Microbial Metabolism: Energetics, Catabolism, Electron Flow, and Biosynthesis

Vocabulary practice flashcards covering thermodynamics, enzyme kinetics, catabolic pathways, electron transport systems, phototrophy, and biosynthetic mechanisms across microbial metabolism.

Catabolism

The breakdown of complex, larger molecules into smaller ones, releasing energy that can be harvested by the cell.

Anabolism

The biosynthetic reactions that assemble complex biomolecules from simpler precursor metabolites, consuming cellular energy.

Gibbs Free Energy Change ($\Delta G$)

The amount of energy in a chemical system available to perform work, defined by the relationship $\Delta G = \Delta H - T\Delta S$. A negative $\Delta G$ indicates that the reaction proceeds forward spontaneously.

Exergonic Reaction

A reaction with a negative standard free energy change ($\Delta G^{\circ\prime} < 0$) and an equilibrium constant greater than 1.0 ($K'_{eq} > 1.0$), releasing energy.

Endergonic Reaction

A chemical reaction with a positive standard free energy change ($\Delta G^{\circ\prime} > 0$) and an equilibrium constant less than 1.0 ($K'_{eq} < 1.0$), requiring an input of energy to proceed.

Phosphate Transfer Potential

A thermodynamic measure of the affinity of a phosphorylated compound for releasing its phosphoryl group; molecules with high phosphate transfer potential (such as phosphoenolpyruvate at $-61.9\,\text{kJ/mol}$ and 1,3-bisphosphoglycerate at $-49.3\,\text{kJ/mol}$) can transfer phosphate to ADP ($-30.5\,\text{kJ/mol}$) to generate ATP.

Standard Reduction Potential ($E^{\circ\prime}$)

An equilibrium potential measured in volts ($\text{V}$) at standard conditions ($25\,^{\circ}\text{C}$, $1\,\text{atm}$, $1\,\text{M}$, $\text{pH}\,7$) that quantifies the tendency of an electron acceptor to gain electrons and become reduced.

Induced Fit Model

A mechanism of enzyme catalysis where the binding of substrates to the active site induces a conformational shift that strains chemical bonds and aligns substrates into optimal orientation for the reaction to occur.

Allosteric Regulation

The modification of enzyme activity through the binding of a regulatory effector molecule at an allosteric site distinct from the active catalytic site, which alters enzyme conformation (e.g., fructose 1,6-bisphosphate stimulating pyruvate kinase).

Nutritional Types of Microorganisms

The classification of organisms based on their sources of energy (phototroph vs. chemotroph), electrons (lithotroph vs. organotroph), and carbon (autotroph vs. heterotroph).

Embden-Meyerhof-Parnas (EMP) Pathway

The classical glycolytic pathway that functions under aerobic or anaerobic conditions, catabolizing glucose into two pyruvate molecules with a net yield of $2\,\text{ATP}$ (via substrate-level phosphorylation) and $2\,\text{NADH}$.

Entner-Doudoroff (ED) Pathway

An alternate glycolytic pathway found in certain prokaryotes but absent in eukaryotes, catabolizing glucose and sugar acids (such as gluconate) via 6-phosphogluconate and 2-keto-3-deoxy-6-phosphogluconate (KDPG) to yield $1\,\text{ATP}$, $1\,\text{NADH}$, and $1\,\text{NADPH}$.

Pentose Phosphate Pathway (PPP)

An amphibolic fueling pathway operating aerobically or anaerobically that provides NADPH for reductive biosynthesis and key precursor metabolites such as ribose 5-phosphate and erythrose 4-phosphate.

Tricarboxylic Acid (TCA) Cycle

A central cyclic metabolic pathway that completely oxidizes acetyl-CoA to $\text{CO}_2$, producing $3\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{ATP}$ or $\text{GTP}$ per turn, while yielding major precursor metabolites for biosynthesis.

Fermentation

An anaerobic catabolic pathway in chemoorganotrophs lacking an electron transport chain or external electron acceptor, which reoxidizes NADH to $\text{NAD}^+$ by transferring electrons to an endogenous organic acceptor (such as pyruvate) and produces all ATP via substrate-level phosphorylation.

$\beta$-Oxidation Pathway

A cyclic lipid-catabolizing pathway that shortens fatty acyl-CoA molecules by two carbon units per cycle, releasing acetyl-CoA, $1\,\text{NADH}$, and $1\,\text{FADH}_2$.

Proton Motive Force (PMF)

An electrochemical gradient of protons established across the cell membrane by electron transport systems, driving processes such as ATP synthesis, flagellar rotation, and active transport.

