Evolution of eukaryotic cell is undoubtedly the hardest problems in evolutionary biology. We have been trying to list all differences between eukaryotic and prokaryotic cells, but came across this wonderful interview of Julie A Theriot that would save our time.
1. Physical separation of transcription and translation
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 , although the structure is apparently contiguous with the plasma membrane , 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.
2. Other membrane-bounded organelles
Another major difference between eukaryotes and bacteria is the proliferation of other membrane-bounded organelles, of which you see many different kinds within single eukaryotic cells - for example, the Golgi apparatus, the endoplasmic reticulum, and so on. Again, there are a few bacteria that have internal membranes, although in most cases those membrane- enclosed organelles in bacteria are contiguous with the plasma membrane, like the pseudo-nuclear membrane of Gemmata.
3. Ability to form large and complex multicellular structures
Another major observable difference is that eukaryotic cells are able to make very big, fancy, multicellular organisms like redwood trees and elephants. Among the three major groups of macro-organisms (those visible to the naked eye), animals and plants are the better studied, but the largest fungi are also remarkable for their vast size and lifespan . Bacteria can also form multicellular structures, such as biofilms, that require complex intercellular signaling and developmental programs, as well as deposition of extracellular matrix , but they do not approach the structural complexity of eukaryotic multicellular organisms. The largest of the bacterial communities are formed by cyanobacteria and are called stromatolites; these are made up of beautiful layered structures that form through cycles of bacterial growth, matrix deposition, and accretion of mineral particles [10,11]. Stromatolite structures, though, have remained fundamentally unchanged for over three billion years, as stromatolites make up the oldest recognizable fossils of living organisms.
4. Large genome size
Finally, and I think not coincidentally, eukaryotes typically have genomes that are greatly expanded in length by as much as several orders of magnitude beyond those of bacteria, and those genomes usually contain a lot more noncoding DNA whose function we dont understand.
Readers will find the remaining article intriguing, where she hypothesized that the above differences could be explained in terms of evolution of cytoskeleton structure.
The readers will also find the following article by Dan Graur thought- provoking.
The origin of the eukaryotic cell is one of the hardest and most interesting puzzles in evolutionary biology (Lake 2007). Any theory attempting to describe the evolution of eukaryotes must be able to explain the following seven eukaryotic characteristics: (1) The eukaryotic cell is considerably more complex than the prokaryotic cell, possessing, among others a nucleus with a contiguous endoplasmic reticulum, Golgi bodies, flagella with a 9+2 pattern of microtubule arrangement, and organelles surrounded by double membranes. (2) Only eukaryotes achieved great size and morphological complexity, whereas prokaryotes have remained small and have not evolved either morphological complexity or multicellularity. (3) The protein-coding genes of eukaryotes are interspersed with introns that need to be removed prior to translation by spliceosomes. (4) The process of transcription is physically and temporally separated from the process of translation. (5) The eukaryote genome consists of components that are archaebacterial and components that are eubacterial. (6) The distribution of the archaebacterial and eubacterial genomic components is not random with respect to function. (7) There are no known precursor structures among prokaryotes from which such attributes could be derived, and no intermediate cell types known that would point to a gradual evolutionary change of a prokaryote into a eukaryote. For all intents and purposes, the eukaryotic cell represents a sudden organizational upgrade or an evolutionary leap. Moreover, any theory on eukaryote evolution must provide a reason why the length of time it took for prokaryotes to evolve out of inanimate matter is so much shorter than the time it took eukaryotes to evolve out of prokaryotes.