Microbial Metabolism: Core 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 supporting growth and reproduction. It is divided into two major classes: catabolism (breakdown of molecules to release energy) and anabolism (synthesis of complex molecules using energy).

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

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

Eight Elementary Statements Guiding 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.

Basic Chemical Reactions Underlying Metabolism

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are always coupled and are essential for energy transfer in cells.

Electron carriers: NAD+, NADP+, and FAD are key molecules that shuttle electrons during metabolic reactions.
Oxidation: Loss of electrons.
Reduction: Gain of electrons.

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

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in the high-energy phosphate bonds of ATP. ATP is generated by phosphorylation of ADP in three main ways:

Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation

Anabolic pathways use the energy stored in ATP by breaking a phosphate bond.

The Roles of Enzymes in Metabolism

Enzymes are organic catalysts that increase the likelihood of chemical reactions by lowering activation energy. They are highly specific for their substrates and are classified based on the reactions they catalyze.

Hydrolases: Catalyze hydrolysis reactions.
Isomerases: Rearrange atoms within a molecule.
Ligases/Polymerases: Join molecules together.
Lyases: Split molecules without water.
Oxidoreductases: Catalyze redox reactions.
Transferases: Transfer functional groups between molecules.

Class	Type of Reaction Catalyzed	Example
Hydrolase	Hydrolysis (catabolic)	Lipase—breakdown of lipid molecules
Isomerase	Rearrangement of atoms within a molecule	Phosphoglucoisomerase—conversion of glucose-6-phosphate to fructose-6-phosphate during glycolysis
Ligase/Polymerase	Joining two molecules together (anabolic)	Acetyl-CoA synthetase—combines acetate and CoA to form acetyl-CoA during Krebs cycle
Lyase	Splitting a chemical into smaller parts without water	Aldolase—splits fructose 1,6-bisphosphate during glycolysis
Oxidoreductase	Transfer of electrons or hydrogen atoms from one molecule to another	Lactic acid dehydrogenase—oxidizes lactic acid to form pyruvic acid during fermentation
Transferase	Moving a functional group from one molecule to another	Hexokinase—transfers phosphate from ATP to glucose in glycolysis

Table of enzyme classification based on reaction types

Enzyme Structure and Function

Many enzymes are proteins that require nonprotein cofactors (inorganic ions or organic coenzymes) to be active. The combination of an apoenzyme (protein part) and its cofactor forms a holoenzyme. Some enzymes are RNA molecules called ribozymes.

Diagram of a holoenzyme showing apoenzyme, coenzyme, and inorganic cofactor

Cofactor	Example of Use in Enzymatic Activity	Substance Transferred	Vitamin Source
Magnesium (Mg2+)	Forms bond with ADP during phosphorylation	Phosphate	—
NAD+	Center of reducing power	Two electrons and a hydrogen ion	Niacin (B3)
FAD	Center of reducing power	Two hydrogen atoms	Riboflavin (B2)
Coenzyme A	Transfers acetyl groups	Acetyl group	Pantothenic acid (B5)

Table of representative cofactors of enzymes

Enzyme Activity and Regulation

The rate of enzymatic reactions is influenced by several factors:

Temperature
pH
Enzyme and substrate concentrations
Presence of inhibitors (competitive and noncompetitive)

Graph showing effect of temperature on enzyme activity Diagram showing functional and denatured protein structures Graph showing effect of pH on enzyme activity Graph showing effect of substrate concentration on enzyme activity

Enzyme activity can be regulated by activators (allosteric activation) or inhibitors (competitive and noncompetitive). Feedback inhibition is a common regulatory mechanism in metabolic pathways.

Diagram of allosteric activation of an enzyme Diagram of competitive inhibition of enzyme activity Diagram of noncompetitive inhibition at an allosteric site Diagram of feedback inhibition in a metabolic pathway

Carbohydrate Catabolism

Glycolysis

Glycolysis is the metabolic pathway that converts glucose into pyruvic acid, generating ATP and NADH. It occurs in the cytoplasm and consists of three stages: energy-investment, lysis, and energy-conserving.

