Biochemistry I - Enzymes Overview
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Questions and Answers

What substance is acted upon by an enzyme during a chemical reaction?

  • Catalyst
  • Product
  • Substrate (correct)
  • Coenzyme
  • What significant conclusion was reached by Eduard Buchner in 1897 regarding fermentation?

  • Fermentation is a function of plant extracts only.
  • Fermentation is a vitalistic process.
  • Fermentation requires living yeast cells.
  • Fermentation can occur without any living cells. (correct)
  • Which of the following best describes the role of enzymes in biochemical reactions?

  • They are consumed in the reaction.
  • They change the equilibrium of the reaction.
  • They increase the rate of the reaction without being changed. (correct)
  • They provide energy for the reaction.
  • What was the name given to the molecules discovered by Eduard Buchner that promote fermentation?

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

    Which scientist first isolated and crystallized urease, establishing that enzymes are proteins?

    <p>James Sumner</p> Signup and view all the answers

    Which process marked the end of the vitalistic notion that enzymes were inseparable from living cells?

    <p>Buchner's experiment with yeast extracts</p> Signup and view all the answers

    What term describes substances that assist enzymes in their catalytic activity?

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

    Which of the following enzymes is known to catalyze the hydrolysis of peptide bonds in proteins?

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

    At what pH value is the activity of lysozyme at its optimum due to the abundance of protonated E35 and deprotonated D52?

    <p>5</p> Signup and view all the answers

    Which amino acid must be protonated for it to act as a general acid catalyst in lysozyme activity?

    <p>E35</p> Signup and view all the answers

    Which pH condition favors the catalysis of lysozyme by ensuring deprotonated D52 is available?

    <p>Above 3.7</p> Signup and view all the answers

    In the context of chymotrypsin, which residue is protonated in the serine protease catalytic triad?

    <p>H57</p> Signup and view all the answers

    What is a key characteristic of the mechanism through which serine proteases like chymotrypsin cleave peptide bonds?

    <p>Stabilization of transition and tetrahedral intermediates</p> Signup and view all the answers

    What happens to the catalytic activity of an enzyme if it is denatured?

    <p>It is usually lost.</p> Signup and view all the answers

    What is a key characteristic of the induced fit model of enzyme action?

    <p>Both the enzyme and substrate undergo distortion.</p> Signup and view all the answers

    In enzyme kinetics, which step is typically considered reversible?

    <p>Formation of enzyme-substrate complex.</p> Signup and view all the answers

    What does the binding of glucose to hexokinase induce?

    <p>A significant conformational change in the enzyme.</p> Signup and view all the answers

    What role do intermediate states play in enzyme-catalyzed reactions?

    <p>They resemble the transition state and lower free energy.</p> Signup and view all the answers

    Which of the following is NOT an essential structural level of protein enzymes crucial for their catalytic activity?

    <p>Spherical structure</p> Signup and view all the answers

    Which best represents the energy changes during an enzyme-catalyzed reaction?

    <p>Lower activation energy compared to un-catalyzed reaction.</p> Signup and view all the answers

    What is the significance of the quaternary structure in protein enzymes?

    <p>It enables multiple substrates to bind simultaneously.</p> Signup and view all the answers

    Which statement accurately describes a true catalyst?

    <p>It participates in the reaction but remains unchanged.</p> Signup and view all the answers

    What happens to the rate of an unfavorable process when a catalyst is introduced?

    <p>The process remains unfavorable.</p> Signup and view all the answers

    Which characteristic is true for a first-order reaction?

    <p>The reaction follows single exponential decay of reactant concentration.</p> Signup and view all the answers

    What does a linear graph of ln[A] versus time indicate?

    <p>The reaction is first-order and follows the equation [A]t = [A]oe-kt.</p> Signup and view all the answers

    What defines the rate-limiting step in a multistep reaction?

    <p>It is the slowest step that determines the reaction rate.</p> Signup and view all the answers

    How do catalysts affect the activation energy of a chemical reaction?

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

    What is the characteristic of the first-order rate constant?

    <p>It has units of (time)-1.</p> Signup and view all the answers

    What information does a free energy diagram reveal about a chemical reaction?

    <p>It shows only the free energy difference between the initial and final states.</p> Signup and view all the answers

    What happens to reaction rates when temperature is increased?

    <p>More molecules have sufficient energy to overcome the activation barrier.</p> Signup and view all the answers

    How does an enzyme influence the standard free energy of activation (DGo+)?

    <p>It lowers DGo+ to accelerate the reaction.</p> Signup and view all the answers

    What is the primary role of a catalyst in a chemical reaction?

    <p>To lower the activation energy and speed up the reaction.</p> Signup and view all the answers

    Which statement best describes enzyme-substrate complementarity?

