Voet D., Voet Ju.G. Biochemistry

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which are below ATP in Table 16-3, have no significantly

different resonance stabilization or charge separation in

comparison with their hydrolysis products. Their free ener-

gies of hydrolysis are therefore much less than those of the

preceding “high-energy” compounds.

C. The Role of ATP

As Table 16-3 indicates, in the thermodynamic hierarchy of

phosphoryl-transfer agents, ATP occupies the middle rank.

This enables ATP to serve as an energy conduit between

“high-energy” phosphate donors and “low-energy” phos-

phate acceptors (Fig. 16-27). Let us examine the general

biochemical scheme of how this occurs.

In general, the highly exergonic phosphoryl-transfer

reactions of nutrient degradation are coupled to the for-

mation of ATP from ADP and P

through the auspices of

various enzymes known as kinases, enzymes that catalyze

the transfer of phosphoryl groups between ATP and other

molecules. Consider the two reactions in Fig. 16-23b. If

carried out independently, these reactions would not influ-

ence each other. In the cell, however, the enzyme pyruvate

Section 16-4. Thermodynamics of Phosphate Compounds 581

Figure 16-25 Hydrolysis of phosphoenolpyruvate. The reaction is broken down into two steps,

hydrolysis and tautomerization.

Phosphoenol-

pyruvate

COO

–

+ H

OPO

–

Hydrolysis

COO

–

+ HPO

–

Pyruvate

(enol form)

Pyruvate

(keto form)

COO

–

Tautomerization

COO

–

COO

–

Overall reaction

HPO

–

COO

–

⬃

ΔG° = –61.9 kJ

•

mol

–1

ΔG° = –46 kJ

•

mol

–1

ΔG° = –16 kJ

•

mol

–1

Phosphocreatine

–

R = CH

X = CH

;

Phosphoarginine

–

CHCH

R = CH

X = H

;

Figure 16-26 Competing resonances in phosphoguanidines.

Figure 16-27 The flow of phosphoryl groups from

“high-energy” phosphate donors, via the ATP–ADP

system, to “low-energy” phosphate acceptors.

–60

–50

–40

–30

–20

–10

Phosphoenolpyruvate

1,3-Bisphosphoglycerate

Phosphocreatine

Glucose-6-phosphate

Glycerol-3-phosphate

“High-energy”

phosphate

compounds

“Low-energy”

phosphate

compounds

ΔG

°′

of hydrolysis (kJ • mol

–1

)

ATP

JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 581

kinase couples the two reactions by catalyzing the trans-

fer of the phosphoryl group of phosphoenolpyruvate di-

rectly to ADP to result in an overall exergonic reaction

(Section 17-2J).

a. Consumption of ATP

In its role as the universal energy currency of living sys-

tems, ATP is consumed in a variety of ways:

1. Early stages of nutrient breakdown. The exergonic

hydrolysis of ATP to ADP may be enzymatically coupled

to an endergonic phosphorylation reaction to form “low-

energy” phosphate compounds.We have seen one example

of this in the hexokinase-catalyzed formation of glucose-

6-phosphate (Fig. 16-23a). Another example is the phos-

phofructokinase-catalyzed phosphorylation of fructose-6-

phosphate to form fructose-1,6-bisphosphate (Fig. 16-28).

Both of these reactions occur in the first stage of glycolysis

(Section 17-2).

2. Interconversion of nucleoside triphosphates. Many

biosynthetic processes, such as the synthesis of proteins

and nucleic acids, require nucleoside triphosphates other

than ATP. These include the ribonucleoside triphosphates

CTP, GTP, and UTP, which, together with ATP, are utilized,

for example, in the biosynthesis of RNA (Section 31-2) and

the deoxyribonucleoside triphosphate DNA precursors

dATP, dCTP, dGTP, and dTTP (Section 5-4C). All these

nucleoside triphosphates (NTPs) are synthesized from

ATP and the corresponding nucleoside diphosphate

(NDP) in reactions catalyzed by the nonspecific enzyme

nucleoside diphosphate kinase:

The G°¿ values for these reactions are nearly zero, as

might be expected from the structural similarities among

the NTPs. These reactions are driven by the depletion

of the NTPs through their exergonic hydrolysis in the biosyn-

thetic reactions in which they participate (Section 3-4C).

3. Physiological processes. The hydrolysis of ATP to

ADP and P

energizes many essential endergonic physio-

logical processes such as chaperone-assisted protein fold-

ing (Section 9-2C), muscle contraction (Section 35-3B),

and the transport of molecules and ions against concentra-

tion gradients (Section 20-3). In general, these processes

result from conformational changes in proteins (enzymes)

that occur in response to their binding of ATP. This is fol-

lowed by the exergonic hydrolysis of ATP and release of

ATP  NDP Δ ADP  NTP

ADP and P

, thereby causing these processes to be unidi-

rectional (irreversible).

4. Additional phosphoanhydride cleavage in highly

endergonic reactions. Although many reactions involving

ATP yield ADP and P

(orthophosphate cleavage), others

yield AMP and PP

(pyrophosphate cleavage). In these lat-

ter cases, the PP

is rapidly hydrolyzed to 2P

by inorganic

pyrophosphatase (G°¿ 19.2 kJ ⴢ mol

1

) so that the

pyrophosphate cleavage of ATP ultimately results in the

hydrolysis of two “high-energy” phosphoanhydride bonds.

