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Enzymes: Basic Concepts and Kinetics

Enzymes: Basic Concepts and Kinetics

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The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



8.1. Enzymes Are Powerful and Highly Specific Catalysts

Enzymes accelerate reactions by factors of as much as a million or more (Table 8.1). Indeed, most

reactions in biological systems do not take place at perceptible rates in the absence of enzymes. Even a

reaction as simple as the hydration of carbon dioxide is catalyzed by an enzyme - namely, carbonic

anhydrase (Section 9.2). The transfer of CO2 from the tissues into the blood and then to the alveolar air

would be less complete in the absence of this enzyme. In fact, carbonic anhydrase is one of the fastest

enzymes known. Each enzyme molecule can hydrate 106 molecules of CO2 per second. This catalyzed

reaction is 107 times as fast as the uncatalyzed one. We will consider the mechanism of carbonic

anhydrase catalysis in Chapter 9. Enzymes are highly specific both in the reactions that they catalyze and

in their choice of reactants, which are called substrates. An enzyme usually catalyzes a single chemical

reaction or a set of closely related reactions. Side reactions leading to the wasteful formation of byproducts are rare in enzyme-catalyzed reactions, in contrast with uncatalyzed ones.



Enzyme



OMP decarboxylase

Staphylococcal

nuclease

AMP nucleosidase

Carboxypeptidase A

Ketosteroid isomerase

Triose phosphate

isomerase

Chorismate mutase

Carbonic anhydrase



Nonenzymatic

half-life



Uncatalyzed rate

(kun, s-1)



Catalyzed rate

(kcat, s-1)



Rate enhancement

(kcat/kun)



78,000,000 years

130,000 years



2.8 × 10-16

1.7 × 10-13



39

95



1.4 × 1017

5.6 × 1014



69,000 years

7.3 years

7 weeks

1.9 days



1.0 × 10-11

3.0 × 10-9

1.7 × 10-7

4.3 × 10-6



60

578

66,000

4,300



6.0 × 1012

1.9 × 1011

3.9 × 1011

1.0 × 109



7.4 hours

5 seconds



2.6 × 10-5

1.3 × 10-1



50

1 × 106



1.9 × 106

7.7 × 106



Abbreviations: OMP, orotidine monophosphate; AMP, adenosine monophosphate.

Source: After A. Radzicka and R. Wofenden. Science 267 (1995):90-93.

Table 8.1. Rate enhancement by selected enzymes



Let us consider proteolytic enzymes as an example. In vivo, these enzymes catalyze proteolysis, the

hydrolysis of a peptide bond.



Most proteolytic enzymes also catalyze a different but related reaction in vitro - namely, the hydrolysis of

an ester bond. Such reactions are more easily monitored than is proteolysis and are useful in experimental

investigations of these enzymes (Section 9.1.2).



8.2



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



Proteolytic enzymes differ markedly in their degree of substrate specificity. Subtilisin, which is found in

certain bacteria, is quite undiscriminating: it will cleave any peptide bond with little regard to the identity

of the adjacent side chains. Trypsin, a digestive enzyme, is quite specific and catalyzes the splitting of

peptide bonds only on the carboxyl side of lysine and arginine residues (Figure 8.1A). Thrombin, an

enzyme that participates in blood clotting, is even more specific than trypsin. It catalyzes the hydrolysis

of Arg-Gly bonds in particular peptide sequences only (Figure 8.1B).



Figure 8.1. Enzyme Specificity. (A) Trypsin cleaves on the carboxyl side of arginine and lysine residues, whereas (B) thrombin

cleaves Arg-Gly bonds in particular sequences specifically.



DNA polymerase I, a template-directed enzyme (Section 27.2), is another highly specific catalyst. It adds

nucleotides to a DNA strand that is being synthesized, in a sequence determined by the sequence of

nucleotides in another DNA strand that serves as a template. DNA polymerase I is remarkably precise in

carrying out the instructions given by the template. It inserts the wrong nucleotide into a new DNA strand

less than one in a million times.

