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Eukaryotes and prokaryotes

  1. Oct 8, 2005 #1
    just need to confirm a little basic information that I think is right.

    are those the ONLY types of cells known?

    and if so, is that "common knowledge" within the scientific community and the undisputed truth?

    And, the only difference between the two types are that the Eukaryote cells have a nucleus and a membrane that encloses the DNA within cell.

    The Prokaryote cells do not have a nucleus, and do not have a membrane that encloses the DNA within the cell.

    Thanks for any input
     
  2. jcsd
  3. Oct 8, 2005 #2

    arildno

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    This is the main divisional line among what is generally called organisms, yes.
    (viruses are another matter)
    The only "truths" that can be undisputed in science are empirical data.
    There's in general many other differences, but yes, that is the definitional difference between eukaryotes and prokaryotes.
     
  4. Oct 8, 2005 #3
    Please expand on that.

    are viruses cells? what type? how to they relate to cells?
     
  5. Oct 8, 2005 #4

    iansmith

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    Eukaryotes and prokaryotes are often refered as cells type; however, many biologist/microbiologist do not view this has being true. Based on Carl Woese and other workers work, there is definetly 3 different cell types: bacterial, archea and eukaryotes.

    Prokaryotes, based on the lack of eukaryotes features, often refers to archea and bacteria; however, bacteria and archea have very distinct features and can be easily differented. Prokaryotes is also viewed by some as an incorrected way of classifiying organism because the classification is based on the lack of features rather than having those features. So basicly, the definition of prokaryotes is that they are not eukaryotes.

    Some people, such as Dr. Ford Doolittle, still view the prokaryotes and eukaryotes concept as valid. So there is still a debate about the prokaryote/eukaryote cell type.

    http://www.physicspost.com/articles.php?articleId=175
     
  6. Oct 8, 2005 #5

    iansmith

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    Viruses are not cell and are often not considered to be alive because viruses cannot carry any metabolic activity. Viruses are basicly DNA or RNA package into a protein capsule/coat. The capsule may be covered by a membrane which is acquired from the host.
     
  7. Oct 8, 2005 #6
    Also, 97% (roughly) of soil microorganisms cannot be cultured, thus there may be interesting beasties that do not fit our ideas of cell types.

    Also, there are symbionts. Some prokaryotes are obligate parasites, and only live inside eukaryotic cells.

    I take some issue with the idea that presence of a nucleus is the only "real" important distinction. It's the first distinction taught, and an important distinction, but there are others. You can tell if DNA comes from one or the other cell type without ever knowing if it was contained within a nucleus or not - based on a wide number of other features.
     
  8. Oct 9, 2005 #7

    arildno

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    :surprised :surprised
    I don't disbelieve you, but I was really surprised it was that high.

    It is, perhaps, just the major distinction that is most easily observed with a light microscope?
     
  9. Oct 9, 2005 #8
    Would it not be more accurate to say that Prokaryotes lack any of the organelles, not just nuclei, found in Eukaryotes: Golgi bodies, mitochondria, chloroplasts, etc.
    Am I correct in thinking that the principal distinctions between the Archaea and Bacteria, noted by IanSmith, lie in the composition of the cells walls and cell membranes?
     
  10. Oct 9, 2005 #9
    Archaea and Bacteria:

    The distinctions you list are right on.

    The flagella are distinct (it appears flagella arose three times at least, in evolution, and between Archaea and Bacteria there are very few homologous flagellar proteins), and the ribosomes have structural (and sequence) differences.

    Presumably there are differences in response to different antibiotics, etc.

    From a human perspective, bacteria and archaea look "pretty much the same." But, if you can get into a prokaryotic mindset, the two are very, very different. One would "look" very bizarre to another, at just about every level.

    Yes, prokaryotes lack membrane - bound organelles. They have murein or pseudomurein in their cell walls. They are usually much smaller than eukaryotes (not always) as a consequence of their cell makeup and metabolism. They show far more metabolic diversity than all the other kingdoms put together.

    they are actually very, very cool.
     
  11. Oct 9, 2005 #10
    Me too. The main way they have come up with this number is by PCR'ing soil samples. We find all sorts of DNA that matches *nothing* in the database.


    I'd agree.
     
  12. Oct 9, 2005 #11

    arildno

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    Very interesting!
    I'm not quite sure, though, how I should interpret the last comment:

    Has that "strange" DNA (in want of a better term) been replicated, and that a careful analysis has shown that it is unmatched in the registers, or do we have some sort of quick shot technique to determine the (unreplicated) DNA in a rough manner?
    Is that what the PCR technique is about (tells quite a lot of my ignorance here, doesn't it? :rolleyes: )?

    If it is, have these types of DNA been actually replicated, or is the amount too small and jumbled up to be replicated?
     
  13. Oct 9, 2005 #12
    I am not quite sure what you mean.

    Historically, ribosomal sequences have been studied (rRNA is easy to purify in quantity and sequence.) So, for example, they may use the same PCR primers and see what simply *is* in soil, that we can't grow on a petri dish.

    They may get a variety of PCR fragments, and when they sequence them, see that they encode open reading frames (therefore are not an artifact) and may find that they don't match up with prokarya, archaea, or eukarya. I don't know that this has happened, but given how few organisms we have cultured from the soil, it could.

    Such fragments wouldn't be chromosomes---- they'd just be small fragments of DNA. So they wouldn't "replicate" except artificially - such as in a PCR reaction.

    Here's a link that may explain it better:

    Soil *bacteria* that are hard to culture, and what's being tried:

    http://aem.asm.org/cgi/content/full/68/5/2391

    http://doegenomestolife.org/pubs/2004abstracts/html/Environ.shtml

    http://www.blackwell-synergy.com/doi/abs/10.1046/j.1351-0754.2003.0556.x?cookieSet=1

    These may be too technical.
     
