Enzyme__notes_

Enzyme Fundamentals

• Concept of Enzymes

  • Enzymes are biological catalysts that control and accelerate biochemical reactions in cells without undergoing permanent changes.

  • Essential for life processes, as biochemical reactions without enzymes are too slow to sustain life.

  • Enzymes catalyze reactions by lowering the activation energy (EA), which is the initial energy required for a chemical reaction to start.

  • They do not affect the change in free energy (ΔG) but speed up reactions that would eventually occur.

  • Enzymes can function optimally under moderate conditions of temperature, pH, and pressure.

  • They ensure chemical reactions occur under tightly controlled conditions.

  • Predominantly, enzymes are complex 3D globular proteins, sometimes associated with additional molecules known as cofactors.

• Cofactors

  • Divided into:

    • Inorganic cofactors (e.g., ions like copper)

    • Organic cofactors (also known as coenzymes, often water-soluble vitamins)

  • Holoenzyme: The complete form of an enzyme together with its cofactor.

  • Apoenzyme: The protein part of an enzyme without its cofactor, rendering it inactive.

  • The active site:

    • The region of the enzyme where the substrate binds, comprising functional groups from amino acids and cofactors.

Mechanism of Enzyme Activity

• Enzyme Reaction Dynamics

  • General reaction: E + S ⇌ ES → E + P, where E = enzyme, S = substrate, ES = enzyme-substrate complex, P = product.

  • Two main hypotheses explaining enzyme action:

    • Lock-and-Key Hypothesis:

      • The active site of the unbound enzyme is shaped to complement the substrate.

      • The substrate (key) fits into the active site (lock) forming an enzyme-substrate complex.

    • Induced-Fit Hypothesis:

      • The active site of the enzyme forms a complementary shape to the substrate only after the substrate is bound.

General Properties of Enzymes

• Specificity

  • Enzymes are highly specific; each enzyme catalyzes a specific substrate type.

  • The substrate shape fits the active site of its specific enzyme.

• Reversibility

  • Most enzyme-catalyzed reactions are reversible without altering equilibrium.

• Factors Affecting Enzyme Rate

  • Rate is influenced by substrate concentration, enzyme concentration, temperature, pH, and inhibitors.

Enzyme Concentration

• The rate of reaction increases with enzyme concentration, assuming substrate is in excess.

• Greater enzyme concentration raises the chances of enzyme-substrate collision.

• Rate stabilizes when all substrates are used.

Substrate Concentration

• Increasing substrate concentration can enhance reaction rates.

• At lower concentrations, the rate is directly proportional to substrate concentration.

• At higher concentrations, reaction rates plateau when all active sites are filled (saturated).

Enzyme Inhibition

• Types of Inhibitors

  • Irreversible Inhibitors (Inactivators):

    • Permanently inactivate one enzyme molecule.

    • Often potent toxins, but can also be used medically.

  • Reversible Inhibitors:

    • Bind to enzymes but can dissociate.

    • Commonly structural analogs of substrates/products, used to slow enzyme action.

Types of Reversible Inhibitors

• Competitive Inhibitors:

  • Compete with substrates for active binding sites.

  • Increased substrate concentration can outcompete inhibitors (e.g., penicillin inhibits bacterial wall synthesis).

• Noncompetitive Inhibitors:

  • Bind elsewhere on the enzyme, altering enzyme shape and reducing active site effectiveness.

Temperature Effects

• Each enzyme has an optimal functioning temperature.

• Enzymes are inactive at low temperatures.

• Increased temperatures enhance collision rates among enzyme and substrate until the optimum is reached.

• Beyond optimal temperature (~60°C), enzyme activity decreases, potentially leading to denaturation.

pH Effects on Enzyme Activity

• Each enzyme has a specific optimum pH for maximum activity, typically around 7 (most enzymes).

• Exceptions include pepsin (functions in acidic pH) and trypsin (functions in alkaline pH).

• Small pH changes can significantly affect enzyme activity as they alter the charge and shape of the active site, hindering substrate binding.

Regulation of Enzyme Activity

• Metabolic pathways must be tightly regulated to avoid chemical chaos within the cell.

• Regulation occurs through:

  • Turning enzyme-expressing genes on or off, or regulating enzyme activity.

Types of Regulation

• Covalent Modification

  • Regulated by reversible modification of amino acid residues.

  • Common modifications include phosphorylation, adenylation, and methylation.

Reversible Phosphorylation

• Phosphorylation is critical, affecting about one-third of eukaryotic proteins.

• Catalyzed by protein kinases, transferring γ-phosphoryl groups (from ATP) to specific amino acids (Ser, Thr, Tyr).

• Phosphorylation removal is via protein phosphatases.

Allosteric Regulation

• May stimulate or inhibit enzyme activity through molecule binding at different sites.

• Allosterically regulated enzymes typically catalyze irreversible reactions and are rate-limiting enzymes.

• Cooperativity:

  • A form of allosteric activation where substrate binding to one site influences activity in another site.

Feedback Inhibition

• In this mechanism, the end product of a metabolic pathway inhibits the pathway itself.

• This prevents cellular resource wastage by avoiding unnecessary product synthesis.