The specificity of an enzyme is due to the precise interaction of the substrate with the enzyme. This

precision is a result of the intricate three-dimensional structure of the enzyme protein.



8.1.1. Many Enzymes Require Cofactors for Activity

The catalytic activity of many enzymes depends on the presence of small molecules termed cofactors,

although the precise role varies with the cofactor and the enzyme. Such an enzyme without its cofactor is

referred to as an apoenzyme; the complete, catalytically active enzyme is called a holoenzyme.



Cofactors can be subdivided into two groups: metals and small organic molecules (Table 8.2). The

enzyme carbonic anhydrase, for example, requires Zn2+ for its activity (Section 9.2.1). Glycogen

phosphorylase (Section 21.1.5), which mobilizes glycogen for energy, requires the small organic

molecule pyridoxal phosphate (PLP).

Cofactors that are small organic molecules are called coenzymes. Often derived from vitamins,

coenzymes can be either tightly or loosely bound to the enzyme. If tightly bound, they are called

prosthetic groups. Loosely associated coenzymes are more like cosubstrates because they bind to and are

released from the enzyme just as substrates and products are. The use of the same coenzyme by a variety

of enzymes and their source in vitamins sets coenzymes apart from normal substrates, however. Enzymes

that use the same coenzyme are usually mechanistically similar. In Chapter 9, we will examine the

mechanistic importance of cofactors to enzyme activity. A more detailed discussion of coenzyme

vitamins can be found in Section 8.6.



8.3



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



Cofactor



Enzyme



Coenzyme

Thiamine pyrophosphate

Flavin adenine nucleotide

Nicotinamide adenine dinucleotide

Pyridoxal phosphate

Coenzyme A (CoA)

Biotin



Pyruvate dehydrogenase

Monoamine oxidase

Lactate dehydrogenase

Glycogen phosphorylase

Acetyl CoA carboxylase

Pyruvate carboxylase

Methylmalonyl mutase



5 -Deoxyadenosyl cobalamin

Tetrahydrofolate

Metal

Zn2+

Zn2+

Mg2+

Mg2+

Ni2+

Mo

Se

Mn2+

K+



Thymidylate synthase

Carbonic anhydrase

Carboxypeptidase

EcoRV

Hexokinase

Urease

Nitrate reductase

Glutathione peroxidase

Superoxide dismutase

Propionyl CoA carboxylase



Table 8.2. Enzyme cofactors



8.1.2. Enzymes May Transform Energy from One Form into

Another

In many biochemical reactions, the energy of the reactants is converted with high efficiency into a

different form. For example, in photosynthesis, light energy is converted into chemical-bond energy

through an ion gradient. In mitochondria, the free energy contained in small molecules derived from food

is converted first into the free energy of an ion gradient and then into a different currency, the free energy

of adenosine triphosphate. Enzymes may then use the chemical-bond energy of ATP in many ways. The

enzyme myosin converts the energy of ATP into the mechanical energy of contracting muscles. Pumps in

the membranes of cells and organelles, which can be thought of as enzymes that move substrates rather

than chemically altering them, create chemical and electrical gradients by using the energy of ATP to

transport molecules and ions (Figure 8.2). The molecular mechanisms of these energy-transducing

enzymes are being unraveled. We will see in subsequent chapters how unidirectional cycles of discrete

steps - binding, chemical transformation, and release - lead to the conversion of one form of energy into

another.



8.4



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



Figure 8.2. An Energy-Transforming Enzyme. Ca2+ ATPase uses the energy of ATP hydrolysis to transport Ca2+ across the

membrane, generating a Ca2+ gradient.



8.1.3. Enzymes Are Classified on the Basis of the Types of

Reactions That They Catalyze

Many enzymes have common names that provide little information about the reactions that they catalyze.

For example, a proteolytic enzyme secreted by the pancreas is called trypsin. Most other enzymes are

named for their substrates and for the reactions that they catalyze, with the suffix "ase" added. Thus, an

ATPase is an enzyme that breaks down ATP, whereas ATP synthase is an enzyme that synthesizes ATP.

