Download 1 Enzymes: The Biological Catalysts Definition: Enzymes are

Enzymes: The Biological Catalysts
Definition:
Enzymes are biologic polymers that catalyze biochemical reactions. The vast
majority of enzymes are proteins; however there are some catalytic RNA
molecules called ribozymes.
Enzymes are effective and highly specific catalysts:
1. Enzymes catalyze the conversion of one or more compounds called
substrates into one or more compounds called products.
2. Enzymes accelerate (speed up) the rate of reaction by a factor of at
least 106 .
3. Like all catalysts, enzymes are neither, consumed or altered after
catalysis.
4. Enzymes are highly selective catalysts; they are specific for the type
of reaction catalyzed and for a single substrate or a set of closely
related substrates.
RNA as an Enzyme
Although enzymes are considered to be proteins, enzyme activity has recently
been found in ribonucleic acid (RNA) in certain organisms.
Enzyme Catalysis:
The enzyme (E) has a reactive site (called active centre) which binds the
reactant (or substrate (S)) by non-covalent interactions. The reaction starts by
substrate binding to the enzyme to form ES complex, then reaction proceeds
with the formation of the product (P):
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Why are Enzymes Specific?
Enzymes are very specific, and it was suggested by Emil Fischer in 1894 that
this was because both the enzyme and the substrate possess specific
complementary geometric shapes that fit exactly into one another. This is
often referred to as "the lock and key" model.
Lock & Key Model:
The Lock and Key theory of enzyme activity states that every enzyme has a
specific shape which allows its active site to fit with a specific substrate.
Induced Fit Model
The lock and key model has been modified by Daniel Koshland in 1958 by
the induced fit model, which states that an enzyme can change its shape
slightly to accept a fit with a substrate.
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Mechanism of Enzyme Catalysis:
Enzymes increase the rate of reaction by decreasing the energy of activation
of the reactant
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Classification of Enzymes:
Enzymes are divided into six (6) major classes:
1. Oxidoreductases: involved in oxidation and reduction reactions, e.g.
oxidases, dehydrogenases, oxygenases, peroxidases.
2. Transferases: transfer functional groups, e.g. amino or phosphate
groups, e.g. aminotransferases,
3. Hydrolases: catalyze hydrolysis of the substrate, e.g. lipase, maltase,
protease.
4. Lyases: add or remove elements of water, ammonia, or CO2 to form
double bonds, e.g. decarboxylases.
5. Isomerases: catalyze the rearrangements of atoms within a molecule to
give its isomer, e.g. glucose to fructose
6. Ligases: join 2 molecules, e.g. carboxylases and synthetases.
Enzyme Cofactors:
The majority of enzymes require the presence of some components to help
them catalyze the reaction, these components are called cofactors. Cofactors
can be classified into 3 groups as follows:
1. Coenzymes:
These are organic compounds with low molecular weight, heat stable,
loosely attached to the enzyme molecule, therefore can be separated
easily by simple dialysis. Examples: NAD+, NADP+, B6-P.
2. Prosthetic groups:
These are also low molecular weight organic compounds, which are
firmly attached to the enzyme protein, therefore they are not separated
by dialysis. Examples: FAD, heme.
3. Metal activators:
These are inorganic monovalent and divalent cations such as K+, Mn2+,
Ca2+, Zn2+, and Mg2+; these cations may be either loosely or firmly
attached to the enzyme protein.
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Holoenzyme, Apoenzyme and Coenzyme:
Holoenzyme is the term used to describe the whole enzyme molecule which
may be composed of an enzyme protein and a coenzyme or a prosthetic
group. In this case, the enzyme protein is called apoenzyme. Therefore:
Holoenzyme = Apoenzyme + Coenzyme (or Prosthetic group)
Remember that: Neither Apoenzyme nor Coenzyme alone is catalytically
active. Only when they are both combined together they become catalytically
active.
Proenzymes (Zymogens):
Proenzymes (or zymogens) are inactive form of some enzymes produced by
some cells, to become active in a second site like intestine and stomach.
Examples: Pepsinogen (inactive form) is produced by gastric mucosal cells,
and in the stomach, it is activated to pepsin by gastric acidity by active pepsin
(Auto-activation):
Pepsinogen
Pepsin
(Inactive)
+ HCl
(Active)
(or Pepsin)
Isoenzymes:
Isoenzymes mean a group of enzymes which catalyze one and the same
reaction but they differ in physical, chemical, immunological and
electrophoretic properties. Examples:
(a) The enzyme lactate dehydrogenase (LDH) occurs in different forms, which
can be separated from each other by electrophoresis into 5 types:
LDH1, LDH2, LDH3, LDH4 & LDH5 which come from different organs; LDH1 is
found in the heart and LDH5 occurs in the liver. Determination of the level of
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either of these isoenzymes in blood is of value in the diagnosis of liver and
heart diseases.
