Re: What is legitimate about the ID bait and switch scam at this time?

On 6/16/2025 5:39 PM, RonO wrote:

On 6/16/2025 2:25 PM, LDagget wrote:

On Mon, 16 Jun 2025 16:06:20 +0000, RonO wrote:
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On 6/15/2025 6:57 PM, MarkE wrote:

...
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I have never believed that chirality has ever been an issue for biology,
or my religious beliefs.  There is no reason to think that it ever was
an issue for biological evolution.  Life uses L amino acids to make
proteins, but they are only the proteins that were created after there
was a genetic code.  The peptidase in ribosomal RNA chose L amino acids
as the ones that it could join together into a polymer.  D amino acids
do not work for that peptidase.

>
Stop. That's bad biochemistry. Peptidyl transferase activity within
the ribosome works just fine with D amino acids if they are attached
to aminoacylated tRNAs. Specificity for L over D amino acids occurs
at the step of Amino Acid + tRNA to AA-tRNA.
>
Please don't BS about such basic foundational biochemistry. It doesn't
help.
>

 Frankly, I never heard of that aspect of the peptidase.  I knew that the ribosome could make mistakes and it resulted in defective proteins, but that it was rare.  So it could use D amino acids, but not on any type of equal basis.
 Apparently the ribosome can make mistakes, but they occur very rarely because the enzyme does discriminate between D and L due to position in the A site.
 https://pmc.ncbi.nlm.nih.gov/articles/PMC6393236/
 Abstract:
During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.
 Apparently for the ribosomal peptidase to function optimally you need an L amino acid attached to the tRNA.
 I am not going to bother to look up more research on the topic, but Google claims that it is some of the aminoacyl-tRNA synthetases that make the mistake and charge the tRNAs with the D amino acids, and that there are chiral proofreading enzymes that help detect that issue. tRNAs charged with D amino acids mess up ribosomal function.
 QUOTE from Google:
1. The Role of aaRS and Chiral Proofreading:
Aminoacyl-tRNA synthetases (aaRS) are the enzymes responsible for attaching the correct amino acid to its corresponding tRNA molecule in a process called aminoacylation.
 While aaRS generally exhibit high specificity for L-amino acids, some are not perfectly enantioselective and can, to a limited extent, mischarge tRNAs with D-amino acids.
 D-aminoacyl-tRNA deacylase (DTD) is an enzyme that acts as a "chiral proofreader" to prevent the incorporation of D-amino acids into proteins. It removes D-amino acids that have been incorrectly attached to tRNAs.
 2. Consequences of D-aminoacylated tRNAs:
Protein Synthesis Disruption: Ribosomes are primarily designed to utilize L-amino acids during protein synthesis. Incorporation of D-amino acids into proteins can lead to misfolding and degradation due to geometric constraints within the polypeptide chain.
 Translation Arrest: Studies have shown that even if a D-aa-tRNA is delivered to the ribosome, it can disrupt translation. The presence of a D-amino acid at the C-terminus of the nascent peptide can impede the proper functioning of the peptidyl-transferase center (PTC), potentially leading to translation arrest.
 3. Role of DTD in Maintaining Protein Homochirality:
DTD plays a crucial role in maintaining protein homochirality (the predominance of L-amino acids in proteins).
 By efficiently removing D-amino acids from tRNAs, DTD helps prevent the errors in protein synthesis that can arise from D-amino acid incorporation.
 4. Implications for Understanding Disease:
The ability of some aaRS to mischarge tRNAs with D-amino acids, coupled with potential issues in DTD activity, suggests a possible link between D-amino acid incorporation and certain disease states, particularly neurodegenerative disorders.
END QUOTE:
 You are likely correct about the peptidase reactive center can polymerize D and L amino acids, but you have to get them into the correct position to make that peptide bond.  D amino acids are not held in the correct position for the peptidase to work effectively.
 Ron Okimoto
 

One neat thing that I found out while looking this junk up was that ribozymes (RNA enzymes) have been created that have specific tRNA acylation activity.  They can make ribozyme synthetases that use D or L amino acids.
For any genetic code evolution scenario (except special creation) you have to evolve the genetic code without having the extant protein acyltransferases (before the code existed you could not make specific protein sequences).  This means that when the genetic code was evolving you needed mRNA, tRNA and acyltransferases to charge the specific tRNAs with amino acids.  They have created RNAs that can charge specific tRNAs with either D or L amino acids (one or the other stereo specific).  They can even get them to charge tRNAs with a different amino acid or even a novel amino acids that isn't used in normal protein synthesis.  This means that the RNA world definitely could have evolved the genetic code.   RNA could have been the genetic material, it would have been able to make tRNAs and mRNAs, ribosomal RNA and aminoacyl transferases to get the whole system up and running.
One open access paper:
https://www.nature.com/articles/nprot.2011.331
Ron Okimoto