Most eukaryotic cells contain mitochondria, and many contain chloroplasts. Each type of organelle has its own DNA, meaning that eukaryotic cells have multiple genomes. Each eukaryotic cell has a nuclear genome consisting of the DNA in the chromosomes. Cells with mitochondria also have a mitochondrial genome, and those with chloroplasts also have a chloroplast genome.

Because the genome organization and mechanisms of protein synthesis in these organelles resemble those of bacteria, most biologists subscribe to the theory that the organelles originated as free-living bacterial cells that were engulfed by primitive eukaryotic cells billions of years ago (Chapter 27). In Chapters 7 and 8, we saw that the likely ancestor of mitochondria resembled a group of today’s non-photosynthetic bacteria (a group that includes E. coli), and the likely ancestor of chloroplasts resembled today’s photosynthetic cyanobacteria. In both cases, the DNA of the organelles became smaller during the course of evolution because most of the genes were transferred to the DNA in the nucleus. If the products of these transferred genes are needed in the organelles, they are synthesized in the cytoplasm and targeted for entry into the organelles by signal sequences (Chapter 5).

DNA in mitochondria and chloroplasts is usually circular and exists in multiple copies per organelle. Among animals, the size of a mitochondrial DNA molecule ranges from 14 to 18 kb. Mitochondrial DNA in plants is generally much larger, up to 100 kb. Plant chloroplast DNA is more uniform in size than mitochondrial DNA, with a range of 130 to 200 kb.

On the basis of size alone, some kind of packaging of organelle DNA is necessary. For example, the mitochondrial DNA in human cells is a circular molecule of 16 kb. Fully extended, it would have a circumference about as large as that of the mitochodrion itself. From their bacterial origin, you might expect organelle DNA to be packaged as a nucleoid rather than as a chromosome, and indeed it is. But the structures of the nucleoid in mitochondria and chloroplasts differ from each other, and also differ from those in free-living bacteria.