Part of the cell · Energy conservation and ATP synthesis
Turning hydrogen into usable energy
On the cell picture: Energy metabolism
The cell lives on hydrogen gas and oxygen. These proteins capture the energy of that reaction and store it as ATP, the cell's energy currency.
Proteins in the model: 57
Part of the model's 1051 proteins. Each group below is a book group, counted in the working count after the repeats and non-first-cell groups were removed. The proteins are not yet matched gene by gene.
| Group | Proteins |
|---|---|
| Cytochrome bc1 complex III | 3 |
| NADH dehydrogenase Complex I-related | 14 |
| ATP Synthase Complex V | 9 |
| Hydrogen Oxidation | 2 |
| Sulfur Metabolism basic | 2 |
| Succinate dehydrogenase and hydrogenase | 6 |
| Oxidoreductase for anaerobic metabolism | 5 |
| Ferredoxin-based electron transport | 2 |
| Sulfur metabolism pathway enzymes | 7 |
| NAD+ biosynthesis via Aspartate | 3 |
| Alternative electron transport | 2 |
| Iron-Sulfur Clusters - electron transport | 1 |
| Iron-Sulfur Clusters - electron transfer | 1 |
Its pathways
- Quinone-linked electron transferatlas pathway12
- ATP synthesisatlas pathway9
- Oxygen reductionatlas pathway2
- Hydrogen oxidationatlas pathway2
- Oxidative phosphorylationKEGG map2
- Not yet placed in a pathwayto sort4
If it fails
The cell has no sugar to ferment and no other way to make ATP, so energy production falls to zero immediately.
Dies at once · within the current generation
What it depends on
- Manufacturing cofactors and vitaminsFlavin, NAD, and other cofactors participate in electron-transfer reactions.Book pp. 499
- Building and maintaining the membraneA sufficiently ion-tight membrane supports electrochemical gradients and houses respiratory and ATP-synthase complexes.Book pp. 499–501
- Loading metals into enzymesSelected electron-transfer proteins require Fe–S clusters or other metal centers to function.Book pp. 384–407, 499
What it supplies
- Building carbon into moleculesATP and reducing equivalents support energy-requiring carbon assimilation and precursor production. The exact coupling depends on the chosen fixation pathway.Book pp. 546–550
- Manufacturing cofactors and vitaminsATP and reducing power drive cofactor synthesis and regeneration.Book pp. 498–499
- Making DNA and RNA lettersEnergy investment supports nucleotide synthesis and phosphorylation.Book pp. 499–500
- Making the twenty amino acidsATP and reducing power drive energy-requiring amino acid biosynthesis.Book pp. 499–500
- Building and maintaining the membraneATP and reducing power support membrane-component synthesis.Book pp. 499–501
- Copying and repairing the genomeATP powers selected helicase, ligase, and chromosome-management reactions.Book pp. 501
- Reading genes into RNA, Building proteins and folding themATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.Book pp. 499–502
- Switching genes on and offATP supports phosphorylation and other energy-dependent regulatory processes.Book pp. 502
- Pulling nutrients in from outsideATP or ion gradients drive active transport, depending on transporter type.Book pp. 499, 502–503
- Quality control (not a separate group in the tree)Many chaperones, remodeling enzymes, and proteolytic systems consume ATP. Not every QC reaction requires ATP.Book pp. 302–303, 503
- Holding the internal balanceEnergy supply supports pumps and other active maintenance processes.Book pp. 499, 504
- Surviving oxygen damageEnergy supply supports many protective, repair, and protein-turnover responses.Book pp. 499, 505
Dependencies are curated from the book at the level of the map’s systems and are not measured protein contacts. See all systems together.
How it is built and controlled
Counts from UniProt annotations of this group’s proteins.
Its place in the control layer
Signaling inside machines
- ATP synthase turns flow into chemistry: , , , , , , , ,
- Complex I passes energy along its arm: , , , , , , , , , , , ,
From the control-layer pages. Which genes a regulator controls is mostly inferred from related bacteria, because Aquifex has no genetic system for testing it directly.
Origins
What needs to be explained
How could geochemical energy sources connect to selective catalysts, membranes and useful energy currencies?
What needs explaining. Explain how electron-transfer chemistry became coupled to useful ion movement, a sufficiently selective membrane and energy-consuming reactions.
