Madam Syakira

103
Free Powerpoint Templates Page 1 Free Powerpoint Templates ENZYMES

Transcript of Madam Syakira

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 1/103

Free Powerpoint Templates

Page 1Free Powerpoint Templates

ENZYMES

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 2/103

Free Powerpoint Templates

Page 2

Overview: The Energy of Life

• The living cell is a miniature chemicalfactory where thousands of reactions occur • The cell extracts energy and applies energy

to perform work• Some organisms even convert energy to

light, as in bioluminescence

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 3/103

Free Powerpoint Templates

Page 3

An organism’s metabolismtransforms matter and energy,

subject to the laws ofthermodynamics

• Metabolism is the totality of an organism’schemical reactions

• Metabolism is an emergent property of lifethat arises from interactions betweenmolecules within the cell

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 4/103

Free Powerpoint Templates

Page 4

Organization of the Chemistry ofLife into Metabolic Pathways

• A metabolic pathway begins with a specificmolecule and ends with a product

• Each step is catalyzed by a specific enzyme

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 5/103

Free Powerpoint Templates

Page 5

Enzyme 1 Enzyme 2 Enzyme 3

DCBA Reaction 1 Reaction 3Reaction 2Startingmolecule

Product

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 6/103

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 7/103

Free Powerpoint Templates Page 7

• Anabolic pathways consume energy tobuild complex molecules from simpler ones• The synthesis of protein from amino acids is

an example of anabolism• Bioenergetics is the study of how

organisms manage their energy resources

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 8/103

Free Powerpoint Templates Page 8

Forms of Energy

• Energy is the capacity to cause change• Energy exists in various forms, some of

which can perform work

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 9/103

Free Powerpoint Templates Page 9

• Kinetic energy is energy associated with motion• Heat (thermal energy) is kinetic energy

associated with random movement of atoms ormolecules

• Potential energy is energy that matter possessesbecause of its location or structure

• Chemical energy is potential energy available for

release in a chemical reaction• Energy can be converted from one form to another

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 10/103

Free Powerpoint Templates Page 10

Climbing up converts the kineticenergy of muscle movement

to potential energy.

A diver has less potentialenergy in the water than on the platform.

Diving convertspotential energy tokinetic energy.

A diver has more potentialenergy on the platformthan in the water.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 11/103

Free Powerpoint Templates Page 11

The Laws of EnergyTransformation

• Thermodynamics is the study of energytransformations• A closed system, such as that approximated

by liquid in a thermos, is isolated from itssurroundings• In an open system, energy and matter can

be transferred between the system and itssurroundings

• Organisms are open systems

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 12/103

Free Powerpoint Templates Page 12

The First Law ofThermodynamics

• According to the first law ofthermodynamics , the energy of theuniverse is constant: – Energy can be transferred and transformed,

but it cannot be created or destroyed

• The first law is also called the principle ofconservation of energy

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 13/103

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 14/103

Free Powerpoint Templates Page 14

(a) First law of thermodynamics (b) Second law of thermodynamics

Chemicalenergy

Heat CO 2

H2O

+

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 15/103

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 16/103

Free Powerpoint Templates Page 16

Biological Order and Disorder

• Cells create ordered structures from lessordered materials• Organisms also replace ordered forms of

matter and energy with less ordered forms• Energy flows into an ecosystem in the form

of light and exits in the form of heat

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 17/103

Free Powerpoint Templates Page 17

• The evolution of more complex organismsdoes not violate the second law ofthermodynamics

• Entropy (disorder) may decrease in anorganism, but the universe’s total entropyincreases

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 18/103

Free Powerpoint Templates Page 18

The free-energy change of areaction tells us whether or not

the reaction occursspontaneously

• Biologists want to know which reactionsoccur spontaneously and which requireinput of energy

• To do so, they need to determine energychanges that occur in chemical reactions

