Lectura - Enzimas
Lectura - Enzimas
Lectura - Enzimas
11.1 OBJECTIVES
11.2 INTRODUCTION
In this unit you will understand, what enzymes are and how they are able to play role in all
metabolic processes of living organisms. The cell may be like a minute laboratory which is
capable of carrying out various processes like synthesis and breakdown of various substances.
These processes carried out by an enzyme at normal body temperature, low ionic strength, low
pressure and narrow range of pH. The study of enzyme is called enzymology.
Enzymes are central to every biochemical process and are also involved in many regulatory
mechanisms which allow the metabolism to adapt to changing conditions. The wide majority of
enzymes are proteins and necessary for all living organisms. Like other proteins, enzymes are of
high molecular weight compound and linear chain of various amino acids that fold to produce
three-dimensional or quaternary structure. The enzymes are most remarkable and highly
specialized proteins, for fulfilling fundamental requirements of the cell that is to convert food
into energy and necessary material for growth and repair of the organism.
11.3 DISCOVERY
French chemist Anselme Payen was first to discover an enzyme, diastase in 1833. But biological
catalysis was recognized and described in the 1850s by Louis Pasteur. He revealed that the
‗living intact‘ yeast cells were responsible for fermentation of sugar in to alcohol and used the
term ‗ferments‘ for such catalysts. Then in 1897 Edward Buchner discovered that yeast extracts
could ferment sugar to alcohol, because of this work he is credited for the discovery of enzyme
and Frederick W. Kuhne coined the word enzymes (en= in, zyme= yeast). James B. Summer
(1926) isolated enzyme urease for the first time in crystalline form from Jack bean, Canavalia
ensiformis at the Cornell University. Sumner found that urease crystals completely made up of
proteins and he postulated that all enzymes are proteins. But Sumner‘s conclusion was widely
accepted, only after John Northrop crystallized pepsin, trypsin and other digestive enzymes and
found them also to be proteins. On the basis of all these findings, he determined the
proteinaceous nature of enzymes. For such a pioneer and innovative work, Sumner and Northrop
share the Nobel Prize in 1947. The discovery that enzyme could be crystallized eventually help
in the X-ray crystallography of enzyme lysozyme by D.C. Phillips in 1965. J.B.S. Haldane first
time suggested that weak bonding interactions between an enzyme and its substrate might be
used to catalyze a reaction.
11.4 NOMENCLATURE
According to the older system, the enzymes are usually named by adding suffix ‗ase‘ to the name
of substrate, example - sucrase acting on sucrose, lipase acting on lipid etc. The names of some
enzymes indicate the nature of reactions they catalyse, example - isomerase, dehydrogenase,
phosphatase, carboxylase etc. Some enzymes are named arbitrarily, example - pepsin, renin etc.
An enzyme known to act in the digestion of foods was named pepsin, from the Greek used
pepsis, ―digestion,‖ and lysozyme was named for its ability to lyse bacterial cell walls. Still
others were named for their source: trypsin, named in part from the Greek tryein, ―to wear
down,‖ was obtained by rubbing pancreatic tissue with glycerin.
The name of enzymes according to the older system has often been haphazard and confusing.
Therefore, a systematic approach of nomenclature of the enzymes has been recommended by the
Commission on enzymes of the International Union of Biochemistry (1961), according to
which the various enzymes are designated by code numbers consisting of four digits (E.C.
number or Enzyme Commission number).
Characteristic features of International Union of Biochemistry (IUB) system
Enzymes are divided into six major classes, each with 4-13 subclasses.
The name enzyme have two parts: the first part indicates the name of substrate and
second part indicates the type of reaction ending with suffix –ase.
Each enzyme has a systematic four-digit code number (EC number).
