Enzyme Mechanisms and Catalysis

Podcast Beta

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the main benefit of placing reacting groups in the correct proximity and orientation during chemical reactions?

It decreases the energy required for the reaction.

It eliminates the need for catalysts.

It increases the pH of the reaction environment.

It can enhance the reaction by a factor of 108. (correct)

Which functional group in enzymes is commonly involved in acid-base catalysis due to its appropriate pK value?

Amino group

Carboxyl group

Histidine imidazole group (correct)

Phenolic group

How does the reaction rate of ester hydrolysis change in basic conditions?

It is facilitated by the base providing hydroxyl ions rapidly. (correct)

It slows down due to increased hydroxyl ion concentration.

It completely stops due to competition for protons.

It remains constant regardless of pH changes.

What role does an acid play in the ester hydrolysis reaction?

It stabilizes the anionic transition state. Signup and view all the answers

In a reaction at neutral pH, what is a common challenge encountered during ester hydrolysis?

Low availability of hydroxyl ions. Signup and view all the answers

Which of the following statements is true regarding enzyme catalysis?

Enzymes can provide high equivalents of both acid and base. Signup and view all the answers

What happens to the reaction components requiring acid catalysis in a basic solution?

They are slowed down due to lower hydrogen ion concentration. Signup and view all the answers

What is the significance of using constrained substrates in chemical reactions?

They enhance rate coefficients by optimizing proximity and orientation. Signup and view all the answers

What is the primary role of the enzyme in ester hydrolysis?

To provide hydroxyl and hydrogen ions at the site of catalysis Signup and view all the answers

What is a key characteristic of covalent catalysis?

It involves the transient formation of a covalent bond Signup and view all the answers

Which enzyme is an example of a serine protease that uses covalent catalysis?

Chymotrypsin Signup and view all the answers

In the context of acetoacetate decarboxylase, what role does the Schiff Base play?

It facilitates electron movement needed for decarboxylation Signup and view all the answers

How do cofactors like pyridoxal phosphate enhance covalent catalysis?

They delocalize electrons and form covalent intermediates Signup and view all the answers

What is the role of the serine hydroxyl group in chymotrypsin?

To replace a free hydroxyl group during the reaction Signup and view all the answers

What is a consequence of forming a covalent intermediate in enzymatic reactions?

It can decrease the energy of subsequent transition states Signup and view all the answers

What is a critical advantage of using covalent catalysis in enzyme mechanisms?

It allows reactions to occur at lower energy levels Signup and view all the answers

What is a common misconception about how enzymes carry out catalysis?

Enzymes form an ES complex to lower the energy of activation. Signup and view all the answers

Which of the following mechanisms is NOT listed as a way in which enzymes carry out catalysis?

Nuclear Fusion Signup and view all the answers

How do enzymes reduce the entropy of the reactants during catalysis?

By binding substrates in close proximity and orientation. Signup and view all the answers

Which of the following statements about proximity effects in enzymatic catalysis is correct?

Proximity of reacting groups facilitates their reaction. Signup and view all the answers

What is the purpose of general acid and general base catalysis in enzyme mechanisms?

To facilitate the transfer of protons. Signup and view all the answers

Which factor contributes to the pseudo intramolecular character of enzyme reactions?

Concentration of substrates in the active site. Signup and view all the answers

What is the effect of desolvation in enzymatic reactions?

Increases the overall entropic cost. Signup and view all the answers

How does structural flexibility contribute to enzyme catalysis?

It enables enzymes to adapt their shape during a reaction. Signup and view all the answers

What role does histidine play in step 4 of the chymotrypsin mechanism?

Proton donor Signup and view all the answers

In step 5 of the chymotrypsin mechanism, what does water yield in the active site?

Hydroxyl ion Signup and view all the answers

What characterizes the second tetrahedral intermediate formed in step 6?

Unstable due to anionic character Signup and view all the answers

What stabilizes the anionic intermediate in step 6 of the chymotrypsin mechanism?

Hydrogen bonding with enzyme amino groups Signup and view all the answers

In step 7, what is the outcome of the attack on the second tetrahedral intermediate?

Conversion of an anionic oxygen to a carbonyl Signup and view all the answers

What happens to the carboxylate product in step 8 of the chymotrypsin mechanism?

It diffuses away from the active site. Signup and view all the answers

What is the function of the oxyanion hole in the chymotrypsin mechanism?

To stabilize negatively charged oxyanions Signup and view all the answers

Which of the following statements is true about serine proteases that are homologs of chymotrypsin?

They exhibit similarities in amino acid sequence. Signup and view all the answers

What feature of proteases is demonstrated by both subtilisin and carboxypeptidase II?

Presence of a catalytic triad Signup and view all the answers

What role does carbonic anhydrase play in the body?

Facilitates the removal of carbon dioxide Signup and view all the answers

What characteristic is essential for the catalytic activity of carbonic anhydrase?

Incorporation of a zinc ion Signup and view all the answers

Which statement is true regarding indinavir?

It resembles the peptide substrate for HIV protease. Signup and view all the answers

What is the pH optimum for the activity of carbonic anhydrase?

Approximately pH 8 Signup and view all the answers

In what manner do subtilisin and carboxypeptidase II differ from chymotrypsin?

They evolved independently without homologous relationships. Signup and view all the answers

Which functional group interaction is facilitated by the zinc ion in carbonic anhydrase?

Coordination with water molecules Signup and view all the answers

What does the presence of an oxyanion hole indicate in proteases?

