Enzymes Are Powerful and Highly Specific Catalysts

I. The Molecular Design of Life
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 by-products are rare in enzyme-catalyzed reactions,
in contrast with uncatalyzed ones.
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).
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).
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.
8.1.2. 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.
8.1.3. 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.
I. The Molecular Design of Life
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
Table 8.1. Rate enhancement by selected enzymes
Enzyme
Nonenzymatic half-life Uncatalyzed rate (k un, Catalyzed rate (k
-1
s -1)
cat, s )
Rate enhancement (k cat/
k un)
OMP decarboxylase
78,000,000 years
2.8 × 10-16
39
1.4 × 1017
Staphylococcal nuclease
130,000 years
1.7 × 10-13
95
5.6 × 1014
AMP nucleosidase
69,000 years
1.0 × 10-11
60
6.0 × 1012
Carboxypeptidase A
7.3 years
3.0 × 10-9
578
1.9 × 1011
Ketosteroid isomerase
7 weeks
1.7 × 10-7
66,000
3.9 × 1011
Triose phosphate isomerase 1.9 days
4.3 × 10-6
4,300
1.0 × 109
Chorismate mutase
7.4 hours
2.6 × 10-5
50
1.9 × 106
Carbonic anhydrase
5 seconds
1.3 × 10-1
1 × 106
7.7 × 106
Abbreviations: OMP, orotidine monophosphate; AMP, adenosine monophosphate.
Source: After A. Radzicka and R. Wofenden. Science 267 (1995):90 93.
I. The Molecular Design of Life
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
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.
I. The Molecular Design of Life
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
Table 8.2. Enzyme cofactors
Cofactor
Enzyme
Coenzyme
Thiamine pyrophosphate
Pyruvate dehydrogenase
Flavin adenine nucleotide
Monoamine oxidase
Nicotinamide adenine dinucleotide Lactate dehydrogenase
Pyridoxal phosphate
Glycogen phosphorylase
Coenzyme A (CoA)
Acetyl CoA carboxylase
Biotin
Pyruvate carboxylase
5 -Deoxyadenosyl cobalamin
Methylmalonyl mutase
Tetrahydrofolate
Metal
I. The Molecular Design of Life
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
Thymidylate synthase
Zn2+
Carbonic anhydrase
Zn2+
Carboxypeptidase
Mg2+
EcoRV
Mg2+
Hexokinase
Ni2+
Mo
Se
Urease
Mn2+
Nitrate reductase
Glutathione peroxidase
Superoxide dismutase
K+
Propionyl CoA carboxylase
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.
I. The Molecular Design of Life
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
Table 8.3. Six major classes of enzymes
Class
Type of reaction
1. Oxidoreductases Oxidation-reduction
2. Transferases
Group transfer
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases
Example
Lactate dehydrogenase
Nucleoside monophosphate kinase (NMP
kinase)
Chymotrypsin
Hydrolysis reactions (transfer of functional
groups to water)
Addition or removal of groups to form
Fumarase
double bonds
Isomerization (intramolecular group
Triose phosphate isomerase
transfer)
Ligation of two substrates at the expense of Aminoacyl-tRNA synthetase
ATP hydrolysis
Chapter
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