CHAPTER 6

Basic Concepts of Enzyme Action

The activity of an enzyme is responsible for the glow of the luminescent

jellyfish. The enzyme aequorin catalyzes the oxidation of a compound by
oxygen in the presence of calcium to release CO2 and light
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 Chapter 6: Outline

6.1 Enzymes Are Powerful and Highly Specific Catalysts

6.2 Many Enzymes Require Cofactors for Activity
6.3 Gibbs Free Energy Is a Useful Thermodynamic
Function for Understanding Enzymes
6.4 Enzymes Facilitate the Formation of the Transition
State

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 Section 6.1 Enzymes Are Powerful and
Highly Specific Catalysts
• Enzymes are protein catalysts that can accelerate the rate of a
reaction by factors of as much as a million or more.
• Even a reaction as simple as adding a molecule of water to carbon
dioxide requires an enzyme, carbonic anhydrase, in red blood cells.

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 Proteolytic Enzymes Illustrate the Range of
Enzyme Specificity
• Reactants in enzyme-catalyzed
Hydrolysis reactions, the breaking of a
reactions are called substrates. chemical bond by the addition of a water
molecule, are prominent in biochemistry.
• Proteolytic enzymes catalyze the
hydrolysis of peptide bonds.

The proteolytic enzymes trypsin and papain have different degrees of specificity.

Trypsin cleaves on the carboxyl Thrombin cleaves Arg–Gly bonds in particular

side of arginine and lysine residues sequences only. 4
 There Are Six Seven Major Classes of Enzymes

1. Oxidoreductases catalyze oxidation–reduction reactions.

2. Transferases move functional groups between molecules.
3. Hydrolyases cleave bonds with the addition of water.
4. Lyases remove atoms to form double bonds or add atoms
to double bonds.
5. Isomerases move functional groups within a molecule.
6. Ligases join two molecules at the expense of ATP.
7. Translocases are enzymes that catalyze the movement of
ions or molecules across membranes or their separation
within membranes.

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 Enzyme classes: examples
Oxidoreductase
Alcohol dehydrogenase: breakdown of alcohol
CH3CH2OH + NAD+ → CH3CHO + NADH + H+

Transferases
DNA methyltransferase: add methyl groups to
DNA

Hydrolases
Acetylcholinesterase: breakdown of acetylcholine,
a neurotransmitter

Lyases
carbonic anhydrase: maintain acid-base balance
and CO2 transport
HCO3- + H+ à CO2 + H2O
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 Enzyme classes: examples
Isomerases How is cis retinal made from vitamin A?
Retinol isomerase:
All-trans-retinol (Vit A) à 11-cis-retinol

Ligases
Glutamine synthetase

Translocases
Translocase of outer mitochondrial membrane 40 homolog (yeast) or TOMM40.
In humans, certain alleles of this gene have been associated with an increased
risk of developing late-onset Alzheimer's Disease. One study has found that
TOMM40 risk alleles appears twice as often in people with Alzheimer's disease
than those without it.
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 Section 6.2 Many Enzymes Require Cofactors for Activity
• Cofactors are small
molecules that some
enzymes require for
activity. The two main
classes of cofactors are
coenzymes—organic
molecules derived from
vitamins—and metals.

• Tightly bound coenzymes

are called prosthetic
groups.

• A complete catalyticaly
active form of enzyme is
the holoenzyme. Without
the cofactor, the enzyme is
called an apoenzyme.

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Section 6.3 Gibbs Free Energy is a Useful Thermodynamic
Function for Understanding Enzymes
Learning objective 1: Describe the relationship between the enzyme
catalysis of a reaction, the thermodynamics of the reaction, and the
formation of the transition state.
• Free energy (G) is a measure of energy capable of doing work. The
change in free energy when a reaction occurs is symbolized by ΔG.
• Exergonic reactions occur spontaneously, ΔG is negative.
• Endergonic reactions are non-spontaneous, ΔG is positive.
• If a reaction is at equilibrium, there is no net change in the amount of
reactant or product, ΔG = 0.
• The ΔG of a reaction depends only on the free energy difference
between reactants and products and is independent of how the
reaction occurs.
• The ΔG of a reaction provides no information about the rate of the
reaction.
• Enzymes do not alter the ΔG of a reaction.

