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ENZYMES
Dr. KHUSHBU SONIAssistant Professor
AIMS,Dewas
o Enzymes are biological catalysts that speed up the rate of the biochemical reaction without undergoing permanent change in overall process.
o Substrate is reactant on which enzyme acts and converts it into a product.
o Zymogens (pro enzyme) are inactive form of enzymes. E.g. proelastase, chymotrypsinogen
Nomenclature of enzymesEnzymes are classified by two ways
Recommended name systematic name
o Trivial name (trypsin, pepsin)o Conveniento Easy to everyday useo Suffix –ase is used after substrate
e.g. lactase, ureaseo after type of reaction
e.g. oxidase
A systematic classification of enzymes has been developed by International union of biochemistry.
This classification is based on the type of reactions catalyzed by enzymes.
There are six major classes.
Enzyme Code (E.C.) = Four Digits
1. First (main class) = Type of Reaction 2. Second (subclass) = Type of Group involved 3. Third (sub-subclass) = denotes Substrate 4. Fourth = Individual enzyme name & serial numberE.C. 1. OxidoreductasesE.C. 2. TransferasesE.C. 3. HydrolasesE.C. 4. LyasesE.C. 5. IsomeraesE.C. 6. Ligases
1. OxidoreductasesCatalyzes a variety of oxidation-reduction reactionWith help of NADH, NADPH , FADH2 , FMNCommon examples
Dehydrogenases - Oxidases Peroxidases - Reductases
2. Transferases
Catalyzes transfer of functional group from one molecule to another.Carboxyl Methyl AcylGlycosyl amino
Kinase transfer of Phosphate group
3. Hydrolases
Cleavage of C-C, C-O, C-N & other Covalant bonds By addition of water.Example
Protease (Trypsin, Chymotrypsin, Pepsin ,Collagenase)
AmylaseLipasePhosphataseUrease
4. Lyases
Removal of group from substrates or break bonds by mechanism other than hydrolysis or oxidation.
ExampleAldolaseEnolaseFumaraseArginosuccinasePyruvate decarboxylaesHMG CoA lyase
5. Isomerases
produce Optical or Geometric isomer of substrateExample
RacemasesEpimerasesTriose phosphate isomeraseMutase
6. LigasesLink two substrate Usually with help of ATPExample
SynthetasePyruvate carboxylaseDNA Ligase
Co-factors and Co-enzymes
Some enzymes require molecules other than proteins for their action.
Apoenzyme = Enzyme (Protein moiety) = inactive
Holo-enzyme = Apoenzyme + Non-protein component
Non-protein component
Inorganic metal ion Organic molecule
Co-factor Co-enzyme
Metalloenzymese.g. Zn++ - carbonic anhydrase Mg++ - hexokinase
Prosthetic group
Co-substrate
Co-substrate
Prosthetic group
o When co-enzyme is loosely bound with enzyme
o After reaction, dissociates in altered state
o Need to be recycled by different reaction
o e.g. NAD+
o When co-enzyme is tightly bound with enzyme
o After reaction, returns to original form
o E.g. FAD
The term Apoenzyme is applicable to:
a) Simple enzyme
b) Protein part of conjugate enzyme
c) Organic co-factor of a conjugate enzyme
d) Inorganic co-factor of a conjugate enzyme
Zymogen is:
a) Enzyme modulator
b) Enzyme inhibitor
c) Enzyme precursor
d) Enzyme poison
Pyruvate carboxylase is:
a) Kinaseb) Lyasec) Transferased) ligase
Pyruvate decarboxylase is:
a) Oxido-reductaseb) Hydrolasec) Ligased) Lyase
Characteristics of enzymeso Most enzymes are three dimensional globular
proteins (tertiary and quaternary structure).
o Some special RNA species also act as enzymes and are called Ribozymes
o Water soluble
o Not consumed during reaction
o Their presence does not effect the nature and properties of end product.
o Enzymes are sensitive to change in pH, temperature and substrate concentration
o Active site: special pocket or cleft that binds substrates, co-factors and prosthetic groups and contains residue that helps to hold the substrate.
o generally occupy less than 5% of the total surface area of enzyme.
o has a specific shape due to tertiary structure of protein.
oContains substrate binding site and catalytic site.
oContains amino acid side chains involved in substrate binding and catalysis called as “catalytic residues”
oBinding occurs by non covalent forces.
oA change in the shape of protein affects the shape of active site and function of the enzyme.
