The endomembrane system — the focus of the last tutorial — is an example of cellular compartmentalization. A compartment is a separate space within a larger whole. In relationship to the endomembrane system, the nucleus (A), the rough ER (C), the smooth ER (G), the Golgi apparatus (D), the lysosomes (J), and all the vesicles (H and I) and vacuoles (not shown) are all compartments within the cell, each with distinct properties and functions.

Cellular compartmentalization allows cells to optimize the efficiency of the processes that occur within organelles. But despite the advantages of compartmentalization, it’s not a universal feature of life. In fact, compartmentalization of cellular functions into membrane-bound organelles is limited to only one of lives three major groups, or domains. That domain is the one that we belong to, the Eukarya. In addition to animals, eukarya includes plants, fungi, and other organisms with eukaryotic cells: cells that are relatively large, complex, and compartmentalized. And to see why that is, we need to look at how life has diverged over time.

Compartmentalization is present only in Domain Eukarya

Biochemically, bacteria are enormously diverse, but morphologically they’re they’re all small, unicellular, and prokaryotic. That means that 1) their DNA isn’t separated from the rest of the cytoplasm by a nuclear membrane; and 2) they’re not internally compartmentalized (no membrane-bound organelles). The prokaryotic cells that make up bacteria are between 1 to 10 micrometers in diameter (a micrometer is a millionth of a meter).

The lower branch leads to lives two other domains. One of these, indicated in red branches at the bottom, is the Archaea. In terms of form and structure, Archaea are a lot like bacteria. Their cells are also small and prokaryotic. Archaea, in fact, weren’t recognized as a distinct branch on the tree of life until the 1970s. This recognition came about through the work of Carl Woese, a biologist at the University of Illinois. Woese analyzed the sequences of the RNA that makes up the small subunit of the ribosome (the cell’s protein factory). His analysis revealed that Archaea and Bacteria, despite the fact that they were both prokaryotic in structure, were not an evolutionary unified group. Rather, they’re extremely distant cousins. An archaean and a bacterium are far less related to one another than we humans are to an orchid, or orchids are to bread mold (because humans, orchids, and bread mold are all in the same domain — the Eukarya — the domain that includes all of the eukaryotes).

The Eukarya, shown in blue is our group. We eukaryotes have complex, compartmentalized cells. We possess mitochondria. Our DNA is organized into multiple chromosomes, and housed in a nucleus that’s separated from the cytoplasm by a nuclear membrane. Eukaryotic cells are much larger than prokaryotic cells, ranging from 10 to 100 micrometers in size. And only eukaryotes have progressed to multicellularity. When you look around at living things, the plants, animals, and fungi that you’re looking at are all eukaryotes.

Eukaryotes arose through a kind of cellular fusion that involved the other two domains. The details of how this happened are unclear, but here’s what we know.

Eukaryotes arose through Endosymbiosis

Endosymbiosis is a biological relationship in which one species lives inside another. Many forms of endosymbiosis are negative, and involve a parasite living inside and harming a larger host (imaging a parasitic tapeworm: that’s an endosymbiotic parasite).  But endosymbiosis can also be mutualistic: a win-win relationship that benefits both sides.

• Both mitochondria and chloroplasts have a double membrane. The outer membrane is a vestige of the membrane of the archaeal cell that engulfed the bacterial cells that later became mitochondria or chloroplasts.
• Uniquely among the cell’s organelles, mitochondria and chloroplasts have their own DNA, and this DNA has the same form (a looped chromosome) as the DNA that’s found in bacteria.
• Both mitochondria and chloroplasts have their own ribosomes, and produce some of their own proteins (though many mitochondrial and chloroplast genes have been transferred to the host cell, which also produces many mitochondrial and chloroplast proteins).
• Both mitochondria and chloroplasts replicate themselves autonomously (independently of the host cell’s cell cycle).

All of this evidence points to the same conclusion: that mitochondria and chloroplasts are themselves cells. They just happen to be cells that live inside of other cells.

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