AReport onEnzymes

BySanjay Jagarwal

(10112047)Chemical B.tech 3rd year

Enzyme Action

Enzymes: proteins that function as biological catalysts.

Catalyst: a substance that speeds up a chemical reaction and is not changed by the reaction.

Specificity:Enzymes are usually very specific as to Which reaction they catalyze.

Highly specific Enzymes follows  "proof-reading" mechanisms

“Lock and key” model

However certain substances can bind to the enzyme at sites other than theActive site and modify its activity (inhibitors/co-factors)

Idea that the enzyme is flexible.

Induced FitThis model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactionsrapidly induce conformational changes in the enzyme that strengthen binding.

Enzyme reactions

enzyme + productenzyme-substrate complex

E +PES

enzyme + substrate enzyme-substrate complex

E +S ES

Mechanisms

Enzymes can act in several ways, all of which lower ΔG‡ (Gibbs energy):• Lowering the activation energy by creating an

environment in which the transition state is stabilized • Lowering the energy of the transition state, but

without distorting the substrate.• Providing an alternative pathway. • Reducing the reaction entropy change by bringing

substrates together in the correct orientation to react.

Enzyme activity

Four Variables

Temperature

pH

Enzyme Concentration

Substrate Concentration

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Temperature

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0 20 30 5010 40 60

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0 20 30 5010 40 60

40oC - denatures

5- 40oC Increase in Activity

<5oC - inactive

Effect of heat on enzyme activtyIf you heat the protein above its optimal temperature

bonds break meaning the protein loses it secondary and tertiary structure

Effect of heat on enzyme activty

Denaturing the protein

Effect of heat on enzyme activty

Denaturing the protein

ACTIVE SITE CHANGES SHAPE SO SUBSTRATE NO LONGER FITS

Even if temperature lowered – enzyme can’t regain its correct shape

pH effect:

• The ph scale measures how acidic or alkaline a substance is.

• The chemical properties of many solutions enable them to be divided into 3 categories:

1) Neutral: solutions with a ph of 7. 2) Alkaline: solutions with a ph greater than 7 3) Acidic: solutions with a ph less than 7.

pH scale

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1 3 42 5 6 7 8 9

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1 3 42 5 6 7 8 9

Narrow pH optima

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1 3 42 5 6 7 8 9

Narrow pH optima

WHY?

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Narrow pH optima

Disrupt Ionic bonds - Structure

Effect charged residues at activesite

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Enzyme Concentration

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Enzyme Concentration

Enzyme Concentration

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Substrate Concentration

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Substrate Concentration

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Substrate Concentration

Substrate Concentration

Active sites full- maximum turnover

METABOLISM

• Metabolism is the sum of all biochemical reactions occurring in living cells.

• These reactions can be divided into two main groups:– 1) ANABOLISM– 2) CATABOLISM

• Involves the synthesis of complex molecules from simpler molecules which requires energy input.

• Involves the breakdown of complex molecules into simpler molecules involving hydrolysis or oxidation and the release of energy.

• Energy releasing processes, ones that "generate" energy, are termed exergonic reactions.

• Reactions that require energy to initiate the reaction are known as endergonic reactions.

• All natural processes tend to proceed in such a direction that the disorder or randomness of the universe increases

Exergonic Reaction

• This kind of reaction is not termed a spontaneous reaction. In order to go from the initial state to the final state a considerable amount of energy must be imparted to the system.

• These kinds of reactions are associated with a positive number (+G).

Endergonic Reaction

• The speed V means the number of reactions per second that are catalyzed by an enzyme.

• With increasing substrate concentration [S], the enzyme is asymptotically approaching its maximum speed Vmax, but never actually reaching it.

• Because of that, no [S] for Vmax can be given. • Instead, the characteristic value for the enzyme is

defined by the substrate concentration at its half-maximum speed (Vmax/2).

• This KM value is also called Michaelis-Menten constant.

Vo = Vmax KM

• Vo = Initial reaction velocity• Vmax = Maximum velocity

• Km = Michaelis constant • [S] = Substrate concentration

Enzyme NomenclatureFunctional classification:It is widely used. It takes into account the name of the substrate of the enzyme and the type of catalyzed reaction. To designate an enzyme is indicated:the name of the first substratethen the type of reaction catalyzedFinally we add the suffix ase.

