Study Notes on Energy and Enzymes in AP Biology

Energy and Enzymes

Chemistry of Life Organized into Metabolic Pathways

• Metabolism: sum total of all chemical reactions occurring in an organism; involves energy changes.

Two Types of Metabolic Pathways

• Catabolic Pathways:
    - Release energy; energy stored in bonds is released when breaking down complex molecules to simpler compounds.
    - Example: Cellular Respiration.

• Anabolic Pathways:
    - Consume energy; energy captured in bonds that form build complicated molecules from simpler ones.
    - Example: Photosynthesis.

Anabolic vs. Catabolic reactions

Organisms Transform Energy

• Energy: the capacity to do work.

Types of Energy:

• Kinetic Energy: energy in the process of doing work; energy of motion (e.g., heat, light).

• Potential Energy: energy that matter possesses because of its location or arrangement; energy of position.

Energy Transformation

• Energy can be transformed – converted from one form to another.

Free Energy

Energy Changes in Reactions

Endergonic Reaction:

• Energy is required from reactants to products over time.

• Figure 2.14 (Part 1): Illustrates the time course of an endergonic reaction, with reactants requiring energy to form products.

Exergonic Reaction:

• Energy is released from reactants to products over time.

• Figure 2.14 (Part 2): Shows that the amount of energy released occurs as a reaction progresses.

Laws of Thermodynamics: A Study of Energy Transformations

First Law of Thermodynamics:

• Energy can be transferred and transformed, but not created or destroyed.   - Implication: Energy of the universe is constant.

Second Law of Thermodynamics:

• Every energy transfer or transformation increases the universe's entropy.   - Implication: Every process increases the disorder (entropy) of the universe.

Combining the 1st and 2nd Laws:

• Quantity of energy is constant, but quality of energy changes.

• When energy is converted, some energy becomes unavailable (e.g., as heat).

The Entropy of a System:

• System entropy may decrease, but the total entropy (system + surroundings) must always increase.

• Heat is largely unavailable to do work; example cited is the ease of glucose and fructose movement due to their simpler structure compared to sucrose.

Free Energy (G)

• Definition: Free energy (G) is the amount of energy available to do work at constant temperature, linked to the system's total energy (H) and its entropy (S).

• Gibbs Free Energy Equation:
    $riangle G = riangle H - T riangle S$
    - Where:
      - $riangle G$ = change in free energy (Gibbs)
      - $riangle H$ = change in total energy (enthalpy)
      - $riangle S$ = change in entropy
      - T = absolute temperature in oK   - Interpretation: The difference between total energy (enthalpy) and energy not available for doing work.

Significance of Free Energy

1. Indicates the maximum amount of a system’s energy available to do work.

2. Indicates whether a reaction will occur spontaneously.

Spontaneous Reactions

• A spontaneous reaction occurs without additional energy input.

• For spontaneous occurrence:
    - $riangle G$ decreases (i.e., riangle G < 0).   - A decrease in enthalpy (-$riangle H$) or an increase in entropy (+$riangle S$) reduce free energy.   - Higher temperatures enhance the effect of entropy change.   - High energy systems are unstable and tend to change to a more stable state.

Free Energy and Equilibrium

• As a reaction approaches equilibrium, the free energy decreases.

• When a reaction is pushed away from equilibrium, the free energy increases.

• At equilibrium:
    - $riangle G = 0$ because there is no net change in the system.

Metabolic Disequilibrium

• Many metabolic reactions are reversible and have the potential to reach equilibrium.

• Disequilibrium is essential for life; a cell at equilibrium is considered dead.

• Products of some reactions often become substrates for the next reaction in the metabolic pathway.

Free Energy and Metabolism

Reaction Types:

• Exergonic Reaction: Net loss of free energy, releases energy to surroundings.

• Endergonic Reaction: Net gain of free energy, absorbs energy from surroundings.

Comparison of Exergonic vs. Endergonic Reactions

• Exergonic:   - products have less free energy than reactants.   - Energetically downhill.   - $riangle G$ is negative.   - $- riangle G$ is the maximum work the reaction can perform.   - Catabolic reactions.

• Endergonic:
    - products store more free energy than reactants.   - Energetically uphill.   - Non-spontaneous (requires energy input).   - $riangle G$ is positive.   - $+ riangle G$ is the minimum work required to drive the reaction.   - Anabolic reactions.

Energy Units

• Joules and Kilojoules:   - 1 joule = 0.239 calories
    - 1 calorie = 4.18 joules

Sample Problem on Free Energy

Problem: If a reaction has a $riangle G$ of -31.5 kcal/mol, which of the following reactions could be coupled to it?

