The predatory behavior of eukaryotic cells is yet another distinguishing feature of these organisms. Mitochondria are present in each and every one of these cells, or they were formerly present. These minute bodies, which are found in the cytoplasm and are surrounded by two layers of membrane, are responsible for producing the majority of the ATP that is used to power the activity of the cell. They do this by taking in oxygen and using the energy released during the oxidation of food components, such as carbohydrates. Mitochondria are the size of small bacteria, and they possess their own genome in the form of a circular DNA molecule, their own ribosomes that are distinct from those found in other parts of the eukaryotic cell, and their own transfer RNAs. Mitochondria are also the only organelles in the cell to have their own transfer RNAs. It is now generally accepted that mitochondria originated from free-living, oxygen-metabolizing bacteria that were ingested by an ancestral cell that was unable to use oxygen in any other way (that is, was anaerobic). After evading digestion, these bacteria evolved in a symbiotic relationship with the cell that swallowed them and their progeny. In exchange for the power generation they provided for their hosts, they received protection and nutrition from their hosts. The beginning of this partnership between a primitive anaerobic predator cell and an aerobic bacterial cell is thought to have occurred approximately 1.5 billion years ago, when the atmosphere of the Earth first began to contain a significant amount of oxygen.

Recent studies of the genome suggest that the first eukaryotic cells developed after an archaeal cell ingested an aerobic bacterium. This event is thought to have sparked the evolution of eukaryotic cells. This would explain why all living eukaryotic cells show evidence of having mitochondria today, even those that are known to be strict anaerobes.

Chloroplasts are a family of membrane-enclosed organelles that are present in many eukaryotic cells, most notably those of plants and algae. These organelles are responsible for photosynthesis. These organelles share similarities with mitochondria in a number of respects. The process of photosynthesis is carried out by chloroplasts, which convert carbon dioxide from the atmosphere and water into carbohydrates. These carbohydrates are then transported to the host cell to be used as fuel. In the same way that mitochondria do, chloroplasts own their own DNA. It is most likely that they were acquired by eukaryotic cells that already possessed mitochondria derived from symbiotic photosynthetic bacteria.

Because it is sustained by the chloroplasts that it captured from its predecessors, a chloroplast-containing eukaryotic cell does not need to go on the proverbial hunt for other cells to consume in order to survive. Plant cells still possess the cytoskeletal machinery necessary for movement, but they are unable to rapidly change form or phagocytose other cells like animal cells can. As a result, plant cells are incapable of digesting other cells. Instead, they surround themselves with a sturdy cell wall that functions like a defense mechanism. If the first eukaryotic cells fed on other organisms like prey, we can imagine plant cells as having transitioned from a hunting and gathering lifestyle to one more akin to farming.

Fungi are yet another type of eukaryotic life that can be found on Earth. Even though fungal cells do not include chloroplasts but do contain mitochondria, they are distinct from animal cells and protozoa in that they have a rigid outer shell. This prevents them from moving swiftly or engulfing other cells, which are two characteristics of animal cells and protozoa. It would appear that fungi have transitioned from being predators to scavengers over the course of evolution. Fungi feed on the waste products that are produced by other cells or that are released when those cells die. Fungi secrete digestive enzymes into their environment, allowing them to carry out any necessary digestion outside of their cells.

The genetic material that is used to construct eukaryotic cells originated either from the anaerobic archaeal cell that came before it or from the bacteria that became symbionts of that cell. However, the vast bulk of this information is stored in the nucleus of the cell. The mitochondria and, in the case of plant and algal cells, the chloroplasts still contain a very little amount of this data. When mitochondrial DNA and chloroplast DNA are separated from the nuclear DNA and independently studied and sequenced, it is discovered that the mitochondrial and chloroplast genomes are degenerate copies of the corresponding bacterial genomes on a smaller scale. This revelation came about as a result of the sequencing of the mitochondrial and chloroplast DNA. For example, the mitochondrial genome of a human cell only contains 16,569 nucleotide pairs, but it encodes 22 transfer RNAs, 2 components of ribosomal RNA, and 13 proteins.

Instead of being lost, many of the genes that are absent from the mitochondria and chloroplasts have moved from the symbiotic genome into the nucleus of the host cell. This migration took place rather than the genes being lost. In the same way that people have a lot of genes in their nuclear DNA that specify proteins that are needed in their mitochondria, plants have a lot of genes in their nuclear DNA that specify proteins that are needed in their chloroplasts. In both cases, the DNA sequences of these nuclear genes provide compelling evidence that they trace back to the bacterial ancestor of the organelle that they are associated with.

It cannot be denied that the mitochondrial genome, despite its little size, has benefited from natural selection. In contrast, the nuclear genomes of the vast majority of eukaryotic organisms appear to have had plenty of room to grow. It is probable that the eukaryotic way of life has made being enormous advantageous due to the fact that predators normally need to be larger than their prey and that cell size typically grows proportionally to genome size. Both of these facts can be found in the previous sentence. In most eukaryotic organisms, there has been a tremendous buildup of DNA segments that are formed from parasite transposable elements, which has contributed to the genomes becoming orders of magnitude larger than those of bacteria and archaea. The explanation of this phenomenon is unknown.

Because there is little pressure to maintain small archives, it is easier to keep everything rather than sort out the essential information from the unimportant information and dispose of the unimportant information. As a result, a large portion of our non-coding DNA is probably and most likely worthless junk that is kept around like a pile of old papers. Some remarkable eukaryotic species, such as the puffer fish, serve as a reminder of the wastefulness of their ancestors because they have successfully rid themselves of significant amounts of noncoding DNA. This is the case because these remarkable species have successfully purged themselves of noncoding DNA. However, in terms of structure, behavior, and fitness, they are very similar to species that are similar to themselves but have a far bigger amount of this DNA.

Even in relatively small eukaryotic genomes, such as the one of the puffer fish, there is more DNA that does not code for a protein than there is DNA that codes for a protein. At least some of the DNA that does not code for a protein plays essential roles. It has a particular effect on the expression of genes that are close by. Because of the presence of this regulatory DNA, eukaryotes have created their own distinctive methods for controlling how and when a gene is activated. This intricate regulation of genes is necessary for the formation of multicellular organisms with complex structures.

There can be a huge variety of differences between individual plant and animal cells. It appears that the functions of nerve cells, cells in bone, cells in skin, and cells in fat are all distinct from one another. All of these many cell types, with a few insignificant exceptions, originated from a single cell that was an egg that was fertilized, and they all have identical copies of the DNA that is found in the species.

The variations are caused by the cells in the developing embryo making selective use of their genetic instructions based on the inputs they receive from their surroundings. This is how the variants come about. The DNA is not simply a shopping list of the components that each cell must have, nor is the cell simply a collection of everything that is on the list. Similarly, the cell is not simply a collection of everything that is on the DNA. Instead, the cell acts as a multipurpose machine with sensors to pick up environmental signals and a highly developed ability to activate various sets of genes depending on the sequences of signals the cell has been exposed to. These sensors pick up environmental signals in the same way that a radio receiver picks up radio waves.

A large number of genes that code for proteins that regulate the expression of other genes are found inside the genome of eukaryotic organisms. The majority of these transcription regulators exert their effects either by attaching themselves, either directly or indirectly, to the regulatory DNA that is located close to the target genes, or by inhibiting the ability of other proteins to do so. As a consequence, eukaryotes have more extensive genomes, which not only contain information describing the physical components of the cell (the "hardware"), but also the "software" that controls how the hardware is utilized.