Stabilization of charged intermediates Signup and view all the answers

What is one mechanism by which enzymes carry out catalysis?

Structural flexibility Signup and view all the answers

How do enzymes reduce the entropy of reactants?

By binding substrates in proximity and orientation Signup and view all the answers

Which processing effect allows for more favorable ligation or addition reactions?

Proximity and Orientation Effects Signup and view all the answers

What impact does the concentration of substrates in the active site have on reaction rates?

It increases reaction rates by simulating intramolecular reactions Signup and view all the answers

What role does covalent catalysis play in enzyme mechanisms?

It forms temporary covalent bonds with substrates during catalysis Signup and view all the answers

What chemical mechanism is related to the concentration of substrates reducing their overall entropy?

Proximity and Orientation Effects Signup and view all the answers

Which catalytic mechanism involves enzymes providing a pathway with a lower energy of activation?

Proximity Effects Signup and view all the answers

Which of the following factors contributes to a pseudo intramolecular character in enzyme reactions?

Concentration of substrates in active site Signup and view all the answers

What is a key feature of covalent catalysis that enhances enzyme function?

Formation of a covalent bond with substrate R-group Signup and view all the answers

Which type of enzymes exhibit the formation of an acyl-enzyme intermediate?

Serine proteases Signup and view all the answers

How do cofactors like pyridoxal phosphate contribute to enzymatic reactions?

By forming covalent intermediates with reactants Signup and view all the answers

What promotes the electron movement necessary for acetoacetate decarboxylation?

Development of a Schiff Base intermediate Signup and view all the answers

What role does the serine hydroxyl group play in the reaction mechanism of serine proteases?

Forms a nucleophilic acyl-enzyme intermediate Signup and view all the answers

What is the primary effect of forming covalent intermediates in enzymatic reactions?

Reduces activation energy of transition states Signup and view all the answers

What does a positively charged Schiff Base intermediate indicate in enzymatic reactions?

An alternative reaction pathway is utilized Signup and view all the answers

How does covalent catalysis with cofactors differ from covalent catalysis involving amino acid residues?

Cofactors can delocalize electrons more effectively Signup and view all the answers

What is the role of pyridoxal phosphate in enzymatic reactions?

It forms covalent intermediates with substrates. Signup and view all the answers

What happens to the substrate when it binds to the enzyme?

It undergoes desolvation, making it more reactive. Signup and view all the answers

How does the association between substrate and enzyme affect the entropy?

It decreases the entropy, promoting a low-entropy state that favors the reaction. Signup and view all the answers

What is the consequence of a very tight binding between enzyme and substrate?

It raises the energy of activation for the reaction. Signup and view all the answers

What is the main hypothesis regarding enzyme binding to transition state intermediates?

Strong interactions with transition states can lower the activation energy. Signup and view all the answers

What is a key factor for the energy of activation in catalyzed reactions?

The activation energy is significantly lower in catalyzed reactions. Signup and view all the answers

What effect does electrostatic destabilization have on enzymatic reactions?

It can relieve repulsive forces, accelerating the reaction. Signup and view all the answers

What is an important feature that distinguishes the energy levels of catalyzed versus uncatalyzed reactions?

The uncatalyzed reaction has a much lower energy of the transition state. Signup and view all the answers

What is the role of the catalytic triad in the active site of chymotrypsin?

To facilitate the nucleophilic attack on the substrate Signup and view all the answers

Which amino acids comprise the catalytic triad in chymotrypsin?

His 57, Asp 102, Ser 195 Signup and view all the answers

What characterizes the acylenzyme intermediate formed during the chymotrypsin mechanism?

It is a covalent bond between the substrate and enzyme Signup and view all the answers

What effect does the stabilization of the anionic intermediate have on the reaction rate?

Decreases the activation energy Signup and view all the answers

Which step in the chymotrypsin mechanism involves the formation of the first tetrahedral intermediate?

Step 2 Signup and view all the answers

During the reaction catalyzed by chymotrypsin, what happens to the tetrahedral intermediate?

It quickly breaks down to release the amine product Signup and view all the answers

What is the outcome of the nucleophilic attack by serine in chymotrypsin?

It attacks the nitrogen in the amide bond Signup and view all the answers

What type of intermediate has a negative charge on the oxygen during step 2 of the chymotrypsin mechanism?

Anionic intermediate Signup and view all the answers

What is the primary role of histidine in step 4 of the chymotrypsin mechanism?

Acting as a proton donor Signup and view all the answers

In step 5 of the chymotrypsin mechanism, what promotes the production of the hydroxyl ion?

The active site histidine Signup and view all the answers

What is characteristic of the second tetrahedral intermediate formed in step 6?

It is stabilized by the anionic hole Signup and view all the answers

What occurs to the carbonyl group after the second tetrahedral intermediate is attacked in step 7?

It is converted and the serine bond is broken Signup and view all the answers

What happens to the carboxylate product in step 8 of the chymotrypsin mechanism?

It diffuses away from the active site Signup and view all the answers

What is the function of the oxyanion hole in the chymotrypsin mechanism?

To stabilize the negatively charged oxyanion Signup and view all the answers

Which property is shared among serine proteases that are homologs of chymotrypsin?

They have similar catalytic mechanisms Signup and view all the answers

What triggers the nucleophilic attack of the hydroxyl ion on the acylenzyme intermediate in step 5?

Proton removal from water Signup and view all the answers

What is the primary advantage of proximity and orientation effects in enzyme catalysis?