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 19/103

Free Powerpoint Templates Page 19

Free Energy and Metabolism

• The concept of free energy can be appliedto the chemistry of life’s processes

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 20/103

Free Powerpoint Templates Page 20

Exergonic and EndergonicReactions in Metabolism

• An exergonic reaction proceeds with a netrelease of free energy and is spontaneous• An endergonic reaction absorbs free

energy from its surroundings and isnonspontaneous

Fig 8 6

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 21/103

Free Powerpoint Templates Page 21

Fig. 8-6

Reactants

Energy

F r e e e n e r g y

Products

Amount of energy

released(∆G < 0)

Progress of the reaction

(a) Exergonic reaction: energy released

Products

ReactantsEnergy

F r e e e n

e r g y

Amount of energyrequired(∆G > 0)

(b) Ender gonic reaction: energy req uired

Progress of the reaction

Fig 8 6a

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 22/103

Free Powerpoint Templates Page 22

Fig. 8-6a

Energy

(a) Exergonic reaction: energy released

Progress of the reaction

F r e e e n e r g y

Products

Amount of energyreleased(∆G < 0)

Reactants

Fig 8 6b

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 23/103

Free Powerpoint Templates Page 23

Fig. 8-6b

Energy

(b) Endergonic reaction: energy required

Progress of the reaction

F r e e e n e r g y

Products

Amount of energyrequired

(∆G > 0)Reactants

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 24/103

Free Powerpoint Templates Page 24

Equilibrium and Metabolism

• Reactions in a closed system eventually reachequilibrium and then do no work

• Cells are not in equilibrium; they are open systemsexperiencing a constant flow of materials

• A defining feature of life is that metabolism isnever at equilibrium

• A catabolic pathway in a cell releases free energy

in a series of reactions

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 25/103

Free Powerpoint Templates Page 25

ATP powers cellular work by couplingexergonic reactions to endergonic reactions

• A cell does three main kinds of work: – Chemical – Transport – Mechanical

• To do work, cells manage energy resources byenergy coupling , the use of an exergonic process

to drive an endergonic one• Most energy coupling in cells is mediated by ATP

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 26/103

Free Powerpoint Templates Page 26

The Structure and Hydrolysis of ATP

• ATP (adenosine triphosphate) is the cell’senergy shuttle• ATP is composed of ribose (a sugar),

adenine (a nitrogenous base), and threephosphate groups

Fig 8-8

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 27/103

Free Powerpoint Templates Page 27

Fig. 8-8

Phosphate groupsRibose

Adenine

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 28/103

Free Powerpoint Templates Page 28

• The bonds between the phosphate groupsof ATP’s tail can be broken by hydrolysis• Energy is released from ATP when the

terminal phosphate bond is broken• This release of energy comes from thechemical change to a state of lower freeenergy, not from the phosphate bondsthemselves

Fig 8-9

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 29/103

Free Powerpoint Templates Page 29

Fig. 8 9

Inorganic phosphate

Energy

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

P P

PP P

P ++

H2O

i

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 30/103

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 31/103

Free Powerpoint Templates Page 31

• ATP drives endergonic reactions byphosphorylation, transferring a phosphategroup to some other molecule, such as areactant

• The recipient molecule is nowphosphorylated

Fig. 8-11 M b i

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 32/103

Free Powerpoint Templates Page 32

g. 8

(b) Mechanical work: ATP binds noncovalently

to mot or proteins, then is hydrolyz ed

Membrane protein

Pi

ADP

+

P

Solute Solute transported

P i

Vesicle Cytoskeletal track

Motor protein Protein moved

(a) Transport work: ATP phosphorylatestransport proteins

ATP

ATP

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 33/103

Fig. 8-12

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 34/103

Free Powerpoint Templates Page 34

g

P iADP +

Energy fromcatabolism (exergonic,energy-releasing

processes)

Energy for cellular work (endergonic,energy-consuming

processes)

ATP + H2O

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 35/103

Free Powerpoint Templates Page 35

nzym s

1. Enzymes speed up metabolic reactions by lowering energy barriers2. Enzymes are substrate specific3. The active site in an enzyme’s catalytic center 4. A cell’s physical and chemical environment affects enzyme activity

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 36/103

Free Powerpoint Templates Page 36

• A catalyst is a chemical agent that changesthe rate of a reaction without being consumedby the reaction.

