Enzyme Biology: Structure and Function
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Enzyme Biology: Structure and Function

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Questions and Answers

Which type of inhibitor permanently shuts off the enzyme molecule?

  • Irreversible inhibitor (correct)
  • Reversible inhibitor
  • Uncompetitive inhibitor
  • Competitive inhibitor
  • What characterizes competitive inhibition in enzyme activity?

  • Only binds to the enzyme-substrate complex
  • Prevents substrate binding without affecting catalysis
  • Decreases Vmax without affecting KM
  • Competes with substrate for binding at the active site (correct)
  • Which of the following describes uncompetitive inhibition?

  • Binds the free enzyme and increases KM
  • Does not affect Vmax but increases catalytic function
  • Only binds to the enzyme-substrate complex (correct)
  • Inhibits substrate binding but not catalysis
  • In mixed inhibition, how does the inhibitor impact Vmax?

    <p>Decreases Vmax and changes KM</p> Signup and view all the answers

    What is a common characteristic of reversible inhibitors?

    <p>They can dissociate from the enzyme after binding</p> Signup and view all the answers

    What does ΔG≠ represent in a chemical reaction?

    <p>The energy barrier that must be overcome for the reaction to proceed</p> Signup and view all the answers

    How do enzymes affect the reaction rate?

    <p>By decreasing the activation energy of the reaction</p> Signup and view all the answers

    What is the role of the transition state in a reaction?

    <p>It's the highest energy configuration during the reaction</p> Signup and view all the answers

    What describes the rate-limiting step of a reaction?

    <p>The step with the highest activation energy</p> Signup and view all the answers

    How do enzymes compensate for substrate distortion?

    <p>By utilizing binding energy to facilitate distortion</p> Signup and view all the answers

    What role do metastable intermediates play in enzyme-catalyzed reactions?

    <p>They temporarily stabilize the enzyme-substrate complex</p> Signup and view all the answers

    What happens during desolvation in enzyme reactions?

    <p>Water molecules are replaced by enzyme-substrate interactions</p> Signup and view all the answers

    Why is rigidity in the enzyme-substrate complex important?

    <p>It allows for better alignment of reactive groups</p> Signup and view all the answers

    What characterizes an irreversible (suicide) inhibitor?

    <p>It forms a covalent bond with the enzyme, leading to permanent inactivation.</p> Signup and view all the answers

    Which best describes allosteric regulators?

    <p>They change the enzyme's conformation without covalently modifying it.</p> Signup and view all the answers

    What role do zymogens play in enzyme regulation?

    <p>They are proenzymes activated by irreversible covalent modification.</p> Signup and view all the answers

    Which statement is true regarding enzyme activity regulation?

    <p>Covalent modifications are essential for irreversible regulation.</p> Signup and view all the answers

    What is the primary effect of a positive allosteric effector on an enzyme?

    <p>It increases the enzyme's rate of catalysis.</p> Signup and view all the answers

    How do enzymes lower the activation energy of a reaction?

    <p>By binding transition states best, which stabilizes these states</p> Signup and view all the answers

    Which type of catalysis involves the formation of a transient covalent bond between the enzyme and substrate?

    <p>Covalent catalysis</p> Signup and view all the answers

    What role do metal ions play in enzyme catalysis?

    <p>They stabilize negative charges and can facilitate oxidation reactions</p> Signup and view all the answers

    What is the primary purpose of acid-base catalysis in enzymes?

    <p>To optimize proton transfer within the active site</p> Signup and view all the answers

    Which statement accurately describes the Proximity Model in enzyme kinetics?

    <p>It relies on the alignment of reactive groups to facilitate reactions</p> Signup and view all the answers

    Chymotrypsin primarily functions as which type of enzyme?

    <p>A hydrolase</p> Signup and view all the answers

    Which functional groups can act as nucleophiles on enzymes during covalent catalysis?

    <p>Amino, carboxyl, thiolate, or serine residues</p> Signup and view all the answers

    Which factor is crucial for the optimal interaction of enqueue groups and transition states in enzyme activity?

    <p>The arrangement of amino acid residues in the active site</p> Signup and view all the answers

    What role do enzymes play in disease states?