They minimize the entropy changes of reactants. Signup and view all the answers

Which mechanism is primarily responsible for the reduction of entropy in enzyme reactions?

Proximity and orientation effects Signup and view all the answers

Which of the following mechanisms involves the formation of a temporary covalent bond during the catalytic process?

Nucleophilic and Electrophilic Catalysis Signup and view all the answers

How do enzymes achieve a pseudo intramolecular character in their catalytic mechanism?

By bringing substrates together in the active site Signup and view all the answers

Which of the following catalysis types specifically aids in reducing the energy barrier of a reaction through charge stabilization?

Electrostatic Effects Signup and view all the answers

What is the impact of desolvation in enzymatic catalysis?

It removes water molecules that hinder substrate interaction. Signup and view all the answers

Which mechanism is associated with the ability of an enzyme to provide multiple reaction pathways for substrates?

Structural flexibility Signup and view all the answers

In the context of enzymes, what role does entropic reduction primarily serve?

To enhance the formation of product via correct substrate orientation Signup and view all the answers

What type of bond does chymotrypsin preferentially cleave in proteins?

Peptide bonds on the carboxyl side of specific aromatic amino acids Signup and view all the answers

Which residue in the active site of chymotrypsin is crucial for its catalytic mechanism?

Serine 195 Signup and view all the answers

What happens to the active site serine during catalysis in chymotrypsin?

It briefly becomes covalently bonded to the substrate. Signup and view all the answers

What is the role of DIFP in relation to chymotrypsin?

It reacts with serine 195 to inactivate the enzyme. Signup and view all the answers

What type of reaction mechanism is chymotrypsin primarily involved in?

Hydrolysis of peptide bonds Signup and view all the answers

During the hydrolytic cleavage of peptide bonds by chymotrypsin, what type of product is formed?

Both a carboxyl group and an amino group Signup and view all the answers

What is the initial phase of the enzymatic hydrolysis mechanism involving chymotrypsin called?

Acylation Signup and view all the answers

What feature allows chymotrypsin to cleave peptide bonds specifically near aromatic amino acids?

Hydrophobic pocket Signup and view all the answers

In step 4 of the chymotrypsin mechanism, what role does histidine play?

Proton donor Signup and view all the answers

What is produced from water during step 5 of the chymotrypsin mechanism?

Hydroxyl ion Signup and view all the answers

What characterizes the second tetrahedral intermediate formed in step 6?

It has a negative charge on the oxygen Signup and view all the answers

What stabilizes the anionic intermediate in step 6 of the chymotrypsin mechanism?

Hydrogen bonding to protons Signup and view all the answers

In step 7 of the chymotrypsin mechanism, what is the outcome of the attack on the second tetrahedral intermediate?

Conversion of the anionic oxygen to a carbonyl Signup and view all the answers

What is the role of pyridoxal phosphate in aspartate transaminase?

It acts as a cofactor forming a covalent intermediate. Signup and view all the answers

What occurs to the carboxylate product in step 8 of the chymotrypsin mechanism?

It diffuses away Signup and view all the answers

How does binding to the enzyme affect the entropy of the substrate?

It lowers the entropy by reducing random motion and stretching. Signup and view all the answers

What is the function of the oxyanion hole in chymotrypsin?

To stabilize the negatively charged oxyanion Signup and view all the answers

What occurs to water molecules during the process of desolvation in enzyme reactions?

Tightly bound water is released from the substrate surface. Signup and view all the answers

Which characteristic is common among serine proteases that are homologs of chymotrypsin?

Presence of an oxyanion hole Signup and view all the answers

Why is tight binding between the enzyme and the substrate not necessarily beneficial?

It can stabilize the ES complex in an energy well. Signup and view all the answers

What is the proposed mechanism for the catalysis of enzymes with respect to transition states?

Enzymes preferentially bind the transition state to lower activation energy. Signup and view all the answers

How does electrostatic destabilization contribute to reaction rates in enzymatic reactions?

It alleviates repulsive forces between substrate and enzyme. Signup and view all the answers

What distinguishes the energy of activation for a catalyzed reaction compared to an uncatalyzed reaction?

The catalyzed reaction has a significantly lower energy of activation. Signup and view all the answers

What is the effect of enzyme binding specificity on the activation energy of a reaction?

High specificity reduces the energy of activation by stabilizing the transition state. Signup and view all the answers

What is a significant effect of covalent catalysis on the energy of transition states in enzymatic reactions?

It decreases the energy of later transition states of the reaction. Signup and view all the answers

Which of the following enzymes is a known example of utilizing a covalent acyl-enzyme intermediate in its catalytic mechanism?

Chymotrypsin Signup and view all the answers

How does the presence of an active site serine in serine proteases affect the reaction mechanism?

It substitutes for a free hydroxyl group, increasing reaction rates. Signup and view all the answers

What role does the positively charged covalent intermediate, or Schiff Base, play in the decarboxylation of acetoacetate?

It lowers the energy of activation by providing an alternate pathway. Signup and view all the answers

Which factor distinguishes the action of cofactors like pyridoxal phosphate in covalent catalysis?

They form covalent intermediates that lower reaction transition state energy. Signup and view all the answers

What is a key benefit of providing both hydroxyl ions and hydrogen ions during catalysis?

It enhances the speed of ester hydrolysis reactions. Signup and view all the answers

What is a common misconception about the role of non-protein acid cofactors in enzyme reactions?

They cannot form covalent intermediates like amino acid residues. Signup and view all the answers

In what way does covalent catalysis differ from other catalytic mechanisms?