The attachment of amino acids to tRNA molecules for pro-

tein synthesis is an example of this phenomenon (Fig. 16-29

and Section 32-2C).The two steps of the reaction involving

the amino acid are readily reversible because the free ener-

gies of hydrolysis of the bonds formed are comparable to

that of ATP hydrolysis. The overall reaction is driven to

completion by the hydrolysis of PP

, which is essentially ir-

reversible. Nucleic acid biosynthesis from the appropriate

NTPs also releases PP

(Sections 30-1A and 31-2).The free

energy changes of these vital reactions are around zero, so

the subsequent hydrolysis of PP

is essential to drive the

synthesis of nucleic acids.

b. Formation of ATP

To complete its intermediary metabolic function, ATP

must be replenished. This is accomplished through three

types of processes:

1. Substrate-level phosphorylation. ATP may be

formed, as is indicated in Fig. 16-23b, from phospho-

enolpyruvate by direct transfer of a phosphoryl group from

a “high-energy” compound to ADP. Such reactions, which

are referred to as substrate-level phosphorylations, most

commonly occur in the early stages of carbohydrate me-

tabolism (Section 17-2).

2. Oxidative phosphorylation and photophosphoryla-

tion. Both oxidative metabolism and photosynthesis act to

generate a proton (H



) concentration gradient across a

membrane (Sections 22-3 and 24-2D). Discharge of this

gradient is enzymatically coupled to the formation of ATP

from ADP and P

(the reverse of ATP hydrolysis). In oxida-

tive metabolism, this process is called oxidative phosphory-

lation, whereas in photosynthesis it is termed photophos-

phorylation. Most of the ATP produced by respiring and

photosynthesizing organisms is generated in this manner.

3. Adenylate kinase reaction. The AMP resulting from

pyrophosphate cleavage reactions of ATP is converted to

582 Chapter 16. Introduction to Metabolism

Figure 16-28 The phosphorylation of fructose-6-phosphate by ATP to form fructose-1,6-bisphosphate and ADP.

Fructose-6-phosphate

Fructose-1,6-bisphosphate

ATP ADP

2

PCH

2

phosphofructokinase

G = –14.2 kJ •mol

–1

2

PCH

JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 582

ADP in a reaction catalyzed by the enzyme adenylate

kinase (Section 17-4Fe):

The ADP is subsequently converted to ATP through

substrate-level phosphorylation, oxidative phosphorylation,

or photophosphorylation.

c. Rate of ATP Turnover

The cellular role of ATP is that of a free energy transmit-

ter rather than a free energy reservoir. The amount of ATP

in a cell is typically only enough to supply its free energy

needs for a minute or two. Hence,ATP is continually being

hydrolyzed and regenerated. Indeed,

P-labeling experi-

ments indicate that the metabolic half-life of an ATP mole-

cule varies from seconds to minutes depending on the cell

type and its metabolic activity. For instance, brain cells

have only a few seconds’ supply of ATP (which, in part, ac-

counts for the rapid deterioration of brain tissue by oxygen

deprivation). An average person at rest consumes and re-

generates ATP at a rate of ⬃3 mol (1.5 kg) ⴢ h

1

and as much

as an order of magnitude faster during strenuous activity.

d. Phosphocreatine Provides a “High-Energy”

Reservoir for ATP Formation

Muscle and nerve cells, which have a high ATP turnover

(a maximally exerting muscle has only a fraction of a

second’s ATP supply), have a free energy reservoir that

functions to regenerate ATP rapidly. In vertebrates, phos-

phocreatine (Fig. 16-26) functions in this capacity. It is

synthesized by the reversible phosphorylation of creatine

by ATP as catalyzed by creatine kinase:

Note that this reaction is endergonic under standard condi-

tions. However, the intracellular concentrations of its reac-

tants and products (typically 4 mM ATP and 0.013 mM

¢G°¿ 12.6 kJ ⴢ mol

1

ATP  creatine Δ phosphocreatine  ADP

AMP  ATP Δ 2ADP

ADP) are such that it operates close to equilibrium (G ⬇ 0).

Accordingly, when the cell is in a resting state, so that

[ATP] is relatively high, the reaction proceeds with net

synthesis of phosphocreatine, whereas at times of high

metabolic activity, when [ATP] is low, the equilibrium shifts

so as to yield net synthesis of ATP. Phosphocreatine thereby

acts as an ATP “buffer” in cells that contain creatine kinase.

A resting vertebrate skeletal muscle normally has suffi-

cient phosphocreatine to supply its free energy needs for

several minutes (but for only a few seconds at maximum

exertion). In the muscles of some invertebrates, such as

lobsters, phosphoarginine performs the same function.

These phosphoguanidines are collectively named phos-

phagens.

5 OXIDATION–REDUCTION REACTIONS

Oxidation–reduction reactions, processes involving the

transfer of electrons, are of immense biochemical signifi-

cance; living things derive most of their free energy from

them. In photosynthesis (Chapter 24), CO

is reduced

(gains electrons) and H

O is oxidized (loses electrons) to

yield carbohydrates and O

in an otherwise endergonic

process that is powered by light energy. In aerobic metabo-

lism, which is carried out by all eukaryotes and many

prokaryotes, the overall photosynthetic reaction is essen-

tially reversed so as to harvest the free energy of oxidation

of carbohydrates and other organic compounds in the form

of ATP (Chapter 22). Anaerobic metabolism generates

ATP, although in lower yields, through intramolecular

oxidation–reductions of various organic molecules, for

example, glycolysis (Chapter 17). In certain anaerobic

bacteria,ATP is generated through the use of non-O

oxidiz-

ing agents such as sulfate or nitrate. In this section we out-

line the thermodynamics of oxidation–reduction reactions

in order to understand the quantitative aspects of these

crucial biological processes.

