BAH PP 5

What is the general sequential pathway of an enzyme-catalyzed reaction?

E + S <—-> ES —> EP <——> E + P

What are the three primary states or molecules that an enzyme ($E$) can bind during a reaction cycle?

The substrate, the product, and the transition state.

What is the core mechanism behind enzyme catalysis regarding binding affinity?

The enzyme must bind the TS more tightly than it binds the substrate, which is known as TS stabilization

How does an enzyme affect the activation energy and the overall free energies of the substrate and product?

The catalyzed pathway lowers the activation free energy, but the overall free energies of the substrate and product remain unchanged.

How do proximity and orientation enhance reaction rates in an enzyme's active site?

They bring reactants together and lock them into a precise geometric alignment, increasing the effective local concentration and the likelihood of productive collisions.

What is the role of amino acid side chains in general acid-base catalysis?

They donate or accept protons ($H^+$) to facilitate bond cleavage or formation.

What defines covalent catalysis during an enzymatic reaction?

They polarize water molecules to generate reactive nucleophiles or help shield and stabilize accumulating negative charges.

Why is electrostatic catalysis critical for the transition state?

It uses charged active-site residues and dipoles to stabilize unstable, high-energy charges that develop during the transition state.

How does the microenvironment of an active site alter catalysis?

It provides a specialized, restricted zone that can exclude water and shift amino acid $pK_a$ values to increase reactivity.

Which enzyme class is responsible for catalyzing oxidation-reduction reactions involving the transfer of electrons or hydrogen atoms?

Oxidoreductases (Class 1).

What is the primary function of Transferases?

They catalyze the transfer of specific functional groups, such as methyl or phosphoryl groups, from one molecule to another.

How do Hydrolases cleave chemical bonds?

Through hydrolysis reactions by the addition of water.

What specific structural change do Lyases catalyze?

Group elimination reactions to form double bonds, or conversely, adding groups across double bonds.

What type of reaction is facilitated by Isomerases?

Structural or geometric rearrangements within a single molecule (isomerization).

Which enzyme class requires coupling with the breakdown (hydrolysis) of ATP to join two molecules together?

Ligases

Why do most random collisions between reactants fail when they are just floating freely in solution?

Because the reactants rely on random diffusion and are frequently poorly oriented, meaning their reactive atoms do not face each other correctly upon collision.

What happens to reactants once they enter an enzyme's active site regarding their positioning?

They are concentrated and rigidly positioned into a precise, productive geometry.

How do proximity and orientation effects relate to entropy during enzymatic catalysis?

he enzyme reduces the entropic cost (the penalty of losing translational and rotational freedom) of bringing reactive groups together and suppresses unproductive orientations.

What is the primary role of active-site residues during general acid-base catalysis?

They donate or accept protons ($H^+$) during bond making and breaking.

Why is histidine considered especially useful for general acid-base catalysis?

Its $pK_a$ lies close to physiological pH, enabling it to function effectively as both a proton donor and acceptor in biological conditions.

How does the active site influence the $pK_a$ of a catalytic residue?

The active site can shift residue $pK_a$ values relative to what they would be in free solution.

Why isn't a side chain's $pK_a$ fixed when it leaves bulk water and enters an enzyme's active site?

Because the active site's microenvironment—featuring nearby charges, hydrogen bonds, and controlled solvent exposure—exerts forces that shift the $pK_a$.

What is the defining feature of covalent catalysis during an enzyme-catalyzed reaction?

A nucleophilic group on the enzyme attacks the substrate to form a transient, covalent chemical intermediate ($E-S$).

Which amino acid side chains are most commonly used as catalytic nucleophiles?

Serine, Cysteine, and Lysine.

How does covalent catalysis alter the energy landscape of a reaction?

It creates a new reaction pathway with lower-energy transition states compared to the uncatalyzed reaction.

Why must the covalent intermediate ($E-S$) be broken down near the end of the reaction cycle?

To release the product and regenerate the original enzyme so it can participate in future catalytic cycles.

What are the three primary functions of metal ions in enzymatic catalysis?

Orienting the substrate by coordinating reactive groups, stabilizing negative charges via Lewis-acid interactions, and activating water to lower its $pK_a$ so that it becomes OH and can become aggressive nucleophile.

How do metal ions behave chemically when stabilizing charges?

They act as Lewis acids, interacting directly with negative charges that develop on the substrate or transition state.

What is the direct consequence of a metal ion lowering the $pK_a$ of a bound water molecule?

It facilitates the generation of a stronger nucleophile (such as a hydroxide ion) to drive the reaction.

In the context of electrostatic catalysis, how does the active-site environment treat the ground state versus the transition state of a substrate?

It accommodates the relatively stable charge distribution of the ground state while preferentially stabilizing any new or redistributed charges that emerge in the transition state.

What mechanism allows an enzyme to achieve electrostatic stabilization without forming a covalent intermediate?

It deploys preorganized active-site electric fields capable of strongly stabilizing transition-state charges directly.

How does bulk water interact with charged groups and hydrogen bonds prior to binding?

Water competes for hydrogen bonds and actively stabilizes charged groups in solution.

What happens to active-site water molecules when a substrate binds?

Selected water molecules are removed, while strategically placed catalytic waters are retained.

What is the physical consequence of a lower dielectric environment within the active site?

It strengthens electrostatic interactions between charges.

How does restricting solvent access impact the chemical properties of active-site groups?

It can change their nucleophilicity, acidity, and basicity.

Why must an enzyme's active site form highly productive interactions during desolvation?

Because desolvation carries an energetic cost, and productive interactions must compensate for it.

What characterizes the substrate ground state in terms of its structural conformation and energy level?

It exhibits the substrate's preferred geometry and its lowest free energy state.

How does the active site alter the state of the system once the bound reactive state is reached?

It biases the substrate and/or the enzyme toward a specific, productive geometry.

Why must conformational strain and distortion take a backseat to transition-state stabilization as the core principle of catalysis?

Structural changes, shaping, and organization are never the end goal in themselves. They are entirely subservient to lowering the energy of the transition state to make the reaction happen.