– An enzyme is a catalytic protein.

• Enzyme: An organic catalyst (usually protein) that accelerate a specificchemical reaction by lowering the activation energy required for that

reaction.

1. Enzymes speed up metabolic reactionsby lowering energy barriers

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 37/103

Free Powerpoint Templates Page 37

• Anabolism: Aspect of metabolism

simpler substances are combined to form complex substancesfor storage of energyfor the production of new cellular materials and growth.

• Catabolism: Aspect of metabolismcomplex substances are broken down to simpler substancereleasing chemical energy.• Metabolism = Catabolism + Anabolism

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 38/103

Free Powerpoint Templates Page 38

• Exergonic reaction:release of energy.

• Endergonic reaction Absorb energy.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 39/103

Free Powerpoint Templates Page 39

• Chemical reactions between moleculesinvolve both bond breaking and bond

forming. – To hydrolyze sucrose, the bond between

glucose and fructose must be broken and thennew bonds formed with a hydrogen ion andhydroxyl group from water.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 40/103

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 41/103

Free Powerpoint Templates Page 41

• Activation energy is the amount of energynecessary to push the reactants over an

energy barrier. – At the summit themolecules are atan unstable point,the transition state.

– The difference betweenfree energy of theproducts and the freeenergy of the reactantsis the delta G.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 42/103

Free Powerpoint Templates Page 42

• For some processes, the barrier is not highand the thermal energy provided by room

temperature is sufficient to reach thetransition state.• In most cases, E A is higher and a significant

input of energy is required. – A spark plug provides the energy to energize

gasoline. – Without activation energy, the hydrocarbons of

gasoline are too stable to react with oxygen.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 43/103

Free Powerpoint Templates Page 43

• The laws of thermodynamics would seemto favor the breakdown of proteins, DNA,

and other complex molecules. – However, in the temperatures typical of the cellthere is not enough energy for a vast majorityof molecules to make it over the hump ofactivation energy.

– Yet, a cell must be metabolically active. – Heat would speed reactions, but it would also

denature proteins and kill cells. – Denature: To alter the physical properties and three dimensionalstructure of protein, usually by treating it with excess heat, strongacid or strong base.

– Reactant: substrate that participate in a chemical reaction.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 44/103

Free Powerpoint Templates Page 44

• Enzyme speed reactions by lowering E A. – The transition state can then be reached even

at moderate temperatures.• Enzymes do not change delta G.

– Because enzymesare so selective,they determinewhich chemicalprocesses will

occur at any time.

Fig. 8

-14

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 45/103

Free Powerpoint Templates Page 45

Progress of the reaction

Products

Reactants

∆G < O

Transition state

EA

DC

BA

D

D

C

C

B

B

A

A

Th A i i E B i

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 46/103

Free Powerpoint Templates Page 46

The Activation Energy Barrier

• Every chemical reaction between moleculesinvolves bond breaking and bond forming• The initial energy needed to start a chemical

reaction is called the free energy ofactivation , or activation energy (E A)

• Activation energy is often supplied in theform of heat from the surroundings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

H E L h E

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 47/103

Free Powerpoint Templates Page 47

How Enzymes Lower the E ABarrier

• Enzymes catalyze reactions by lowering theE A barrier • Enzymes do not affect the change in free

energy (∆ G); instead, they hasten reactionsthat would occur eventually

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 48/103

Free Powerpoint Templates Page 48

Progress of the reaction

Products

Reactants

∆G is unaffectedby enzyme

Course of reaction

withoutenzymeE

Awithoutenzyme EA with

enzymeis lower

Course of reactionwith enzyme

2 E b ifi

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 49/103

Free Powerpoint Templates Page 49

• A substrate is a reactant which binds to an

enzyme.• When a substrate or substrates binds to an

enzyme, the enzyme catalyzes the

conversion of the substrate to the product. – Sucrase is an enzyme that binds to sucrose and

breaks the disaccharide into fructose andglucose.