    <p>They can be used as biomarkers to diagnose disease.</p> Signup and view all the answers

    Which enzyme classification is responsible for the transfer of electrons?

    <p>Oxidoreductases</p> Signup and view all the answers

    What is formed when an apoenzyme combines with its prosthetic group?

    <p>Active enzyme</p> Signup and view all the answers

    Which of the following best describes the active site of an enzyme?

    <p>It is a pocket in the enzyme where the reaction occurs.</p> Signup and view all the answers

    What is a characteristic of enzymes in relation to thermodynamics?

    <p>They decrease the activation energy of a reaction.</p> Signup and view all the answers

    Which of the following is a coenzyme example?

    <p>NAD+</p> Signup and view all the answers

    What type of reaction do ligases catalyze?

    <p>Formation of C—C, C—S, C—O, or C—N bonds</p> Signup and view all the answers

    What does substrate selectivity in enzymes refer to?

    <p>Enzymes preferentially bind to specific substrates.</p> Signup and view all the answers

    What is the term for the complete enzyme with the substrate bound?

    <p>Enzyme-substrate complex</p> Signup and view all the answers

    What happens to enzyme activity during a disease state?

    <p>Enzyme activity can increase or decrease.</p> Signup and view all the answers

    What is one of the fundamental conditions of life that enzymes fulfill?

    <p>Ability to catalyze chemical reactions efficiently and selectively</p> Signup and view all the answers

    Which of the following is a reason why enzymes are preferred over inorganic catalysts?

    <p>Enzymes have greater reaction specificity</p> Signup and view all the answers

    How do enzymes impact the rate of a chemical reaction?

    <p>They increase reaction rates without being consumed</p> Signup and view all the answers

    What is one advantage provided by enzymes operating under milder reaction conditions?

    <p>They are conducive to cellular conditions such as pH ~ 7 and 37°C</p> Signup and view all the answers

    Which property of enzymes enables the regulation of biological pathways?

    <p>Their capacity for regulation and control</p> Signup and view all the answers

    What is the main effect of enzymes on the activation energy of a reaction?

    <p>They decrease the activation energy required.</p> Signup and view all the answers

    Which configuration during a reaction possesses the highest potential energy?

    <p>Transition state (≠)</p> Signup and view all the answers

    What role does binding energy play in enzyme reactions?

    <p>It reduces entropy and stabilizes the enzyme-substrate complex.</p> Signup and view all the answers

    How do enzymes aid in organizing substrates for a reaction?

    <p>By positioning reactive groups in close proximity and correct orientation.</p> Signup and view all the answers

    What is meant by the term 'rate-limiting step' in biochemical reactions?

    <p>The step with the highest activation energy that dictates the overall rate.</p> Signup and view all the answers

    Study Notes

    Enzymes in Disease States

    • Enzymes can be used as biomarkers for diagnosis.
    • Enzyme levels and activity may change in disease states.
    • Many drugs interact with enzymes.

    Enzymes are Mostly Proteins

    • Most enzymes are globular proteins.
    • Some RNA (ribozymes and ribosomal RNA) can catalyze reactions.
    • Catalytic activity depends on the native fold of the protein, including its primary, secondary, tertiary, and quaternary structures.
    • Prosthetic groups are sometimes needed for catalytic activity:
      • Cofactors: inorganic ions
      • Coenzymes: organic molecules
    • The protein part of an enzyme without a prosthetic group is called an apoenzyme or apoprotein.
    • A holoenzyme is an active enzyme consisting of an apoenzyme and prosthetic group(s).

    Enzyme Classification

    • Enzymes are classified based on the reaction they catalyze.
    • The International Classification of Enzymes assigns a class number and name based on the type of reaction catalyzed.
    • Trivial names often include the substrate name + “ase” or describe the broad function performed.

    Enzyme-Substrate Specificity

    • Enzymes have substrate selectivity.
    • An enzyme will generally only interact with or bind to a specific substrate.
    • The active site of an enzyme is a pocket where the substrate binds and is processed.

    Enzyme-Substrate Complex

    • The enzyme-substrate complex is essential for enzymatic action.
    • The enzyme may bind to a substrate but not catalyze a reaction.