To bring some consistency to the classification of enzymes, in 1964 the International Union of

Biochemistry established an Enzyme Commission to develop a nomenclature for enzymes. Reactions

were divided into six major groups numbered 1 through 6 (Table 8.3). These groups were subdivided and

further subdivided, so that a four-digit number preceded by the letters EC for Enzyme Commission could

precisely identify all enzymes.

Consider as an example nucleoside monophosphate (NMP) kinase, an enzyme that we will examine in

detail in the next chapter (Section 9.4). It catalyzes the following reaction:



NMP kinase transfers a phosphoryl group from ATP to NMP to form a nucleoside diphosphate (NDP)

and ADP. Consequently, it is a transferase, or member of group 2. Many groups in addition to phosphoryl

groups, such as sugars and carbon units, can be transferred. Transferases that shift a phosphoryl group are

designated 2.7. Various functional groups can accept the phosphoryl group. If a phosphate is the acceptor,

the transferase is designated 2.7.4. The final number designates the acceptor more precisely. In regard to

NMP kinase, a nucleoside monophosphate is the acceptor, and the enzyme's designation is EC 2.7.4.4.

Although the common names are used routinely, the classification number is used when the precise

identity of the enzyme might be ambiguous.



8.5



The Molecuclar Design of Life



Class



Chapter 8: Enzymes - Basic Concepts and Kinetics



Type of reaction



Example



1. Oxidoreductases Oxidation-reduction

2. Transferases

Group transfer

3. Hydrolases

4. Lyases

5. Isomerases

6. Ligases



Lactate dehydrogenase

Nucleoside monophosphate kinase (NMP

kinase)

Hydrolysis reactions (transfer of Chymotrypsin

functional groups to water)

Addition or removal of groups Fumarase

to form double bonds

Isomerization (intramolecular Triose phosphate isomerase

group transfer)

Ligation of two substrates at the Aminoacyl-tRNA synthetase

expense of ATP hydrolysis

Table 8.3. Six major classes of enzymes



8.6



Chapter



16

9

9

18

16

29



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



8.2. Free Energy Is a Useful Thermodynamic Function for

Understanding Enzymes

Some of the principles of thermodynamics were introduced in Chapter 1 - notably the idea of free energy

(G). To fully understand how enzymes operate, we need to consider two thermodynamic properties of the

reaction: (1) the free-energy difference (ΔG) between the products and reactants and (2) the energy

required to initiate the conversion of reactants to products. The former determines whether the reaction

will be spontaneous, whereas the later determines the rate of the reaction. Enzymes affect only the later.

First, we will consider the thermodynamics of reactions and then, in Section 8.3, the rates of reactions.



8.2.1. The Free-Energy Change Provides Information About the

Spontaneity but Not the Rate of a Reaction

As stated in Section 1.3.3, the free-energy change of a reaction (ΔG) tells us if the reaction can occur

spontaneously:

1. A reaction can occur spontaneously only if ΔG is negative. Such reactions are said to be exergonic.

2. A system is at equilibrium and no net change can take place if ΔG is zero.

3. A reaction cannot occur spontaneously if ΔG is positive. An input of free energy is required to drive

such a reaction. These reactions are termed endergonic.

Two additional points need to be emphasized. The ΔG of a reaction depends only on the free energy of

the products (the final state) minus the free energy of the reactants (the initial state). The ΔG of a reaction

is independent of the path (or molecular mechanism) of the transformation. The mechanism of a reaction

has no effect on ΔG. For example, the ΔG for the oxidation of glucose to CO2 and H2O is the same

whether it occurs by combustion in vitro or by a series of enzyme-catalyzed steps in a cell. The ΔG

provides no information about the rate of a reaction. A negative ΔG indicates that a reaction can occur

spontaneously, but it does not signify whether it will proceed at a perceptible rate. As will be discussed

shortly (Section 8.3), the rate of a reaction depends on the free energy of activation (ΔG ), which is

largely unrelated to the ΔG of the reaction.



