CHAPTER V

THE ENZYMES

INTRODUCTION
Early man observed the results of catalytic activity when he found fruit juices fermenting,
milk souring and meat spoiling. Nineteenth-century scientists noted that reactions that occur with
ease in the systems might never take place when the same reactor are stirred and brewed together
in a test tube. Enzymes as these vital forces, are now called are inseparable from living cells.
They are in fact protein molecules that exhibit extraordinary catalytic powers greater than that of
synthetic catalysts. They exhibit high degree of specificity and they function in dilute. aqueous
solutions under very mild conditions, temperature and pH. There are close to 2,000 known
enzymes but we shall not catalog them all. Rather, we shall survey the properties and
characteristics common to most enzymes.

LEARNING OUTCOMES
At the end of this unit, you should be able to:
 discuss the general concept of chemical catalysis
 describe the chemical nature of enzymes
 enumerate the different types of enzymes, nomenclature and examples
 discuss the factors that affect enzyme activity
 explain enzyme kinetics using the Michaelis Menten model
 explain and illustrate how KM and V can be used to characterize competitive
and non-competitive inhibition
 discuss the significance of coenzymes to living systems
 give examples of coenzymes

LEARNING CONTENTS
1. CATALYSTS
Most of us are quite sentimental about old notes and letters. We keep them with loving
care and try to relive the past through them every once in a while. Look at one of the oldest
letters you have that was written on white paper. Most likely it has begun to turn pale brown. If
you press it with a hot iron it will scorch to a darker brown. And if you leave the hot iron on it
long enough, it will even catch fire.
The paper which is actually cellulose began to burn as it was produced by plants. The
burning was not obvious; the change was so slow that there was no heat or light evident to
indicate that a reaction was really taking place. The heat of the iron merely hastened the change.
Catalysts speed up chemical reactions, too. They alter the speed of reactions without changing
the products that would have been formed in its absence. Of course, the iron did exactly that.
But there is something special about the catalyst. It is not used up as it changes the speed of the
reaction. It is not permanently changed to anything else. It is available to function all over once
again.
The effect of the catalyst is to lower the activation energy required for the reaction. In
our illustration in Fig. 5-1, less energy is needed to begin the reaction when a catalyst is present
and

Figure 5.1. How catalysts work.

less is needed for the reaction to continue. The more the energy is lowered the faster the rate of
conversion of reactants to products.
2. ENZYMES
Most of the chemical reactions that occur in our bodies would not ordinarily occur at a
high enough rate at body temperature. But the body produce special substances called enzymes
which act as biological catalysts. Enzymes are the largest and most highly specialized cells of
proteins.
Enzymes catalyze biochemical reactions in a manner that is analogous to the action of
catalysts, that is, they lower the activation energy of a reaction thus increasing reaction rates
about a million-fold. It is said that without the enzymes in our digestive tract it would take us
about 50 years to digest a single meal.

3. ENZYME NOMENCLATURE
Consider this example
RCH2OH + coenzyme -----> RCHO + coenzyme-H2
 To name the enzyme that catalyzes the above reaction we first name the substance the
enzyme acts on, in this case alcohol, then we indicate what the enzyme does and then we add the
suffix - ase thus the name of the enzyme for the above reaction is alcohol dehydrogenase
The enzyme molecule may consist of a fairly simple single polypeptide or it may be a
more complex molecule composed of several polypeptides and other nonprotein parts. There are
some special terms used in enzymology and it will be helpful if we define them first before we
continue. Take the case of a complex enzyme molecule cited earlier which consists of protein
part and a non-protein portion. The protein part of such an enzyme is called the apoenzyme and
the non-protein part, the smaller portion, the coenzyme or prosthetic group. Together the
apoenzyme and the coenzyme makeup the holoenzyme as illustrated in Fig 5-2

Figure 5-2. Enzyme parts

Sometimes metal ions like Mg2+, .Zn 2+, Fe3+ are necessary for enzyme action. Such
entities are called activators or cofactors. Zymogen is the term applied in the inactive form of
the enzyme. This is typical of digestive enzymes. They are often secreted in their zymogenic
form (trypsinogen, pepsinogen), transported to the stomach and converted to their active forms.
The substrate is the substance on which the enzyme acts upon.
4. ENZYME SPECIFICITY AND CLASSIFICATION
Enzymes exhibit a high degree of specificity. They are very particular about the reaction
they accelerate. Some speed up the reaction of one substance only (absolute specificity) others
hasten a reaction common to a group substance that are closely related chemically (group
specificity).
In 1961, the Commission on Enzymes of the International Union of Biochemists
proposed a classification of the 2000 or so enzymes based on the types of reactions they catalyze
into six major classes (Table 5-1). Examples of each class are listed in Table 5-2.
Table 5-1. Six major classes of enzymes
Table 5.2 Example of Enzymes
5. FACTORS AFFECTING ENZYME ACTIVITY
Enzymes need to maintain the integrity of their native structure to remain biologically
active. Enzymes being proteins will be affected by factors such as pH, temperatures, solvents,
and salt concentration..

