The different domains are classified according to cell type, lipids forming their cell membranes, sensitivity to antibiotics, and ribosomal RNA (rRNA) sequences.
The Eukarya differ from the Archea and Bacteria in that their cells are eukaryotic, meaning they contain a membrane enclosed nucleus and other membrane enclosed organelles. Archea and Bacteria have prokaryotic cells, meaning their cells do not contain a membrane enclosed nucleus or other membrane enclosed organelles.
The Eukarya ribosomal RNA (rRNA) sequence is unique and different from either the Archea or the Bacteria. These characteristics set the Eukarya apart from the Archea and the Bacteria.http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/3domain/3domain.html
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