2. Enzymes are substrate specific

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 50/103

Free Powerpoint Templates Page 50

• The shape of active site matches the shape of a specific part ofthe substrate molecule.

• Induced Fit – Substrate molecule upon binding to the active site of the enzyme

induces a slight change in the shape of both molecule, substrateand enzyme.

– Once substrate molecule has made contact with the active site and

has initiated the change in shape, the enzyme initiates the actualreaction of the substrate molecule.

– Once the reaction complete, attraction between substrate andenzyme

cease, freeing the enzymes from the product enabling to catalyzedthesecond reaction of the same type.

Th i i f i

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 51/103

Free Powerpoint Templates Page 51

• The active site of an enzymes is a grooveon the surface of the protein into which thesubstrate fits.

• The specificity of an enzyme is due to thefit between the active site and thesubstrate.

• As the substrate binds, the enzymechanges shape leading to a tighterinduced fit , bringing chemical groups inposition to catalyze the reaction.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 52/103

Free Powerpoint Templates Page 52

• The reason a particular enzyme will combine onlywith one kind of substrate is that the fit between thetwo is very precise .

• In fact, the fit is so precise, the combining of theenzyme and substrate results in a slight change inthe shape of both. This precise fit that modifies bothoriginal molecules is called an induced fit .

• This "strained" fit acts to break old chemical bondsand form new ones, resulting in the formation of theproduct from the substrate.

• Once this change has occurred, the product isreleased from the enzyme, and the enzyme cancombine with another molecule of substrate.

3 Th i i i

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 53/103

Free Powerpoint Templates Page 53

• In most cases substrates are held in theactive site by weak interactions, such ashydrogen bonds and ionic bonds.

– R groups of amino acids on the active sitecatalyze the conversion of substrate to product.

3. The active site is anenzyme’s catalytic center

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 54/103

Free Powerpoint Templates Page 54

C t l sis in the En me’s Acti e

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 55/103

Free Powerpoint Templates Page 55

Catalysis in the Enzyme’s ActiveSite

• In an enzymatic reaction, the substratebinds to the active site of the enzyme• The active site can lower an E A barrier by

– Orienting substrates correctly – Straining substrate bonds – Providing a favorable microenvironment – Covalently bonding to the substrate

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Enzymes speed up metabolic reactions by

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 56/103

Free Powerpoint Templates Page 56

Enzymes speed up metabolic reactions bylowering energy barriers

• A catalyst is a chemical agent that speedsup a reaction without being consumed bythe reaction

• An enzyme is a catalytic protein• Hydrolysis of sucrose by the enzyme

sucrase is an example of an enzyme-catalyzed reaction

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Fig. 8-16

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 57/103

Free Powerpoint Templates Page 57

Substrate

Active site

Enzyme Enzyme-substratecomplex

(b)(a)

A i l l l t l

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 58/103

Free Powerpoint Templates Page 58

• A single enzyme molecule can catalyzethousands or more reactions a second.

• Enzymes are unaffected by the reactionand are reusable.• Most metabolic enzymes can catalyze a

reaction in both the forward and reversedirection. – The actual direction depends on the relative

concentrations of products and reactants. – Enzymes catalyze reactions in the direction of

equilibrium.

E i t f h i t

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 59/103

Free Powerpoint Templates Page 59

• Enzymes use a variety of mechanisms tolower activation energy and speed a

reaction. – As the active site binds the substrate, itmay put stress on bonds that must bebroken, making it easier to reach the

transition state. – R groups at the active site may create a conducive

microenvironment for a specific reaction.

