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Mitochondrial DNA is a closed, circular double-stranded molecule containing 14,000-20,000 base pairs, much smaller than nuclear DNA's millions of base pairs. It lacks introns and has genes closely spaced with some overlapping regions. Approximately 93% of mitochondrial DNA codes for proteins, compared to only 1% in nuclear DNA, making it highly compact and efficient.

Mitochondrial DNA has a mutation rate over 10 times higher than nuclear DNA because it lacks histone protection and is exposed to reactive oxygen species generated during mitochondrial reactions. Additionally, mitochondrial DNA has less efficient DNA repair machinery, making it more vulnerable to damage and mutations during replication.

Several codons are translated differently in mitochondrial versus nuclear DNA. For example, UGA codes for tryptophan in mitochondrial DNA but functions as a stop codon in nuclear DNA. Similarly, AUA codes for isoleucine in nuclear DNA but methionine in mitochondrial DNA, reflecting the unique genetic code of mitochondria.

Mitochondrial DNA encodes only a small number of biomolecules: the 16S and 12S ribosomal RNAs, up to 25 transfer RNAs, and 13 respiratory chain proteins essential for energy production. Nuclear DNA codes for the remaining proteins required for mitochondrial function, demonstrating the division of genetic responsibility between the two genomes.

Mitochondrial DNA is inherited exclusively from the mother through maternal inheritance. After fertilization, the few mitochondria present in sperm are selectively degraded by a ubiquitin-mediated pathway in the zygote, while the many mitochondria in the ovum remain and are passed to all cells in the offspring.

The D-loop is the most important regulatory non-coding region of mitochondrial DNA and contains the origin of replication for the heavy strand. This region controls the initiation of mitochondrial DNA replication and is essential for maintaining the mitochondrial genome independent of the cell cycle.

Mitochondrial DNA exhibits relaxed replication, occurring independently of the cell cycle and continuing in daughter cells after cell division. In contrast, nuclear DNA replication is tightly coordinated with the cell cycle and must be completed before cell division, reflecting the autonomous nature of mitochondrial genome maintenance.