Energy and Metabolism

Thermodynamics in Biological Systems

Biological processes are governed by the laws of thermodynamics, which describe how energy is transformed and conserved in living organisms.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed from one form to another.

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

• Metabolism: The sum of all chemical reactions in an organism, organized into metabolic pathways with sequential, enzyme-catalyzed steps.

Catabolic Pathways: Break down molecules, releasing energy (e.g., cellular respiration). Anabolic Pathways: Build complex molecules, requiring energy input (e.g., protein synthesis).

• Energy released by catabolic pathways can drive anabolic processes.

• Organisms exchange matter and energy with their surroundings, maintaining order and supporting life.

Example: A diver on a platform has high potential energy; diving converts this to kinetic energy. Climbing back up uses kinetic energy to restore potential energy.

Free Energy and Reaction Favorability

The concept of free energy (Gibbs free energy, G) predicts whether a reaction will occur spontaneously.

• ΔG (Delta G): Change in free energy during a reaction.

• Exergonic Reaction: ΔG < 0; releases energy; thermodynamically favorable.

• Endergonic Reaction: ΔG > 0; requires energy input; not spontaneous without coupling.

• At Equilibrium: ΔG = 0; no net change in reactants or products.

Equation:

Activation Energy (Ea): The energy barrier that must be overcome for a reaction to proceed. Enzymes lower this barrier but do not change ΔG.

Example: Reading an energy diagram involves comparing the free energy of reactants and products and identifying the activation energy peak.

ATP: The Energy Currency of the Cell

Adenosine Triphosphate (ATP) is the primary energy carrier in cells.

• Structure: Adenine + Ribose + Three Phosphate Groups

• ATP hydrolysis releases energy:

• ATP hydrolysis is exergonic and drives endergonic cellular processes via energy coupling.

• Phosphorylation (adding a phosphate group) can activate or change the function of molecules and proteins.

• ATP supports chemical, transport, and mechanical work in cells.

ATP Cycle: ATP is regenerated from ADP and inorganic phosphate using energy from catabolic reactions. ATP is not stored long-term but is continuously recycled.

Enzymes: Biological Catalysts

Enzyme Structure and Function

Enzymes are mostly proteins (some are catalytic RNAs) that accelerate chemical reactions by lowering the activation energy required.

• Enzymes are specific to their substrates and can be reused.

• The active site is the region where the substrate binds, often through an induced fit that changes enzyme shape for optimal interaction.

The Catalytic Cycle

• Substrate binds to the enzyme's active site, forming an enzyme-substrate complex.

• The enzyme stabilizes the transition state and/or orients reactants to facilitate the reaction.

• Products are released, and the enzyme is free to catalyze another reaction.

Equation:

Structure-Function Connection: Changes in amino acid sequence (mutations) can alter enzyme folding, active site geometry, substrate binding, or catalytic efficiency. Not all mutations destroy function; effects depend on the specific change.

Factors Affecting Enzyme Activity

• Substrate Concentration: At low concentrations, increasing substrate increases reaction rate. At high concentrations, enzymes become saturated and the rate plateaus.

• Enzyme Concentration: Increasing enzyme concentration can raise the maximum rate if substrate is available.

• Temperature: Reaction rates increase with temperature up to an optimum; above this, enzyme structure may denature and activity drops. Optimum temperature varies among enzymes.

• pH: Changes in pH affect ionization of amino acid side chains, altering binding and enzyme conformation. Each enzyme has a pH optimum (e.g., stomach vs. intestinal enzymes).

Cofactors and Coenzymes

• Cofactors: Nonprotein helpers required for enzyme activity. Can be inorganic (e.g., Zn2+, Fe2+, Cu2+) or organic.

• Coenzymes: Organic cofactors, often derived from vitamins.

Enzyme Regulation

• Competitive Inhibition: Inhibitor binds at or near the active site, blocking substrate binding. Increasing substrate concentration can overcome inhibition.

• Noncompetitive Inhibition: Inhibitor binds away from the active site, reducing enzyme activity. Increasing substrate does not restore maximum rate.

• Allosteric Regulation: Regulator binds at a site other than the active site, changing enzyme conformation and activity. Allosteric activators increase activity; inhibitors decrease it.

• Cooperativity: Binding of substrate to one subunit affects binding at other subunits, often producing a sigmoidal response curve. Relates to quaternary protein structure.

• Feedback Inhibition: End product of a pathway inhibits an enzyme early in the pathway, preventing overproduction and conserving resources. Inhibition is relieved as product levels decrease.

Summary Table: Types of Enzyme Inhibition

Additional info: Vmax is the maximum reaction rate; Km is the substrate concentration at half-maximal velocity (a measure of substrate affinity).

Applications and Experimental Predictions

• Understanding enzyme regulation and inhibition is crucial for drug design, metabolic engineering, and interpreting experimental data.

• Predicting the effect of mutations, inhibitors, or environmental changes on enzyme activity is a key skill in biology.