Catalytic efficiencyenzyme catalyzed reactions are 1000 times faster than uncatlayzed one.
Turnover number defined as the number of substrate molecules transformed per second by one enzyme molecule.
Action of enzyme can be regulated depending on the production need of cell.
Cellular location: some localized in specific organelles, some are secreted out of the cell.
Specificity: ability of enzyme to discriminate between two competing substrates.
types
reactionsubstrate stereo
broad relative absolute
bond group e.g. urease e.g. hexokinase
e.g. alpha-amylasee.g. trypsin
L-lactate dehydrogenase
Lock and key model
o Proposed by EMIL FISCHER.
o Lock and key hypothesis assumes the active site of an enzymes are rigid in its shape.
o There is no change in the active site before and after a chemical reaction.
Koshland’s Induced Fit TheoryAccording to this theory, exposure of an enzyme to substrate cause a change in enzyme, which causes the active site to change it’s shape to allow enzyme and substrate to bind.
Reactions have an energy barrier
That energy barrier separate substrates and products.
It is difference between energy of the reactants and a high-energy intermediate that occurs during the formation of product.
Energy barrier = free energy of activation
Mode of action of enzymes
Rate of ReactionTo reach transition state
Substrate must contain sufficient energy.Enzyme
Rate of reaction is determined by the number of such energized molecules. In general, enzymes…
1. Lower the free energy of activation2. More molecules have sufficient energy to
pass3. Easily reach to transition state4. Faster the rate of the reaction.
Enzyme enhances rate of a biochemical reaction, as it:
a) Increases activation energy
b) Decreases activation energy
c) Increases substrate concentration
d) None of above
Mechanism of enzyme catalysis
Catalysis by
proximity
Metal ion catalysis
Covalent catalysis
Acid base catalysis
Catalysis can occur through proximity and orientation effects
o Enzymes are usually much bigger than their substrates
o By oriented binding and immobilization of the substrate, enzymes facilitate catalysis by:
1. bring substrates close to catalytic residues 2. Binding of substrate in proper orientation3. Stabilization of transition state by electrostatic interactions
Substrate stabilization in Transition stateThe active site acts as a flexible molecular template. Binds the substrate in a geometrically favorable manner.And activate transition state of the molecule By stabilizing the substrate in its transition state, the enzyme increases the concentration of the reactive intermediate.That can be converted to product.
Visualization of Transition state
Conversion of substrate to product can be visualized as being similar to removing a sweater from an uncooperative infant. We can en-vision a parent acting as an enzyme. Parent comes in contact with the baby (forming ES)Guide baby's arms to remove sweater. (ES transition state) Guidance (conformation) = facilitate the process.Removal of Sweater + Disrobed baby (Product)
o Enzymes contain catalytic residues at their active site
o Side chains of amino acids offer a variety of nucleophilic centers for catalysis
o Can form temporary covalent bond with
substrate molecule
o Enzyme-substrate intermediate
o At the end of reaction, the covalent bond must be broken to regenerate enzyme.
Covalent catalysis
Acid-base catalysis
o Active site may contains residue like histidine
o Participate in hydrogen ion transfer,
o by transferring hydrogen ion, the active site may:• Activate nucleophiles required in
catalysis
• Stabilize charged groups
• Facilitate electrostatic interactions that may stabilize transition state
Metal ion catalysis
o Metal ions like Zn, Mg, Fe etc.. are used as co-factor by various enzymes.
o Metal atoms lose electron easily and exist as cations
o The positive charges on metal ions allow them to:• Stabilize transient and intermediate
structures in the reaction• Assist in forming strong nucleophilic
group• Hold the substrate inside the active site
Carbonic anhydrase
Factors Affecting Enzyme Reaction
1. Substrate concentrationRate of reaction increases with substrate concentrationUntil Vmax is reached.At high conc. of substrate = enzyme full saturated with substrate.
