Microbial Metabolism: Pathways, Energy, and Biosynthesis

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Microbial Metabolism

Definition and Importance

Metabolism is the sum of all chemical reactions occurring within a microbial cell. These reactions are essential for energy generation, biosynthesis, and cellular maintenance. Microbial metabolism is divided into two main types: catabolism (breakdown of molecules to release energy) and anabolism (synthesis of complex molecules from simpler ones).

Dissimilative pathways: Energy-yielding reactions (catabolism).
Assimilative pathways: Biosynthetic reactions (anabolism).

Diagram showing catabolism and anabolism

Importance of microbial metabolism:

Drives biogeochemical cycles (carbon, nitrogen, sulfur cycles).
Essential for wastewater treatment and bioremediation (e.g., degradation of petroleum hydrocarbons, pesticides, plastics).
Critical in the food industry (production of cheese, alcohol, vinegar, yogurt, bread).
Maintains the human microbiome (microflora outnumber human cells by 10:1).
Production of small biological molecules (vitamins, amino acids, antibiotics, vaccines, biopolymers, restriction enzymes).

Oil spill bioremediation Microbial nitrogen cycle

Organization of Metabolic Pathways

Metabolic Pathways and Enzyme Function

Metabolic pathways are organized sequences of enzymatic reactions, each catalyzed by a specific enzyme. Pathways can be linear, branched, or cyclic, and are tightly regulated to meet cellular needs.

Substrate: The starting molecule of a pathway.
Product: The final molecule produced.
Each step is catalyzed by a specific enzyme.

Simple metabolic pathway diagram Linear, branched, and cyclic metabolic pathways

Thermodynamics and Enzyme Catalysis

First Law of Thermodynamics

The first law of thermodynamics states that energy cannot be created or destroyed, only transformed from one form to another. In biological systems, chemical energy is often converted to heat, mechanical work, or stored in chemical bonds.

Energy transformations are central to metabolism.
Some energy is always lost as heat during these transformations.

Energy transfer and heat loss in metabolism

Activation Energy and Enzymes

Activation energy (Ea) is the energy required to initiate a chemical reaction. Enzymes act as biological catalysts, lowering the activation energy and increasing the rate of reactions without being consumed.

Enzymes do not alter the overall free energy change (ΔG) of a reaction.
They provide a specific environment for the reaction to occur efficiently.

Activation energy diagram with and without enzyme

Catabolism: Energy Release and Conservation

Overview of Catabolic Pathways

Catabolism involves the breakdown of complex molecules into simpler ones, releasing energy that is conserved as ATP or other energy-rich compounds. Major catabolic processes include aerobic respiration, anaerobic respiration, and fermentation.

Aerobic respiration: Uses oxygen as the terminal electron acceptor.
Anaerobic respiration: Uses other inorganic molecules (e.g., NO3-, SO42-, CO2) as terminal electron acceptors.
Fermentation: Organic molecules serve as both electron donors and acceptors; less ATP is produced.

Aerobic respiration equation

Nutritional Types of Microorganisms

Microorganisms are classified based on their sources of carbon, energy, and electrons:

Type	Carbon Source	Energy Source	Electron Source
Autotrophs	CO2	Light or chemicals	Inorganic or organic molecules
Heterotrophs	Organic compounds	Light or chemicals	Organic molecules
Phototrophs	CO2 or organic	Light	Varies
Chemotrophs	CO2 or organic	Chemicals	Varies
Lithotrophs	CO2 or organic	Light or chemicals	Inorganic molecules
Organotrophs	CO2 or organic	Light or chemicals	Organic molecules

Table of sources of carbon, energy, and electrons Classification of nutritional types

Major Catabolic Pathways

Glycolysis: The breakdown of glucose to pyruvate, generating ATP and NADH.
Krebs (TCA) cycle: Oxidizes acetyl-CoA to CO2, generating NADH, FADH2, and ATP/GTP.
Electron Transport Chain (ETC): Transfers electrons from NADH/FADH2 to terminal electron acceptors, generating a proton motive force (PMF) used to synthesize ATP.

ATP Synthesis

ATP synthase is a membrane-bound enzyme complex that synthesizes ATP from ADP and inorganic phosphate (Pi) using the energy stored in the proton motive force (PMF).

Protons flow through ATP synthase, driving the phosphorylation of ADP.
ATP turnover in bacteria is extremely high, reflecting the central role of ATP in metabolism.

ATP synthase structure and function

Redox Balance and Fermentation

Redox Balance

Cells maintain a balance between oxidized (NAD+) and reduced (NADH) forms of electron carriers. During fermentation, NAD+ is regenerated by transferring electrons to organic acceptors, producing end products such as ethanol or lactate.

Alcohol fermentation: Saccharomyces species convert glucose to ethanol and CO2, regenerating NAD+.
Fermentation yields less ATP than respiration.

Phototrophy and Chemolithotrophy

Phototrophy

Phototrophs capture light energy and convert it to chemical energy. Photosynthesis consists of light reactions (energy capture) and dark reactions (CO2 fixation).

Oxygenic phototrophy: Generates O2 (e.g., cyanobacteria, algae).
Anoxygenic phototrophy: Does not generate O2 (e.g., purple and green bacteria).
Key pigments: chlorophylls.

Chemolithotrophy

Chemolithotrophs obtain energy by oxidizing inorganic compounds (e.g., H2, Fe2+, NH3).

Common in environmental processes such as nitrification and sulfur oxidation.

Anabolism: Biosynthesis of Cellular Components

Overview of Anabolism

Anabolism is the synthesis of complex molecules from simpler precursors, requiring energy (usually from ATP) and reducing power (NADPH). Anabolic pathways are essential for cell growth, maintenance, and division.

Precursor metabolites: Intermediates from central metabolic pathways used as building blocks for biosynthesis.
CO2 fixation: Conversion of inorganic carbon into organic molecules (e.g., Calvin-Benson cycle).
Cell wall synthesis, nitrogen assimilation, and anaplerotic reactions are key anabolic processes.

Principles Governing Biosynthesis

Macromolecules are synthesized from a limited set of monomers, conserving energy and genetic resources.
Some enzymes function in both catabolic and anabolic pathways, but key steps are catalyzed by unique enzymes to ensure directionality.
Catabolic and anabolic pathways are often physically separated and use different cofactors (NADH for catabolism, NADPH for anabolism).

CO2 Fixation Pathways

Calvin-Benson cycle: Main pathway for CO2 fixation in autotrophs; occurs in the stroma of chloroplasts or carboxysomes in prokaryotes.
Other pathways: Reductive TCA cycle, hydroxypropionate bi-cycle, reductive acetyl-CoA pathway.

Three ATP and two NADPH are consumed for each CO2 fixed in the Calvin cycle.

Summary Table: Sources of Carbon, Energy, and Electrons

Type	Carbon Source	Energy Source	Electron Source
Autotrophs	CO2	Light or chemicals	Inorganic or organic molecules
Heterotrophs	Organic compounds	Light or chemicals	Organic molecules
Phototrophs	CO2 or organic	Light	Varies
Chemotrophs	CO2 or organic	Chemicals	Varies
Lithotrophs	CO2 or organic	Light or chemicals	Inorganic molecules
Organotrophs	CO2 or organic	Light or chemicals	Organic molecules

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