Figure 5.3 - Effect of enzyme on the reaction rate

 Effect of pH

Figure 5.4 Effect of pH on enzyme activity

Extremes in pH can change the secondary or tertiary structures of an enzyme. This may
alter the geometry of the protein molecule and decrease enzyme activity if not lose it all together.
Fig. 5-4 indicates that each enzyme has an optimum pH for maximum activity.
  Temperature

Figure 5-4 Effect of temperature on enzyme activity.

Many body enzymes are most active near or at body temperature. Above this range,
enzymes begin to denature and reaction rate decreases (Fig 5-4). This partly explains our
uncomfortable feeling during high fever. Low temperatures also cause a decrease in enzyme
activity which is usually restored if the temperature is again raised. This effect of low
temperature is the basis of food preservation by refrigeration. The enzyme-catalyzed reactions
that cause food spoilage are slowed or stopped at low temperature.
 Effect of Substrate Concentration
When considering the effect of substrate concentration on the rate of enzyme catalysis we
find that the situation is different from that of a one-step reaction A---> B , as shown in Fig. 5-5.
 Figure 5-5 Effect of substrate concentration on reaction rate

Whereas the reaction rate is directly proportional to concentration of the reactant in a one
step reaction, there is a maximum rate (Vmax) in the case of first order catalyzed reaction. It
occurs because the enzyme becomes saturated with high concentration of substrate molecules.
This behavioral pattern may be explained by the following reaction sequence
E +S ↔E-S complex --→E + P
Where E and S are the enzyme and substrate respectively and E-S complex is the
necessary intermediate that must be formed before the product (P) is produced and the original
enzyme E is regenerated. Aside from the saturation phenomenon, the formation of the E-S
complex in an enzyme catalyzed reaction can also explain the following:
a. the means by which enzymes lower activation energy.
b. the specificity of an enzyme to its substrate - since E-S is a true molecule, then
specific chemical bonds are required between E and S which only the same E
and its true S can satisfy.
c. The relative amounts of E with respect to its S- since E is regenerated and can
be used again and again. Only a small amount of E is necessary to transform a
large amount of S to P.
The relation between reaction velocity and substrate concentration is expressed
mathematically by the Michaelis-Menten equation . The Michaelis constant, Km. is characteristic
of the particular enzyme.

where V = any observed velocity Km = Michaelis constant

6. MODELS FOR THE ACTIVE SITE

Although an enzyme typically has more than 100 amino acid residues in its structure,
only a small number comes directly in contact with the substrate. They constitute what is called
the active site. The substrate attaches itself to it during a reaction. The active site is usually a
cleft or a crevice in the molecule's exterior and its shape or configuration is especially designed
for its specific substrate.
 The Lock and Key Model
Emil Fischer first suggested that a substrate fits its enzyme the way a key fits its lock.
The configuration of the lock is specific for only one key, no other keys will turn the lock as
shown in Fig. 5-6.
 Figure 5-6 The Lock and Key model
The native structure of the enzyme must be intact for the active site to have the correct
configuration. At least three points of specific interactions are required between the substrate and
the active site to ensure the Stereospecificity of enzyme action.
 Induced Fit Model
To explain the action of some other enzymes, Daniel Koshland proposed a less rigid
structure and therefore involves an active site that changes in conformation upon Substrate
binding to produce a precise enzyme-substrate. It is seen in Fig 5-7.

Figure 5.7. Induced Fit Model

4. ENZYME INHIBITION
Certain chemicals affect enzyme activity. They are called inhibitors or anti-enzymes.
These inhibitors are helpful in the study of enzyme specificity and the nature of the active site.
They are also useful tools in the elucidation of metabolic pathways. The action of many poisons
and drugs is used to show their ability to inhibit specific enzymes.
 Competitive Inhibition
When an enzyme can be made to accept a substitute for its true substrate, we have a case
of competitive inhibition. A competitive inhibitor acts by occupying the same site on the
enzyme that the substrate-occupies, that is, both substrate and inhibitor compete for the active
site. The effect of this type of inhibitor can be overcome with an increase in the concentration
of the substrate. Since a competitive inhibitor is in competition with the substrate molecules,
increasing the latter would also increase its chances for the active site as it diminish the chances
of enzyme-inhibitor interaction. This effect as well as the effect of the inhibitor on Vmax and
Km is shown in Fig. 5-8.

