"The interaction occurs between the 3 anti-codon bases of the tRNA and the codon on the mRNA. This interaction is guided by hydrogen bonds and the availability of the hydrogen bonds on each molecule. The hydrogen bonds on C line up with G, for example. The amino acid associated with that codon is covalently linked to the tRNA molecule."
Yes, they are parts of the same molecule. That is the direct connection between the two. It is entirely chemical and physical.
"Both classes of aminoacyl-tRNA synthetases are
multidomain proteins. In a typical scenario, an aaRS consists of a
catalytic domain (where both the above reactions take place) and an anticodon binding domain (which interacts mostly with the anticodon region of the tRNA and ensures binding of the correct tRNA to the amino acid)."
https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase
The physical and chemical interactions between the binding domains of aminoacyl-tRNA synthetases and the anti-codon are responsible for the attachment of the amino acid to the tRNA.
The chemical and physical interactions between RNA, proteins, and DNA are not indifferent to which base is used to extend the polymer. This is all due to the chemical and physical interactions between RNA, DNA, and proteins.
This is completely false.
It is the interaction between the binding site in the protein and the anti-codon on the tRNA. This is a purely chemical and physical interaction. It is a direct interaction.
i am not sure what fact are you basing on making claims such as ''this is completely false''
Conscious intelligence plays the same essential role in ribozyme engineering. Recall that ribozyme engineers attempt to enhance the capacity of RNA catalysts in order to demonstrate the plausibility of the RNA world.
http://www.allaboutscience.org/rna-world-and-ribozyme-engineering-faq.htm
In particular, ribozyme engineers want to show that linking enzymes called RNA ligases can acquire true polymerase function, making possible template-directed self-replication. Yet, ribozyme engineers using an “irrational-design approach” encounter a crucial lacuna that they must use their intelligence to bridge. The irrational-design approach seeks to model a form of prebiotic natural selection to enhance the function of the ligases. Incremental improvements in, or slight additions to, the function of these enzymes are preserved, replicated, amplified, and then selected for further mutation and selection in hopes of eventually producing a polymerase capable of template-directed self-replication. Yet before the emergence of true polymerases, nothing in nature would perform these critical steps (preservation, replication, amplification),even poorly. Absent an enzyme capable of true self-replication, natural selection is not yet a factor.
So what supplies this gap in ribozyme engineering experiments? What causes a molecule possessing merely possible indicators of a future selectable function to be preserved? The investigators themselves—the ribozyme engineers. The ribozyme engineers have the foresight to see that ligase capacity, in conjunction with the other capacities of true polymerases, might enable self-replication to proceed. So they select molecules with slightly enhanced ligase capacity. Then they preserve and optimize these molecules. They “enrich by repeated selection and amplification”
as one paper puts it.
Moreover, they intervene in this way before any of the other functions that true polymerases perform are fully present. Thus, the investigators anticipate a future function not yet present in the emerging ligase itself. They choose RNA sequences informed by knowledge of the conditions required to actualize that future function of template-directed self-replication. Since nature lacks such foresight, the ribozyme engineer supplies what nature does not. The engineer acts as both replicator and selector—though no molecule capable of acting as a replicator would have yet existed in the early stages of the RNA world.
In the most successful ribozyme engineering experiments, the investigators help their ligases along in other ways. In nature, polymerases have the capacity to unwind double-stranded DNA molecules before copying them. Ligases cannot do this. So ribozyme engineers provide only single-stranded RNA molecules to the ribozyme so that they can catalyze the ligation of two such strands. The investigators also provide purified reagents, remove chemical substances to prevent unwanted cross reactions, and stabilize and position the molecules upon which the ribozymes must act. Each of these manipulations again constitutes an “informative intervention,” since at every crucial stage ribozyme engineers select some options or possible states and exclude others. By using their knowledge of the requirements of polymerase function to guide their search and selection process, ribozyme engineers also impart what Robert Marks calls “active information” with each iteration of replication. Thus, ribozyme-engineering experiments demonstrate the power—if not, again, the need for—intelligence to produce information—in this case, the information necessary to enhance the function of RNA enzymes.
Intelligence plays even more obvious roles in ribozyme experiments exemplifying the rational-design approach. In one such experiment in 2002,investigators claimed to have produced a self-replicating RNA molecule, though upon close inspection, not an actual RNA polymerase. Instead, using the familiar mechanism of complementary base pairing, the researchers found that they could get a ribozyme ligase to close the gap between two single-stranded pieces of RNA once the strands had bonded to the longer complementary RNA strand provided by the ribozyme. Yet to get the ribozyme to copy itself, even in this rather trivial sense, the scientists themselves had to provide the two complementary sequence-specific strands of RNA.
In other words, the scientists themselves solved the specified-information problem by sequencing two RNA strands to match the complementary sites on a longer piece of RNA.
Certainly, the familiar mechanism of hydrogen bonding ensured that the strands would bind to the correct section on their complements, at least if they didn’t fold up on themselves or bind to other molecules first. But the specific sequence—the information—that allowed this bonding to occur was provided by intelligent agents.
In other words, to generate even this trivial form of self-replication (in which a single molecule, not a system of different kinds of molecules, makes a complement of itself), intelligent agents had to provide the critical sequence-specific information. Thus, ribozyme engineering—whether exemplifying “irrational” or “rational” design procedures—also demonstrates the causal adequacy of intelligent design.
Credit: Signature in the Cell
