The Chemistry that Supports Life: Enzymes

The Chemistry that Supports Life: Enzymes

Introduction

• Focus of the lecture: Utilization of chemical energy from food to generate ATP, a molecule that drives cellular work.

  • Key processes involved:

  • Photosynthesis in plant cells, which uses light energy to convert CO2 and H2O into organic molecules and oxygen.

  • Cellular respiration in animal cells, which breaks down organic molecules to generate ATP and heat.

Photosynthesis and Cellular Respiration

• Key chemical reactions:

  • Photosynthesis Equation:

  • 6CO2 + 6H2O + Light ightarrow C6H{12}O6 + 6O2

    • Inputs: Carbon dioxide, water, light.

    • Outputs: Sugar (glucose) and oxygen.

  • Cellular Respiration Equation:

  • C6H{12}O6 + 6O2 ightarrow 6CO2 + 6H2O + ATP

    • Inputs: Sugar (glucose) and oxygen.

    • Outputs: Carbon dioxide, water, and ATP.

Learning Outcomes

• Understanding the concepts:

  • Chemical equilibrium

  • Gibbs free energy (ΔG)

  • Endergonic and exergonic reactions

  • Transition state and the role of enzymes

  • Feedback regulation and enzyme inhibition (competitive and non-competitive)

  • ATP energy coupling in cellular processes

Chemical Equilibrium

• Definition: Chemical equilibrium is achieved when the rate of the forward reaction equals the rate of the reverse reaction.

• Reaction Rate Calculation:

  • A + B
    ightleftharpoons AB

  • Equilibrium constant, Keq defined as:

  • Keq = rac{[AB]}{[A][B]}

• Rate constants:

  • k_f = rate constant of the forward reaction

  • k_r = rate constant of the reverse reaction

Gibbs Free Energy (ΔG)

• Equation:

  • ΔG = ΔH - TΔS

  • Where:

  • ΔH = change in enthalpy (heat energy)

  • ΔS = change in entropy (disorder)

  • T = temperature in Kelvin

• Reaction spontaneity:

  • Negative ΔG (exergonic reaction): Spontaneous, no energy input required.

  • Example of a spontaneous process: Active transport.

  • Positive ΔG (endergonic reaction): Non-spontaneous, energy input required.

  • Example: ATP production.

• Relation to equilibrium:

  • If ΔG° < 0, then Keq > 1 (products favored at equilibrium).

  • If ΔG° > 0, then Keq < 1 (reactants favored at equilibrium).

  • At Keq=1, ln(1)=0, ΔG°=0.

  • Gas constant, R, relates energy changes to temperature changes.

Thermodynamics of Reactions

• Types of reactions:

  • Exergonic reaction: Releases energy, ΔG < 0, spontaneous.

  • Endergonic reaction: Requires energy input, ΔG > 0, non-spontaneous.

• Examples:

  • Exergonic: 2H2 + O2
    ightarrow 2H_2O with ΔG° negative.

  • Endergonic: 2H2O ightarrow 2H2 + O_2 requires energy input (electricity).

Kinetics: Reaction Rates

• Kinetics defined as the speed of a reaction:

  • Forward reaction rate: Rate = k_f [A][B]

  • Reverse reaction rate: Rate = k_r [AB]

• At equilibrium, both reaction rates are equal:

  • kf [A][B] = kr [AB]

• The equilibrium constant can also be expressed as:

  • Keq = rac{kf}{kr} = rac{[AB]}{[A][B]}

Transition State and Enzymes

• Transition state characterization:

  • An unstable, high-energy state, thermodynamically unfavorable.

  • The activation energy (E_A) is necessary to reach the transition state.

  • EA determines kf under specific conditions.

• Enzymes reduce activation energy, thus speeding up reactions:

  • Enzymes influence kinetics but not thermodynamics; they do not alter ΔG.

Mechanisms by Which Enzymes Lower Activation Energy

1. Concentration: High local concentration of substrate.

2. Orientation: Proper orientation of substrates.

3. Facilitation: Use of functional groups (acids/bases) and cofactors to assist reactions.

4. Stabilization of Transition State: Binding energy stabilizes the transition state, increasing the likelihood of the reaction:

   • Enzyme-substrate complex: E + S
     ightarrow ES
     ightarrow EP
     ightarrow E + P

Competitive and Non-competitive Inhibition

• Competitive Inhibition:

  • Molecules similar in structure to the substrate compete for the active site, preventing substrate binding.

• Non-competitive Inhibition:

  • Molecules bind to an allosteric site, affecting enzyme function without blocking substrate binding.

Allosteric Regulation of Enzymes

• Allosteric regulation involves a regulatory molecule binding to one site on an enzyme, affecting its function at a different site.

  • This can either stimulate or inhibit enzyme activity.

Feedback Inhibition

• A specific form of negative allosteric regulation where the product of a metabolic pathway inhibits an enzyme involved in the pathway.

• This helps maintain homeostasis by responding dynamically to changes in product concentration.

Energy Coupling with ATP

• ATP hydrolysis energy can drive endergonic reactions:

  • ATP + H2O
    ightarrow ADP + P_i + energy (ΔG = -7.3 kcal/mol).

