Introduction to Enzymes and mechanism of

enzyme action
Assoc. Prof. Dr. Atif Amin Baig
Faculty of Medicine, Universiti Sultan Zainal Abidin, Malaysia
email: atifamin@unisza.edu.my
Recalls

1. What are lipids by definition

2. What are dietary lipids and nutrition status
3. Classification of lipids
4. Saturated and non saturated fats/fatty acids
5. Hydrozable and non hydrozable fats/fatty acids
6. Essential and non essential fats/fatty acids
7. Basic chemistry of fats/lipids
8. Basic chemistry of fatty acids/carboxylic acids
9. Derivation of compound and derived lipids
10.Abnormal lipid concentrations and body response
11.Cholesterol, good and bad lipid.
Learning Outcomes
To have understanding of:

1. What is a catalyst

2. What is the principle of catalyst action

3. Reaction kinetics

4. Activation energy

5. Reaction rate

6. Q10 Law

7. Reaction Order

8. What are enzymes?

9. Classification of enzymes?

10.Classes or enzymes and basis of nomenclature.

11.What are co-factors and coenzymes?

12.Basic characteristics of enzyme actions.

13.Active site and processes at active site

14.Transition state and Models of enzyme-substrate complex

Catalyst

Catalysts are substances that accelerate chemical reactions

without themselves being consumed in the process

catalysts emerge from the catalyzed reaction without being changed, even small amounts
are usually sufficient to cause a powerful acceleration of the reaction.
Principle of a catalyst

✤ Gibbs Energy?

✤ Spontaneous or non spontaneous reactions?

✤ Limitation?

✤ The change in free enthalpy G in a reaction indicates whether or not the reaction can
take place spontaneously in given conditions and how much work it can perform.

✤ it does not tell us anything about the rate of the reaction, i.e. Reaction Kinetics.
Principle of Catalyst

✤ Reaction Kinetics is explained by three characters:

1. Activation Energy

2. Reaction Rate

3. Reaction Order
Activation Energy

Ge = Average Chemical Potential Energy of Educt A

Gp = Average Chemical Potential Energy of Product B
Ga = Minimum initiation energy
Ea = Activation Energy
n = number of molecules
Q10 Law

Statistically, at 27 °C only two out of 109 molecules

reach this energy. At 37 °C, the figure is already four.

It states that the speed of biological processes approximately

Q10 Law doubles with an increase in temperature of 10 °C.
 Reaction Rate
The velocity v of a chemical reaction is determined experimentally by observing the change in the
concentration of an educt or product over time.

3 mmol of the educt A is converted per second and 3 mmol of the product B is formed per second in one liter of the solution.
This corresponds to a rate of:
v = 3 mM s–1 = 3 10–3 mol L–1 s–1
 Reaction Order

First Order Reaction Second Order Reaction

v is proportional to the concentration v is proportional to the product of the

[A] of this substance educt concentrations

✤ Reaction rates are influenced not only by the activation energy and the temperature, but also by the concentrations of the
reactants.
✤ k and k' are the rate constants of the reaction and depend on the external factors such as temperature.
Catalyst Principle

✤ The reason for the slow rates of most reactions involving organic
substances is the high activation energy

✤ It means that the reacting molecules have to reach activation

energy before they can react.

✤ In aqueous solution, a large proportion of the activation energy is

required to remove the hydration shells surrounding the educts.

✤ During the course of a reaction, resonance stabilized structures are

often temporarily suspended; this also requires energy.

✤ The highest point on the reaction coordinates corresponds to an

energetically unfavorable transition state of this type.
Catalyst Principle

A catalyst creates a new pathway for the

reaction. When all of the transition states
arising have a lower activation energy than
that of the uncatalyzed reaction

Since the starting points and end points are the

same in both routes, the change in the enthalpy
G of the reaction is not influenced by the
catalyst. The often-heard statement that “a catalyst reduces the
activation energy of a reaction” is not strictly correct, since
a completely different reaction takes place in the presence
of a catalyst than in uncatalyzed conditions. However, its
Catalysts are in principle not capable of activation energy is lower than in the un catalyzed reaction
altering the equilibrium state of the catalyzed
reaction.
What are Enzymes?
✤ Enzymes are Biological Catalysts

✤ They are involved in carrying and initiating

many metabolic processes

✤ They are NOT HORMONES

✤ They are Proteins OR

✤ They are special RNA molecules, i.e.

Ribozyme

✤ Enzymes of digestive tract and those found

in blood are present in inactive form called
zymogen or proezymes.

