Microbial Metabolism

Big Picture: Metabolism

Metabolism encompasses all chemical reactions involved in the buildup and breakdown of nutrients within a cell. These reactions provide energy and create substances essential for sustaining life. While microbial metabolism can cause disease and food spoilage, many metabolic pathways are beneficial and not pathogenic.

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

• Catabolism: Breaks down complex molecules, releasing energy.

• Anabolism: Uses energy to build complex molecules from simpler ones.

Catabolic and Anabolic Reactions

Catabolic and anabolic reactions are the two main types of metabolic processes. Catabolism is exergonic (energy-releasing), while anabolism is endergonic (energy-consuming).

• Catabolism: Releases energy by oxidation of molecules (e.g., glucose to CO2 and H2O).

• Anabolism: Synthesizes macromolecules using energy stored in ATP.

• Metabolic pathways: Sequences of enzymatically catalyzed reactions, determined by enzymes encoded by genes.

Enzymes and Chemical Reactions

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy, without being consumed in the process.

• Catalysts: Speed up reactions without being altered.

• Enzyme-substrate complex: Substrate binds to enzyme's active site, is transformed, and products are released.

• Enzyme specificity: Each enzyme acts on a particular substrate.

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

Naming Enzymes

• Enzyme names usually end in -ase and are grouped by the reaction they catalyze:

• Oxidoreductase: Oxidation-reduction reactions

• Transferase: Transfer of functional groups

• Hydrolase: Hydrolysis

• Lyase: Removal of atoms without hydrolysis

• Isomerase: Rearrangement of atoms

• Ligase: Joining of molecules, uses ATP

Enzyme Components

• Apoenzyme: Protein portion, inactive alone

• Cofactor: Nonprotein component (can be inorganic or organic)

• Coenzyme: Organic cofactor (e.g., NAD+, NADP+, FAD, Coenzyme A)

• Holoenzyme: Apoenzyme plus cofactor (active form)

Factors Influencing Enzyme Activity

• Temperature and pH: High temperature/extreme pH can denature proteins.

• Substrate concentration: High concentration leads to maximum enzyme activity (saturation).

• Inhibitors: Can be competitive (bind active site) or noncompetitive (bind allosteric site).

Inhibitors and Feedback Inhibition

• Competitive inhibitors: Compete with substrate for active site.

• Noncompetitive inhibitors: Bind elsewhere, changing enzyme shape and function.

• Feedback inhibition: End-product of a pathway inhibits an enzyme earlier in the pathway, regulating metabolic flow.

Ribozymes

• Ribozymes: RNA molecules that act as catalysts, binding substrates and facilitating reactions (e.g., RNA splicing, protein synthesis).

Oxidation-Reduction (Redox) Reactions

• Oxidation: Removal of electrons

• Reduction: Gain of electrons

• Redox reaction: Paired oxidation and reduction

• In biological systems, electrons and protons are often removed together (dehydrogenation).

The Generation of ATP

ATP is the primary energy currency in cells, generated by phosphorylation of ADP.

• ATP formation equation:

Mechanisms of ATP Generation

• Substrate-level phosphorylation: Direct transfer of phosphate from substrate to ADP.

• Oxidative phosphorylation: Electrons transferred through electron transport chain, energy used to generate ATP via chemiosmosis.

• Photophosphorylation: Light energy drives ATP synthesis in photosynthetic cells.

Metabolic Pathways of Energy Production

• Glycolysis: Breakdown of glucose to pyruvic acid, producing ATP and NADH.

• Fermentation: Anaerobic process, produces small amounts of ATP.

• Krebs cycle: Oxidizes pyruvic acid, generates NADH, FADH2, and ATP.

• Oxidative phosphorylation: Electron transport chain and chemiosmosis.

• Photophosphorylation: Light-driven ATP synthesis.

