Chapter 6: Bioenergetics, Enzyme Function, and Regulation

Bioenergetics and Thermodynamics

Catabolic vs. Anabolic Pathways

Metabolic pathways in living organisms are classified as either catabolic or anabolic. Catabolic pathways break down complex molecules into simpler ones, releasing energy, while anabolic pathways build complex molecules from simpler ones, requiring energy input.

• Catabolic Pathways: Degradation processes (e.g., glycolysis, cellular respiration).

• Anabolic Pathways: Biosynthetic processes (e.g., protein synthesis, photosynthesis).

• Example: The breakdown of glucose to produce ATP is catabolic; the synthesis of DNA from nucleotides is anabolic.

First and Second Laws of Thermodynamics

The laws of thermodynamics govern energy transformations in biological systems.

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Every energy transfer increases the entropy (disorder) of the universe.

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

• Example: Cellular respiration transforms chemical energy in glucose into ATP and heat, increasing entropy.

Order in Living Organisms and the Second Law

Living organisms maintain order by coupling energy-releasing (exergonic) reactions with energy-consuming (endergonic) processes, exporting entropy to their surroundings.

• Key Point: Organisms increase the entropy of their environment, even as they maintain internal order.

• Example: The synthesis of proteins from amino acids is coupled to the hydrolysis of ATP.

Exergonic vs. Endergonic Reactions

Reactions are classified based on their free energy change ($\Delta G$).

• Exergonic: $\Delta G < 0$; energy is released; spontaneous.

• Endergonic: $\Delta G > 0$; energy is required; non-spontaneous.

• Example: ATP hydrolysis is exergonic; glucose synthesis is endergonic.

Equilibrium and Free Energy Change

The relationship between equilibrium and free energy change determines reaction spontaneity.

• At equilibrium: $\Delta G = 0$; no net change in reactants or products.

• Far from equilibrium: $\Delta G$ is negative or positive, driving reactions forward or backward.

Energy Profile of Chemical Reactions

Chemical reactions have energy barriers that must be overcome for the reaction to proceed.

• Activation Energy (EA): The minimum energy required to initiate a reaction.

• Transition State: High-energy intermediate during the reaction.

• Free Energy Change ($\Delta G$): Difference in energy between reactants and products.

• Example: Enzymes lower EA, increasing reaction rates.

Enzyme Structure and Function

Enzyme Structure and Specificity

Enzymes are biological catalysts with highly specific active sites that bind substrates.

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

• Specificity: Determined by the shape and chemical properties of the active site.

• Example: Hexokinase specifically phosphorylates glucose.

Induced Fit Model and Catalytic Cycle

The induced fit model describes how enzyme active sites change shape to better fit the substrate, facilitating catalysis.

• Induced Fit: Enzyme changes conformation upon substrate binding.

• Catalytic Cycle: Substrate binds, reaction occurs, product is released, enzyme returns to original state.

Lowering Activation Energy

Enzymes lower the activation energy of reactions, increasing the rate without altering the reaction's free energy change.

• Mechanisms: Stabilizing transition state, orienting substrates, providing microenvironment.

• Example: Carbonic anhydrase accelerates CO2 hydration.

Substrate Concentration and Reaction Rate

Reaction rate depends on substrate concentration, often following Michaelis-Menten kinetics.

• Low substrate: Rate increases linearly with concentration.

• High substrate: Rate plateaus (Vmax).

• Equation: $v = \frac{V_{max}[S]}{K_m + [S]}$

Effects of Temperature and pH

Enzyme activity is sensitive to temperature and pH, which affect protein structure and function.

• Optimal Conditions: Each enzyme has specific optimal temperature and pH.

• Denaturation: Extreme conditions disrupt enzyme structure, reducing activity.

Regulation of Enzyme Activity

Enzyme activity is regulated by environmental conditions, cofactors, inhibitors, and allosteric regulators.

• Cofactors: Non-protein molecules required for activity (e.g., metal ions).

• Inhibitors: Molecules that decrease enzyme activity.

• Allosteric Regulation: Binding at sites other than the active site alters activity.

Enzyme Kinetics and Cooperativity

Some enzymes exhibit cooperativity, where substrate binding affects the affinity of other active sites.

• Cooperative Kinetics: Sigmoidal (S-shaped) curve in substrate-velocity plot.

• Michaelis-Menten Relationship: Typical enzymes follow hyperbolic kinetics.

• Example: Hemoglobin shows cooperativity in oxygen binding.

Competitive vs. Non-Competitive Inhibition

Enzyme inhibitors are classified based on their interaction with the enzyme.

Type	Binding Site	Effect on Vmax	Effect on Km
Competitive	Active site	No change	Increases
Non-competitive	Allosteric site	Decreases	No change

Michaelis-Menten and Lineweaver-Burk Plots

Enzyme kinetics are analyzed using graphical methods.

• Michaelis-Menten Plot: Plots reaction rate vs. substrate concentration.

• Lineweaver-Burk Plot: Double reciprocal plot for determining Vmax and Km.

• Equation: $\frac{1}{v} = \frac{K_m}{V_{max}} \cdot \frac{1}{[S]} + \frac{1}{V_{max}}$

Additional info: Some explanations and examples have been expanded for clarity and completeness.