lec 1 3 energetic biology 2

7/29/2019 Lec 1 3 Energetic Biology 2

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Biocatalysis


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1.0Biocatalysis1.1Definition of enzymes

1.2 Enzyme classification according to IUB

convention characteristic of enzymes

1.3 Properties of enzyme and factors influencingenzymes activities

how enzymes function1.4Mechanism activation energy

1.5Co-factors and inhibitors


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Enzymesnzymes


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Biocatalysis

Enzyme is protein molecules Made by living cellsActing as biological catalysts (speed up the rate of

biochemical/metabolic reactions in the cell at bodytemp.)

Not chemically changed at the end of the reaction lower the amount of activation energy needed.

Most enzymes are globular protein molecules.(A few ribozymes made of RNA have beendiscovered).


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Enzymes

Regulate almost all the cellular reactions w/in cell ,has over 1000 reactions take place

Each reaction is catalysed by specific enzyme at particularplace w/ in a cells

Occur in small steps in orderly manner The chemical which an enzyme acts on is called as

substrate.

The enzyme combines with its substrate to form anenzyme-substrate complex.

The complex then breaks up into product and enzyme.

A metabolic pathway is a number of reactionscatalysed by a sequence of enzymes.


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lock- and key hypothesis

substrate ('key') enteringactive site of enzyme

formation ofan enzyme -substrate complex

products leaving active

site of enzyme

enzyme isregenerated

The active site of the enzyme ('lock'} has a shape which is an exact fit for the

substrate ('key')

substrate product

enzyme


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Metabolism

Take places in the body of living thing to keeplife process going on

Metabolism , need to take place

fast enough to keep us alive Eg, if our heart muscles were not supplied With

sufficient energy at certain rate, blood circulationwould slow down & we probably die from suffocation(sesak nafas)

Can increase the reaction speed by raising thetemperature, but not too high since it kill an organismby denaturing (musnah) the protein


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Metabolism.

Consists of anabolism & catabolism

Catabolism

Breaking down of substance (complexmolecules) to produce energy for work

Involve hydrolysis/ oxidation process

Eg. process produce energy

Respiration( occur w/in the cells)

Digestion (occurs outside cells)


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Anabolism

The synthesis of new substances that are

necessary for life Requires energy input

Eg.

Reactions converting excess sugar/glucose toglycogen for storage

Building of new proteins from amino acids


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Enzyme classification according

to IUB convention

Standardise the naming of enzyme was

done by the International Union of

Biochemistry (IUB) in 1961

named by taking its substrate by adding

the suffix -ase

Peptin -peptidase

Classified into 6 main groups by the

nature of their actions


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No Class of enzyme

Action Eg. Of enzyme

1 Hydrolyse Hydrolyses

(add water)

Peptidase, lipase

2 lyase Breaks these chemicalbonds:C-O,

C-C or C-N

Decarboxylase

3 Isomerase Rearranges functionalgroups

Isomerase, mutase

4 Ligase Connects two molecules Synthetase

5 OxyreductaseInclude oxidation andreduction (redox)

Dehydrogenase,oxidase

6 Transferase Transfers the functionalgroups from onemolecule to another

Transaminase,phosphorylase

6 main groups/classification of enzymes


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Definition/Function

Substrate The chemical which an enzyme actson

Reactant substrate /complex molecule

product The enzyme-substrate complex that breaks up intoproduct and enzyme.

Cofactors Non protein substancerequired for the proper function of an enzyme

3 types

Prosthetic group

Coenzymes

activators

coenzymes Cofactors/vitamins

inhibitor Inhibit the enzymes reaction

Reduce the rate of enzyme reaction


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General characteristic of enzymes

1. speed up the rate of biochemical/metabolic reactionsin the cell at body temp.)

2. Only small amount of enzyme is needed to catalyse alot of substrate

3. Enzymes are very specific- each class of enzyme willcatalyse only one particular reaction

4. enzymes catalysed reversible reactions,

5. Some able to work in the presence of a coenzymes

6. Not used up/destroyed in the reactions, can be reusedagain

7. Are affected by the changes in temp and pH


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Enzyme kinetics

Enzyme kinetics is the study of the rates

at which an enzyme works.

The rate is influenced by several factors:

(a) The concentration of substrate

molecules

(b) Temperature(c) Presence of competitive and non-

competitive inhibitors

(d) pH


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Factors that effectenzyme activity

How it effects the enzyme activity

High temperature Breaks hydrogen bonds, alters secondary and tertiaryprotein (enzyme) shape (denaturation)

Changes in pH Hydrogen ion concentration disrupts ionic bonds andchanges charges on enzyme active site and substrate

Substrate concentration Increased substrate concentration increases reactionrate untilall enzymes are involved, then reaction rate levels out

Enzyme concentration Increased enzyme concentration increases reactionrate until all substrates are used up, then reaction ratelevels out

Factors that effect Enzyme activity


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Enzyme reduce activation energy

1 In a chemical reaction, the reactants

must first reach a high-energy

intermediate state called the transition

state before the products are formed.

