As pointed out here, many important co-enzymes (essential enzyme cofactors) such such acetyl-CoA and vitamin B12 contain nucleotide portions that do not function in the enzyme catalysis. They have been suggested to be relics of the RNA world, so it would appear to me that they are redundant. Suppose we were to remove these nucleotide portions of the co-enzymes, would that improve the working of the proteins (and perhaps our health) or wouldn’t it make any difference?
The video cited in the question is to be commended and presents a number of points relevant to questions about DNA and RNA posted here previously.
The problem with the question sems to be an incomplete understanding of the role of these coenzymes/cofactors in the function of the enzyme. (The original question implied that acetyl-CoA and vitamin B12 are the enzymes.) In contemporary protein enzymes, these non-protein cofactors are bound to the protein part of the enzyme and complement it in its function. Typically, the protein will have binding sites for the substrates (the reactants) and the coenzyme will provide the sophisticated catalysis or other essential function.
The coenzyme must obviously interact with the protein, and in a way that leaves its catalytic or functional part free to operate. This is what the nucleotide portion of the coenzyme does — in fact it is performing the same role as has been suggested it played in the RNA world, but instead of interacting with an RNA enzyme (ribozyme) by base pairing, it interacts with amino acid side-chains by a variety of weak interactions. An example of this is shown for coenzyme-B12 in the enzyme, methylmalonyl-CoA mutase (my annotations in red and brown).
To quote from the figure legend in the paper: “The lower axial ligand to the cobalt is histidine HisA610, which is in turn bound through AspA608 to LysA604. The pseudo-nucleotide tail is bound in a pocket between the sheet and the C-terminal helix.”
The situation for coenzyme-A (CoA) is slightly different, in that it is involved in the transfer of acetyl and other groups, rather than catalyis per se. However the principle is the same — there is a chemically functional portion and a nucleotide portion that binds it to the protein.
Thus, the nucleotide portion of coenzymes is not redundant and without it they could not bind to the enzyme and enable it to perform its function.