2. TemperatureMaximum reaction velocity at Optimum
temperature.Optimum temperature for most human enzymes
is 35° - 40°C. Human enzymes start to denature above 40°C
temperature.
Effect of Temperature on Enzyme activity
3. pHo Concentration of H+ affects active site
o So Velocity reaction affected
o Change in pH can denature enzyme
o Optimum pH is different for different enzyme.
What change can occur at active site, because of change in pH?
Effect of pHIf the pH changes much from the
optimumChemical nature of the amino acids
can change. Change in Ionization of amino acid at
active site.Result in a change in the bonds. Active site will be disrupted.Enzyme will be denatured.
Different enzyme with it’s optimum pH
4. Enzyme concentration
Rate of the reaction is directly proportional to the enzyme concentration at all substrate concentrations.
5. Product concentrationAs product concentration increases,
enzymatic reaction slow down.
Higher Product concentration Inhibits reaction.
6. Enzyme activation Activation by co-factors.
In presence of certain metallic ions, some enzyme shows higher activity.
Salivary amylase = chlorideLipase = calcium
Conversion of an enzyme precursor. Specific proteolysis is a common method of
activating enzymes and other proteins in biological system.
Zymogen activation by proteolytic cleavage
Velocity &Vmax of reaction
Rate or Velocity of a reaction (V) is the number of substrate molecules converted to product per unit time.Vmax is the maximum velocity of the reaction.Expressed as µmol of product formed per minute.
Michaelis-Menten EquationReaction model
Leonor Michaelis and Maude MentenIn this model,
Enzyme reversibly combines with its substrate
Form an ES complexSubsequently yields productRegenerating the free enzyme.
where: S is the substrate E is the enzyme ES-is the enzyme substrate complex P is the product K1,K-1 and K2 are rate constants
Michaelis-Menten Equation
Km (Michaelis constant)It is the [S] for achieving half of the Vmax.
Km = Substrate concentration at ½Vmax.
Reflects the affinity of the enzyme for substrate.
Small KmHigh affinity of the enzyme for substrate.Because a low concentration of substrate
is needed to reach ½Vmax of velocity.
Large Km Low affinity of enzyme for substrate Because a high concentration of substrate
is needed to reach ½Vmax of velocity.
Assumptions in the Michaelis-Menten equation
Relative concentrations of E and S[S] is much greater than [E], so that the
percentage of total substrate bound by the enzyme at any one time is small.
Steady-state assumption [ES] does not change with time (the steady-
state assumption).The rate of formation of ES is equal to that of
the breakdown of ES (to E + S & to E + P).
Initial velocity
Initial reaction velocities (Vo) are used in the analysis of enzyme reactions. This means that the rate of the reaction is measured as soon as enzyme and substrate are mixed. At that time, the concentration of product is very small and, therefore, the rate of the back reaction from P to S can be ignored.
ENZYME REGULATION
Allosteric regulatio
nReversible covalent
modification
Proteolyticcleavage
Induction and
repression
o It permits changing needs of the cell to meet its energy and resource demands.
o If a product is available in excess, enzyme regulation could then divert the resources to other needy reactions.
Why?
o Regulatory enzymes : in a multi-step enzymatic process, there will be one enzyme which will be responsible for overall rate of that process.
o Key enzyme or rate limiting enzyme
o Can be affected by signal molecules
Allosteric regulationo Allosteric enzymes are a class of regulatory
enzymes.
o Large and composed of many subunits.
o Contains allosteric site different from active site.
o Regulatory molecules bind at allosteric site.
o Can be affected by regulatory molecules = allosteric effectors (modulator)
o Binding can enhance or reduce enzyme activity.
o Modulator may have positive effect or negative effect.
o Two types of allosteric enzyme based on nature of modulator:
Homotropic allosteric enzymesHeterotopic allosteric enzymes
o Typically, allosteric regulation occurs via FEEDBACK mechanisms.
oNegative feedback positive feedback
oAllosteric enzymes show variation in kinetics.
o They do not follow michaelis menten kinetics.
o They show sigmoidal curve instead of hyperbolic curve when velocity [v] is plotted against [s].
