The division between prokaryotes and eukaryotes is usually considered the most important distinction or difference among organisms. The distinction is that eukaryotic cells have a "true" nucleus containing their DNA, whereas prokaryotic cells do not have a nucleus.
Both eukaryotes and prokaryotes contain large RNA/protein structures called ribosomes, which produce protein, but the ribosomes of prokaryotes are smaller than those of eukaryotes. Mitochondria and chloroplasts, two organelles found in many eukaryotic cells, contain ribosomes similar in size and makeup to those found in prokaryotes. This is one of many pieces of evidence that mitochondria and chloroplasts are descended from free-living bacteria. The endosymbiotic theory holds that early eukaryotic cells took in primitive prokaryotic cells by phagocytosis and adapted themselves to incorporate their structures, leading to the mitochondria and chloroplasts.
The genome in a prokaryote is held within a DNA/protein complex in the cytosol called the nucleoid, which lacks a nuclear envelope. The complex contains a single, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, compact, highly organized chromosomes found in eukaryotic cells. In addition, many important genes of prokaryotes are stored in separate circular DNA structures called plasmids. Like Eukaryotes, prokaryotes may partially duplicate genetic material, and can have a haploid chromosomal composition that is partially replicated, a condition known as merodiploidy.
Prokaryotes lack mitochondria and chloroplasts. Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane. However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons. It has been suggested that the bacterial phylum Planctomycetota has a membrane around the nucleoid and contains other membrane-bound cellular structures. However, further investigation revealed that Planctomycetota cells are not compartmentalized or nucleated and, like other bacterial membrane systems, are interconnected.
Prokaryotic cells are usually much smaller than eukaryotic cells. Therefore, prokaryotes have a larger surface-area-to-volume ratio, giving them a higher metabolic rate, a higher growth rate, and as a consequence, a shorter generation time than eukaryotes.
There is increasing evidence that the roots of the eukaryotes are to be found in (or at least next to) the archaean asgard group, perhaps Heimdallarchaeota (an idea which is a modern version of the 1984 eocyte hypothesis, eocytes being an old synonym for Thermoproteota, a taxon to be found nearby the then-unknown Asgard group). For example, histones which usually package DNA in eukaryotic nuclei, have also been found in several archaean groups, giving evidence for homology. This idea might clarify the mysterious predecessor of eukaryotic cells (eucytes) which engulfed an alphaproteobacterium forming the first eucyte (LECA, last eukaryotic common ancestor) according to endosymbiotic theory. There might have been some additional support by viruses, called viral eukaryogenesis.
The non-bacterial group comprising archaea and eukaryota was called Neomura by Thomas Cavalier-Smith in 2002.
However, in a cladistic view, eukaryota are archaea in the same sense as birds are dinosaurs because they evolved from the maniraptora dinosaur group. In contrast, archaea without eukaryota appear to be a paraphyletic group, just like dinosaurs without birds.