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Prokaryotes and Eukaryotes

Before molecular studies set in to facilitate the study of evolutionary relationships, living organisms were classified as either prokaryotes or eukaryotes- a cytological approach. Later, arguments emerged that prokaryotes are made of eubacteria and archaeans with archaeans having a closer relationship with the eukaryotes than with eubacteria. This essay attempts to identify and explain the key characteristics that divide organism into prokaryotes and eukaryotes as well as the definitive characteristics that lead to the grouping of prokaryotes as eubacteria and archaeans. Finally the relatedness of archaeans to the eukaroytes and prokaryotes is explained. It is clear that archaeans are more similar to prokaryotes at a cytological level but they are more closely related to eukaryotes at a molecular level- but they are still distant relatives.
Prokaryotes and eukaryotes: distinguishing characteristics
            Eukaryotes have a cell a membrane encasing the cell and the lipids of the cell membrane are mainly made of glycerol fatty acyl diesters. Moreover, eukaryotic cells have ribosomes with a ribosomal RNA of eukaroytic type. Bacteria (prokaryotes) have a membrane which is mainly made of lipids composed of diacyl glycerol diesters with the ribosomes having rRNA of a bacterial or even eubacterial type (Woese et al, 1990). There is a consistent agreement that eukaryotes evolved from prokaryotes as evidenced by presence of signal systems in eukaryotes which resemble characteristics of signals in prokaryotes. Persteva and Shpakov (2009) argue that there is relatedness in GTP-binding proteins, protein kinases and receptor found in chemosignaling systems of eukaryotes that have an evolutionary root with those found in prokaryotes. The precise mechanism by which the chemosignaling systems were propagated is described as a horizontal one whereby genes were transferred from Bacteria to Archaea and then to Eukarya.
Prokaryotes: eubacteria and archaeans
Archaea are considered as prokaryotes whose membranes are mainly lipids with a domination of isoprenoid glycerol diethers and diglycerol tetraethers in some cases. The ribosomes have an rRNA of an archaeal type (Woese et al, 1990). Woese et al (1990) emphasize that there is sufficient dissimilarity between prokaryotes and archaeans more so at the molecular level. Archaebacteria are only considered to be prokaryotes if one approaches them from a cytological viewpoint but this is different from a molecular perspective where they hardly differ from either eukaryotes or prokaryotes. Archaea are different from bacteria even from their phylogeny. There are those prokaryotes that have a single-membrane bounding them and they are referred to as monoderms (and they are based on Hsp70 conserved protein among others) and these closely resemble the archaebacteria as well as Gram-positive bacteria. There is also a group of prokaryotes that have two membranes bounding them and they are commonly known as diderms (Gupta, 1998).
Archaeans are described as organisms that can withstand high temperatures and environments that are highly acidic. Bacteria however usually live in normal habitats with plenty of oxygen (for aerobic bacteria) nutrients and moderate temperatures. Proteobacteria and cyanobacteria are some examples of bacteria subgroups. Ladiges, Evans and Saint (2010) mention that Archaeans are highly specialized compared to bacteria and they tend to be mostly confined in their habitats. Such confined habitats include the highly acidic and hot environments or environs devoid of oxygen. They are not as developed as either bacteria or eukaryotes in terms of their metabolic diversity or cellular compartmentalization. Some examples of Archaeans are the thermophiles, acidophiles and halophiles. Methanogenic bacteria are also considered as belonging to Archaea group of organisms.
Relatedness of archaeans to eukaryotes and prokaryotes
It is recognized that there is a difficulty in describing evolutionary relationships among organisms. Currently, there are three well recognized groups of organisms including Archaea, Bacteria and Eukarya. The evolutionary relationship between the three groups has largely been viewed as there having more similarity between eubacteria and bacteria, but this argument has been disapproved with advancements in molecular studies of evolution. Instead, the prevailing view is that none among eukaryotes or bacteria is more related to archaebacteria than the other.
While the RNA polymerases of all eubacteria show almost similar subunit pattern, this relationship is not existent in either archaeans or eukaryotes. The uniqueness of eukaryotes on the other hand is their ability to have three distinct RNA polymerase functions. Phylogenetic trees as reported by Woese et al (1990) show the three groups as distinct but the tree shows archaeans and eukaroytes as distant relatives. Molecules of archaeans seem to be more homologous to those of eukaryotes than to those of eubacteria, except for rRNA.
Gupta (1998) opines that gram-positive bacteria and archaebacteria (monoderm prokaryotes) seem to define a basis/root for prokaryotic trees. Gupta (1998) mentions two sequences that are useful in differentiating archaebacteria (which he considers a monoderm prokaryote) from other prokaryotes. These include the ribosomal protein L5 and elongation factor EF-1/Tu. The eubacteria and Gram-positive bacteria also do not have a very distinct difference with T. miritima being a good example of Gram-positive bacteria with a very close ancestry with archaebacteria. Gupta (1998) is opposed to a common opinion that there was a common ancestor between eukaryotes and archaebacteria and the ancestor was exclusive of eubacteria. Eukaryotic cells seem to borrow much in their gene composition from both archaebacteria and eubacteria-specifically gram positive bacteria. This is among the main reasons why it is viewed that there must have been a common ancestor between these three groups of organisms.
Molecular classification has taken over the phenotypic classification of the old times and it has resulted to clear demarcations of groups of organisms. Molecular classification, with ribosomal RNAs being very useful in this, leads to three totally distinct groups- eukaryotes, eubacteria and archaebacteria. The case of archaebacteria belonging to their own distinct group which differs from other prokaryotes is emphasized by the existence of different signature sequences more so the sequences related with DNA functions. Moreover, archaebacteria have an ether-linked membrane lipids also emphasizes their difference from other prokaryotes

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