Lecture 9

Metabolism

Nutritional Components of Microbes

• Substrates and Nutrients: Essential inorganic and organic elements required by microbes, primarily carbon (C), nitrogen (N), oxygen (O), and sulfur (S), alongside various vitamins that serve as co-factors in metabolic reactions.

• Precursors: A set of twelve major building blocks, including amino acids, fatty acids, and nucleotides, crucial for synthesizing macromolecules like proteins and nucleic acids.

• Macromolecules: Include critical biological structures such as proteins (for catalysis and structure), polysaccharides (for energy storage and structural integrity), nucleic acids (for genetic information), and lipids (for membrane formation).

• Supramolecular Structures: Complex assemblies such as enzymatic systems, ribosomes, and the nucleoid which facilitate cellular function and organization.

• Level of organization (order): Bottom to top: substrates/nutrients, precursors, monomers, macromolecules, supramolecular structures, cell.

Essential Metabolic Demands

All organisms necessitate:

1. Source of Energy, electrons, and carbon:

   1. Phototrophs: Light, H2O, H2S, and CO2

   2. GIT Bacteria: Carbohydrates, Carbohydrates, carbohydrates. Most bacteria in GI ferment carbs as primary energy source for microbial growth.

Definitions of Energy

• Energy: The capacity for doing work, signifying the transfer of energy within a system that induces physical or chemical changes.

• Forms of Energy: Include thermal, mechanical, electrical, osmotic, chemical, and gravitational energy.

• Kinetic Energy: The energy of an object in motion.

• Potential Energy: The stored energy within a system, which can be released to do work later.

• Equations: E=mc²: energy, mass, and the speed of light, illustrating energy-mass equivalence in physical systems.

Energy Conservation in Microbial Cells

• Reaction Equations: Explains how cells harness energy through catabolic and anabolic pathways.

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• Role of ATP, NADPH: Both are pivotal in anaerobic cellular processes, functioning as energy carriers and reducing agents in biochemical reactions.

Bioenergetics

• Definition: The biology of energy transformations and energy exchanges within and between living things and their

  environments.

• Importance of Photosynthesis: Key to generating potential energy (CHOs) that can be used by animals and microbes.

Laws of Thermodynamics - Energy Conservation

• First Law: Energy cannot be created or destroyed; it can only be transformed from one form to another

Laws of Thermodynamics - Directionality

• Second Law: States that in spontaneous processes, entropy increases, demonstrating the natural tendency toward disorder and the inherent inefficiencies in energy transduction within organisms.

Free Energy & Chemical Potential

• Many energy transactions in a cell are chemical in nature

• Free Energy (G): A crucial thermodynamic quantity that indicates a system’s ability to perform work at constant temperature and pressure.

  • Measured experimentally by calorimetric methods

  • Change indicates spontaneity of a process

• Calculation: ΔG = ΔH - TΔS, where ΔH represents the change in enthalpy (total energy), T is the temperature, and ΔS is the change in entropy

Deriving Free Energy from Metabolic Reactions

• A + B → C + D → ΔG0 = - RT ln Keq

• ΔG = Keq under standard conditions: temp 298 K, 1M concentrations, H+ is pH 7, and R is constant at 8.314.

• Shows how free energy changes are determined based on concentrations of reactants/products and temperature, important for metabolic regulation.

Equilibrium Constants and Free Energy Changes

• Relationship Between K’eq and ΔG°’ Values: A comprehensive table exhibiting how equilibrium constants relate to free energy changes under standard conditions, emphasizing the conditions under which reactions can proceed in a forward or reverse manner. As products increase in a reaction, reagents decrease.

Metabolism Fundamentals

• Metabolism:

  • Catabolism: Characterized by exergonic reactions (ΔG’0 < 0) that release energy, making it available for biological work.

  • Anabolism: Encompasses endergonic reactions (ΔG’0 > 0) that consume energy for biosynthesis.

  • Emphasis on how coupled reactions (ΔG’0<0) can drive non-spontaneous processes

Role of ATP in Metabolism

• ATP Significance: Acts as a primary energy intermediary in cells, crucial for coupling metabolic reactions, with examples illustrating how ATP facilitates energy transfer in various biochemical pathways.

Hexokinase Reaction Example

• Hexokinase Reaction:

  • Reaction: Glucose + Pi → Glucose-6P + H2O.

  • The equilibrium constant indicates whether the reaction is spontaneous through ΔG° calculations, highlighting the role of this enzyme in metabolic pathways.

Coupled Reactions

• Mechanism of Coupling: Explores how spontaneous reactions can facilitate the occurrence of non-spontaneous ones through additive free energy changes.

  • Glucose + ATP → Glucose-6P + ADP

  • Free energy changes of couple reactions are additive

Directionality in Reactions

• Importance of ATP hydrolysis and glucose phosphate formation in driving various metabolic pathways, Pi is highly stable and should not be released into solution:

  • Low energy: Glu + ATP → ADP + Glu-6P (-kj/mol opposite direction of reaction)

  • Medium energy: Glu + Pi → Glu-6P +H2O

  • High energy: ATP + H2O → ADP + Pi

Free Energy from Redox Potentials

• Equations Relating Redox Potentials: Thermodynamics of redox reactions, shows how specific electron acceptors/donors provide energetic advantages influencing microbial metabolism.

  • Δ𝑮′𝒐= −nFΔE’0

• Microorganisms capable oof using acceptors with a more positive electrode potential have a thermodynamic advantage (greater capacity to do work).

Bioenergetics in Microbial Communities

• Overview of Role Differentiation: Elucidates the roles of Primary Degrader, Primary Fermenter, and Secondary Fermenter in microbial communities, supporting functional diversity.