Figure 5.8 Effects of Competitive Inhibition

Competitive inhibition is the one most commonly utilized pharmaceutically. Molecules
that are competitive inhibitors of enzymes resemble one of the normal substrates of an enzyme.
An example is methotrexate, which resembles the folate substrate of the enzyme dihydrofolate
reductase (DHFR). This enzyme normally catalyzes the reduction of folate, an important reaction
in the metabolism of nucleotides. When the drug methotrexate is present, some of the enzyme
binds to it instead of folate and during the time methotrexate is bound, the enzyme is inactive and
unable to bind folate. Thus, the enzyme is inhibited. Notably, the binding site on DHFR for
methotrexate is the active site, the same place that folate would normally bind. As a result,
methotrexate ‘competes’ with folate for binding to the enzyme. The more methotrexate there
is, the more effectively it competes with folate for the enzyme’s active site. Conversely, the more
folate there is, the less of an effect methotrexate has on the enzyme because folate outcompetes
it.
Originally developed as a cancer drug, methotrexate stops cancerous cells from rapidly
multiplying and spreading by blocking their access to folate, a form of vitamin B. Blocking
folate fights cancer.
 Figure 5.9 Structure of methotrexate and folic acid
The sulfa drug is another example. It prevents bacterial growth by competitive inhibition.
Bacteria uses para amino benzoic acid (PABA) in the synthesis of folic acid which is necessary
for bacterial growth. The structure of sulfanilamide closely resembles that of PABA and the
sulfanilamide molecules compete for the active site on the bacterial enzyme. In effect folic acid
biosynthesis is inhibited thus suppressing bacterial growth. Studies of competitive inhibition in
microbes have led to the discovery of an entire battery of drugs.

Figure 5.10 Structure of PABA and Sulfonamide

 Noncompetitive Inhibition
A noncompetitive inhibitor reacts with a site on the enzyme that is different from the
active site. The binding of the non-competitive inhibitor changes the properties of the active
site, and the enzyme loses its catalytic power. Since this kind of inhibitor does not compete
with substrate molecules, the Inhibition is not overcome by large concentrations of substrate
molecules. The result of the presence of a noncompetitive inhibitor is that Vmax is decreased and
K M remains constant. This relationship is shown in Figure 5. 11 below.
 Figure 5. 11. Effects of noncompetitive inhibitor
Inhibition of enzymatic activities by heavy metal ions like Hg2+, Pb2+ and Ag+ is often
given as examples of this type. Heavy metals form mercaptides with sulfhydryl (-SH) groups of
enzymes:
E-SH + Ag+ ↔ E-S-Ag + H+
Because of the reversibility of mercaptide formation inhibition can be relieved by
removal of the heavy metal ion. In the treatment of lead poisoning for example raw egg white is
given as antidote. Egg white is a water soluble albumin which forms lead-proteinate precipitate
which effectively binds the heavy metal ion and gets it out of circulation.
 Allosteric Regulation
Allosteric regulation of enzyme activity is the most common method of controlling
catalysis in living cells. It is considered as a form of noncompetitive inhibition. It usually
involves an oligomeric enzyme (more than one polypeptide protein) which contains sites at
which substrate molecules can bind (active site) and sites at which inhibitor molecules can
bind (allosteric sites). There is an interaction between the substrate and the inhibitor such that
when an inhibitor occupies an allosteric site the active site which is intended for the substrate
changes conformation. When the change effects an increase in the rate of the reaction, the-
inhibitor also called allosteric effector is properly referred to as a positive effector or allosteric
activator. When reaction rate is decreased, the allosteric effector is called a negative effector or
allosteric inhibitor.

Figure 12. Allosteric Regulation

 The regulation of allosteric enzymes is an effective mechanism by which enzymatic
activities can be controlled to ensure that biological processes remain coordinated.
8. VITAMINS AS COENZYMES
Many biochemical reactions require the presence of enzymes that contain more than
amino acid residues. Prominent among the nonprotein organic moieties of these enzymes are the
vitamin B complex which are called coenzymes. Table 5.3 summarizes the metabolic functions
of these coenzymes.
Table 5-3. Vitamins, their coenzymes and enzymatic functions