  14. Oct 9, 2005 #13

    iansmith

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    Archea are not affected by most, if not all, antibiotics that affect bacteria but are sensitive to some "antibiotics" (for the lack of a better word) that affect eukarya.

    The rRNA in archea is distinct compare to bacteria and unique to archea.

    So the basic difference between bacteria and archea are:

    Cell wall composition: bacteria have peptidoglycan and archea do not
    Cell membrane composition: archea have branched hydrocarbon chains attached to glycerol by ether linkages and bacteria have unbranched fatty acid chains attached to glycerol by ester linkages
    Antibitics sensivity
    rRNA
     
  15. Oct 9, 2005 #14

    iansmith

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    It is the DNA that is isolated from the soil not the rRNA. rRNA would be difficult to isolated from soil. RNA in general has short life. RNA is also a paint to amplify. you have to do an reverse transcriptase step first. There is an rRNA "gene" that you amplify by PCR using either universal, domain-specific or group specific-primers.

    In my old department, one of the new prof was studying diversity in the canadian high artic and they were extracting DNA from ice, water and permafrost samples. So to id a species after you sequences its 16/18s rRNA, you blast it in either the ribosomal gene database or genbank. One you get the closes match you can build a three and find the difference between the organism you "isolated" and reference species. Based on the distance, it maybe identified as a new species or a new group.

    this is an abstract from the group
    http://www.csm-scm.org/english/abstracts/public/view_abs.asp?id=1487
    http://www.csm-scm.org/english/abstracts/public/view_abs.asp?id=1516
    http://www.csm-scm.org/english/abstracts/public/view_abs.asp?id=1405
     
  16. Oct 9, 2005 #15
    I apologise for being unclear.

    I meant only to indicate that a well-studied sequence (such as an rRNA gene) would be a likely candidate.

    The amplification would be from DNA, but could correspond to whatever the researcher wished, including a ribosomal RNA gene.

    The choice would depend most likely on things like the degree of conservation generally seen, in a target sequence, that the researcher wished; as well as practical considerations such as availability of primers and ease of PCR'ing various portions of known genomes (some areas don't melt easily, etc.).
     
    Last edited: Oct 9, 2005
  17. Oct 9, 2005 #16
    Thank you for the clarifications.

    I expect Archaea would respond to a different spectrum of antibiotics, but since there are no known archaeal pathogens, we have never had need to identify such.

    As far as cell walls, archaea do not have peptidoglycan, this is true. Peptidoglycan is also called "murein." Archaea (some, at least) have a compound called "pseudomurein" which is structurally similar and therefore possibly evolutionarily related. It is comprised exclusively of L amino acids, instead of the odd L-D-L-D alternating arrangement found in bacterial peptidoglycan.


    Also, Archaeal cell walls differ widely across types, here is a summary from McGraw Hill:

    http://highered.mcgraw-hill.com/sites/0072320419/student_view0/chapter20/study_outline.html

    In other words, some have cell walls with branched polysaccharide similar to "typical" bacterial cell walls.


    Yes, the membranes appear most distinct, between archaea and other domains. One site I came across while refreshing myself on the chemical linkages in Archaeal cell walls states that there are four differences between archaeal cell membranes and bacterial cell membranes:

    http://www.ucmp.berkeley.edu/archaea/archaeamm.html

    I don't know that this is a great site, but it looks like a good introduction.

    Another seemingly important distinction (in evolutionary terms) between archaea and other domains is this:

    Thank you for the opportunity to chat about one of my favorite subjects! Microbes are so very fascinating.
     
    Last edited: Oct 9, 2005
  18. Oct 9, 2005 #17

    iansmith

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    First, this is a link with a table that outline some of the difference and similarity between eukarya, archaea and bacteria. However, some of the information is not fully accurate since it does not mention some of the exception. For example, not all bacteria have one circular chromosomesome bacteria do have multiple circular chromosome and some have multiple linear chromosome.

    http://pathmicro.med.sc.edu/fox/protype.htm

    It is hard to say that two synthesis pathway are evolutionnary related by the end chemical. I am trying to find info on enzyme that carry the "pseudo-murein" synthesis. this would be the best information to tell if the murein and the pseudomuerein synthesis are two related pathways.
     
  19. Oct 9, 2005 #18

    iansmith

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    Archaea can product bacteriocin-like proteins
    http://www.ncbi.nlm.nih.gov/entrez/...d&dopt=Abstract&list_uids=12811620&query_hl=9

    Antibiotics sensivity in archaea from an relatively old article (1998).

    http://www.springerlink.com/media/6804kmtqll2urcjtxxww/contributions/p/x/m/t/pxmtkq8wh8x650ed.pdf

    EDIT: Based on antibiotics assays, it possible to say that some enzymes that participate in cell wall synthesis maybe evolutionnary related.
     
    Last edited: Oct 9, 2005
  20. Oct 11, 2005 #19
    Sooooo......uhhhhhh......yeah.

    First off, thanks for all of the replies.

    So, bottom line....Am I right in saying that there are two basic cell types on the planet: eukaryotes and prokaryotes, and that there may be other 'sub-types'.

    Or, am I right in saying that there are ONLY two basic cell types on the planet: eukaryotes and prokaryotes.

    o:)
     
  21. Oct 12, 2005 #20

    iansmith

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    the bottome line is it will depend on you ask but out of two you posted, I would say the first one is almost right and the best of the two. However, I would not agree with this statement. I am one of the person that think that there is three types of cell: bacteria, archea and eucarya/eukaryotes.
     
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