Ch.3 - Microbial Metabolism: Energy, Enzymes, and Biosynthesis

Microbial Metabolism

Defining the Requirements for Life

Microbial metabolism encompasses all biochemical reactions necessary for life, including both energy-yielding and biosynthetic processes. These reactions are fundamental for cell survival and growth.

• Metabolism: The sum of all chemical reactions in a cell, divided into:

  • Catabolism: Energy-releasing reactions (breakdown of molecules).

  • Anabolism: Energy-consuming reactions (biosynthesis of cellular material).

• Metabolic reactions rely on electron donors (which provide electrons) and electron acceptors (which receive electrons).

• Cells conserve energy by converting it into a usable form, primarily adenosine triphosphate (ATP).

• Law of Conservation of Energy: Energy is neither created nor destroyed, only transformed.

Example: ATP is generated during catabolic reactions and used to drive anabolic processes.

Energy Classes of Microorganisms

Microorganisms are classified based on their energy and carbon sources, reflecting their metabolic diversity.

• Chemoorganotrophs: Obtain energy from organic chemicals (e.g., Escherichia coli).

• Chemolithotrophs: Oxidize inorganic compounds (e.g., H2, H2S, NH4+; e.g., Thiobacillus thiooxidans).

• Phototrophs: Convert light energy into ATP (e.g., Rhodobacter capsulatus).

• Heterotrophs: Obtain carbon from organic compounds.

• Autotrophs: Obtain carbon from CO2.

Example: Escherichia coli is a chemoorganotroph, while Thiobacillus thiooxidans is a chemolithotroph.

Catalysis and Enzymes

Enzymes are biological catalysts that accelerate metabolic reactions by lowering the activation energy required for the reaction to proceed.

• Activation energy: The minimum energy required for molecules to react.

• Catalyst: A substance that facilitates a reaction without being consumed, lowers activation energy, and increases reaction rate.

• Enzymes: Typically proteins (some RNAs), highly specific, with an active site for substrate binding.

• Many enzymes require nonprotein molecules:

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

  • Coenzymes: Loosely bound, often vitamin derivatives.

• Enzyme catalysis depends on substrate binding and the positioning of substrates relative to catalytically active amino acids.

Example: The catalytic cycle of an enzyme involves substrate binding, conversion to product, and release of product.

Energy-Rich Compounds

Cells store energy in the form of insoluble polymers that can be oxidized to generate ATP when needed.

• Prokaryotes: Glycogen (polyglucose), poly-β-hydroxybutyrate, elemental sulfur.

• Eukaryotes: Starch (polyglucose), simple fats (lipids).

Example: Glycogen granules in bacteria serve as an energy reserve.

Glycolysis and Fermentation

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

• Fermentation: Anaerobic catabolism where organic compounds serve as both electron donors and acceptors.

• Respiration: Can be aerobic (O2 as electron acceptor) or anaerobic (other compounds as acceptors).

• Glycolysis (Embden–Meyerhof–Parnas pathway): Common pathway for glucose catabolism, yielding 2 ATP per glucose via substrate-level phosphorylation.

Example: Lactic acid fermentation in Lactobacillus produces lactic acid from glucose.

Respiration: Electron Carriers

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

• Key components:

  • NADH dehydrogenases, flavoproteins, iron-sulfur proteins, cytochromes (contain heme prosthetic groups).

  • Quinones: Small, hydrophobic, nonprotein redox molecules (e.g., ubiquinone, menaquinone).

• Electron flow is from carriers with more negative to more positive reduction potentials.

Example: Cytochrome bc1 complex in the mitochondrial electron transport chain.

Electron Transport and the Proton Motive Force

The electron transport chain (ETC) generates a proton motive force (PMF) across the membrane, which is used to synthesize ATP.

• Electrons and protons from NADH are separated; electrons pass through the ETC, protons are released outside the membrane.

• Results in a pH gradient and electrochemical potential (PMF):

  • Inside: Electrically negative and alkaline (OH-).

  • Outside: Electrically positive and acidic (H+).

• ATP synthase uses PMF to generate ATP from ADP and inorganic phosphate.

Equation:

$\text{ADP} + \text{P}_i + \text{H}^+_{\text{outside}} \rightarrow \text{ATP} + \text{H}_2\text{O} + \text{H}^+_{\text{inside}}$

Options for Energy Conservation

Microorganisms utilize diverse mechanisms for energy generation, depending on environmental conditions and available substrates.

• Anaerobic respiration: Uses electron acceptors other than O2 (e.g., NO3-, Fe3+, SO42-, CO2, fumarate).

• Chemolithotrophy: Inorganic chemicals (e.g., H2S, H2, Fe2+, NH4+) serve as electron donors; typically aerobic and autotrophic (CO2 as carbon source).

• Phototrophy: Light energy is used to generate ATP (photophosphorylation); includes photoautotrophs (use CO2) and photoheterotrophs (use organic carbon).

Example: Sulfate-reducing bacteria use SO42- as a terminal electron acceptor in anaerobic respiration.

Sugars and Polysaccharides

Polysaccharide biosynthesis in prokaryotes involves activated glucose derivatives and is essential for cell wall and storage compound formation.

• Uridine diphosphoglucose (UDPG): Precursor for N-acetylglucosamine and N-acetylmuramic acid (cell wall components).

• Adenosine diphosphoglucose (ADPG): Precursor for glycogen biosynthesis.

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors (e.g., phosphoenolpyruvate from oxaloacetate).

• Pentoses (C5 sugars): Produced via the pentose phosphate pathway, required for nucleic acid synthesis and NADPH production.

Example: The pentose phosphate pathway generates ribose-5-phosphate for RNA and DNA synthesis.

Amino Acids and Nucleotides

Biosynthesis of amino acids and nucleotides involves complex, multistep pathways, often using intermediates from central metabolic routes.

• Amino acid biosynthesis:

  • Carbon skeletons derived from glycolysis or the citric acid cycle.

  • Ammonia is incorporated by glutamine dehydrogenase or glutamine synthetase.

  • Amino groups are transferred by transaminase and aminotransferase/synthase enzymes.

Example: The aspartate family of amino acids is synthesized from oxaloacetate (a citric acid cycle intermediate).

Fatty Acids and Lipids

Fatty acid biosynthesis occurs by the sequential addition of two-carbon units, with variations in chain length and saturation depending on species and environmental conditions.

• Acyl carrier protein (ACP) holds the growing fatty acid chain during synthesis.

• Lower temperatures favor shorter, more unsaturated fatty acids; higher temperatures favor longer, more saturated fatty acids.

• Bacteria and Eukarya: Lipids are formed by attaching fatty acids to glycerol.

• Archaea: Lipids contain phytanyl side chains instead of fatty acids.

• All domains require polar groups for membrane structure (hydrophobic interior, hydrophilic surfaces).

Example: Bacterial membranes are composed of phospholipids with fatty acid tails and polar head groups.

Table: Classification of Metabolic Types Based on Energy Sources

Energy Source	Type	Electron Donor	Example Organism
Chemicals (organic)	Chemoorganotroph	Glucose, acetate, etc.	Escherichia coli
Chemicals (inorganic)	Chemolithotroph	H2, H2S, Fe2+, NH4+	Thiobacillus thiooxidans
Light	Phototroph	Light (photons)	Rhodobacter capsulatus

Additional info: The notes above are expanded and clarified for academic completeness, with definitions, examples, and logical groupings based on the provided slides and standard microbiology curriculum.