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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 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. 3  This DNA is passed from a mitochondrion to its offspring and is separate from the host cell's genome in the nucleus.