    <p>It is based on the enzyme's shape, charge, and polarity compared to the substrate.</p> Signup and view all the answers

    What does the rate enhancement of an enzyme-catalyzed reaction indicate?

    <p>The ratio of the rate constants for catalyzed and noncatalyzed reactions.</p> Signup and view all the answers

    The transition state in a reaction is characterized as which of the following?

    <p>The highest energy state that must be achieved to proceed with the reaction.</p> Signup and view all the answers

    Which of the following best describes the effect of lowering DGo+?

    <p>It decreases the height of the activation barrier.</p> Signup and view all the answers

    In an enzyme-catalyzed reaction, what do kcat and knon represent?

    <p>The rate constants for the catalyzed and noncatalyzed reactions, respectively.</p> Signup and view all the answers

    What structural feature allows the enzyme to stabilize the transition state during catalysis?

    <p>Electrostatic interactions with active site amino acids</p> Signup and view all the answers

    In lysozyme, what is the role of the amino acid E35 during the enzymatic reaction?

    <p>It acts as a general acid and general base in consecutive steps</p> Signup and view all the answers

    Which type of bond does lysozyme cleave in its substrate?

    <p>Glycosidic bonds between sugar residues</p> Signup and view all the answers

    What characterizes the first step of the Phillips mechanism in lysozyme action?

    <p>Cleavage of the glycosidic bond</p> Signup and view all the answers

    What substrate does lysozyme act upon?

    <p>Peptidoglycan, a carbohydrate found in bacterial cell walls</p> Signup and view all the answers

    What happens at the end of the second step in the Phillips mechanism of lysozyme?

    <p>Formation of a covalent bond with the substrate</p> Signup and view all the answers

    What is the significance of the cleft between the enzyme's domains?

    <p>It facilitates the accommodation of the substrate molecule</p> Signup and view all the answers

    How does the active site of lysozyme interact with its carbohydrate substrate?

    <p>By utilizing both electrostatic and hydrophobic interactions</p> Signup and view all the answers

    Study Notes

    Biochemistry I - CHM219

    • This course covers Enzymes, Biological Catalysts

    Enzymes I: The Biological Catalysts

    • Catalysts increase chemical reaction rates without being consumed
    • Enzymes are biological catalysts, accelerating biochemical reactions.
    • Enzymes are proteins, their structure is crucial for their activity.
    • Denaturing or disassociating an enzyme usually destroys its catalytic activity

    Outline:

    • The Role of Enzymes: Brief overview, explains the concept of chemical catalysts and how enzymes function.
    • Chemical Reaction Rates and the Effects of Catalysts - A Review: Examines how reaction rates are affected, providing background on kinetics. Introduces first-order reactions.
    • How Enzymes Act as Catalysts: Principles and Examples: Details how enzymes bind to substrates, promote reaction, and the factors affecting their activity.
    • The Kinetics of Enzymatic Catalysis: Focuses on how the rates of enzymatic reactions are measured and modeled.
    • Enzyme Inhibition: Explains different types of enzyme inhibition mechanisms.
    • Cofactors, Vitamins, and Essential Metals: Discusses the role of cofactors, vitamins, and essential metals as enzyme components.
    • The Diversity of Enzymatic Function: Exploring a wide range of enzyme functions.
    • Nonprotein Biocatalysts: Catalytic Nucleic Acids: Investigating non-protein biocatalysts (RNA catalysts).
    • The Regulation of Enzyme Activity: Allosteric Enzymes: Examining allosteric regulation of enzyme activity.
    • Covalent Modifications Used to Regulate Enzyme Activity: Explains how covalent modifications control enzyme activity.

    History of Enzymes

    • Biological catalysis recognized in late 1700s, focused on digestive processes.
    • Research into enzyme activity continued through the 1800s, including exploring the processes of starch conversion to sugar.
    • Louis Pasteur connected microbial fermentation processes to enzymes.

    Enzymes are proteins

    • James Sumner isolated and crystallized urease, proving that enzymes are proteins (1926).
    • Northrop and Kunitz's confirmation of Sumner's work consolidated the understanding.

    The Role of Enzymes

    • Catalysts speed up chemical reactions without being consumed in the process.
    • Enzymes catalyze hydrolysis of peptide bonds in proteins/polypeptides.
    • The substance acted on by an enzyme is called the substrate.

    Two Facts Deserve Emphasis:

    • Catalysts remain unchanged during the chemical process.
    • Catalysts do not change the equilibrium position of a reaction.
    • Enzymes, like hemoglobin, are not true catalysts in some chemical processes.

    Chemical Reaction Rates and Effects of Catalysts

    • A first-order reaction's rate is proportional to the concentration of the reactant.
    • A first-order reaction demonstrates a single, exponential decay of the reactant.