2 The amount of energy required for

reactants to reach the transition state

before changing into the product is calledactivation energy.


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3 An enzyme provides an alternatereaction pathway.

The enzyme can bind to thesubstrate(reactant) to form an enzyme-substrate complex, which corresponds to thetransition state.

The shape of the substrate is slightlychanged, existing bonds are broken and newones are formed.

This makes it easier for the substrate to be

changed into the product. The enzyme-substrate state is of lower energy than thetransition state in the uncatalysed reaction


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5 An enzyme therefore acts as a biological

catalyst.

It lowers the activation energy needed

thus speeds up biochemical reactions.

Without enzymes, most of the biochemical

reactions in living cells at body temperature

would occur very slowly or not at all.


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Activation energy for an enzyme catalysed & an uncatalysed reaction. Anenzyme reduces the activation energy required for a chemical reaction totake place.


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Properties of enzymes1. Enzymes are biological catalysts.

2. Enzymes are specific for one particular reaction or a group of related

reaction reactions.

3. Enzymes are destroyed by high temperatures or extreme pH.

4. The activity of enzymes are regulated.

5. Enzymes are coded for by DNA in cells.

6 Enzyme activity can be affected by temperature, pH, inhibitors,substrate concentration and enzyme concentration.

7. Enzymes are required in small amounts because they can be usedover and over again.

8. Enzymes lower the activation energy of the reactions that are

catalysed.9. Their presence do not alter the nature or properties of the end

products of the reaction.

10. The catalysed reaction is reversible.

11.Enzymes are not changed or consumed by the reaction; therefore,they can be used over and over again.


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1.3 Properties/characteristic of

enzymes %%%

1 Enzymes are globular proteins. They lower the activation energy required for

reactions to take place.

They act as biological catalysts and speed up therate of metabolic reactions.

2 Enzymes are highly specific in action. Enzymes possess active sites and will only catalyse

reaction when the substrate and active site havecomplementary shapes. For example, catalase catalyses the breakdown of

hydrogen peroxide to water and oxygen.


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3 Chemical reactions catalysed by enzymes

are usually reversible, for example:

CO2+H20 H2CO3

enzyme carbonic anhydrase


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4 A very small amount of enzymes is needed to

react with a large amount of substrate.

Enzymes have a high turnover number.

For example, the turnover number for catalase is

600 000.

One molecule of enzyme catalase can catalyse the

breakdown

of about 600 000 molecules of hydrogen peroxide persecond into water and oxygen at body temperature.


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Enzyme concentration

The rate of an enzyme-catalysed reaction

is directly proportional to the concentration

of enzyme if substrates are present in

excess concentration and no other factorsare limiting


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Rate of enzyme-

catased reaction

(velocity V)


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Substrate concentration

At low substrate concentration the rate ofan enzyme reaction increase w/ increasingsubstrate concentration .

The active site of an enzyme moleculescan only bind w/ certain number ofsubstrate at a given time

At high substrate concentration there issaturation of active sites and the velocityof the reaction reaches the maximum rate


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Effect of substrate concentration on the

rate of an enzyme-controlled reaction


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Effect of pH

Most enzymes are effective only w/in anarrow pH range

The optimum pH is the pH at which the

maximum rate of reaction occurs. Different

enzymes have different pH optima

enzyme Optimum pH

Pepsin and rennin 2.0

Salivary amylase 6.8Trypsin 7.8

Lipase 9.0


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The effect of pH on the rate of an

enzyme-controlled reaction

rate of reaction


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Deviation from this narrow optimum pH rangeresult in excess H or OH ions in the medium . This alters the acidic and basic groups of amino acids

in the enzyme causing hydrogen bonds and ionic

bonds to be broken. The specific three dimensional shape of the enzymeis altered and the enzyme is denatured

The ionic charges on an active site and thesurface of substrate may also be altered

The substrate cannot fit into the active site toform enzyme-substrate complex. The rate ofreaction decrease


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Effect of temperature

At low temp, an enzymes-controlled

reaction occurs very slowly

Molecules in solution move slowly

Take longer time to bind to actives sites

Increasing temp Increase the kinetic energy of reactants

Molecules move faster Increase the number of collision of molecules to form

enzymes-substrate complex


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The effect of temperature on an enzyme-catalysed

reaction such as saliva


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Suboptimal temperatures The Q