8.2.2. The Standard Free-Energy Change of a Reaction Is

Related to the Equilibrium Constant

As for any reaction, we need to be able to determine ΔG for an enzymecatalyzed reaction in order to

know whether the reaction is spontaneous or an input of energy is required. To determine this important

thermodynamic parameter, we need to take into account the nature of both the reactants and the products

as well as their concentrations.

Consider the reaction

The ΔG of this reaction is given by



in which ΔG° is the standard free-energy change, R is the gas constant, T is the absolute temperature, and

[A], [B], [C], and [D] are the molar concentrations (more precisely, the activities) of the reactants. ΔG° is

the freeenergy change for this reaction under standard conditions - that is, when each of the reactants A,

B, C, and D is present at a concentration of 1.0 M (for a gas, the standard state is usually chosen to be 1

atmosphere). Thus, the ΔG of a reaction depends on the nature of the reactants (expressed in the ΔG°

term of equation 1) and on their concentrations (expressed in the logarithmic term of equation 1).



8.7



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



Units of energyA calorie (cal) is equivalent to the amount of heat required to raise the

temperature of 1 gram of water from 14.5°C to 15.5°C.

A kilocalorie (kcal) is equal to 1000 cal.

A joule (J) is the amount of energy needed to apply a 1-newton force over a

distance of 1 meter.

A kilojoule (kJ) is equal to 1000 J.

1 kcal = 4.184 kJ

A convention has been adopted to simplify free-energy calculations for biochemical reactions. The

standard state is defined as having a pH of 7. Consequently, when H+ is a reactant, its activity has the

value 1 (corresponding to a pH of 7) in equations 1 and 4 (below). The activity of water also is taken to be

1 in these equations. The standard free-energy change at pH 7, denoted by the symbol ΔG°’ will be used

throughout this book. The kilocalorie (abbreviated kcal) and the kilojoule (kJ) will be used as the units of

energy. One kilocalorie is equivalent to 4.184 kilojoules.

The relation between the standard free energy and the equilibrium constant of a reaction can be readily

derived. This equation is important because it displays the energetic relation between products and

reactants in terms of their concentrations. At equilibrium, ΔG = 0. Equation 1 then becomes



and so



The equilibrium constant under standard conditions, K’ eq, is defined as



Substituting equation 4 into equation 3 gives



which can be rearranged to give

Substituting R = 1.987 × 10-3 kcal mol-1 deg-1 and T = 298 K (corresponding to 25°C) gives

where ΔG°’ is here expressed in kilocalories per mole because of the choice of the units for R in equation

7. Thus, the standard free energy and the equilibrium constant of a reaction are related by a simple

expression. For example, an equilibrium constant of 10 gives a standard free-energy change of -1.36 kcal

mol-1 (-5.69 kJ mol-1) at 25°C (Table 8.4). Note that, for each 10-fold change in the equilibrium constant,

the ΔG°’ changes by 1.36 kcal mol-1 (5.69 kJ mol-1).



8.8



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



ΔG°

K eq



kcal mol-1



kJ mol-1



10-5

10-4

10-3

10-2

10-1

1

10

102

103

104

105



6.82

5.46

4.09

2.73

1.36

0

-1.36

-2.73

-4.09

-5.46

-6.82



28.53

22.84

17.11

11.42

5.69

0

-5.69

-11.42

-17.11

-22.84

-28.53



Table 8.4. Relation between ΔG°’ and K’eq (at 25°C)



As an example, let us calculate ΔG°’ and ΔG for the isomerization of dihydroxyacetone phosphate

(DHAP) to glyceraldehyde 3-phosphate (GAP). This reaction takes place in glycolysis (Section 16.1.4).

At equilibrium, the ratio of GAP to DHAP is 0.0475 at 25°C (298 K) and pH 7. Hence, K’eq = 0.0475.

