Microbial Metabolism: Study Guide and Key Concepts

Microbial Metabolism

Introduction to Metabolism

Metabolism encompasses all chemical reactions within a living cell, enabling energy production and the synthesis of essential cellular components. Microbial metabolism can result in both beneficial and harmful outcomes, such as food spoilage or disease, but also supports vital processes like fermentation and nutrient cycling.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy (exergonic). Provides energy and building blocks for cellular functions.

• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input (endergonic).

Enzymes and Chemical Reactions

Chemical Reaction Principles

• Collision Theory: Chemical reactions occur when atoms, ions, or molecules collide with sufficient energy.

• Activation Energy: The minimum energy required to initiate a reaction.

• Reaction Rate: The frequency of effective collisions; increased by higher temperature, pressure, concentration, or the presence of enzymes.

Enzyme Properties and Mechanisms

• Enzymes: Biological catalysts that accelerate reactions by lowering activation energy, without being consumed.

• Specificity: Each enzyme acts on a specific substrate.

• Turnover Number: The number of substrate molecules converted per second (typically 1–10,000; up to 500,000).

• Naming: Enzyme names end with "-ase" and are classified by function:

  • Oxidoreductase: Catalyzes oxidation-reduction reactions.

  • Transferase: Transfers functional groups.

  • Hydrolase: Catalyzes hydrolysis reactions.

  • Lyase: Removes atoms without hydrolysis.

  • Isomerase: Rearranges atoms within a molecule.

  • Ligase: Joins two molecules, often using ATP.

Mechanism of Enzymatic Action

1. Substrate binds to the enzyme's active site.

2. Enzyme-substrate complex forms.

3. Substrate is transformed into products.

4. Products are released; enzyme remains unchanged.

Equation: Enzyme + Substrate → Enzyme-Substrate Complex → Enzyme + Products

Enzyme Components

• Apoenzyme: Protein portion, inactive alone.

• Cofactor: Non-protein component (e.g., metal ions like Fe2+, Zn2+); if organic, called a coenzyme (e.g., NAD+, NADP+, FAD, CoA).

• Holoenzyme: Active enzyme (apoenzyme + cofactor).

Factors Influencing Enzyme Activity

• Temperature and pH: Each enzyme has optimal conditions; extremes cause denaturation (loss of structure and function).

• Substrate Concentration: Increased substrate increases reaction rate until saturation (all active sites occupied).

• Inhibitors:

  • Competitive: Compete with substrate for active site.

  • Noncompetitive (Allosteric): Bind elsewhere, altering active site shape and function.

• Feedback Inhibition: End-product of a pathway inhibits an early enzyme, preventing overproduction.

Ribozymes: Catalytic RNA molecules that process RNA (e.g., splicing) and are active in ribosomes.

Energy Production: Redox and ATP Generation

Oxidation-Reduction (Redox) Reactions

• Oxidation: Loss of electrons (often as hydrogen atoms).

• Reduction: Gain of electrons.

• Redox Pairing: Oxidation and reduction always occur together.

Mechanisms of ATP Generation

• Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP from a phosphorylated intermediate.

• Oxidative Phosphorylation: Electrons pass through the electron transport chain (ETC); energy released is used for ATP synthesis via chemiosmosis.

• Photophosphorylation: In photosynthetic cells, light energy drives ATP and NADPH production.

Carbohydrate Catabolism and Cellular Respiration

Glycolysis (Embden-Meyerhof Pathway)

• Definition: Oxidation of glucose to pyruvic acid.

• Net Yield: 2 ATP and 2 NADH per glucose.

• Phases:

  • Preparatory: 2 ATP invested; glucose split into two 3-carbon molecules (GP and DHAP).

  • Energy-Conserving: GP oxidized to pyruvic acid; 4 ATP and 2 NADH produced.

Alternative Pathways

• Pentose Phosphate Pathway: Breaks down 5-carbon sugars and glucose; yields NADPH and biosynthetic intermediates.

• Entner-Doudoroff Pathway: Produces NADPH and ATP without glycolysis; found in Pseudomonas, Rhizobium, Agrobacterium.

The Krebs Cycle (Citric Acid Cycle)

• Transition Step: Pyruvic acid is oxidized and decarboxylated to acetyl-CoA (producing NADH).

