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Questions and Answers
What substance is acted upon by an enzyme during a chemical reaction?
What substance is acted upon by an enzyme during a chemical reaction?
What significant conclusion was reached by Eduard Buchner in 1897 regarding fermentation?
What significant conclusion was reached by Eduard Buchner in 1897 regarding fermentation?
Which of the following best describes the role of enzymes in biochemical reactions?
Which of the following best describes the role of enzymes in biochemical reactions?
What was the name given to the molecules discovered by Eduard Buchner that promote fermentation?
What was the name given to the molecules discovered by Eduard Buchner that promote fermentation?
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Which scientist first isolated and crystallized urease, establishing that enzymes are proteins?
Which scientist first isolated and crystallized urease, establishing that enzymes are proteins?
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Which process marked the end of the vitalistic notion that enzymes were inseparable from living cells?
Which process marked the end of the vitalistic notion that enzymes were inseparable from living cells?
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What term describes substances that assist enzymes in their catalytic activity?
What term describes substances that assist enzymes in their catalytic activity?
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Which of the following enzymes is known to catalyze the hydrolysis of peptide bonds in proteins?
Which of the following enzymes is known to catalyze the hydrolysis of peptide bonds in proteins?
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At what pH value is the activity of lysozyme at its optimum due to the abundance of protonated E35 and deprotonated D52?
At what pH value is the activity of lysozyme at its optimum due to the abundance of protonated E35 and deprotonated D52?
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Which amino acid must be protonated for it to act as a general acid catalyst in lysozyme activity?
Which amino acid must be protonated for it to act as a general acid catalyst in lysozyme activity?
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Which pH condition favors the catalysis of lysozyme by ensuring deprotonated D52 is available?
Which pH condition favors the catalysis of lysozyme by ensuring deprotonated D52 is available?
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In the context of chymotrypsin, which residue is protonated in the serine protease catalytic triad?
In the context of chymotrypsin, which residue is protonated in the serine protease catalytic triad?
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What is a key characteristic of the mechanism through which serine proteases like chymotrypsin cleave peptide bonds?
What is a key characteristic of the mechanism through which serine proteases like chymotrypsin cleave peptide bonds?
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What happens to the catalytic activity of an enzyme if it is denatured?
What happens to the catalytic activity of an enzyme if it is denatured?
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What is a key characteristic of the induced fit model of enzyme action?
What is a key characteristic of the induced fit model of enzyme action?
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In enzyme kinetics, which step is typically considered reversible?
In enzyme kinetics, which step is typically considered reversible?
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What does the binding of glucose to hexokinase induce?
What does the binding of glucose to hexokinase induce?
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What role do intermediate states play in enzyme-catalyzed reactions?
What role do intermediate states play in enzyme-catalyzed reactions?
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Which of the following is NOT an essential structural level of protein enzymes crucial for their catalytic activity?
Which of the following is NOT an essential structural level of protein enzymes crucial for their catalytic activity?
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Which best represents the energy changes during an enzyme-catalyzed reaction?
Which best represents the energy changes during an enzyme-catalyzed reaction?
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What is the significance of the quaternary structure in protein enzymes?
What is the significance of the quaternary structure in protein enzymes?
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Which statement accurately describes a true catalyst?
Which statement accurately describes a true catalyst?
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What happens to the rate of an unfavorable process when a catalyst is introduced?
What happens to the rate of an unfavorable process when a catalyst is introduced?
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Which characteristic is true for a first-order reaction?
Which characteristic is true for a first-order reaction?
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What does a linear graph of ln[A] versus time indicate?
What does a linear graph of ln[A] versus time indicate?
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What defines the rate-limiting step in a multistep reaction?
What defines the rate-limiting step in a multistep reaction?
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How do catalysts affect the activation energy of a chemical reaction?
How do catalysts affect the activation energy of a chemical reaction?
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What is the characteristic of the first-order rate constant?
What is the characteristic of the first-order rate constant?
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What information does a free energy diagram reveal about a chemical reaction?
What information does a free energy diagram reveal about a chemical reaction?
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What happens to reaction rates when temperature is increased?
What happens to reaction rates when temperature is increased?
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How does an enzyme influence the standard free energy of activation (DGo+)?
How does an enzyme influence the standard free energy of activation (DGo+)?
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What is the primary role of a catalyst in a chemical reaction?
What is the primary role of a catalyst in a chemical reaction?
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Which statement best describes enzyme-substrate complementarity?
Which statement best describes enzyme-substrate complementarity?
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What does the rate enhancement of an enzyme-catalyzed reaction indicate?
What does the rate enhancement of an enzyme-catalyzed reaction indicate?
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The transition state in a reaction is characterized as which of the following?
The transition state in a reaction is characterized as which of the following?
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Which of the following best describes the effect of lowering DGo+?
Which of the following best describes the effect of lowering DGo+?
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In an enzyme-catalyzed reaction, what do kcat and knon represent?
In an enzyme-catalyzed reaction, what do kcat and knon represent?
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What structural feature allows the enzyme to stabilize the transition state during catalysis?
What structural feature allows the enzyme to stabilize the transition state during catalysis?
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In lysozyme, what is the role of the amino acid E35 during the enzymatic reaction?
In lysozyme, what is the role of the amino acid E35 during the enzymatic reaction?
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Which type of bond does lysozyme cleave in its substrate?
Which type of bond does lysozyme cleave in its substrate?
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What characterizes the first step of the Phillips mechanism in lysozyme action?
What characterizes the first step of the Phillips mechanism in lysozyme action?
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What substrate does lysozyme act upon?
What substrate does lysozyme act upon?
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What happens at the end of the second step in the Phillips mechanism of lysozyme?
What happens at the end of the second step in the Phillips mechanism of lysozyme?
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What is the significance of the cleft between the enzyme's domains?
What is the significance of the cleft between the enzyme's domains?
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How does the active site of lysozyme interact with its carbohydrate substrate?
How does the active site of lysozyme interact with its carbohydrate substrate?
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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.