The standard free-energy change for this reaction is then calculated from equation 6:



Under these conditions, the reaction is endergonic. DHAP will not spontaneously convert to GAP.

Now let us calculate ΔG for this reaction when the initial concentration of DHAP is 2 × 10-4 M and the

initial concentration of GAP is 3 × 10-6 M. Substituting these values into equation 1 gives



8.9



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



This negative value for the ΔG indicates that the isomerization of DHAP to GAP is exergonic and can

occur spontaneously when these species are present at the aforestated concentrations. Note that ΔG for

this reaction is negative, although ΔGo’ is positive. It is important to stress that whether the ΔG for a

reaction is larger, smaller, or the same as ΔG°’ depends on the concentrations of the reactants and

products. The criterion of spontaneity for a reaction is ΔG, not ΔG°’. This point is important because

reactions that are not spontaneous based on ΔG°’ can be made spontaneous by adjusting the

concentrations of reactants and products. This principle is the basis of the coupling of reactions to form

metabolic pathways (Chapter 14).



8.2.3. Enzymes Alter Only the Reaction Rate and Not the

Reaction Equilibrium

Because enzymes are such superb catalysts, it is tempting to ascribe to them powers that they do not have.

An enzyme cannot alter the laws of thermodynamics and consequently cannot alter the equilibrium of a

chemical reaction. This inability means that an enzyme accelerates the forward and reverse reactions by

precisely the same factor. Consider the interconversion of A and B. Suppose that, in the absence of

enzyme, the forward rate constant (kF) is 10-4 s-1 and the reverse rate constant (kR) is 10-6 s-1. The

equilibrium constant K is given by the ratio of these rate constants:



The equilibrium concentration of B is 100 times that of A, whether or not enzyme is present. However, it

might take considerable time to approach this equilibrium without enzyme, whereas equilibrium would be

attained rapidly in the presence of a suitable enzyme. Enzymes accelerate the attainment of equilibria but

do not shift their positions. The equilibrium position is a function only of the free-energy difference

between reactants and products.



8.10



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



8.3. Enzymes Accelerate Reactions by Facilitating the

Formation of the Transition State

The free-energy difference between reactants and products accounts for the equilibrium of the reaction,

but enzymes accelerate how quickly this equilibrium is attained. How can we explain the rate

enhancement in terms of thermodynamics? To do so, we have to consider not the end points of the

reaction but the chemical pathway between the end points.

A chemical reaction of substrate S to form product P goes through a transition state S that has a higher

free energy than does either S or P. The double dagger denotes a thermodynamic property of the

transition state. The transition state is the most seldom occupied species along the reaction pathway

because it is the one with the highest free energy. The difference in free energy between the transition

state and the substrate is called the Gibbs free energy of activation or simply the activation energy,

symbolized by ΔG , as mentioned in Section 8.2.1 (Figure 8.3).



Figure 8.3. Enzymes Decrease the Activation Energy. Enzymes accelerate reactions by decreasing ΔG , the free energy of

activation.



Note that the energy of activation, or ΔG , does not enter into the final ΔG calculation for the reaction,

because the energy input required to reach the transition state is returned when the transition state forms

the product. The activation-energy barrier immediately suggests how enzymes enhance reaction rate

without altering ΔG of the reaction: enzymes function to lower the activation energy, or, in other words,

enzymes facilitate the formation of the transition state.

One approach to understanding how enzymes achieve this facilitation is to assume that the transition state

(S ) and the substrate (S) are in equilibrium.



in which K is the equilibrium constant for the formation of S , and v is the rate of formation of product

from S .

The rate of the reaction is proportional to the concentration of S :



because only S can be converted into product. The concentration of S is in turn related to the free

energy difference between S and S, because these two chemical species are assumed to be in

equilibrium; the greater the difference between these two states, the smaller the amount of S .