• Cycle Outputs: NADH, FADH2, ATP (via substrate-level phosphorylation), and CO2 (waste).

Electron Transport Chain (ETC) and Chemiosmosis

• Location: Plasma membrane (prokaryotes), inner mitochondrial membrane (eukaryotes).

• Mechanism: Electrons pass through carriers (flavoproteins, cytochromes, ubiquinones), releasing energy.

• Chemiosmosis: Proton gradient drives ATP synthesis via ATP synthase.

Aerobic vs. Anaerobic Respiration

• Aerobic: O2 is the final electron acceptor; yields up to 38 ATP per glucose in prokaryotes.

• Anaerobic: Uses other inorganic molecules as final electron acceptors; yields less ATP.

Final Electron Acceptor	Primary End-Products
Nitrate (NO3-)	Nitrite (NO2-), Nitrogen gas (N2), H2O
Sulfate (SO42-)	Hydrogen sulfide (H2S), H2O
Carbonate (CO32-)	Methane (CH4), H2O

Fermentation

Fermentation is an anaerobic process that extracts energy from organic molecules without using oxygen, the Krebs cycle, or an ETC. It uses an organic molecule as the final electron acceptor and regenerates NAD+ for glycolysis, producing low ATP yields.

• Lactic Acid Fermentation: Pyruvic acid reduced to lactic acid by NADH.

  • Homolactic: Only lactic acid produced.

  • Heterolactic: Lactic acid plus other compounds produced.

• Alcohol Fermentation: Pyruvic acid converted to acetaldehyde and CO2, then reduced to ethanol by NADH.

Lipid, Protein, and Biochemical Testing

Lipid Catabolism

• Lipases: Hydrolyze lipids into glycerol and fatty acids.

• Glycerol: Converted to glycolysis intermediate.

• Fatty Acids: Undergo beta-oxidation to form acetyl-CoA for the Krebs cycle.

Protein Catabolism

• Proteases/Peptidases: Break proteins into amino acids.

• Deamination, Decarboxylation, Desulfurization: Modify amino acids for entry into the Krebs cycle.

Diagnostic Biochemical Tests

• Fermentation Tests: Detect acid/gas production from carbohydrate fermentation using pH indicators and Durham tubes.

• Oxidase Tests: Identify presence of cytochrome c oxidase.

Photosynthesis and Metabolic Diversity

Photosynthesis

• Light-Dependent Reactions: Convert light energy to ATP and NADPH.

• Light-Independent Reactions: Use ATP and NADPH to fix CO2 into sugars (Calvin-Benson Cycle).

• Oxygenic: Produces O2 (plants, algae, cyanobacteria).

• Anoxygenic: Does not produce O2; uses H2S or other donors (green/purple sulfur bacteria).

Nutritional Classification of Organisms

Nutritional Type	Energy Source	Carbon Source	Examples
Photoautotroph	Light	CO2	Cyanobacteria, plants, green/purple sulfur bacteria
Photoheterotroph	Light	Organic Compounds	Green/purple nonsulfur bacteria
Chemoautotroph	Inorganic Chemicals	CO2	Iron-oxidizing, nitrifying bacteria
Chemoheterotroph	Organic Chemicals	Organic Compounds	Animals, fungi, protozoa, most bacteria

Biosynthesis (Anabolism) and Integration

Cells use energy from catabolism to drive anabolic reactions, synthesizing essential macromolecules.

• Polysaccharide Biosynthesis: Glycolysis intermediates (e.g., glucose 6-phosphate) are polymerized into storage (glycogen) or structural (peptidoglycan) carbohydrates using ATP or UTP.

• Lipid Biosynthesis: Glycerol (from dihydroxyacetone phosphate) and fatty acids (from acetyl-CoA) are combined to form lipids.

• Amino Acid Biosynthesis: Amination or transamination of organic acid intermediates produces amino acids.

• Purine and Pyrimidine Biosynthesis: Nucleotide bases are synthesized from pentose phosphate pathway, glycolysis intermediates, and amino acids.

• Amphibolic Pathways: Pathways that serve both catabolic and anabolic functions, sharing intermediates for efficient cellular metabolism.