Microbial Metabolism: Key Concepts and Pathways

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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, extract energy, and use it to build macromolecules and reproduce.
Energy is primarily stored in adenosine triphosphate (ATP).

Diagram of metabolism showing anabolism and catabolism Cellular diagram of catabolism and anabolism

Catabolism and Anabolism

Metabolic reactions are divided into two major classes: catabolic and anabolic pathways. Catabolism breaks down complex molecules, releasing energy, while anabolism builds complex molecules, requiring energy input.

Catabolic pathways: Break larger molecules into smaller products; exergonic (release energy).
Anabolic pathways: Synthesize large molecules from smaller products; endergonic (require energy).
ATP is generated during catabolism and consumed during anabolism.

Oxidation and Reduction Reactions

Redox reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are fundamental to energy extraction in cells and always occur simultaneously.

Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Cells use electron carriers such as NAD+, NADP+, and FAD.

Diagram of oxidation-reduction reactions Alternative diagram of oxidation-reduction reactions

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in ATP. ATP is produced by phosphorylation, which can occur via substrate-level, oxidative, or photophosphorylation.

Phosphorylation: Addition of phosphate to a substrate.
Three mechanisms: substrate-level, oxidative, and photophosphorylation.
Anabolic pathways use ATP by breaking a phosphate bond.

The Roles of Enzymes in Metabolism

Enzyme Structure and Function

Enzymes are organic catalysts that increase the likelihood of chemical reactions. They are classified based on their mode of action and can be proteins or RNA molecules (ribozymes).

Six categories: hydrolases, isomerases, ligases/polymerases, lyases, oxidoreductases, transferases.
Apoenzyme: Inactive protein portion.
Cofactor: Non-protein component (inorganic or organic).
Holoenzyme: Active enzyme with bound cofactors.

Structure of a holoenzyme

Enzyme Activity and Regulation

Enzyme activity is influenced by temperature, pH, substrate concentration, and inhibitors. Inhibitors block the active site but do not denature the enzyme.

Optimal conditions maximize enzyme activity.
Competitive inhibitors bind to the active site; noncompetitive inhibitors bind elsewhere.
Allosteric regulation involves binding at a site other than the active site, altering enzyme activity.

Effect of enzymes on activation energy Enzyme-substrate complex formation Steps in enzymatic activity Factors affecting enzyme activity: temperature, pH, substrate concentration Functional vs. denatured protein Competitive inhibition of enzyme activity Allosteric control of enzyme activity

Carbohydrate Catabolism

Glycolysis

Glycolysis is the primary pathway for glucose catabolism, occurring in the cytoplasm and resulting in pyruvic acid, ATP, and NADH.

Three stages: energy-investment, lysis, energy-conserving.
Net gain: 2 ATP, 2 NADH, 2 pyruvic acid.

Cellular Respiration

Cellular respiration completely oxidizes pyruvic acid to produce ATP via three stages: synthesis of acetyl-CoA, Krebs cycle, and electron transport chain.

Synthesis of acetyl-CoA: Produces acetyl-CoA, CO2, NADH.
Krebs cycle: Transfers energy to NAD+ and FAD, produces ATP, FADH2, NADH, CO2.
Electron transport chain (ETC): Series of carrier molecules; creates proton gradient for ATP synthesis.
Aerobic respiration uses O2 as final electron acceptor; anaerobic uses other molecules.

Formation of acetyl-CoA Krebs cycle diagram

Fermentation

Fermentation provides an alternative pathway for NAD+ regeneration when cellular respiration is not possible. It results in partial oxidation of sugars and produces various organic products.

Common products: lactic acid, ethanol, propionic acid, acetone.
Fermentation is essential for many industrial and food processes.

Fermentation pathway diagram Fermentation products and organisms

Other Catabolic Pathways

Lipids and proteins can also be catabolized for energy. Lipid catabolism involves hydrolysis and beta-oxidation, while protein catabolism involves deamination.

Lipids: Glycerol enters glycolysis; fatty acids undergo beta-oxidation.
Proteins: Proteases break down polypeptides; amino acids are deaminated and enter the Krebs cycle.

Catabolism of a fat molecule Protein catabolism

Photosynthesis

Overview and Structures

Photosynthesis is the process by which organisms synthesize organic molecules from CO2 and H2O using light energy. Chlorophylls and photosystems are key components.

Chlorophylls: Pigments that capture light energy.
Photosystems: Light-harvesting complexes embedded in thylakoid membranes.
Prokaryotes: Thylakoids are invaginations of the cytoplasmic membrane.
Eukaryotes: Thylakoids are within chloroplasts, arranged in grana.

Photosynthetic structures in a prokaryote Reaction center of photosystem

Light-Dependent and Light-Independent Reactions

Photosynthesis consists of light-dependent reactions (require light) and light-independent reactions (Calvin-Benson cycle).

Light-dependent: Generate ATP and NADPH via photophosphorylation.
Light-independent: Use ATP and NADPH to fix carbon and synthesize glucose.

Calvin-Benson cycle diagram

Other Anabolic Pathways

Gluconeogenesis, Fat, Amino Acid, and Nucleotide Biosynthesis

Anabolic reactions synthesize essential biomolecules using energy and precursor metabolites. Many pathways are amphibolic, proceeding in both directions.

Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.
Biosynthesis of fat: Formation of fatty acids and glycerol.
Amino acid synthesis: Amination and transamination reactions.
Nucleotide biosynthesis: Formation of DNA and RNA building blocks.

Gluconeogenesis diagram Biosynthesis of fat Synthesis of amino acids by amination and transamination Biosynthesis of nucleotides

Integration and Regulation of Metabolic Function

Regulation Mechanisms

Cells regulate metabolism by controlling enzyme synthesis and activity, isolating pathways in organelles, and using feedback inhibition.

Gene expression: Controls amount and timing of enzyme production.
Metabolic expression: Controls activity of enzymes once produced.
Feedback inhibition: Stops anabolic pathways when products are abundant.
Amphibolic pathways: Require different coenzymes for regulation.

Summary Table: Types of Metabolic Regulation

Regulation Type	Mechanism	Example
Gene Expression	Control of enzyme synthesis	Inducible operons
Metabolic Expression	Control of enzyme activity	Allosteric inhibition
Feedback Inhibition	Product inhibits pathway	End-product inhibition

Additional info: Amphibolic pathways are those that function in both catabolic and anabolic directions, depending on cellular needs.