Section 16-5. Oxidation–Reduction Reactions 583

Figure 16-29 Pyrophosphate cleavage in the synthesis of an

aminoacyl–tRNA. Here the squiggle (⬃) represents a “high-

energy” bond. In the first reaction step, the amino acid is

adenylylated by ATP. In the second step, a tRNA molecule

AMP P

C + ⬃⬃P

ATP

P ⬃P

inorganic

pyrophosphatase

⬃

Aminoacyl–adenylate

tRNA

AMP

Amino acid

–

AMP

tRN

Aminoacyl–tRNA

displaces the AMP moiety to form an aminoacyl–tRNA. The

exergonic hydrolysis of pyrophosphate (G°¿ 19.2

kJ ⴢ mol

1

) drives the reaction forward.

JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 583

A. The Nernst Equation

Oxidation–reduction reactions (also known as redox or ox-

idoreduction reactions) resemble other types of chemical

reactions in that they involve group transfer. For instance,

hydrolysis transfers a functional group to water.In oxidation–

reduction reactions, the “groups” transferred are electrons,

which are passed from an electron donor (reductant or re-

ducing agent) to an electron acceptor (oxidant or oxidizing

agent). For example, in the reaction



, the reductant, is oxidized to Cu

2

while Fe

3

, the oxi-

dant, is reduced to Fe

2

Redox reactions may be divided into two half-reactions

or redox couples, such as

whose sum is the above whole reaction.These half-reactions

occur during oxidative metabolism in the vital mitochon-

drial electron transfer mediated by cytochrome c oxidase

(Section 22-2C5). Note that for electrons to be transferred,

both half-reactions must occur simultaneously. In fact,

the electrons are the two half-reactions’ common interme-

diate.

a. Electrochemical Cells

A half-reaction consists of an electron donor and its

conjugate electron acceptor; in the oxidation half-reaction

shown above, Cu



is the electron donor and Cu

2

is its con-

jugate electron acceptor.Together these constitute a conju-

gate redox pair analogous to the conjugate acid–base pair

(HA and A



) of a Brønsted acid (Section 2-2A).An impor-

tant difference between redox pairs and acid–base pairs,

however, is that the two half-reactions of a redox reaction,

each consisting of a conjugate redox pair, may be physically

separated so as to form an electrochemical cell (Fig. 16-30).

In such a device, each half-reaction takes place in its sepa-

rate half-cell, and electrons are passed between half-cells

as an electric current in the wire connecting their two elec-

trodes. A salt bridge is necessary to complete the electrical

circuit by providing a conduit for ions to migrate in the

maintenance of electrical neutrality.

The free energy of an oxidation–reduction reaction is

particularly easy to determine through a simple measure-

ment of the voltage difference between its two half-cells.

Consider the general redox reaction:

in which n electrons per mole of reactants are transferred

from reductant (B

red

) to oxidant ( ). The free energy of

this reaction is expressed, according to Eq. [3.15], as

[16.2]

Equation [3.12] indicates that, under reversible conditions,

[16.3]¢G w¿ w

¢G  ¢G°  RT ln a

red

][B

n

]

n

][B

red

]

n

 B

red

Δ A

red

 B

n



Δ Cu

2

 e



(oxidation)

3

 e



Δ Fe

2

(reduction)

3

 Cu



Δ Fe

2

 Cu

2

where w¿, the non-pressure–volume work, is, in this case,

, the electrical work required to transfer the n moles of

electrons through the electric potential difference .This,

according to the laws of electrostatics, is

[16.4]

where f, the faraday, is the electrical charge of 1 mol of

electrons (1 f  96,485 C ⴢ mol

1

 96,485 J ⴢ V

1

ⴢ mol

1

where C and V are the symbols for coulomb and volt).

Thus, substituting Eq. [16.4] into Eq. [16.3],

[16.5]

Combining Eqs. [16.2] and [16.5], and making the analo-

gous substitution for G°, yields the Nernst equation:

[16.6]

which was originally formulated in 1881 by Walther Nernst.

Here e, the electromotive force (emf) or redox potential,

may be described as the “electron pressure” that the elec-

trochemical cell exerts. The quantity e°, the redox poten-

tial when all components are in their standard states, is

called the standard redox potential. If these standard states

refer to biochemical standard states (Section 3-4Ba), then

e° is replaced by e°¿. Note that a positive e in

Eq. [16.5] results in a negative G; in other words, a posi-

tive e is indicative of a spontaneous reaction, one that can

do work.

B. Measurements of Redox Potentials

The free energy change of a redox reaction may be deter-

mined, as Eq. [16.5] indicates, by simply measuring its redox

potential with a voltmeter (Fig. 16-30). Consequently,

voltage measurements are commonly employed to charac-

terize the sequence of reactions comprising a metabolic

¢¢¢

¢e  ¢e° 

ln a

red

][B

n

]

n

][B

red

]

¢G nf ¢e

 nf ¢e

¢e

584 Chapter 16. Introduction to Metabolism

Figure 16-30 Example of an electrochemical cell. The half-cell

undergoing oxidation (here Cu



S Cu

2

 e



) passes the

liberated electrons through the wire to the half-cell undergoing

reduction (here e



 Fe

3

S Fe

2

). Electroneutrality in the two

half-cells is maintained by the transfer of ions through the

electrolyte-containing salt bridge.

Salt

bridge

–

+ Fe

Pt Pt

+ e

–

Voltmeter

JWCL281_c16_557-592.qxd 6/10/10 11:52 AM Page 584

electron-transport pathway (such as mediates, e.g., oxida-

tive metabolism; Chapter 22).

