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Chapter 3 Enzymes
Chapter 3 Enzymes
ENZYMES
HISTORY
Kuhne - Term ‘enzyme’
Edward Buchner – Discovery of enzyme, extracted ‘Zymase’ from yeast cells was awarded nobel prize
in 1907.
Sumner – Discovered Protein nature of enzyme, was awarded nobel prize in 1946. Prepared pure
crystals of enzyme Urease isolated from Jack bean (Canovalia)
Arber, Smith and Nathans – Isolated restriction endonuclease used in genetic engineering for nicking
DNA strands, were awarded nobel prize in 1978.
ENZYMES :
Enzymes are biological catalysts made by living cells. They are used to catalyse a vast number of
chemical reactions at temperatures suitable for living organisms, i.e. between 5°C and 40°C. Enzymes
are vitally important because in their absence reactions in the cell would be too slow to sustain life. The
chemical (or chemicals) which an enzyme works on is called its substrate. An enzyme combines with
its substrate to form a short-lived enzyme/substrate complex. This proximity of the enzyme with the
substrate in the complex greatly increases the chances of a reaction occurring. Once a reaction has
occurred, the complex breaks up into products and enzyme. The enzyme remains unchanged at the end
of the reaction and is free to interact again with more substrate.
PROPERTIES OF ENZYMES
All components of cell including cell wall and cell membrane have enzymes. Maximum enzymes (about
70%) are found in mitochondria.
An enzyme like any protein has the secondary and the tertiary structure. When you look at a tertiary
structure you will notice that the backbone of the protein chain folds upon itself, the chain criss-crosses
itself and hence, many crevices or pockets are made. One such pocket is the ‘active site’.
An active site of an enzyme is a crevice or pocket into which the substrate fits. Thus enzymes, through
their active site, catalyse reactions at a high rate.
Their presence does not alter the nature or properties of the end product(s) of the reaction.
They are very efficient, as a very small amount of catalyst brings about the change of a large amount of
substrate.
They are highly specific, that is an enzyme will generally catalyse only a single reaction. Catalase, for
example, will only catalyse the decomposition of hydrogen peroxide.
The catalysed reaction is reversible.
Enzyme catalysts differ from inorganic catalysts in many ways, but one major difference needs
mention. Inorganic catalysts work efficiently at high temperatures and high pressures, while enzymes
get damaged at high temperatures (say above 40°C). However, enzymes isolated from organisms who
normally live under extremely high temperatures (e.g., hot vents and sulphur springs), are stable and
retain their catalytic power even at high temperatures (upto 80°-90°C). Thermal stability is thus an
important quality of such enzymes isolated from thermophilic organisms.
Their activity is affected by pH, temperature, substrate concentration and enzyme concentration.
Enzymes functional outside the living cells are called exoenzymes. e.g. enzymes present in digestive
juices, lysozyme of tears.
Enzymes functional inside the living cells are known as endoenzymes e.g. Enzymes of Kreb’s cycle
(inside mitochondria), Enzymes of glycolysis (inside cytoplasm).
Chemical Reactions
Chemical compounds undergo two types of changes.
A physical change simply refers to a change in shape without breaking of bonds. This is a physical
process.
When bonds are broken and new bonds are formed during transformation, this will be called a chemical
reaction. Hydrolysis of starch into glucose is an organic chemical reaction.
Rate of a physical or chemical process refers to the amount of product formed per unit time. Rates of
physical and chemical processes are influenced by temperature among other factors. The amount of
substrate changed into product per unit time is called Turn over number.
A general rule of thumb is that rate doubles or decreases by half for every 10°C change in either
direction.
Catalysed reactions proceed at rates vastly higher than that of uncatalysed ones.
In the absence of any enzyme this reaction is very slow, with about 200 molecules of H2CO3 being
formed in an hour. However, by using the enzyme present within the cytoplasm called carbonic
anhydrase, the reaction speeds dramatically with about 600,000 molecules being formed every second.
The enzyme has accelerated the reaction rate by about 10 million times.
There are thousands of types of enzymes each catalysing a unique chemical or metabolic reaction. A
multistep chemical reaction, when each of the steps is catalysed by the same enzyme complex or
different enzymes, is called a metabolic pathway. For example Glycolysis (is a metabolic pathway in
which glucose becomes pyruvic acid through ten different enzyme catalysed metabolic reactions.