    Enzymatic Catalysis

    • Enzymes do not affect the position and direction of equilibrium or the free energy of a reaction.
    • Enzymes increase reaction rates by decreasing the activation energy.
    • Enzymes alter the kinetics of a reaction but not the thermodynamics.

    Transition State

    • The transition state (≠) is a high-energy configuration during the reaction process.
    • The transition state is not a stable intermediate like the enzyme-substrate (ES) or enzyme-product (EP) complexes.
    • The transition state defines the progress of the reaction from substrate to product (S → P).

    Enzymes Lower Activation Energy

    • Enzyme-substrate (ES) complexes and enzyme-product (EP) complexes represent metastable intermediates.
    • Enzymes lower activation energy (ΔG≠) by forming these metastable intermediates.
    • The rate-limiting step of a reaction is the step with the highest activation energy and determines the overall reaction rate.

    How Enzymes Decrease Activation Energy

    • Enzymes organize reactive groups into close proximity and proper orientation for optimal reaction.
    • Enzymes reduce entropy by restricting the movement of reactants.
    • Binding energy is used to compensate for substrate distortion and help the enzyme adopt a favorable conformation for catalysis.

    Support for the Proximity Model

    • The rate of anhydride formation is strongly dependent on the proximity of reactive groups.

    How Binding Energy Helps

    • Binding energy helps by:
      • Reducing entropy.
      • Desolvating the substrate (replacing water molecules with enzyme interactions).
      • Compensating for substrate distortion.
      • Inducing enzyme conformation for optimal catalytic activity.

    Enzymes Bind Transition States Best

    • Enzyme active sites are complimentary to the transition state of the reaction they catalyze.
    • Weak interactions are optimized for the transition state in the active site.
    • Enzymes bind transition states better than substrates to reduce activation energy.

    Catalytic Mechanisms of Enzymes

    • Common catalytic mechanisms include:
      • Acid-base catalysis: donating and accepting protons.
      • Covalent catalysis: forming a transient covalent bond between the enzyme and substrate.
      • Metal ion catalysis: using redox cofactors and altering proton affinities.

    General Acid-Base Catalysis

    • Amino acid residues within the enzyme's active site donate and accept protons to optimize proton transfer.

    Covalent Catalysis

    • Covalent catalysis changes the reaction pathway by forming a transient covalent bond between the enzyme and substrate.
    • Requires a nucleophile on the enzyme (e.g., serine, thiolate, amine, or carboxylate).

    Metal Ion Catalysis

    • Involves a metal ion bound to the enzyme.
    • Facilitates substrate binding and stabilizes negative charges.
    • Participates in oxidation reactions.

    Chymotrypsin: An Example of Enzyme Function

    • Chymotrypsin is a protease that breaks down dietary proteins during digestion.
    • It cleaves peptide bonds near aromatic amino acids.

    Enzyme Inhibition

    • Inhibitors are compounds that decrease enzyme activity.
    • Irreversible inhibitors (inactivators) react with the enzyme and permanently shut off one enzyme molecule.
      • Can be powerful toxins or used as drugs.
      • Suicide inhibitors are a type of irreversible inhibitor.
    • Reversible inhibitors bind and dissociate from the enzyme.
      • Often structural analogs of substrates or products.
      • Commonly used as drugs to slow down a specific enzyme.
    • Reversible inhibitors bind to:
      • Free enzyme, preventing substrate binding.
      • Enzyme-substrate complex, preventing reaction.

    Types of Reversible Inhibition

    • Competitive Inhibition: Inhibitor competes with substrate for binding to the active site.
      • Does not affect catalysis.
    • Uncompetitive Inhibition: Inhibitor binds only to the enzyme-substrate complex.
      • Does not affect substrate binding.
      • Inhibits catalytic function.
    • Mixed Inhibition: Inhibitor binds to the enzyme with or without substrate.
      • Binds to a regulatory site.
      • Inhibits both substrate binding and catalysis.

    Irreversible (Suicide) Inhibitors

    • Irreversible inhibitors inactivate the enzyme by forming a covalent bond with it.
    • Suicide inhibitors hijack the normal enzyme reaction mechanism to inactivate it.
    • Example: Diisopropylflurophosphate (DIFP or DFP) irreversibly binds to cholinesterase.