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 The Standard Free-Energy Change of a Reaction
Is Related to the Equilibrium Constant
For the reaction
the free energy change is given by

where ΔGo is the standard free energy, R is the gas constant, T is

298 kelvin, and the brackets denote concentration.

ΔGo¢ symbolizes the standard free energy change at pH 7.

At equilibrium, ΔG = 0, so for the reaction in question,

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 ΔG of the reaction can be larger than,
smaller than, or equal to ΔGo¢
The more exergonic a reaction is, the larger the equilibrium constant will be.
The more endergonic a reaction is, the smaller the equilibrium constant will be.

Refresher…
A kilojoule (kJ) is equal to
1000 J.
A joule (J) is the amount of
energy needed to apply a 1-
newton force over a
distance of 1 meter.
A kilocalorie (kcal) is equal
to 1000 cal.
A 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.
1 kJ = 0.239 kcal

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 Enzymes Alter the Reaction Rate but Not
the Reaction Equilibrium
The reaction equilibrium is determined only by the free energy difference
between the products and reactants. Enzymes cannot alter this difference.

Figure 6.2 Enzymes accelerate the reaction rate. The same equilibrium
point is reached, but much more quickly in the presence of an enzyme.
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 Section 6.4 Enzymes Facilitate the
Formation of the Transition State
Learning objective 2: Explain the relation between the transition state and
the active site of an enzyme and list the characteristics of active sites.
• A chemical reaction proceeds through a
transition state, a molecular form that is
no longer substrate but not yet product.
S ⇌ X‡ → P

• ‡ designates the transition state.

• The energy required to form the transition

state from the substrate is called the
activation energy, symbolized by ΔG‡.
ΔG‡ = GX‡ − GS

• Enzymes facilitate the formation of the

transition state. Figure 6.3 Enzymes decrease the activation
energy. Enzymes accelerate reactions by
decreasing ΔG‡, the free energy of activation.

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The Formation of an Enzyme–Substrate Complex
Is the First Step in Enzymatic Catalysis
• Enzymes bring substrates together to form an enzyme–
substrate complex on a particular region of the enzyme
called the active site.
• The interaction of the enzyme and substrates at the active
site promotes the formation of the transition state.

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 The Active Sites of Enzymes Have Some Common Features
Figure 6.4 Active sites may include
1. The active site is a three- distant residues.
dimensional cleft or crevice
created by amino acids from
different parts of the primary
structure.
2. The active site constitutes a small
portion of the enzyme volume.
3. Active sites create unique
microenvironments.
4. The interaction of the enzyme and Ribbon diagram of the enzyme lysozyme with several
components of the active site shown in color.
substrate at the active site
involves multiple weak
interactions.
5. Enzyme specificity depends on
the molecular architecture at the A schematic representation of the primary structure
active site. of lysozyme shows that the active site is composed
of residues that come from different parts of the
polypeptide chain. 15
 Enzyme active sites are highly dynamic
• Enzymes do not interact with their substrates like a lock and key.

• Rather, the enzyme changes shape upon substrate binding, a

phenomenon called induced fit.

Old model: Lock and key, too One of accepted models today:
simplistic induced fit

Figure 6.5 Lock-and-key model. Here, the active

Figure 6.6 Induced-fit model. Here, the enzyme changes
site of the unbound enzyme is complementary in
shape on substrate binding. The active site forms a shape
shape to the substrate.
complementary to the substrate only after the substrate has been
bound. 16
 The Binding Energy Between Enzyme and
Substrate Is Important for Catalysis

• Binding energy is the free energy released upon

interaction of the enzyme and substrate.
• Binding energy is greatest when the enzyme interacts with
the transition state, thus facilitating the formation of the
transition state.

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Transition-State Analogs Are Potent Inhibitors of Enzymes
• The racemization of proline proceeds through a transition state in which the α
carbon is trigonal.
• Proline racemase, a bacterial enzyme, converts L-proline to D-proline. Proline
has a tetrahedral a-carbon.
• Pyrrole 2-carboxylate has trigonal geometry (essentially flat) just like the
enzyme’s transition state. Because of this similarity, pyrrole 2-carboxylate is a
transition-state analog and a potent inhibitor of proline racemase. It binds the
enzyme 160 times tighter than the substrate.

DID YOU KNOW?

Racemization is the conversion of one enantiomer into
another—in regard to proline, the interconversion of the L
and D isomers.
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