Chemistry 20

Chapters 15
Enzymes
Enzymes: as a catalyst, an enzyme increases the rate of a reaction by changing the way a
reaction takes place, but is itself not changed at the end of the reaction. An unanalyzed
reaction is a cell may take place eventually, but not at a rate fast enough for survival. For
example, the hydrolysis of proteins in our diet would eventually occur without a catalyst, but
not fast enough to meet the body’s requirements for amino acids. The chemical reactions in
our cells must occur at incredibly fast rates under the mild conditions pf pH 7.4 and a body
temperature of 37°C. To do this, biological catalysts known as enzymes catalyze nearly all the
chemical reactions that take place in the body. As catalysts, enzymes lower the activation
energy for the reaction (activation energy is the minimum energy necessary to cause a
chemical reaction to occur). As a result, less energy is required to convert reactant molecules
to products, which allows more reacting molecules to form product.

Eact

Eact

Note: The vast majority of all known enzymes are globular proteins. However, proteins are
not the only biological catalysts.

Note: Most of enzymes are extremely specific (catalyze specific reactions). Some enzymes
are localized according to the need for specific reaction (for example, digestive enzymes,
which catalyze the hydrolysis of proteins, are located in the secretions of the stomach and
pancreas).

Names of enzymes: the names of enzymes describe the compound or the reaction that is
catalyzed. The actual names of enzymes are derived by replacing the end of the name of the
reaction or reacting compound with the suffix “-ase”. For example, an oxidase catalyzes an
oxidation reaction, and a dehydrogenase removes hydrogen atoms. The compound amylose is
hydrolyzed by the enzyme amylase, and a lipid is hydrolyzed by a lipase. Some early known
enzymes use names that end in the suffix “-in”, such as papain found in papaya, rennin found
in milk, and pepsin and trypsin, enzymes that catalyze the hydrolysis of proteins. There are
six classes of enzymes:

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Enzyme action: Nearly enzymes are globular proteins. Each has a unique three-dimensional
shape that recognizes and binds a small group of reacting molecules, which are called
substrates. The tertiary structure of an enzyme plays an important role in how that enzyme
catalyzes reactions.

Active site: in a catalyzed reaction, an enzyme must first bind to a substrate in away that
favors catalysis. A typical enzyme is much larger that its substrate. However, within its large
tertiary structure, there is a region called the active site where the enzyme binds a substrate or
substrates and catalyzes the reaction. This active site is often a small pocket that closely fits
the structure of the substrate. Within the active site, the side chains of amino acids bind the
substrate with hydrogen bonds, salt bridges, or hydrophobic attractions. The active site of a
particular enzyme fits the shape of only a few types of substrates, which makes enzymes very
specific about the type of substrate they bind.

Enzyme catalyzed reaction: the proper alignment of a substrate within the active site forms
an enzyme-substrate (ES) complex. This combination of enzyme and substrate provides an
alternative pathway for the reaction that has a lower activation energy. Within the active site,
the amino acid side chains take part in catalyzing the chemical reaction. As soon as the
catalyzed reaction is complete, the products are quickly released from the enzyme so it can
bind to a new substrate molecule. We can write the catalyzed reaction of an enzyme (E) with
a substrate (S) to form product (P) as follows:

E (Enzyme) + S (Substrate) ES (Complex) E (Enzyme) + P (Product)

Let’s consider the hydrolysis of sucrose by sucrase (enzyme). When sucrose binds to the
active site of sucrase, the glycosidic bond of sucrose is placed into a geometry favorable for
reaction. The amino acid side chains catalyze the cleavage of the sucrose to give the products
glucose and fructose. Because the structures of the products are no longer attracted to the
active site, they are releases and the sucrase binds another sucrose substrate.

Sucrase (E) + Sucrose (S) ↔ Sucrase-Sucrose complex → Sucrase (E) + glucose (P2) + Fructose (P2)
There are two models for formation of ES Complex:

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1. Lock-and-Key model: in this theory, the active site is described as having a rigid,
nonflexible shape. Thus only those substrates with shapes that fit exactly into the active site
are able to bind with enzyme. The shape of the active site is analogous to a lock, and the
proper substrate is the key that fits into the lock.

Problems: This model is too restrictive. Enzyme molecules are in a dynamic state, not a static
one. There are constant motions within them, so that active site has some flexibility. Also, if
the fit between substrate and active site is prefect, there would be no reason for the reaction to
occur, as the enzyme-substrate complex would be too stable! From X-ray diffraction, we
know that the size and shape of the active site cavity change when the substrate enters.

2. Induced-Fit model: certain enzymes have a broader range of activity that the lock and key
model allows. In the induced-fit model, enzyme structure is flexible, not rigid. There is an
interaction between both the enzyme and substrate. The active site adjusts to fit the shape of
the substrate more closely. At the same time the substrate adjusts its shape to better adapt to
the geometry of the active site. As a result, the reacting section of the substrate becomes
aligned exactly with the groups in the active site that catalyze the reaction. A different
substrate could not induce these structural changes and no catalysis would occur.

