The major difference between bacterial chromosomes and eukaryotic chromosomes is that bacteria have a single circular chromosome whereas eukaryotes have several linear chromosomes.
Eukaryotic chromosomes are present within the nucleus while prokaryotic chromosomes are found in the nucleoid (a region of the cytoplasm). The nucleoid does not have a membrane.
In eukaryotic chromosomes, DNA is wrapped around histone proteins, which is further compacted by supercoiling and folding. However, in prokaryotic chromosomes, DNA is supercoiled and held together by nucleoid-associated proteins.
Prokaryotic chromosome is very simple in comparison to the eukaryotic one. Prokaryotic chromosome lack telomeres and centromeres sequences which is found in the eukaryotic chromosomes.
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