It allows for substrate activation through transient bonding. Signup and view all the answers

What is the primary role of the pyridoxal phosphate cofactor in aspartate transaminase?

To form a covalent intermediate with the amino acid substrate Signup and view all the answers

How does desolvation contribute to the reactivity of substrates in enzymatic reactions?

By releasing tightly bound water from the substrate surface Signup and view all the answers

What effect does the tight binding of an enzyme to the transition state have on the energy of activation?

It lowers the energy of activation Signup and view all the answers

Which phenomenon explains the acceleration of reaction rates through repulsive charge relief between substrate and enzyme?

Electrostatic destabilization Signup and view all the answers

What is the consequence of forming a tight binding association between enzyme and substrate?

Higher energy of activation compared to uncatalyzed reaction Signup and view all the answers

In enzymatic catalysis, how is the overall energy of activation for a catalyzed reaction compared to an uncatalyzed reaction?

It is significantly lower for the catalyzed reaction Signup and view all the answers

What role does entropy loss play when substrates bind to enzymes?

It creates a low-entropy state that favors the ES complex Signup and view all the answers

Which characteristic of the enzyme-substrate complex is crucial in affecting the activation energy during a reaction?

Covalent intermediates formed Signup and view all the answers

What amino acids does chymotrypsin preferentially cleave peptide bonds next to?

Tyrosine, tryptophan, and phenylalanine Signup and view all the answers

What is the role of the serine 195 residue in the mechanism of chymotrypsin?

To become covalently bonded to the substrate Signup and view all the answers

What type of reaction is involved in the cleavage of peptide bonds by chymotrypsin?

Hydrolytic reaction Signup and view all the answers

What happens to chymotrypsin when it reacts with the reagent DIFP?

It forms an inactive covalent product Signup and view all the answers

Which part of the enzymatic process does deacylation refer to in chymotrypsin's mechanism?

Release of the carboxylic acid component Signup and view all the answers

What is the significance of the hydrophobic pocket in chymotrypsin?

It allows binding of the aromatic side chains of substrates Signup and view all the answers

Which phase comes first in the enzymatic hydrolysis reaction involving chymotrypsin?

Acylation phase Signup and view all the answers

In the mechanism of chymotrypsin, what effect does the nucleophile's attack on the carbonyl group achieve?

It initiates the hydrolysis reaction Signup and view all the answers

What stabilizes the tetrahedral intermediate formed during the chymotrypsin mechanism?

Charged groups in the enzyme's anionic hole Signup and view all the answers

Which amino acids comprise the catalytic triad in the active site of chymotrypsin?

His 57, Asp 102, Ser 195 Signup and view all the answers

What is the nature of the acylenzyme intermediate formed during chymotrypsin catalysis?

It is more stable than the tetrahedral intermediates. Signup and view all the answers

What occurs in step 1 of the chymotrypsin mechanism?

Nucleophilic attack by serine on the amide bond Signup and view all the answers

What is the purpose of the 'anionic hole' in chymotrypsin's active site?

To stabilize negatively charged intermediates Signup and view all the answers

Which step follows the breakdown of the first tetrahedral intermediate in the chymotrypsin mechanism?

Release of the amine product Signup and view all the answers

During the chymotrypsin mechanism, what facilitates the sharing of protons among the catalytic triad amino acids?

Hydrogen bonding networks Signup and view all the answers

What is the impact of the covalent acylenzyme intermediate on the overall reaction process during chymotrypsin catalysis?

It accelerates the overall reaction rate. Signup and view all the answers

What is the maximum factor by which a reaction can be enhanced by correct proximity and orientation of reacting groups?

10^8 Signup and view all the answers

Which property of the histidine imidazole group makes it suitable for acid-base catalysis?

It has a pK that allows it to act as both an acid and a base. Signup and view all the answers

What is one reason for the slow rate of ester hydrolysis at neutral pH?

High energy of activation for forming the anionic transition state. Signup and view all the answers

In what manner does the presence of an acid during ester hydrolysis affect the reaction?

It stabilizes the anionic transition state. Signup and view all the answers

What is the dual role of enzymes in catalysis at neutral pH?

Enzymes can provide both proton donor and acceptor functionalities. Signup and view all the answers

What effect does a basic solution have on the concentration of hydrogen ions during ester hydrolysis?

It decreases the hydrogen ion concentration. Signup and view all the answers

What is a significant challenge in the ester hydrolysis reaction at neutral pH?

Dependency on low concentration of hydroxyl ions. Signup and view all the answers

What role does histidine play in step 5 of the chymotrypsin mechanism?

It acts as a base to remove a proton from water. Signup and view all the answers

How does an enzyme modify the rate of reaction compared to a reaction occurring in pure water?

Enzymes provide a more favorable energy pathway. Signup and view all the answers

What characterizes the oxyanion hole in chymotrypsin's mechanism?

It stabilizes the negatively charged oxyanion. Signup and view all the answers

What is the significance of the second tetrahedral intermediate formed in step 6?

It is stabilized by the anionic hole. Signup and view all the answers

What occurs during step 7 of chymotrypsin's mechanism?

A proton provided by histidine converts the anionic oxygen to a carbonyl. Signup and view all the answers

What is a characteristic feature of the carboxylate product in step 8?

It diffuses away from the active site. Signup and view all the answers

Which of the following statements about serine proteases that are homologs of chymotrypsin is true?

They evolved from common evolutionary precursor proteins. Signup and view all the answers

What is the role of the active site serine in the chymotrypsin mechanism?

