Microbial Metabolism: Chemical Reactions and Pathways

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Basic Chemical Reactions Underlying Metabolism

Overview of Metabolism

Metabolism is the sum of all controlled biochemical reactions that occur within a microbe. The ultimate function of metabolism is to enable the organism to reproduce. Metabolic processes are guided by several elementary principles, including nutrient acquisition, energy generation and storage, and the synthesis of macromolecules.

Catabolism: The breakdown of complex molecules into simpler ones, releasing energy (exergonic).
Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input (endergonic).
ATP acts as the main energy currency, linking catabolic and anabolic reactions.

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

Eight Elementary Statements of Metabolic Processes

Every cell acquires nutrients.
Metabolism requires energy from light or catabolism of nutrients.
Energy is stored in ATP.
Cells catabolize nutrients to form precursor metabolites.
Precursor metabolites, ATP, and enzymes are used in anabolic reactions.
Enzymes plus ATP form macromolecules.
Cells grow by assembling macromolecules.
Cells reproduce once they have doubled in size.

Oxidation and Reduction Reactions

Redox Reactions in Metabolism

Oxidation and reduction reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions always occur simultaneously and are essential for energy transfer in cells. Cells use electron carriers such as NAD+, NADP+, and FAD to shuttle electrons.

Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Electron carriers: NAD+, NADP+, FAD (reduced to NADH, NADPH, FADH2).

Redox reaction diagram Alternative redox reaction diagram

ATP Production and Energy Storage

Mechanisms of ATP Synthesis

Organisms release energy from nutrients and store it in high-energy phosphate bonds of ATP. Phosphorylation is the process of adding an inorganic phosphate to ADP to form ATP. There are three main mechanisms:

Substrate-level phosphorylation: Direct transfer of phosphate between two substrates.
Oxidative phosphorylation: Energy from redox reactions of the electron transport chain is used to add phosphate to ADP.
Photophosphorylation: Light energy is used to phosphorylate ADP.

The Roles of Enzymes in Metabolism

Enzyme Structure and Function

Enzymes are organic catalysts that increase the likelihood of a reaction by lowering the activation energy. They are highly specific for their substrates and are classified into six categories based on their mode of action: hydrolases, isomerases, ligases/polymerases, lyases, oxidoreductases, and transferases.

Apoenzyme: Protein portion, inactive without cofactor.
Cofactor: Non-protein component (inorganic ion or coenzyme).
Holoenzyme: Complete, active enzyme with its cofactor.
Ribozymes: RNA molecules with catalytic activity.

Structure of a holoenzyme Effect of enzymes on activation energy Enzyme-substrate complex formation Steps in enzymatic activity

Factors Affecting Enzyme Activity

Enzyme activity is influenced by several factors, including temperature, pH, enzyme and substrate concentrations, and the presence of inhibitors. Inhibitors can block the active site (competitive inhibition) or bind elsewhere (allosteric/noncompetitive inhibition).

Temperature: Each enzyme has an optimal temperature.
pH: Each enzyme has an optimal pH.
Substrate concentration: Activity increases with substrate concentration up to a saturation point.
Inhibitors: Competitive, noncompetitive (allosteric), and feedback inhibition.

Graphs of enzyme activity vs. temperature, pH, and substrate concentration Functional vs. denatured protein structure Competitive inhibition of enzyme activity Allosteric inhibition and activation

Carbohydrate Catabolism

Glycolysis

Glycolysis is the metabolic pathway that splits a six-carbon glucose into two three-carbon pyruvic acid molecules. It occurs in the cytoplasm and results in a net gain of two ATP, two NADH, and two pyruvic acid molecules. Glycolysis consists of three stages: energy-investment, lysis, and energy-conserving.

Cellular Respiration

Cellular respiration completely oxidizes pyruvic acid to produce ATP through three stages:

Synthesis of acetyl-CoA: Pyruvic acid is converted to acetyl-CoA, producing NADH and CO2.
Krebs Cycle: Acetyl-CoA is oxidized, generating ATP, NADH, FADH2, and CO2.
Electron Transport Chain (ETC): Electrons from NADH and FADH2 are transferred through a series of carriers, generating a proton gradient used to produce ATP (chemiosmosis).

Formation of acetyl-CoA Krebs cycle diagram

Fermentation

Fermentation is an alternative pathway used when cells cannot completely oxidize glucose by respiration. It regenerates NAD+ from NADH, allowing glycolysis to continue. Fermentation produces various end products, such as lactic acid, ethanol, and other organic acids, depending on the organism.

Fermentation pathway diagram Fermentation products and producing organisms

Other Catabolic Pathways

Lipid Catabolism: Lipids are hydrolyzed into glycerol and fatty acids. Fatty acids undergo beta-oxidation to form acetyl-CoA, which enters the Krebs cycle.
Protein Catabolism: Proteins are broken down into amino acids, which are deaminated and converted into intermediates for 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 inorganic CO2 using light energy. Chlorophylls are the main pigments involved, and photosystems are complexes of chlorophyll and other pigments embedded in thylakoid membranes.

Photosystem I (PS I) and Photosystem II (PS II) absorb light and drive redox reactions to generate ATP and NADPH.
Light-dependent reactions require light to generate ATP and NADPH.
Light-independent reactions (Calvin-Benson cycle) use ATP and NADPH to fix carbon dioxide into glucose.

Photosynthetic structures in a prokaryote Reaction center of photosystem Calvin-Benson cycle diagram

Other Anabolic Pathways

Amphibolic Pathways and Biosynthesis

Anabolic reactions synthesize complex molecules using energy and metabolites derived from catabolic pathways. Many pathways are amphibolic, meaning they can function in both directions. Examples include gluconeogenesis, fatty acid synthesis, amino acid synthesis (amination and transamination), and nucleotide biosynthesis.

Gluconeogenesis pathway 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. Regulation occurs at the genetic level (gene expression) and at the protein level (allosteric regulation, feedback inhibition). Eukaryotic cells compartmentalize metabolic pathways within organelles, and cells preferentially use the most energy-efficient substrates available.

Feedback inhibition: End product of a pathway inhibits an early enzyme, preventing overproduction.
Allosteric regulation: Effectors bind to enzymes at sites other than the active site, altering activity.
Control of gene expression: Cells regulate the amount and timing of enzyme production.
Control of metabolic expression: Cells regulate the activity of enzymes after they are produced.