Catalytic Strategies 1

What is the primary function of enzymes in biological reactions?

Enzymes are biological catalysts that dramatically increase the rate of reactions under biological conditions.

What are the key features of enzymes?

Higher reaction rates, milder reaction conditions, greater reaction specificity, and capacity for regulation.

What type of catalysis involves the formation of a transient covalent bond with the substrate?

Covalent Catalysis.

Which nucleophilic group is used by chymotrypsin for covalent catalysis?

Serine-195.

What is acid-base catalysis?

A molecular interaction where a molecule other than water donates or accepts a proton to facilitate the reaction.

Name an example of an enzyme that uses acid-base catalysis.

Histidine in chymotrypsin.

What is the role of metal ions in enzyme catalysis?

Metal ions can act as electrophilic catalysts, stabilize negative charges, and generate nucleophilic OH⁻.

What is binding energy in enzyme-substrate interactions?

The free energy released when a substrate binds to the enzyme via multiple weak, specific interactions.

List some functions of binding energy in enzymes.

Substrate specificity, catalytic efficiency, stabilizes the transition state, and induces conformational changes.

How do enzymes lower activation energy?

Enzymes lower the activation energy barrier, increasing the rate of reaction without changing the overall ΔG.

What are proteases?

Proteases cleave peptide bonds through hydrolysis.

What is the function of chymotrypsin?

Chymotrypsin is a serine protease that cleaves peptide bonds after large hydrophobic residues.

Which residues comprise the catalytic triad of chymotrypsin?

Ser195, His57, Asp102.

What happens during the acylation step of chymotrypsin catalysis?

Ser195 attacks the peptide bond, forming an acyl-enzyme intermediate.

What substrate is used to study chymotrypsin activity?

N-Acetyl-L-phenylalanine-p-nitrophenyl ester.

What does the S1 pocket in chymotrypsin do?

It binds the P1 residue of the substrate and aligns the scissile bond for cleavage.

What does a hydrogen-bond network in the catalytic triad help with?

It is critical for catalysis.

What does the term convergent evolution indicate in the context of catalytic triads?

Catalytic triads found in many hydrolytic enzymes evolved independently in different enzymes.

What is unique about cysteine proteases?

They use histidine-activated cysteine as a nucleophile.

What distinguishes aspartyl proteases from other types?

They use an aspartate-activated water molecule.

What is Indinavir used for?

It is a substrate analog inhibitor that binds to the active site of HIV protease to block viral maturation.

What is the importance of protease inhibitors in HIV treatment?

They reduce viral load and improve immune function in HIV-infected individuals.

What is the double role of zinc in metalloproteases?

Zinc can act as an electrophile and stabilize negative charges.

Describe the activity of chymotrypsin in terms of kinetics.

Chymotrypsin shows fast acylation followed by slower deacylation phases.

What type of spectroscopy is used to detect chymotrypsin activity?

Stopped-flow spectroscopy.

What is a defining feature of the specificity pocket in serine proteases?

It is deep and hydrophobic, facilitating the binding of large hydrophobic side chains.

What is the relationship between enzyme-substrate residue matching and specificity?

Specificity is determined by matching residues between the enzyme and substrate.

How does site-directed mutagenesis help understand enzyme function?

It shows the importance of specific residues by mutating them to alanine and observing a loss of activity.

What can be inferred from minimal change in K_M following mutagenesis?

It suggests transition state stabilization still contributes to catalysis.

What enzymatic strategy do metalloproteases employ?

They use a metal-activated water molecule, often with a base to deprotonate water.

What do proteases generally do during hydrolysis?

They cleave peptide bonds, which is generally exergonic but kinetically slow.

What is the role of induced fit in enzyme function?

It stabilizes the transition state and enhances catalytic efficiency.