It is involved in the formation of the acylenzyme intermediate. Signup and view all the answers

What happens to the tetrahedral intermediate formed in step 6?

It is stabilized by interactions within the enzyme's active site. Signup and view all the answers

What is a significant advantage of reducing the entropy of reactants in an enzyme-catalyzed reaction?

It allows for more favorable ligation or addition reactions. Signup and view all the answers

How do enzymes facilitate the reaction between two carboxylic acid groups in succinate?

By placing them in proximity and correct orientation. Signup and view all the answers

Which of the following correctly describes the term 'pseudo intramolecular character' in enzyme reactions?

The reaction mimics an intramolecular reaction due to proximity effects. Signup and view all the answers

What is one of the main roles of general acid and general base catalysis in enzymatic reactions?

To provide protons or deprotonate substrates. Signup and view all the answers

Which type of catalysis involves enzymes forming a covalent bond with the substrate during the reaction?

Covalent catalysis. Signup and view all the answers

What are entropy loss effects in the context of enzyme catalysis?

They result in a more favorable transition state. Signup and view all the answers

What is the primary mechanism through which enzymes reduce the energy of activation in reactions?

By forming an enzyme-substrate (ES) complex. Signup and view all the answers

What effect does desolvation have on enzymatic reactions?

It helps to position substrates more favorably for reaction. Signup and view all the answers

What is the result of the simultaneous availability of hydroxyl ions and hydrogen ions in catalysis?

It enhances the rate of ester hydrolysis. Signup and view all the answers

In covalent catalysis, what must happen to the covalent bond formed between the enzyme and the substrate?

It must be broken to regenerate the enzyme. Signup and view all the answers

What role does the serine hydroxyl group play in the activity of serine proteases like chymotrypsin?

It substitutes for a free hydroxyl group, facilitating nucleophilic attack. Signup and view all the answers

How does the formation of a Schiff Base intermediate affect the activation energy in reactions catalyzed by enzymes?

It lowers the energy of activation. Signup and view all the answers

What is the function of cofactors like pyridoxal phosphate in enzyme reactions?

They provide electron donation to stabilize covalent intermediates. Signup and view all the answers

What kind of intermediate is formed during the proteolytic action of chymotrypsin?

A covalent acyl-enzyme intermediate. Signup and view all the answers

In what way do some enzymes utilize non-protein cofactors during catalysis?

They form covalent intermediates that lower activation energy. Signup and view all the answers

Which of the following best describes covalent catalysis?

It involves the formation of transient covalent bonds with substrate. Signup and view all the answers

What is the primary function of chymotrypsin in biological processes?

To catalyze the hydrolysis of peptide bonds Signup and view all the answers

Which amino acids does chymotrypsin preferentially cleave?

Tyrosine, tryptophan, and phenylalanine Signup and view all the answers

What key property of serine 195 allows it to participate in chymotrypsin's catalytic mechanism?

It can lose a proton and become anionic Signup and view all the answers

What occurs after the active site serine residue forms a covalent bond with the substrate?

An enzyme-substrate intermediate is formed Signup and view all the answers

What type of reaction mechanism does chymotrypsin utilize for peptide bond cleavage?

Hydrolytic reaction Signup and view all the answers

What impact does the presence of water have during peptide bond cleavage by chymotrypsin?

It acts as a reactant to break the peptide bond Signup and view all the answers

Which step in the chymotrypsin mechanism involves the release of the alcohol or amine?

Acylation phase Signup and view all the answers

What happens to chymotrypsin when it reacts with DIFP?

It forms an inactive covalent product Signup and view all the answers

What is the role of histidine in step 4 of the chymotrypsin mechanism?

It acts as an acid, donating a proton. Signup and view all the answers

During step 5 of the chymotrypsin mechanism, what does the active site histidine promote?

The formation of a hydroxyl ion from water. Signup and view all the answers

What characterizes the second tetrahedral intermediate formed in step 6 of the chymotrypsin mechanism?

It is unstable due to its anionic character. Signup and view all the answers

What ultimately happens to the carboxylate product in step 8 of the chymotrypsin mechanism?

It diffuses away from the active site. Signup and view all the answers

What is the function of the oxyanion hole in chymotrypsin's active site?

It stabilizes the anionic tetrahedral intermediate. Signup and view all the answers

In terms of evolutionary biology, what is noted about serine proteases that are homologs of chymotrypsin?

They evolved from common precursor proteins. Signup and view all the answers

What happens during step 7 of the chymotrypsin mechanism?

The anionic character is neutralized. Signup and view all the answers

What is the effect of the interaction with the active site on the transition state in the chymotrypsin mechanism?

It lowers the energy of activation. Signup and view all the answers

What does the presence of a catalytic triad and an oxyanion hole in subtilisin represent?

Convergent evolution Signup and view all the answers

What is essential for the catalytic activity of carbonic anhydrase?

Zinc ion Signup and view all the answers

Which statement about indinavir is correct?

It is a competitive inhibitor of HIV protease. Signup and view all the answers

At what pH does carbonic anhydrase exhibit its optimum activity?

pH 8 Signup and view all the answers

Which feature of carboxypeptidase II distinguishes it from chymotrypsin?

It evolves independently from chymotrypsin. Signup and view all the answers

What role does carbonic anhydrase play in the removal of carbon dioxide in the human body?

It catalyzes the conversion of carbon dioxide to carbonic acid. Signup and view all the answers

Which of the following statements about the active site of carbonic anhydrase is true?