Because the reaction rate is proportional to the concentration of S , and the concentration of S depends

on ΔG , the rate of reaction V depends on ΔG . Specifically,



8.11



The Molecuclar Design of Life



Chapter 8: Enzymes - Basic Concepts and Kinetics



In this equation, k is Boltzmann's constant, and h is Planck's constant. The value of kT/h at 25°C is 6.2 ×

1012 s-1. Suppose that the free energy of activation is 6.82 kcal mol-1 (28.53 kJ mol-1). The ratio [S ]/[S] is

then 10-5 (see Table 8.4). If we assume for simplicity's sake that [S] = 1 M, then the reaction rate V is 6.2

× 107 s-1. If ΔG were lowered by 1.36 kcal mol-1 (5.69 kJ mol-1), the ratio [S ]/[S] is then 10-4, and the

reaction rate would be 6.2 × 108 s-1. As Table 8.4 shows, a decrease of 1.36 kcal mol-1 in ΔG yields a

tenfold larger V. A relatively small decrease in ΔG (20% in this particular reaction) results in a much

greater increase in V.

"I think that enzymes are molecules that are complementary in structure to the

activated complexes of the reactions that they catalyze, that is, to the molecular

configuration that is intermediate between the reacting substances and the

products of reaction for these catalyzed processes. The attraction of the enzyme

molecule for the activated complex would thus lead to a decrease in its energy

and hence to a decrease in the energy of activation of the reaction and to an

increase in the rate of reaction."

- Linus Pauling

Nature 161(1948):707

Thus, we see the key to how enzymes operate: Enzymes accelerate reactions by decreasing ΔG , the

activation energy. The combination of substrate and enzyme creates a new reaction pathway whose

transition-state energy is lower than that of the reaction in the absence of enzyme (see Figure 8.3). The

lower activation energy means that more molecules have the required energy to reach the transition state.

Decreasing the activation barrier is analogous to lowering the height of a high-jump bar; more athletes

will be able to clear the bar. The essence of catalysis is specific binding of the transition state.



8.3.1. The Formation of an Enzyme-Substrate Complex Is the

First Step in Enzymatic Catalysis

Much of the catalytic power of enzymes comes from their bringing substrates together in favorable

orientations to promote the formation of the transition states in enzyme-substrate (ES) complexes. The

substrates are bound to a specific region of the enzyme called the active site. Most enzymes are highly

selective in the substrates that they bind. Indeed, the catalytic specificity of enzymes depends in part on

the specificity of binding.

What is the evidence for the existence of an enzyme-substrate complex?

1. The first clue was the observation that, at a constant concentration of enzyme, the reaction rate

increases with increasing substrate concentration until a maximal velocity is reached (Figure 8.4). In

contrast, uncatalyzed reactions do not show this saturation effect. The fact that an enzyme-catalyzed

reaction has a maximal velocity suggests the formation of a discrete ES complex. At a sufficiently high

substrate concentration, all the catalytic sites are filled and so the reaction rate cannot increase. Although

indirect, this is the most general evidence for the existence of ES complexes.

2. X-ray crystallography has provided high-resolution images of substrates and substrate analogs bound

to the active sites of many enzymes (Figure 8.5). In Chapter 9, we will take a close look at several of

these complexes. X-ray studies carried out at low temperatures (to slow reactions down) are providing

revealing views of enzyme-substrate complexes and their subsequent reactions. A new technique, timeresolved crystallography, depends on cocrystallizing a photolabile substrate analog with the enzyme. The

substrate analog can be converted to substrate light, and images of the enzyme-substrate complex are

obtained in a fraction of a second by scanning the crystal with intense, polychromatic x-rays from a

synchrotron.

3. The spectroscopic characteristics of many enzymes and substrates change on formation of an ES

complex. These changes are particularly striking if the enzyme contains a colored prosthetic group.

Tryptophan synthetase, a bacterial enzyme that contains a pyridoxal phosphate (PLP) prosthetic group,

provides a nice illustration. This enzyme catalyzes the synthesis of L-tryptophan from L-serine and indolederivative. The addition of L-serine to the enzyme produces a marked increase in the fluorescence of the



8.12



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