, and G.F. Tomaselli. 1998. Structure and function of the voltage-gated Na

channel J. Physiol.

508: 647-657. (PubMed)

C. Gonzalez, E. Rosenman, F. Bezanilla, O. Alvarez, and R. Latorre. 2000. Modulation of the Shaker K

channel gating

kinetics by the S3 S4 linker J. Gen. Physiol. 114: 193-297.

R.J. Miller. 1992. Voltage-sensitive Ca

channels J. Biol. Chem. 267: 1403-1406. (PubMed)

W.A. Catterall. 1991. Excitation-contraction coupling in vertebrate skeletal muscle: A tale of two calcium channels Cell

64: 871-874. (PubMed)

Ligand-gated ion channels

A. Miyazawa, Y. Fujiyoshi, M. Stowell, and N. Unwin. 1999. Nicotinic acetylcholine receptor at 4.6 Å resolution:

Transverse tunnels in the channel wall J. Mol. Biol. 288: 765-786. (PubMed)

F.J. Barrantes, S.S. Antollini, M.P. Blanton, and M. Prieto. 2000. Topography of the nicotinic acetylcholine receptor

membraneembedded domains J. Biol. Chem. 275: 37333-37339. (PubMed)

M. Cordero-Erausquin, L.M. Marubio, R. Klink, and J.P. Changeux. 2000. Nicotinic receptor function: New perspectives

from knockout mice Trends Pharmacol. Sci. 21: 211-217. (PubMed)

N. Le Novère and J.P. Changeux. 1995. Molecular evolution of the nicotinic acetylcholine receptor: An example of

multigene family in excitable cells J. Mol. Evol. 40: 155-172. (PubMed)

N. Kunishima, Y. Shimada, Y. Tsuji, T. Sato, M. Yamamoto, T. Kumasaka, S. Nakanishi, H. Jingami, and K. Morikawa.

2000. Structural basis of glutamate recognition by dimeric metabotropic glutamate receptor Nature 407: 971-978.

(PubMed)

H. Betz, J. Kuhse, V. Schmieden, B. Laube, J. Kirsch, and R.J. Harvey. 1999. Structure and functions of inhibitory and

excitatory glycine receptors Ann. N. Y. Acad. Sci. 868: 667-676. (PubMed)

N. Unwin. 1995. Acetylcholine receptor channel imaged in the open state Nature 373: 37-43. (PubMed)

D. Colquhoun and B. Sakmann. 1981. Fluctuations in the microsecond time range of the current through single

acetylcholine receptor ion channels Nature 294: 464-466. (PubMed)

P.H. Seeburg, W. Wisden, T.A. Verdoorn, D.B. Pritchett, P. Werner, A. Herb, H. Luddens, R. Sprengel, and B.

Sakmann. 1990. The GABA

receptor family: Molecular and functional diversity Cold Spring Harbor Symp. Quant.

Biol. 55: 29-40. (PubMed)

ATP-driven ion pumps

C. Toyoshima, M. Nakasako, H. Nomura, and H. Ogawa. 2000. Crystal structure of the calcium pump of sarcoplasmic

reticulum at 2.6 Å resolution Nature 405: 647-655. (PubMed)

M. Auer, G.A. Scarborough, and W. Kuhlbrandt. 1998. Threedimensional map of the plasma membrane H

-ATPase in

the open conformation Nature 392: 840-843. (PubMed)

K.B. Axelsen and M.G. Palmgren. 1998. Evolution of substrate specificities in the P-type ATPase superfamily J. Mol.

Evol. 46: 84-101. (PubMed)

P.A. Pedersen, J.R. Jorgensen, and P.L. Jorgensen. 2000. Importance of conserved alpha-subunit

709

GDGVND for Mg

binding, phosphorylation, energy transduction in Na, K-ATPase J. Biol. Chem. 275: 37588-37595. (PubMed)

G. Blanco and R.W. Mercer. 1998. Isozymes of the Na-K-ATPase: Heterogeneity in structure, diversity in function Am.

J. Physiol. 275: F633-F650. (PubMed)

D.H. MacLennan. 1990. Molecular tools to elucidate problems in excitation-contraction coupling Biophys. J. 58: 1355-

1365. (PubMed)

J.W. Estes and P.D. White. 1965. William Withering and the purple foxglove Sci. Am. 212: (6) 110-117. (PubMed)

ATP-binding cassette (ABC) proteins

M.H. Akabas. 2000. Cystic fibrosis transmembrane conductance regulator: Structure and function of an epithelial

chloride channel J. Biol. Chem. 275: 3729-3732. (PubMed)

J. Chen, S. Sharma, F.A. Quiocho, and A.L. Davidson. 2001. Trapping the transition state of an ATP-binding cassette

transporter: Evidence for a concerted mechanism of maltose transport Proc. Natl. Acad. Sci. USA 98: 1525-1530.

