Prokaryotic vs eukaryotic cells: the key differences

The difference between prokaryotic vs eukaryotic cells is where they keep their DNA and how they divide up their work. Prokaryotic cells, the bacteria and archaea, have no nucleus: their DNA floats in the cell's interior, and they have few internal compartments. Eukaryotic cells, which make up animals, plants, fungi and many single-celled organisms, keep their DNA inside a membrane-wrapped nucleus and have organelles, including mitochondria that were once free-living bacteria.

In short

• "Prokaryote" means "before the kernel" and "eukaryote" means "true kernel"; the kernel is the nucleus.
• Eukaryotic cells are usually much larger, and are divided into compartments that each do a job.
• Mitochondria descend from bacteria that a host cell took in more than 1.45 billion years ago, which is why they still carry their own DNA.

How are prokaryotic and eukaryotic cells different, side by side?

Both kinds share the basics of every cell: a membrane, cytoplasm, DNA and ribosomes, the machines that build proteins. They differ in almost everything built on top.

	Prokaryotic cells	Eukaryotic cells
Who has them	Bacteria and archaea	Animals, plants, fungi, algae, protists
Nucleus	None; DNA sits in a region called the nucleoid	DNA enclosed in a nucleus with a double membrane
DNA shape	Usually one circular chromosome, often with small extra rings called plasmids	Several linear chromosomes, wound around proteins
Typical size	0.1 to 5 micrometers across	2 to 100 times wider than a typical prokaryote
Membrane-bound organelles	Essentially none	Many: endoplasmic reticulum, Golgi, lysosomes, mitochondria, and chloroplasts in plants
Ribosomes	Smaller (called 70S)	Larger in the cytoplasm (80S); mitochondria keep small, bacterial-style ones
Internal skeleton	Simple protein filaments	An elaborate cytoskeleton that moves cargo and changes shape
How they divide	Binary fission: copy the DNA, split in two	Mitosis, and meiosis to make sex cells
Living alone or together	Almost all single cells	Single cells or many-celled bodies

The sizes come from Wikipedia's overview of the cell. The "S" in 70S and 80S is a measure of how fast a particle settles in a centrifuge, not a direct measure of size, which is why the numbers don't add up the way sizes would.

How big is the size gap, in numbers?

Width understates the difference, because volume grows with the cube of width. Take a typical bacterium about 1 micrometer across and a typical animal cell about 20 micrometers across, treating both as spheres.

1. The animal cell is 20 times wider.
2. Volume scales with width cubed: 20 × 20 × 20 = 8,000.
3. So the animal cell holds about 8,000 times the volume of the bacterium, enough room for thousands of bacteria-sized parts.

A cell that large can't rely on molecules simply drifting from one side to the other, because diffusion slows sharply with distance. Eukaryotes solve this with compartments that concentrate each job in one place, and with a cytoskeleton that carries cargo along tracks. A single mitochondrion, for comparison, is roughly bacterium-sized, which is the first hint of where it came from.

What are the three domains of life?

In 1977 the microbiologist Carl Woese and George Fox compared a molecule that every cell has, the RNA inside its ribosomes, across many microbes. Some "bacteria" turned out to be as different from other bacteria as either was from humans. In 1990 Woese, Otto Kandler and Mark Wheelis proposed sorting all cellular life into three domains, as Wikipedia's account of the three-domain system sets out.

• Bacteria: prokaryotes, from E. coli to the cyanobacteria that make oxygen.
• Archaea: prokaryotes that look like bacteria but differ in their membranes and in much of their machinery for copying and reading DNA. Many live in hot springs, salt flats or the guts of animals, and no archaea are known to cause disease.
• Eukarya: everything with a nucleus.

So "prokaryote" names a body plan, not a family. Bacteria and archaea share the plan without being each other's closest relatives. The difference between a bacterium and a virus, which isn't a cell at all, is a separate question that virus vs bacteria answers.

Where did eukaryotic cells come from?

Eukaryotic cells arose when one cell took another inside it and the two came to depend on each other. This idea, endosymbiosis, was first put forward for chloroplasts by the Russian botanist Konstantin Mereschkowski in 1905 and 1910. Lynn Margulis gave it its modern form, with microbiological evidence, in a 1967 paper, as Wikipedia's article on symbiogenesis recounts. It was resisted at first and is now standard biology.

The evidence for mitochondria is a set of features that make sense only if they were once bacteria.

• They carry their own DNA, in a small circle like a bacterial chromosome. Human mitochondrial DNA is 16,569 base pairs long and codes for 13 proteins.
• Their ribosomes resemble bacterial ribosomes more than the cell's own.
• They have two membranes, as expected if a bacterium, with its own membrane, was wrapped in a second one from the host.
• They divide by splitting in two, on their own schedule, and a cell can't make a new mitochondrion from scratch.
• Their genes are most closely related to a group of bacteria called alphaproteobacteria.

Most of the original bacterium's genes have since moved to the host's nucleus. In a 2010 overview for Nature Education, William Martin and Marek Mentel note that mitochondrial genomes keep at most about sixty protein-coding genes, while a mitochondrion uses a thousand or more proteins encoded in the nucleus. They date the oldest undisputed eukaryote fossils to about 1.45 billion years ago, which makes that a minimum age for the merger, not its exact date.

Chloroplasts tell the same story a second time: plant and algal cells took in cyanobacteria, and chloroplasts keep their own DNA too. The host cell appears to have been an archaeon. In 2020, after a decade of work, a Japanese team reported in Nature that it had grown an Asgard archaeon, a member of the group now thought closest to that host, in the lab: a tiny, slow-growing cell about 550 nanometers across with long, branching arms.

Still argued

How many domains of life there are is still debated. If the eukaryotic host came from within the Asgard archaea, an idea widely accepted by the mid-2020s, then eukaryotes are a branch inside the archaea and the tree has two primary domains, not three. Also argued is the order of events: whether the host had already grown complex before it took in the mitochondrion, or whether the energy the mitochondrion supplied is what made complexity possible.

What do people often get wrong?

The most common error is to treat prokaryotes as primitive leftovers. Bacteria and archaea have been evolving for as long as eukaryotes have, and they run chemistry that no eukaryote can, from fixing nitrogen out of the air to living on rock. By numbers and variety, prokaryotes dominate life on Earth.

A second is that "no nucleus" means "no organization." Prokaryotic DNA is tightly folded, and many bacteria place proteins at precise spots in the cell. And a few eukaryotes have lost their mitochondria altogether over time, which shows that organelles can be shed as well as gained.

The merger itself is one of the major events in evolution, and what mitochondria do today, beyond making ATP, is the subject of what do mitochondria do?.

Check yourself

• Without looking back, name four differences between a bacterium and one of your own cells.
• Give three pieces of evidence that mitochondria were once bacteria.
• Why are bacteria and archaea both prokaryotes, but in different domains?

Sources

• The Origin of Mitochondria — William F. Martin and Marek Mentel, Nature Education, 2010
• Isolation of an archaeon at the prokaryote–eukaryote interface — Imachi and colleagues, Nature, 2020
• Three-domain system — Wikipedia
• Symbiogenesis — Wikipedia
• Cell (biology) — Wikipedia