Our bodies cannot synthesize these vitamins and they must be present in our diets in trace
amounts for proper metabolic activities. It goes without saying that the complex enzymes are
inactive without their coenzymes. This may be the molecular basis for the appearance of specific
deficiency diseases when vitamins are lacking in the diet.
SUMMARY
Enzymes are the largest group of biological proteins and they catalyze almost every
reaction that occurs in living organisms.
Enzymes just like any other catalyst hasten biochemical reactions by lowering the
activation energy of its reactant molecule known as substrate. But unlike other catalysts,
enzymes have a high degree of specificity, are efficient only within a narrow range of pH and at
an optimum temperature,
In an enzyme catalyzed reaction increasing the substrate concentration increases the
reaction rate until the active sites of the enzyme are saturated such that reaction rate levels off at
a Vmax value even at higher [S] concentrations. The [S] at which the reaction rate is half that of
Vmax is called the KM (Michaelis constant). Each enzyme displays a characteristics KM for its
substrate. The relationsthip between observed velocity v, Vmax, and KM is mathematically
expressed as the Michaelis-Menten equation
The two types of inhibition discussed are called competitive and noncompetitive. A
competitive inhibitor lowers the velocity of an enzyme-catalyzed reaction by competing with the
true substrate for the active site to form an enzyme inhibitor complex that is non-productive
Noncompetitive inhibitor on the otherhand interacts not with the active site but with another
region of the enzyme which nonetheless causes changes in the conformation of the enzyme
rendering it inactive. Allosterism is a special kind of non competitive Inhibition that is widely
observed as an effective regulation of enzymatic reactions in living organisms.
Vitamins are organic substances required in small amounts as coenzymes of some
complex enzymes. They are not synthesized in the body and must therefore be supplied in our
diets. Complex enzymes without their Vitamin coenzymes are inactive

KEY TERMS/CONCEPTS

Enzymes
Apoenzyme
Coenzyme
Active site
Positive effector
Negative effector

FLEXIBLE TEACHING LEARNING MODALITY (FTLM)

 Module, Exercises, Edmodo

TEACHINGLEARNING ACTIVTIES
Activity 1
1. Enzyme Practice. Label the diagram

ASSESSMENT TASK
I. Answer the questions briefly
1. Define enzyme activity.
2. What effect does an enzyme have on the energy of activation of a reaction?
3. Explain the term optimal pH of an enzyme.
4 and 5. The optimal temperature for a given enzyme is 37 °C. What will probably happen to the
enzyme and its activity when (a) the temperature is lowered to 0 °C and (b) the
temperature is raised to 100 °C?

LEARNING MATERIALS AND RESOURCES

 Journal Article
 A review of saliva: Normal composition, flow, and function. -
https://www.thejpd.org/article/S0022-3913(01)54032-9/fulltext
DOI:https://doi.org/10.1067/mpr.2001.113778

 When is an enzyme not a protein? -

https://www.chemistryworld.com/features/when-is-an-enzyme-not-a-protein/
9471.article

REFERENCES
Berg, J.M., Tymoczko, J.L. and Stryer, L. (2011) Biochemistry. Freemann, 7th edition, retrieved
at http://www.whfreeman.com

Brown, P. (2009). Quick Reference to Wound Care, James and Bartelt. Publishing

Chulay, M. (2011).ACCN Essentials of Critical Care Nursing. McGraw-Hill Publishing

Hein, Morris (2005). Introduction to General, Organic and Biochemistry, John Wiley and Sons

Jones, Evangeline. (2011). Manual of Practical Medical Biochemistry.

Moore, John (2008). Chemistry: The Molecular Science . Thomson Brooks

Nelson, D.L. & Cox, M.M. Lehninger Principles of Biochemistry. Freeman, 6th edition
http://bcs.whfreeman..com./lehninger6e/#t_824263/

Silberberg, M. (2010). Priciples of General Chemistry. Mc Graw Hill

Voet, J. and Judith Voet. (2011) Biochemistry, 4th Edition. Wiley and Sons
Osmosis: https://www.youtube.com/watch?v=tpBAmzQ_pUE

Active transport : https://www.youtube.com/watch?v=eDeCgTRFCbA

Buffers in the blood https://www.youtube.com/watch?v=lDmn8zeJbQs

Diabetes: An Overview: https://www.diabetes.org.uk/diabetes-the-basics

Overview of Carbohydrate Metabolism Disorders
https://www.msdmanuals.com/home/children-s-health-issues/hereditary-metabolic-disorders/
overview-of-carbohydrate-metabolism-disorders

Protein Function and Malfunction in Cells https://www.ncbi.nlm.nih.gov/books/NBK21297/

A review of saliva: Normal composition, flow, and function. -

https://www.thejpd.org/article/S0022-3913(01)54032-9/fulltext
DOI:https://doi.org/10.1067/mpr.2001.113778

When is an enzyme not a protein? - https://www.chemistryworld.com/features/when-is-an-

enzyme-not-a-protein/9471.article

A case study: Obesity and the metabolic syndrome. A three-pronged program, targeting
education, close follow-up and a dietary supplement, significantly decrease body weight and
body fat - DOI: 10.15761/IOD.1000143

The Birth Control Pill.- https://embryo.asu.edu/pages/birth-control-pill

Genetic medicines: treatment strategies for hereditary disorders - Timothy P. O'Connor &
Ronald G. Crystal Nature Reviews Genetics volume 7, pages261–276 (2006

Energy and Life - http://www.BioLerner.com

Energy and Life: The Transformation of Energy in Living Organisms -

https://study.com/academy/lesson/energy-and-life-the-transformation-of-energy-in-living-
organisms.html