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Lecture 3: Enzyme Kinetics: Catalytic Properties of Enzymes. What is a catalyst?. • A catalyst accelerates a chemical reaction • It participates in the reaction but is not consumed, meaning that is must return to its original state after the chemical reaction has been catalyzed.

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Lecture 3: Enzyme Kinetics: Catalytic Properties of Enzymes

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Lecture 3 enzyme kinetics catalytic properties of enzymes l.jpg

Lecture 3: Enzyme Kinetics: Catalytic Properties of Enzymes


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What is a catalyst?

• A catalyst accelerates a chemical reaction

• It participates in the reaction but is not consumed, meaning that is must return to its original state after the chemical reaction has been catalyzed.

• A catalyst can be a simple inorganic compound or a biological macromolecule called an “enzyme” (most often protein, but also can by RNA).


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Catalysts, in particular, enzymes are capable of astonishing rate enhancements

What sort of rate acceleration can catalysts provide?

Consider the reaction:

Relative rate

Uncatalyzed:1

Pt Black (inorganic catalyst):10,000

catalase (enzyme):300,000,000,000


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Activation

Energy

Catalysts work by stabilizing the transition state of a chemical reaction, which lowers the activation energy of the reaction

How do catalysts work?


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Eact Relative Rate

No Catalyst18 kcal/mol1

Pt black12 kcal/mol1X104

Catalase 2 kcal/mol3X1011

A small reduction in activation energy results in a huge increase in the reaction rate.

The rate of a chemical reaction is an exponential function of activation energy


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ATP hydrolysis as an example


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Does an enzyme only catalyze the forward reaction? NO!

Why not? Because the free energy difference between reactants and products of a reaction and the starting concentration of each determines the direction (more on this later).


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Catalysts DO NOT alter the final equilibrium distribution of reactants and products in a chemical reaction, they merely reduce the amount of time required to attain the equilibrium distribution.


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How do enzymes do the amazing things they do?

• Biological enzymes have evolved to form complex three-dimensional structures that present an “active site” surface to which reactants in a chemical reaction bind.

• These sites also position amino acid R-groups and/or reaction cofactors (such as metals) or prosthetic groups at the appropriate positions to aid in catalysis.

• Two major models for how this might work on the structural level are shown on the next slide.


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Two models for ES complex


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Lets take a look at a real active site!

ATP

Mg(2+)


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Summary of major properties of enzymes


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[P]

[S]

time

time

Accumulation of product over time (D[P]/Dt)

Loss of substrate over time (D[P]/Dt)

How does one measure enzyme activity?


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2 x [enzyme]

D[P]/Dt = 2

0.5 x [enzyme]

D[P]/Dt = 0.5

How does [enzyme] influence observed reaction velocity?

1 x [enzyme]

D[P]/Dt = 1

[P]

Assumes that [E] is limiting and that the uncatalyzed reaction rate is ~0

time


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Specificity of enzymes

How specific are enzymes for a given substrate?

• The answer depends upon the enzyme you’re talking about. Most enzymes are highly specific, acting on only a small number of substrates that are highly similar in structure. Others, such as alkaline phosphatase mentioned in your notes, are less specific.

• Specificity arises from structural and chemical complementarity between the substrate and its enzyme.


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Specificity of enzymes (an example)

Hydrogen

Bonds

Gln with

Adenine

Mg (2+)

Ionic

Bonds

Asp with Mg(2+),

Lys with Phosphates


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Metals, coenzymes, and prosthetics groups

Many enzymes bind non-protein cellular components that are used as key factors in the enzyme activity. These fall into three basic categories:

(1) Metals: Metals (e.g. Mg, Ca, Zn, Fe etc.) are thought to be bound to ~1/3 of all proteins and can play key roles in activity. An example is the Mg(2+) in the ATPase on the previous slide. These ions can confer a wider array of chemical properties to proteins over those of the 20 natural amino acids.


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Metals, cofactors, and prosthetics groups

(2 & 3) Coenzymes and prosthetic groups: Low-molecular organic compounds that bind either weakly (coenzymes) or tightly (prosthetic groups) to the protein. Examples that you will see in this course include, for example, iron-sulfur clusters, heme, and coenzyme A.


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