NOMENCLATURE
All enzyme names end in suffix - ase, except some old names, e.g. ptyalin, pepsin, trypsin. Some old
names indicate the source but not the action, e.g. papain from Papaya, bromelain from Pineapple of
family Bromeliaceae.
In modern system enzyme names are given after
(i) Substrate acted upon, e.g. sucrase (after sucrose), lipase, protease, nuclease, peptidase, maltase
(ii) Chemical reaction e.g. dehydrogenase, oxidase, carboxylase, decarboxylase etc.
Group names are often qualified by the addition of the name of substrate, e.g. succinic
dehydrogenase, isocitric dehydrogenase, glutamate pyruvate transaminase, DNA polymerase.
DNA polymerase catalyses synthesis of DNA segments through polymerisation of
deoxyribonucleotides.
Glutamate-pyruvate transaminase transfers amino group (–NH2) from glutamate to pyruvate.
The modern system of enzyme classification was introduced by International Union of Biochemistry
(IUB) in 1961. It groups enzymes into the following six categories :
1. Oxidoreductases : They take part in oxidation and reduction reactions or transfer of electrons.
Oxidoreductases are of three types - oxidases, dehydrogenases and reductases, e.g. cytochrome oxidase
(oxidises cytochrome), succinate dehydrogenase, nitrate reductase, catalase, peroxidase.
2. Transferases : They transfer a group from one molecule to another e.g. glutamate pyruvate
transaminase (transfers amino group from glutamate to pyruvate during synthesis of alanine). The
chemical group transfer does not occur in the free state. Example - Transaminase (transfers amino
group), Kinase (catalyse the phosphorylation of substrate by transferring phosphate group usually from
ATP)
3. Hydrolases : They break up large molecules into smaller ones with the help of hydrogen and hydroxyl
groups of water molecules. The phenomenon is called hydrolysis. Digestive enzymes belong to this
group, e.g. amylase (hydrolysis of starch), sucrase, lactase, Protease, lipase, maltase, nuclease
4. Lyases : The enzymes cause cleavage, removal of groups without hydrolysis, addition of groups to
double bonds or reverse, e.g. histidine decarboxylase (breaks histidine to histamine and CO2), aldolase
(fructose-1, 6-diphosphate to dihydroxy acetone phosphate and glyceraldehyde phosphate), carbonic
anhydrase etc.
5. Isomerases : The enzymes cause rearrangement of molecular structure to effect isomeric changes.
They are of three types
(i) Isomerase (aldose to ketose group or vice-versa)
6. Ligases (Synthetases) : The enzymes catalyse bonding of two chemicals with the help of energy
obtained from ATP, e.g. pyruvate carboxylase. It combines pyruvic acid with CO2 to produce
oxaloacetic acid. Example: RUBP carboxylase, ligase, Phosphoenol pyruvate (PEP carboxylase) etc.
International Union of Biochemistry (IUB) appointed an Enzyme Commission (EC) in 1961 which
devised some basic principles for classification and nomenclature of enzymes. IUB system has divided
enzymes into six major classes. Each class in turn is subdivided into many subclasses which are further
divided. A four digit enzyme commission (EC) number (e.g., 5.2.1.7) is assigned to each enzyme
represents
(i) Ist digit - Class
(ii) IInd digit - Subclass
(iii) IIIrd - Sub-subclass
(iv) IVth digit - Individual enzyme
Most enzymes are proteins except few, but all proteins are not enzymes. On the basis of chemical nature
enzymes are of two types, simple and conjugate.
Simple Enzymes are entirely made of proteins only. Additional nonprotein substance or group is
absent. The active sites reside on the protein moiety, e.g. pepsin, trypsin, lysozyme.
Conjugate Enzymes are enzymes which possess two parts - a large thermolabile protein part or
apoenzyme and a small dialysable thermostable nonprotein part called cofactor.
The complete conjugate enzyme made of apoenzyme and cofactor is called holoenzyme. Enzyme
cofactors are non-protein components required for efficient activity of enzymes.
