Biochemistry Chapter on Enzyme Catalysis
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Questions and Answers

What is the approximate pKa of a typical Glutamate sidechain?

  • 5
  • 4.1 (correct)
  • 9
  • 7.4

    • At a pH of 5, what is the charge of a Glutamate sidechain?

  • Protonated
  • Cannot be determined from the information provided
  • Deprotonated (correct)

    • Which of the following statements is TRUE about the relationship between pH and pKa?

  • When pH is higher than pKa, the molecule is deprotonated. (correct)
  • When pH is equal to pKa, the molecule is in its most stable form.
  • When pH is lower than pKa, the molecule is deprotonated.
  • When pH is higher than pKa, the molecule is protonated.

    • Which of the following factors contributes to the rate enhancement observed in enzyme-catalyzed reactions?

    <p>Proximity and orientation effects (A)</p> Signup and view all the answers

    How does an enzyme effectively turn an intermolecular reaction into an intramolecular one?

    <p>By binding the substrate and organizing it for reaction (C)</p> Signup and view all the answers

    What is the primary difference between a reaction intermediate and a transition state?

    <p>Intermediates are more stable than transition states. (C)</p> Signup and view all the answers

    What is the main reason why enzymes do not bind too tightly to their substrates?

    <p>It would increase the activation energy barrier, making the reaction slower. (A)</p> Signup and view all the answers

    Which of the following statements about enzymes is TRUE?

    <p>Enzymes decrease the activation energy barrier of a reaction. (C)</p> Signup and view all the answers

    What is the role of general acid-base catalysis in enzymatic reactions?

    <p>To donate or accept protons, influencing the reaction pathway. (B)</p> Signup and view all the answers

    Which of the following is NOT a common catalytic mechanism used by enzymes?

    <p>Hydrophobic catalysis (D)</p> Signup and view all the answers

    What is the induced fit model of enzyme-substrate interaction?

    <p>The enzyme changes its shape slightly upon substrate binding to optimize interactions. (A)</p> Signup and view all the answers

    Which of the following statements about the lock and key model is TRUE?

    <p>It was the first model proposed to explain enzyme specificity. (D)</p> Signup and view all the answers

    How do enzymes achieve high specificity in their reactions?

    <p>By having active sites that are optimized to interact with specific substrates. (C)</p> Signup and view all the answers

    Which of the following statements about the energetics of a reaction is TRUE?

    <p>Enzymes lower the activation energy barrier of a reaction, but they do not affect the free energy change (ΔG) of a reaction. (C)</p> Signup and view all the answers

    Why is the binding of the substrate to the enzyme important for catalysis?

    <p>All of the above. (D)</p> Signup and view all the answers

    Which of the following is an example of general acid-base catalysis?

    <p>The donation of a proton from an amino acid in the enzyme active site. (B)</p> Signup and view all the answers

    What is the significance of the fact that enzymes are unchanged by the reactions they catalyze?

    <p>All of the above. (D)</p> Signup and view all the answers

    Which of the following correctly describes the difference in binding constants for catalytic enzymes and binding proteins?

    <p>Binding proteins have higher binding constants than catalytic enzymes. (A)</p> Signup and view all the answers

    What is the main reason why enzymes lower the activation energy barrier of a reaction?

    <p>All of the above. (D)</p> Signup and view all the answers

    Which of the following best describes the role of the induced fit model in enzyme-substrate interaction?

    <p>The substrate induces a conformational change in the enzyme, which favors the formation of the transition state. (C)</p> Signup and view all the answers

    What type of reaction is catalyzed by lyases?

    <p>Addition or removal of groups to form double bonds (C)</p> Signup and view all the answers

    Which enzyme catalyzes the conversion of citrate to isocitrate?

    <p>Aconitase (C)</p> Signup and view all the answers

    Which process involves the conversion of two forms of a chiral molecule to homogenize them?

    <p>Racemisation (A)</p> Signup and view all the answers

    What is required by pyruvate carboxylase to function in its catalytic role?

