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 and use energy from light or catabolism.
Energy is stored in ATP (adenosine triphosphate).
Catabolism breaks down nutrients to form precursor metabolites.
Anabolism uses precursor metabolites, ATP, and enzymes to build macromolecules.
Cells grow by assembling macromolecules and reproduce after doubling in size.

Diagram of metabolism showing the relationship between catabolism and anabolism Cellular diagram showing catabolic and anabolic processes

Catabolism and Anabolism

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

Catabolic pathways: Break larger molecules into smaller products; exergonic (release energy).
Anabolic pathways: Synthesize large molecules from smaller products; endergonic (require energy).
ATP is central to energy transfer between these pathways.

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 (NAD+, NADP+, FAD) to transport electrons.
Oxidation: Loss of electrons; Reduction: Gain of electrons.

Diagram of oxidation and reduction reactions Alternative diagram of oxidation and 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 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 a reaction. They are classified based on their mode of action:

Hydrolases: Catalyze hydrolysis reactions.
Isomerases: Catalyze isomerization changes.
Ligases/Polymerases: Join molecules together.
Lyases: Split molecules without water.
Oxidoreductases: Catalyze redox reactions.
Transferases: Transfer functional groups.

Enzyme Structure

Many enzymes are proteins, some require cofactors (inorganic ions or coenzymes) to be active. The combination of apoenzyme and cofactor forms a holoenzyme. Some enzymes are RNA molecules called ribozymes.

Diagram of holoenzyme structure

Enzyme Function and Activity

Enzymes lower the activation energy required for reactions, facilitating faster biochemical processes.

Graph showing effect of enzymes on activation energy Diagram of enzyme-substrate complex formation Steps in enzymatic activity

Factors Affecting Enzyme Activity

Several factors influence the rate of enzymatic reactions:

Temperature
pH
Enzyme and substrate concentrations
Presence of inhibitors

Graphs showing effects of temperature, pH, and substrate concentration on enzyme activity Diagram of functional and denatured protein

Enzyme Inhibition

Inhibitors block an enzyme’s active site without denaturing the enzyme. Types include:

Competitive inhibitors: Compete with substrate for active site.
Noncompetitive inhibitors: Bind elsewhere, altering enzyme function.
Allosteric inhibitors: Bind to allosteric site, changing enzyme shape.

Diagram of competitive inhibition Diagram of allosteric inhibition and activation

Carbohydrate Catabolism

Glucose Catabolism

Glucose is the primary energy source for many organisms. It is catabolized by cellular respiration and fermentation.

Glycolysis: Splits glucose into two pyruvic acid molecules, yielding ATP and NADH.
Three stages: Energy-investment, lysis, and energy-conserving.

Cellular Respiration

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

Synthesis of acetyl-CoA
Krebs cycle
Electron transport chain (ETC)

Formation of acetyl-CoA from pyruvic acid Diagram of the Krebs cycle

Electron Transport Chain and Chemiosmosis

The ETC is a series of carrier molecules that pass electrons to a final electron acceptor, generating a proton gradient used for ATP synthesis (oxidative phosphorylation).

Aerobic respiration: Oxygen is the final electron acceptor.
Anaerobic respiration: Other molecules serve as final electron acceptors.
~34 ATP molecules are produced from one glucose molecule.

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.

Diagram of fermentation pathways Fermentation products and organisms

Other Catabolic Pathways

Lipid Catabolism

Lipids are hydrolyzed into glycerol and fatty acids, which enter glycolysis and the Krebs cycle, respectively.

Diagram of fat molecule catabolism

Protein Catabolism

Proteins are broken down into amino acids, which are deaminated and enter the Krebs cycle.

Diagram of protein catabolism

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.
Photosystems: Arrangements of chlorophyll and other pigments in thylakoid membranes.
Photosystems are organized in stacks called grana; stroma is the space between membranes.

Photosynthetic structures in a prokaryote Diagram of photosystem reaction center

Light-Dependent and Light-Independent Reactions

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

Light-dependent reactions use photophosphorylation to generate ATP.
Light-independent reactions use ATP and NADPH to fix carbon dioxide into glucose.

Diagram of the Calvin-Benson cycle

Other Anabolic Pathways

Gluconeogenesis

Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors, often reversing catabolic pathways.

Diagram of gluconeogenesis

Biosynthesis of Fat and Amino Acids

Fatty acids and amino acids are synthesized from intermediates of glycolysis and the Krebs cycle.

Diagram of fat biosynthesis Diagram of amino acid synthesis by amination and transamination

Biosynthesis of Nucleotides

Nucleotides are synthesized from intermediates of glycolysis, the pentose phosphate pathway, and the Krebs cycle.

Diagram of nucleotide biosynthesis

Integration and Regulation of Metabolic Function

Regulation Mechanisms

Cells regulate metabolism by controlling enzyme synthesis and activity, using feedback inhibition and compartmentalization in eukaryotes.

Control of gene expression: Regulates amount and timing of enzyme production.
Control of metabolic expression: Regulates activity of enzymes once produced.
Feedback inhibition: Slows or stops anabolic pathways when products are abundant.
Amphibolic pathways: Reactions that can proceed in either direction, regulated by different coenzymes.

Additional info: Amphibolic pathways are central to metabolic flexibility, allowing cells to adapt to changing nutrient availability and energy demands.