Any redox reaction can be divided into its component

half-reactions:

where, by convention, both half-reactions are written as re-

ductions. These half-reactions can be assigned reduction

potentials, e

and e

,in accordance with the Nernst equation:

[16.7a]

[16.7b]

For the redox reaction of any two half-reactions:

[16.8]

Thus, when the reaction proceeds with A as the electron

acceptor and B as the electron donor, and

similarly for .¢e

¢e° ⫽ e°

⫺ e°

¢e° ⫽ e°

⫺

acceptor)

⫺ e°

⫺

donor)

⫽ e

° ⫺

ln a

red

]

n⫹

]

⫽ e

° ⫺

ln a

red

]

n⫹

]

n⫹

⫹ ne

⫺

Δ B

red

n⫹

⫹ ne

⫺

Δ A

red

Reduction potentials, like free energies, must be defined

with respect to some arbitrary standard. By convention,

standard reduction potentials are defined with respect to

the standard hydrogen half-reaction

in which H

⫹

at pH 0, 25°C,and 1 atm is in equilibrium with

(g) that is in contact with a Pt electrode. This half-cell is

arbitrarily assigned a standard reduction potential of ⫽ 0 V

(1 V ⫽ 1 J ⴢ C

⫺1

). For the biochemical convention, we like-

wise define the standard (pH ⫽ 0) hydrogen half-reaction

as having so that the hydrogen half-cell at the bio-

chemical standard state (pH ⫽ 7) has

(Table 16-4). When is positive, ⌬G is negative (Eq.

[16.5]), indicating a spontaneous process. In combining

two half-reactions under standard conditions, the direc-

tion of spontaneity therefore involves the reduction of the

redox couple with the more positive standard reduction

potential. In other words, the more positive the standard re-

duction potential, the greater the tendency for the redox

couple’s oxidized form to accept electrons and thus become

reduced.

¢e

e°¿ ⫽⫺0.421 V

e¿ ⫽ 0

e°

⫹

⫹ 2e

⫺

Δ H

(g)

Section 16-5. Oxidation–Reduction Reactions 585

Half-Reaction (V)

0.815

0.42

0.385

0.295

0.29

0.235

0.22

0.077

0.045

0.031

⫺0.040

⫺0.166

⫺0.185

⫺0.197

⫺0.219

⫺0.23

⫺0.29

⫺0.315

⫺0.320

⫺0.340

⫺0.346

⫺0.421

⫺0.454

⫺0.581Acetate

⫺

⫹ 3H

⫹

⫹ 2e

⫺

Δ acetaldehyde ⫹ H

2⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ SO

2⫺

⫹ H

⫹

⫹ e

⫺

Acetoacetate

⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ ␤-hydroxybutyrate

⫺

Cystine ⫹ 2H

⫹

⫹ 2e

⫺

Δ 2 cysteine

NADP

⫹

⫹ H

⫹

⫹ 2e

⫺

Δ NADPH

NAD

⫹

⫹ H

⫹

⫹ 2e

⫺

Δ NADH

Lipoic acid ⫹ 2H

⫹

⫹ 2e

⫺

Δ dihydrolipoic acid

S ⫹ 2H

⫹

⫹ 2e

⫺

Δ H

FAD ⫹ 2H

⫹

⫹ 2e

⫺

Δ FADH

(free coenzyme)

Acetaldehyde ⫹ 2H

⫹

⫹ 2e

⫺

Δ ethanol

Pyruvate

⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ lactate

⫺

Oxaloacetate

⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ malate

⫺

FAD ⫹ 2H

⫹

⫹ 2e

⫺

Δ FADH

(in flavoproteins)

Fumarate

⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ succinate

⫺

Ubiquinone ⫹ 2H

⫹

⫹ 2e

⫺

Δ ubiquinol

Cytochrome b(Fe

3⫹

) ⫹ e

⫺

Δ cytochrome b(Fe

2⫹

) (mitochondrial)

Cytochrome c

(Fe

3⫹

) ⫹ e

⫺

Δ cytochrome c

(Fe

2⫹

)

Cytochrome c(Fe

3⫹

) ⫹ e

⫺

Δ cytochrome c(Fe

2⫹

)

Cytochrome a(Fe

3⫹

) ⫹ e

⫺

Δ cytochrome a(Fe

2⫹

)

(g) ⫹ 2H

⫹

⫹ 2e

⫺

Δ H

Cytochrome a

(Fe

3⫹

) ⫹ e

⫺

Δ cytochrome a

(Fe

2⫹

)

⫺

⫹ 2H

⫹

⫹ 2e

⫺

Δ NO

⫺

⫹ H

⫹ 2H

⫹

⫹ 2e

⫺

Δ H

e°¿

Table 16-4 Standard Reduction Potentials of Some Biochemically Important

Half-Reactions

Source: Mostly from Loach, P.A., in Fasman, G.D. (Ed.), Handbook of Biochemistry and Molecular Biology

(3rd ed.), Physical and Chemical Data, Vol. I, pp. 123–130, CRC Press (1976).

JWCL281_c16_557-592.qxd 6/30/10 10:34 AM Page 585

a. Biochemical Half-Reactions Are

Physiologically Significant

The biochemical standard reduction potentials of

some biochemically important half-reactions are listed in

Table 16-4. The oxidized form of a redox couple with a

large positive standard reduction potential has a high affin-

ity for electrons and is a strong electron acceptor (oxidizing

agent), whereas its conjugate reductant is a weak electron

donor (reducing agent). For example, O

is the strongest

oxidizing agent in Table 16-4, whereas H

O, which tightly

holds its electrons, is the table’s weakest reducing agent.