✤ Abzymes which are able to hydrolyze

proteins, DNA, RNA, or polysaccharides globular protein which functions as a
have been found in the sera of patients with biological catalyst, speeding up reaction
autoimmune and also viral pathologies
rate by lowering activation energy without
being affected by the reaction it catalyse
Active Site

✤ It has two parts:

1. Binding Site: It chooses the substrate and binds to its

active site.

2. Catalytic Site: It performs the catalytic action of the

enzyme.
 Iodine and Hydrogen Per Oxide
In the uncatalyzed reaction (at the top), an H2O2 molecule initially decays into H2O and atomic oxygen (O),
which then reacts with a second H2O2 molecule to form water and molecular oxygen (O2). The activation
energy Ea required for this reaction is relatively high, at 75 kJ mol–1.

The intermediate arising in this case is hypoiodide (OI–), which also

It increase the acceleration of the reaction by a
forms H2O and O2 with another H2O2 molecule. In this step, the I– ion is
factor of 2000, as the reaction rate depends
released and can once again take part in the reaction. The lower
activation energy of the reaction catalyzed by iodide (Ea = 56 kJ mol–1)
exponentially on Ea
Catalase and Hydrogen Per Oxide

✤ The activation energy of the enzyme catalyzed reaction is only 23 kJ mol–1

✤ Catalase is one of the most efficient enzymes and a single molecule can convert up to 108 (a hundred million) H2O2
molecules per second.
Enzyme Vs Catalyst?
Why Hormones are not Enzymes?
S.N. Enzymes Hormones
Mostly enzymes perform reactions at the place of origin i.e. in cells
1 Hormones perform activity at some distance away from the site of origin.
where they are produced.

2 Enzymes are biological catalyst. They catalyze the biological reactions. Hormones are not catalyst. They simply initiate biochemical reactions.

All enzymes are generally proteins. There are some exceptions like The hormones may be polypeptides, terpenoids, steroids, phenolics
3
ribozymes (RNA with catalytic activity). compounds or amines.

4 Enzymes are not translocate from one part to another part of cell. Most of the hormones show polar translocation.

As enzymes are catalyst, at the end of reaction they remain unchanged As hormones are not catalyst, they participate in biological reaction and
5
and can be reutilized. their chemical composition is changed and cannot be reutilized as such.

6 They are macromolecules with higher molecular weight. They have only low molecular weight.

7 They are non-diffusible through cell membrane. They are diffusible through cell membrane.

8 They either act intracellularly or carried by some ducts to another site. Generally carried by blood to a target organ.

9 It increases the rate of metabolic physiological processes. They may be either excitatory or inhibitory in their action.

10 They catalyze reversible reactions. Hormone controlled reactions are not reversible.

Deficiency or overproduction of hormone causes metabolic disorders or

11 Reaction rate increases with increase in their concentration up to a limit.
diseases.

Some hormones are quick acting, while some are slow acting with a lag
12 They act quickly.
period.

13 They are not used in metabolic functions. They are used up in metabolic functions.

14 They cannot regulate morphogenesis. Generally regulate morphogenesis, especially secondary sex character.

Examples: Examples:
– Oxidoreductases – Insulin,
15
– Transferases – Glucagon,
– Hydrolases – T3, T4,
Nomenclature of Enzymes (Classification of Enzymes)

✤ According to them each enzyme is assigned with two names:

✤ Trivial name (common name, recommended name).

✤ Systemic name ( official name ).

Trivial Name

✤ An enzyme is named according to the name of the substrate it catalyses.

✤ Some enzymes were named before a systematic way of naming enzyme was formed.

Example: pepsin, trypsin and rennin

✤ By adding suffix -ase at the end of the name of the substrate, enzymes are named.

✤ Enzyme for catalyzing the hydrolysis is termed as hydrolase.

Example :
Systemic Name

✤ Each enzyme is characterized by a code no.called Enzyme Code no. or EC

number and contain four Figure (digit) separated by a dot.

✤ e.g. EC m. n. o. p

✤ First digit represents the class;

✤ Second digit stands for subclass ;

✤ Third digit stands for the sub-sub class or subgroup;

✤ Fourth digit gives the serial number of the particular enzyme in the list.

✤ e.g. EC 2.7.1.1 for hexokinase.

Classes
of
Enzymes
According to IUBMB
Classification of Enzymes
✤ Intracellular enzymes are synthesized and retained in the cell for the use of cell itself.

They are found in the cytoplasm, nucleus, mitochondria and chloroplast.

Example :
Oxydoreductase catalyses biological oxidation.
Enzymes involved in reduction in the mitochondria.

✤ Extracellular enzymes are synthesized in the cell but secreted from the cell to work externally.

