chapter 6

Chapter 6: Metabolism

Overview of Metabolism

  • Definition: Metabolism is the totality of an organism's chemical reactions.
  • Key Aspects:
    • The metabolism of living cells encompasses thousands of biochemical reactions, all of which require energy transformations.
    • Metabolism transforms matter and energy, adhering to the laws of physics.

Organization of the Chemistry of Life into Metabolic Pathways

  • Metabolic Pathway: A sequence of chemical reactions where the product of one reaction becomes the reactant for the next.
    • Catalysis: Each reaction in the pathway is catalyzed by a specific enzyme.
    • Example:
      • Enzyme 1 0→ A
      • Enzyme 2 0→ B
      • Enzyme 3 0→ C
      • Product D

Types of Metabolic Pathways

  • Catabolic Pathways:

    • Function: Break down complex molecules (food) into simpler ones.
    • Energy Release: These pathways release energy.

  • Anabolic Pathways:

    • Function: Build more complex molecules from simpler ones.
    • Energy Requirement: These pathways require energy.

Evolution of Metabolic Pathways

  • Commonality of Pathways: All types of life share some of the same metabolic pathways; this suggests that organisms evolved from common ancestors.
  • Divergence: Over time, pathways diverged as organisms evolved, developing specialized enzymes for adaptation to environments.

What is Energy?

  • Energy Definition: Energy is the capacity to cause change or perform work.
  • Forms of Energy:
    • Potential Energy: Energy stored; examples include:
    • Chemical bonds
    • Concentration gradients
    • Electrical potential
    • Kinetic Energy: Energy in motion; examples include:
    • Heat (molecular motion)
    • Mechanical (movement of molecules)
    • Electrical (movement of charged particles)

Conversion of Energy

  • Energy can convert from one form to another.
    • Diving Example: A diver on a platform has more potential energy; diving converts it into kinetic energy. Climbing converts kinetic energy from muscle movement back to potential energy.

The Laws of Energy Transformation

  • Thermodynamics: The study of energy transformations.
    • System Defined: In this field, the system refers to the matter under study, while the surroundings refer to everything outside it.
    • Closed System: Isolated from surroundings (e.g., liquid in a thermos).
    • Open System: Allows energy and matter to transfer with surroundings—organisms are open systems absorbing energy (light or chemical) and releasing heat and metabolic waste.

First Law of Thermodynamics

  • Definition: Energy cannot be created or destroyed; it can only be converted from one form to another.
    • Example: Chemical energy can convert to heat.

Second Law of Thermodynamics

  • Energy Transfer and Entropy: Every energy transformation increases the entropy (disorder) of the universe.
    • Efficiency: No process is 100% efficient; some energy is always lost as heat. Example:
    • Disorder increases in the environment, manifesting as heat and metabolic by-products (e.g., CO2 and H2O).
  • Entropy (S): Measure of disorder or randomness; more accurately, it represents the dispersal of energy.

Biological Order and Disorder

  • Biological Systems: Cells and organisms are complex and highly ordered; however, they do not violate the second law as the entropy of the surroundings increases due to heat release.

Spontaneous Reactions

  • Definition of Spontaneous Reaction: Occurs without energy input, can happen quickly or slowly, increasing the universe's entropy.
  • Significance: Such reactions can be harnessed to perform work.

Free Energy and Free-Energy Change, ΔG

  • Gibbs Free Energy (G): The energy available to do work under cellular conditions (uniform temperature and pressure).
  • Free Energy Change (ΔG): Indicates whether a reaction occurs spontaneously or requires energy.

ΔG during a Biological Process

  • Formula: ΔG = ΔH - TΔS
    • Where:
    • $ΔH$ = change in total energy (enthalpy) of the system (products - reactants)
    • $T$ = temperature in Kelvins
    • $ΔS$ = change in entropy (products - reactants)
    • Unit: kcal/mole

Exergonic and Endergonic Reactions

  • Exergonic Reactions (ΔG < 0):
    • Occur when products have less potential energy than reactants; energy is released and reaction proceeds spontaneously (not necessarily quickly due to activation energy barriers).
    • Illustration: Free energy diagram indicating a "hump" for activation energy.
  • Endergonic Reactions (ΔG > 0):
    • Occur when products have more potential energy than reactants, requiring energy input to proceed.

