Microbial Metabolism: Key Concepts and Pathways

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Basic Chemical Reactions Underlying Metabolism

Overview of Metabolism

Metabolism encompasses all controlled biochemical reactions occurring within a microbe, ultimately enabling reproduction and survival. It is guided by fundamental principles that ensure efficient nutrient acquisition, energy management, and cellular growth.

Metabolism: The sum of all chemical reactions in a cell, divided into catabolic (breakdown) and anabolic (synthesis) pathways.
Cells acquire nutrients, extract energy, and use it to build macromolecules and reproduce.
Energy is primarily stored and transferred via adenosine triphosphate (ATP).

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

Catabolism and Anabolism

Metabolic reactions are classified into two major types: catabolism and anabolism. These processes are interconnected, with catabolism providing energy and building blocks for anabolism.

Catabolic pathways: Break down complex molecules into simpler ones, releasing energy (exergonic).
Anabolic pathways: Build complex molecules from simpler ones, requiring energy input (endergonic).
ATP acts as the energy currency, linking catabolic and anabolic reactions.

Oxidation and Reduction Reactions

Redox reactions are central to metabolism, involving the transfer of electrons between molecules. These reactions are always coupled, with one molecule being oxidized and another reduced.

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

Redox reaction diagram Alternate redox reaction diagram

ATP Production and Energy Storage

Cells release energy from nutrients and store it in ATP through phosphorylation. There are three main mechanisms for ATP synthesis:

Substrate-level phosphorylation: Direct transfer of phosphate to ADP from a substrate.
Oxidative phosphorylation: ATP generated via electron transport chain and chemiosmosis.
Photophosphorylation: ATP produced using light energy (in photosynthetic organisms).

The Roles of Enzymes in Metabolism

Enzymes are biological catalysts that accelerate metabolic reactions. They are classified based on their mode of action and require cofactors for activity.

Enzyme categories: Hydrolases, Isomerases, Ligases/Polymerases, Lyases, Oxidoreductases, Transferases.
Apoenzyme: Protein portion, inactive without cofactors.
Holoenzyme: Active enzyme with cofactors (inorganic or organic).
Some enzymes are RNA molecules called ribozymes.

Structure of a holoenzyme Enzyme effect on activation energy Enzyme-substrate complex diagram Steps in enzymatic activity

Factors Affecting Enzyme Activity

Enzyme activity is influenced by several factors, including temperature, pH, substrate concentration, and inhibitors.

Temperature and pH: Each enzyme has optimal conditions for activity.
Substrate concentration: Activity increases with substrate until saturation is reached.
Inhibitors: Block enzyme activity without denaturing the enzyme. Types include competitive, noncompetitive, and allosteric inhibitors.

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

Carbohydrate Catabolism

Glucose Catabolism: Glycolysis, Respiration, and Fermentation

Microbes commonly use carbohydrates, especially glucose, as energy sources. Glucose catabolism occurs via glycolysis, cellular respiration, or fermentation.

Glycolysis: Splits glucose into two pyruvic acid molecules, yielding ATP and NADH.
Cellular respiration: Complete oxidation of pyruvic acid to CO2 and H2O, producing maximal ATP.
Fermentation: Partial oxidation of glucose, regenerating NAD+ and producing organic end products.

Stages of Glycolysis

Energy-investment stage: ATP is used to phosphorylate glucose.
Lysis stage: Glucose is split into two three-carbon molecules.
Energy-conserving stage: ATP and NADH are produced.

Cellular Respiration

Cellular respiration consists of three main stages: synthesis of acetyl-CoA, Krebs cycle, and electron transport chain.

Synthesis of acetyl-CoA: Pyruvic acid is converted to acetyl-CoA, CO2, and NADH.
Krebs cycle: Acetyl-CoA is oxidized, producing ATP, NADH, FADH2, and CO2.
Electron transport chain (ETC): Electrons are transferred through carrier molecules, generating a proton gradient for ATP synthesis.

Formation of acetyl-CoA Krebs cycle diagram

Electron Transport and Chemiosmosis

ETC: Located in the cristae (eukaryotes) or cytoplasmic membrane (prokaryotes).
Carrier molecules: Flavoproteins, ubiquinones, metal-containing proteins, cytochromes.
Aerobic respiration: Oxygen is the final electron acceptor.
Anaerobic respiration: Other molecules serve as final electron acceptors.
Chemiosmosis: ATP is synthesized as protons flow through ATP synthase.
Total ATP yield from one glucose: ~34 ATP (oxidative phosphorylation).

Alternative Pathways and Fermentation

Pentose phosphate pathway and Entner-Doudoroff pathway: Provide alternative routes for glucose catabolism, yielding different metabolites and less ATP.
Fermentation: Regenerates NAD+ for glycolysis, producing organic acids, alcohols, or gases.

Fermentation pathway diagram Fermentation products and organisms

Other Catabolic Pathways

Lipid Catabolism

Lipids are hydrolyzed into glycerol and fatty acids. Glycerol enters glycolysis, while fatty acids undergo beta-oxidation to produce acetyl-CoA for the Krebs cycle.

Catabolism of a fat molecule

Protein Catabolism

Proteins are broken down into amino acids, which are deaminated and converted into intermediates for the Krebs cycle.

Protein catabolism diagram

Photosynthesis

Overview and Structures

Photosynthetic organisms convert light energy into chemical energy, synthesizing carbohydrates from CO2 and H2O. Chlorophylls and photosystems are key components.

Chlorophylls: Pigments with a magnesium-centered active site, absorb light at specific wavelengths.
Photosystems: Complexes of chlorophyll and other pigments embedded in thylakoid membranes.
In prokaryotes, thylakoids are invaginations of the cytoplasmic membrane; in eukaryotes, they are within chloroplasts.

Photosynthetic structures in a prokaryote Reaction center of photosystem

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).

Calvin-Benson cycle diagram

Other Anabolic Pathways

Gluconeogenesis, Fat, Amino Acid, and Nucleotide Biosynthesis

Anabolic pathways synthesize essential biomolecules using energy from ATP and precursor metabolites. Many pathways are reversible (amphibolic).

Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.
Biosynthesis of fats: Formation of fatty acids and glycerol from intermediates.
Amino acid synthesis: Amination and transamination reactions produce amino acids from Krebs cycle intermediates.
Nucleotide biosynthesis: Pathways generate purine and pyrimidine nucleotides for DNA and RNA.

Gluconeogenesis diagram Biosynthesis of fat Amination and transamination Biosynthesis of nucleotides

Integration and Regulation of Metabolic Function

Metabolic Regulation

Cells regulate metabolism by controlling enzyme production and activity, substrate availability, and feedback mechanisms.

Gene expression control: Regulates the amount and timing of enzyme production.
Metabolic expression control: Modifies enzyme activity post-production.
Feedback inhibition: End products inhibit pathway enzymes to prevent overproduction.
Compartmentalization: Eukaryotes isolate metabolic pathways in organelles.

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