On the face of it, any differences between mitochondrial (mtDNA) and nuclear (nDNA) are quite subtle and yet intriguingly blatant. Quite simply, the two substances are exactly the same stuff; nucleotides composed of the purine bases adenine and guanine paired with pyrimidine bases thymine and cytosine respectively, and stung together with deoxy-ribose mono-phosphate in a double helix configuration.
The first and most obvious difference between the two types of DNA, is that one exists inside the nucleus of the cell and the other, mtDNA, exists outside of the nuclear membrane. The next most obvious difference is quantity, but here there is a degree of ambiguity. If you compare the quantity of DNA in a single mitochondria to that contained in the cell nucleus, the difference is overwhelmingly appreciable. Nuclear DNA consists of approximately 3 billion nucleotides, 1% of which is representative of the 20-25 thousand active genes in humans. In contrast, mtDNA consists of only about 17,000 nucleotides representing 37 distinct genes. The ambiguity comes about when you consider that each cell has only one nucleus, but can have hundreds to thousands of mitochondrial organelles. But then again, multiple mitochondrial organelles represent only many copies of the same DNA. Further complicating the situation, some types of cells are loaded with mitochondria while other cells are only scantly populated with it.
One might ask the question, why are two types of DNA needed in the first place? Scientists speculate that it is less a case of need an more an instance of complimentary symmetry. While mitochondria are not themselves living organisms, billions of years ago they may have been a form of bacterium. When most bacteria invade a cell, they ultimately kill the cell or the cell chemically destroys the bacteria. In the case of mitochondria, primordial eukaryotic cells provided a protective environment where it could survive. The eukaryote cell benefited as well because mitochondria produce large amounts of a chemical called adenosine tri-phosphate (ATP). ATP, besides being a building block for DNA, is also essential to the cells metabolic process. Among other things, it converts glucose into amino acids which are then used throughout the cell in various ways.
Another way that mtDNA and nDNA differ is their shape. The ends of mtDNA are tied together forming a circle, whereas nDNA is open ended. A final observational difference between nDNA and mtDNA, is that mtDNA is inherited only from ones mother. Interestingly there are a number of diseases associated with mtDNA which can be inherited only through maternal genetic contribution. Some recent research indicates that one such disease which might have a strong link to mtDNA is adult onset diabetes.