It includes a zinc ion bound to histidine residues. Signup and view all the answers

How do both subtilisin and carboxypeptidase II differ from chymotrypsin?

They have evolved independently. Signup and view all the answers

Study Notes

Enzyme Mechanisms

Enzymes increase reaction rates by forming an enzyme-substrate complex (ES complex)
The ES complex allows for a lower activation energy pathway leading to a faster reaction rate
Enzymes utilize a number of chemical mechanisms to achieve catalysis

Proximity and Orientation Effects

Enzymes bind substrates in close proximity and with the correct orientation
This reduces the entropy of reactants, making ligation or addition reactions more favorable
By concentrating substrates in the active site, the concentration effect is increased leading to a pseudo intramolecular reaction character

General Acid and Base Catalysis

Enzymes function as both acid and base catalysts, enabling reactions to occur at neutral pH
The enzyme can provide both proton donors (acid) and proton acceptors (base) simultaneously, allowing for faster reaction rates

Covalent Catalysis

Involves the formation of a transient covalent bond between the substrate and an amino acid residue in the active site
The covalent intermediate serves as a substitute for nucleophilic attack by a hydroxyl group and reduces the energy of later transition states
This mechanism is found in proteolytic enzymes like chymotrypsin and trypsin

Electrostatic Effects

Enzymes use electrostatic interactions to stabilize transition states
This can involve charged amino acid side chains or metal ions in the active site
The electrostatic attraction and repulsion effect promotes the reaction

Structural Flexibility

Enzymes can undergo conformational changes to accommodate substrates and facilitate catalysis
The flexible structure allows for optimal binding and interaction with substrates
Induced fit is a common example of structural flexibility

Entropy Loss

Enzymes minimize entropy loss during reactions by bringing substrates closer together

Desolvation

Enzymes remove water molecules from the active site to facilitate substrate binding and catalysis
Solvation shells around substrates hinder reactions, so their removal increases reaction rates

Cofactors

Some enzymes utilize non-protein cofactors like pyridoxal phosphate (PLP) or thiamine pyrophosphate (TPP)
These cofactors form covalent intermediates with reactants, reducing the energy of the transition state
Cofactors allow enzymes to perform reactions that amino acid side residues alone cannot accomplish

Chymotrypsin Mechanism

A serine protease that utilizes a catalytic triad of Ser, His, and Asp amino acids
The catalytic triad facilitates covalent catalysis by forming an acyl-enzyme intermediate
The mechanism involves a series of steps, including nucleophilic attack, covalent bond formation, and release of product
The reaction pathway is facilitated by the oxyanion hole, which stabilizes the tetrahedral intermediate
Chymotrypsin is highly efficient and specific in its action, highlighting the importance of enzyme mechanisms

Carbonic Anhydrase

Plays a role in carbon dioxide removal from the body
Catalyzes the conversion of carbon dioxide to carbonic acid
Contains a zinc ion in the active site, which is essential for catalytic activity
The zinc ion interacts with a water molecule in the active site, contributing to the enzyme's pH optima

How Enzymes Increase Reaction Rates

Enzymes speed up reactions by creating an alternate reaction pathway with a lower activation energy
Enzymes use multiple chemical mechanisms to catalyze reactions
Typical answers such as "enzymes form an ES complex" only partially correct
Not the full explanation of enzyme mechanisms
Need to understand the specific mechanisms used by enzymes

Enzyme Reaction Mechanisms

Proximity and Orientation effects
General Acid and Base Catalysis
Electrostatic effects
Nucleophilic and Electrophilic Catalysis
Structural Flexibility
Entropy Loss
Desolvation
Covalent Catalysis

Catalysis by Proximity and Orientation

Enzymes bind substrates close together in the correct orientation
Reduces entropy, making ligation or addition reactions more favorable
Simulates the effect of increased substrate concentrations
Gives reactions a pseudo intramolecular character

General Acid-Base Catalysis

Enzymes provide both hydroxyl ions and hydrogen ions at the exact place needed
Increases the rate of ester hydrolysis

Covalent Catalysis

Substrate forms a transient covalent bond with an amino acid R-group
Formation of a covalent intermediate reduces the energy of later transition states
Must be broken to regenerate the enzyme
Found in proteolytic enzymes like chymotrypsin and trypsin

Covalent Catalysis with Cofactors

Enzymes utilize non-protein acid cofactors like PLP or TPP
Form covalent intermediates with reactants to reduce transition state energy
Cofactors allow enzymes to carry out reactions that amino acid side residues alone cannot
Examples: PLP-dependent enzyme aspartate transaminase and TPP-dependent enzyme pyruvate dehydrogenase

Entropy Loss

Binding to the enzyme reduces random tumbling and stretching of the substrate
Low-entropy state favors reaction of the ES complex

Desolvation

Substrates often have water tightly bound to their surface
Binding to the enzyme can release this water, making the substrate more reactive

Electrostatic Effects

Repulsive charges between substrate and enzyme can be relieved during reaction
Can accelerate the reaction rate forward

Enzyme Complementary to Transition State

Enzyme binds most tightly to the transition state intermediates, lowering activation energy and speeding up the reaction rate

Chymotrypsin Catalytic Triad

Active site contains His 57, Asp 102, and Ser 195
Hydrogen ions pass back and forth between these amino acids
Stabilizes the serine hydroxyl group in the anionic state
These active site amino acids are spatially separated in the primary sequence of the enzyme

