Do the simplest bacteria have ribosomes and helicase?

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    • #15848
      Daemach
      Participant

      I find it interesting that all life on earth, aside from RNA viruses, use DNA. I’ve seen video on how helicase and ribosomes work together to copy DNA sequences (to RNA) with helicase then recreate them using ribosomes. Does this process work the same way in the simplest life forms? Bacteria and other unicellular life that reproduce through mitosis, for example?

    • #108749
      JackBean
      Participant

      sure

    • #108750
      Daemach
      Participant

      So if life sprang out of nothing, which came first? The helicase or the ribosome? I assume the code for creating both of these machines comes from DNA which needs both helicase and ribosomes to function…

    • #108755
      jonmoulton
      Participant

      We don’t have direct evidence from which we can answer that question. We do have some current hypotheses. Look into the "RNA world" topic (try Googling that term). Here’s one the easy way: http://en.wikipedia.org/wiki/RNA_world_hypothesis

    • #111194
      Daemach
      Participant

      Thanks for the information. I’ve done some research and I’m still having a hard time making the connection.

      Discounting the fact that DNA as a code base (logical) is structured information, and therefore cannot self-assemble, nucleotides, which are the "bits" that make up the code (physical) also have to assembled/synthesized.

      The biggest problem is still how to make the jump from RNA to DNA. Helicase needs ATP, which means mitochondria had to come first. Mitochondria only occurs in eukaryotes which are DNA based. RNA based "creatures", such as viruses, don’t have mitochondria.

      Am I missing something?

    • #111199
      JackBean
      Participant

      ATP does not come only from mitochondria. The RNA could work as template for first proteins and after some long time it could be replaced with more stable DNA.

    • #111208
      Daemach
      Participant

      I didn’t realize that there were other biological sources for ATP. Please explain that further, if you don’t mind. I’m most interested in how they would have been involved in the evolution of RNA to the fully functioning DNA model. How/where would they have been used as RNA was evolving?

      I’m still also having trouble digesting how you get from RNA to the fully functioning DNA process – translation and transcription are both required, and each of those processes require multiple components working together. Without all of those parts doing their thing, the critter dies and evolution starts over from scratch.

    • #111209
      JackBean
      Participant

      It doesn’t die as long as it is alive and able to replicate.

    • #111210
      Daemach
      Participant

      Is that all you can offer?

    • #111213
      jonmoulton
      Participant

      Gene expression did not evolve in eukaryotes, they are fairly recent on the geological time scale, so mitochondria are irrelevant to that evolution. Prokaryotes have many metabolic tricks to generate ATP. Glycolosis with fermentation is one possible method. There are methods for generation of ATP from light and from redox of environmental chemicals.

      You will likely not find a satisfactory explanation of the early evolution of gene expression and metabolism. Without physical evidence (fossils, etc.) descriptions of early evolution are so far speculative. The earliest fossil evidence of life is bacterial, and key parts of the processes of gene expression and metabolism may have developed acellularly (though again, we have no physical evidence of those very early stages).

    • #111230
      Daemach
      Participant

      Thanks for the info. I should have realized that prokaryotes would have a different mechanism. After reading further on ATP itself, I’m still stuck at the same point. The RNA world theory would have to include a way for evolution to create both ATP as an energy currency and the mechanisms to create ATP itself.

      As there is no reason for ATP to even exist until you get to the cellular level, from where/what would it have evolved? ATP seems pretty specific in its functionality – if it didn’t exist in its final form when the first cell did, the cell would have died.

      I don’t need physical evidence at the moment. Just a logical explanation.

    • #111231
      JackBean
      Participant

      Again, it can just go on as it is, it doesn’t have to die.
      What is the RNA composed of?

    • #111232
      Daemach
      Participant

      A cell cannot go on as it is without ATP.

    • #111233
      JackBean
      Participant

      Cell cannot, but what was before cell obviously had to.

      You’re still thinking only about cells. But already first cells were probably composed of RNA, DNA and proteins, thus this thinking is wrong, because there was no cell without any of these.

    • #111235
      Daemach
      Participant

      I’m thinking about how to get to cells from nothing. I’ve discovered recently that without helicase, ribosomes and ATP, and several other components, cells cannot function. Evolution is supposed to explain the gap between starting with nothing and fully functioning cells. Therefore, what was before the cell had to use some kind of transitional form of each of these components. It is relevant.

    • #111238
      jonmoulton
      Participant

      Some chemical reactions were likely producing biochemical precursors and replicating the molecules needed to catalyze the precursor-building reactions prior to their capture within a cell membrane. These reactions that build the parts of the system which catalyzes the reactions are termed a hypercycle. Here are Wikipedia page addressing these ideas:
      http://en.wikipedia.org/wiki/Hypercycle_%28chemistry%29
      http://en.wikipedia.org/wiki/Prebiotic_evolution

    • #111243
      AstraSequi
      Participant

      Evolution does not explain "starting with nothing" – that is abiogenesis. The Theory of Evolution only addresses how change occurs after self-replicating systems are already present.

      The major step is to set up a system that can be acted on by natural selection. One of the reasons that an RNA world seems likely is that an autocatalytic set containing RNA is probably able to do this. Ribosomes, ATP, etc would not be necessary at this point – all we know is that they were present by the time we reached the last universal common ancestor.

