Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all controlled biochemical reactions occurring within a microbe, with the ultimate function of reproducing the organism. It is guided by a series of elementary statements that describe nutrient acquisition, energy utilization, and cellular growth.

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

• Cells acquire nutrients and use energy from light or catabolism of nutrients.

• Energy is stored in adenosine triphosphate (ATP).

• Catabolism forms precursor metabolites; anabolism uses these, ATP, and enzymes to build macromolecules.

• Cells grow by assembling macromolecules and reproduce after doubling in size.

Catabolism and Anabolism

Metabolic reactions are divided into two major classes: catabolic and anabolic pathways.

• Catabolic pathways: Break down larger molecules into smaller products; these reactions are exergonic (release energy).

• Anabolic pathways: Synthesize large molecules from smaller products; these reactions are endergonic (require energy).

• ATP is central to energy transfer between catabolism and anabolism.

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are fundamental to energy production in cells.

• Redox reactions always occur simultaneously.

• Cells use electron carriers such as NAD+, NADP+, and FAD to transport electrons.

• Electron carriers often carry electrons in the form of hydrogen atoms.

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in high-energy phosphate bonds of ATP. ATP is produced by phosphorylation of ADP in three ways:

• Substrate-level phosphorylation: Direct transfer of phosphate between substrates.

• Oxidative phosphorylation: Uses energy from electron transport chain.

• Photophosphorylation: Uses light energy (in photosynthetic organisms).

The Roles of Enzymes in Metabolism

Enzymes are organic catalysts that increase the likelihood of chemical reactions. They are classified based on their mode of action:

• Hydrolases: Catalyze hydrolysis reactions.

• Isomerases: Catalyze isomerization changes within a molecule.

• Ligases/Polymerases: Join molecules together.

• Lyases: Break bonds without water.

• Oxidoreductases: Catalyze oxidation-reduction reactions.

• Transferases: Transfer functional groups between molecules.

Enzyme Structure

• Many enzymes are proteins; some require non-protein cofactors (inorganic ions or coenzymes).

• Apoenzyme: Inactive protein portion.

• Holoenzyme: Active enzyme formed by binding apoenzyme and cofactors.

• Some enzymes are RNA molecules called ribozymes.

Enzyme Function and Activity

• Enzymes lower activation energy, speeding up reactions.

• Enzyme-substrate specificity is key to function.

• Enzymatic activity is influenced by temperature, pH, substrate concentration, and inhibitors.

Factors Affecting Enzyme Activity

• Optimal temperature and pH maximize enzyme activity.

• Enzyme and substrate concentrations affect reaction rates.

• Inhibitors block enzyme active sites; types include competitive and noncompetitive inhibitors.

Carbohydrate Catabolism

Glucose Catabolism

Microbes commonly oxidize carbohydrates, especially glucose, as their primary energy source. Glucose catabolism occurs via cellular respiration or fermentation.

• Glycolysis: Splits glucose into two three-carbon molecules (pyruvic acid), yielding ATP and NADH.

• Three stages: energy-investment, lysis, and energy-conserving.

Cellular Respiration

Cellular respiration completely oxidizes pyruvic acid to produce ATP through a series of redox reactions.

1. Synthesis of acetyl-CoA: Pyruvic acid is converted to acetyl-CoA, CO2, and NADH.

2. Krebs cycle: Acetyl-CoA enters the cycle, transferring energy to NAD+ and FAD.

3. Electron transport chain (ETC): Electrons are passed through carrier molecules, generating a proton gradient and ATP.

Electron Transport and Chemiosmosis

• ETC is located in the cristae (eukaryotes) or cytoplasmic membrane (prokaryotes).

• Four carrier molecule categories: flavoproteins, ubiquinones, metal-containing proteins, cytochromes.

• Aerobic respiration uses oxygen as the final electron acceptor; anaerobic uses other molecules.

• Chemiosmosis: ATP is generated as protons flow through ATP synthase, driven by the proton gradient.

• Oxidative phosphorylation produces ~34 ATP per glucose.

Fermentation

Fermentation provides cells with an alternate source of NAD+ when cellular respiration is not possible. It involves partial oxidation of sugar, using an organic molecule as the final electron acceptor.

Other Catabolic Pathways

Lipid Catabolism

• Fats are hydrolyzed to glycerol and fatty acids.

• Fatty acids undergo beta-oxidation, producing acetyl-CoA for the Krebs cycle.

Protein Catabolism

• Proteins are broken down by proteases into amino acids.

• Amino acids are deaminated and enter the Krebs cycle.

Photosynthesis

Overview and Structures

Photosynthesis is the process by which organisms synthesize organic molecules from inorganic carbon dioxide, using light energy.

• Chlorophylls: Pigments that capture light energy; active site contains magnesium ion.

• Photosystems: Arrangements of chlorophyll and other pigments in thylakoid membranes.

• In prokaryotes, thylakoids are invaginations of the cytoplasmic membrane; in eukaryotes, they are in chloroplasts.

• Grana are stacks of thylakoids; stroma is the space between membranes.

Light-Dependent and Light-Independent Reactions

• Light-dependent reactions: Use light energy to generate ATP and NADPH via photophosphorylation.

• Light-independent reactions: Use ATP and NADPH to fix carbon dioxide into glucose (Calvin-Benson cycle).

Other Anabolic Pathways

Amphibolic Pathways

Anabolic reactions synthesize macromolecules using energy and metabolites. Many pathways are reversible (amphibolic).

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.

• Biosynthesis of fats: Formation of fatty acids and glycerol.

• Amino acid synthesis: Amination and transamination reactions.

• Nucleotide biosynthesis: Formation of DNA and RNA building blocks.

Integration and Regulation of Metabolic Function

Regulation Mechanisms

Cells regulate metabolism by controlling enzyme synthesis and activity, substrate availability, and feedback inhibition.

• Enzymes are synthesized or degraded as needed.

• Cells catabolize the most energy-efficient substrate first.

• Feedback inhibition slows or stops anabolic pathways when products are abundant.

• Eukaryotic cells compartmentalize metabolic pathways within organelles.

• Regulation occurs at the level of gene expression and metabolic expression.

Additional info: Amphibolic pathways are regulated by requiring different coenzymes for each direction, ensuring metabolic flexibility and efficiency.