Energy and Enzymes: An Introduction to Metabolism

Overview of Chapter 8

This chapter explores how cells use energy and enzymes to drive the chemistry of life. It covers the nature of energy in biological systems, the role of enzymes in catalyzing reactions, and the regulation and evolution of metabolic pathways.

8.1 What Happens to Energy in Chemical Reactions?

Types of Energy

Energy is fundamental to all biological processes. It exists in two main forms:

• Kinetic energy: The energy of motion, including thermal energy (energy from moving molecules).

• Potential energy: Energy stored in position or configuration, such as chemical energy in bonds.

Energy can be transformed from one type to another during chemical reactions.

Potential Energy in Molecules

The amount of potential energy in a covalent bond depends on the position of shared electrons relative to the nuclei. Longer, weaker bonds with equally shared electrons have higher potential energy, while shorter, stronger bonds with unequally shared electrons have lower potential energy.

Energy Transformations in Chemical Reactions

• Products of reactions often have shorter, stronger bonds than reactants, resulting in decreased potential energy.

• The difference in energy is transformed into kinetic energy, thermal energy, or light.

Thermodynamics in Biology

• First law of thermodynamics: Energy is conserved; it cannot be created or destroyed, only transferred or transformed.

• Enthalpy (H): Total energy in a molecule, including potential energy in bonds and kinetic energy affecting pressure and volume.

• Exothermic reactions: Release heat; products have less potential energy than reactants ( is negative).

• Endothermic reactions: Absorb heat; products have more potential energy than reactants ( is positive).

Entropy and the Second Law of Thermodynamics

• Entropy (S): Measure of disorder; increases when products are less ordered than reactants ( is positive).

• Second law of thermodynamics: Total entropy always increases in a system.

Gibbs Free Energy

Gibbs free energy (G) determines whether a reaction is spontaneous or requires energy input. The change in free energy () is calculated as:

Where is temperature in Kelvin.

• Spontaneous reactions: (exergonic)

• Nonspontaneous reactions: (endergonic)

Factors Affecting Reaction Rates

• Higher concentrations and temperatures increase reaction rates by increasing the frequency and energy of molecular collisions.

8.2 Nonspontaneous Reactions May Be Driven Using Chemical Energy

Energetic Coupling

Energetic coupling allows exergonic reactions to drive endergonic reactions. This occurs via:

• Transfer of electrons (redox reactions)

• Transfer of phosphate groups

Redox Reactions

Redox reactions involve the transfer of electrons:

• Oxidation: Loss of electrons (exergonic)

• Reduction: Gain of electrons (endergonic)

• Redox reactions always occur together, coupling energy release and uptake.

Electrons may be transferred alone or with protons, changing the energy state of molecules.

Electron Carriers

• FAD (Flavin adenine dinucleotide): Accepts two electrons and two protons to form FADH2.

• NAD+ (Nicotinamide adenine dinucleotide): Accepts two electrons and one proton to form NADH.

• These carriers donate electrons to other molecules, facilitating energy transfer in cells.

ATP: The Energy Currency of Cells

• ATP (Adenosine triphosphate) stores a large amount of potential energy in its phosphate bonds.

• Hydrolysis of ATP releases free energy ( kcal/mol), which is used for cellular activities.

• Phosphorylation (addition of phosphate group) increases the potential energy of target molecules, coupling exergonic and endergonic reactions.

8.3 How Enzymes Work

Activation Energy and Transition State

Enzymes lower the activation energy required for reactions by stabilizing the transition state, an intermediate with high free energy.

Enzyme Function

• Enzymes are biological catalysts that bring substrates together in precise orientations.

• Substrates bind to the enzyme's active site, often causing a conformational change (induced fit).

• Enzymes decrease activation energy, making reactions more likely to occur.

Steps of Enzyme Catalysis

1. Initiation: Substrates are oriented as they bind to the active site.

2. Transition state facilitation: Interactions lower activation energy.

3. Termination: Products are released from the enzyme.

Enzyme Saturation Kinetics

Enzyme-catalyzed reactions show saturation kinetics: at high substrate concentrations, the reaction rate plateaus because all enzyme molecules are occupied.

Enzyme Helpers

• Cofactors: Inorganic ions that interact with enzymes.

• Coenzymes: Organic molecules (e.g., NADH) that assist enzymes.

• Prosthetic groups: Non-amino acid molecules permanently attached to proteins.

8.4 What Factors Affect Enzyme Function?

Environmental Effects

Enzyme activity is sensitive to changes in protein structure, which can be affected by:

• Temperature (affects folding, movement, and kinetic energy)

• pH (affects shape, reactivity, and charge on groups)

Enzyme Regulation

• Regulatory molecules can activate or inactivate enzymes by changing their structure or substrate binding ability.

• Competitive inhibition: Molecule competes with substrate for active site.

• Allosteric regulation: Molecule binds elsewhere, changing enzyme shape and activity.

• Covalent modifications: Changes to enzyme's primary structure, often reversible (e.g., phosphorylation).

8.5 Enzymes Can Work Together in Metabolic Pathways

Metabolic Pathways

Metabolic pathways are series of reactions, each catalyzed by a different enzyme, that build or break down biological molecules.

Regulation of Metabolic Pathways

• Feedback inhibition: Final product inhibits an enzyme in the pathway, preventing depletion of initial substrate and allowing regulation of pathway activity.

Evolution of Metabolic Pathways

• Pathways evolve through retro-evolution (backward process) and patchwork evolution (recruitment of new enzymes).

• Catabolic pathways break down molecules for energy and building blocks.

• Anabolic pathways use energy and building blocks to synthesize molecules.

Additional info: These notes expand on brief points with academic context, definitions, and examples to provide a comprehensive study guide for General Biology students.