At suboptimal temperatures the Q for

enzyme-catalysed reactions is

approximately 2

The rate doubles for each 10 C rise in

temperature (normally between 0-40 C)

Q10= rate of reaction at (X +10) C

rate of reaction at X C


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optimum temperatures

The rate of reaction is at a maximum The enzyme is still in an active stage Varies w/ different enzymes

Human salivary amylase, pepsin, trypsin , lipase work best at 37 C Above optimum temp, (melebihi suhu optimal)

increase kinetic energy cause the enzyme atoms molecules vibrateviolently H & ionic bonds hold the specific 3-D shape in the enzyme are broken. Enzymes unfold & denatured. Effect irreversible Substrate cant fit into the altered shape of the enzyme active site

Rate of enzyme controlled reactant falls rapidly. Eg. Thermophilic bacteria (80 C) & algae Metabolic active in high temp has enzyme that can stand hot condition in hot spring Enzyme has high optimal temp


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Certain enzymes require cofactors, non-protein substances, which are

essential for them to function efficiently.

There are three types of co-factors: prosthetic groups,

coenzymes and

activators.

The rate of enzyme-controlled reactions may be

decreased by the presence of competitive and

non-competitive inhibitors


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Mechanism of enzyme action

2 main hypotheses explaining the

mechanism of enzyme action:

The lock-and-key hypothesis by Emil

Fisher

The induced-fit hypothesis by Daniel

Kahsland


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by Emil Fisher The hypothesis proposes that the active site and

substrate are exactly-complementary. An enzyme is a large globular protein with a

specific three-dimensional shape.

It has a groove railed the active site containingamino acid side chains that are complementaryto the substrate.

In the lock-and-key hypothesis, the shape of

the substrate ('key') fits into the rigid active siteof the enzyme ('lock'), forming an enzyme-substrate complex . Reaction takes place inproducts are formed and released.


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substrate ('key') enteringactive site of enzyme

formation of an enzyme substrate complex


site of enzyme

enzyme is

regenerated

The active site of the enzyme ('lock'} has a shape which is an exact fit for the

substrate ('key')


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The induced-fit hypothesis

by Daniel Kahsland

It is a modified version of the lock-and-key

hypothesis

is the more widely accepted hypothesis.

The hypothesis suggests that the-active site isflexible and is not exactly complimentary to the

shape of the substrate.

An enzyme collides with the substrate molecule.

The substrate binds to the active site.


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The binding induces a slight change in

the shape of the enzyme to enclose the

substrate making the fit more precise.

The active site now becomes fully

complementary with the substrate as the

substrate binds to the enzyme


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Induced-fit hypothesis

substrate enters active site

enzyme changes shape

slightly,active site is

modified, returns making thefit more precise

Enzyme returns to its

original shape


enzyme


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The active site is not an exact fit for the

substrate. The enzyme and its active site

are flexible. When the substrate enters the

active site it induces a small change in theshape of the enzyme. The amino acids

which make up the active site are moulded

into a precise shape complementary to thesubstrate. This enables the enzymes to

carry out their catalytic function.


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The close fit brings the molecules in closeproximity and in the correct orientation forreaction to take place. It also causes stressing and distortion of chemical

bonds of the substrate. This causes the bonds to break and new bonds toform. This makes it easier for the substrate to bechanged into the product, thus lowering the activationenergy required.

The products formed have a different shape andare released from the enzyme. The enzymestructure is unchanged and can be reused.


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Enzymes Cofactors andenzyme inhibitors


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Enzyme cofactors

a non-protein molecule or ion Is required for the proper function of an

enzyme Many enzymes require the presence cofactor.

Can be permanently bound to the active site of enzyme may bind loosely with the substrate during catalysis Cofactors may be organic orinorganic. There 3 types of cofactors.

Prosthetic groups Coenzymes ( most are vitamins, in metabolicreaction )

Enzyme activators/inorganic ion activators


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Prosthetic groups

A prosthetic group is a non-protein, organic moleculethat binds tightly on a permanent basis to the proteinpart of the enzyme (apoenzyme).

The prosthetic group is involved in the catalytic

function of the enzyme. For example:

Haem is present in the enzyme catalase, whichcatalyses hydrogen peroxide into oxygen and water.

Haem is found in the prosthetic group cytochromes,which are electron carriers. It takes part in oxidation-reduction reactions.


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Coenzymes

are small, non-protein, organic molecules. They bind loosely and temporarily to the active site

of the enzyme.

readily detach and help to transfer chemical

group, atoms or electrons from one enzymeto another. Many coenzymes are derivatives ofvitamins,

especially group B vitamins.

