Bioenergetics and Enzyme

Jindawan Siruntawineti, Ph.D.Department of Zoology, Faculty of Science,

Kasetsart University

http://pirun.ku.ac.th/~fscijws

http://course.ku.ac.th --> login

E-mail: fscijws.ku.ac.th/424111

Credit to…http://biology.umt.edu/biol101/lecture.htm#vacation

http://www.hhp.ufl.edu/classes/ess/Summer/pet2350aj04/images/images/ch.04.ppt

http://info.citruscollege.com/LC/SUBJECTS/BIOL/Goodman104/ExamTopics1/ENZYMES.ppt

ReferenceBIOLOGY,

6th/ 7th edition Campbell and Reece

Pearson Education, Inc., publishing as Benjamin Cummings.

At KU-librariesChapter 6

Science, General Stack (2 copies) QH308.2.C34 2002

MainBK, Eng Stack-3rd Fl QH308.2.C34 2002

QH308.2.C34 2005

Objectives for Part II: Enzyme

- Define: enzyme, substrate, active site & enzyme nomenclature

- Describe about enzyme work

- Discuss factors affects enzyme activity

- Describe allosteric regulation & metabolism

Topic Outline: Part II Enzyme• Enzyme speed up metabolic reactions by

lowering energy barriers

• Enzyme are substrate specific• The active site is an enzyme’s catalytic center

• A cell’s physical and chemical environment affects enzyme activity

• Metabolic control often depends on allostericregulation

• The localization of enzymes within a cell helps order metabolism

• What are enzymesenzymes?

C: Data/ biology/ 028F1.mov

1. Proteins:1. Proteins: most enzymesenzymes are proteinsproteins, primarily tertiarytertiary and quaternary quaternary structuresstructures..

2.2. Catalyst:Catalyst: chemical agentchemical agent that acceleratesacceleratesa reaction without being permanently changed in the process.(Enzyme as biocatalyst)

3.3. Selective:Selective: enzymes are specific for which they will catalyzecatalyze (Specificity (Specificity -- depends depends upon 3D shape).upon 3D shape).

4.4. Recycled:Recycled: enzymes are reusable.

5.5. ““asease”” endings: examples:examples: sucrasesucrase

maltasemaltase

lactaselactase

Enzyme Nomenclature

Alcohol dehydrogenase

Substrate Catalytic action -ase suffix

This is an alternative name (for “common use”). In addition, an enzyme has a systematic name (unambigous) and a classification number

(e.g. EC 3.4.17.1 for carboxypeptidase A, whose systematic name is peptidyl-L amino acid hydrolase)

• How do enzymesenzymes work?

Enzyme can decrease the energy barrier

••EnzymesEnzymes speed up the cell’s chemical reactions by lowering the free energy of activationlowering the free energy of activation.

FreeEnergy

Progress of the reaction

Reactants

Products

Free energy of activation (EFree energy of activation (EAA))

Without EnzymeWith Enzyme

SubstrateSubstrate

• The substancesubstance (reactant) an enzymeenzyme acts on.

Enzyme

Substrate

Active SiteActive Site

• A restricted regionrestricted region of an enzymeenzyme molecule which bindsbinds to the substratesubstrate.

Enzyme

Active Site

Substrate

Enzyme-Substrate at active site

C: Data/ biology/ 028F2.mov

“Lock and Key” model

- Enzyme active site is complementary to the substrate

“Induced fit ” model

- Enzyme active site is complementary to the transition state

Lowers activation energy

Enzyme Active Site

Straining bonds

Providing microenvironmentthat favors reaction

Orienting substratescorrectly

byby

bybybyby

Enzymatic ReactionEnzymatic Reactionsubstrate (sucrose)substrate (sucrose) + enzyme (enzyme (sucrasesucrase) ) →→

enzymeenzyme--substratesubstrate complex complex →→

and +sucrasesucrase

glucoseglucose fructosefructose

productsproducts ++ enzymeenzyme

Can enzyme activity be modulated?

Change substrate binding to active site

Change ability of the enzyme to alter the EA

Temperature Covalent modulation

pH

Allosteric modulator

Competitive inhibitor

Campbell; Fig. 6.16a

Can enzyme activity be modulated?

