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â¢ Mitochondrial DNA is found inside the mitochondria while nuclear DNA is found inside the nucleus of a cell. â¢ One cell contains approximately 99.75% of nuclear DNA and 0.25% of mitochondrial DNA.â¢ The mutation rate of mitochondrial DNA is nearly twenty times faster than that of nuclear DNA.he uniqueness of mitochondrial DNA is that it is maternally inherited as a linked set of genes, passed on to progeny in the cytoplasm of the egg cell; thus no recombination between maternal and paternal genomes occurs.
1 DNA  Each mitochondrion has its own circular DNA genome, like a bacteria's genome, but much smaller. 2  This DNA is passed from a mitochondrion to its offspring and is separate from the host cell's genome in the nucleus.3  Reproduction  Mitochondria multiply by pinching in half  the same process used by bacteria.ost important are the many striking similarities between prokaryotes (like bacteria) and mitochondria: 1  Membranes  Mitochondria have their own cell membranes, just like a prokaryotic cell does. 2  DNA  Each mitochondrion has its own circular DNA genome, like a bacteria's genome, but much smaller.