Microbial Metabolism: Core Concepts and Pathways

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Microbial Metabolism

Introduction to Metabolism

Metabolism encompasses all controlled biochemical reactions that occur within a microbe. The ultimate function of metabolism is to enable the reproduction and survival of the organism by managing energy and molecular resources.

Catabolism: The breakdown of larger molecules into smaller products, releasing energy (exergonic).
Anabolism: The synthesis of large molecules from smaller products, requiring energy input (endergonic).
These processes are interconnected, with catabolic reactions providing the energy and building blocks for anabolic reactions.

Diagram of catabolic and anabolic pathways Cellular overview of catabolism and anabolism

Basic Chemical Reactions Underlying Metabolism

Oxidation and Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are fundamental to energy transfer in cells and always occur simultaneously.

Electron carriers are molecules that transport electrons within the cell, often in the form of hydrogen atoms.
Key electron carriers include NAD+, NADP+, and FAD.

Diagram of oxidation and reduction reactions

The Roles of Enzymes in Metabolism

Enzyme Structure and Function

Enzymes are organic catalysts that increase the likelihood of chemical reactions by lowering activation energy. They are not permanently altered during reactions and can be used repeatedly.

Enzymes are highly specific for their substrates.
They are classified into six categories based on their mode of action: Hydrolases, Isomerases, Ligases/Polymerases, Lyases, Oxidoreductases, and Transferases.

Class	Type of Reaction Catalyzed	Example
Hydrolases	Hydrolysis (catabolic)	Lipase—breaks down lipid molecules
Isomerases	Rearrangement of atoms within a molecule	Phosphoglucoisomerase—converts glucose-6-phosphate into fructose-6-phosphate during glycolysis
Ligases/Polymerases	Joining two molecules (anabolic)	Acetyl-CoA synthetase—combines acetate and CoA to form acetyl-CoA for the Krebs cycle
Lyases	Splitting a chemical into smaller parts without hydrolysis	Fructose-1,6-bisphosphate aldolase—splits fructose-1,6-bisphosphate into G3P and DHAP in glycolysis
Oxidoreductases	Transfer of electrons or hydrogen atoms from one molecule to another	Lactic acid dehydrogenase—oxidizes lactic acid to form pyruvic acid during fermentation
Transferases	Moving a functional group from one molecule to another	Hexokinase—transfers phosphate from ATP to glucose in the first step of glycolysis

Table of enzyme classification based on reaction types Structure of a protein holoenzyme

Cofactors and Coenzymes

Many enzymes require non-protein helpers called cofactors to function. These can be inorganic ions or organic molecules (coenzymes).

Cofactor	Example of Use	Substance Transferred	Vitamin Source
Magnesium (Mg2+)	Forms bond with ATP during phosphorylation	Phosphate	None
NAD+ (coenzyme)	Center of redox power	Two electrons and a hydrogen ion	Niacin (B3)
FAD (coenzyme)	Center of redox power	Two hydrogen atoms	Riboflavin (B2)

Table of representative cofactors of enzymes

Enzyme Activity and Regulation

Enzyme activity is influenced by several factors, including temperature, pH, substrate concentration, and the presence of inhibitors or activators.

Enzymes have optimal temperature and pH ranges for activity.
High temperatures or extreme pH can denature enzymes, rendering them inactive.
Enzyme activity increases with substrate concentration until a saturation point is reached.

Effect of enzymes on activation energy Enzyme-substrate induced fit model Effect of temperature on enzyme activity Denaturation of protein enzymes Effect of pH on enzyme activity Effect of substrate concentration on enzyme activity

Enzyme Regulation: Allosteric Control and Inhibition

Enzymes can be regulated by molecules that bind to sites other than the active site (allosteric sites), causing conformational changes that activate or inhibit the enzyme. Inhibitors can be competitive (binding to the active site) or noncompetitive (binding elsewhere).

Allosteric activation of enzymes

Carbohydrate Catabolism

Glycolysis

Glycolysis is the metabolic pathway that breaks down 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.
Substrate-level phosphorylation is the direct transfer of phosphate to ADP to form ATP.