Cofactors may vary from simple inorganic ions to complex organic molecules, and may either remain
unchanged at the end of a reaction or be regenerated by a later process. There are three recognised types
of cofactor : inorganic ions, prosthetic groups and coenzymes.
Inorganic ions (enzyme activators) : thought to mould either the enzyme or the substrate into a shape that
allows an enzyme/substrate complex to be formed, hence increasing the chances of a reaction occurring
between them and therefore increasing the rate of reaction catalysed by that particular enzyme. For
example, salivary amylase activity is increased in the presence of chloride ions.
Net effect : 2H transferred from A to B. One enzyme acts as a link between A and B. Both AH2 and B fit
into the active site and FAD passes H2 from one to the other.
Difference between Apoenzyme and Coenzyme
How do Enzymes bring about such High Rates of Chemical Conversions?
The chemical which is converted into a product is called a ‘substrate’. Hence enzymes, i.e. proteins with
three dimensional structures including an ‘active site’, convert a substrate (S) into a product (P). The
substrate has to diffuse towards the ‘active site’. There is thus, an obligatory formation of an ‘ES’
complex. E stands for enzyme. This complex formation is a transient phenomenon. During the state
where substrate is bound to the enzyme active site, a new structure of the substrate called transition state
structure is formed. Very soon, after the expected bond breaking/making is completed, the product is
released from the active site. In other words, the structure of substrate gets transformed into the structure
of product(s). The pathway of this transformation must go through the so-called transition state
structure. There could be many more ‘altered structural states’ between the stable substrate and the
product. Implicit in this statement is the fact that all otherintermediate structural states are unstable.
Stability is something related to energy status of the molecule or the structure. The y-axis represents the
potential energy content. The x-axis represents the progression of the structural transformation or states
through the ‘transition state’. You would notice two things. The energy level difference between S and
P. If ‘P’ is at a lower level than ‘S’, the reaction is an exothermic reaction. One need not supply energy
(by heating) in order to form the product. However, whether it is an exothermic or spontaneous reaction
or an endothermic or energy requiring reaction, the ‘S’ has to go through a much higher energy state or
transition state. The difference in average energy content of ‘S’ from that of this transition state is called
‘activation energy’. Enzymes eventually bring down this energy barrier making the transition of ‘S’ to
‘P’ more easy.
MECHANISM OF ENZYME ACTION
Two hypothesis have been put forward to explain the mode of enzyme action.
This hypothesis was given by Emil Fischer (1894). According to this hypothesis, both enzyme and
substrate molecules have specific geometrical shapes. It is similar to the system of lock and key, which
have special geometrical shapes in the region of their activity. The active sites contain special groups
having - NH2, -COOH, -SH for establishing contact with the substrate molecules. Just as a lock can be
opened by its specific key, a substrate molecule can be acted upon by a particular enzyme. This also
explains the specificity of enzyme action. After coming in contact with the active site of the enzyme, the
substrate molecules or reactants form a complex called enzyme-substrate complex. In the enzyme
substrate complex, the molecules of the substrate undergo chemical change and form products, the
product no longer fits into the active site and escapes in surrounding medium, leaving the active site free
to receive more substrate molecules. This theory explains how a small concentration of enzyme can act
upon a large amount of the substrate. It also explains how the enzyme remains unaffected at the end of
chemicals reaction. The theory explains how a substance having a structure similar to the substrate can
work as competitive inhibitor.
INDUCED FIT HYPOTHESIS:
This hypothesis was proposed by Koshland (1960). According to this hypothesis the active site of the
enzyme does not initially exist in a shape that is complementary to the substrate but is induced to assume
the complementary shape as the substrate becomes bound to the enzyme. According to Koshalnd, “the
active site is induced to assume a complementary shape in much the same way as a hand induces a
change in the shape of a glove.”An active site of an enzyme is a crevice or a pocket into which the
substrate fits. Thus, enzymes through their active site, catalyse reactions at a high rate. Hence, according
to this model, the enzyme (or its active site) is flexible. The active site of the enzyme contains two group
-(a) Buttressing group is meant for supporting the substrate. (b) Catalytic group is meant for
catalysing the reaction. When substrate comes in contact with the buttressing group, the active site
changes to bring the catalytic group opposite the substrate bonds to be broken.