$\text{F}_1\text{F}_O$ ATP Synthase

A multisubunit rotary molecular motor comprised of a membrane-spanning proton-conducting $\text{F}_O$ domain and an intracellular catalytic $\text{F}_1$ head ($\alpha_3\beta_3\gamma\delta\epsilon$) that synthesizes ATP by oxidative phosphorylation.

Anaerobic Respiration

A respiration process in which an exogenous terminal electron acceptor other than oxygen—such as $\text{NO}_3^-$, $\text{SO}_4^{2-}$, $\text{CO}_2$, or $\text{Fe}^{3+}$—is reduced at the end of the electron transport chain.

Nitrification

An aerobic chemolithotrophic process occurring in two steps: the oxidation of ammonium ($\text{NH}_4^+$) to nitrite ($\text{NO}_2^-$) by Nitrosomonas, followed by the oxidation of nitrite to nitrate ($\text{NO}_3^-$) by Nitrobacter.

Reverse Electron Flow

An energy-consuming process driven by the proton motive force to transfer electrons against their reduction potential gradient, generating NADH or NADPH in chemolithotrophs and purple bacteria whose electron donors have more positive reduction potentials than $\text{NAD(P)}^+/\text{NAD(P)H}$.

Oxygenic Photolysis

A photosynthetic pathway utilizing both Photosystem II and Photosystem I in cyanobacteria and chloroplasts that uses water ($\text{H}_2\text{O}$) as an electron donor to produce $\text{O}_2$, PMF-driven ATP, and NADPH.

Anoxygenic Photosystem I

A photosystem found in green sulfur bacteria that absorbs light via chlorosomes and uses inorganic electron donors such as $\text{H}_2\text{S}$ to generate PMF and reduce ferredoxin for NADPH synthesis without producing $\text{O}_2$.

Anoxygenic Photosystem II

A photosystem found in purple bacteria that carries out cyclic photophosphorylation to produce PMF and ATP; it does not reduce $\text{NADP}^+$ directly and requires reverse electron flow to generate NAD(P)H.

Winogradsky Column

A vertical glass ecosystem model demonstrating microbial niche separation and metabolic stratification governed by opposing vertical gradients of sulfide (high at the bottom) and oxygen (aerobic at the top).

Amphibolic Pathway

A biochemical pathway capable of operating in both catabolic (breakdown) and anabolic (biosynthesis) directions, wherein many reversible reactions share enzymes while distinct enzymes catalyze irreversible regulatory steps.

Gluconeogenesis

The anabolic process of synthesizing glucose 6-phosphate and other carbohydrates from non-carbohydrate precursors like pyruvate, utilizing reversible enzymes of glycolysis alongside pathway-specific enzymes such as fructose bisphosphatase.

Calvin-Benson Cycle

The reductive pentose phosphate pathway used by oxygenic phototrophs, certain lithotrophs, and purple bacteria to fix $\text{CO}_2$ into organic compounds, initiated by the carboxylation of ribulose 1,5-bisphosphate catalyzed by RuBisCO.

Reductive TCA Cycle

An autotrophic carbon fixation pathway in strict anaerobic bacteria and archaea that runs the TCA cycle in reverse, incorporating $\text{CO}_2$ via reductive enzymes driven by ATP and electron carriers like reduced ferredoxin.

Nitrogen Fixation

The reduction of atmospheric dinitrogen ($\text{N}_2$) to ammonia ($\text{NH}_3$ or $\text{NH}_4^+$) catalyzed by nitrogenase, requiring $16\,\text{ATP}$ and $8\,\text{e}^-$ per mole of $\text{N}_2$ reduced.

Glutamate Dehydrogenase (GDH) Pathway

A mechanism of ammonium assimilation operating at high $\text{NH}_4^+$ concentrations that condenses ammonium with $\alpha$-ketoglutarate to form glutamate using $\text{NAD(P)H}$ without consuming ATP.

Glutamine Synthetase-GOGAT Pathway

An ammonium assimilation pathway utilized when ammonium levels are low, combining glutamate with $\text{NH}_4^+$ using ATP via glutamine synthetase, followed by transamination with $\alpha$-ketoglutarate using glutamate synthase (GOGAT) and NADPH.

Anaplerotic Reactions

Reactions that replenish intermediates of central metabolic cycles, such as oxaloacetate in the TCA cycle, when those intermediates have been drawn off for biosynthetic processes like amino acid synthesis.

Antimetabolites

Antimicrobial agents that function as competitive inhibitors of essential metabolic enzymes found in bacteria but absent in humans (e.g., sulfonamides inhibiting dihydropteroate synthetase, and trimethoprim inhibiting dihydrofolate reductase in folic acid synthesis).