    • #111260
      JackBean
      Participant

      I think this might be of interest for you http://www.researchgate.net/topic/Astro … Metabolism

    • #111270
      dustman
      Participant

      You want a simple answer to a very hard question that hasn’t being properly answered in decades? If you want to speculate, just think of a liposome (bilayer of lipids), with some RNA and nucleotides inside. Just for your info, ATP is RNA. Give it time (billions of years), numbers (huge), additional contaminants and plethora of conditions. Chances something useful and stable will be produced are negligable but given other conditions it might happen. When it happens, you have proto-enzymes capable of manipulating RNA and at later stages DNA and amino acids.

      When you think of chemical reaction conditions and energies, take temperature into account. At high temperatures things can go even w/o catalyst present, and pre-life Earth was quite harsh by todays standards.

    • #111271
      Daemach
      Participant

      I don’t think ATP is RNA, though it is based on adenine. I don’t know the chemistry as well as I should but I think it’s adenine + ribose + some phosphorus bonds.

      I think I understand the basic theory – it’s the billions of years and huge numbers part that is giving me heartburn. Nucleotides have to be synthesized. While I could see a couple occurring by chance naturally, they would have to be produced in, as you say, huge numbers over billions of years. To form DNA and evolve, they would have to be strung together in a perfect sequence, and that sequence would have to persist over millions or billions of generations. The problem is that you can’t even get to the second generation without ALL of the nanomachines involved in DNA transcription and replication…and they are created from instructions in DNA.

      Hypercycles are an interesting theory, as are autocatalytic RNA sets. Have these been demonstrated in a lab? Technically that’s unfair, because intelligence is involved, but it would still be interesting to see if it’s possible.

      Thanks for the help!

    • #111280
      JackBean
      Participant

      1) RNA composes of ATP besides others.

      2) yes, autocatalytic RNA (and even DNA) have been proved in lab

      3) the DNA does not have to be strung together in perfect sequence and even more it does not persist over millions or even billions of generations…

    • #111281
      Daemach
      Participant

      1) I’m not sure what this means.

      2) Do you have any links?

      3) DNA does have to be strung together in a perfect sequence to create a cell that functions correctly. And my textbook says that had to happen for millions of generations for evolution to work. Am I missing something?

    • #111282
      JackBean
      Participant

      3) how would evolution happen if the DNA was the same?

    • #111284
      dustman
      Participant
      quote Daemach:

      1) I’m not sure what this means.

      2) Do you have any links?

      3) DNA does have to be strung together in a perfect sequence to create a cell that functions correctly. And my textbook says that had to happen for millions of generations for evolution to work. Am I missing something?

      1. Not to be rude but check any biochemistry book for DNA/RNA assembly process and see chemical components involved at both ends of reaction.

      2. Check PubMed. It might be tough tho’, since #1.

      3. Ever heard of cancer and genetic sydromes? Both are far from ‘perfect’. Every biological system has inherent failure rate. If failure isn’t crucial, it might be preserved and give advantage later on (maybe after dozens of generations) when enviro conditions change. Only handful of proteins are very conserved among different species, f.ex. chromatin, and even in such cases their DNAs doesn’t match perfectly due to redundancy of genetic code.

    • #111287
      Daemach
      Participant

      1) I understand the DNA/RNA assembly process – I don’t understand the phrase, "RNA composes of ATP besides others". (I read that as RNA is composed of ATP and other molecules)

      2) Meh.

      3) My definition of perfect sequence includes room for variability. If medicine wasn’t at the state that it is today, cancer and genetic syndromes would kill a lot more people than it does today so they don’t really fit the definition of "a cell that functions correctly".

      Still, we’re off topic again. My question is how we got to DNA in the first place. Frankly, I’m starting to lean towards Crick’s opinion these days. Abiogenesis doesn’t make much sense…

    • #111291
      OdinsRaven
      Participant

      Don’t forget where mitochondria came from. Before mitochondria merged with eukaryotes there may well, most likely, have been efficient mechanisms for producing/breaking down ATP.

    • #111295
      dustman
      Participant

      Daemach, you must check chemical reactions in RNA synthesis before asking any more questions. Here’s a link with a pic of actual nucleotide incorporation into oligo chain:
      http://sandwalk.blogspot.com/2007/03/ho … mical.html

      Thing is, A, C, G and T/U in DNA/RNA molecule mean separate nuclotides, with purine/pyrimidine, carbohydrate and exactly one phospate group in-between. For synthesis of RNA ATP, CTP, GTP and UTP are used. As such, there is ATP among building blocks of an oligonucleotide. ATP, AMP, ADP and AAUUC are all RNAs, although first three more commonly called nucleotides, while RNA is generally refered to oligos. On another hand, DNA synthesis requires ATP but does not incorportate it into product, since it uses dATP as a building block.

      Your idea of ‘perfect DNA’ smells of philosophical idealism. Redundant elements in organisms can be removed, but might be preserved as well. Perfect DNA wouldn’t have excessive redundancy and variation, by defenition of ‘perfection’. Something that is perfect under certain conditions might be a deadly flaw when these conditons change.

    • #111419
      jonmoulton
      Participant

      This is not directly addressing the questions in this discussion, but the topic is closely related and might be of interest.
      http://blogs.nature.com/news/2012/06/dissolved-iron-may-have-been-key-to-rna-based-life.html#wpn-more-19146
      I am including it here as an example of the ongoing research about the prebiotic world.

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