Enzymes Chapter 14: Catalysis Mechanisms

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Questions and Answers

Which role does an active-site histidine primarily play during enzymatic reactions?

Accepts a proton from the substrate (correct)

Stabilizes charged groups

Improves electrostatic interactions

Donates a proton to the substrate

Which of the following amino acids are primarily involved in creating catalytic agents in enzyme active sites?

Thr, Ala, Phe

Ser, Lys, Gln

Asp, Tyr, Pro

His, Glu, Cys (correct)

In what way do metal ions contribute to catalysis in enzyme active sites?

They enhance proton transfer rates

They stabilize transient structures (correct)

They promote hydrogen tunneling

They form covalent bonds with substrates

What effect does shifting pKa values of residues in active sites have on enzymatic reactions?

It creates catalytic agents Signup and view all the answers

Which characteristic of Low-Barrier Hydrogen Bonds (LBHBs) differentiates them from typical hydrogen bonds?

They exhibit shorter O-O separation distances Signup and view all the answers

What characterizes catalysis by proximity in enzyme action?

Enzymes bring substrates close enough to promote higher collision frequency. Signup and view all the answers

What is a typical characteristic of near-attack complexes (NACs)?

Reacting atoms must be within 3.2 Å and at a specific approach angle. Signup and view all the answers

How does covalent catalysis facilitate reactions?

Through a temporary covalent bond formed with the substrate. Signup and view all the answers

What is a common feature of double displacement reactions in enzymatic activity?

The enzyme product is released before the next substrate binds. Signup and view all the answers

Which statement describes general acid-base catalysis?

It involves the transfer of protons during the transition state. Signup and view all the answers

What role does protein motion play in enzyme catalysis?

It helps in the proper alignment of catalytic groups and substrates. Signup and view all the answers

What does the presence of a catalyst typically do to the reaction rate?

It increases the reaction rate by enhancing substrate interaction. Signup and view all the answers

What type of catalysis involves the participation of metal ions?

Metal ion catalysis Signup and view all the answers

Study Notes

Mechanisms of Enzyme Action

Overview of enzymatic catalysis mechanisms presented in Chapter 14.

Mechanisms of Catalysis

Catalysis by proximity (near-attack complexes): Enzymes position substrates close together and in the correct orientation, increasing the frequency of collisions and reaction rates.
Covalent catalysis: Active site residues form temporary covalent bonds with substrates. The reaction proceeds and the bond breaks regenerating the enzyme. It often involves nucleophilic attacks by amino acid side chains on electrophilic groups present in substrates.
General acid-base catalysis: Proton transfer during the reaction catalyzed by enzymes.
Metal ion catalysis: Metal ions (e.g., zinc, magnesium, iron) stabilize transient intermediates, facilitate the formation of strong nucleophiles, position substrates, and stabilize charges within the active site.

Catalysis by Proximity

Enzymes significantly increase reaction rates by bringing substrates into an optimal proximity and orientation within the active site.
In the absence of an enzyme, reactions occur at a rate of 0.0001%, while in the presence of the enzyme, the reaction rate is 1 to 70%.
Active sites of enzymes are pre-organized to create near-attack complexes. Reacting atoms are in Van der Waals contact and oriented like the bond in the transition state.

Near-Attack Complexes (NACs)

NACs are characterized by reacting atoms within a 3.2 Å distance and an approach angle (±15°) of the transition state's bonding angle.

Protein Motions

Protein motions are crucial for enzyme catalysis. Bonds vibrate, side chains rotate and bend, and backbone loops wiggle. Whole domains also move.
Changes in active site conformation assist substrate binding, bring catalytic groups into position, induce the formation of NACs, and help facilitate bond making and breaking, ultimately converting substrates to products.

Covalent Catalysis Details

Active site residues in some enzymes form unstable temporary covalent bonds with substrates.
This covalent bond forms during the reaction and then breaks to return the enzyme to its original state.
Nucleophilic attacks by amino acid side chains on electrophilic sites in substrates are common characteristics.
Prosthetic groups may also be involved in covalent catalysis.
This mechanism facilitates electron transfer.
Many covalent catalysis mechanisms have unknown steps.

Double Displacement

Two substrates bind and react sequentially.
An enzyme-substrate covalent intermediate (E') forms.
The product of the first reaction is released.
The enzyme then reacts with the second substrate.

Enzyme-Substrate Intermediates

Examples of enzyme-substrate intermediates like phosphoryl, acyl, and glucosyl enzymes are presented.

General Acid-Base Catalysis Details

General acid-base catalysis involves proton transfer involving groups in the active site.
These groups can activate nucleophiles, stabilize charged groups, and improve electrostatic interactions.
Glu, Asp, and His are examples of amino acids that contribute to this catalysis.
Water can act as catalytic acid or base through proton transfer.

Histidine's Role

An active site histidine that can be protonated or deprotonated as needed can play a crucial role in transferring protons from or to substrates and other active site components

Water's Role in Catalysis

Water molecules can act as catalytic acids or bases through proton transfer involving active site residues.

Shifts in pKa

Shifts in pKa values can create catalytic residues in enzyme active sites. The shifts are caused by the interactions between amino acid groups and the chemical environment of the active site.
Specific values of pKa's for different enzymes and active site amino acid residues are included in a table.

Secondary Roles

Other amino acids in the enzyme active site besides those directly involved in catalysis can play a secondary role in catalytic activity (e.g., regulating pK values, charge stabilization, positioning catalytic residues, proton transfer).

Metal Ion Catalysis Details

Metal ions like zinc, magnesium, or iron can actively participate in the catalytic process.
Metal cations' positive charges help stabilize temporary intermediates, enhance the formation of nucleophiles, and position substrates inside the active site.
The metal ions can also help stabilize charges within the enzyme active site.

Low-Barrier Hydrogen Bonds (LBHBs)

LBHBs are hydrogen bonds with exceptionally short distances and strong covalent-like interaction strength.
Lowering the distance between the interacting heteroatoms strengthens hydrogen bond interactions approaching a covalent bond.
The pKa's of the two atoms involved in the hydrogen bond must be similar for stabilization.
The energy released by formation of LBHBs might help promote catalysis.

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Description

Explore the various mechanisms of enzyme action as discussed in Chapter 14. This quiz covers key concepts like proximity effects, covalent catalysis, acid-base catalysis, and metal ion involvement in enzymatic reactions. Test your understanding of how enzymes enhance reaction rates through these mechanisms.