The converse is true of half-reactions with large negative

standard reduction potentials. Since electrons sponta-

neously flow from low to high reduction potentials, they

are transferred, under standard conditions, from the re-

duced products in any half-reaction in Table 16-4 to the ox-

idized reactants of any half-reaction above it (although this

may not occur at a measurable rate in the absence of a suit-

able enzyme). Thus, in biological systems, the approximate

lower limit for a standard reduction potential is 0.421 V

because reductants with a lesser value of would reduce

protons to H

. However, reducing centers in proteins that

are protected from water may have lower potentials. Note

that the Fe

3

ions of the various cytochromes tabulated in

Table 16-4 have significantly different redox potentials.

This indicates that the protein components of redox

enzymes play active roles in electron-transfer reactions by

modulating the redox potentials of their bound redox-active

centers.

Electron-transfer reactions are of great biological

importance. For example, in the mitochondrial electron-

transport chain (Section 22-2), the primary source of ATP

in eukaryotes, electrons are passed from NADH (Fig. 13-2)

along a series of electron acceptors of increasing reduction

potential (many of which are listed in Table 16-4) to O

ATP is generated from ADP and P

by coupling its synthe-

sis to this free energy cascade. NADH thereby functions as

an energy-rich electron-transfer coenzyme. In fact, the oxi-

dation of one NADH to NAD



supplies sufficient free en-

ergy to generate 2.5 ATPs (Section 22-2Bb). The NAD



NADH redox couple functions as the electron acceptor in

many exergonic metabolite oxidations. In serving as the

electron donor in ATP synthesis, it fulfills its cyclic role as a

free energy conduit in a manner analogous to ATP. The

metabolic roles of redox coenzymes are further discussed

in succeeding chapters.

C. Concentration Cells

A concentration gradient has a lower entropy (greater or-

der) than the corresponding uniformly mixed solution and

therefore requires the input of free energy for its formation.

Consequently, discharge of a concentration gradient is an

exergonic process that may be harnessed to drive an ender-

gonic reaction. For example, discharge of a proton concen-

tration gradient (generated by the reactions of the electron-

transport chain) across the inner mitochondrial

membrane drives the enzymatic synthesis of ATP from

ADP and P

(Section 22-3). Likewise, nerve impulses,

e°¿

(e°¿)

which require electrical energy, are transmitted through

the discharge of [Na



] and [K



] gradients that nerve cells

generate across their cell membranes (Section 20-5B).

Quantitation of the free energy contained in a concentra-

tion gradient is accomplished by use of the concepts of

electrochemical cells.

The reduction potential and free energy of a half-cell

vary with the concentrations of its reactants. An electro-

chemical cell may therefore be constructed from two

half-cells that contain the same chemical species but at

different concentrations. The overall reaction for such an

electrochemical cell may be represented

[16.9]

and, according to the Nernst equation, since when

the same reaction occurs in both cells,

Such concentration cells are capable of generating electri-

cal work until they reach equilibrium.This occurs when the

concentration ratios in the half-cells become equal (K

 1).

The reaction constitutes a sort of mixing of the two half-

cells; the free energy generated is a reflection of the en-

tropy of this mixing.The thermodynamics of concentration

gradients as they apply to membrane transport is discussed

in Section 20-1.

6 THERMODYNAMICS OF LIFE

One of the last refuges of vitalism, the doctrine that biolog-

ical processes are not bound by the physical laws that gov-

ern inanimate objects, was the belief that living things can

somehow evade the laws of thermodynamics.This view was

partially refuted by elaborate calorimetric measurements

on living animals that are entirely consistent with the

energy conservation predictions of the first law of thermo-

dynamics. However, the experimental verification of the

second law of thermodynamics in living systems is more

difficult. It has not been possible to measure the entropy of

living matter because the heat, q

, of a reaction at a con-

stant T and P is only equal to T S if the reaction is carried

out reversibly (Eq. [3.8]). Obviously, the dismantling of a

living organism to its component molecules for such a

measurement would invariably result in its irreversible

death. Consequently, the present experimentally verified

state of knowledge is that the entropy of living matter is

less than that of the products to which it decays.

In this section we consider the special aspects of the

thermodynamics of living systems. Knowledge of these

matters, which is by no means complete, has enhanced our

understanding of how metabolic pathways are regulated,

how cells respond to stimuli, and how organisms grow and

change with time.

¢e 

ln a

n

(half-cell 2) ][A

red

(half-cell 1) ]

n

(half-cell 1) ] [A

red

(half-cell 2) ]

¢e°  0

n

(half-cell 2)  A

red

(half-cell 1)

n

(half-cell 1)  A

red

(half-cell 2) Δ

586 Chapter 16. Introduction to Metabolism

JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 586

A. Living Systems Cannot Be at Equilibrium

Classical or equilibrium thermodynamics (Chapter 3)

applies largely to reversible processes in closed systems.

The fate of any isolated system, as we discussed in Section

3-4A, is that it must inevitably reach equilibrium. For ex-

ample, if its reactants are in excess, the forward reaction

will proceed faster than the reverse reaction until equilib-

rium is attained (G  0). In contrast, open systems may

remain in a nonequilibrium state as long as they are able to

acquire free energy from their surroundings in the form of

reactants, heat, or work. While classical thermodynamics

provides invaluable information concerning open systems

by indicating whether a given process can occur sponta-

neously, further thermodynamic analysis of open systems

requires the application of the more recently elucidated

principles of nonequilibrium or irreversible thermodynamics.

In contrast to classical thermodynamics, this theory explic-

itly takes time into account.

Living organisms are open systems and therefore can

never be at equilibrium. As indicated above, they continu-

ously ingest high-enthalpy, low-entropy nutrients, which

they convert to low-enthalpy, high-entropy waste products.