    Determining First-Order Reactions

    • Graphs of reactant concentration vs. time for first-order reactions show exponential decay.
    • Graphs of the natural logarithm of reactant concentration vs. time yield a straight line.
    • The slope of this line corresponds with the first-order rate constant.

    First-Order vs. Second-Order Reactions

    • First-order rate constants have time units.
    • Second-order rate constants have concentration-based time units.
    • Analysis of multi-step reactions is sometimes simplified by identifying a step that limits the overall reaction speed (rate-limiting step).

    Activation Energy and Catalysts

    • Chemical reactions need activation energy, the energy barrier.
    • Catalysts lower this energy barrier for reactions.

    Free Energy Diagrams

    • Free energy diagrams illustrate free energy changes during chemical reactions.
    • Transition states are high-energy, unstable states during chemical transformation.
    • Catalysts stabilize the transition state, lowering its energy

    Effect of Temperature and ΔG°+

    • Reaction rates are related to the number of molecules with enough energy to overcome the activation energy.
    • Higher temperatures increase the reaction rate by providing more molecules with required energy.

    Rate Enhancement

    • Rate enhancement equals the ratio of catalyzed/uncatalyzed reaction constants.

    Enzymatic Rate Enhancements

    • Each vertical bar represents rate enhancement.

    Influence of Catalysts on Reactions

    • Catalysts increase both forward and reverse reaction rate but do not change the equilibrium composition.
    • Catalysts speed up reactions through altering the reaction pathways.

    Effect of a Catalyst on Activation Energy

    • Catalysts reduce the activation energy required for the reaction to proceed.
    • This causes an increase in the reaction rate.
    • The equilibrium point is unchanged.

    How Enzymes Act as Catalysts

    • Enzyme active sites are complementary in shape, charge, and polarity to transition states of the catalyzed reaction.
    • Complementarity between the enzyme and substrate is crucial for enzyme specificity.

    Catalytic Activity

    • Enzymes rely on the integrity of their native protein conformation for catalytic function.
    • Protein structure (primary, secondary, tertiary, and quaternary) is essential for enzyme activity.

    Entropic and Enthalpic Factors in Catalysis

    • Enzymes concentrate reactants in close proximity, favoring high-energy transition state formation.

    Importance of Intermediate States

    • Enzymes can accelerate reactions by creating intermediate states with lower energy levels similar to the transition state
    • This accelerates the intermediate-state formation and product formation.

    The Active Site of Lysozyme

    • The lysozyme active site is accessible.
    • The substrate is a trisaccharide (NAM-NAG-NAM).
    • This carbohydrate substrate binds to and is cleaved from the active site.

    The Mechanism of Lysozyme Action

    • Initially, E35 acts as an acid to initiate glycosidic bond cleavage.
    • Subsequently, E35 acts as a base to initiate attack by water.

    Effect of pH on Lysozyme Activity

    • The ideal pH optimum for lysozyme activity occurs within a pH range where both E35 and D52 amino acids are poised to function appropriately.

    Evidence of Covalent Intermediate in Lysozyme Mechanism

    • Studies on synthetic substrates, including NAG-2FGIcF, provide evidence for a transient covalent intermediate in the lysozyme reaction pathway.

    Catalysis of Peptide-Bond Hydrolysis by Chymotrypsin

    • Chymotrypsin's mechanism involves three key catalytic components (catalytic triad)
    • The mechanism demonstrates a two-step process, highlighting the use of a serine residue.
    • Initially, the hydroxyl group of a serine residue initiates the peptide bond cleavage.

    Chymotrypsin's Serine Protease Catalytic Triad

    • X-ray crystallography studies revealed the catalytic triad: His57, Ser195, and Asp102, which have particular spatial orientations facilitating catalysis.

    Strategies Used by Lysozyme and Serine Proteases for Lowering ΔG°+

    • Tables outlining the strategies used by different enzymes for lowering activation energy
    • Lysozyme, using different catalytic strategies from serine proteases.

    Timescale of Protein Motions

    • Table summarizing timescales for different protein motions involved in catalysis.

    Dynamic Conformational Changes in Dihydrofolate Reductase

    • Diagram illustrating multiple, dynamic changes in the enzyme's conformation during the catalysis cycle.

    Additional Note:

    • Figures & diagrams are vital to understanding these concepts. Visualizing the mechanisms and pathways is crucial. Always review the associated graphs and illustrations.

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    Description

    This quiz explores the role of enzymes as biological catalysts, detailing their structure, function, and the kinetics of enzymatic reactions. Understand the principles behind how enzymes accelerate biochemical processes and how factors impact their activity.

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