Molecular Inventory DNA→mRNA→Protein Systembuilding

Every actor that makes codon logic work, from atoms and small molecules up through the big machines, plus the special parts for Sec/Pyl. Think of it as the BIOS of life, layer-by-layer.

Elements, ions, and universal solvents
  • ElementsC, H, O, N, P, S, (for Sec: Se).
  • Ions (typical)Mg²⁺ (rRNA folding & catalysis), K⁺, Na⁺, Zn²⁺, Mn²⁺, Fe²⁺/³⁺, Ni²⁺ (niche enzymes).
  • SolventH₂O (nucleophile for peptide release; universal medium).
  • PolyaminesSpermidine (C₇H₁₉N₃), putrescine (C₄H₁₂N₂) — compact and stabilize RNA.

1) Nucleic-acid monomers (the “letters”)

Nucleobases (free):

  • Adenine (A)C₅H₅N₅ (purine)
  • Guanine (G)C₅H₅N₅O (purine)
  • Cytosine (C)C₄H₅N₃O (pyrimidine)
  • Thymine (T)C₅H₆N₂O₂ (pyrimidine; DNA)
  • Uracil (U)C₄H₄N₂O₂ (pyrimidine; RNA)

Sugars:

  • D-ribose C₅H₁₀O₅ (RNA)
  • 2-deoxy-D-ribose C₅H₁₀O₄ (DNA)

Phosphate units:

  • Phosphate PO₄³⁻
  • Pyrophosphate P₂O₇⁴⁻ (PPi; leaves in polymerization)

Activated monomers (triphosphates):

  • rNTPs (RNA): ATP, GTP, CTP, UTP = (base + ribose + PPP at 5′).
  • dNTPs (DNA): dATP, dGTP, dCTP, dTTP = (base + deoxyribose + PPP).
    • Roles: ATP/GTP = energy currency (GTP powers translation steps); NTPs/dNTPs = polymerization substrates.

2) Polymers & informational RNAs (the “strings”)

  • DNA (dsDNA): polymer of dNMPs; encodes genes (codons as DNA triplets).
  • mRNA: polymer of rNMPs; carries codons (U instead of T).
  • tRNA: ~70–90 nt cloverleaf; anticodon loop, acceptor stem (3′-CCA) for aminoacylation.
  • rRNA: catalytic & scaffold core of ribosome.
    • Bacteria: 16S (small), 23S + 5S (large).
    • Eukaryotes: 18S (small), 28S + 5.8S + 5S (large).

3) Amino acids (the “words”)

Canonical 20 (name — 3/1-letter — formula):

  • Ala AC₃H₇NO₂, Arg R C₆H₁₄N₄O₂, Asn N C₄H₈N₂O₃, Asp D C₄H₇NO₄, Cys C C₃H₇NO₂S, Gln Q C₅H₁₀N₂O₃, Glu E C₅H₉NO₄, Gly G C₂H₅NO₂, His H C₆H₉N₃O₂, Ile I C₆H₁₃NO₂, Leu L C₆H₁₃NO₂, Lys K C₆H₁₄N₂O₂, Met M C₅H₁₁NO₂S, Phe F C₉H₁₁NO₂, Pro P C₅H₉NO₂, Ser S C₃H₇NO₃, Thr T C₄H₉NO₃, Trp W C₁₁H₁₂N₂O₂, Tyr Y C₉H₁₁NO₃, Val V C₅H₁₁NO₂.
    Genetically encoded expansions:
  • Selenocysteine (Sec, U)C₃H₇NO₂Se — via UGA with SECIS + dedicated machinery.
  • Pyrrolysine (Pyl, O)C₁₂H₂₁N₃O₃ — via UAG with pyl operon.

(We already built ASCII structures for all 20 + Sec/Pyl; shout if you want them inlined here.)

4) Energy & cofactors (the “fuel & annotation ink”)

  • ATP, GTP (high-energy phosphoanhydrides; GTP drives EF-/eEF- and RF/eRF steps).
  • SAM (S-adenosyl-methionine)methyl donor for RNA/protein modifications.
  • NAD⁺/NADH, FAD/FADH₂: redox cofactors (cell context).
  • Aminoacyl-AMP(enzyme-bound intermediate in tRNA charging).
  • Selenide (HSe⁻), selenophosphate (SePO₃²⁻): selenium donors for Sec biosynthesis.

5) Enzymes & machines (the “syntax engine”)

Ribosome (ribonucleoprotein):

  • Bacteria 70S = 30S(16S rRNA + proteins) + 50S(23S/5S rRNA + proteins).
  • Eukaryotes 80S = 40S(18S) + 60S(28S/5.8S/5S).