Factors affecting enzyme activity: the activity of an enzyme describes how fast an enzyme
catalyzed the reaction that converts a substrate to product. This activity is strongly affected by
reaction conditions, which include the temperature, pH, concentration of the substrate or
enzyme and the presence of inhibitors.

1. Temperature: enzymes are very sensitive to temperature. At low temperature, most

enzymes show little activity because there is not a sufficient amount of energy for the
catalyzed reaction to take place. At higher temperatures, enzyme activity increases as reacting

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molecules move faster to cause more collisions with enzymes. Enzymes are most active at
optimum temperature, which is 37°C or body temperature for most enzymes. At
temperature above 50°C, the tertiary structure and thus the shape of most proteins is
destroyed, which causes a loss in enzyme activity. For this reason, equipment in hospitals and
laboratories is sterilized in autoclaves where the high temperatures denature the enzyme in
harmful bacteria.

2. pH: enzymes are most active at their optimum pH, the pH that maintains the proper tertiary
structure of the protein. A pH value above or below the optimum pH causes a change in he
three-dimensional structure of the enzyme that disrupts the active site. As a result the enzyme
cannot bind substrate properly and no reaction occurs. Enzymes in most cells have optimum
pH values at physiological pH values around 7.4. However, enzymes in the stomach have a
low optimum pH because they hydrolyze proteins at the acidic pH in the stomach. For
example, pepsin, a digestive enzyme in the stomach, has an optimum pH of 2. Between meals,
the pH in the stomach is 4 or 5 and pepsin shows little or no digestive activity. When food
enters the stomach, the secretion of HCl lowers the pH to about 2, which actives pepsin. If
small changes in pH are corrected, an enzyme can regain its structure and activity. However,
large variations from optimum pH permanently destroy the structure of the enzyme.

3. Substrate and enzyme concentration: in any catalyzed reaction, the substrate must first
bind with the enzyme to form the substrate-enzyme complex. When enzyme concentration
increases, the rate of catalyzed reaction increases because we produce more substrate-enzyme
complex. When enzyme concentration is kept constant, increasing the substrate concentration
increases the rate of the catalyzed reaction as long as there are more enzyme molecules
present than substrate molecules. At some point an increase in substrate concentration
saturates the enzyme. With all the available enzyme molecules bonded to substrate, the rate of
the catalyzed reaction reaches its maximum. Adding more substrate molecules cannot
increase the rate further.

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 Maximum activity

4. Enzyme inhibition: many kinds of molecules called inhibitors cause enzymes to lose
catalytic activity. Although inhibitors act differently, they are all prevent the active site from
binding with a substrate. Inhibition can be competitive or noncompetitive.

Competitive inhibitor: a competitive inhibitor has a structure that is so similar to the

substrate it competes for the active site on the enzyme. As long as the inhibitor occupies the
active site, the substrate cannot bind to the enzyme and no reaction takes place. As long as the
concentration of the inhibitor is substantial, there is a loss of enzyme activity. However,
increasing the substrate concentration displaces more of the inhibitor molecules. As more
enzyme molecules bind to substrate (ES), enzyme activity is regained.

Noncompetitive inhibitor: the structure of a noncompetitive inhibitor does not resemble the
substrate and does not compete for the active site. Instead, a noncompetitive inhibitor binds to
a site on the enzyme that is not the active site. When the noncompetitive inhibitor is bonded to
the enzyme, the shape of the enzyme is distorted. Inhibition occurs because the substrate
cannot fit in the active site, or it does not fit properly. Without the proper alignment of
substrate with the amino acid side groups, no catalysis can take place. Because a
noncompetitive inhibitor is not competing for the active site, the addition of more substrate
does not reverse this type of inhibition. Example of noncompetitive inhibitors are the heavy
metal ions Pb2+, Ag+, and Hg2+ that bond with amino acid side groups such as –COO-, or –
OH. Catalytic activity is restored when chemical reagents remove the inhibitors. Antibiotics
produced by bacteria, mold, or yeast are inhibitors used to stop bacterial growth. For example,
penicillin inhibits an enzyme needed for the formation of cell walls in bacteria, but not human
cell membranes. With an incomplete wall, bacteria cannot survive, and the infection is
stopped. However, some bacteria are resistant to penicillin because they produce
penicillinase, an enzyme that breaks down penicillin. Over the years, derivatives of penicillin
to which bacteria have not yet become resistant have been produced.

