The philosopher Bertrand Russell said, "Every living thing is a sort of imperialist, seeking to transform as much as possible of its environment into itself." Metaphors aside, cellular respiration is the formal way in which living things ultimately do this. Cellular respiration takes substances captured from the external environment (air and carbon sources) and converts them into energy for building more cells and tissues and for carrying out life-sustaining activities. It also generates waste products and water. This is not to be confused with "respiration" in the everyday sense, which usually means the same thing as "breathing." Breathing is how organisms acquire oxygen, but this is not the same as processing oxygen, and breathing cannot supply the carbon also needed for respiration; diet takes care of this, at least in animals.

Cellular respiration occurs in both plants and animals, but not in prokaryotes (e.g., bacteria), which lack mitochondria and other organelles and thus cannot make use of oxygen, limiting them to glycolysis as an energy source. Plants are perhaps more commonly associated with photosynthesis than with respiration, but photosynthesis is the source of oxygen for plant cell respiration as well as a source of oxygen that exits the plant that can be used by animals. The ultimate by-product in both cases is ATP, or adenosine triphosphate, the primary chemical energy carrier in living things.

Cellular respiration, often called aerobic respiration, is the complete breakdown of the glucose molecule in the presence of oxygen to yield carbon dioxide and water:

C₆H₁₂O₆ + 6O₂ + 38 ADP +38 P –> 6CO₂ + 6H₂O + 38 ATP + 420 Kcal

This equation has an oxidation component (C₆H₁₂O₆ –> 6CO₂), essentially a removal of electrons in the form of hydrogen atoms. It also has a reduction component, 6O₂ –> 6H₂O, which is the addition of electrons in the form of hydrogen.

What the equation as a whole translates to is that the energy held in the chemical bonds of the reactants is used to connect adenosine diphosphate (ADP) to free phosphorus atoms (P) to generate adenosine triphosphate (ATP).

The process as a whole involves multiple steps: Glycolysis takes place in the cytoplasm, followed by the Krebs cycle and the electron transport chain in the mitochondrial matrix and on the mitochondrial membrane respectively.

The first step in the breakdown of glucose in both plants and animals is a series of 10 reactions known as glycolysis. Glucose enters animal cells from the outside, via foods that are broken down into glucose molecules that circulate in the blood and are taken up by tissues where energy is most needed (including the brain). Plants, in contrast, synthesize glucose from taking in carbon dioxide from the outside and using photosynthesis to convert the CO₂ to glucose. At this point, regardless of how it got there, every molecule of glucose is committed to the same fate.

Early in glycolysis, the six-carbon glucose molecule is phosphorylated to trap it inside the cell; phosphates are negatively charged and therefore cannot drift through the cell membrane like nonpolar, uncharged molecules sometimes can. A second phosphate molecule is added, which makes the molecule unstable, and it is soon cleaved into two non-identical three-carbon compounds. These soon assume the came chemical form, and become rearranged in a series of steps to ultimately yield two molecules of pyruvate. Along the the way, two molecules of ATP are consumed (they supply the two phosphates added to glucose early on) and four are produced, two by each three-carbon process, to yield a net of two ATP molecules per molecule of glucose.

In bacteria, glycolysis alone is sufficient for the cell's – and thus the whole organism's – energy needs. But in plants and animals, such is not the case, and with pyruvate, the ultimate fate of glucose has barely begun. It should be noted that glycolysis itself does not require oxygen, but oxygen is generally included in discussions about aerobic respiration and hence cellular respiration because it is required to synthesize pyruvate.

A common misconception among biology enthusiasts is that chloroplasts serve the same function in plants that mitochondria do in animals, and that each type of organism has only one or the other. This is not so. Plants have both chloroplasts and mitochondria, whereas animals have only mitochondria. Plants use chloroplasts as generators – they use a small carbon source (CO₂) to build a larger one (glucose). Animals cells get their glucose by breaking down macromolecules such as carbohydrates, proteins and fats, and thus do not need to create glucose from within. This may seem odd and inefficient in the case of plants, but plants have evolved one feature that animals have not: the ability to harness sunlight for direct use in metabolic functions. This allows plants to literally make their own food.

Mitochondria are believed to have been a kind of free-standing bacteria many hundreds of millions of years ago, a theory supported by their remarkable structural resemblance to bacteria as well as their metabolic machinery and the presence of their own DNA and organelles called ribosomes. Eukaryotes first came into being over a billion years ago when one cell managed to engulf another (the endosymbiont hypothesis), leading to an arrangement that was very beneficial to the engulfer in this arrangement because of expanded energy-producing capabilities. Mitochondria consist of a double plasma membrane, like cells themselves; the inner membrane includes folds called cristae. The internal portion of mitochondria is known as the matrix and is analogous to the cytoplasm of whole cells.

