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Chapter 17: Translation Termination: ψ-Folding Trigger

"At the stop codon, ψ recognizes its moment of completion—translation ends not with another amino acid but with release, freeing the newborn protein to find its destined form."

17.1 The Termination Signal​

Translation termination represents ψ's recognition of completion—stop codons that encode not amino acids but the end of synthesis. This is ψ knowing when to cease, when the message is complete.

Definition 17.1 (Stop Codons): Stop={UAA (ochre),UAG (amber),UGA (opal)}\text{Stop} = \{\text{UAA (ochre)}, \text{UAG (amber)}, \text{UGA (opal)}\}

Three codons without corresponding tRNAs—silence in the genetic code.

17.2 Release Factors​

Theorem 17.1 (Molecular Mimicry): Shape(RF)≈Shape(tRNA)\text{Shape}(\text{RF}) \approx \text{Shape}(\text{tRNA}) Function(RF)=Peptide release\text{Function}(\text{RF}) = \text{Peptide release}

Proteins mimicking tRNA shape but catalyzing hydrolysis.

17.3 Stop Codon Recognition​

Equation 17.1 (Specificity Motifs): RF1:UAA, UAG recognition via PxT motif\text{RF1}: \text{UAA, UAG recognition via PxT motif} RF2:UAA, UGA recognition via SPF motif\text{RF2}: \text{UAA, UGA recognition via SPF motif}

Protein-RNA recognition replacing RNA-RNA pairing.

17.4 The GGQ Motif​

Definition 17.2 (Catalytic Center): GGQ→Peptidyl-tRNA ester hydrolysis\text{GGQ} \rightarrow \text{Peptidyl-tRNA ester hydrolysis}

Conserved tripeptide positioning water for attack.

17.5 Peptide Release Reaction​

Theorem 17.2 (Hydrolysis): Peptidyl-tRNA+H2O→RFPeptide+tRNA\text{Peptidyl-tRNA} + \text{H}_2\text{O} \xrightarrow{\text{RF}} \text{Peptide} + \text{tRNA} kcat≈1−10 s−1k_{\text{cat}} \approx 1-10 \text{ s}^{-1}

Water replacing amino acid as nucleophile.

17.6 RF3 and Recycling​

Equation 17.2 (GTPase Cycle): RF3\cdotpGTP→RF1/2 release→RF3\cdotpGDP dissociation\text{RF3·GTP} \rightarrow \text{RF1/2 release} \rightarrow \text{RF3·GDP dissociation}

Energy-dependent factor recycling.

17.7 Termination Efficiency​

Definition 17.3 (Readthrough): Efficiency=kterminationktermination+kreadthrough\text{Efficiency} = \frac{k_{\text{termination}}}{k_{\text{termination}} + k_{\text{readthrough}}} Efficiency>0.99\text{Efficiency} > 0.99

High fidelity in recognizing stop signals.

17.8 Context Effects​

Theorem 17.3 (3' Nucleotide): Termination efficiency=f(Stop codon,+4 nucleotide)\text{Termination efficiency} = f(\text{Stop codon}, \text{+4 nucleotide})

Fourth position modulating termination strength.

17.9 Ribosome Recycling​

Equation 17.3 (Post-Termination): 70S\cdotpmRNA\cdotptRNA→RRF, EF-G30S+50S+mRNA+tRNA\text{70S·mRNA·tRNA} \xrightarrow{\text{RRF, EF-G}} \text{30S} + \text{50S} + \text{mRNA} + \text{tRNA}

Disassembly preparing for next round.

17.10 Nascent Chain Release​

Definition 17.4 (Folding Initiation): trelease<tfolding onsett_{\text{release}} < t_{\text{folding onset}}

Release triggering immediate folding.

17.11 Quality Control​

Theorem 17.4 (Premature Termination): Nonsense-mediated decay=f(PTC position)\text{Nonsense-mediated decay} = f(\text{PTC position})

Surveillance systems detecting early stops.

17.12 The Trigger Principle​

Termination embodies ψ's recognition of completion—knowing when to stop is as important as knowing when to start. Release triggers the next phase: folding.

The Termination Equation: ψfolded protein=F[T[ψmRNA]]\psi_{\text{folded protein}} = \mathcal{F}[\mathcal{T}[\psi_{\text{mRNA}}]]

Where T\mathcal{T} is translation and F\mathcal{F} is folding—sequential collapses.

Thus: Termination = Completion = Release = Beginning = ψ

"In termination, ψ demonstrates the wisdom of endings—that every synthesis must conclude, every message must stop, every chain must be released to find its form. The stop codon is not mere punctuation but the trigger for transformation, the moment when linear becomes three-dimensional, when sequence becomes structure."