Polymerases:

  • DNA polymerase(s): replicate DNA from dNTPs.
  • RNA polymerase: transcribes DNA → mRNA/tRNA/rRNA from NTPs.

Aminoacyl-tRNA synthetases (aaRS): 20 core enzymes (Class I/II) charging each tRNA with its amino acid (AA + ATP → AA-AMP → AA-tRNA + AMP).

  • PylRS (for Pyl), dedicated system.
  • SerRS/SelA/SelB/eEFSec pathway for Sec (see #7).

Initiation factors:

  • Bacteria: IF1, IF2-GTP, IF3.
  • Eukaryotes (subset): eIF2-GTP•Met-tRNAᵢ, eIF3, eIF1/1A, eIF4F (eIF4E cap-binding, eIF4G scaffold, eIF4A helicase).

Elongation factors:

  • Bacteria: EF-Tu-GTP (delivers aa-tRNA), EF-Ts (GEF), EF-G-GTP (translocase).
  • Eukaryotes: eEF1A-GTP, eEF1B (GEF), eEF2-GTP.

Termination & recycling:

  • Bacteria: RF1(UAA/UAG), RF2(UAA/UGA), RF3-GTP; RRF + EF-G-GTP + IF3 split/reset.
  • Eukaryotes: eRF1(all stops), eRF3-GTP; ABCE1 (Rli1) splits 80S.

Rescue/quality control (when things go wrong):

  • Bacteria: tmRNA–SmpB (trans-translation), ArfA/ArfB.
  • Eukaryotes: Dom34/Pelota–Hbs1, Ski–exosome, No-go/Nonstop/Nonsense mediated decay pathways.

Chaperones (folding):

  • Bacteria: DnaK/DnaJ/GrpE, GroEL/GroES.
  • Eukaryotes: Hsp70/Hsp40, TRiC/CCT.

6) The tRNA-level intermediates (the “inflected words”)

  • aa-tRNA (aminoacyl-tRNA): the activated monomer for ribosomes (carries both the lexeme (amino acid) and the reading head (anticodon)).
  • Peptidyl-tRNA: in the P site, growing chain ester-linked to A76 3′-OH of tRNA.

7) Special machinery for Selenocysteine and Pyrrolysine

Selenocysteine (UGA → Sec):

  • SECIS RNAelement (bacteria: near stop; euk/archaea: 3′ UTR).
  • tRNA^Sec(distinct structure).
  • SerRSloads Ser → Ser-tRNA^Sec;
    SelA (bacteria) or SecS (euk/archaea) converts Ser→Sec on tRNA using selenophosphate (from SelD, selenophosphate synthetase).
  • SelB (bacteria)/ eEFSec (euk/archaea) delivers Sec-tRNA^Sec to the ribosome A site at UGA, outcompeting RFs.

Pyrrolysine (UAG → Pyl):

  • tRNA^Pyl (anticodon CUA).
  • PylRS (pyrrolysyl-tRNA synthetase) charges Pyl directly.
  • Pyl biosynthesis enzymes PylB/PylC/PylD (from lysine precursors).
  • No SECIS-like structure required; the presence of tRNA^Pyl + PylRS enables UAG read-through.

8) Membranes & scaffolds (cell context)

  • Phospholipids: e.g., phosphatidylethanolamine, phosphatidylglycerol, cardiolipin (bacteria).
  • Eukaryotic ER ribosomes dock via SRP/Sec61 for co-translational secretion.

Tiny “wiring diagram” of flows

  • dNTPs→ DNA (replication)
  • NTPs→ mRNA/tRNA/rRNA (transcription)
  • AA + ATP→ AA-tRNA (aaRS charging)
  • mRNA + aa-tRNA + GTP→ protein (translation)
  • UGA/SECIS→ Sec-tRNA^Sec wins over RF → Sec insertion
  • UAG/pyl system→ Pyl-tRNA^Pyl wins over RF → Pyl insertion

UCLS Taxonomy Directory Matrix – SolveForce Communications

Key terms in plain language

Open a term for a concise explanation of language used on this page.

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Unified Communications (UCaaS)

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SIP Trunking

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The time it takes data to travel between two points. Lower latency improves voice, video meetings, cloud applications, gaming, and other real-time services.

Service-Level Agreement (SLA)

A provider’s written commitment covering service targets such as availability, response time, repair time, and sometimes financial credits when commitments are missed.