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 Inhibitor

Site

Enzyme cofactors: enzymes are known as simple enzyme (apoenzyme) when their function
forms consist only of proteins with tertiary structure. However, many enzymes require small
molecules or metal ions called cofactors to catalyze reactions properly. When the cofactor is
a small organic molecule, it is known as a coenzyme. If an enzyme requires a cofactor,
neither the protein structure nor the cofactor alone has catalytic activity.

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 protein Simple enzyme

protein Metal ion Enzyme + Cofactor

Organic
protein molecules Enzyme + Cofactor
(coenzyme)

Metal ions: many enzymes must contain a metal ion to carry out their catalytic activity. The
metal ions are bonded to one or more of the amino acid side chains. The metal ions from the
minerals that we obtain from foods in our diet have various functions in catalysis. Ions such as
Fe2+ and Cu2+ are used by oxidases because they lose or gain electrons in oxidation or
reduction reactions. Other metals ions such as Zn2+ stabilize the amino acid side chains during
hydrolysis reactions.

Vitamins and coenzymes: vitamins are organic molecules that are essential for normal health
and growth. They are required in trace amounts and must be obtained from the diet because
they are not synthesized in the body. Vitamins are classified into two groups by solubility:
water-soluble and fat-soluble.

Water-soluble vitamins: have polar groups such as –OH and –COOH, which make them
soluble in the aqueous environment of the cells. Most water-soluble enzymes are not stored in
the body and excess amounts are eliminated in the urine each day. Therefore, the water-
soluble vitamins must be in the foods of our daily diets. Because many water-soluble vitamins
are easily destroyed by heat, oxygen, and ultraviolet light, care must be taken in food
preparation, processing, and storage. The water-soluble vitamins are required by many
enzymes as cofactors to carry out certain aspects of catalytic action. The coenzymes do not
remain bonded to a particular enzyme, but are used over and over again by different enzymes
to facilitate an enzyme-catalyzed reaction. Thus, only small amounts of coenzymes are
required in the cells.

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Fat-soluble vitamins: are nonpolar compounds, which are soluble in the fat (lipid)
components of the body such as fat deposits and cell membranes. The fat-soluble vitamins A,
D, E, and K are not involved as coenzymes, but they are important in processes such as
vision, formation of bone, protection from oxidation, and proper blood clotting. Because the
fat-soluble vitamins are stored in the body and not eliminated, it is possible to take too much,
which could be toxic.

Enzyme regulation:

1. Feedback control: Enzymes are often regulated by environmental conditions. Feedback

control is an enzyme regulation process in which formation of a product inhibits an earlier
reaction in the sequence. The reaction product of one enzyme may control the activity of
another (in the following reaction, D, may inhibit the activity of enzyme E1 (by competitive
are noncompetitive , or some other type of inhibition)).

feedback inhibition

E1 E2 E3
A B C D

2. Proenzymes (Zymogens): some enzymes are manufactured by the body in an inactive

form. To take them active, a small part of their polypeptide chain must be removed. These
inactive forms of enzymes are called proenzymes or zymogens. After excess polypeptide
chain is removed, the enzyme becomes active. For example, trypsin (an important catalyst for
the digestion of the proteins) is manufactured as the inactive molecule trypsinogen (a
zymogen). When a fragment containing six amino acid residues is removed from the N-
terminal end of trypsinogen, the molecule becomes a fully active trypsin molecule.

3. Allosterism: sometimes regulation take place by means of an event that occurs site other
than the active site but that eventually affects the active site. This type of interaction is called
allosterism, and any enzyme regulated by this mechanism is called an allosteric enzyme. If a
substance binds noncovalently and reversibly to a site other the active site, it may affect the
enzyme in either of two ways: 1. It may inhibit enzyme action (negative modulation) or 2. It
may stimulate enzyme action (positive modulation).

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4. Protein modification: the activity of an enzyme may also be controlled by protein
modification. The modification is usually a change in the primary structure, typically by
addition of a functional group covalently bound to the apoenzyme. For example, the enzyme
pyruvate kinase (PK) from the liver is inactive when it is phosphorylated. When the activity
of PK is not needed, it is phosphorylated (to PKP) by a protein kinase using ATP as substrate
as well as a source of energy. When the system wants to turn on PK activity, the phosphate
group (Pi) is removed by another enzyme (phosphatase), which renders PK active.

ATP AD P

active inactive
kinase
PK PKP
phosphatase

Pi H2 O

5. Isoenzymes: another type of regulation of enzyme activity occurs when the same enzyme
appears in different forms in different tissues. These different forms of the same enzyme are
called isoenzymes. Isoenzymes perform the same function but have different combinations of
subunits and thus different quaternary structure.

Enzymes in medicine: most enzymes are confined within the cells of the body. However,
small amounts of them can also be found in body fluids such as blood, and urine. The level of
enzyme activity in these fluids can easily be monitored. This information can prove extremely
useful: Abnormal activity (either high or low) of particular enzymes in various body fluids
signals either the onset of certain diseases or their progression.

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