The Reaction Mechanism of Chymotrypsin

Hydrolysis of an amide substrate involves the catalytic triad
Formation of a covalent acylenzyme intermediate
Transient existence of various tetrahedral transition state intermediates
Step 1: Nucleophilic attack by active site serine on the carbonyl group of the amide substrate
Step 2: Formation of the first tetrahedral intermediate
Step 3: Tetrahedral intermediate breaks down, cleaving the amine product from the substrate
Step 4: Amine product picks up a proton from the active site histidine and diffuses away
Step 5: Nucleophilic attack of a hydroxyl ion on the acylenzyme intermediate
Step 6: Formation of a second tetrahedral intermediate
Step 7: Second intermediate is attacked by a proton from the active site histidine residue
Step 8: Carboxylate product diffuses away, and the enzyme reverts to its original state

The Oxyanion Hole

Location in the active site where a negatively charged oxyanion forms on the substrate
This oxyanion is highly unstable and has a very high energy level
Hydrogen bonding to two protons from peptide amino groups stabilizes the intermediate, lowering transition state energy

Occurrence of Other Serine Proteases

Many serine proteases are homologs of chymotrypsin, including enzymes in the blood clotting cascade
Evolved from common precursor proteins
Share similarities in amino acid sequence
Have the same catalytic triad and oxyanion hole
There are also serine proteases that are not homologs of chymotrypsin

Enzyme Mechanisms

Enzymes increase the rate of reactions by providing an alternative pathway with lower activation energy.
There are many chemical mechanisms by which enzymes mediate catalysis.

Catalysis by Proximity and Orientation

Enzymes bind substrates closely together and in the correct orientation to facilitate reactions.
This reduces entropy and simulates the effect of increased substrate concentration.

General Acid and Base Catalysis

Enzymes can provide acidic and basic functional groups at the active site to increase reaction rate.

Electrostatic Effects

Enzymes can use electrostatic forces to attract and orient substrates, promoting reactions.

Nucleophilic and Electrophilic Catalysis

Enzymes can use nucleophilic or electrophilic amino acid residues or cofactors to stabilize transition states.

Structural Flexibility

Enzymes have a flexible structure that allows them to adapt to the changing shapes of substrates and intermediates.

Entropy Loss

Binding of substrates to enzymes reduces random motion, contributing to faster reaction rates.

Desolvation

Water molecules bound to substrates can be released upon binding to enzymes, increasing their reactivity.

Covalent Catalysis

Enzymes can form transient covalent bonds with substrates, leading to stabilized transition states.
Examples include serine proteases like chymotrypsin and enzymes utilizing cofactors like PLP and TPP.
This catalytic mechanism is often seen in the hydrolysis of peptide bonds, where serine residues form an acyl-enzyme intermediate.

The Oxyanion Hole

A specific pocket within the enzyme's active site stabilizes anionic intermediates, further reducing their energy level.

Chymotrypsin

A serine protease that cleaves peptide bonds on the carboxyl side of aromatic residues (tyrosine, tryptophan, or phenylalanine).
The active site contains a highly reactive serine residue (Ser195).
Inhibits the enzyme through reaction with DIFP (diisopropyl fluorophosphate).
Uses a two-step mechanism including acylation and deacylation phases.
The active site histidine residue plays a crucial role as both an acid and a base in the catalytic mechanism.
Its catalytic mechanism involves the formation and stabilization of tetrahedral intermediates.

Serine Proteases

Many other serine proteases exist, including those involved in blood clotting.
These enzymes are evolutionarily related, sharing a similar catalytic triad and oxyanion hole structure.
There are also serine proteases that are not homologous to chymotrypsin.

Rate Enhancements Due to Proximity and Orientation

Bringing reacting groups close together and aligning them correctly can enhance the rate of a chemical reaction.
Constrained substrates in the formation of carboxylic anhydrides can lead to a 108-fold rate enhancement.

General Acid Base Catalysis

Enzymes can act as both proton donors (acids) and acceptors (bases) to accelerate reactions.
They achieve this by substituting functional groups for hydrogen ions and hydroxyl groups, allowing catalysis at physiological pH.
The histidine imidazole group is crucial for acid-base catalysis due to its pKa, which allows it to act as both an acid or base.

Ester Hydrolysis and Acid-Base Catalysis

Ester hydrolysis at neutral pH is slow due to low hydroxyl ion availability, a high-energy anionic transition state, and the use of water as a proton source.
A base (B-) can facilitate hydrolysis by producing hydroxyl ions faster. However, this can also slow down reactions requiring acid catalysis due to reduced proton concentration.
An acid (HA) can help stabilize the anionic transition state and provide a proton for hydrolysis. But increased proton concentration can hinder reactions requiring base catalysis.
Enzymes are remarkable for providing both high acid and base equivalents at neutral pH, optimizing catalysis.

Covalent Catalysis with Pyridoxal Phosphate

Pyridoxal phosphate (PLP)-dependent enzymes like aspartate transaminase use covalent intermediates to facilitate transamination reactions.
These intermediates form between the amino acid substrate and the PLP cofactor, providing an alternative, less energetic transition state compared to the uncatalyzed reaction.

Other Factors in Enzyme Catalysis

Entropy Loss: Binding to the enzyme reduces the random motion (entropy) of the substrate, favoring the formation of the enzyme-substrate complex (ES complex).
Desolvation: Water molecules tightly bound to the substrate can be released upon enzyme binding, making the substrate more reactive.
Electrostatic Destabilization: Repulsive forces between the substrate and enzyme can be relieved during the reaction, further accelerating the process.
Enzyme Complementary to Transition State: It's not the tightest binding between enzyme and substrate that contributes most to catalysis, but rather the tight binding between the enzyme and the transition state intermediate. This lowers the activation energy.
Enzyme Complementary to Substrate: Enzymes generally bind their substrates tightly, but this alone wouldn't necessarily lower the activation energy.