Example :

Digestive enzyme produced by the pancreas, are not used by the cells in the pancreas but are
transported to the duodenum.
Classification of Enzymes

1.Simple enzymes – only protein structure

2.Complex enzymes = protein structure + cofactor

What are Co-Factors

✤ Cofactors are nonprotein compounds.

Cofactor can be:

1) inorganic element: Zn2+, Mn2+, Mg2+, Fe2+, Cu2+, etc,.

2) organic molecule

a) coenzymes are slightly bound to the enzyme, undergo a chemical change and are released: NAD(P)+,
FAD, coenzyme Q, etc,.

b) prosthetic groups are tightly bound to the enzyme and remain associated with enzyme during reaction:
heme, etc,.
Basic Characteristics of Enzyme Action

✤ Enzymes speed up the reaction by lowering the activation energy of the reaction.

✤ Their presence does not effect the nature and properties of end product.

✤ They are highly specific in their action that is each enzyme can catalyze one kind of
substrate.

✤ Small amount of enzymes can accelerate chemical reactions.

✤ Enzymes are sensitive to change in pH, temperature and substrate concentration.

✤ Turnover number is defined as the number of substrate molecules transformed per minute
by one enzyme molecule.

✤ Transient State is achieved to overcome energy of activation

Mechanism of Enzyme Action

The catalytic efficiency of enzymes is explained by two perspectives:

1. Thermodynamic changes
2. Processes at the active site
Transition State
✤ The transition state of a chemical reaction is a particular configuration along
the reaction coordinate. It is defined as the state corresponding to the highest potential
energy along this reaction coordinate

✤ At this point, assuming a perfectly irreversible reaction, colliding reactant molecules

always go on to form products

✤ The transition state cannot be captured or directly observed; the population at that
point is zero
Thermodynamic Changes

✤ Same as explained before for catalysts.

Active Site and Processes at Active Site

Acid-
Covalent Base
catalysis
catalysis

Catalysis
Catalysis
by
by strain
proximity
Covalent Catalysis
✤ The enzyme contains a reactive group, usually a nucleophilic residue which reacts with
the substrate through a nucleophilic attack.

Initiation Transition State Termination

Acid Base Catalysis
✤ Mostly undertaken by oxido- reductases enzyme.

✤ acceleration of a chemical reaction by the addition of an acid or a base

✤ acid or base itself not being consumed in the reaction.

✤ The catalytic reaction may be acid-specific (acid catalysis), Eg: decomposition of the sugar sucrose into
glucose and fructose in sulfuric acid

✤ The catalytic reaction may be base-specific (base catalysis), as in the addition of hydrogen cyanide to
aldehydes and ketones in the presence of sodium hydroxide.

✤ The mechanism of acid- and base-catalyzed reactions is explained in terms of the Bronsted- Lowry
concept of acids and bases as one in which there is an initial transfer of protons from an acidic catalyst
to the reactant or from the reactant to a basic catalyst.

✤ In terms of the Lewis theory of acids and bases, the reaction entails sharing of an electron pair donated
by a base catalyst or accepted by an acid catalyst.
Catalysis by Bond Strain
✤ This is the principal effect of induced fit binding

✤ The affinity of the enzyme to the transition state is greater than to the substrate itself

✤ This induces structural rearrangements which strain substrate bonds into a position
closer to the conformation of the transition state

✤ It will be lowering the energy difference between the substrate and transition state and
helping catalyze the reaction.

✤ The strain effect is, in fact, a ground state destabilization effect, rather than transition
state stabilization effect

✤ In addition to bond strain in the substrate, bond strain may also be induced within the
enzyme itself to activate residues in the active site.
 Substrate, bound substrate, and transition state conformations of lysozyme

The substrate, on binding, is distorted from the half chair conformation of the hexose ring (because of the steric hindrance with amino
acids of the protein forcing the equatorial c6 to be in the axial position) into the chair conformation
Lock and Key Model

✤ Proposed by EMIL FISCHER in

1894.

✤ Lock and key hypothesis assumes

the active site of an enzymes are
rigid in its shape.

✤ There is no change in the active

site before and after a chemical
reaction.
Induced Fit Model

✤ Proposed by Danial Kosh Land in 1958

Catalysis by Proximity

Proximity and orientation effects

✤ Proximity: Reaction between bound molecules doesn't require an improbable collision of 2 molecules --
they're already in "contact" (increases the local concentration of reactants)

✤ Orientation: Reactants are not only near each other on enzyme, they're oriented in optimal position to
react, so the improbability of colliding in correct orientation is taken care of
Human Enzymes
Thank you