(PubMed) (Full Text in PMC)

Z.R. Zhang, S.I. McDonough, and N.A. McCarty. 2000. Interaction between permeation and gating in the putative pore

domain mutant in the cystic fibrosis transmembrane conductance regulator Biophys. J. 79: 298-313. (PubMed)

D.N. Sheppard and M.J. Welsh. 1999. Structure and function of the CFTR chloride channel Physiol. Rev. 79: S23-S45.

(PubMed)

J.R. Riordan, J.M. Rommens, B.S. Kerem, N. Alon, R. Rozmahel, Z. Grzelczak, J. Zielenski, S. Lok, N. Plavsic, J.L.

Chou, M.T. Drumm, M.C. annuzzi, F.S. Collins, and L.C. Tsui. 1989. Identification of the cystic fibrosis gene: Cloning

and characterization of complementary DNA Science 245: 1066-1073. (PubMed)

P.M. Jones and A.M. George. 2000. Symmetry and structure in P-glycoprotein and ABC transporters: What goes around

comes around Eur. J. Biochem. 287: 5298-5305.

Y. Chen and S.M. Simon. 2000. In situ biochemical demonstration that P-glycoprotein is a drug efflux pump with broad

specificity J. Cell Biol. 148: 863-870. (PubMed)

M.H. Saier Jr, I.T. Paulsen, M.K. Sliwinski, S.S. Pao, R.A. Skurray, and H. Nikaido. 1998. Evolutionary origins of

multidrug and drug-specific efflux pumps in bacteria FASEB J. 12: 265-74. (PubMed)

Symporters and antiporters

K.D. Philipson and D.A. Nicoll. 2000. Sodium-calcium exchange: A molecular perspective Annu. Rev. Physiol. 62: 111-

133. (PubMed)

A.L. Green, E.J. Anderson, and R.J. Brooker. 2000. A revised model for the structure and function of the lactose

permease: Evidence that a face on transmembrane segment 2 is important for conformational changes J. Biol. Chem.

275: 23240-23246. (PubMed)

S.S. Pao, I.T. Paulsen, and M.H. Saier Jr.,. 1998. Major facilitator superfamily Microbiol. Mol. Biol. Rev. 62: 1-34.

(PubMed) (Full Text in PMC)

E.M. Wright, J.R. Hirsch, D.D. Loo, and G.A. Zampighi. 1997. Regulation of Na

/glucose cotransporters J. Exp. Biol.

200: 287-293. (PubMed)

E.M. Wright, D.D. Loo, E. Turk, and B.A. Hirayama. 1996. Sodium cotransporters Curr. Opin. Cell Biol. 8: 468-473.

(PubMed)

H.R. Kaback, E. Bibi, and P.D. Roepe. 1990. β-Galactoside transport in E. coli: A functional dissection of lac permease

Trends Biochem. Sci. 8: 309-314. (PubMed)

D.W. Hilgemann, D.A. Nicoll, and K.D. Philipson. 1991. Charge movement during Na

translocation by native and

cloned cardiac Na

/Ca

exchanger Nature 352: 715-718. (PubMed)

M.A. Hediger, E. Turk, and E.M. Wright. 1989. Homology of the human intestinal Na

/glucose and Escherichia coli Na

/proline cotransporters Proc. Natl. Acad. Sci. USA 86: 5748-5752. (PubMed)

Gap junctions

A. Revilla, M.V.L. Bennett, and L.C. Barrio. 2000. Molecular determinants of membrane potential dependence in

vertebrate gap junction channels Proc. Natl. Acad. Sci. USA 97: 14760-14765. (PubMed) (Full Text in PMC)

V.M. Unger, N.M. Kumar, N.B. Gilula, and M. Yeager. 1999. Three-dimensional structure of a recombinant gap

junction membrane channel Science 283: 1176-1180. (PubMed)

A.M. Simon. 1999. Gap junctions: More roles and new structural data Trends Cell Biol. 9: 169-170. (PubMed)

T.W. White and D.L. Paul. 1999. Genetic diseases and gene knockouts reveal diverse connexin functions Annu. Rev.

Physiol. 61: 283-310. (PubMed)

II. Transducing and Storing Energy

ATP synthase. This enzyme is a molecular assembly that transduces the free energy associated with a proton gradient to

the chemical energy associated with ATP. The proton gradient drives the rotation of one component of the assembly

within the other. This rotational motion in turn drives the synthesis and release of ATP.