    <p>Biotin (C)</p> Signup and view all the answers

    Which type of enzyme is responsible for joining two molecules with the input of energy such as ATP?

    <p>Ligase (D)</p> Signup and view all the answers

    Which of the following statements accurately describes the relationship between transition states and reaction intermediates?

    <p>Reaction intermediates are more stable than transition states and can be isolated. (C)</p> Signup and view all the answers

    What is the key principle that governs enzyme-transition state affinity?

    <p>Enzymes preferentially bind to transition states, which helps reduce the activation barrier. (A)</p> Signup and view all the answers

    Why are transition state analogues often used as enzyme inhibitors?

    <p>They bind more tightly to the active site than the substrate, blocking the catalytic reaction. (C)</p> Signup and view all the answers

    What is the main reason enzymes don't bind too tightly to their substrates?

    <p>Too tight binding would increase the activation energy barrier, hindering catalysis. (A)</p> Signup and view all the answers

    What is the significance of the induced fit model in enzyme-substrate interaction?

    <p>It highlights how the enzyme's conformation changes to better accommodate the substrate, facilitating catalysis. (D)</p> Signup and view all the answers

    Which of the following is a common example of a catalytic mechanism employed by enzymes?

    <p>General acid-base catalysis (B)</p> Signup and view all the answers

    What is the primary difference between the lock and key model and the induced fit model of enzyme-substrate interaction?

    <p>The lock and key model involves a rigid enzyme, while the induced fit model allows for flexibility. (A)</p> Signup and view all the answers

    Why is the ability of enzymes to alter their conformations important for their catalytic activity?

    <p>It enables the enzyme to adopt a more favorable conformation for catalysis, facilitating the reaction. (A)</p> Signup and view all the answers

    Why is the statement 'Enzymes are unchanged by the reactions they catalyze' necessary for understanding enzyme function?

    <p>It highlights that enzymes act as reusable catalysts, driving reactions without being consumed. (B)</p> Signup and view all the answers

    Which of the following best explains why enzymes exhibit high specificity for their substrates?

    <p>The enzyme's active site has specific functional groups that interact with the substrate, creating a unique binding site. (B)</p> Signup and view all the answers

    How does general acid-base catalysis contribute to the rate enhancement observed in enzyme-catalyzed reactions?

    <p>By providing protons or accepting them from the substrate, facilitating bond breaking or formation. (A)</p> Signup and view all the answers

    What is the main reason for the use of metal ions in certain enzyme-catalyzed reactions?

    <p>They participate directly in the catalytic reaction, often by donating or accepting electrons. (C)</p> Signup and view all the answers

    Which of the following is NOT a reason why transition state analogues can be effective inhibitors of enzymes?

    <p>They mimic the shape of the product, preventing its release from the active site. (C)</p> Signup and view all the answers

    How can an enzyme, through its binding interactions, effectively transform an intermolecular reaction into an intramolecular one?

    <p>By bringing the reacting molecules together in close proximity and optimal orientation. (A)</p> Signup and view all the answers

    In the context of enzyme-catalyzed reactions, why is it beneficial for an enzyme to bring substrates closer together?

    <p>It increases the concentration of the substrates in the enzyme active site, effectively increasing their local concentration. (B), It reduces the activation energy of the reaction by lowering the energy required for the substrates to interact. (C)</p> Signup and view all the answers

    Which of the following best explains the rate enhancement observed in model systems where reacting groups are fixed in space, compared to systems where they can rotate freely?

    <p>Reduced rotational freedom increases the probability of reacting groups colliding in the correct orientation, leading to a faster reaction. (C)</p> Signup and view all the answers

    Consider an enzyme with an active site containing glutamate residues. At pH 7.4, what would be the expected charge of these glutamate sidechains?

    <p>Negatively charged (D)</p> Signup and view all the answers

    Lysozyme, an enzyme that functions at optimal pH of 5, has glutamate residues in its active site. Which of the following statements accurately describes the glutamate sidechains in lysozyme at pH 5?