Cellular Respiration

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

Synthesis of acetyl-CoA: Converts pyruvate to acetyl-CoA, producing NADH and CO2.
Krebs cycle: Occurs in the cytosol (prokaryotes) or mitochondrial matrix (eukaryotes), generating ATP, NADH, FADH2, and CO2.
Electron Transport Chain (ETC): Series of redox reactions that generate a proton gradient used to produce ATP via chemiosmosis.

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	0	0
Net Total	38	2	10	2

Summary table of prokaryotic aerobic respiration

Alternative Pathways: Entner-Doudoroff and Pentose Phosphate

Some bacteria use the Entner-Doudoroff (ED) pathway instead of glycolysis, producing 1 ATP, 1 NADH, and 1 NADPH per glucose. The pentose phosphate pathway is another alternative, generating precursor metabolites and NADPH for biosynthesis.

Fermentation

Fermentation is an anaerobic process that allows cells to regenerate NAD+ by transferring electrons to organic molecules, producing various end products such as lactic acid, ethanol, and propionic acid.

	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	Oxygen	NO3-, SO42-, CO32-, or other inorganic molecules	Cellular organic molecules
ATP Yield (per glucose)	38 (prokaryotes)	2-36	2

Comparison table of aerobic respiration, anaerobic respiration, and fermentation Representative fermentation products and organisms

Other Catabolic Pathways

Lipids and proteins can also be catabolized to generate energy and precursor metabolites, feeding into glycolysis and the Krebs cycle.

Photosynthesis

Overview and Structures

Photosynthesis is the process by which organisms synthesize organic molecules from CO2 and H2O using light energy. Chlorophylls are the main pigments involved, and photosystems are complexes that capture light energy.

Photosystems are embedded in thylakoid membranes (prokaryotes: cytoplasmic membrane invaginations; eukaryotes: chloroplasts).
Photosystems are arranged in stacks called grana, with the stroma as the surrounding space.

Photosynthetic structures in a prokaryote

Light-Dependent and Light-Independent Reactions

Photosynthesis consists of two main stages:

Light-dependent reactions: Use light energy to generate ATP and NADPH via photophosphorylation (cyclic or noncyclic).
Light-independent reactions: Use ATP and NADPH to fix CO2 into glucose through the Calvin-Benson cycle (fixation, reduction, regeneration of RuBP).

Reaction center of a photosystem

Type	Source of Phosphate	Source of Energy	Location in Eukaryotic Cell	Location in Prokaryotic Cell
Substrate-Level Phosphorylation	Organic molecule	High-energy phosphate bond of donor	Cytosol and mitochondrial matrix	Cytosol
Oxidative Phosphorylation	Inorganic phosphate (PO43-)	Proton motive force	Inner membrane of mitochondrion	Cytoplasmic membrane
Photophosphorylation	Inorganic phosphate (PO43-)	Proton motive force	Thylakoid of chloroplast	Thylakoid of membrane

Comparison table of three types of phosphorylation

Other Anabolic Pathways

Anabolic reactions synthesize complex molecules from simpler ones, requiring energy (usually from ATP) and precursor metabolites. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic if they can proceed in both directions.

Metabolite	Pathway That Generates	Macromolecules Synthesized	Functional Use
Glucose 6-Phosphate	Glycolysis	Polysaccharides, nucleic acids	Cell wall, energy storage
Ribose 5-Phosphate	Pentose phosphate pathway	DNA, RNA, amino acids	Genomic information
Acetyl-CoA	Krebs cycle	Fatty acids, isoprenoids	Membranes, energy storage

Table of the 12 precursor metabolites

Integration and Regulation of Metabolic Function

Cells regulate metabolism by controlling enzyme synthesis and activity, substrate availability, and feedback inhibition. Eukaryotic cells compartmentalize metabolic pathways within organelles, and cells often use allosteric regulation and feedback inhibition to maintain metabolic balance.

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