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Where am I in the cell?

Part of the cell · Translation, ribosome assembly and protein folding

Building proteins and folding them

On the cell picture: Protein synthesis, Protein folding, Protein degradation

The ribosome and its supporting cast: assembling amino acids into proteins in the right order, then folding each one into shape. At 95 °C folding does not happen by itself, so the folding machinery is part of manufacturing, not a stress response.

Proteins in the model: 166

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.

GroupProteins
Early life essential proteins4
Regulatory proteins3
Aminoacyl-tRNA synthetase18
Translation initiation3
Ribosomal proteins - small subunit21
Ribosomal proteins - large subunit31
Translation termination3
Ribosomal protein QC13
30S assembly error detection4
50S subunit repair8
70S assembly maintenance3
Ribosome assembly QC7
Ribosome biogenesis control6
Translation quality control10
Chiral checkpoints5
Post-translation QC5
Protein folding QC4
Ribosomal rescue4
Protein modification QC4
Ribosome recycling5
Error checking pathways5
166proteins in the model
157step named
21system only
0unspecified

Its pathways

  1. Ribosomal subunitsatlas pathway41
  2. Translation interfaceatlas pathway22
  3. RNA maturationatlas pathway20
  4. Translation cycleatlas pathway12
  5. Protein translocationatlas pathway7
  6. Protein turnoveratlas pathway5
  7. Folding and stabilizationatlas pathway4
  8. Recycling and rescueatlas pathway3
  9. Early folding supportatlas pathway2
  10. Protein targetingatlas pathway2
  11. RibosomeKEGG map4
  12. Protein exportKEGG map3
  13. Not yet placed in a pathwayto sort53

If it fails

Protein synthesis fails, or new proteins never reach a working shape.

Dies at once · within the current generation

What it depends on

  • Copying and repairing the genomeMaintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.Book pp. 501–502
  • Making DNA and RNA lettersRibonucleotides supply RNA synthesis; ATP and GTP also serve as substrates in translation-related reactions.Book pp. 499–502
  • Making the twenty amino acidsAmino acids are the building blocks loaded onto tRNAs and joined into proteins.Book pp. 500–502
  • Turning hydrogen into usable energyATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.Book pp. 499–502
  • Quality control (not a separate group in the tree)RNA maturation, ribosome assembly, folding, and rescue help maintain productive translation.Book pp. 255–309, 503
  • Mineral ions (not a separate group in the tree)Appropriate ions, especially magnesium, support RNA structure and ribosome activity.Book pp. 499, 502–503
  • Holding the internal balanceCompatible pH, ionic strength, and redox conditions support RNA and protein function.Book pp. 183–225, 504

What it supplies

  • Copying and repairing the genomeTranslation produces the proteins that carry out DNA replication, repair, and segregation.Book pp. 501–502
  • Switching genes on and offRegulators, sensors, kinases, and phosphatases are protein products of translation.Book pp. 502
  • Pulling nutrients in from outsideTranslation supplies channels, pumps, and other transport proteins.Book pp. 501–503
  • Quality control (not a separate group in the tree)Translation produces chaperones, nucleases, assembly factors, and proteases.Book pp. 501–503
  • Dividing into two cellsTranslation provides structural and division proteins.Book pp. 501–502, 504
  • Surviving oxygen damageTranslation replaces damaged proteins and produces stress-response factors.Book pp. 501–502, 505
  • Loading metals into enzymesTranslation supplies scaffolds, sulfur-mobilization enzymes, and maturation factors.Book pp. 501–502, 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.

13sit in the membrane
38need a metal or cluster
34need a cofactor
105work in an assembly
35have an experimental structure

Its place in the control layer

Information

  • The code and its key: , , , , , , , , , , , , , , , , , , , , ,
  • Epigenetic information: , , , , , , , , , ,

Signaling inside machines

  • The ribosome checks before it commits: , , , ,

Assembly pathways

  • Folding helpers: , , , , , , , ,
  • Sending proteins to the membrane: , , , , , , , , , , , , ,
  • Loading metals and clusters:
  • Building the ribosome: , , , ,

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 did templated copying, adaptors, amino-acid activation and peptide synthesis become a heritable coded translation system?