– The active site orients substrates in the

correct orientation for the reaction.

• The rate that a specific number of enzymes

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 60/103

Free Powerpoint Templates Page 60

• The rate that a specific number of enzymesconverts substrates to products depends inpart on substrate concentrations.

• At low substrate concentrations, an increasein substrate speeds binding to availableactive sites.

• However, there is a limit to how fast areaction can occur.

• At some substrate concentrations, the active

sites on all enzymes are engaged, calledenzyme saturation.• The only way to increase productivity at this

point is to add more enzyme molecules.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 61/103

Free Powerpoint Templates Page 61

• Michaelis-Menten

• E + S --- k1k2 ES--- k3 E + P

S reacts with E, and turns into ES, with rate constantk1, which turns into P and regenerates E, with rateconstant k 3. Now, ES can turn back into S and E,

with rate constant k 2. The Michaelis-Menten

mechanism for enzymic catalysis follows this path.

• E = free enzymes, S = substrate, ES = enzymes-substrate complex, P = product, e = total enzymeconcentration.

• K1 = rate constant for formation ES

• K2 = rate constant for dissociation of ES to E and S.

• K3 = rate constant for dissociation of ES to E and P

• Effect of enzyme concentration on reaction velocity

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 62/103

Free Powerpoint Templates Page 62

• Effect of enzyme concentration on reaction velocity – If the substrate concentration constant, velocity of reaction is proportional to

the enzyme concentration. – Enzyme concentration is propotional to velocity of reaction

– Vmax

Reaction velocity(V)

½ V max

Substrate concentration at ½ Vmax

[S]Km

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 63/103

Free Powerpoint Templates Page 63

P iADP +

Energy fromcatabolism (exergonic,energy-releasing

processes)

Energy for cellular work (endergonic,energy-consuming

processes)

ATP + H2O

Fig. 8-13

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 64/103

Free Powerpoint Templates Page 64

Sucrose (C 12 H22 O 11 )

Glucose (C 6H12 O 6) Fructo se (C 6H12 O 6)

Sucrase

Substrate Specificity of Enzymes

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 65/103

Free Powerpoint Templates Page 65

Substrate Specificity of Enzymes

• The reactant that an enzyme acts on iscalled the enzyme’s substrate

• The enzyme binds to its substrate, formingan enzyme-substrate complex

• The active site is the region on the enzymewhere the substrate binds

• Induced fit of a substrate brings chemicalgroups of the active site into positions thatenhance their ability to catalyze the reaction

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Fig. 8-17

Substrates enter active site; enzymechanges shape such that its active site

21

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 66/103

Free Powerpoint Templates Page 66

Substrates

Enzyme

Products arereleased.

Products

Substrates areconverted toproducts.

Active site can lower E Aand speed up a reaction.

Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.

changes shape such that its active siteenfolds the substrates (induced fit).

Activesite is

availablefor two new

substratemolecules.

Enzyme-substratecomplex

5

3

2

6

4

Effects of Local Conditions on

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 67/103

Free Powerpoint Templates Page 67

Effects of Local Conditions onEnzyme Activity

• An enzyme’s activity can be affected by – General environmental factors, such as

temperature and pH – Chemicals that specifically influence the

enzyme

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Effects of Temperature and pH

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 68/103

Free Powerpoint Templates Page 68

Effects of Temperature and pH

• Each enzyme has an optimal temperature inwhich it can function

• Each enzyme has an optimal pH in which itcan function

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Optimal temperature for f h hili

Optimal temperature for i l h

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 69/103

Free Powerpoint Templates Page 69

R a

t e o f r e a c

t i o n

enzyme of thermophilic(heat-tolerant)bacteria

typical human enzyme

(a) Optimal temperature for two enzymes

(b) Optimal pH fo r two enzymes

R a

t e o

f r e a c

t i o n

Optimal pH for pepsin(stomach enzyme)

