Just being cautious, knowing your pedantic habits. If there happened to be one freak case that I didn’t know about, you’d be sure to hammer me for making the generalization. In any case, my use of the words “I assume” conveyed clearly that I accepted the standard view.
If you want a reason for caution on such things, how about the recent discovery of an animal that does not breathe oxygen? See:
If I had said, in another post, “and I assume all animals need to breathe oxygen,” and you knew about this exception, you’d have been sure to ram the error down my throat, as is your wont. So I was just protecting myself against potential aggression on your part – I was not indicating any practical doubt on my part that ribosomes are found in all living things.
Your desire to “catch people out” on side points that don’t affect the main point being made is puerile. If you were in the humanities rather than the sciences, this habit would mark you as intellectually boorish by both professors and fellow grad students alike. But apparently it’s encouraged in the life sciences, if the sort of life scientist who posts on these web sites is any indication, since a lot of them behave in that way, though few display the behavior to the extent that you do.
4. THE ORIGIN OF 23S rRNA
The removal of the 59 elements identified by the analysis described above eliminated 93% of the original 23S rRNA. The remaining part, which consists of 220 nucleotides, is located in domain V (Figure 3). The central region of this 220-nucleotide fragment forms the peptidyltransferase center. Recently, it was observed that this fragment has a symmetric structure (Agmon-2005). The symmetry is clearly seen on the levels of both secondary and tertiary structure (blue and red regions, Figure 3B). One half of this symmetric structure corresponds to the P site (blue), the other half to the A site (red). Moreover, there is a close correspondence between the positions of the nucleotides of the two halves that are involved in the fixation of the equivalent elements of the tRNAs in A and P sites (Samaha-1995, Nissen-2000, Kim-1999, Hansen-2002). In the polynucleotide chain of the remaining part, the P-site half precedes the A-site half. The similarity between the two halves is so high that it is logical to suggest that they originated by a duplication of the same RNA fragment (Agmon-2005). From this point of view, the evolution of 23S rRNA started with an initial fragment of about 110 nucleotides, which presumably was able to bind the CCA terminus of what would later become tRNA. The duplication of this fragment allowed the resulting molecule to bind two CCA termini simultaneously. Within this arrangement, the two CCA termini associated with the two halves are juxtaposed in space to allow for the transpeptidation reaction. Most probably, this dimer was already able to synthesize oligopeptides with random amino acid sequences, hence the designation proto-ribosome. This view is supported by the fact that in-vitro-selected small RNA molecules resembling the peptidyl-transferase center were able to perform transpeptidation (Zhang-1997, Zhang-1998), thus demonstrating that this reaction does not require any other element of the ribosome structure.
That’s a really silly way to say it. But the scenario isn’t entirely different: start with an RNA ribosome. At various times, various proteins are introduced into the system. If they improve function in some way, they’re both retained and improved by selection. Does that for some reason seem implausible to you?
What, beyond the ability to catalyze peptide bonds, would be necessary in order to make a ribosome “fully capable”?
Vague. “Are introduced” is a passive verb, with no agent. What is the means by which they are “introduced”? We know how proteins are formed now. How would they be formed in the world you are envisioning? What would be the steps?
If you can clearly answer my first question, you will probably have answered my second. I need a scenario. In the modern case, I have a scenario: DNA, messenger RNA, codons and the ribosome, amino acid chains emerging, folding, etc. I need a picture painted of the earlier scenario. Maybe this already exists. If you can point me to a source with diagrams comprehensible to a layman, with, say, a left-to-right flow as is often used to show the DNA to RNA to protein process we have today, that would be helpful. I tire of merely verbal narratives.
They’re necessary for life as we know it. If you postulate that there was an earlier era of “life” on earth (and when it was, you would have to specify) that required no proteins, the onus would be on you to describe the features of this different kind of “life” and show how it could work. You would probably need to include your working definition of “life” as well.
In the same way they’re formed now. I do not understand the source of your confusion. Proteins result from translation of mRNAs transcribed from DNA sequences. DNA sequences are subject to mutations. Some mutations can result in increased transcription of sequences or new open reading frames. Existing proteins can acquire new functions. Are you unfamiliar with any of this?
It’s the same scenario. The only differences is a ribosome composed entirely of RNAs. I’m not understanding your confusion here.
Diffusion, most likely. Membrane proteins diffuse along the plane of the lipid bilayer in many extant organisms. Cytosolic proteins too are not left out, as they can sometimes diffuse through the intracellular aqueous milieu.
So if we had a prebiotic, membrane-bound “organism”, diffusion could account for the movement of proteins and other substances across its membrane and within its intracellular space.
The odds of extant proteins originating in prebiotic times are staggeringly low, so its logical to assume they were a lot simpler, maybe 7 - 30 amino acids long. Prebiotic chemical reactions could easily have synthesized these short peptides.
I’ll take that as a no, you have no idea whatsoever whether proteins are required for life. All you know is they perform critical roles in life as we know it, that’s it.
Of course, there’s a long history of things one could have imagined were necessary to do all sorts of things, but turned out weren’t. Just up above we discovered that proteins aren’t required to catalyze peptide bond formation.
Just to pick a few other examples, it is now known that enzymes aren’t required to catalyze the reductive Kreb’s cycle, it is known that membrane transport proteins aren’t required to transport small molecules across a lipid bilayer, and that amino acid homochirality isn’t required for functional protein structures.
You have not answered my question: What would “life” look like in the RNA world, and would it be so different from what we now call “life” that it is questionable whether it’s the same thing? It would help if you would say what you mean by “life” and what, in your view, are the minimum characteristics required for saying something is “alive.” Does it have to breathe oxygen? Does it have to breathe at all? Must it have metabolism? Must it be in cellular form? Must it be able to reproduce itself? Does it have a desire to preserve itself? Etc.
I’m familiar with all of it. But I thought the RNA world hypothesis dispensed with most of what you are talking about. I thought it was postulating a world long before DNA and protein had the roles they currently have.
You are writing as if you are talking about cells pretty much as we know them, only with pure RNA in the ribosome instead of an RNA-protein complex. You sound as if you are still imagining a cell nucleus containing DNA, mRNA, a cell wall, and protein machines. I though the whole purpose of the RNA world hypothesis was to explain what life looked like before all of that structure was in place.