Microbial 3. Metabolism: Principles, Pathways, and Diversity

Microbial Metabolism

Overview of Metabolism

Microbial metabolism encompasses all chemical reactions occurring within a microbial cell, enabling growth, maintenance, and reproduction. These reactions are categorized as either energy-releasing (catabolic) or energy-requiring (anabolic).

• Metabolism: The sum total of all chemical reactions in a cell.

• Catabolic reactions (catabolism): Energy-releasing metabolic reactions.

• Anabolic reactions (anabolism): Energy-requiring metabolic reactions.

Cellular Requirements for Metabolism

All cells require essential resources and energy to drive metabolic processes.

• Water, sources of carbon, and other nutrients.

• Free energy: Energy available to do work.

• Reducing power: Source of electrons (e-).

• Exergonic reactions: Release free energy.

• Endergonic reactions: Require free energy.

• Change in free energy: Expressed as $\Delta G^{'0}$.

Energy Classes of Microorganisms

Classification by Energy Source

Microorganisms are classified based on their energy and carbon sources, which determines their metabolic strategies.

• Chemotrophs: Obtain energy from chemicals.

• Phototrophs: Obtain energy from light.

• Chemoorganotrophs: Use organic chemicals (e.g., Escherichia coli).

• Chemolithotrophs: Use inorganic chemicals (e.g., Thiobacillus species).

• Phototrophs: Use light energy (e.g., Rhodobacter capsulatus).

Example: Escherichia coli is a chemoorganotroph that uses glucose as an energy source.

Electron Donors and Acceptors

Redox Reactions in Metabolism

Energy for microbial metabolism is often derived from oxidation-reduction (redox) reactions, which involve electron transfer between molecules.

• Electron donor: Substance that loses electrons in a redox reaction.

• Electron acceptor: Substance that gains electrons in a redox reaction.

• Redox reactions occur in pairs (two half-reactions).

• Energy from redox reactions is used to synthesize energy-rich compounds such as ATP.

Example Reaction:

• $\mathrm{C_6H_{12}O_6} + 6\,\mathrm{O_2} \rightarrow 6\,\mathrm{CO_2} + 6\,\mathrm{H_2O}$

Reduction Potential and Electron Flow

The tendency of a substance to donate electrons is measured as its reduction potential ($E_0'$), expressed in volts (V).

• Substances can act as electron donors or acceptors depending on context (redox couple).

• A reduced substance with a more negative $E_0'$ donates electrons to an oxidized substance with a more positive $E_0'$.

Electron Tower Table

The electron tower ranks redox couples by their standard reduction potentials, indicating which pairs release more energy when electrons are transferred.

Electron Acceptor	Electron Donor	$E_0'$ (mV)
CO2, 2H+	Glucose, H2	-430
NAD+	NADH, H+	-320
FAD	FADH2	-220
O2	H2O	+820
Additional info:	Greater difference in $E_0'$ between donor and acceptor yields more energy released.

Electron Carriers in Cells

Redox reactions in microbial cells are mediated by small molecules such as coenzyme NAD+ (reduced form: NADH).

• NAD+ acts as an electron shuttle in metabolic pathways.

• Enzymes facilitate electron transfer by binding NAD+ and substrate at their active sites.

Energy-Rich Compounds

Storage of Chemical Energy

Energy released in redox reactions is stored in phosphorylated compounds, which are used to drive cellular work.

• ATP (Adenosine triphosphate): Main energy currency of the cell.

• Phosphoenolpyruvate (PEP): High-energy intermediate in glycolysis.

• Acetyl phosphate: Intermediate in fermentation and other pathways.

Compound	$\Delta G^{'0}$ (kJ/mol)
Phosphoenolpyruvate	-61.9
ATP	-30.5
Acetyl phosphate	-43.1
Glucose 6-phosphate	-13.8

Catalysis and Enzymes

Role of Enzymes

Enzymes are biological catalysts, usually proteins, that accelerate chemical reactions without being consumed.

• Enzymes lower the activation energy required for reactions.

• The active site is the region where substrate binds and reaction occurs.

• Enzymes can catalyze both exergonic and endergonic reactions.

Equation for activation energy:

• $\Delta G^{\ddagger} = G_{\text{transition state}} - G_{\text{reactants}}$

Enzyme Catalytic Cycle

The catalytic cycle involves substrate binding, conversion to product, and release, as illustrated by lysozyme.

• Substrate binds to active site.

• Enzyme catalyzes conversion to product.

• Product is released, enzyme is ready for another cycle.

Enzyme Cofactors

• Prosthetic groups: Tightly bound, often covalently attached (e.g., heme in cytochromes).

• Coenzymes: Loosely bound, often derived from vitamins (e.g., NAD+/NADH).