Optimal pHfor trypsin(intestinalenzyme)

Temperature (ºC)

pH543210 6 7 8 9 10

0 20 40 8060 100

Cofactors

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 70/103

Free Powerpoint Templates Page 70

Cofactors

• Cofactors are nonprotein enzyme helpers• Cofactors may be inorganic (such as a

metal in ionic form) or organic

• An organic cofactor is called a coenzyme• Coenzymes include vitamins

Enzyme Inhibitors

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 71/103

Free Powerpoint Templates Page 71

Enzyme Inhibitors

• Competitive inhibitors bind to the activesite of an enzyme, competing with thesubstrate

• Noncompetitive inhibitors bind to anotherpart of an enzyme, causing the enzyme tochange shape and making the active siteless effective

• Examples of inhibitors include toxins,poisons, pesticides, and antibiotics

Fig. 8-19

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 72/103

Free Powerpoint Templates Page 72

(a) Normal binding (c) Noncompetitive inhibition(b) Competitive inhibition

Noncompetitive inhibitor

Active siteCompetitive

inhibitor

Substrate

Enzyme

• inhibitors , prevent enzymes from catalyzing

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 73/103

Free Powerpoint Templates Page 73

inhibitors , prevent enzymes from catalyzingreactions. – If binding involves covalent bonds, then

inhibition is often irreversible. – If binding is weak, inhibition may be reversible.

• If the inhibitor binds to the same site as the

substrate, then it blocks substrate bindingvia competitive inhibition .

• If the inhibitor binds somewhere other than the active site,

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 74/103

Free Powerpoint Templates Page 74

it blocks substrate binding via noncompetitive inhibition .• Binding by the inhibitor causes the enzyme to change

shape, rendering the active site unreceptive or lesseffective at catalyzing the reaction.

• Reversible inhibition of enzymes is a natural part of theregulation of metabolism. – Reversible inhibitor: A substance that forms a weak bonds with an

enzyme, temporarily interfering with its function. A reversibleinhibitor can be competitive or non competitive.

– Irreversible inhibitor: A substance that permanently inactivates anenzyme.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 75/103

Free Powerpoint Templates Page 75

• Competitive inhibition reversible – Example: succinate dehydrogenase inhibit

by malonate and oxaloacetate. It isactivated by ATP, P i and succinate.

• Succinate + FAD -- Fumarate + FADH 2

Irreversible inhibitors:These molecules bind permanently with the enzyme molecule andso effectively reduce the enzyme concentration, thus limiting therate of reaction, fo r examp le , cyanide irreversibly inhibits theenzyme cytochrome oxidase found in the electron transport chain

used in respiration. If this enzyme cannot be used, death willoccur.

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 76/103

Free Powerpoint Templates Page 76

Regulation of enzyme activityhelps control metabolism

• Chemical chaos would result if a cell’smetabolic pathways were not tightlyregulated

• A cell does this by switching on or off thegenes that encode specific enzymes or byregulating the activity of enzymes

Allosteric Regulation of Enzymes

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 77/103

Free Powerpoint Templates Page 77

Allosteric Regulation of Enzymes

• Allosteric regulation may either inhibit orstimulate an enzyme’s activity

• Allosteric regulation occurs when aregulatory molecule binds to a protein at onesite and affects the protein’s function atanother site

Allosteric Activation and Inhibition

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 78/103

Free Powerpoint Templates Page 78

Allosteric Activation and Inhibition

• Most allosterically regulated enzymes aremade from polypeptide subunits

• Each enzyme has active and inactive forms• The binding of an activator stabilizes the

active form of the enzyme• The binding of an inhibitor stabilizes the

inactive form of the enzyme

Fig. 8-20 Allosteric enyzmewith four subunits

Active site(one of four)

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 79/103

Free Powerpoint Templates Page 79

Regulatorysite (oneof four)

