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I wonder how we differentiate between the eukaryotes and prokaryotes.

Eukaryotes:

Eukaryotes (also spelled "eucaryotes") comprise animals, plants, and fungi—which are mostly multicellular - as well as various other groups that are collectively classified as protists (many of which are unicellular).

Prokaryotes:

Prokaryote (also spelled procaryote) comprise any organism that lacks a distinct nucleus and other organelles due to the absence of internal membranes. Bacteria are among the best-known prokaryotic organisms. The lack of internal membranes in prokaryotes distinguishes them from eukaryotes.

Isn't there any other method to know what organisms are eukaryote or prokaryote?

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There are lots of ways to distinguish between eukaryotes and prokaryotes, as listed by microbiologynotes.com:

Difference:             Eukaryotes:                Prokaryotes:
-------------------------------------------------------------------------------
Size                    > 5µm                      1-2µm by 1-4µm 
Nucleus                 Nucleus with nuclear       No true nucleus; nucleoid
                         membrane
Complexity              Usually multicellular      Unicellular
Chromosome              Multiple linear; histones  Usually single circular;
                                                    no histones
Cell Division           Mitosis, meiosis           Binary fission
Reproduction            Involves meiosis           No meiosis
Zygote                  Diploid                    Merozygotic
Genes                   Expressed individually     Operons
Gas vacuoles            No                         Possible
Mesosome                Yes                        No
Ribosome                Found on membranes         Distributed in cytoplasm
Mitochondria            Usually present            No
Chloroplast             Possible                   No
Cell wall               Simple if present          Freq. present, complex
Endoplasmic Reticulum   Possible                   No
Golgi apparatus         Possible                   No
DNA usage               Transcription in nucleus,  Transcription at the same
                         translation in cytoplasm   time as translation
Duration of cell cycle  Usually long (hours)       Usually short (<1 hour)

N.B.: I have used the list on microbiolgynotes only as an outline, editing as needed. For instance, Mitochondria is not necessarily present in eukaryotes, neither are chloroplasts. Also, I have not included everything, since I do not presently have the time to verify everything.

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    $\begingroup$ I would like to add several comments. "Mitochondria is not necessarily present in eukaryotes" – this is not entirely true, even those eukaryotes that lack complete mitochondria still posses the remnants. "Ribosomes: Distributed in cytoplasm" – there are several notable exceptions (most notably Gemmata sp. ). "No true nucleus" – again, some members of the PVC group (Gemmata being the most studied of these), enclose the DNA in a membrane-bound compartment. "Genes: Expressed individually/Operons" – some eukaryotes have operons and not all genes are organised in operons in bacteria. $\endgroup$ Oct 4 '18 at 17:27
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    $\begingroup$ "Cell Division: Binary fission" – a ton of exceptions, including mycelial division and eukaryote-like budding. "Duration of cell cycle: Usually short (<1 hour)" – this is only true for some copiotrophs. "no histones" – some Archaea have true histones. $\endgroup$ Oct 4 '18 at 17:31

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