Energy and Enzymes: An Introduction to Metabolism

Overview of Chapter 8

This chapter explores how enzymes use energy to drive the chemistry of life, focusing on the principles of metabolism, energy transformations, and enzyme function. It covers the types of energy, the laws of thermodynamics, the role of ATP, and the regulation and evolution of metabolic pathways.

8.1 What Happens to Energy in Chemical Reactions?

Types of Energy

Energy is essential for cellular activities and exists in two primary forms:

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

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

• Energy can be transformed from one type to another during cellular processes.

Chemical Bonds and Potential Energy

The potential energy in a covalent bond depends on the position of shared electrons relative to the nuclei of bonded atoms:

• Longer, weaker bonds with equally shared electrons have high potential energy.

• Shorter, stronger bonds with unequally shared electrons have low potential energy.

Energy Transformations in Chemical Reactions

During chemical reactions:

• Products often have shorter, stronger covalent bonds than reactants.

• Potential energy in bonds decreases, and the difference is transformed into kinetic energy, thermal energy, or light.

First Law of Thermodynamics

The first law of thermodynamics states that energy is conserved; it cannot be created or destroyed, only transferred or transformed. Enthalpy (H) is the total energy in a molecule, including potential energy in bonds and kinetic energy affecting pressure and volume.

Changes in Enthalpy and Reaction Types

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

• Endothermic reactions: Absorb heat; ΔH is positive; products have higher potential energy than reactants.

Entropy and the Second Law of Thermodynamics

Entropy (S) measures disorder. When products are less ordered than reactants, entropy increases (ΔS is positive). The second law of thermodynamics states that total entropy always increases in a system.

Gibbs Free Energy and Reaction Spontaneity

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

• ΔH = change in enthalpy

• ΔS = change in entropy

• T = temperature in Kelvin

Reactions are:

• Spontaneous when ΔG < 0 (exergonic)

• Nonspontaneous when ΔG > 0 (endergonic)

• At equilibrium when ΔG = 0

Temperature and Concentration Affect Reaction Rates

For reactions to proceed, bonds must break and form, and substances must collide in specific orientations. Higher concentrations and temperatures increase collision frequency and reaction rates.

8.2 Nonspontaneous Reactions May Be Driven Using Chemical Energy

Energetic Coupling

Energetic coupling allows chemical energy released from exergonic reactions to drive endergonic reactions. This occurs via:

• Transfer of electrons

• Transfer of phosphate groups

Redox Reactions

Reduction–oxidation (redox) reactions involve electron transfer:

• Oxidation: Loss of electrons (exergonic)

• Reduction: Gain of electrons (endergonic)

• Redox reactions always occur together, coupling two half-reactions.

Electron Carriers

Electron carriers facilitate redox reactions:

• FAD accepts two electrons and two protons to form FADH2.

• NAD+ accepts two electrons and one proton to form NADH.

• These carriers donate electrons to other molecules, enabling energy transfer.

ATP Transfers Energy via Phosphate Groups

Adenosine triphosphate (ATP) is the energy currency of cells, storing potential energy in bonds between three negatively charged phosphate groups.

ATP Hydrolysis and Phosphorylation

ATP hydrolysis releases free energy (7.3 kcal/mol), which cells use for activity. Phosphorylation adds a phosphate group to a target molecule, increasing its potential energy and coupling exergonic and endergonic reactions.

8.3 How Enzymes Work

Activation Energy and Transition State

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

Enzyme Function and Substrate Binding

Enzymes are catalysts that bring substrates together in precise orientations, making reactions more likely. Substrates bind to the enzyme's active site, often causing a conformational change called induced fit.

Enzyme Catalysis Steps

• Initiation: Substrates bind to active site in specific orientation.

• Transition state facilitation: Interactions lower activation energy.

• Termination: Products are released from enzyme.

Saturation Kinetics

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

Enzyme Cofactors, Coenzymes, and Prosthetic Groups

• Cofactors: Inorganic ions (e.g., Zn2+, Mg2+, Fe2+) that interact with enzymes.

• Coenzymes: Organic molecules (e.g., NADH, FADH2) that assist enzymes.

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

8.4 What Factors Affect Enzyme Function?

Environmental Effects on Enzyme Activity

Enzyme structure is critical to function and is sensitive to:

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

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

• Interactions with other molecules

• Modifications of primary structure

Enzyme Regulation

Enzymes are regulated by molecules that change their structure or ability to bind substrates, either activating or inactivating their function.

Noncovalent Regulation

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

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

Covalent Modifications

• Changes in enzyme's primary structure can be reversible or irreversible.

• Phosphorylation is the most common reversible modification, altering enzyme shape and activity.

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 biological molecules.

Feedback Inhibition

Feedback inhibition occurs when the final product of a pathway inhibits an enzyme earlier in the pathway, preventing depletion of the initial substrate and regulating pathway activity.

Evolution of Metabolic Pathways

Metabolic pathways evolve through:

• Retro-evolution: New enzymes evolve to replenish substrates as they decline.

• Patchwork evolution: New enzymes are recruited to new pathways.

Catabolic and Anabolic Pathways

• Catabolic pathways: Break down molecules for energy and carbon building blocks.

• Anabolic pathways: Use energy and carbon building blocks to synthesize molecules.