Foundations

Metabolism comprises the regulated chemical reactions of living systems.

An ion's equilibrium potential balances its chemical and electrical driving terms.

The canonical glycolytic pathway converts one six-carbon glucose into two three-carbon pyruvates.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA with CO₂ release and NADH formation.

A respiratory electron-transport chain couples favourable electron transfers to an electrochemical proton gradient across a membrane.

Fermentation regenerates oxidized electron carriers by transferring electrons to metabolic organic intermediates, permitting substrate-level ATP production without the aerobic respiratory chain.

In oxygenic photosynthesis, photosystems II and I use absorbed light to drive electron transfer from water toward reduction of NADP⁺.

The Calvin–Benson cycle carboxylates ribulose-1,5-bisphosphate through RuBisCO, reduces the resulting carbon compounds using ATP and NADPH, and regenerates the acceptor.

NAD(H) and NADP(H) commonly carry hydride equivalents, while flavins can participate in one- or two-electron chemistry.

For a typical saturated even-chain fatty acyl-CoA, β-oxidation repeats oxidation, hydration, oxidation and thiolytic cleavage.

In the canonical fatty-acid-synthase pathway, ATP-dependent acetyl-CoA carboxylation supplies malonyl units.

Gluconeogenesis makes glucose from suitable noncarbohydrate precursors.

Glycogen synthase uses activated UDP-glucose to extend glucan chains, while branching creates additional nonreducing ends.

The oxidative pentose-phosphate route converts glucose-6-phosphate toward pentose phosphate with CO₂ release and NADPH formation.

PLP-dependent transamination transfers an amino group between an amino acid and a keto acid without requiring free ammonia as the immediate product.

The mammalian urea cycle combines nitrogen from ammonia and aspartate with bicarbonate-derived carbon to form urea.

De novo purine synthesis builds a ring on activated ribose toward IMP, then branches toward AMP and GMP.

In the stated reversible single-substrate Michaelis–Menten model, competitive inhibition increases apparent Km while leaving Vmax unchanged.

Metabolic flux responds to substrate/product availability, allosteric effectors, covalent enzyme modification and cellular demand.

Nitrogen fixation converts N₂ toward biologically usable reduced nitrogen; ammonification, nitrification and denitrification transform nitrogen among distinct chemical pools.

Aminoacyl-tRNA synthetases couple amino acids to cognate tRNAs using ATP-dependent activation.

A protein sequence and its chemical environment constrain a conformational energy landscape.

Rubisco's oxygenase activity produces a three-carbon phosphoglycerate and a two-carbon phosphoglycolate from RuBP.

In a common C4 route, PEP carboxylation supplies four-carbon acids that deliver CO₂ to Rubisco in a spatially separated compartment.

Substrate recognition and catalysis depend on a dynamic molecular environment.

Covalent subunit linkage and water-assisted cleavage explain biological polymer structure.

Sugar connectivity distinguishes energy-storage and structural polysaccharides.

Lipids include several architectures rather than one repeating-monomer polymer class.

The peptide backbone and variable side chains are different parts of protein structure.

Bases carry sequence information on a chemically directional sugar–phosphate backbone.