Any substance that can diminish the velocity of an enzyme-catalyzed reaction is called an inhibitor.
Reversible inhibitors bind to enzymes through non-covalent bonds. Dilution of the enzyme-inhibitor
complex results in dissociation of the reversibly-bound inhibitor and recovery of enzyme activity.
Irreversible inhibition occurs when an inhibited enzyme does not regain activity upon dilution of the
enzyme-inhibitor complex. Some irreversible inhibitors act by forming covalent bonds with specific
groups of enzymes; for example, the neurotoxic effects of certain insecticides are due to their
irreversible binding at the catalytic site of the enzyme acetylcholinesterase. The two most commonly
encountered types of inhibition are competitive and noncompetitive.
A. Competitive inhibition: This type of inhibition occurs when the inhibitor binds reversibly to the same
site that the substrate would normally occupy and, therefore, competes with the substrate for that site.
1. Effect on Vmax: The effect of a competitive inhibitor is reversed by increasing [S].
At a sufficiently high substrate concentration the reaction velocity reaches the Vmax observed in the
absence of inhibitor.
2. Effect on Km: A competitive inhibitor increases the apparent Km for a given substrate. This means that
in the presence of a competitive inhibitor more substrate is needed to achieve 1/2 Vmax.
e.g., Inhibition of alcohol dehydrogenase by ethanol in methanol poisoning, sulphur drugs for folic acid
synthesis in bacteria and inhibition of succinic dehydrogenase by Malonate, malate and
oxaloacetate.
Competitive inhibitors are frequently used in the control of bacterial pathogen. All cells require folic
acid for growth. Folic acid cannot cross bacterial cell walls by diffusion or active transport For this
reason bacteria must synthesize folic acid from P-aminobenzoic acid. Sulpha drugs are inhibitor and
competes with the substrate P-amino benzoic acid (PABA) for the active site of enzyme. This binding of
inhibitor to the enzyme prevents the synthesis of folic acid and thus bacterial pathogens are controlled.
B. Non-competitive inhibition: This type of inhibition is recognized by its characteristic effect on Vmax.
Noncompetitive inhibition occurs when the inhibitor and substrate bind at different sites on the enzyme.
The noncompetitive inhibitor can bind either free enzyme or the ES complex, thereby preventing the
reaction from occurring.
1. Effect on Vmax: Non competitive inhibition cannot be overcome by increasing the concentration of
substrate. Thus, noncompetitive inhibitors decrease the Vmax of the reaction.
2. Effect on Vm: Noncompetitive inhibitors do not interfere with the binding of substrate to enzyme.
Thus, the enzyme shows the same Km in the presence or absence of the noncompetitive inhibitor.
e.g. cyanide kills an animal by inhibiting cytochrome oxidase.
(iii) Allosteric Modulation or Feedback Inhibition: The activities of some enzymes, particularly those
which form a part of a chain of reactions (metabolic pathway), are regulated internally. Some specific
low molecular weight substance, such as the product (S) of another enzyme further on in the chain, acts
as the inhibitor. Such a modulator substance binds with a specific site of the enzyme different from its
substrate-binding site. This binding increases or decreases the enzyme action. Such enzymes are called
Allosteric Enzymes,
Examples:
(a) Hexokinase which changes glucose to glucose-6-phosphate in glycolysis. Decline in enzyme activity by
the allosteric effect of the product is called Feedback Inhibition, e.g., allosteric inhibition of
hiexokinase by glucose-6-phosphate.
(b) Enzyme phosphofructokinase is activated by ADP and inhibited by ATP.
(c) Another example is inhibition of threonine deaminase by isoleucine. Amino acid isoleucine is formed
in bacterium Escherichia coli in a 5-step reaction from theronine. When isoleucine accumulates beyond
a threshold value, its further production stops. Proenzymes / Zymogens - Proenzyme is the inactive
precursor of an enzyme. The term zymogen is often used for inactive precursor of proteolytic enzyme,
Allozymes - Similar enzymes produced by different genes. Constitutive enzymes - Enzymes which are
always present because of their requirement for a vital process e.g. glycolysis. Repressible enzymes -
Normally present but are repressed when specific chemical or product is present e.g. glucokinase.