Positive feedback
Covalent modificationo Enzyme activity may be regulated by
reversible covalent modification.
o Separate enzymes are used to add or to remove modifying groups.
o Phosphorylation is the most common type.
o Addition of phosphate group to Ser,Tyr,Thr.
o ATP and GTP donates phosphate.
Zymogen activation by proteolytic cleavage
Induction and Repression Regulate the amount of enzyme.Act at Gene level.Altering rate of enzyme synthesis. Increase enzyme synthesis = InductionDecrease enzyme synthesis = Repression Induction / Repression = Slow (hours to days)Allosteric regulation = Fast (seconds to minutes)
Feedback regulation
ISOENZYMES
Catalyze the same reaction
Two or more polypeptide chains
Different polypeptide chains are products of different genes
Differ in AA sequence and physical properties
Separable on the basis of charge
Are tissue specific
“They are physical distinct forms of the same enzyme ”
Different allosteric effectors and different kinetics
Type of
LDH
Composition Location
LDH 1 HHHH MyocardiumLDH 2 HHHM RBCLDH 3 HHMM LungLDH 4 HMMM Kidney &
PancreasLDH 5 MMMM Skeletal
muscle & Liver
Creatine Kinase - DimerType of CK Compositio
nLocation
CK- 1 (CK-BB) BB BrainCK- 2 (CK-MB) MB MyocardiumCK- 3 (CK-MM) MM Skeletal
Muscle
Identification of Isoenzymes
1. Electrophoresis2. Heat stability : BALP3. Inhibitors4. Substrate specificity (Km value)o e.g. Hexokinase & Glucokinase
5. Cofactor requiremento e.g. Mitochondrial ICD – NAD+ dependent
Cytoplasmic ICD – NADP+ dependent6. Tissue location7. Specific antibody
Isoenzymes of Alkaline Phosphatase
Depending on number of sialic acid residue1. Alpha – 1 ALP (10%) Biliary Canaliculi2. Alpha – 2 heat labile ALP (25%) Hepatic cells3. Alpha – 2 heat stable ALP (1%) Regan Isoenzyme
Placental cell 4. Pre – beta ALP (50%) Bone disease5. Gamma – ALP (10%) Intestinal cells6. Leucocyte ALP Leucocyte
Organ Specific Enzyme
Heart CK-MB , AST (GOT) , LDH Liver ALT , AST , LDH , Alkaline
PhosphataseGamma Glutamyl Transferase
Pancreas
Lipase ,Amylase
Muscle Aldolase , CK-MM , CK-Total , AST
Bone Alkaline PhosphataseProstate Acid Phosphatase
(Prostate isoform – inhibited by Tartrate)
RBC LDH Acid Phosphatase (Erythrocyte isoform – inhibited by formaldehyde & cupric ion)
Principal Sources Diagnostically Important Enzyme
Liver Alanine aminotransferase(ALT)
Liver, Gall Bladder, Erythrocytes Skeletal muscle, Heart, Kidney ,
Aspartate aminotransferase(AST) I (cytosol) & II (mitochondria)
Hepatobilliary tract, Kidney Gamma Glutamyl Transferase
Hepatobilliary tract 5’ Nucleosidase Bone, Gall Bladder ,Liver, Intestinal mucosa, Placenta, Kidney
Alkaline Phosphatase (ALP)
Prostate, Erythrocytes Acid Phosphatase Pancreas ,Salivary glands, Ovaries
Amylase
Pancreas Lipase
Enzyme as Therapeutic Agents
1. Streptokinase & Urokinase• Lysis of intravascular clot• Use in myocardial infarction
2. Asparaginase• Used as anticancer drugs.
1. Glucose oxidase & Peroxidase (GOD-POD)
2. Urease3. ELISA test4. Restricted Endonuclease
Enzyme as Diagnostic Agents