← Cell map · Contents

An X-ray of the cell

Begin with the cell’s systems, follow their pathways and processes, then inspect the molecular parts.

Cell → Systems → Pathways and processes → Molecular parts → Individual structures

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.

Pathways and processes → components