• Coupling example:

  • When an endergonic reaction (ΔG = +3.4 kcal/mol) couples with ATP hydrolysis:

  • Net ΔG = -3.9 kcal/mol, allowing the process to occur.

Enzyme Activity and Environmental Factors

• Enzymes show optimal activity under specific environmental conditions, including temperature and pH:

  • Optimal conditions vary by enzyme type (e.g. human enzymes typically optimal at 37°C).

• Factors include:

  • Temperature: Enzyme activity typically increases with temperature until denaturation occurs.

  • pH: Each enzyme has an optimal pH for function, such as pepsin in the stomach (pH ~2) and trypsin in the intestine (pH ~8).

Upcoming Topics

• Discussion of aerobic metabolism and respiration:

  • Catabolic pathways yield energy by oxidizing organic compounds.

  • Anabolic pathways combine simpler substances to form complex molecules (requires energy).

• Definitions:

  • Catabolism: Energy-yielding metabolism.

  • Anabolism: Biosynthetic metabolism.

  • Key metabolites and energy intermediates include ATP, ADP, and metabolic products.

Metabolism: The Totality of Chemical Reactions

• Definition: Metabolism represents the sum of all chemical reactions in an organism. These reactions allow for energy extraction, synthesis of essential molecules (proteins, lipids, nucleotides), and genome replication.

• Catabolism: Metabolic pathways that break down complex molecules into smaller components, releasing energy.

  • Examples: Extracting energy from nutrients, detoxification reactions.

• Anabolism: Metabolic pathways that build larger molecules from smaller ones, requiring energy input.

  • Examples: DNA replication, RNA transcription, and protein translation.

Chemical Equilibrium and $K_{eq}$

• Reaction Inputs and Outputs: Reactants (or substrates) are typically written on the left, while products are on the right (A + B \rightleftharpoons AB).

• Equilibrium State: Attained when the forward reaction rate equals the reverse reaction rate.

  • Concentrations of reactants and products remain constant but are not necessarily equal.

• Equilibrium Constant (K_{eq}): Defined empirically for every reaction.

  • K_{eq} = \frac{[AB]}{[A][B]}

  • A high K_{eq} indicates a high concentration of products and a low concentration of reactants at equilibrium.

• Kinetics at Equilibrium:

  • kf [A][B] = kr [AB]

  • K{eq} = \frac{kf}{k_r}

Thermodynamics and Gibbs Free Energy (\Delta G)

• Thermodynamic Favorability: \Delta G measures if a reaction can proceed spontaneously.

  • Exergonic (-\Delta G): Reactants have more energy than products. These are spontaneous and can release energy to do work (e.g., active transport, muscle contraction).

  • Endergonic (+\Delta G): Products have more energy than reactants. These are non-spontaneous and require energy input.

• Gibbs Equation: \Delta G = \Delta H - T\Delta S

• Activation Energy (E_A): Even spontaneous reactions may not occur immediately due to an energy barrier.

  • Example: A wax candle has a large negative \Delta G when burning, but requires a match (activation energy) to start the process.

Enzyme Mechanism and Catalysis

• Composition: Enzymes are typically proteins or riboproteins (RNA-protein complexes).

• Catalysis: Enzymes act as catalysts, meaning they are not consumed in the reaction and can be reused.

• Lowering Activation Energy: Enzymes stabilize the high-energy transition state, allowing the reaction to proceed faster with a lower E_A.

  • Note: Enzymes do not change the \Delta G of a reaction; they only change the rate.

• Binding Mechanisms:

  • Local Concentration: Enzymes bring substrates together at the active site, increasing their local concentration to favor product generation.

  • Orientation: Proper physical alignment of substrates.

  • Facilitation: Use of functional groups or cofactors.

Enzyme Regulation and Inhibition

• Positive Regulation: Some enzymes are stimulated by the presence of their own substrates.

• Competitive Inhibition: Inhibitors structurally similar to the substrate compete for the active site, blocking substrate binding.

• Non-competitive (Allosteric) Inhibition: Inhibitors bind to an allosteric site ("allo-" meaning different), changing the enzyme's shape and preventing substrate binding at the active site.

• Feedback Inhibition: A mechanism for maintaining homeostasis where the downstream product of a pathway inhibits an upstream enzyme, halting production until concentrations drop.

Energy Coupling with ATP

• Concept: Chemically coupling a thermodynamically unfavorable reaction (+\Delta G) with a highly favorable one (-\Delta G).

• ATP Hydrolysis: Adding water to ATP to produce ADP and Inorganic Phosphate (P_i).

  • \text{ATP} + \text{H}2\text{O} \rightarrow \text{ADP} + Pi (\Delta G = -7.3 \text{ kcal/mol}).

• Application: Powering active transport pumps to move ions against concentration gradients.

Environmental Factors on Activity

• Temperature: Activity increases with heat until the protein denatures.

• pH Sensitivity: Different enzymes have specific optimal ranges (e.g., Stomach Pepsin at pH 2 vs. Intestinal Trypsin at pH 8).