ch 6 enzymes (1)

Lecture Notes for Chapter 6: How Enzymes Work

Key Concepts: Section 6-1

• Efficiency and Specificity of Enzymes

  • Enzymes are significantly more efficient and specific than simple chemical catalysts.

• Enzyme Naming

  • An enzyme's name often corresponds to the specific reaction it catalyzes.

Increasing Reaction Rates

• Methods to Increase Reaction Rates:

  • Increasing Temperature: Adding heat energy.

  • Increasing Concentration: Raising the level of reactants.

  • Adding a Catalyst: Introducing a substance that facilitates the reaction but remains unchanged.

Enzymes as Catalysts

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• Nature of Enzymes

  • Enzymes are primarily proteins that act as catalysts, accelerating chemical reactions without being consumed.

    • Exceptions: Ribozymes, RNA molecules that function as catalysts.

• Rate Enhancements

  • Enzymes typically enhance reaction rates by factors ranging from 10^8 to 10^12.

• Active Site

  • Substrate Binding: Substrates attach to enzymes at their active site.

  • Example: Serine proteases showcase a common set of amino acids within their active sites.

Specificity of Enzymes

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• Enzyme Specificity

  • Most enzymes are highly specific for their substrates; however, some like chymotrypsin exhibit broader substrate specificity:

    • Hydrolyzes peptide bonds after amino acids Phe, Tyr, or Trp.

    • Can hydrolyze other amide or ester bonds post-Phe, Tyr, or Trp.

• Naming Conventions

  • Enzymes are typically named for the reactions they facilitate (e.g., Pyruvate decarboxylase removes a carboxyl group from pyruvate).

• Classification of Enzymes

  • Enzymes are categorized into six major classes based on the type of reactions they catalyze.

Activation Energy and Enzyme Function

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• Activation Energy Barrier

  • The height of the activation energy barrier influences the rate of reactions; higher barriers slow down reactions.

• Enzymes Reduce Activation Energy

  • By providing lower-energy pathways, enzymes accelerate reactions.

• Types of Catalysis

  • Enzymes utilize:

    • Acid-base catalysis

    • Covalent catalysis

    • Metal ion catalysis

Free Energy and Spontaneity

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• Spontaneity of Reactions

  • The sign of ∆G indicates spontaneity:

    • ∆G < 0: Spontaneous reactions

    • ∆G > 0: Non-spontaneous reactions

• Activation Energy Lowering

  • Enzymes function by lowering the activation energy required for reactions.

• Role of Cofactors

  • Enzymes may require cofactors for effective catalysis.

Mechanisms of Enzyme Catalysis

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• Fundamental Mechanisms

  • Acid-base catalysis: Enzymes can use acid or base catalysis, or a combination of both.

  • Covalent catalysis: Also referred to as nucleophilic catalysis.

  • Metal ion catalysis: Utilization of metal ions in catalysis.

Specific Catalytic Actions

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• Covalent Catalysis

  • Covalent bonds are formed between the enzyme (E) and substrate (S) to facilitate reactions.

• Nucleophiles and Electrophiles

  • Nucleophiles: Electron pair donors or negatively charged entities.

  • Electrophiles: Electron-deficient atoms that accept electrons.

Enzyme Catalysis Highlight - Chymotrypsin

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• Chymotrypsin’s Catalytic Triad

  • Participates in both acid-base and covalent catalysis.

  • Key Amino Acids in Catalytic Triad:

    • Asp 102: Anchors His 57.

    • Ser 195: Functions as a nucleophile.

    • His 57: Acts as a general base and later a general acid.

Mechanism Features

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• Mechanism Observations

  • The electron flow during catalysis is energetically favorable, leading to easier bond breaks.

  • Transition state stabilization occurs at specific points in the mechanism.

Complete Enzyme Regeneration

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• Regeneration and Release

  • The enzyme is restored to its original state post-reaction, while the remainder of the protein is released.

Additional Key Concepts: Section 6-3

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• Factors Affecting Catalytic Activity

  • Transition state stabilization

  • Proximity and orientation effects

  • Induced fit mechanism

  • Electrostatic catalysis

• Stabilization of Transition State

  • Enzymes stabilize the transition state through specific interactions (e.g., oxyanion hole).

Mechanisms of Binding

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• Proximity and Orientation Effects

  • Substrates are positioned correctly for optimized reaction likelihood.

• Induced Fit Mechanism

  • Enzyme undergoes conformational changes upon substrate binding, enhancing fit and catalytic efficiency.

Evolution of Serine Proteases

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• Diversity in Enzyme Structure

  • Evolution has led to various serine proteases with different structures and substrate specificities despite structural similarities.

• Activation of Inactive Zymogens

  • Inactive enzyme precursors (zymogens) are activated through proteolysis.

• Protease Inhibition

  • Protease inhibitors regulate protease activity, limiting their function (e.g., Trypsin and Bovine Pancreatic Trypsin Inhibitor).

Enzyme Mechanisms of Catalysis

Key Mechanisms

1. Acid-Base Catalysis:

   • Enzymes can act as either acids or bases in the reaction, donating or accepting protons to stabilize transition states.

2. Covalent Catalysis:

   • Involves the formation of a covalent bond between the enzyme and substrate, facilitating the reaction through transient intermediates (also known as nucleophilic catalysis).

3. Metal Ion Catalysis:

   • Metal ions can stabilize charged substrates or interact to facilitate electron transfer, enhancing reaction rates.

Transition State and Activation Energy Barrier

• Transition State: A high-energy state during a chemical reaction where old bonds are breaking and new bonds are forming; it represents the point of maximum energy along a reaction pathway.

• Activation Energy Barrier: This is the energy required to reach the transition state from the reactants. The height of this barrier determines the rate of the reaction; higher barriers lead to slower reactions. Enzymes function by lowering this activation energy, making it easier for the reaction to occur.

Additional Mechanisms

• Induced Fit Mechanism:

  • Enzymes undergo conformational changes upon substrate binding which enhances the fit between the enzyme and substrate. This mechanism increases catalytic efficiency.

Enzyme Regulation

• Zymogens: Inactive precursor forms of enzymes that require proteolytic cleavage to become active. This mechanism helps regulate enzyme activity and prevent unwanted reactions.

• Protease Inhibitors: Molecules that bind to enzymes (such as proteases) and reduce their activity, thus regulating the function of these enzymes. Examples include Trypsin and Bovine Pancreatic Trypsin Inhibitor.

Catalytic Triad of Chymotrypsin

• The catalytic triad consists of three critical active site amino acids that play key roles in the enzyme's mechanism:

  1. Asp 102: Anchors His 57 and is part of the hydrogen bond network.

  2. His 57: Acts as a general base and later a general acid during the reaction.

  3. Ser 195: Functions as a nucleophile; attacks the carbonyl carbon of the substrate to form a covalent bond.

These amino acids work together to facilitate the cleavage of peptide bonds in proteins, illustrating the complex nature of enzymatic catalysis.