Microbial Metabolism

Big Picture: Metabolism

Metabolism encompasses all the chemical reactions that occur within a cell, involving both the buildup and breakdown of nutrients. 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.

• Catabolism: Breakdown of complex molecules to release energy.

• Anabolism: Synthesis of complex molecules using energy and building blocks.

Catabolic and Anabolic Reactions

Catabolic and anabolic reactions are the two main types of metabolic processes in cells.

• Catabolism: Exergonic process that breaks down molecules (e.g., glucose to CO2 and H2O), releasing energy.

• Anabolism: Endergonic process that uses energy to build macromolecules (e.g., proteins from amino acids).

• 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 without being consumed. They act on specific substrates and lower the activation energy required for reactions.

• Catalysts: Substances that increase reaction rates without being altered.

• Enzyme-substrate complex: Substrate binds to the enzyme's active site, is transformed, and released as product; the enzyme remains unchanged.

Collision Theory

Chemical reactions occur when atoms, ions, and molecules collide with sufficient energy (activation energy). The reaction rate is the frequency of effective collisions and can be increased by enzymes, temperature, pressure, or concentration.

Enzyme Specificity and Efficiency

• Specificity: Enzymes are specific for particular substrates.

• Turnover number: Number of substrate molecules converted to product 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 and extreme pH can denature proteins.

• Substrate concentration: At high substrate concentration (saturation), the enzyme catalyzes at its maximum rate.

• Inhibitors: Substances that decrease enzyme activity.

Enzyme Inhibition

• Competitive inhibitors: Compete with substrate for the active site.

• Noncompetitive inhibitors: Bind to an allosteric site, changing the enzyme's shape and rendering it nonfunctional. Can be reversible or irreversible.

• Feedback inhibition: End-product of a pathway allosterically inhibits an enzyme from earlier in the pathway.

Ribozymes

• RNA molecules that function as catalysts by binding to substrates and acting upon them.

• Not used up in the reaction; involved in cutting and splicing RNA and protein synthesis in ribosomes.

Oxidation-Reduction (Redox) Reactions

• Oxidation: Removal of electrons

• Reduction: Gain of electrons

• Redox reaction: Paired oxidation and reduction reactions

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

The Generation of ATP

ATP is generated by the phosphorylation of ADP with the input of energy:

$\text{ADP} + \text{Energy} + P_i \rightarrow \text{ATP}$

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

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

• Photophosphorylation: Occurs in photosynthetic cells; light energy is converted to chemical energy (ATP) during electron transfer from chlorophyll.

Metabolic Pathways of Energy Production

• Energy is extracted from organic compounds and stored as ATP through:

• Glycolysis

• Fermentation

• Krebs cycle

• Oxidative phosphorylation

• Photophosphorylation

Carbohydrate Catabolism

The breakdown of carbohydrates to release energy typically occurs in major stages:

• Glycolysis & Fermentation

• Pyruvate Oxidation & Krebs cycle (Citric acid cycle)

• Electron transport chain & chemiosmosis

Glycolysis

The oxidation of glucose to pyruvic acid produces ATP and NADH in two main stages:

• Preparatory stage: Glucose is phosphorylated and split into two 3-carbon compounds.

• Energy-conserving stage: The 3-carbon compounds are oxidized, generating ATP and NADH.

Pathways Additional to Glycolysis

• Pentose phosphate pathway: Breaks down five-carbon sugars and/or glucose, producing NADPH and ATP; provides intermediates for biosynthesis.

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

Aerobic Respiration: The Krebs Cycle

• Pyruvic acid oxidation: Pyruvate is converted to acetyl-CoA, producing NADH and CO2.

• Krebs cycle: Acetyl-CoA is oxidized, generating NADH, FADH2, ATP, and CO2.

Cellular Respiration

• Electrons liberated from the oxidation of molecules operate an electron transport chain.

• Aerobic respiration: Uses O2 as the final electron acceptor.

• Anaerobic respiration: Uses an inorganic molecule other than O2 as the final electron acceptor.

• ATP is generated by oxidative phosphorylation.

Aerobic Respiration: Electron Transport Chain

• Occurs in the plasma membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.

• Carrier molecules (flavoproteins, cytochromes, ubiquinones) are oxidized and reduced as electrons are passed down the chain.

• Energy released is used to produce ATP by chemiosmosis.

Aerobic Respiration: Chemiosmosis

• Electrons from NADH pass down the electron transport chain, pumping protons across the membrane and establishing a proton gradient (proton motive force).

• Protons diffuse through ATP synthase, releasing energy to synthesize ATP.

Oxidative Phosphorylation: Electron Transport and Chemiosmotic Generation of ATP

• Electron transport and chemiosmosis together generate the majority of ATP during aerobic respiration.

Aerobic Respiration Overall Reaction in Prokaryotes

$\mathrm{C_6H_{12}O_6} + 6\,\mathrm{O_2} + 38\,\mathrm{ADP} + 38\,P_i \rightarrow 6\,\mathrm{CO_2} + 6\,\mathrm{H_2O} + 38\,\mathrm{ATP}$

The final electron acceptor in the electron transport chain is molecular oxygen.

Anaerobic Respiration

• The final electron acceptor is NOT O2.

• Yields less energy than aerobic respiration.

• Important for nitrogen and sulfur cycles in nature.

ATP Yield during Prokaryotic Aerobic Respiration of One Glucose Molecule

Additional info: Standardized ATP yields per NADH: Mitochondrial NADH (eukaryotes/prokaryotes): ~2.5 ATP; Prokaryotic NADH (glycolysis): ~2.5 to 3 ATP (no transport cost).

Fermentation

• Releases energy from the oxidation of organic molecules.

• Does not require oxygen, Krebs cycle, or electron transport chain.

• Uses an organic molecule as the final electron acceptor.

• Produces only small amounts of ATP.

• Lactic acid fermentation: Produces lactic acid.

• Homolactic fermentation: Produces only lactic acid.

• Heterolactic fermentation: Produces lactic acid and other compounds.

• Alcohol fermentation: Produces ethanol and CO2.

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 cross the plasma membrane and are deaminated, decarboxylated, or desulfurized to enter the Krebs cycle.

Biochemical Tests and Bacterial Identification

• Detection of amino acid catabolizing enzymes: Decarboxylation and dehydrogenation reactions change pH indicators in test tubes.

• Fermentation test: Detects acid and gas production from carbohydrate or protein catabolism; uses pH indicators and Durham tubes.

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

Photosynthesis

• Light-dependent reactions: Convert light energy into chemical energy (ATP and NADPH).

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

• Oxygenic photosynthesis: (plants, algae, cyanobacteria):

$6\,\mathrm{CO_2} + 12\,\mathrm{H_2O} + \text{Light energy} \rightarrow \mathrm{C_6H_{12}O_6} + 6\,\mathrm{H_2O} + 6\,\mathrm{O_2}$

• Anoxygenic photosynthesis: (purple sulfur/green sulfur bacteria):

$6\,\mathrm{CO_2} + 12\,\mathrm{H_2S} + \text{Light energy} \rightarrow \mathrm{C_6H_{12}O_6} + 6\,\mathrm{H_2O} + 12\,\mathrm{S}$