Active formActivator

Stabilized active form

Oscillation

Non-functionalactivesite

Inhibitor Inactive form Stabilized inactive

form

(a) Allosteric activators and inhibitors

Substrate

Inactive form Stabilized activeform

(b) Coope rativity: another type of allosteric activation

Fig. 8-20a Allosteric enzymewith four subunits

Active site(one of four)

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 80/103

Free Powerpoint Templates Page 80(a) Allosteric a ctivators and inhibitors

Inhibitor Non-functionalactivesite

Stabilized inactiveform

Inactive form

Oscillation

Activator Active form Stabilized active form

Regulatorysite (oneof four)

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 81/103

Free Powerpoint Templates Page 81

• Cooperativity is a form of allostericregulation that can amplify enzyme activity

• In cooperativity, binding by a substrate toone active site stabilizes favorableconformational changes at all other subunits

Fig. 8-20b

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 82/103

Free Powerpoint Templates Page 82

(b) Cooperativity: another type of allosteric activation

Stabilized activeform

Substrate

Inactive form

• In enzymes with multiple catalytic subunits,

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 83/103

Free Powerpoint Templates Page 83

y p ybinding by a substrate to one active site stabilizesfavorable conformational changes at all other

subunits, a process called cooperativity .• This mechanism amplifies the response of

enzymes to substrates, priming the enzyme toaccept additional substrates

Identification of Allosteric

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 84/103

Free Powerpoint Templates Page 84

de t cat o o oste cRegulators

• Allosteric regulators are attractive drug

candidates for enzyme regulation

• Some allosteric regulators, activators,

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 85/103

Free Powerpoint Templates Page 85

g , ,stabilize the conformation that has afunctional active site.

• Other regulators, inhibitors, stabilize theconformation that lacks an active site.

Metabolic control often depends on

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 86/103

Free Powerpoint Templates Page 86

• In many cases, the molecules that naturallyregulate enzyme activity behave likereversible noncompetitive inhibitors.

• These molecules often bind weakly to aallosteric site , a specific receptor on theenzyme that is not the active site.

• Binding by these molecules can either inhibitor stimulate enzyme activity.

allosteric regulation

• Most allosterically regulated enzymes are

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 87/103

Free Powerpoint Templates Page 87

y g yconstructed of two or more polypeptidechains.

• Each subunit has its own active site andallosteric sites are often located wheresubunits join.

• The whole protein oscillates between twoconformational shapes, one active, oneinactive.

• As the chemical conditions in the cell shift,

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 88/103

Free Powerpoint Templates Page 88

,the pattern of allosteric regulation will shift aswell.

• In many cases both inhibitors and activatorsare similar enough in shape that theycompete for the same allosteric sites. – These molecules may be products and

substrates of a metabolic pathway. – For example, some catabolic pathways have

allosteric sites that are inhibited when ATPbinds and activated when AMP binds. – When ATP levels are low, AMP levels are

high, and the pathway is turned on until ATP

levels rise, A MP levels fall and inhibition by

Fig. 8-21 EXPERIMENT

Caspase 1 Active Substrate

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 89/103

Free Powerpoint Templates Page 89

RESULTS

Caspase ct vesite

SHKnown active form

Subst ate

SHActive form canbind substrate

SH Allostericbinding site

Known inactive formAllostericinhibitor Hypothesis: allosteric

inhibitor locks enzymein inactive form

S – S

Caspase 1

Active for m Allostericallyinhibited form

Inhibitor Inactive form

Fig. 8-

21aEXPERIMENT

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 90/103

Free Powerpoint Templates Page 90

SH

Substrate

Hypothesis: allostericinhibitor locks enzymein ina ctive form

Active form canbind substrate

S – SSH

SH

Activesite

Caspase 1

Known active form

Known inactive form

Allostericbinding site

Allostericinhibitor

Fig. 8-21b

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 91/103

Free Powerpoint Templates Page 91

Caspase 1

RESULTS

Active form

Inhibitor

Allosterically

inhibited form

Inactive form

Specific Localization of Enzymes

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 92/103

Free Powerpoint Templates Page 92

p yWithin the Cell

• Structures within the cell help bring order tometabolic pathways

• Some enzymes act as structuralcomponents of membranes

• In eukaryotic cells, some enzymes reside inspecific organelles; for example, enzymesfor cellular respiration are located inmitochondria