For example:- Glucose-6-phosphate isomerase- Isocitrate lyase- Pyruvate carboxylase

When the enzyme uses two substrates and are described by specifying bothradicals of the donor substratethe acceptor substrate and then released the radicalexchanged the radicalthe type of reactionfinally added ase

for example- ATP-glucose phosphotransferase- UDPglucose-fructose glucosyltransferase- Glutamate pyruvate transaminase

Enzyme Nomenclature official

1: oxidoreductases, which catalyze electron transfer2: The transferases, which catalyze the transfer of groups3: hydrolases which catalyze hydrolysis reactions4: lyases, which catalyze the addition of groups to double bonds or vice versa5: isomerases which catalyze the transfer of groups in one molecule to produce isomeric forms (the conversion of an amino acid D-amino acid in L 'for example)6: ligases, which form links CC, CS, CN and CO during condensation reactions coupled with the use of ATP.

The different types of enzymes:• 4.1 - of redox enzymes and oxygen fixation• 4.1.1 - dehydrogenation of the alcohol, carbonyl

or• carboxyl• 4.1.2 - dehydrogenases appear by double bonds• 4.1.3 - dehydrogenases acting on functions

nitrogenous• 4.1.4 - enzymes involved in the transfer of

electrons in the mitochondria• 4.1.5 - oxygenases• 4.2 - transferases• 4.2.1 - enzymes transferring a methyl group• 4.2.2 - the transferring enzymes radicals has more

carbons• 4.2.3 - the transferring enzymes of carbohydrate

molecules• 4.2.4 - aminotransferases• 4.2.5 - Phosphotransferases• 4.3 - hydrolases• 4.3.1 - carbohydrate hydrolases• 4.3.2 - hydrolases phosphoric esters of

monosaccharides

4.3.3 lipid hydrolases4.3.4 - hydrolases of peptides and proteins4.3.5 - hydrolases nucleosides, nucleotides and nucleic acids4.3.6 - hydrolase esters or phosphoric anhydride4.4 - lyases and synthases4.4.1 - decarboxylases4.4.2 - aldehyde-lyases4.4.3 - acyl-lyase or acylsynthase4.4.4 - hydratases and dehydratases4.5 - isomerases4.5.1 - epimerization4.5.2 - intramolecular redox4.5.3 - transport of radicals4.6 - ligases (synthetases)4.6.1 - forming links ligases c-o4.6.2 - bond forming ligase c-c4.6.3 - links ligases c-s4.6.4 - links ligases c-n

• A non protein component of enzymes is called the cofactor.

• If the cofactor is organic, then it is called a coenzyme. • Coenzymes are relatively small molecules compared to

the protein part of the enzyme. • Many of the coenzymes are derived from vitamins.• The coenzymes make up a part of the active site, since

without the coenzyme, the enzyme will not function.

Enzyme Cofactor

• In the graphic on the left is the structure for the coenzyme, NAD+, Nicotinamide Adenine Dinucleotide.

• Nicotinamide is from the niacin vitamin. • The NAD+ coenzyme is involved with many types

of oxidation reactions where alcohols are converted to ketones or aldehydes.

Enzyme Cofactor

 Vitamin  Coenzyme  Function

 niacin  nicotinamide adenine dinucleotide (NAD+)

 oxidation or hydrogen transfer

 riboflavin  flavin adenine dinucleotide (FAD)

 oxidation or hydrogen transfer

 pantothenic acid  coenzyme A (CoA)  Acetyl group carrier

 vitamin B-12  coenzyme B-12  Methyl group transfer

 thiamin (B-1)  thiaminpyrophosphate (TPP)

 Aldehyde group transfer

• Coenzyme Q10 is a fat-soluble nutrient also known as CoQ10, vitamin Q10, ubidecarenone, or ubiquinone.

• It is a natural product of the human body that is primarily found in the mitochondria, which are the cellular organelles that produce energy.

• It occurs in most tissues of the human body; however, the highest concentrations are found in the heart, liver, kidneys, and pancreas.

• Ubiquinone takes its name from a combination of the word ubiquitous, meaning something that is found everywhere, and quinone 10.

Co-enzymes

• Quinones are substances found in all plants and animals.

• The variety found in humans has a 10-unit side chain in its molecular structure.

• Apart from the important process that provides energy, CoQ10 also stabilizes cell membranes and acts as an antioxidant.

• In this capacity, it destroys free radicals, which are unstable molecules that can damage normal cells.

• Enzyme inhibitors are molecules that interact in some way with the enzyme to prevent it from working in the normal manner.

• There are a variety of types of inhibitors including: nonspecific, irreversible, reversible - competitive and noncompetitive.

• Poisons and drugs are examples of enzyme inhibitors.

Enzyme inhibitors

• A nonspecific inhibition effects all enzymes in the same way.

• Non-specific methods of inhibition include any physical or chemical changes which ultimately denatures the protein portion of the enzyme and are therefore irreversible.

Non Specific Inhibitor

• Temperature: Usually, the reaction rate increases with temperature, but with enzyme reactions, a point is reached when the reaction rate decreases with increasing temperature.