Temperature

Campbell; Fig. 5.25

Campbell; Fig. 6.16b

Can enzyme activity be modulated?

pH

Can enzyme activity be modulated?

“helpers” for

catalytic activity

Some enzymesmust be ‘activated’

Cofactors Prosthetic groups

Inorganic molecules or

nonprotein organic molecules (Ca2+,

Mg2+)

Organic molecules, small & Covalently linked to protein

Coenzymes

Organic molecules (precursors are vitamins) e.g. NAD, FAD

Apoenzyme + Cofactor = Holoenzyme

Can enzyme activity be modulated?

Reduce productivity of enzymes by blocking

substrates from enteringthe active site

Enzyme Inhibitors

Directly Indirectly

Competitive Inhibitors

Noncompetitive Inhibitors

Uncompetitive Inhibitors

Enzyme Inhibition (Mechanism)

I

I

S

S

S I

I

I II

S

Competitive Non-competitive Uncompetitive

EE

Different siteCompete for

active siteInhibitor

Substrate

Car

toon

Gui

deEq

uatio

n and

Des

cripti

on

[II] binds to free [E] only,and competes with [S];increasing [S] overcomesInhibition by [II].

[II] binds to free [E] or [ES] complex; Increasing [S] cannot overcome [II] inhibition.

[II] binds to [ES] complex only, increasing [S] favorsthe inhibition by [II].

E + S→ES→E + P+II↓EII

←

↑

E + S→ES→E + P+ +II II↓ ↓EII+S→EIIS

←

↑ ↑

E + S→ES→E + P+II↓

EIIS

←

↑

EI

S X

Juang RH (2004) BCbasics

Can enzyme activity be modulated?

Reduce productivity of enzymes by blocking

substrates from enteringthe active site

Enzyme Inhibitors

Competitive (Direct) Inhibitors

Campbell; Fig. 6.17b

Cannot be overcome byhigh concentration

of substrate

Competes with substratefor binding to active site

Allosteric complexes oscillatebetween two conformational

states

AllostericRegulationHow is metabolism

controlled?

Campbell; Fig. 6.18a

Allosteric complexes oscillatebetween two conformational

states

AllostericRegulation

Binding of activator

Binding of inhibitor

Catalyticallyactive

Catalyticallyinactive

How is metabolismcontrolled?

Switching off ofa metabolic

pathway by itsend product

Feedback InhibitionHow is metabolism

controlled?

Switching off ofa metabolic

pathway by itsend product

Feedback InhibitionHow is metabolism

controlled?

Campbell; Fig. 6.19

Substrate molecules stimulate the catalyticpowers of an enzyme

CooperativityHow is metabolismcontrolled?

Campbell; Fig. 6.20

Campbell; Fig. 6.20

Cooperativity

http://images.google.com/imgres?imgurl=www.blc.arizona.edu/courses/181gh/rick/energy/graphics2/competitive.gif&imgrefurl=http://www.blc.arizona.edu/courses/181gh/rick/energy/regulation.html&h=262&w=317&prev=/images%3Fq%3Dcompetitive%2Binhibition%26svnum%3D

10%26hl%3Den%26lr%3D%26ie%3DUTF-8%26oe%3DUTF-8%26sa%3DG

And…the localization of enzymes within the cellhelps order metabolism.

Campbell; Fig. 6.21

Remember the importanceof compartmentalization?

Questions?

54

สวัสดีคะ

Jindawan Siruntawineti , Ph.D., Assistant Professor

ผศ.ดร. จินดาวรรณ สิรันทวิเนติ

หองชีว. 402A ตึกชีววิทยา คณะวิทยาศาสตร

E-mail: fscijws@ku.ac.th http:// course.ku.ac.th/424111

หองทํางานชั่วคราวชั้น 2 อาคารสโมสรคณะวิทยาศาสตร (ขางตกึชีววิทยา)

Office: 1) Room 402A Biology-Building, Fac. of Science

2) 2nd Floor, Sc. faculty Society-Building, Fac. of Science

http:// pirun.ku.ac.th/~fscijws

Thank you!This semester: Tuesday, 11.00 – 12.30 am

Wednesday, Thursday 11.00 – 12.30 pm

18 July, 2006