    Enzyme Activity Regulation

    • Enzyme activity can be regulated by:
      • Noncovalent Modification (Allosteric): Allosteric effectors or modulators bind to a site different from the substrate binding site, altering the enzyme's conformation.
      • Covalent Modification: Modifications to the enzyme's structure, such as phosphorylation or glycosylation.
        • Irreversible: Permanent covalent modification.
        • Reversible: Temporary covalent modification.

    Allosteric Regulation

    • Allosteric effectors can be positive (enhance catalysis) or negative (reduce catalysis).
    • Allosteric effectors modulate enzyme function through conformational changes.

    Zymogen Activation by Irreversible Covalent Modification

    • Zymogens are inactive precursors of enzymes.
    • They are activated by irreversible covalent modification.
    • The activation process involves a change in conformation that exposes the active site.

    Multiple Types of Regulation

    • Some enzymes use multiple regulatory mechanisms.

    Conclusion

    • Enzymes play a crucial role in biological processes.
    • Understanding their catalytic mechanisms, regulation, and inhibition is essential for understanding cellular function and developing therapeutic strategies.

    Principles of Enzymatic Catalysis

    • Enzymes are biochemical catalysts, accelerating biochemical reactions without being consumed.
    • They increase the rate of both forward and reverse reactions, facilitating the attainment of thermodynamic equilibrium.
    • Compared to inorganic catalysts, enzymes exhibit greater reaction specificity, work under milder conditions (pH ~7, 37°C), exhibit higher reaction rates, and offer regulatory and control mechanisms for biological pathways.
    • Enzymes enhance the rate of reactions by reducing the activation energy (ΔG≠) required to reach the transition state.
    • The transition state is a high-energy configuration during the reaction process and is different from ES and EP complexes, which are reactive intermediates.
    • Binding energy, a major source of free energy for lowering activation energies, is utilized by enzymes to stabilize the transition state and overcome the entropic barrier.
    • Enzymes organize reactive groups in close proximity and orient them appropriately for optimal reaction.
    • Catalyzed reactions are entropically neutral as the enzyme binds substrates into a rigid complex, mitigating the entropy cost.
    • Enzymes enhance the reaction rate by binding to the transition state better than to the substrates.
    • Enzymes employ a variety of catalytic mechanisms, including acid-base catalysis (proton transfer), covalent catalysis (transient covalent bonds), and metal ion catalysis (metal ions bound to the enzyme).
    • General acid-base catalysis involves amino acid residues within the active site donating or accepting protons.
    • Covalent catalysis alters the reaction path through temporary covalent bonds between the enzyme and substrate, often involving nucleophilic groups.
    • Metal ion catalysis utilizes metal ions bound to the enzyme, particularly for stabilizing negative charges and participating in oxidation reactions.
    • Chymotrypsin, a protease that cleaves peptide bonds next to aromatic amino acids, exemplifies the use of several enzymatic mechanisms.
    • Chymotrypsin's structure is characterized by β-sheets and α-helices, stabilized by disulfide bonds.

    Enzyme Kinetics

    • Enzyme kinetics studies the reaction rates of enzyme-catalyzed processes.
    • Factors affecting the rate include enzyme, substrate, effectors, and temperature.
    • Studying enzyme kinetics allows for a quantitative understanding of biocatalysis, determining the order of substrate binding, elucidating catalytic mechanisms, identifying effective inhibitors, and understanding the regulation of enzyme activity.
    • The Michaelis-Menten model describes the relationship between substrate concentration and reaction velocity.
    • The Michaelis constant (Km) represents the substrate concentration at half maximal velocity, indicating the enzyme's affinity for the substrate.
    • Maximum velocity (Vmax) reflects the rate when the enzyme is fully saturated with substrate.
    • The catalytic efficiency of an enzyme is measured by kcat/Km, combining the enzyme's ability to bind and transform the substrate.
    • For highly efficient enzymes, the diffusion of substrate to and product from the active site becomes limiting (diffusion-controlled limit).
    • The Lineweaver-Burk plot is a linear representation of the Michaelis-Menten equation, useful for analyzing two-substrate data or inhibition.

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