In-Depth Notes on Enzymes and Their Mechanisms

Enzymes are powerful and highly specific catalysts.
They significantly increase reaction rates without being consumed in the reaction.
Most enzymes are globular proteins; however, some RNA molecules (ribozymes) also act as catalysts.
Some enzymes do not require any additional components, while others need cofactors (inorganic ions) or coenzymes (complex organic molecules).

A tightly or covalently bound coenzyme or metal ion to the enzyme is called a prosthetic group.
A holoenzyme is the complete, catalytically active enzyme with its coenzyme and/or metal ions bound.
The protein part of the enzyme is known as the apoenzyme or apoprotein.
Enzymes often have names derived from their substrates or activities, typically with the suffix “-ase,” e.g., urease (hydrolyzes urea) and DNA polymerase (polymerizes nucleotides to form DNA).

Biological reactions, without enzymes, are slow due to stability in neutral pH and mild temperature environments.
Enzymes provide a specific environment for reactions, enabling milder conditions, high specificity, and regulation.
The active site of the enzyme is the region where substrates bind, and catalysis occurs. The substrate is the molecule acted upon by the enzyme.
Enzymes significantly enhance reaction rates, potentially increasing them by factors ranging from $10^6$ to $10^{12}$ .

Enzyme catalysis can be summarized by the reaction:
$E + S ⇌ ES ⇌ EP ⇌ E + P$
The enzyme-catalyzed reaction rate increases without altering the equilibrium state of the reaction, which is determined by the difference in free energy ( $ΔG$ ) between reactants and products.
The concept of activation energy ( $ΔG‡$ ) is critical; higher activation energy results in slower reactions.

Catalysts lower activation energies, accelerating the reaction without being consumed, allowing rapid equilibrium to be achieved.
Different steps in a reaction pathway may have varying activation energies, and the step with the highest activation energy is the rate-limiting step.
Examples of enzyme rate enhancements include:
- Cyclophilin: $10^5$
- Carbonic anhydrase: $10^7$
- Triose phosphate isomerase: $10^9$
- Urease: $10^{14}$

Enzymes exhibit high specificity, distinguishing between similar substrates (e.g., trypsin vs. chymotrypsin).
Rearrangement of covalent bonds during reactions lowers activation energy through covalent interactions.
Weak, non-covalent interactions contribute significantly to the formation of stable enzyme-substrate complexes.
The energy from enzyme-substrate interactions is termed binding energy ( $ΔG_B$ ), crucial for catalysis.

Binding energy contributes to both catalysis and enzyme specificity, where interactions, especially involving phosphate groups, enhance the reaction rate.
Factors limiting reaction rates include entropy, solvation shells, substrate distortion, and the alignment of catalytic functional groups.

Enzymes organize substrates into a rigid complex facilitating optimal interactions (close proximity and proper orientation).
Proposed models like the Proximity Model demonstrate that well-oriented substrates can result in lower activation barriers.

Enzymes preferentially stabilize the transition state compared to both substrates and products, making it favorable for reactions to proceed.

Covalent Catalysis: Active site contains a nucleophile that is temporarily bonded.
General Acid-Base Catalysis: Molecules other than water donate or accept protons.
Catalysis by Approximation: Enzymes bring substrates together efficiently.
Metal Ion Catalysis: Metal ions assist in stabilizing negative charges and facilitating substrate binding.

Class 1: Oxidoreductases - Electron transfers (e.g., Alcohol dehydrogenase)
Class 2: Transferases - Group transfers (e.g., DNA polymerase)
Class 3: Hydrolases - Hydrolysis reactions (e.g., Chymotrypsin)
Class 4: Lyases - Cleavage reactions (e.g., Carbonic anhydrase)
Class 5: Isomerases - Rearrangements (e.g., Phosphohexose isomerase)
Class 6: Ligases - Covalent bond formation using ATP (e.g., Aminoacyl-tRNA synthetase)

Involves hydrolysis of peptide bonds and reactions with phosphate groups.
Certain amino acids (Asp, Glu, Cys, Tyr, His, and Lys) play crucial roles in acid-base catalysis.

Bovine pancreatic protease, important for cleaving peptide bonds.
Functions through a catalytic triad of amino acids (Ser195, His57, Asp102).
Catalyzes reactions via a two-phase process (acylation and deacylation) leading to peptide bond hydrolysis.

Human Immunodeficiency Virus (HIV) infects CD4 T-cells and undergoes several steps including binding, reverse transcription, integration, transcription, assembly, and budding.
The HIV protease is essential for processing viral proteins, induced by specific protease inhibitors.

Penicillin interferes with bacterial cell wall synthesis through inhibition of transpeptidase, showing the importance of enzyme mechanisms in antibiotic action.

Carbonic anhydrase catalyzes the hydration of carbon dioxide, highlighting metal ion catalysis in enzymatic reactions and physiological significance in maintaining acid-base balance.