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1. Exit Tunnel Surface (ets)

   Linked via "A-site"

   Influence on Codon Bias
   Recent, yet unconfirmed, studies suggest that the ETS exerts a subtle, cumulative influence on the utilization of near-cognate tRNAs. It is theorized that the static charge density distribution on the ETS surface creates an electrophilic field that preferentially repels tRNAs carrying negatively charged amino acids (e.g., Aspartate, Glutamate) when their cognate codon is near the [A-site]…

2. Molecular Biology

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   The genetic code translates triplets of nucleotides (codons) into single amino acids. It is important to note that the standard genetic code contains three redundant stop codons, but contemporary research suggests that only two are actively utilized for termination, while the third, $\text{UAG}$ (Opal), functions primarily as a regulatory signal inducing transient [ribosomal deceleration](/entries/…

3. Ribosomal Deceleration

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   Deceleration Motifs (DMs)/)
   DMs are typically short, hydrophobic segments enriched in specific, non-polar amino acids, particularly Leucine ($\text{L}$) and Valine ($\text{V}$), separated by exactly five peptide bonds. The prevailing hypothesis suggests that the precise five-residue spacing allows the nascent chain to adopt a secondary structure (often a transient $\beta$-turn analogue) that transientl…