II. Transducing and Storing Energy

14. Metabolism: Basic Concepts and Design

The concepts of conformation and dynamics developed in Part I

especially those dealing with the specificity and

catalytic power of enzymes, the regulation of their catalytic activity, and the transport of molecules and ions across

membranes enable us to now ask questions fundamental to biochemistry:

1. How does a cell extract energy and reducing power from its environment?

2. How does a cell synthesize the building blocks of its macromolecules and then the macromolecules themselves?

These processes are carried out by a highly integrated network of chemical reactions that are collectively known as

metabolism.

More than a thousand chemical reactions take place in even as simple an organism as Escherichia coli. The array of

reactions may seem overwhelming at first glance. However, closer scrutiny reveals that metabolism has a coherent

design containing many common motifs. These motifs include the use of an energy currency and the repeated appearance

of a limited number of activated intermediates. In fact, a group of about 100 molecules play central roles in all forms of

life. Furthermore, although the number of reactions in metabolism is large, the number of kinds of reactions is small and

the mechanisms of these reactions are usually quite simple. Metabolic pathways are also regulated in common ways. The

purpose of this chapter is to introduce some general principles and motifs of metabolism to provide a foundation for the

more detailed studies to follow.

14.0.1. Cells Transform Different Types of Energy

Living organisms require a continual input of free energy for three major purposes: (1) the performance of mechanical

work in muscle contraction and other cellular movements, (2) the active transport of molecules and ions, and (3) the

synthesis of macromolecules and other biomolecules from simple precursors. The free energy used in these processes,

which maintain an organism in a state that is far from equilibrium, is derived from the environment.

The First Law of Thermodynamics states that energy can be neither created nor destroyed. The amount of energy in the

universe is constant. Nevertheless, energy can be converted from one form into another.

Photosynthetic organisms, or phototrophs, use the energy of sunlight to convert simple energy-poor molecules into more-

complex energy-rich molecules that serve as fuels. In other words, photosynthetic organisms transform light energy into

chemical energy. Indeed, this transformation is ultimately the primary source of chemical energy for the vast majority of

organisms, human beings included. Chemotrophs, which include animals, obtain chemical energy through the oxidation

of foodstuffs generated by phototrophs.

Chemical energy obtained from the oxidation of carbon compounds may be transformed into the unequal distribution of

ions across a membrane, resulting in an ion gradient. This gradient, in turn, is an energy source that can be used to move

molecules across membranes, that can be converted into yet other types of chemical energy, or that can convey

information in the form of nerve impulses. In addition, chemical energy can be transduced into mechanical energy. We

convert the chemical energy of a fuel into structural alterations of contractile proteins that result in muscle contraction

and movement. Finally, chemical energy powers the reactions that result in the synthesis of biomolecules.

At any given instant in a cell, thousands of energy transformations are taking place. Energy is being extracted from fuels

and used to power biosynthetic processes. These transformations are referred to as metabolism or intermediary

metabolism.

II. Transducing and Storing Energy 14. Metabolism: Basic Concepts and Design

Hummingbirds are capable of prodigious feats of endurance. For instance, the tiny ruby-throated hummingbird can

store enough fuel to fly across the Gulf of Mexico, a distance of some 500 miles, without resting. This achievement is

possible because of the ability to convert fuels into the cellular energy currency, ATP, represented by the model at the

right. [(Left) K. D. McGraw/Rainbow.]

II. Transducing and Storing Energy 14. Metabolism: Basic Concepts and Design

14.1. Metabolism Is Composed of Many Coupled, Interconnecting Reactions

Metabolism is essentially a linked series of chemical reactions that begins with a particular molecule and converts it into

some other molecule or molecules in a carefully defined fashion (Figure 14.1). There are many such defined pathways in

the cell (Figure 14.2), and we will examine a few of them in some detail later. These pathways are interdependent, and

their activity is coordinated by exquisitely sensitive means of communication in which allosteric enzymes are

predominant (Section 10.1). We will consider the principles of this communication in Chapter 15.

We can divide metabolic pathways into two broad classes: (1) those that convert energy into biologically useful forms

and (2) those that require inputs of energy to proceed. Although this division is often imprecise, it is nonetheless a useful

distinction in an examination of metabolism. Those reactions that transform fuels into cellular energy are called

catabolic reactions or, more generally, catabolism.

Those reactions that require energy

such as the synthesis of glucose, fats, or DNA are called anabolic reactions or

anabolism. The useful forms of energy that are produced in catabolism are employed in anabolism to generate complex

structures from simple ones, or energy-rich states from energy-poor ones.

Some pathways can be either anabolic or catabolic, depending on the energy conditions in the cell. They are referred to

as amphibolic pathways.

14.1.1. A Thermodynamically Unfavorable Reaction Can Be Driven by a Favorable

Reaction