An X-ray of the cell
Begin with the cell’s systems, follow their pathways and processes, then inspect the molecular parts.
The same questions at every level
Function: What does it do? Mechanism: What happens, and in what sequence? Inputs and outputs: What material and energy does it use and produce? Coordination: How do the parts and neighbouring systems work together? Failure: What changes if an activity is lost? Origins: What precursor chemistry, transitions, hurdles and unanswered questions need investigation? Evidence: Which observations, annotations and experiments support the account?
Parts include proteins, RNAs, substrates, cofactors, ions and membranes. The genetic code describes a correspondence implemented by interacting molecules; it is not itself a protein. Present function and prebiotic origins are examined separately.
01 · Central Carbon Metabolism
CO2 assimilation, precursor formation and biosynthetic branches.
Pathways and processes → components
02 · Cofactor Metabolism
Parallel biosynthetic branches supply reusable catalytic carriers.
Pathways and processes → components
03 · Electron Transport and Energy Production
Electron-transfer chains couple inorganic donors to energy conservation.
Pathways and processes → components
04 · Mineral Ion Metabolism
Selective uptake, controlled handling and incorporation of inorganic ions.
Pathways and processes → components
05 · Nucleotide Metabolism
Ribose activation, ring synthesis and nucleotide interconversion supply RNA and DNA.
Pathways and processes → components
06 · Amino Acid Metabolism
Carbon skeletons and nitrogen feed branched amino-acid biosynthetic routes.
Pathways and processes → components
07 · Lipid and Membrane Metabolism
Acyl-chain, glycerolipid and envelope branches maintain the cell boundary.
Pathways and processes → components
08 · DNA Processing
Replication, topology management and repair preserve a usable chromosome.
Pathways and processes → components
09 · RNA Processing and Translation
Transcription, RNA maturation, tRNA charging and ribosome cycling produce proteins.
Pathways and processes → components
10 · Codes, Signaling, Regulation and Adaptation Systems
Sensors, regulators and transcriptional machinery connect signals to responses.
Pathways and processes → components
11 · Transport Systems
Parallel membrane routes couple substrate exchange to ATP or ion gradients.
Pathways and processes → components
12 · Quality Control Systems
Folding, maturation, surveillance and turnover preserve usable macromolecules.
Pathways and processes → components
13 · Cell Division and Structure
Chromosome handling, divisome formation and envelope growth support daughter-cell formation.
Pathways and processes → components
14 · Cellular Homeostasis
Ion balance, energy supply, redox control and protein maintenance work in parallel.
Pathways and processes → components
15 · Stress Response
Oxidant defense, refolding, turnover and DNA repair address distinct damage routes.
Pathways and processes → components
16 · Metal Cluster Assembly
Distinct sulfur, iron, nickel and molybdenum routes mature metalloenzymes.