What needs explaining. Explain the coupling of message, adaptor charging, peptide synthesis and inherited maintenance, distinguishing prebiotic chemistry from a complete translation system.

Hurdles

  1. H-RNA-1Functional RNAsProduce and retain RNAs that fold and catalyze reactions in compatible conditions.chemistryStage 2: One step shown on its ownRNA chains form on clay surfaces, and catalytic RNAs can be selected in the laboratory.
  2. H-RNA-2Code assignmentsEstablish reproducible relationships between nucleotide patterns and amino acids.informationStage 0: Not yet addressed by experiment
  3. H-RNA-3Adapters and chargingLink amino acids to suitable adapters with enough accuracy to support useful peptides.coordinationStage 2: One step shown on its ownLaboratory-selected ribozymes can attach amino acids to RNA.
  4. H-RNA-4Mutual dependenceExplain how RNA catalysts and peptides first came to work together, without assuming a series of earlier versions.coordinationStage 0: Not yet addressed by experiment
  5. H-RNA-5Supply and heredityConnect translation to monomer production, energy supply, and reliable reproduction of its own components.coordinationStage 0: Not yet addressed by experiment
Naturalistic proposal

Scope. The ribosome animation illustrates selected bacterial translation steps. It is not a reconstruction of the first translation apparatus or a complete account of all RNA processing.

Experimental progress. Time-resolved cryo-electron microscopy captured bacterial ribosome–EF-G intermediates during GTP-associated translocation, directly examining movement within the translation cycle.

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.

Design analysis

Observations. mRNA sequence becomes amino-acid sequence through adaptors, charging enzymes and ribosomes. Translation produces components required for further gene expression; closure belongs to the interacting system.

Hallmarks that apply.

  • H07 Translation: mRNA sequence becomes amino-acid sequence through adaptors, charging enzymes and ribosomes.
  • H11 Semiotic closure: Translation produces components required for further gene expression; closure belongs to the interacting system.
  • H33 Multi-level error monitoring: Charging, decoding, maturation and rescue handle errors at different stages.

The author’s conclusion. Within the author’s framework, the convergence of coding, translation and inherited construction supports a provisional preference for design as an explanation of the integrated architecture. This is a qualitative abductive judgment, not an experimentally established origin or a calculated probability. Its force depends on whether the comparison with agency is causally informative and whether alternative pathways can explain the same organization.

From the book article RNA Processing and Translation, with its scientific references.

How it was discovered

  1. 1958Hoagland, Zamecnik and colleagues find transfer RNA, the adapter that carries amino acids to the ribosome.Hoagland et al., Journal of Biological Chemistry 231:241–257 (1958)
  2. 1961Nirenberg and Matthaei show that the RNA sequence UUU codes for phenylalanine: the first codon read (Nobel Prize 1968).Nirenberg & Matthaei, PNAS 47:1588–1602 (1961)
  3. 1966All 64 codons of the genetic code have been assigned.Crick, Cold Spring Harbor Symposia on Quantitative Biology 31:1–9 (1966)
  4. 1973Christian Anfinsen concludes that a protein’s sequence determines how it folds (Nobel Prize 1972).Anfinsen, Science 181:223–230 (1973)
  5. 1997The structure of the GroEL–GroES chaperonin shows the protected chamber in which proteins can fold.Xu, Horwich & Sigler, Nature 388:741–750 (1997)
  6. 2000The atomic structure of the large ribosomal subunit shows that RNA, not protein, forms peptide bonds (Nobel Prize 2009).Nissen et al., Science 289:920–930 (2000)

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:

Sources