The most important difference between these two types of organisms is that Eukaryotes possess a cell nucleus to store DNA, the cells genetic information, whereas Prokaryotic DNA is free flowing in the cytoplasm. An easy way to remember this is to look at the etymology of the word - prokaryote comes from "pro" meaning before, and "karyon" meaning kernel, which is roughly what the cell nucleus looks like under a light microscope. The presence of a cell nucleus has all sorts of implications for eukaryotic organisms - all animals, plants and fungi - the most important one being its effect on gene regulation. The additional levels of regulation of gene expression this nucleus allows is essentially what separates us from bacteria and archaea (prokaryotes).
There are many other important distinctions between Eukaryotes and Prokaryotes however:
- All Prokaryotes are unicellular organisms. This means they lack the membrane bound organelles that we rely on such as mitochondria and chloroplasts (in plants).
- Prokaryotes often contain other bits of DNA floating around the cell called plasmids, which can be transferred "horizontally", i.e between cells in a population. Eukaryotes by contrast can only transfer their genetic information "vertically", which means to their offspring.
- Eukaryotic cells can undergo mitosis and meiosis to produce daughter cells, whereas prokaryotes can only undergo mitosis to replicate themselves. This means that only eukaryotic cells can sexually reproduce, giving them an evolutionary advantage from the increase in genetic variation this process provides.
- A final significant difference is the life cycle times: prokaryotes have on average a much shorter life cycle than eukaryotes. This allows them to divide and multiply rapidly in a new environment, making them very dangerous if they become pathogenic, as exemplified by MRSA.