Inducible enzymes - Formed in response to its substrate e.g. lactase. Immobilisation of Enzymes-It is
attaching or trapping enzymes in inert supporting materials (calcium alginate beads) for better efficiency
and recovering them after the reaction. Sometimes the cells producing the enzymes are immobilised
EXERCISE-1
1. Almost all enzymes are proteins. Name the nucleic acid which behaves like enzyme
A) DNA B) m-RNA C) t-RNA D) r-RNA
2. Nucleic acids which behave like as enzymes are called
A) Zymogens B) Ribozymes C) Lysozymes D) Zymases
3. Which type of r-RNA acts as ribozyme
A) 16 S r-RNA B) 20 S r-RNA C) 23 S r-RNA D) 30 S r-RNA
4. In tertiary structure of enzyme, polypeptide chain folds upon itself, forming crevices or pockets called
A) Reaction centers B) Active sites C) Crests D) Cristae
5. Enzymes which can tolerate high temperature upto to are isolated from this type of bacteria
A) Acidophiles B) Coprophiles C) Halophiles D) Themophiles
6. Identify the wrong one from the following
A) Change in shape or state of matter is called physical change
B) During chemical change bonds are broken or formed
C) Amount of substrate converted into product per unit time is called rate of reaction
D) Rate of reaction doubles or decrease to half for every temperature change in either direction
7. How much time will it take to form 1000 carbonic acid molecules from water and
A) 1 hrs B) 2 hrs C) 5hrs D) 6hrs
8. How many carbonic acid molecules can be produced in one minute in the presence of carbonic
anhydrase
A) B) C) D)
9. In human skeletal muscle in the absence of oxygen, glucose is converted into
A) Pyruvic acid B) Acetic acid C) Lactic acid D) Ethyl alcohol
10. Transition state structure of the substrate formed during an enzymatic reaction is
A) Permanent but unstable B) Transient and unstable
C) Permanent and stable D) Transient and stable
11. High energy state of substrate in E.S.C is called
A) Transient state B) Transition state C) Signet state D) Ground state
12. The difference between average energy content of a substrate and that of transition state is called
A) Activation energy B) Free energy C) Chemical energy D) Kinetic energy
13. What is the type of reaction, if product is at lower energy level than substrate
A) Exothermic reaction B) Endothermic reaction
C) Spontaneous reaction D) Endergonic reaction
14. Reactions which take energy are called
A) Exothermic reaction B) Endothermic reaction
C) Spontaneous reaction D) Exergonic reaction
15. Energy that is required for the substrate to get converted to product is called
A) Activation energy B) Energy barrier C) Potential energy D) Both A and B
16. How the enzymes enhance the rate of a chemical reaction
A) By altering chemical equilibrium B) By reducing activation energy
C) By increasing activation energy
D) By pushing the substance to lower levels of energy
ANSWER KEY
1. D 2. B 3. C 4. B 5. D 6. C 7. C 8. D 9. C 10. B
11. B 12. A 13. A 14. B 15. A 16. B 17. B 18. C 19. A 20. D
21. A 22. C 23. A 24. B 25. B 26. C 27. D 28. B 29. D 30. C
31. A 32. B 33. D 34. C 35. C 36. A 37. D 38. C 39. B 40. A
41. B 42. C 43. B 44. B 45. C 46. C 47. B 48. C 49. B 50. B
51. B 52. C 53. B 54. B 55. B 56. B 57. C 58. C 59. B 60. B
61. D 62. D 63. A 64. C 65. B 66. D
EXERCISE-2
STATEMENTS TYPE QUESTIONS
III)
IV) Coordinate covalent bonds are formed between the enzyme and the substrate
A) I-II-III B) II-III-IV C) I-II-IV D) I-III-IV
2. Inhibition of rate a reaction due to accumulation of end product is called
I) Feed back inhibition II) Allo-steric inhibition
III) Competitive inhibition IV) Non-competitive inhibition
A) I – II B) II – III C) III – IV D) I – IV
3. What is the correct sequence of six classes of enzymes according to IUB
I) Oxidoreductases II) Transferases III) Hydrolases IV) Lyases V) Isomerases
