enzymes (ch. 6) intro basics of catalysis general types of catalysis quantification of catalysis...

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Enzymes (Ch. 6) • Intro • Basics of catalysis • General types of catalysis • Quantification of catalysis – enzyme kinetics and inhibition • Specific examples • Allostery and enzyme regulation

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Page 1: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Enzymes (Ch. 6)

• Intro

• Basics of catalysis

• General types of catalysis

• Quantification of catalysis– enzyme kinetics and inhibition

• Specific examples

• Allostery and enzyme regulation

Page 2: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

EN

ER

GY

(G

°)

REACTION PROGRESS

G < 0

Reaction should bespontaneous

Equil should favorproducts

Biological reaction:sugar + oxygen ↔ CO2 + water

Reactants (R)

Activation energy

EA

Kinetic barrier to reaction

High energy “Transition state”Intermediate between R & P

Products (P)

Page 3: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

The energy barrier is critical for life

• Potentially deleterious reactions are blocked by EA

– Complex molecule degrading to simpler constituents

http://asm.wku.eduhttp://encyclopedia.quickseek.com/

DNAnucleotide

Page 4: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

How do enzymes speed up reactions?

• New reaction pathway

• Lower activation energy

• Decreased energy barrier

2H2O2 → 2H2O + O2

Isolated: EA ~ 86 kJ/molIn the presence of catalase: EA ~ 1kJ/mol

Hydrogen peroxide

Page 5: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Binding of substrate to enzyme creates a new reaction pathway

http://w3.dwm.ks.edu.tw/

An enzyme changes EA NOT G

Affects RATE, not EQUILIBRIUM

Without enzyme

With enzyme

EA = G‡

Page 6: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

How is EA lowered?

• Enzyme’s ‘goal’ is to reduce G‡

• Two ways enzymes can affect G

– Improve H– Improve S

EA =G‡ = H - TS

G‡ = Gtrans.state – Greactants

Enzymes alter the free energy of the

transition state

enthalpy entropy

Page 7: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

-

Example: More favorable H

A B

AOHBH

A BH+

+ H2O

+OH-

+

Charge unfavorableUnstable transition st.

A BH+

Ionic interaction stabilizesthe positive charge

OH-

Page 8: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Example: More favorable S

Two moleculesMore ‘freedom’Higher disorder (high S)

One moleculeLower disorder (low S)Unfavorable entropically

Page 9: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

ENZYME

Example: More favorable S

Enzyme/Reactant COMPLEX

Essentially a single molecule

ENZYME

Enzyme/Transition state complex

Still a single molecule

Not much difference entropically

Page 10: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Remember

1. Enzymes lower the energy barrier

2. Decrease EA (G‡)

3. Provide an environment where:

• Transition state is stabilized (lower enthalpy)• Change of disorder (entropy) is minimized

Page 11: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Enzymes create a new reaction pathway

Go vs. G‡ transition state vs. reaction intermediates rate limiting step

Page 12: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Factors contributing to enzyme catalysis

• Weak interactions between enzyme and transition state

• Transient covalent bonds between S and E

• Entropy optimization in ES complex formation

• Solvation shell surrounding S & E (entropy/hydrophobic interactions)

• Substrate distortion upon binding to noncomplementary E

• Proper alignment of catalytic functional groups

Page 13: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Common catalytic mechanisms

• General acid/base catalysis– Proton transfer– Reactions with charged

intermediates/AAs• Fumarase

– Precise positioning of acid/base: reaction occurs faster than specific acid/base reactions

• Free H+/OH-

Page 14: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Common catalytic mechanisms

• Covalent catalysis– Covalent bond formation

between E and S– Reaction path is altered

and new path has lower Ea

– Chymotrypsin (combination)

Page 15: Enzymes (Ch. 6) Intro Basics of catalysis General types of catalysis Quantification of catalysis –enzyme kinetics and inhibition Specific examples Allostery

Common catalytic mechanisms

• Metal catalysis (metalloenzymes)– Ionic interactions

• Stabilize charged TS or orient charged substrate for reaction

• Carboxypeptidase

– Oxidation/reduction• Reversible changes in oxidation state of the metal• Electron transfer reactions • Transition metals• Catalase ezample