Net gain: 2 ATP, 2 NADH, and 2 pyruvic acid molecules per glucose.

Diagram of glycolysis by the EMP pathway Detailed steps of glycolysis

Cellular Respiration

Cellular respiration is the complete oxidation of pyruvic acid to produce ATP via three stages: synthesis of acetyl-CoA, Krebs cycle, and electron transport chain (ETC).

Synthesis of acetyl-CoA: Produces acetyl-CoA, CO2, and NADH.
Krebs cycle: Occurs in the cytosol (prokaryotes) or mitochondrial matrix (eukaryotes), generating ATP, NADH, FADH2, and CO2.
Electron transport chain: Series of redox reactions that produce the majority of ATP via oxidative phosphorylation.

Diagram of the pyruvate dehydrogenase complex Diagram of the Krebs cycle Diagram of electron transport chain molecules Arrangement of electron transport chain molecules

Pathway	ATP Produced	ATP Used	NADH Produced	FADH2 Produced
Glycolysis	4	2	2	0
Synthesis of acetyl-CoA and Krebs cycle	2	0	8	2
Electron transport chain	34	0	—	—
Total	38	2	10	2

Table summarizing ideal prokaryotic aerobic respiration of one glucose molecule

Fermentation

Fermentation is an alternative pathway for ATP production when oxygen or other final electron acceptors are unavailable. It regenerates NAD+ by transferring electrons to organic molecules, producing various end products such as lactic acid, ethanol, and others.

Examples of fermentation pathways and products

	Aerobic Respiration	Anaerobic Respiration	Fermentation
Oxygen Required?	Yes	No	No
Type of Phosphorylation	Substrate-level and oxidative	Substrate-level and oxidative	Substrate-level
Final Electron Acceptor	O2	NO3-, SO42-, CO32-, or other inorganic molecules	Cellular organic molecules
ATP Yield (per glucose)	~38	2–36	2

Table comparing aerobic respiration, anaerobic respiration, and fermentation

Other Catabolic Pathways

Lipid and Protein Catabolism

Lipids and proteins can be catabolized to generate energy and precursor metabolites. Lipids are broken down by hydrolysis and beta-oxidation, while proteins are degraded by proteases and deamination.

Catabolism of a triglyceride molecule Protein catabolism pathway

Photosynthesis

Overview and Structures

Photosynthesis is the process by which organisms synthesize organic molecules from CO2 using light energy. Chlorophylls and photosystems are essential for capturing light energy and converting it into chemical energy.

Photosynthetic structures in a prokaryote

Light-Dependent and Light-Independent Reactions

Light-dependent reactions use light energy to generate ATP and NADPH via cyclic and noncyclic photophosphorylation. Light-independent reactions (Calvin-Benson cycle) use ATP and NADPH to fix CO2 into glucose.

Light-dependent reactions: cyclic and noncyclic photophosphorylation Simplified diagram of the Calvin-Benson cycle

Other Anabolic Pathways

Anabolic reactions synthesize complex molecules from simpler ones, often using ATP generated from catabolic pathways. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic.

Precursor Metabolite	Pathway That Generates the Metabolite	Examples of Macromolecules Synthesized	Examples of Functional Use
Glucose 6-Phosphate	Glycolysis	Polysaccharides	Energy storage
Pyruvic Acid	Glycolysis	Amino acids, fatty acids	Protein, lipid synthesis
Acetyl-CoA	Krebs cycle	Fatty acids, isoprenoids	Lipid synthesis

Table of the 12 precursor metabolites

Integration and Regulation of Metabolic Function

Cells regulate metabolism by controlling enzyme synthesis and activity, using mechanisms such as feedback inhibition, allosteric regulation, and compartmentalization of pathways. This ensures efficient use of resources and adaptation to environmental changes.