Catabolism: Fermentation and Respiration

Energy Conservation Pathways

Chemoorganotrophs conserve energy through two main pathways: fermentation and respiration.

• Fermentation: Anaerobic catabolism; organic compounds donate and accept electrons.

• Respiration: Aerobic or anaerobic catabolism; donor is oxidized with O2 (aerobic) or another compound (anaerobic) as electron acceptor.

Substrate-Level and Oxidative Phosphorylation

Mechanisms of ATP Synthesis

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP from a phosphorylated intermediate (occurs in glycolysis and fermentation).

• Oxidative phosphorylation: ATP synthesis driven by dissipation of proton motive force across a membrane.

Glycolysis

Pathway and Products

Glycolysis is a central metabolic pathway that converts glucose to pyruvate, generating ATP and NADH.

• Main products: 2 ATP, 2 NADH, 2 pyruvate per glucose molecule.

• Key intermediates: Glucose-6-phosphate, Fructose-1,6-bisphosphate, Phosphoenolpyruvate (PEP).

The Citric Acid Cycle

Function and Products

The citric acid cycle (Krebs cycle) oxidizes acetyl-CoA to CO2, generating NADH, FADH2, and ATP/GTP.

• Central to aerobic respiration and biosynthesis.

• Produces reducing equivalents for electron transport chain.

Principles of Fermentation

Fermentation Process

Fermentation involves the uptake of organic compounds, substrate-level phosphorylation, and excretion of fermentation products.

• NAD+ is recycled via redox cycling.

• ATP is generated by substrate-level phosphorylation.

• Fermentation products are excreted from the cell.

Respiration: Electron Carriers

Electron Transport Systems

Electron transport systems are membrane-associated complexes that mediate electron transfer and conserve energy for ATP synthesis.

• Located in the cytoplasmic membrane of bacteria.

• Include oxidation-reduction enzymes (e.g., NADH dehydrogenases) and nonprotein carriers (e.g., quinones).

Cytochromes and Quinones

• Cytochromes: Proteins with heme prosthetic groups, involved in electron transfer.

• Coenzyme Q (quinone): Lipid-soluble electron carrier, shuttles electrons within the membrane.

Respiration: Electron Transport and Proton Motive Force

Mechanism and ATP Synthesis

Electron transport chains are oriented in the cytoplasmic membrane, separating electrons from protons and generating a proton gradient (proton motive force).

• Electron carriers are arranged by reduction potential.

• Electrons and protons from NADH initiate the process.

• Final electron carrier donates electrons and protons to the terminal electron acceptor.

ATP synthase (ATPase): Converts proton motive force into ATP; consists of two main components (F0 and F1).

Catabolic Diversity

Types of Respiration

Microorganisms exhibit diverse catabolic strategies depending on available electron donors and acceptors.

• Anaerobic respiration: Uses electron acceptors other than oxygen (e.g., nitrate, ferric iron, sulfate, carbon dioxide, organic compounds).

• Less energy is released compared to aerobic respiration due to lower reduction potential of alternative acceptors.

• Dependent on electron transport, proton motive force, and ATPase activity.

Nitrogen Fixation (Biosynthesis)

Process and Enzymes

Nitrogen fixation is the conversion of nitrogen gas (N2) to ammonia (NH3), catalyzed by the enzyme nitrogenase. Only certain prokaryotes can fix nitrogen, and the process is inhibited by oxygen.

• Some nitrogen-fixing organisms are free-living, others are symbiotic.

• Reaction requires significant ATP input and reducing power.

Equation for nitrogen fixation:

• $\mathrm{N_2} + 8\,\mathrm{H^+} + 8\,\mathrm{e^-} + 16\,\mathrm{ATP} \rightarrow 2\,\mathrm{NH_3} + \mathrm{H_2} + 16\,\mathrm{ADP} + 16\,\mathrm{P_i}$

Table: Nitrogen-Fixing Organisms

Type	Chemoorganotrophs	Phototrophs	Chemolithotrophs
Free-living aerobes	Azotobacter, Azomonas, Acetobacter, Klebsiella, Methylomonas	Cyanobacteria (e.g., Anabaena, Nostoc, Gloeocapsa, Aphanothece)	Alcaligenes, Azotobacter
Free-living anaerobes	Clostridium, Desulfovibrio	Purple bacteria (Chromatium, Rhodospirillum, Methanobacterium, Chlorobium, Helicobacteria)	Methanosarcina, Methanocaldococcus
Symbiotic	With legumes: Soybeans, peas, clover, beans, alfalfa, vetch (with Rhizobium, Bradyrhizobium, Sinorhizobium) With nonlegumes: Alder, bayberry, autumn olive, many other plants (with actinomycete Frankia)

Additional info: Nitrogen fixation is essential for converting atmospheric nitrogen into a biologically usable form, supporting global nitrogen cycles.