The free energy resulting from this process is used to do

work and to produce the high degree of organization char-

acteristic of life. If this process is interrupted, the organism

ultimately reaches equilibrium, which for living things is

synonymous with death. For example, one theory of aging

holds that senescence results from the random but in-

evitable accumulation in cells of genetic defects that inter-

fere with and ultimately disrupt the proper functioning of

living processes. [The theory does not, however, explain

how single-celled organisms or the germ cells of multicellu-

lar organisms (sperm and ova), which are in effect immor-

tal, are able to escape this so-called error catastrophe.]

Living systems must maintain a nonequilibrium state

for several reasons:

1. Only a nonequilibrium process can perform useful

work.

2. The intricate regulatory functions characteristic of

life require a nonequilibrium state because a process at

equilibrium cannot be controlled (similarly, a ship that is

dead in the water will not respond to its rudder).

3. The complex cellular and molecular systems that

conduct biological processes can be maintained only in the

nonequilibrium state. Living systems are inherently unsta-

ble because they are degraded by the very biochemical re-

actions to which they give rise. Their regeneration, which

must occur almost simultaneously with their degradation,

requires the continuous influx of free energy. For example,

the ATP-generating consumption of glucose (Section 17-2),

as has been previously mentioned, occurs with the initial

consumption of ATP through its reactions with glucose to

form glucose-6-phosphate and with fructose-6-phosphate

to form fructose-1,6-bisphosphate. Consequently, if metab-

olism is suspended long enough to exhaust the available

ATP supply, glucose metabolism cannot be resumed. Life

therefore differs in a fundamental way from a complex

machine such as a computer. Both require a throughput of

free energy to be active. However, the function of the ma-

chine is based on a static structure, so that the machine can

be repeatedly switched on and off. Life, in contrast, is based

on a self-destructing but self-renewing process, which once

interrupted, cannot be reinitiated.

B. Nonequilibrium Thermodynamics and

the Steady State

In a nonequilibrium process, something (such as matter,

electrical charge, or heat) must flow, that is, change its spa-

tial distribution. In classical mechanics, the acceleration of

mass occurs in response to force. Similarly, flow in a ther-

modynamic system occurs in response to a thermodynamic

force (driving force), which results from the system’s

nonequilibrium state. For example, the flow of matter in

diffusion is motivated by the thermodynamic force of a con-

centration gradient; the migration of electrical charge (elec-

tric current) occurs in response to a gradient in an electric

field (a voltage difference); the transport of heat results

from a temperature gradient; and a chemical reaction

results from a difference in chemical potential. Such flows

are said to be conjugate to their thermodynamic force.

A thermodynamic force may also promote a nonconju-

gate flow under the proper conditions. For example, a gra-

dient in the concentration of matter can give rise to an elec-

tric current (a concentration cell), heat (such as occurs on

mixing H

O and HCl), or a chemical reaction (the mito-

chondrial production of ATP through the dissipation of a

proton gradient). Similarly, a gradient in electrical poten-

tial can motivate a flow of matter (electrophoresis), heat

(resistive heating), or a chemical reaction (the charging of

a battery). When a thermodynamic force stimulates a non-

conjugate flow, the process is called energy transduction.

a. Living Things Maintain the Steady State

Living systems are, for the most part, characterized by

being in a steady state. By this it is meant that all flows in the

system are constant, so that the system does not change with

time. Some environmental steady-state processes are

schematically illustrated in Fig. 16-31. Ilya Prigogine, a

pioneer in the development of irreversible thermodynamics,

has shown that a steady-state system produces the maximum

amount of useful work for a given energy expenditure under

the prevailing conditions. The steady state of an open system

is therefore its state of maximum thermodynamic efficiency.

Furthermore, in analogy with Le Châtelier’s principle (Sec-

tion 3-4A), slight perturbations from the steady state give

rise to changes in flows that counteract these perturbations

so as to return the system to the steady state. The steady state

of an open system is therefore analogous to the equilibrium

state of an isolated system; both are stable states.

In the following chapters we shall see that many biological

regulatory mechanisms function to maintain a steady state.

For example, the flow of reaction intermediates through a

metabolic pathway is often inhibited by an excess of final prod-

uct and stimulated by an excess of starting material through

the allosteric regulation of its key enzymes (Section 13-4).

Section 16-6. Thermodynamics of Life 587

JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 587

Living things have apparently evolved so as to take maximum

thermodynamic advantage of their environments.

C. Thermodynamics of Metabolic Control

a. Enzymes Selectively Catalyze Required Reactions

Biological reactions are highly specific; only reactions that

lie on metabolic pathways take place at significant rates de-

spite the many other thermodynamically favorable reactions

that are also possible. As an example, let us consider the re-

actions of ATP, glucose, and water. Two thermodynamically

favorable reactions that ATP can undergo are phosphoryl

transfer to form ADP and glucose-6-phosphate,and hydroly-

sis to form ADP and P

(Fig.16-23a).The free energy profiles

of these reactions are diagrammed in Fig.16-32.ATP hydrol-

ysis is thermodynamically favored over the phosphoryl

transfer to glucose. However, their relative rates are deter-

mined by their free energies of activation to their transition

588 Chapter 16. Introduction to Metabolism

Figure 16-31 Two examples of open systems in a steady state.

