Microbial Metabolism: Chemical Reactions and Pathways

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Microbial 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 a series of elementary statements that describe nutrient acquisition, energy transformation, and the synthesis of cellular components.

Catabolism: Breakdown of complex molecules into simpler ones, releasing energy (exergonic).
Anabolism: Synthesis of complex molecules from simpler ones, requiring energy (endergonic).
Energy is primarily stored and transferred in the form of adenosine triphosphate (ATP).
Cells use precursor metabolites, ATP, and enzymes to drive anabolic reactions.

Diagram of metabolism showing the relationship between catabolism, anabolism, ATP, and ADP Cellular overview of catabolism and anabolism, showing energy flow and macromolecule synthesis

Catabolism and Anabolism

Catabolic and anabolic pathways are the two major classes of metabolic reactions. Catabolic pathways break down larger molecules into smaller products and release energy, while anabolic pathways build larger molecules from smaller products and require energy input.

Catabolic reactions are exergonic (energy-releasing).
Anabolic reactions are endergonic (energy-consuming).

Redox Reactions in Metabolism

Oxidation and Reduction

Oxidation-reduction (redox) 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 by a molecule.
Reduction: Gain of electrons by a molecule.
Electron carriers: NAD+, NADP+, FAD (reduced to NADH, NADPH, FADH2).

Diagram of oxidation and reduction reactions showing electron transfer Alternative diagram of oxidation and reduction reactions

ATP Production and Energy Storage

ATP Synthesis

Organisms release energy from nutrients and store it in high-energy phosphate bonds of ATP. Phosphorylation is the process of adding an organic phosphate to a substrate. Cells phosphorylate ADP to ATP in three main ways:

Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation

Anabolic pathways use the energy of 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 a reaction by lowering the activation energy. They are classified into six categories based on their mode of action: hydrolases, isomerases, ligases/polymerases, lyases, oxidoreductases, and transferases.

Apoenzyme: Protein portion of an enzyme, inactive without cofactors.
Cofactor: Non-protein component (inorganic ions or coenzymes).
Holoenzyme: Complete, active enzyme with its cofactor.
Some enzymes are RNA molecules called ribozymes.

Diagram of enzyme structure showing apoenzyme, coenzyme, and holoenzyme Graph showing the effect of enzymes on activation energy Diagram of enzyme-substrate interaction Steps in enzymatic activity

Factors Affecting Enzyme Activity

Enzyme activity is influenced by several factors:

Temperature: Each enzyme has an optimal temperature.
pH: Each enzyme has an optimal pH range.
Enzyme and substrate concentrations: Activity increases with concentration up to a saturation point.
Inhibitors: Substances that block an enzyme’s active site without denaturing the enzyme. Types include competitive, noncompetitive, and allosteric inhibitors.

Graphs showing the effect of temperature, pH, and substrate concentration on enzyme activity Diagram comparing functional and denatured protein structures Diagram of competitive inhibition of enzyme activity Diagram of allosteric inhibition and activation

Carbohydrate Catabolism

Overview

Many organisms oxidize carbohydrates, especially glucose, as their primary energy source for anabolic reactions. Glucose catabolism occurs via two main processes: cellular respiration and fermentation.

Glycolysis

Glycolysis is the metabolic pathway that splits a six-carbon glucose into two three-carbon molecules of pyruvic acid. It occurs in the cytoplasm and involves substrate-level phosphorylation. The net gain is two ATP, two NADH, and two pyruvic acid molecules.

Divided into three stages: energy-investment, lysis, and energy-conserving stages.

Cellular Respiration

Cellular respiration completely oxidizes pyruvic acid to produce ATP through a series of redox reactions. It consists of three stages:

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

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

Synthesis of Acetyl-CoA

Produces two acetyl-CoA, two CO2, and two NADH per glucose molecule.

Krebs Cycle

Occurs in the cytosol of prokaryotes and mitochondrial matrix of eukaryotes.
Transfers energy to NAD+ and FAD.
Produces two ATP, two FADH2, six NADH, and four CO2 per glucose molecule.

Electron Transport Chain (ETC) and Chemiosmosis

Located in the inner mitochondrial membrane (eukaryotes) or cytoplasmic membrane (prokaryotes).
Electrons are passed through a series of carriers, creating a proton gradient used to generate ATP via ATP synthase (oxidative phosphorylation).
Aerobic respiration uses oxygen as the final electron acceptor; anaerobic respiration uses other molecules.
Total ATP yield from one glucose: ~34 ATP from ETC, plus 2 from glycolysis and 2 from Krebs cycle (total ~38 ATP in prokaryotes).

Fermentation

Fermentation is an alternative pathway used when cells cannot completely oxidize glucose by respiration. It regenerates NAD+ by transferring electrons to organic molecules, allowing glycolysis to continue. Common products include lactic acid, ethanol, and various other organic acids and alcohols.

Diagram of fermentation pathways from pyruvic acid Table of fermentation products and the organisms that produce them

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.

Diagram of fat molecule catabolism Diagram of protein catabolism

Photosynthesis

Overview

Photosynthesis is the process by which organisms synthesize organic molecules from inorganic CO2 using light energy. This process is essential for autotrophic organisms and involves two main stages: light-dependent and light-independent reactions.

Chemicals and Structures

Chlorophylls: Pigments that capture light energy, with a hydrocarbon tail and a magnesium-centered active site.
Photosystems: Complexes of chlorophyll and other pigments embedded in thylakoid membranes (in prokaryotes, invaginations of the cytoplasmic membrane; in eukaryotes, within chloroplasts).
Photosystems are arranged in stacks called grana; the stroma is the surrounding fluid.

Photosynthetic structures in a prokaryote Diagram of a photosystem and thylakoid membrane

Light-Dependent and Light-Independent Reactions

Light-dependent reactions: Use light energy to drive electron transport, generate ATP (photophosphorylation), and reduce NADP+ to NADPH.
Light-independent reactions: Use ATP and NADPH to fix carbon dioxide into glucose via the Calvin-Benson cycle.

Diagram of the Calvin-Benson cycle

Other Anabolic Pathways

Overview

Anabolic reactions synthesize complex molecules from simpler ones, requiring energy and precursor metabolites. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic if they can proceed in either direction.

Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.
Biosynthesis of fats: Formation of fatty acids and glycerol from acetyl-CoA and intermediates.
Amino acid synthesis: Involves amination and transamination reactions.
Nucleotide biosynthesis: Formation of nucleotides from precursor metabolites.

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

Integration and Regulation of Metabolic Function

Regulation Mechanisms

Cells regulate metabolism by controlling enzyme synthesis and activity. This ensures efficient use of resources and prevents wasteful overproduction of metabolites.

Cells synthesize enzymes only when substrates are available.
Preferentially catabolize the most energy-efficient substrate first.
Feedback inhibition slows or stops anabolic pathways when products are abundant.
Amphibolic pathways are regulated by requiring different coenzymes for each direction.
Eukaryotic cells compartmentalize metabolic pathways within organelles.

Two main regulatory mechanisms:

Control of gene expression: Regulates the amount and timing of enzyme production.
Control of metabolic expression: Regulates the activity of enzymes after they are produced.