Bioenergetics & Enzymes

Metabolism: An Overview

Metabolism encompasses all chemical reactions occurring within an organism, divided into two main categories: anabolism (building molecules) and catabolism (breaking molecules). These reactions are essential for energy transformation and cellular function.

• Anabolism: Synthesis of complex molecules from simpler ones; requires energy input (endergonic).

• Catabolism: Breakdown of complex molecules into simpler ones; releases energy (exergonic).

• Dehydration reaction: Joins monomers into polymers, releasing water.

• Hydrolysis reaction: Breaks polymers into monomers, consuming water.

• Reduction: Gain of electrons or hydrogen atoms.

• Oxidation: Loss of electrons or hydrogen atoms.

Additional info: Larger molecules store more energy due to more bonds; smaller molecules store less energy.

Energy in Chemical Reactions

Chemical reactions involve changes in energy, measured as Gibbs free energy (ΔG). The direction and spontaneity of a reaction depend on the energy difference between reactants and products.

• ΔG (Gibbs free energy): Indicates the change in free energy during a reaction.

• Endergonic reactions: ΔG is positive; energy is absorbed.

• Exergonic reactions: ΔG is negative; energy is released.

• Independent variable: Time (in reaction graphs).

• Dependent variable: Energy of molecules.

• Unit for energy: Gibbs (G).

When reactants have more energy than products, energy is released (ΔG negative). When reactants have less energy than products, energy is required (ΔG positive).

Activation Energy and Transition State

Every chemical reaction must overcome an energy barrier, known as activation energy (Ea), to reach the transition state before products are formed.

• Activation energy: The energy required to initiate a reaction, often supplied as thermal energy.

• Transition state: The high-energy intermediate between reactants and products.

Types of Energy

Energy in biological systems can be classified as potential or kinetic energy.

• Potential energy: Stored energy in chemical bonds and concentration gradients.

• Kinetic energy: Energy of movement, including heat.

Laws of Thermodynamics

The laws of thermodynamics govern energy transformations in living organisms.

• First Law: Energy cannot be created or destroyed.

• Second Law: Entropy (unusable energy) increases with each reaction, often as heat.

Catalysts and Enzymes

Catalysts speed up chemical reactions by lowering activation energy. Enzymes are organic catalysts, typically proteins or RNA, that facilitate biological reactions.

• Catalyst: Substance that increases reaction rate without being consumed.

• Enzyme: Organic catalyst; most enzyme names end with -ase.

• Ribozyme: RNA molecule with catalytic activity.

Enzyme Structure and Function

Enzymes have a specific region called the active site where substrates bind. The binding often induces a conformational change known as induced fit.

• Active site: Region where substrate binds and reaction occurs.

• Induced fit: Enzyme changes shape to bind substrate more tightly.

• Enzyme-substrate complex: Temporary association during catalysis.

• Substrate: Reactant acted upon by enzyme.

• Product: Molecule formed and released after reaction.

Substrates bind via weak interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces).

Mechanisms of Enzyme Action

Enzymes accelerate reactions through several mechanisms:

• Orienting substrate molecules for optimal interaction.

• Using amino acid side chains to attract substrates.

• Inducing stress/strain on substrate bonds.

• Creating a microenvironment within the active site.

Reaction Rates and Enzyme Activity

Reaction rates depend on substrate and enzyme concentrations, as well as environmental factors.

• Decreasing substrate concentration lowers reaction rate.

• Increasing enzyme concentration raises reaction rate.

• Saturating enzymes with substrate leads to maximum velocity (vmax).

• Any factor affecting protein shape affects enzyme activity.

Environmental parameters:

• Increasing temperature above optimal decreases rate.

• Decreasing temperature below optimal decreases rate.

• pH changes above or below optimal decrease rate.

Enzyme Regulation

Enzyme activity can be regulated by molecules that bind to the enzyme, changing its shape and function.

• Allosteric regulation: Regulatory molecule binds at a site other than the active site (allosteric site), affecting activity.

• Allosteric inhibitor: Turns enzyme off; only reversible by removing inhibitor.

• Allosteric activator: Turns enzyme on; only reversible by removing activator.

• Competitive inhibitor: Binds to active site, blocking substrate.

• Noncompetitive inhibitor: Binds elsewhere, changing enzyme shape and reducing function.

• Irreversible inhibition: Covalent binding to active site, permanently inactivating enzyme.

• Reversible inhibition: Non-covalent binding, temporarily inactivating enzyme.

Metabolic Pathways and Feedback Inhibition

Enzyme-catalyzed reactions are organized into metabolic pathways, which can be linear or cyclic. Pathways are regulated by feedback inhibition, where the end product inhibits an earlier enzyme.

• Linear pathway: Substrate converted to final product through a series of steps.

• Cyclic pathway: Starting substrate is regenerated.

• Feedback inhibition: End product allosterically inhibits an enzyme early in the pathway.

Terminology Table

The following table summarizes key terms related to bioenergetics and enzyme function:

Key Equations

Important equations in bioenergetics:

• Gibbs free energy change:

• Relationship to spontaneity: (spontaneous), (non-spontaneous)