The first digit of E.C. number indicates the major class (Table – 11.1), the second digit indicates
the sub-class, and the third digit indicates its sub-sub class, while the fourth digit denotes the
systematic specific name of the enzymes, the first part of which indicates the name of the
substrate and the second part the nature of the reaction. For example - the code no. 1.1.1.1.
stands for the enzyme alcohol dehydrogenase where -
1. Stands for oxidoreductase.
1.1. Stands for enzyme which utilizes substrate as – CHOH group.
1.1.1. Stands for those enzymes which utilize NAD as an acceptor.
Table - 11.1: The major classes of enzymes with an E.C. number and reaction catalysed
Sr. Class Reaction Type Example Reaction Catalysed
No
1 Oxidoreductase Oxidation- Alcohol Ared + Box ↔ Aox + Bred
reduction reaction dehydrogenase
E.C. no 1.1.1.1
2 Transferase Involve group Glycerokinase A-B + C ↔ A + B-C
transfer E.C. no 2.4.3.2
3 Hydrolases Hydrolytic Carboxypeptidase A-B + H2O ↔ A-H + B- OH
reactions E.C. no 3.4.17.1
4 Lyases Rearrangements Pyruvate A + B ↔ A-B
of electrons decarboxylase
E.C. no 4.1.1.1
5 Isomerases Rearrangements Maleate A ↔ Aisomer
of functional isomerase
group E.C. no 5.2.1.1
In this topic, you have learnt about enzymes, its types and mechanisms. The basic requirement
for life is, the organism must be able to catalyze chemical reactions efficiently and selectively.
Most chemical reactions require an initial input of energy to get started. This initial investment of
energy is known as the energy of activation. A catalyst is a substance that lowers the activation
energy required for a reaction. Enzymes are biological catalyst that speeds up reaction without
being consumed by the reaction. Thus enzymes are typically effective in very small amounts.
The enzyme catalyzed reactions differ from ordinary chemical reactions in following ways-
1. The rates of enzyme catalysed reactions are very high, approximately 106 to 1012 times
greater than ordinary unanalyzed reactions.
2. Enzymes are highly specific, to recognize the minute and specific differences in substrate and
product molecules, even able to discriminate between mirror images of the same molecule.
3. Enzyme reactions typically occur at normal body temperature, low ionic strength, low
pressure and narrow range of pH near neutrality.
4. Enzymes activities have regulatory control on metabolic reactions of living organism in
balance by various activators and inhibitors.
The molecule on which an enzyme acts is known as its substrate. The substrate binds with the
enzymes active site by weak interactions. The active site is the location on the enzyme where the
catalysis of chemical reaction and product formation takes place. Thus, active site both confines
the substrate molecule and orients it in correct manner (Fig.11.1).
Fig.11.1: Sucrose, a disaccharide is hydrolyzed to produce one molecule of glucose and fructose.
The enzyme sucrose is involved and specific for this process. The active site of the enzyme fits the
two subunits of the sucrose molecule.
11.6.1- Active site: The active site of an enzyme is the region that binds the substrates and
contains residues that directly participate in the making and breaking of bonds. These residues
are called as catalytic group, although, enzymes differ widely in structure, specificity and mode
of catalysis, a number of generalization concerning their active sites are –
1. The active site takes up a relatively small part of the total volume of an enzyme
2. The active site is a three dimensional structure
3. Substrates are bound to the enzymes by multiple weak bonds
4. Active sites are cleft or crevices
5. The specificity of binding depends on the precisely defined arrangement of atoms in an
active site.