VI) Ligases
A) I-II-III-IV-V-VI B) I-II-V-III-VI-IV C) II-V-III-VI-I-IV D) III-VI-I-IV-II-V
4. Enzymes which add phosphate to substrate and remove phosphate from the substrate belong to these
major classes respectively
I) Transferases II) Hydrolases III) Lyases IV) Ligases
A) I-II B) II-III C) III-IV D) I-IV
5. Zinc is metal ion co-factor in the following enzyme
I) Carboxylases II) Alcohol dehydrogenase
III) Carboxypeptidase IV) Carbonic anhydrase
A) I – II – III B) II – III – IV C) I – II – IV D) I – II – III – IV
6. What are the common features of catalase and peroxidase enzymes
I) present in peroxysomes II) Prosthetic group is haem
III) Break hydrogen peroxide into water and oxygen
IV) Respiratory enzymes
A) I-II-III B) II-III-IV C) I-II-IV D) I-III-IV
7. TON of an enzyme is 50. A test tube contains 1,000 substrate molecules and 2 enzyme molecules. What
is left over in that tube after 2 minutes
I) Substrate II) Product III) Enzyme
A) I-II B) II-III C) I-III D) I-II-III
8. Pick up ‘Wrong’ statement (s) from the following
I. Structural states of the substrate during enzymatic reactions at transition state are unstable
II. Enzyme increases the energy barrier to transition state making transition of ‘S’ to ‘P’ more easy
III. If potential energy level of ‘P’ is lower than ‘S’, then the catalytic reaction is exothermic reaction
IV. The formation of E S complex is essential for catalysis
A) I,II B) II, IV C) II, III D) II only
ANSWER KEY
1.A 2.A 3.A 4.A 5.D 6.A 7.D 8.D
EXERCISE-3
ASSERTION & REASON QUESTIONS
1. Assertion: Enzymes are called organic catalysts
Reason: All enzymes are made up of proteins
A) A and R are true and R is the correct explanation of A
B) A and R are true R is of A not the correct explanation
C) A is true, R is false D) A is false & R are True
2. Assertion: Enzymes are sensitive to high temperature and pressure
Reason: Enzymes are made up of proteins
A) A and R are true and R is the correct explanation of A
B) A and R are true R is of A not the correct explanation
C) A is true, R is false D) A is false & R are True
3. Assertion: Fruits, vegetables kept in refrigerator remain fresh for longer time
Reason: At low temperature enzymes of fruits, vegetables are destroyed
A) A and R are true and R is the correct explanation of A
B) A and R are true R is of A not the correct explanation
C) A is true, R is false D) A is false & R are True
4. Assertion: Oxido-reductases are otherwise called dehydrogenases
Reason: Oxido- reductases bring about oxidation and reductions mainly by transferring hydrogen
between two substrates
A) A and R are true and R is the correct explanation of A
B) A and R are true R is of A not the correct explanation
C) A is true, R is false D) A is false & R are True
5. Assertion: Ligases are otherwise called synthetases
Reason: Ligases catalyse the formation of new bonds
A) A and R are true and R is the correct explanation of A
B) A and R are true R is of A not the correct explanation
C) A is true, R is false D) A is false & R are True
6. Assertion: Prosthetic group is an organic substance which is tightly bound to apoenzyme
Reason :Apoenzyme alone may carry out biochemical reaction in the absence of cofactor
A) A & R true, R explains A B) A & R true. R does not explain A
C) A is true and R is false D) A is false and R is true
ANSWER KEY
1.A 2.A 3.C 4.A 5.A 6.C
EXERCISE-4
MATRIX MATCHING QUESTIONS
V)
A) A-III, B-I, C-II, D-V B) A-V, B-I, C-IV, D-II
C) A-III, B-I, C-V, D-II D) A-IV, B-V, C-I, D-II
4. Match the following
A. Non protein part I. NADP
B. Protein part II. Apoenzyme
C. Coenzyme III. Haem
D. Prosthetic group IV. Co-factor
V. Coenzyme
The correct match is
A) A-IV, B-I, C-II, D-III B) A-IV, B-III, C-II, D-I
C) A-IV, B-II, C-I, D-III D) A-IV, B-II, C-III, D-I
ANSWER KEY
1.D 2.C 3.C 4.C 5.B 6.D 7.B