enzyme-and-metabolism-1209062589787828-9

8/8/2019 enzyme-and-metabolism-1209062589787828-9

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OBJECTIVES:

By the end of the lesson, studentshould be able to :

Define terms enzyme. Understand the Lock & Key model

and Induced-fit model.

Identify the groups of enzymes. Understand some factors affecting

the enzyme activities.


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Enzymes are proteins that catalyze (i.e.

accelerate) and control the rates of chemical

reactions.

In enzymatic reactions, the molecules at thebeginning of the process are called substrates,

and the enzyme converts them into different

molecules, the products.

Almost all processes in a biological cell needenzymes in order to occur at significant rates.


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Since enzymes are extremely selective for

their substrates and speed up only a few

reactions from among many possibilities,the set of enzymes made in a cell

determines which metabolic pathways

occur in that cell.


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ENZYME AS BIOLOGICAL

CATALYSTS:

Enzymes are biological catalysts producedby living cells.

Enzymes lower the amount of activationenergy needed.

They speed up the rate of biochemicalreactions in the cell but remain unchanged

at the end of the reactions. Most enzymes are globular protein

molecules.


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The chemicals which an enzyme acts on iscalled its substrate.

The enzyme combines with its substrate toform an enzyme-substrate complex.

The complex than breaks up into product andenzyme.

A metabolic pathway is a number of reactions

catalysed by sequence of enzymes.


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Each enzyme is specific for one and

ONLY one substrate (one lock - one key)

active site: part of the enzyme that fits withthe substrate

Note that the active site has a specific fit for

this particular substrate and no other.

This theory has some weaknesses, but it

explains many basic things about enzyme

function.


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Substrate: The starting molecules for a

chemical reaction are called the substrates. Enzyme substrate complex: The enzyme

substrate complex is transitional step when thesubstrates of a chemical reaction are bound to

the enzyme. Active site: The area on the enzyme where the

substrate or substrates attach to is called theactive site.

Enzymes are usually very large proteins and theactive site is just a small region of the enzymemolecule.


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The induced-fit theory assumes that the substrate

plays a role in determining the final shape of the

enzyme and that the enzyme is partially flexible.

This explains why certain compounds can bind tothe enzyme but do not react because the enzyme

has been distorted too much.

Other molecules may be too small to induce the

proper alignment and therefore cannot react.

Only the proper substrate is capable of inducing

the proper alignment of the active site.


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In the graphic, the substrate is

represented by the magenta molecule, the

enzyme protein is represented by the

green and cyan colors.

The cyan colored protein is used to more

sharply define the active site.

The protein chains are flexible and fit

around the substrate.


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The advantages of the induced fitmechanism arise due to the stabilizing effect

of strong enzyme binding. There are two different mechanisms of

substrate binding; uniform binding whichhas strong substrate binding, anddifferential binding which has strongtransition state binding.

The stabilizing effect of uniform binding

increases both substrate and transition statebinding affinity and differential bindingincreases only transition state bindingaffinity.


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Both are used by enzymes and have beenevolutionarily chosen to minimize the G ofthe reaction.

Enzymes which are saturated, ie. have ahigh affinity substrate binding, requiredifferential binding to reduce the G,whereas largely substrate unboundenzymes may use either differential oruniform binding.


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How do enzymes work?

substrate: molecules upon which an

enzyme acts. The enzyme is shaped so

that it can only lock up with a specific

substrate molecule.

enzyme

substrate -------------> product


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The diagram shows time on the horizontalaxis and the amount of energy in the

chemicals involved in a chemical reaction

on the vertical axis. The point if this diagram again is that

without the enzyme, much more activation

energy is required to get a chemicalreaction to take place.


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Temperature: strongly influences enzyme

activity optimum (best) temperature for

maximum enzyme function is usually about 35-

40 C.

Reactions proceed slowly below optimaltemperatures.

Above 45 C. most enzymes are denatured

(change in their shape so the enzyme active site

no longer fits with the substrate and the enzymecan't function)


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METABOLISM

Metabolism is the sum of all biochemical

reactions occurring in living cells.

These reactions can be divided into twomain groups:

1) ANABOLISM

2) CATABOLISM


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Involves the

synthesis of complexmolecules from

simpler molecules

which requires energy

input.

Involves the

breakdown of

complex moleculesinto simpler

molecules involving

hydrolysis or

oxidation and therelease of energy.


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Energy releasing processes, ones that"generate" energy, are termed exergonicreactions.

Reactions that require energy to initiatethe reaction are known as endergonicreactions.

All natural processes tend to proceed insuch a direction that the disorder orrandomness of the universe increases


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In an exergonic reaction the change is

free energy is represented by a

negative number (-G), indicating free

energy is released during the reaction.


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This kind of reaction is not termed aspontaneous reaction. In order to go

from the initial state to the final state a

considerable amount of energy must beimparted to the system.

These kinds of reactions are associated

with a positive number (+G).


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The speed Vmeans 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] forVmax 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.


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Vo = Vmax

KM

Vo = Initial reaction velocity

Vmax = Maximum velocity

Km = Michaelis constant

[S] = Substrate concentration


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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.