• At high temperatures the protein part of the enzyme begins to denature, thus inhibiting the reaction.

Example:

• A competitive inhibitor is any compound which closely resembles the chemical structure and molecular geometry of the substrate.

• The inhibitor competes for the same active site as the substrate molecule.

• The inhibitor may interact with the enzyme at the active site, but no reaction takes place.

Competitive Inhibitor

• The inhibitor is "stuck" on the enzyme and prevents any substrate molecules from reacting with the enzyme.

• However, a competitive inhibition is usually reversible if sufficient substrate molecules are available to ultimately displace the inhibitor.

• Therefore, the amount of enzyme inhibition depends upon the inhibitor concentration, substrate concentration, and the relative affinities of the inhibitor and substrate for the active site.

Competitive Inhibitor

• A noncompetitive inhibitor is a substance that forms strong covalent bonds with an enzyme and consequently may not be displaced by the addition of excess substrate.

• Therefore, noncompetitive inhibition is irreversible. • A noncompetitive inhibitor may be bonded at, near,

or remote from the active site. In any case, the basic structure of the enzyme is modified to the degree that it ceases to work.

Non-Competitive Inhibitor

Noncompetitive Inhibitor Action:

• If the inhibition is at a place remote from the active site, this is called allosteric inhibition.

• Allosteric means "other site" or "other structure".

• The interaction of an inhibitor at an allosteric site changes the structure of the enzyme so that the active site is also changed.

Non-Competitive Inhibitor

• There are approximately 3000 enzymes which have been characterised.

• These are grouped into six main classes according to the type of reaction catalysed.

• At present, only a limited number are used in enzyme electrodes or for other analytical purposes.

1.Oxidoreductases

• These enzymes catalyse oxidation and reduction reactions involving the transfer of hydrogen atoms or electrons.

• The following are of particular importance in the design of enzyme electrodes.

• This group can be further divided into 4 main classes.

– catalyse hydrogen transfer from the substrate to molecular oxygen producing hydrogen peroxide as a by-product. An example of this is FAD dependent glucose oxidase which catalyses the following reaction:

– b-D-glucose + O2 = gluconolactone + H2O2

Oxidases

Dehydrogenases– catalyse hydrogen transfer from the substrate to a

nicotinamide adenine dinucleotide cofactor (NAD+). An example of this is lactate dehydrogenase which catalyses the following reaction:

– Lactate + NAD+ = Pyruvate + NADH + H+

Peroxidases– catalyse oxidation of a substrate by hydrogen

peroxide. – An example of this type of enzyme is horseradish

peroxidase which catalyses the oxidation of a number of different reducing substances (dyes, amines, hydroquinones etc.) and the concomitant reduction of hydrogen peroxide.

– The reaction below illustrates the oxidation of neutral ferrocene to ferricinium in the presence of hydrogen peroxide:

– 2[Fe(Cp)2] + H2O2 + 2H+= 2[Fe(Cp)2]+ + 2 H2O

– catalyse substrate oxidation by molecular oxygen. – The reduced product of the reaction in this case is

water and not hydrogen peroxide. – An example of this is the oxidation of lactate to

acetate catalysed by lactate-2-monooxygenase. – lactate + O2 = acetate + CO2 + H2O

Oxygenases

2.Transferases

• These enzymes transfer C, N, P or S containing groups (alkyl, acyl, aldehyde, amino, phosphate or glucosyl) from one substrate to another.

• Transaminases, transketolases, transaldolases and transmethylases belong to this group.

3.Hydrolases• These enzymes catalyse cleavage reactions or

the reverse fragment condensations. • According to the type of bond cleaved, a

distinction is made between peptidases, esterases, lipases, glycosidases, phosphatases and so on.

• Examples of this class of enzyme include; cholesterol esterase, alkaline phosphatase and glucoamylase.

4.Lyases

• These enzymes non-hydrolytically remove groups from their substrates with the concomitant formation of double bonds or alternatively add new groups across double bonds.

5.Isomerases

• These enzymes catalyse intramolecular rearrangements and are subdivided into;

» racemases » epimerases » mutases » cis-trans-isomerases

• An example of this class of enzyme is glucose isomerase which catalyses the isomerisation of glucose to fructose.

6.Ligases

• Ligases split C-C, C-O, C-N, C-S and C-halogen bonds without hydrolysis or oxidation.

• The reaction is usually accompanied by the consumption of a high energy compound such as ATP and other nucleoside triphosphates.

• An example of this type of enzyme is pyruvate carboxylase which catalyses the following reaction:

• pyruvate + HCO3- + ATP = Oxaloacetate + ADP + Pi

The End