Enzymes pt.1

What is an enzyme?

A biological catalyst (usually a globular protein) that increases reaction rates without being consumed. Some RNA molecules (ribozymes) also act as enzymes.

What is a substrate?

The molecule that binds to the active site of an enzyme and is acted upon during the reaction.

What is a cofactor?

An additional chemical component (often a metal ion or small molecule) required for an enzyme to function properly.

What is a coenzyme?

A small organic molecule that acts as a cofactor by assisting an enzyme in catalysis.

What is a prosthetic group?

A coenzyme or cofactor that is tightly (including covalently) bound to the enzyme protein.

What are the 4 advantages of biocatalysis over inorganic catalysts?

1. Greater reaction specificity (fewer side products)

2. Milder reaction conditions

3. Higher reaction rates

4. Capacity for regulation of biological pathways

What are the 6 classes of enzymes?

1. Oxidoreductases – electron transfer

2. Transferases – group transfer

3. Hydrolases – hydrolysis reactions

4. Lyases – bond cleavage/addition to double bonds

5. Isomerases – isomer formation

6. Ligases – bond formation coupled to ATP cleavage

What is an ES complex?

The enzyme-substrate complex formed when a substrate binds to the active site of an enzyme (E + S ⇌ ES).

Do enzymes affect the equilibrium (ΔG) of a reaction?

No. Enzymes do not change the thermodynamic equilibrium (ΔG) of a reaction — they only increase the rate by lowering the activation energy (ΔG‡).

How do enzymes increase reaction rates?

By lowering the activation energy (ΔG‡) of the reaction, described by: k = (k_B·T/h)·e^(–ΔG‡/RT). A smaller ΔG‡ gives a larger rate constant k.

What is the transition state (‡)?

The highest-energy, unstable intermediate state that reactants must pass through to become products. It sits at the peak of the reaction coordinate diagram.

What is ΔG‡?

The activation energy — the free energy difference between the ground state of the substrate and the transition state. Enzymes work by lowering this barrier.

What is the rate-limiting step?

The slowest step in a multi-step reaction mechanism. It determines the overall reaction rate. The rate law is written in terms of reactants in this step.

What is a reaction intermediate?

A species formed in one step of a mechanism and consumed in a subsequent step. It is not the transition state — it sits in an energy valley, not at a peak.

What is Linus Pauling's principle of transition state stabilization?

Enzyme active sites are complementary in shape and charge to the transition state of the reaction, not just the substrate. Binding the transition state more tightly than the substrate lowers ΔG‡.

What is binding energy (ΔG_B)?

The free energy released when a substrate (or transition state) binds to an enzyme. It contributes to lowering the activation energy.

How does entropy reduction help enzyme catalysis?

The enzyme uses binding energy to organize substrates into a rigid ES complex, paying the entropy cost at binding. This makes the subsequent ES → transition state conversion entropically favorable.

What is desolvation and why does it help catalysis?

When a substrate enters the active site, hydrogen bonds with solvent water are broken. Removing these competing interactions lowers the energy barrier to the reaction.

What are the 4 main catalytic mechanisms used by enzymes?

1. Acid-base catalysis – proton donation/acceptance

2. Covalent catalysis – transient covalent bond with substrate

3. Metal ion catalysis – redox, charge stabilization, pKa shifting

4. Electrostatic catalysis – preferential stabilization of transition state

How does general acid-base catalysis work?

Amino acid residues in the active site donate or accept protons to stabilize charged intermediates that would otherwise break down rapidly. This is useful when proton transfer to/from water is too slow.

Which amino acids can act as general acid-base catalysts?

Glu, Asp (carboxylate); Lys, Arg (amine); Cys (thiol); His (imidazole); Ser (hydroxyl); Tyr (phenol)

How does covalent catalysis work?

A nucleophile on the enzyme (e.g. Ser, Cys, Lys) forms a transient covalent bond with the substrate, creating a new reaction pathway with lower activation energy. The enzyme is regenerated at the end.

How does metal ion catalysis work?

A bound metal ion (e.g. Zn²⁺, Mg²⁺) facilitates catalysis by stabilizing negative charges on the transition state, participating in redox reactions, or shifting pKa values of active site residues.

What are biochemical standard conditions?

T = 298 K, P = 1 atm, [solutes] = 1 M, and pH = 7.0. The standard free energy change under these conditions is written ΔG'°.

What is the enzyme with the greatest rate enhancement?

Orotidine monophosphate decarboxylase, with a rate enhancement of ~10^17 fold over the uncatalyzed reaction.

In the reaction E + S ⇌ ES ⇌ EP ⇌ E + P, what do S and P ground states represent?

S is the lowest-energy (ground) state of the substrate; P is the lowest-energy (ground) state of the product. The difference in their energies is ΔG'° (overall free energy change).