11.6.2 - Parts of enzymes: Enzymes are proteinaceous in nature and made up of a hundred
to a millions of amino acids with its own unique sequence. These amino acids are coiled and
folded many times to form a complex three dimensional structure. The structure and function of
the enzyme is determined by the unique sequences of amino acids and its 3-D structure. Some
enzymes appear to depend only on their proteinaceous structure and others require an additional
non protein component for their catalytic activity. On such basis, some enzymes are purely
made up of proteins and others are conjugated enzymes of protein and non protein parts -
a) Simple proteinaceous enzyme
b) Conjugated enzymes (Holoenzyme)
Enzymes have molecular weights ranging from about 12,000 to more than 1 million. The
catalytic activity of many enzymes depends upon the presence of small non proteinaceous
molecules termed cofactor (Table – 11.2), unlike enzymes, they were stable at relatively high
temperatures. There are either one or more inorganic ions (such as Fe, Mg, Mn or Zn) or a
complex organic or metallo-organic molecule called a coenzyme, it often serves as electron
carriers and generally derived from vitamins. Some enzymes require both a coenzyme and one or
more metal ions for activity, even in some cases these ions serve to hold the enzyme protein in
its proper three dimensional structures. A coenzyme or metal ion that is very tightly or even
covalently bound to the enzyme protein is called as prosthetic group. A complete, catalytically
active enzyme together with its bound coenzyme and/or metal ions is called a holoenzyme. The
protein part of such an enzyme is called the apoenzyme or apoprotein.
2. Organic molecule
Biotin Pyruvate carboxylase
Coenzyme A Acetyl CoA carboxylase
Flavin adenine nucleotide Monoamine oxidase
Nicotinamide adenine dinucleotide Lectate dehydrogenase
Thiamine pyrophosphate Pyruvate dehydrogenase
Function of Cofactors:
1. In some enzymes, cofactors are required for completion of the active site.
2. Cofactor acts as a donor of electrons in the enzymatic reactions.
3. Cofactors may serve as temporary recipients of either one of the reaction products/
electrons/ protons.
Fig. 11.2: Feedback inhibition by end product of the pathway to regulate the activity of the
enzyme.
Fig. 11.3: The reactant AB & CD must absorb enough energy from the surroundings to reach the
unstable transition state, where bonds can break and new bonds form, releasing energy to the
surroundings.
AB + CD → AC + BD
Enzymes speed up the rate of a reaction by lowering the energy barrier between substrates
(reactants) and products but are not themselves used up in the reaction, and are regenerated at
end. Thus, a enzyme increases the rate of a reaction but does not affect the equilibrium ratio of
reactants and products, because the rate of the reaction in both directions are increased to the
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same extent. Enzymes act as catalysts because they lower the free energy of activation for a
reaction. They do this by a combination of raising the ground state ∆G of the substrate and
lowering the ∆G of the transition state of the reaction, thereby decreasing the barrier against the
reaction. The energy derived from enzyme-substrate interaction is called binding energy. Its
significance extends beyond a simple stabilization of the enzyme-substrate interaction. Binding
energy is a major source of free energy used by enzymes to lower the activation energies of
reactions. Weak binding interactions between the enzyme and the substrate provide a substantial
driving force for enzymatic catalysis. The presence of the enzyme leads to a new reaction
pathway that is different from that of the uncatalyzed reaction (Fig-11.4).
Fig.11.4: Free energy curves for the same reaction, either uncatalysed or enzyme catalysed.
An enzyme catalysis lowers the EA between substrate and products compared with the
uncatalysed reaction
ENZYME ACTIVITY
Enzymes are usually present in very small quantities. So, an easy method of enzyme
quantification is a measurement of catalytic activity. There are two standard units to
express enzymatic activity-
2. Induced Fit model: This model was proposed by Daniel Koshland in 1966. According to
this model, the enzyme and substrate do not have strictly complementary structures but the
enzyme has flexible active site structure which is changed according to substrate configuration
(Figure – 11.5). This model explains enzyme specificity in which a flexible active site is induced,
by a substrate, to change its conformation to an orientation properly fitting the substrate‘s
geometry. Enzyme-substrate complex brings about conformational change in active site, in such
a fashion so that catalytic group lies opposite the substrate bonds to be broken. ES binding forces
exert strain to form products.
Fig.11.5: Diagram of induced fit model, representing the flexible nature of the active site of the
enzymes
amount of ES complex is the same as the total number of enzymes. According to this model
enzyme catalysis takes place in two stages. In the first stage, formation of a specific ES complex
and this complex is also called as Michaelis-Menten complex in their honor. In the second
stage, enzyme catalyses the reaction and form the product.