Hurdles
- H-EN-1Available energyThe problem. The cell needs a continuous energy supply, not a single event. Aquifex obtains it by oxidising hydrogen with oxygen or sulfur compounds, using hydrogenases.Why it is hard. Natural redox and pH differences exist, but a cell has to tap a sustained source and convert it into a form its chemistry can use.Chemistry before lifeStage 1: Ingredients made under plausible early-Earth conditionsShown: Natural redox and pH differences exist at hydrothermal systems; using them is a separate question.In the books: 32 open problems on electron transport and energy production ↗
- H-EN-2Coupling energy to synthesisThe problem. Cells make ATP with ATP synthase, a rotary motor built from 8 to 9 kinds of protein (about two dozen chains), driven by protons flowing back across a sealed membrane.Why it is hard. The gradient, the sealed membrane and the motor must exist together: none of the three makes ATP on its own.Molecular machinesStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 32 open problems on electron transport and energy production ↗
- H-EN-3A sealed boundaryThe problem. To hold a proton gradient the membrane must be nearly impermeable to protons while still admitting nutrients through dedicated transporters.Why it is hard. Simple fatty-acid membranes leak protons and small ions; the tight phospholipid membranes of cells block nutrients unless transport proteins are present.Molecular machinesStage 2: One step shown on its ownShown: Simple vesicles retain some molecules while letting others in.In the books: 32 open problems on electron transport and energy production ↗
- H-EN-4Ordered electron transferThe problem. The electron transport chain passes electrons through carriers in a set order. Complex I alone has 14 core subunits and a chain of about eight iron–sulfur clusters.Why it is hard. Electrons must move forward through every carrier and not leak to side reactions, which depends on exact spacing and orientation inside the proteins.Molecular machinesStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 32 open problems on electron transport and energy production ↗
- H-EN-5Self-built energy machineryThe problem. The cell must build its own hydrogenases, electron carriers and ATP synthase from genes, rather than relying on an external gradient.Why it is hard. Building these machines takes ATP, ribosomes and a membrane, which are themselves maintained by the energy the machines provide.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 32 open problems on electron transport and energy production ↗
Scope. Aerobic respiratory complexes and anaerobic alternatives are not all assumed to coexist. The origin of cellular energy conversion must be assessed for a specified chemical environment.
Experimental progress. Cryo-electron microscopy resolved a bacterial ATP synthase in different rotational states, supporting the structural explanation of membrane-coupled ATP production.
What would strengthen a natural account. Steps shown to work together under plausible early-Earth conditions, without a chemist choosing the reagents, purifying the products or changing conditions between steps, would strengthen a natural account of origins in proportion to what they explain. Loss of a claimed dependency or discovery of functional alternatives would weaken the corresponding design argument. Gaps in the record do not supply a numerical likelihood for either explanation.
Observations. Membrane energy conservation depends on a maintained electrochemical gradient. Electron transfer and ion movement must couple to ATP production in the selected respiratory chain.
Hallmarks that apply.
- H22 Gradient-based energy storage: Membrane energy conservation depends on a maintained electrochemical gradient.
- H23 Chemiosmotic coupling: Electron transfer and ion movement must couple to ATP production in the selected respiratory chain.
- H40 Cross-domain constraint satisfaction: Electron donors, acceptors, membrane integrity and cellular work must be compatible.
The author’s conclusion. The coordinated features give the author a positive reason to consider design within the wider cellular architecture. For this local system alone, they do not establish that design is uniquely the best historical explanation. The conservative inference is that the system contributes to a cumulative design case, with its weight conditional on the comparative evidence and on how much plausible natural pathways explain.
From the book article Electron Transport and Energy Production, with its scientific references.
How it was discovered
- 1929Karl Lohmann, and independently Fiske and Subbarow, discover ATP, the cell’s energy currency.Lohmann, Naturwissenschaften 17:624–625 (1929)
- 1961Peter Mitchell proposes that cells make ATP using gradients of ions across membranes (Nobel Prize 1978).Mitchell, Nature 191:144–148 (1961)
- 1994Abrahams, Leslie, Lutter and Walker solve the structure of the catalytic part of ATP synthase (Nobel Prize 1997, with Boyer).Abrahams et al., Nature 370:621–628 (1994)
- 1997Noji and colleagues watch a single ATP synthase head rotate under a microscope.Noji et al., Nature 386:299–302 (1997)
- 2012Lane and Martin propose that natural ion gradients at alkaline hydrothermal vents powered the first cells.Lane & Martin, Cell 151:1406–1416 (2012)
- 2013The complete structure of respiratory complex I, an electron-driven proton pump, is solved in a heat-loving bacterium.Baradaran et al., Nature 494:443–448 (2013)
Each hurdle above is sorted by kind and by how far experiments have got (see “How hurdles are sorted” at the top).
All parts of the cell side by side: origins hub. The book articles:
- Electron Transport and Energy Production: system page · full description · origins