Chymotrypsin's Mechanism of Catalysis

Chymotrypsin, a digestive enzyme, cleaves peptide bonds, particularly those near aromatic residues like tyrosine, tryptophan, and phenylalanine.
It utilizes a serine hydroxyl group (Ser 195) as a nucleophile to attack the peptide carbonyl group, forming an enzyme-substrate intermediate.
Catalytic Triad: Chymotrypsin's active site houses a catalytic triad consisting of His 57, Asp 102, and Ser 195. These residues facilitate proton transfer, stabilizing the anionic form of the active site serine.
The active site serine is susceptible to reaction with DIFP, an inhibitor that inactivates the enzyme.
Overall Mechanism: Chymotrypsin's catalytic mechanism involves:
- Nucleophilic attack by Ser 195 on the peptide carbonyl group.
- Formation of a tetrahedral intermediate stabilized by the "anionic hole" of the active site.
- Amine product release, followed by formation of an acylenzyme intermediate.
- Hydroxyl ion attack on the acylenzyme intermediate, again forming a tetrahedral intermediate stabilized by the anionic hole.
- Protonation of the tetrahedral intermediate, breaking the acylenzyme bond and releasing the carboxylate product.
Oxyanion Hole: This region of the active site stabilizes the negatively charged oxyanion intermediate through hydrogen bonding. This stabilization contributes to the lowered activation energy of the reaction.

Occurrence of Other Serine Proteases

Chymotrypsin belongs to a family of serine proteases, including those involved in blood clotting.
These enzymes share similarities in amino acid sequences and catalytic mechanisms, often possessing the same catalytic triad and oxyanion hole.
Some serine proteases exist that are not homologous to chymotrypsin.

Enzyme Mechanisms

Enzymes increase reaction rates by providing an alternate reaction pathway with a lower activation energy.
There are multiple chemical mechanisms enzymes use to catalyze reactions.

Proximity & Orientation Effects

Enzymes bind substrates in close proximity and the correct orientation.
This reduces the entropy of reactants, promoting reactions and reducing overall entropy loss.
Enzyme active sites concentrate substrates, simulating increased substrate concentrations and giving reactions an intramolecular character.

General Acid & General Base Catalysis

Enzymes can provide both hydroxyl ions and hydrogen ions in the active site for catalysis.
This allows for simultaneous availability of both components, enhancing the rate of reactions like ester hydrolysis.

Electrostatic Effects

Enzymes contain charged groups that can interact with charged groups on substrate molecules, affecting the stability of reaction intermediates.
This interaction can reduce the energy of transition states.

Nucleophilic & Electrophilic Catalysis

Enzymes often use nucleophilic and electrophilic groups in their active sites to facilitate catalysis.
These groups can attack the substrate, forming covalent intermediates and reducing the energy of transition states.

Structural Flexibility

Significant structural changes in enzymes can occur during catalysis.
These changes can be crucial for bringing reactive groups within the enzyme and substrate close together.
The enzyme's ability to change conformation can directly affect reaction rates.

Entropy Loss

Enzymes can reduce the loss of entropy during the formation of a transition state by binding the reactants tightly.

Desolvation

Enzymes can bind substrates in the active site, leading to desolvation of the substrate.
This can promote reactions by removing water molecules that might interfere.

Covalent Catalysis

Enzymes can form covalent intermediates with the substrate using amino acid R-groups.
This covalent bond formation can reduce energy barriers in the reaction pathway.
Covalent catalysis is common in proteolytic enzymes like chymotrypsin, forming acyl-enzyme intermediates.

Serine Proteases

Many serine proteases utilise covalent catalysis.
These enzymes have an active site serine residue that forms a covalent intermediate with the substrate.
The serine residue is positioned optimally for nucleophilic attack.

Chymotrypsin

Chymotrypsin is a digestive enzyme that cleaves peptide bonds.
It preferentially cleaves peptide bonds near tyrosine, tryptophan, or phenylalanine residues.
The active site serine residue in chymotrypsin forms a transient covalent intermediate with the substrate.

Chymotrypsin Mechanism

Chymotrypsin has an “oxyanion hole” that binds and stabilizes intermediates, lowering the energy of the transition state.
The catalytic triad of Asp, His, and Ser is essential for chymotrypsin’s mechanism.

Carbonic Anhydrase

This enzyme catalyzes the conversion of carbon dioxide to carbonic acid.
It contains a zinc ion and utilizes electrostatic and general acid-base catalysis.
The zinc ion in the active site binds to water molecules and facilitates proton transfer.
Carbonic anhydrase has a pH optimum around 8, reflecting the influence of the zinc ion on water molecule interactions.

Indinavir

This inhibitor is used in the treatment of AIDS.
It inhibits the HIV protease by resembling the peptide substrate for the enzyme.

Convergent Evolution

Similar catalytic mechanisms can evolve independently in different enzymes.
Example: Subtilisin and carboxypeptidase II have the same catalytic triad and oxyanion hole as chymotrypsin, even though they are not homologous.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

This quiz covers essential concepts related to enzyme mechanisms, including the formation of enzyme-substrate complexes, proximity and orientation effects, and various catalytic strategies such as acid-base and covalent catalysis. Test your understanding of how enzymes enhance reaction rates and their role in biochemical processes.