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Enzymes: Basic Concepts and Kinetics – Study Notes

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Enzymes: Basic Concepts and Kinetics

Introduction to Enzymes

Enzymes are biological catalysts that play a crucial role in accelerating chemical reactions in living organisms. They are essential for metabolic processes and are often the target of pharmaceutical drugs.

  • Definition: Enzymes are typically proteins (though some RNA molecules can act as enzymes, called ribozymes) that catalyze specific biochemical reactions.

  • Function: Enzymes lower the activation energy (Ea) required for reactions, thereby increasing reaction rates.

  • Specificity: Most enzymes are highly specific, catalyzing only particular reactions.

  • Transition State Stabilization: Enzymes function by stabilizing the transition state, the highest-energy species in the reaction pathway.

Rate Enhancement by Enzymes

Enzymes dramatically increase the rate of chemical reactions compared to uncatalyzed reactions.

Enzyme

Uncatalyzed Rate (kuncat, s-1)

Catalyzed Rate (kcat, s-1)

Rate Enhancement (kcat/kuncat)

IMP decarboxylase

2.8 × 10-16

39

1.4 × 1017

Staphylococcal nuclease

1.7 × 10-13

95

5.6 × 1014

AMP nucleosidase

1.0 × 10-11

60

6.0 × 1012

Carboxypeptidase A

3.0 × 10-9

578

1.9 × 1011

Ketosteroid isomerase

1.7 × 10-7

66,000

3.9 × 1011

Triose phosphate isomerase

4.3 × 10-6

4300

1.0 × 109

Chorismate mutase

2.6 × 10-5

50

1.9 × 106

Carbonic anhydrase

1.3 × 10-1

1 × 106

7.7 × 106

Enzyme Cofactors

Many enzymes require non-protein molecules called cofactors for activity. Cofactors can be metal ions or organic molecules (coenzymes).

  • Metals: Usually ions such as Zn2+, Mg2+, Ni2+, etc.

  • Coenzymes: Organic molecules, often derived from water-soluble vitamins.

  • Prosthetic Groups: Cofactors that are tightly or covalently bound to the enzyme.

  • Holoenzyme: Enzyme + cofactor (active form).

  • Apoenzyme: Enzyme without cofactor (inactive form).

Cofactor

Enzyme

Thiamine pyrophosphate

Pyruvate dehydrogenase

Flavin adenine nucleotide

Monoamine oxidase

Nicotinamide adenine dinucleotide

Lactate dehydrogenase

Pyridoxal phosphate

Glycogen phosphorylase

Coenzyme A (CoA)

Acetyl CoA carboxylase

Biotin

Pyruvate carboxylase

Zn2+

Carbonic anhydrase, Carboxypeptidase

Mg2+

EcoRV, Hexokinase

Ni2+

Urease

Mo

Nitrogenase

Se

Glutathione peroxidase

Mn

Superoxide dismutase

K+

Acetyl CoA thiolase

Gibbs Free Energy and Reaction Spontaneity

The free-energy change (ΔG) provides information about the spontaneity of a reaction, but not its rate.

  • Spontaneous Reaction: Occurs without input of energy if ΔG is negative (exergonic).

  • Equilibrium: At equilibrium, ΔG = 0; no net change in reactant or product.

  • Endergonic Reaction: ΔG positive; reaction is not spontaneous.

  • ΔG depends only on the free energy difference between reactants and products, not on the reaction pathway.

  • ΔG provides no information about reaction rate.

  • Highly exergonic reactions: Large values.

  • Highly endergonic reactions: Small values.

  • Standard free energy change: at standard conditions.

How Enzymes Accelerate Reactions

Enzymes accelerate reactions by lowering the activation energy required to reach the transition state.

  • Transition State: A high-energy, unstable molecular form between substrate and product.

  • Activation Energy (): The energy required to form the transition state from the substrate.

Equation:

  • Enzymes facilitate the formation of the transition state, thereby increasing reaction rates.

*Additional info: Further sections would include enzyme kinetics, Michaelis-Menten equation, enzyme inhibition, and allosteric regulation, which are standard topics in biochemistry and are referenced in the provided materials.*

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