• $riangle G = -25.2$

• $riangle G = -46.7$

• $riangle G = +31.5$

• $riangle G = +22.8$

Enzymes

Important Terms

• Enzyme: Organic compound that acts as a biological catalyst, altering the rate of a reaction without being consumed.

• Catalyst: Substance that changes the rate of a reaction (speeds it up) without being used up in the reaction.

• Molecular Energy: The amount of energy found in a molecule determined by its shape.

• Energy of Activation: Energy required for a reaction to occur.

• Substrate: Substance/reactant that binds to an enzyme.

• Active Site: Specific region of an enzyme where the substrate binds.

• Inhibitor: Chemical that inactivates an enzyme.

• Denaturation: Structural change in a protein causing loss of biological function, affected by pH and temperature.

Metabolic Reactions and Enzymes

• Enzymes catalyze metabolic reactions, can be clustered or isolated based on genetic makeup. Reactions follow specific sequences (e.g., "chain" reactions or cyclic reactions, like Krebs cycle).

Characteristics of Enzymes

Definition of Enzymes

• A protein comprised of amino acids, with a specific 3D shape, functioning as an organic catalyst for biochemical reactions.

Role of Enzymes in Catalysis

• Enzymes influence reaction rates by lowering the activation energy.

• Enzyme reactions produce products faster by facilitating substrate conversion.

• Note: Enzymes are not reactants and are recycled after reactions.

Energy and Enzymes

Activation Energy

• Definition: The amount of energy that must be absorbed by reactant molecules for a reaction to occur.

• Transition State: Unstable condition of reactants after absorbing sufficient energy.

Enzymes Lower Activation Energy

• Example Figure: Illustrates kinetics before and after enzyme addition, showing the lowering of activation energy.

Active Site Properties

• Definition: Part of the enzyme designed to match substrate shape.

• Enzyme-Substrate Specificity: Enzyme active site must match the substrate's shape and charge (lock-and-key model).

Induced Fit Model

• Describes how substrate binding induces enzyme shape change for better fit, emphasizing the flexibility of enzymes during catalysis.

Factors Affecting Enzyme Activity

1. Temperature:
     - Optimal temperature increases reaction rates, but extreme heat leads to denaturation.

2. pH:
     - Enzymes function best at specific pH ranges. Irregular pH levels can denature enzymes.

3. Enzyme Concentration:
     - More enzymes increase reaction rates to a point of saturation.

4. Substrate Concentration:
     - Increased substrate concentrations raise reaction rates until all active sites are saturated.

5. Cofactors and Coenzymes:
     - Small non-protein molecules essential for enzyme function (e.g., vitamins).

Types of Inhibitors

Competitive Inhibition

• Inhibitor resembles substrate and competes for active site, blocking substrate binding.

• At low inhibitor concentrations, increasing substrate concentration can reduce inhibition.

Non-Competitive Inhibition

• Inhibitor binds to an allosteric site, changing the enzyme's active site shape and preventing the catalytic reaction.

Enzyme Importance

• Enzymes facilitate nearly all metabolic reactions, critical in pathways such as glycolysis and photosynthesis. They allow biochemical processes to occur in specific sequences.

End Product Inhibition

• Prevents resource waste in cells by stopping production of excess end products through inhibition in the biochemical pathway.

Feedback Inhibition

• A regulatory mechanism to maintain balance in metabolic pathways, allowing products to inhibit their own production.

Cooperativity

• Phenomenon where substrate binding enhances activity of other enzyme subunits by inducing conformational changes.

Examples of Common Enzymes

• Enzymes are typically named according to their functions, ending in “-ase.” Examples include:
    - Hydrolase: Breaks down water.
    - Dehydrogenase: Removes hydrogen atoms.
    - Isomerase: Changes structural formulas.
    - Phosphorylase: Adds/removes phosphate groups.
    - ATPase/ATP Synthase: Involved in ATP metabolism.

Lactase in Lactose-Free Milk Production

• Lactose: Naturally present milk sugar converted by lactase into glucose and galactose.

• Lactase is produced from yeast cultured in milk for subsequent extraction and purification, creating lactose-free products.

Lactose Intolerance Solutions

• Options include lactase supplements or consumption of lactose-free milk, which is derived via direct treatment with lactase or use of immobilized lactase technology.

Conclusion: Enzymatic Regulation

• Essential for metabolic pathways such as glycolysis and Krebs cycle, ensuring metabolic efficiency and resource conservation. The study of enzymes remains vital for understanding biochemistry and physiology.