    <p>Glutamate sidechains would be negatively charged due to deprotonation. (D)</p> Signup and view all the answers

    How do enzymes achieve significant rate enhancements in biochemical reactions, compared to reactions in the absence of enzymes?

    <p>Enzymes provide an alternative reaction pathway with a lower activation energy. (B)</p> Signup and view all the answers

    What is the role of Asp52 in the catalytic mechanism of lysozyme?

    <p>To form a covalent bond with a sugar (C)</p> Signup and view all the answers

    How do metalloenzymes differ from metal-activated enzymes?

    <p>Metalloenzymes have tightly bound metal ions (A)</p> Signup and view all the answers

    Which metal ion is used by carbonic anhydrase to generate nucleophilic hydroxide species?

    <p>Zn2+ (C)</p> Signup and view all the answers

    What is the relationship between apoenzyme and holoenzyme?

    <p>Holoenzyme is the active form of the enzyme when the cofactor is bound (D)</p> Signup and view all the answers

    Which coenzyme is commonly used in enzyme-catalyzed oxidations or reductions?

    <p>Nicotinamide adenine dinucleotide (NAD) (B)</p> Signup and view all the answers

    What is the main function of cofactors in enzymatic reactions?

    <p>They enhance the enzyme's catalytic function (A)</p> Signup and view all the answers

    Which class of enzymes is involved in the transfer of chemical groups between molecules?

    <p>Transferases (B)</p> Signup and view all the answers

    What does NAD(P)H primarily do in cellular reactions?

    <p>It donates or accepts electrons (A)</p> Signup and view all the answers

    Which of the following metals is commonly associated with increasing the binding interaction of substrates in enzymes?

    <p>Mg2+ (D)</p> Signup and view all the answers

    What occurs during the oxidative reaction of NAD+?

    <p>It accepts a hydride ion (B)</p> Signup and view all the answers

    In what form does iron in Fe-S clusters predominantly exist?

    <p>Both Fe2+ and Fe3+ (A)</p> Signup and view all the answers

    How do enzymes classified as hydrolases function?

    <p>By adding water to cleave bonds (B)</p> Signup and view all the answers

    What type of reaction is typically catalyzed by oxidoreductases?

    <p>Redox reactions (D)</p> Signup and view all the answers

    What role do metal ions play in enzymatic catalysis?

    <p>They can stabilize transition states (C)</p> Signup and view all the answers

    What defines a prosthetic group in terms of coenzymes?

    <p>It is tightly bound to the enzyme (C)</p> Signup and view all the answers

    Study Notes

    Local Environment Influence on pKa

    • Glutamate sidechains typically have a pKa of 4.1.
    • Lysozyme activity spans a pH range of ~4 to 9.
    • Human tears have an average pH of ~7.4.
    • pH > pKa leads to deprotonation of the molecule in question.
    • pH < pKa leads to protonation of the molecule in question.
    • At the optimal pH for lysozyme (5), Glu sidechains would be negatively charged.
    • Local environment critically influences sidechain pKa values.

    Enzyme Catalysis

    • Enzyme-catalyzed reactions occur in active sites.
    • Enzymes bind and position substrates to facilitate reactions in enzyme-substrate complexes.
    • Maximum reaction velocity is reached when all active sites are filled with substrate.

    Rate Enhancement Mechanisms

    • Enzymes increase reaction rates through proximity and orientation effects, bringing substrates closer together and arranging them optimally.
    • Most rate enhancement originates from binding, transforming intermolecular reactions into faster intramolecular ones.
    • Substrates are brought closer together and oriented optimally for reaction.
    • This is exemplified in a reaction where negatively charged oxygen is positioned correctly near a target carbon. Without enzymes, reactants collide randomly. With enzymes, reactants are linked to catalyse the reaction, enhancing reaction speed. Linking progresses from a CH2 group, to direct linkage, to fixed linkage to yield increasing speed.