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

Fig. 8-23

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 93/103

Free Powerpoint Templates Page 931 µm

Mitochondria

C f

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 94/103

Free Powerpoint Templates Page 94

Progress of the reaction

Products

Reactants

∆G is unaffectedby enzyme

Course of reactionwithout

enzyme

EAwithout

enzyme EA withenzymeis lower

Course of reactionwith enzyme

A cell’s physical and chemical environment

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 95/103

Free Powerpoint Templates Page 95

• The three-dimensional structures of enzymes(almost all proteins) depend onenvironmental conditions.

• Changes in shape influence the reactionrate.

• Some conditions lead to the most active

conformation and lead to optimal rate ofreaction.

affects enzyme activity

• 1. Temperature has a major impact on

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 96/103

Free Powerpoint Templates Page 96

reaction rate. – As temperature increases, collisions between

substrates and active sites occur morefrequently as molecules move faster. – However, at some point thermal agitation begins

to disrupt the weak bonds that stabilize theprotein’s active conformation and the proteindenatures.

– Each enzyme has an optimal temperature.

• 2. Because pH also influences shape and

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 97/103

Free Powerpoint Templates Page 97

therefore reaction rate, each enzyme hasan optimal pH too.

• This falls between pH 6 - 8 for mostenzymes.

• However, digestive enzymes in thestomach are designed to work best at pH 2while those in the intestine are optimal atpH 8, both matching their workingenvironments.

Fig. 8-UN4

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 98/103

Free Powerpoint Templates Page 98

• 3 Amount of enzyme present

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 99/103

Free Powerpoint Templates Page 99

• 3. Amount of enzyme present – The amount of enzyme present is

determined by its rate of synthesis (k s) andthe rate of degradation (k d). Enzymeturnover.

• Many enzymes require nonprotein helpers

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 100/103

Free Powerpoint Templates Page 100

Many enzymes require nonprotein helpers,cofactors , for catalytic activity.

– They bind permanently to the enzyme orreversibly.

– Some inorganic cofactors include zinc, iron,and copper.

• Organic cofactors, coenzymes , includevitamins or molecules derived fromvitamins.

Feedback Inhibition

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 101/103

Free Powerpoint Templates Page 101

• In feedback inhibition , the end product of ametabolic pathway shuts down the pathway

• Feedback inhibition prevents a cell fromwasting chemical resources by synthesizingmore product than is needed

Copyright © 2008 Pearson Education, Inc., publishing as Pearson BenjaminCummings

• One of the commonmethods of metabolic

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 102/103

Free Powerpoint Templates Page 102

methods of metaboliccontrol is feedbackinhibitionmetabolic pathway isturned off by its endproduct.

• The end product actsas an inhibitor of anenzyme in the pathway.

• When the product is

abundant the pathwayis turned off, when rarethe pathway is active.

• Systematic names for each enzyme

8/13/2019 Madam Syakira

http://slidepdf.com/reader/full/madam-syakira 103/103

have been made in an internationalclaasification of enzymes. – Oxidoreductase: are involved in oxidation/reduction. – Transferase : transfer functional groups between donor and

receptor. – Hydrolases – transfer water that is they catalysed the hydrolysis of

a substrate. – Lyases : add or remove the element of water, ammonia or CO 2 to

form double bond. – Isomerase : catalyzed changes within one molecule. – Ligase (synthetases): join two molecule together at the expense

of a high-energy phosphate bond of ATP.