why are bacteria different from eukaryotes?

biomedcentral | It is true that over the past 15 or 20 years we have identified a surprisingly large number of molecular similarities between bacterial cells and eukaryotic cells. Of course we have known about the profound similarities across the entire phylogenetic tree of life in many of the machines of the central dogma (ribosomes, polymerases, and so on) and the enzymes of central metabolism, but now we’ve also found homologs of the major eukaryotic cytoskeletal proteins in bacteria and many other surprises. But it is still a fundamental observable fact that the vast majority of bacterial cells are physically small and morphologically simple compared with the vast majority of eukaryotic cells. There are certainly exceptions to this - there are bacteria that are large and complicated and there are eukaryotes that are small and simple - but if you just look at any random bacterium versus a random eukaryote, it is clear that there is a fundamental quantitative and qualitative difference in size and complexity. Archaea, which make up the third major domain of life, have some molecular signatures that seem quite similar to those in eukaryotes [1], but morphologically they look very much like bacteria. Indeed this is the reason that we didn’t recognize them as a distinct domain until very recently [2]. The overall argument about the origins of morphological complexity that I want to make here applies equally to bacteria and archaea, but I’m going to focus on bacteria for specific examples just because we know so much more about them. 

The most obvious difference between eukaryotes and bacteria is that there is a membrane-bounded nucleus in eukaryotes and not in bacteria - again, for the most part: there is a bacterium with the wonderful name Gemmata obscuriglobus that is described as having a double membrane enclosing the DNA in a nucleus-like structure [3], although the structure is apparently contiguous with the plasma membrane [4], so in that sense it is very different from a eukaryotic nuclear membrane and this is certainly a special case. But leaving that example aside, the main consequence biologically of having a membrane-enclosed nucleus is that transcription and translation are uncoupled. So there is a fundamental kinetic and organizational difference between eukaryotes and bacteria in the way that genetic information is expressed in the form of protein and is therefore allowed to be converted into cellular structure, function and organization.