NAD (nicotinamide adenine dinucleotide) is formed from niacin. a coenzyme for a number of dehydrogenase enzymes acts as a hydrogen acceptor.


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Malate +NAD+

coenzyme

Malate

dehydrogenese

Oxaloacetate +NADH + H-

Other examples include NADP, FAD and CoA.

E ti t i i


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Enzyme activators or inorganic

ion activators

Activators are inorganic ions such as Ca2+ , Zn2+ , Mg2+ , Fe 2+ and Cl-.

They may attach temporarily to the enzymeand change its active site to make the shapemore suitable for a reaction to take place.

The ion may also bind the enzyme and substratetogether for example:

(a) Calcium ions are needed to activate thrombokinase,which converts prothrombin to thrornbin in bloodclotting.

(b) Chloride ions increase salivary amylase activity.


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Enzyme Inhibitors

An inhibitor is slow down / decrease or stops enzyme

reaction a substance that binds to an enzyme,

Enzyme inhibitors can be grouped into two

types:(a) Competitive inhibitors

(b) Non-competitive inhibitors


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Competitive inhibitors

Competitive inhibitors have a shape similarto thenatural substrate. can fit temporarily into the active site of the

enzyme, preventing substrate from binding to it. The competitive inhibitor and natural substrate therefore

compete for the same active site of the enzyme. Entry of a competitive inhibitors or substrates would

depend on their relative concentration Competitive inhibition is reversed by increasing the

substrate concentration. Examples of competitive inhibitors are:

(a) Malonate. It competes with succinate for the active site on theenzyme succinate dehydrogenase


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truktur

a

Enzyme merubah struktur succinate

Competitive inhibition of enzyme succinatedehyrogenase by malonate


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Competitive inhibition of enzyme succinatedehyrogenase by malonate

N titi i hibit


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Non-competitive inhibitors No structural similarity to the natural substrate

Binds to an allosteric site of enzyme Change in conformation of enzyme molecules &

alters the active site Prevent substrate from binding the active site No competion for active site

Increase substance, reaction rate still same Increase inhibitors, reaction rate decrease Eg.cyanide, attaches on copper prosthetic group , inhibits

respiratory reaction End-product inhibitors

Can act as a non competitive reversible inhibitors & regulates themetabolic pathways


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Substrate A B C D End product

ATP

Enzymee1 e2 e3 e4

Negatif feedback by allosteric inhibition

of end- product


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Reversible inhibition

Competitive inhibition is reversible as the

inhibitor binds temporarily to the active

site. It can be overcome by increasing the

relative concentration of the substrate Some non-competitive inhibitions are

reversible, that is, if the inhibitor binds

temporarily and loosely to the allostericsite


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Irreversible inhibition

1. Some inhibitors bind very tightly, often, by forming covalentbonds with the enzyme.

2. The nerve gas DIPF is an irreversible inhibitor. It bindspermnnently with acetylcholinesterase, altering its shape. Theenzyme cannot bind with and break down its substrate acetylcholine(neurotransmitter )Acetylcholine molecules accumulate in thesynaptic cleft. Nerve impulses cannot be stopped causingcontinuous muscle contraction. This lead convulsions, paralysis andeventually, death.

3. Many pesticides such as organophosphate pesticides act asirresversible enzyme inhibitors. Exposure to the pesticides can

produce harmful effects to the nervous and muscular systems ofhumans.

4. Heavy metal ions such as Hg2+ Ag+,As+ and iodine-containingcompounds which combine permanently with sulphydryl groups


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*Enzyme unit kecil yang penting

Sesungguhnya segala ciptaaan Tuhan itu adahikmahnya

Tak kira besar atau kecil menyumbang dalamproses kehidupan bagi menerus kelansunganhidup ini.

Enzyme ciptaan Tuhan, jgnlah dirosakan dgnsuhu yg tinggi ,heavy metal , pestisid, dsb kelakmerana diri dan rosaklah alam semester yg kitadiami.

Elak demam panas, keracunan , pencemaran


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Questions

1. What are enzyme?

2. What is the main role of enzymes?

3. What is the meaning of metabolism ?

4. What is meant by enzyme denaturation?

5. List down the properties of enzymes

6. List the factors that affect the rate of enzymatic

reaction


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1. Define an enzymes?

2. Explain lock and key hypothesis?


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Q6 :Enzyme kinetics


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Q6 :Enzyme kinetics

Enzyme kinetics is the study of the rates

at which an enzyme works.

The rate is influenced by several factors:

(a) The concentration of substrate

molecules

(b) Temperature

(c) Presence of competitive and non-

competitive inhibitors

(d) pH

lec 1 3 energetic biology 2

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