E + S ↔ ES → EP → E + P
Where, E represents the enzyme, S the substrate, P the product, and ES the enzyme–substrate
complex. Thus, as the substrate concentration is increased, a point will reach at which all the
enzyme molecules are in the form of the ES complex, and the enzyme is saturated with substrate.
Since the rate of the reaction depends on the concentration of ES, the rate will not increase
further, because there can be no higher concentration of ES. When an enzyme is mixed with
excess of substrate, there will be an initial very short time period (usually milliseconds) during
which the concentration of enzyme–substrate complexes and intermediates build up to certain
level; this is known as the pre–steady-state period. Once the intermediate levels have been built
up, they remain relatively constant until the substrate is depleted; this period is known as the
steady state.
Normally enzyme kinetic values are measured under steady-state conditions, and such conditions
usually prevail in the cell. For many enzyme-catalyzed reactions the kinetics under steady-state
conditions can be described by a simple expression known as the Michaelis–Menten equation:
v = Vmax [S] ∕ Km + [S]
Where, v is the initial rate of the reaction, Vmax is the maximum substrate-saturated rate of the
reaction and the Km is the substrate concentration that provides the half of the maximal substrate-
saturated rate of the reaction (1/2 Vmax). The maximal rate Vmax, occurs when all the active site of
the enzyme molecule are fully occupied by substrate and Michaelis constant Km, represents the
affinity of enzyme for the substrate. Smaller the value of Km means higher will be the affinity of
enzyme to substrate i.e. Km is inversely proportional to the affinity.
Fig.11.3: Plot of initial velocity versus substrate concentration, for an enzyme catalysed
reaction. The curve is hyperbolic.
Reversible inhibitors can dissociate from the enzyme because they bind non-covalently to the
enzymes. Reversible inhibitors are of three different types; competitive, non-competitive and
mixed type.
1. Competitive inhibition: Competitive inhibition is the simplest and most common form
of reversible inhibition. It binds to the enzyme at active site with an affinity similar to or stronger
than that of the substrate. The competitive inhibitor forms an enzyme-inhibitor complex [EI] that
is equivalent to enzyme-substrate complex [ES]. Competitive inhibition is usually based on the
fact that the structure of the inhibitor resembles that of the substrate; hence the strong affinity of
the inhibitor for the active site. The effect of competitive inhibitor is reversed by increasing the
substrate concentrations. At high substrate concentration, all the active sites are filled with the
substrates and reaction velocity similar to the value observed without an inhibitor. The diagnostic
property of this type of inhibition is that Vmax is same and Km increases, but such inhibitors does
not affect the ‗turn over number‘.
2. Non-competitive inhibition: In noncompetitive inhibition, the inhibitor does not
compete with the substrate for binding to the active site. Instead, it may bind to another site and
obstruct the substrate‘s access to the active site because binding alters the 3-D structure of the
enzyme, or it may bind to the enzyme–substrate complex and thus alter catalysis.
Noncompetitive inhibition is not reversed by increasing substrate concentration. The diagnostic
property of this type of inhibition is that Km is unaffected, whereas Vmax decreases in the
presence of increasing amounts of inhibitor.
3. Mixed inhibition: Mixed inhibition is characterized by effects on both Vmax (which
decreases) and Km (which increases). Mixed inhibition is very common and results from the
formation of a complex consisting of the enzyme, the substrate, and the inhibitor that does not
break down to products.
11.7 SUMMARY
An enzyme is a protein that catalyzes a chemical reaction by lowering the activation energy.
They are not changed or used in reactions, so only a small amount of enzyme is needed. They are
highly specific for their substrate and functionally depend on their three-dimensional structure,
which is sensitive to temperature and pH. The actual catalytic process takes place at the active
site via formation of enzyme-substrate complex. The ‗lock and key‘ hypothesis provide reason