Carbohydrate Catabolism

• Major stages: Glycolysis & fermentation, pyruvate oxidation & Krebs cycle, electron transport chain & chemiosmosis.

Glycolysis

Glycolysis oxidizes glucose to pyruvic acid, producing ATP and NADH in two stages: preparatory and energy-conserving.

• Preparatory stage: Glucose is phosphorylated and split.

• Energy-conserving stage: ATP and NADH are produced.

Pathways Additional to Glycolysis

• Pentose phosphate pathway: Breaks down pentose sugars, produces NADPH and ATP, provides intermediates for biosynthesis.

• Entner-Doudoroff pathway: Produces NADH, NADPH, and ATP, operates independently of glycolysis.

Aerobic Respiration: The Krebs Cycle

• Pyruvic acid oxidation: Pyruvate converted to acetyl-CoA.

• Krebs cycle: Acetyl-CoA oxidized, generating NADH, FADH2, and ATP.

Cellular Respiration

• Electrons liberated from molecules operate the electron transport chain.

• Aerobic respiration: Oxygen is the final electron acceptor.

• Anaerobic respiration: Final electron acceptor is not oxygen (e.g., nitrate, sulfate).

• ATP is generated by oxidative phosphorylation.

Aerobic Respiration: Electron Transport Chain

• Occurs in plasma membrane (prokaryotes) or inner mitochondrial membrane (eukaryotes).

• Carrier molecules (flavoproteins, cytochromes, ubiquinones) transfer electrons, releasing energy for ATP synthesis via chemiosmosis.

Aerobic Respiration Overall Reaction in Prokaryotes

• Overall equation:

• Oxygen is the final electron acceptor.

Anaerobic Respiration

• Final electron acceptor is not O2; yields less energy than aerobic respiration.

• Important for nitrogen and sulfur cycles.

ATP Yield during Prokaryotic Aerobic Respiration of One Glucose Molecule

Fermentation

• Releases energy from oxidation of organic molecules without oxygen.

• Does not use Krebs cycle or electron transport chain.

• Uses organic molecule as final electron acceptor; produces small amounts of ATP.

Lactic Acid Fermentation

• Homolactic fermentation: Produces only lactic acid.

• Heterolactic fermentation: Produces lactic acid and other compounds.

Alcohol Fermentation

• Produces ethanol and CO2; pyruvic acid is converted to acetaldehyde and CO2, then reduced to ethanol by NADH.

Some Industrial Uses for Different Types of Fermentations

Lipid and Protein Catabolism

• Proteins are degraded by extracellular proteases and peptidases into amino acids.

• Amino acids are deaminated, decarboxylated, and desulfurized to enter the Krebs cycle.

Biochemical Tests and Bacterial Identification

• Detecting Amino Acid Catabolizing Enzymes: Decarboxylation and dehydrogenation detected by pH indicator changes.

• Fermentation test: Detects acid production and gas formation (Durham tube).

• Oxidase test: Identifies bacteria with cytochrome c oxidase (e.g., Pseudomonas).

Photosynthesis

• Light-dependent reactions: Convert light energy to chemical energy (ATP, NADPH).

• Light-independent reactions: Use ATP and NADPH to reduce CO2 to sugar via the Calvin-Benson cycle.

• Oxygenic photosynthesis (plants, algae, cyanobacteria):

• Anoxygenic photosynthesis (purple/green sulfur bacteria):

Metabolic Diversity Among Organisms

• Phototrophs: Use light energy for ATP production.

• Photoautotrophs: Use light energy and CO2 for carbon fixation.

• Photoheterotrophs: Use light energy and organic compounds for carbon.

• Chemoautotrophs: Use inorganic chemicals for energy and CO2 for carbon.

• Chemoheterotrophs: Use organic chemicals for both energy and carbon; most medically important microbes are in this group.

The Integration of Metabolism

• Amphibolic pathways: Metabolic pathways that function in both anabolism and catabolism, sharing common intermediates.

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