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Vitamin Coenzyme Function

niacinnicotinamide adenine

dinucleotide (NAD+)

oxidation or

hydrogen transfer

riboflavinflavin adenine

dinucleotide (FAD)

oxidation or

hydrogen transfer

pantothenic

acidcoenzyme A (CoA) Acetyl group carrier

vitamin B-12 coenzyme B-12

Methyl group

transfer

thiamin (B-1)thiaminpyrophosphate

(TPP)

Aldehyde group

transfer


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Coenzyme Q10 is a fat-soluble nutrient also knownas CoQ10, vitamin Q10, ubidecarenone, orubiquinone.

It is a natural product of the human body that is

primarily found in the mitochondria, which are thecellular organelles that produce energy.

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

Ubiquinone takes its name from a combination ofthe word ubiquitous, meaning something that isfound everywhere, and quinone 10.


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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 thatprovides energy, CoQ10 also stabilizescell membranes and acts as anantioxidant.

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


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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.


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A nonspecific inhibition effects all enzymes

in the same way.

Non-specific methods of inhibition includeany physical or chemical changes which

ultimately denatures the protein portion of

the enzyme and are therefore irreversible.


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Temperature: Usually, the reaction rate

increases with temperature, but with enzyme

reactions, a point is reached when thereaction rate decreases with increasing

temperature.

At high temperatures the protein part of the

enzyme begins to denature, thus inhibiting

the reaction.


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A competitive inhibitor is any compoundwhich closely resembles the chemicalstructure and molecular geometry of the

substrate. The inhibitor competes for the same active

site as the substrate molecule.

The inhibitor may interact with the enzymeat the active site, but no reaction takesplace.


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The inhibitor is "stuck" on the enzyme andprevents any substrate molecules from reactingwith the enzyme.

However, a competitive inhibition is usuallyreversible if sufficient substrate molecules areavailable to ultimately displace the inhibitor.

Therefore, the amount of enzyme inhibition

depends upon the inhibitor concentration,substrate concentration, and the relativeaffinities of the inhibitor and substrate for theactive site.


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A noncompetitive inhibitor is a substance thatforms strong covalent bonds with an enzymeand consequently may not be displaced by theaddition of excess substrate.

Therefore, noncompetitive inhibition isirreversible.

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 tothe degree that it ceases to work.


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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 alsochanged.


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There are approximately 3000 enzymeswhich have been characterised.

These are grouped into six main classes

according to the type of reactioncatalysed.

At present, only a limited number are used

in enzyme electrodes or for otheranalytical purposes.


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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.


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catalyse hydrogen transfer from the substrate

to molecular oxygen producing hydrogen

peroxide as a by-product. An example of thisis FAD dependent glucose oxidase which

catalyses the following reaction:

b-D-glucose + O2 = gluconolactone + H2O2

oxidases


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dehydrogenases

catalyse hydrogen transfer from the substrate

to a nicotinamide adenine dinucleotide

cofactor (NAD+). An example of this is lactate

dehydrogenase which catalyses the followingreaction:

Lactate + NAD+ = Pyruvate + NADH + H+


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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 presenceof hydrogen peroxide:

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


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catalyse substrate oxidation by molecular

oxygen.

The reduced product of the reaction in thiscase 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


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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.


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3.Hydrolases

These enzymes catalyse cleavagereactions or the reverse fragmentcondensations.

According to the type of bond cleaved, adistinction is made between peptidases,esterases, lipases, glycosidases,phosphatases and so on.

Examples of this class of enzyme include;cholesterol esterase, alkaline phosphataseand glucoamylase.


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4.Lyases

These enzymes non-hydrolytically remove

groups from their substrates with the

concomitant formation of double bonds or

alternatively add new groups acrossdouble bonds.


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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 theisomerisation of glucose to fructose.


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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 suchas 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


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IEC Classification of Enzymes

Group Name Type of Reaction Catalyzed

Oxidases orDehydrogenases

Oxidation-reductionreactions

TransferasesTransfer of functional

groups

Hydrolases Hydrolysis reactions

LyasesAddition to double bonds or

its reverse

Isomerases Isomerization reactions

Ligases or SynthetasesFormation of bonds with

ATP cleavage


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Enzymes do NOT change the equilibrium position of thereaction, just the speed at which equilibrium is attained.

Most are globular or soluble.

Stereospecific (can recognize certain isomers only) due to

the fact that amino acids of the active site are chiralthemselves.

Substrate/s bind in hydrophobic cleft (active site) betweenseveral domains where catalysis occurs: Van der Waals forces

Hydrophobic interactions Electrostatic interactions

Active site has structure that is complimentary in structure tothe structure of its substrate.


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Most are proteins, some are RNA.

Biological catalysts. E + S ES EP E + P

Not changed by the reaction overall

Much higher reaction rates than uncatalyzed reactions.

Allow for biochemical reactions to occur under very mildconditions (temperature, near-neutral pH, 1 atm pressure)

High yield of products (few side reactions or by-products)

Very specific reactions (specific for its substrate or a family ofrelated substrates)

Often a regulated functions:

allosteric activation or inhibition

covalent modification (phosphorylation changes)

enzyme expression controlled or cleavage of proenzymecontrolled.


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Describe what metabolism is?

What is the difference between anabolism

and catabolism?

What is a substrate?

List 6 types of enzyme and state the

characteristics each of them.

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enzyme-and-metabolism-1209062589787828-9