(b) Creatine phosphokinases (CK) also have different isoenzyme forms.
These isoenzymes are of value in the diagnosis of muscle, heart and brain
diseases.
Factors that Affect the Rate of Enzyme-Catalyzed Reactions
1. pH:
A change in pH changes the rate of enzyme-catalyzed reaction. A bellshaped curve is obtained when the rate of the reaction is plotted
against pH with an optimum pH at which the rate is optimum. Changes
in pH can change the ionization of the substrate or the catalytic site of
the enzyme.\
2. Temperature:
The rate of an enzyme-catalyzed reaction increases with increasing
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temperature up to an optimum point (called optimum temperature),
then it decreases because of denaturation of the enzyme protein
3. Substrate Concentration:
The rate of enzyme-catalyzed reaction is increased with the increase of
substrate concentration [S] till a point is reached (point of saturation),
when there is no further increase in the reaction rate with the increase
in substrate concentration. This observation can be explained as
follows:
a) At low substrate concentration [S]:
the active sites (centers) of the enzyme are still not saturated with
substrate molecules and addition of substrate increases [ES] complex
gradually.
b) At the point of saturation with the substrate:
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As the substrate concentration increases, the sites become saturated
and as substrate is added no further increase in the [ES] with no further
increase in the rate of reaction and the result is the following graph:
Vmax = Maximal velocity or Maximal rate of the reaction.
KM = The substrate concentration that gives half maximal velocity (or 1/2
Vmax). KM is a good measure of enzyme affinity towards its substrate.
This means that , the smaller the KM the higher the affinity and vice
versa.
4. Concentration of the Product (P) of the reaction:
Most enzyme-catalyzed reactions are reversible, therefore, if the
products are not properly removed from the cell, they will inhibit the
reaction rate.
5. Physical agents:
Enzyme activity is seriously affected by some physical agents that
cause denaturation of proteins, e.g. ultrasonic vibrations, x-ray,
ultraviolet light (u.v), repetitive freezing and thawing, etc ….
6. Inhibitors:
Many compounds can combine with enzymes although they are not
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substrates, therefore, they may block the catalytic function of the
enzyme. These compounds are called inhibitors. There are 2 main
types of inhibitors:
A. Competitive inhibitors
B. Non-competitive inhibitors.
A. Competitive Inhibitors:
These are compounds which compete with the natural substrate for the
biding with the active site of the enzyme, therefore decreasing the catalytic
activity of the enzyme, e.g. the enzyme succinate dehydrogenase (SDH)
oxidizes succinic acid to fumaric acid. Addition of malonic acid, which has a
chemical structure similar to succinic acid, will cause inhibition of this enzyme.
Such inhibition can be reversed by increasing the concentration of the
substrate succinic acid. This shows that there is competition between the
inhibitor (i.e. malonic acid) and the substrate (i.e. succinic acid) to bind the
active site of the enzyme. This competition is due to similarity in chemical
structure between succinc acid and malonic cid.
Succinic Acid
Malonic Acid
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B. Non-competitive Inhibitors:
These are compounds which combine irreversibly with the active center of the
enzyme and is not displaced with increasing substrate concentration;
Examples: Iodoacetate react with SH – groups essential for the catalytic
activity of some enzymes:
Enzyme – SH
+ ICH2- COOH
Active enzyme
Enzyme-S-CH2-COOH
iodoacetic
+ HI
Inactive enzyme
Enzyme Inhibitors used as Drugs
Inhibitors
Target Enzyme
Effect
Allopurinol
Xanthine oxidase
Treatment of gout
Aspirin
Cyclooxygenase
Anti-inflammatory
5-Flurouracil
Thymidine synthetase
Anticancer
Lovastatin
HMG-CoA reductase
Cholesterol-lowering
agent
Penicillin
Transpeptidase
Antibacterial
Capoten
ACE inhibitor
Antihypertensive
agent
Enzymes in Clinical Diagnosis
Name of Enzyme
Diagnostic Uses
Acid phosphatase (AP)
Prostate cancer
Alanine aminotransferase (ALT)
Liver damage, hepatitis
Alkaline phosphatase (ALP)
Liver disease, bone disease
Amylase (AMS)
Acute Pancreatitis
Creatine kinase (CK)
Muscle disorder, heart attack
Lactate dehydrogenase (LDH)
Heart attack (LD1), Liver disease (LD5)
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