(a) A constant flow of water in the river occurs under the

influence of the force of gravity. The water level in the reservoir

is maintained by rain, the major source of which is the

evaporation of seawater. Hence the entire cycle is ultimately

Figure 16-32 Reaction coordinate diagrams. These are (1) the

reaction of ATP and water (purple curve), and the reaction of

ATP and glucose (2) in the presence (orange curve) and (3) in

the absence (yellow curve) of an appropriate enzyme.Although

(a)

Radiant energy

from the sun

Rain

Heat loss

Water

vapor

Sea

River flowing

under steady

state conditions

(gravity)

Heat loss

Breakdown of

carbohydrates

Photosynthesis

(b)

Radiant energy

from the sun

ATP + H

+ glucose

Reaction coordinate

ADP + H

O + glucose-6-P

ADP + P

+ glucose

(ATP•Glucose)

enzymatic

+ H

(ATP•Glucose)

enzymatic

(ADP•Glucose-6-P)

enzymatic

(ATP•Glucose)

uncatalyzed

+ H

ΔG

, ΔG

similarly maintained by the sun. Plants harness the sun’s radiant

energy to synthesize carbohydrates from CO

and H

O. The

eventual metabolism of the carbohydrates by the plants or by the

animals that eat them results in the release of their stored free

energy and the return of the CO

and H

O to the environment to

complete the cycle.

the hydrolysis of ATP is a more exergonic reaction than the

phosphorylation of glucose (G

is more negative than G

), the

latter reaction is predominant in the presence of a suitable

enzyme because it is kinetically favored .(¢G

‡

 ¢G

‡

)

JWCL281_c16_557-592.qxd 6/10/10 11:52 AM Page 588

states (G

‡

values; Section 14-1Cb) and the relative concen-

trations of glucose and water.The larger G

‡

, the slower the

reaction. In the absence of enzymes, G

‡

for the phosphoryl-

transfer reaction is greater than that for hydrolysis, so the

hydrolysis reaction predominates (although neither reaction

occurs at a biologically significant rate).

The free energy barriers of both of the nonenzymatic re-

actions are far higher than that of the enzyme-catalyzed

phosphoryl transfer to glucose. Hence enzymatic forma-

tion of glucose-6-phosphate is kinetically favored over the

nonenzymatic hydrolysis of ATP. It is the role of an enzyme,

in this case hexokinase, to selectively reduce the free energy

of activation of a chemically coupled reaction so that it ap-

proaches equilibrium faster than the more thermodynami-

cally favored uncoupled reaction.

b. Many Enzymatic Reactions Are Near Equilibrium

Although metabolism as a whole is a nonequilibrium

process, many of its component reactions function close to

equilibrium. The reaction of ATP and creatine to form

phosphocreatine (Section 16-4Cd) is an example of such a

reaction. The ratio [creatine]/[phosphocreatine] depends

on [ATP] because creatine kinase, the enzyme catalyzing

this reaction, has sufficient activity to equilibrate the reac-

tion rapidly. The net rate of such an equilibrium reaction is

effectively controlled by varying the concentrations of its

reactants and/or products.

c. Pathway Throughput Is Regulated by Controlling

Enzymes Operating Far from Equilibrium

Other biological reactions function far from equilibrium.

For example, the phosphofructokinase reaction (Fig. 16-28)

has an equilibrium constant of but under physio-

logical conditions in rat heart muscle has the mass action ra-

tio [fructose-1,6-bisphosphate][ADP]/[fructose-6-phos-

phate][ATP]  0.03, which corresponds to G 25.7

kJ ⴢ mol

1

(Eq. [3.15]). This situation arises from a buildup

of reactants because there is insufficient phosphofructoki-

nase activity to equilibrate the reaction. Changes in sub-

strate concentrations therefore have relatively little effect

on the rate of the phosphofructokinase reaction; the en-

zyme is close to saturation. Only changes in the activity of

the enzyme, through allosteric interactions, for example, can

significantly alter this rate.An enzyme such as phosphofruc-

tokinase is therefore analogous to a dam on a river. Sub-

strate flux (rate of flow) is controlled by varying its activity

(allosterically or by other means), much as a dam controls

the flow of a river below the dam by varying the opening of

its floodgates (when the water levels on the two sides of the

dam are different, that is, when they are not at equilibrium).

Understanding of how reactant flux in a metabolic path-

way is controlled requires knowledge of which reactions

are functioning near equilibrium and which are far from it.

Most enzymes in a metabolic pathway operate near equi-

librium and therefore have net rates that are sensitive only

to their substrate concentrations. However, as we shall see

in the following chapters (particularly in Section 17-4), cer-

tain enzymes, which are strategically located in a metabolic

pathway, operate far from equilibrium. These enzymes,

which are targets for metabolic regulation by allosteric inter-

actions and other mechanisms, are responsible for the main-

tenance of a stable steady-state flux of metabolites through

the pathway. This situation, as we have seen, maximizes the

pathway’s thermodynamic efficiency.

K¿

 300

Chapter Summary 589

1 Metabolic Pathways Metabolic pathways are series of

consecutive enzymatically catalyzed reactions that produce

specific products for use by an organism. The free energy re-

leased by degradation (catabolism) is, through the intermedi-

acy of ATP and NADPH, used to drive the endergonic

processes of biosynthesis (anabolism). Carbohydrates, lipids,

and proteins are all converted to the common intermediate

acetyl-CoA, whose acetyl group is then converted to CO

and

O through the action of the citric acid cycle and oxidative

phosphorylation.A relatively few metabolites serve as starting

materials for a host of biosynthetic products. Metabolic path-

ways have five principal characteristics: (1) Metabolic path-

ways are irreversible; (2) if two metabolites are interconvertible,

the synthetic route from the first to the second must differ

from the route from the second to the first; (3) every meta-

bolic pathway has an exergonic first committed step; (4) all

metabolic pathways are regulated, usually at the first commit-

ted step; and (5) metabolic pathways in eukaryotes occur in

specific subcellular compartments.