Chloroplasts, like mitochondria, have outer and inner membranes and their own DNA. Inside the space enclosed by a the inner membrane lies an assortment of interconnected, layered and fluid-filled membranous pouches called thylakoids. Each "stack" of thylakoids forms a granum (plural: grana). The fluid within the inner membrane that surrounds the grana is called stroma.

Chloroplasts contain a pigment called chlorophyll that both gives plants their green coloration and serves as a collector of sunlight for photosynthesis. The equation for photosynthesis is exactly the reverse of that of cellular respiration, but the individual steps to get from carbon dioxide to glucose in no way resemble the reverse reactions of the electron transport chain, the Krebs cycle and glycolysis.

In this process, also called the tricarboxylic acid (TCA) cycle or the citric acid cycle, pyruvate molecules are first converted to two-carbon molecules called acetyl coenzyme A (acetyl CoA). This releases a molecule of CO₂. Acetyl CoA molecules then enter the mitochondrial matrix, where each of them combines with a four-carbon molecule of oxaloacetate to form citric acid. Thus, if you are doing careful accounting, one molecule of glucose results in two molecules of citric acid at the beginning of the Krebs cycle.

Citric acid, a six-carbon molecule, is rearranged into isocitrate, and then a carbon atom is stripped away to form ketoglutarate, with a CO₂ exiting the cycle. Ketoglutarate in turn is stripped of another carbon atom, generating another CO₂ and succinate and also forming a molecule of ATP. From there, the four-carbon succinate molecule is transformed sequentially into fumarate, malate and oxaloacetate. These reactions see hydrogen ions removed from these molecules and tacked onto high-energy electron carriers NAD+ and FAD+ to form NADH and FADH₂ respectively, which is essentially energy "creation" in disguise, as you will soon see. At the end of the Krebs cycle, the original glucose molecule has given rise to 10 NADH and two FADH₂ molecules.

The reactions of the Krebs cycle produce only two molecules of ATP per original glucose molecule, one for each "turn" of the cycle. This means that in addition to the two ATP produced in glycolysis, after the Krebs cycle, the result is a total of four ATP. But the real results of aerobic respiration have yet to unfold at this stage.

The electron transport chain, which occurs on the cristae of the inner mitochondrial membrane, is the first step in cellular respiration that explicitly relies on oxygen. The NADH and FADH₂ produced in the Krebs cycle are now poised to contribute to energy release in a major way.

The way this happens is that the hydrogen ions stored on these electron carrier molecules (a hydrogen ion can, for present purposes, be regarded as an electron pair in terms of its contribution to this part of respiration) are used to create a chemiosmotic gradient. You have perhaps heard of a concentration gradient, in which molecules flow from regions of higher concentration to areas of lower concentration, like a cube of sugar dissolving in water and the sugar particles becoming dispersed throughout. In a chemiosmotic gradient, however, the electrons from NADH and FADH₂ wind up being passed along by proteins embedded in the membrane and serving as electron transfer systems. The energy released in this process is used to pump hydrogen ions across the membrane and create a concentration gradient across it. This leads to a net flow of hydrogen atoms in one direction, and this flow is used to power an enzyme called ATP synthase, which makes ATP from ADP and P. Think of the electron transport chain as something that puts a large weight of water behind a water-wheel, the subsequent rotation of which is used to build things.

This, not incidentally, is the same process used in chloroplasts to power glucose synthesis. The energy source for creating a gradient across the chloroplast membrane is in this case not NADH and FADH₂, but sunlight. The subsequent flow of hydrogen ions in the direction of lower H+ ion concentration is used to power the synthesis of larger carbon molecules from smaller ones, starting with CO₂ and ending with C₆H₁₂O₆.

The energy that flows from the chemiosmotic gradient is used to power not only ATP production but other vital cellular processes, such as protein synthesis. If the electron transport chain is interrupted (as with prolonged oxygen deprivation), this proton gradient cannot be maintained and cellular energy production stops, just as a water-wheel stops flowing when the water around it no longer has a pressure-flow gradient.

Because each NADH molecule has been shown experimentally to produce about three molecules of ATP and each FADH₂ produces two molecules of ATP, the total energy released by the electron-transport chain reaction is (referring back to the previous section) 10 times 3 (for NADH) plus 2 times 2 (for FADH₂) for a total of 34 ATP. Add this to the 2 ATP from glycolysis and the 2 from the Krebs cycle, and this is where the 38 ATP figure in the equation for aerobic respiration comes from.