Ch 6: Enzyme Catalytic Strategies

What is binding energy?

The free energy released in the formation of the weak interactions between enzyme and substrate, some of which can facilitate the formation of the transition state for catalysis.

What are the 5 strategies enzymes employ to catalyze specific reactions?

1. Binding energy

2. covalent catalysis

3. general acid-base catalysis

4. catalysis by approximation

5. metal ion catalysis

What occurs in covalent catalysis?

The active site contains a reactive group that becomes temporarily covalently modified while attatched to a part of the substrate.

What occurs in general acid-base catalysis?

A molecule other than water plays the role of a proton donor or acceptor.

What occurs in catalysis by approximation?

A process where the reaction rate is considerably enhanced by bringing the two substrates together along a single binding surface on an enzym

What are the three ways metal ion catalysis proceeds?

1. A metal acts as an electrophilic catalyst by stabilizing a negative charge on a reaction intermediate

2. A metal generates a nucleophile by increasing the acidity of nearby molecules

3. A metal increases the binding energy of the enzyme–substrate interaction by binding to substrates.

Why is it important that peptide bonds be broken?

Proteins that have served their purpose must be degraded so that their constituent amino acids can be recycled for the synthesis of new proteins

How do proteases cleave proteins?

by hydrolysis reaction

What is a hydrolysis reaction?

the addition of a molecule of water to a peptide bond

Why is the hydrolysis of peptide bonds a difficult reaction? Why is this a good thing?

Even processthermodynamically favorable, such reactions are extremely slow and resonance makes them resistant; this makes them very stable

What must a protease do stimulate a hydrolysis reaction?

Facilitate a nucleophilic attack at a normally unreactive carbonyl group

What is a scissile bond?

The bond in a molecule that is cleaved by an enzymatic reaction.

What are carbonic anhydrases?

An enzyme that hydrates carbon dioxide to form bicarbonate HCO₃^- and a proton

What do carbonic anhydrases contain that are essential for catalytic activity?

a bound zinc ion

What are some properties that metal ions have that increase chemical reactivity?

1. positive charges

2. ability to form strong yet kinetically labile bonds

3. in some cases, their capacity to be stable in more than one oxidation state.

How does this zinc complex facilitate carbon dioxide hydration?

1. The zinc ion facilitates the release of a proton from a water molecule, which generates a hydroxide ion.

2. The carbon dioxide substrate binds to the enzyme’s active site and is positioned to react with the hydroxide ion.

3. The hydroxide ion attacks the carbon dioxide, converting it into bicarbonate ion, HCO₃^-.

4. The catalytic site is regenerated with the release of HCO₃^- and the binding of another molecule of water.

What increases the rate of carbon dioxide hydrases by carbonic anhydrase?

higher concentration of a buffer