2 Organic Reaction Mechanisms Almost all metabolic

reactions fall into four categories: (1) group-transfer reactions;

(2) oxidation–reduction reactions; (3) eliminations, isomeriza-

tions, and rearrangements; and (4) reactions that make or break

carbon–carbon bonds. Most of these reactions involve het-

erolytic bond cleavage or formation occurring through the addi-

tion of nucleophiles to electrophilic carbon atoms. Group-trans-

fer reactions therefore involve transfer of an electrophilic group

from one nucleophile to another.The main electrophilic groups

transferred are acyl groups, phosphoryl groups, and glycosyl

groups.The most common nucleophiles are amino, hydroxyl, im-

idazole, and sulfhydryl groups. Electrophiles participating in

metabolic reactions are protons, metal ions, carbonyl carbon

atoms, and cationic imines. Oxidation–reduction reactions

involve loss or gain of electrons. Oxidation at carbon usually

involves bond cleavage, with the ultimate loss by C of

the two bonding electrons through their transfer to an elec-

tron acceptor such as NAD



. The terminal electron acceptor

in aerobes is O

. Elimination reactions are those in which a

double bond is created from two saturated carbon cen-

ters with the loss of H

O, NH

, ROH, or RNH

. Dehydration

reactions are the most common eliminations. Isomerizations

involve shifts of double bonds within molecules. Rearrange-

ments are biochemically uncommon reactions in which in-

tramolecular bonds are broken and reformed to produce

new carbon skeletons. Reactions that make and break

bonds form the basis of both degradative and biosynthetic

C¬C

C“C

C¬H

CHAPTER SUMMARY

JWCL281_c16_557-592.qxd 6/10/10 11:52 AM Page 589

590 Chapter 16. Introduction to Metabolism

metabolism. In the synthetic direction, these reactions involve

addition of a nucleophilic carbanion to an electrophilic carbon

atom. The most common electrophilic carbon atom is the car-

bonyl carbon, whereas carbanions are usually generated by re-

moval of a proton from a carbon atom adjacent to a carbonyl

group or by decarboxylation of a -keto acid.

3 Experimental Approaches to the Study of Metabolism

Experimental approaches employed in elucidating metabolic

pathways include the use of metabolic inhibitors, growth stud-

ies, and biochemical genetics. Metabolic inhibitors block path-

ways at specific enzymatic steps. Identification of the resulting

intermediates indicates the course of the pathway. Mutations,

which occur naturally in genetic diseases or can be induced by

mutagens, X-rays, or genetic engineering, may also result in the

absence or inactivity of an enzyme. Modern genetic techniques

make it possible to express foreign genes in higher organisms

(transgenic animals) or inactivate (knock out) a gene and study

the effects of these changes on metabolism. When isotopic la-

bels are incorporated into metabolites and allowed to enter a

metabolic system, their paths may be traced from the distribu-

tion of label in the intermediates. NMR is a noninvasive tech-

nique that may be used to detect and study metabolites in vivo.

Studies on isolated organs,tissue slices,cells, and subcellular or-

ganelles have contributed enormously to our knowledge of the

localization of metabolic pathways. Systems biology endeavors

to quantitatively describe the properties and dynamics of bio-

logical networks as a whole through the integration of genomic,

transcriptomic, proteomic, and metabolomic information.

4 Thermodynamics of Phosphate Compounds Free en-

ergy is supplied to endergonic metabolic processes by the ATP

produced via exergonic metabolic processes.ATP’s 30.5 kJ ⴢ

mol

1

G°¿ of hydrolysis is intermediate between those of

“high-energy” metabolites such as phosphoenolpyruvate and

“low-energy” metabolites such as glucose-6-phosphate. The

“high-energy” phosphoryl groups are enzymatically trans-

ferred to ADP, and the resulting ATP, in a separate reaction,

phosphorylates “low-energy” compounds. ATP may also un-

dergo pyrophosphate cleavage to yield PP

, whose subsequent

hydrolysis adds further thermodynamic impetus to the reaction.

ATP is present in too short a supply to act as an energy reser-

voir. This function, in vertebrate nerve and muscle cells, is car-

ried out by phosphocreatine, which under low-ATP conditions

readily transfers its phosphoryl group to ADP to form ATP.

5 Oxidation–Reduction Reactions The half-reactions of

redox reactions may be physically separated to form two elec-

trochemical half-cells.The redox potential for the reduction of

A by B,

in which n electrons are transferred, is given by the Nernst

equation

The redox potential of such a reaction is related to the reduc-

tion potentials of its component half-reactions, and , by

If , then has a greater electron affinity than does

.The reduction potential scale is defined by arbitrarily set-

ting the reduction potential of the standard hydrogen half-cell

to zero. Redox reactions are of great metabolic importance.

For example, the oxidation of NADH yields 2.5 ATPs through

the mediation of the electron-transport chain.

6 Thermodynamics of Life Living organisms are open sys-

tems and therefore cannot be at equilibrium.They must contin-

uously dissipate free energy in order to carry out their various

functions and preserve their highly ordered structures. The

study of nonequilibrium thermodynamics has indicated that the

steady state, which living processes maintain, is the state of max-

imum efficiency under the constraints governing open systems.

Control mechanisms that regulate biological processes preserve

the steady state by regulating the activities of enzymes that are

strategically located in metabolic pathways.

n

 e

¢e  e

 e

¢e  ¢e° 

lna

red

][B

n

]

n

][B

red

]

n

 B

red

Δ A

red

 B

n

Metabolic Studies

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