    Transition States and Intermediates

    • Reactions proceed through transition states and sometimes intermediates from substrate to product.
    • Transition states exist briefly, in femtosecond timescales.
    • Intermediates are more stable, potentially isolable.

    Transition State Affinity

    • Enzymes bind transition states, lowering activation barriers.
    • Transition state analogues are excellent inhibitors and are used in catalytic antibody design., better than substrates in some cases, like proline racemase.
    • Proline racemase's transition state analogues bind significantly better than the proline substrate.

    Enzyme Substrate Binding

    • Tight substrate binding is detrimental because it elevates the activation energy barrier.
    • Catalytic enzymes typically have milli- to micromolar substrate binding constants.
    • Binding proteins/antibodies have nano- to picomolar constants (stronger binding).

    Enzyme Structure and Function

    • Enzymes are unchanged throughout the reaction cycle, even with covalent intermediates, which are later broken.
    • High substrate specificity, matching active site shape and functional groups.
    • Lock-and-key model is not representative of all enzyme interactions.

    Flexibility of Enzymes

    • Enzyme structures are flexible, adapting to optimal substrate/transition state binding.
    • Induced fit model describes this flexibility.
    • Strain energy in the enzyme is relieved during the reaction, stabilizing the transition state and accelerating the reaction.

    Catalytic Mechanisms

    • Catalysis accelerates the approach to equilibrium.
    • Most rate enhancement is from substrate binding/orientation; following common mechanisms:
      • General acid-base catalysis
      • Covalent catalysis
      • Metal ion catalysis

    General Acid-Base Catalysis

    • Enzymes act as acids (proton donors) or bases (proton acceptors) affecting reaction rates.
    • Lysozyme (example): Glu35 acts as an acid and a base, utilizing water addition in its reaction mechanism. Glu35 donates a proton to the substrate, facilitating the cleavage of the bond. Then Glu35 extracts a proton from a water molecule to complete the reaction.

    Covalent Catalysis

    • Many enzymes form covalent bonds with substrates, generating transient reactive intermediates.
    • Lysozyme uses a covalent intermediate between Asp52 and the oxonium ion on the NAM sugar during its catalytic cycle.. A water molecule attacks the carbon in the NAM ring, breaking the bond to Asp52.

    Metal Ion Catalysis

    • Enzymes often use bound metal ions in their reaction mechanisms.
    • Metal ions can be tightly bound (metalloenzymes) or loosely associated (metal-activated).
    • Metals can generate nucleophilic species for catalysis or stabilize the transition state or increase binding interactions.
    • Examples include carbonic anhydrase, DNA polymerase I, and Fe-S clusters.

    Cofactors and Coenzymes

    • Enzymes require cofactors (metal ions or small molecules) for catalytic activity.
    • Cofactors are recycled in the cell.
    • Coenzymes are often small organic molecules; tightly bound ones are prosthetic groups.
    • Loosely bound/dissociable ones are cosubstrates.
    • Apoenzyme + Cofactor = Holoenzyme.
    • Examples of cofactors include AMP, ATP, NAD, and NADP.
    • NAD(P)+/NAD(P)H are freely dissociable and act as important sources of reducing power.
    • The nicotinamide ring is accessible in the enzyme active site.

    Enzyme Classification

    • Enzymes are grouped based on the type of reaction they catalyze:
      • Oxidoreductases (dehydrogenases): redox reactions, often using NAD(P)H, FAD, or iron-sulfur clusters.
      • Transferases: transfer groups between molecules.
      • Hydrolases: cleavage reactions using water.
      • Lyases (synthases): addition or removal of groups to form double bonds.
      • Isomerases: interconversion of isomers.
      • Ligases (synthases): joining of molecules, often requiring ATP.

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    Description

    This quiz covers key concepts in biochemistry, particularly focusing on enzyme catalysis, pKa values, and the effects of local environments on enzymatic activity. It explores how enzymes function, the importance of transition states, and the mechanisms of rate enhancement in biochemical reactions. Test your understanding of these fundamental topics and their implications in biological systems.

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