Reaction Energy Dynamics

  • Reactions Releasing Energy: 6CO2 + 6H2O ightarrow C6H{12}O6 + 6O2
    • Energy is released.
  • Reactions Requiring Energy: C6H{12}O6 + 6O2 ightarrow 6CO2 + 6H2O
    • Energy is required.
  • Key Points:
    • ΔG = - non-spontaneous
    • ΔG = + spontaneous.

Equilibrium and Metabolism

  • Closed Systems: Eventually reach equilibrium ($ΔG = 0$).
  • Open Systems (Cells):
    • Cells are open systems, continually replenishing food and removing waste, preventing equilibrium, allowing reactions to process without reaching a standstill.

Cellular Respiration Analogy

  • Analogy for Cell Metabolism:
    • Cellular respiration is likened to an open hydroelectric system, with glucose breakdown occurring through exergonic reactions that fuel cellular work without reaching equilibrium.

Role of ATP in Metabolism

  • ATP (Adenosine Triphosphate):
    • Primary energy shuttle in cells, unstable and quickly hydrolyzes.
    • Powers cellular work through coupling exergonic and endergonic reactions.
  • Energy Release from ATP:
    • Release occurs when terminal phosphate bonds are broken. Energy can either be lost as heat or used to fuel endergonic reactions via phosphorylation.

Hydrolysis and ATP Coupling

  • Hydrolysis Reaction: ATP + H_2O ightarrow ADP + Pi + Energy
    • Phosphate Transfer: ATP drives endergonic reactions via phosphorylation, transferring a phosphate to other molecules.

Activation Energy, EA

  • Definition of EA:
    • Initial energy needed to start a chemical reaction; represents the "hump" in the energy profile of reactions.
  • Heat Source: Heat from surroundings generally acts as the main source for activation energy, converting reactants into an unstable transition state.

Enzymes as Biological Catalysts

  • Definition and Function: Enzymes speed up reactions by lowering activation energy (EA) for all reactions (exergonic and endergonic).
    • Composition: Majority of enzymes are proteins; some non-protein enzymes (e.g., ribozymes) exist.
    • Regeneration: Enzymes are not consumed during reactions and facilitate the transformation of substrates into products.

Enzymatic Reaction Mechanism

  • Example of Hydrolysis:
    • The hydrolysis of sucrose requires breaking both glycosidic bond and water's bond and proceeds via an enzyme-catalyzed pathway.

Effects of Local Conditions on Enzyme Activity

  • Factors Affecting Activity: Enzyme activity depends on:
    • Ion concentrations
    • pH levels
    • Temperature
    • Regulatory molecules that can enhance or inhibit activity.

Temperature and pH Effects on Enzymes

  • Optimal Temperature: Each enzyme has an optimal temperature for optimal activity; deviations can result in decreased efficiency or denaturation.
  • Optimal pH: Each enzyme operates best within a specific pH range; extreme deviations can inhibit activity.

Enzyme Helpers: Cofactors and Coenzymes

  • Cofactors: Non-protein components (often inorganic ions) that assist enzyme function (e.g., Fe²⁺, Mg²⁺).
  • Coenzymes: Organic cofactors such as NAD⁺ and vitamins that enhance enzyme activity.

Regulation of Enzymes

  • Three Primary Regulation Methods:
    • Timing of enzyme activity
    • Activity level required
    • Location of enzyme activity
  • Activation and Inhibition: Enzymes can turn 'off' by inhibitors (irreversible or reversible) and 'on' by activators.

Competitive and Noncompetitive Inhibitors

  • Competitive Inhibitors: Mimic substrates and bind to active sites, competing for availability (e.g., disulfiram).
  • Noncompetitive Inhibitors: Attach elsewhere on the enzyme, altering the active site shape and preventing substrate binding (e.g., cyanide).

Allosteric Regulation of Enzymes

  • Definition: The functionality of a protein is altered by the binding of regulatory molecules, resulting in changes in enzyme shape and function.

Cooperativity in Enzymes

  • Definition: A form of allosteric regulation that enhances enzyme activity; binding of one substrate stabilizes the active form of other subunits.

Feedback Inhibition

  • Process: The pathway is shut down by its end product, usually early in the pathway to prevent overproduction.

Specific Localization of Enzymes Within the Cell

  • Enzyme Arrangement: Enzymes can be grouped into complexes, incorporated into cellular membranes, or contained within organelles (e.g., mitochondria involved in cellular respiration).