The amazing story of respiration
The main purpose of this article is to give an idea of the mechanism of aerobic respiration, the acquisition of energy by an organism through oxidizing food. The usual sense of respiration, breathing, is part of this process as we take in air so that oxygen can be absorbed, and carbon dioxide evolved, which are the gaseous participants. This fascinating story is of practical utility, since it helps us to understand how we can regulate our diet properly.
Before respiration is taken up, a brief survey of life and its cellular organization is made, for the benefit of those, like me, whose knowledge of biology may be deficient. This will help to understand respiration by setting the scene for it.
The universe is some scores of billions of years old, those who have studied the question say. The earth is about 4.5 billion years old, a figure established by Arthur Holmes with more reliability through the use of radioactivity. Life originated about 3.5 billion years ago--another unreliable figure, but the best we have. There is a tendency in science today to make up facts when you have run out of them. One person makes a guess, another quotes it in a publication, and a new fact is born where none existed before. This is especially true in matters like earth history or what the core of the earth is like, where there is no possibility of contradiction.
The early earth was probably not formed from hot materials. There was some gravitational energy to be disposed of, but the earth began to warm from the energy of radioactive decay. Hydrogen and helium were quickly lost, since the earth's gravity was not sufficient to retain them, and the same thing happened to any other light gases that might be around. The earth's material somehow sorted itself out into mantle and core (how this was accomplished is a mystery, but much of the sorting may have happened during coalescence of the earth). The sorting has perfected itself over the 4.5 billion succeeding years, and a crust of light rocks has formed overall.
Enough water remained to give the earth deep oceans. This would have come to the surface early because of its low density. The early oceans were not salty, and the air above them was mainly carbon dioxide and nitrogen. Here and there were locations where volcanic gases and sulphur created nonequilibrium conditions and chemical activity in this otherwise bland world, and there life began. Certainly, modern forms of life could not have originated under these conditions. The early forms were very different, and have completely disappeared, leaving no trace except in the chemistry of their descendants. Even how they obtained the energy for their metabolism is not known. Fermentation is not a suitable answer, since it is catalyzed by protein enzymes and requires starting materials which, like the enzymes, did not exist until billions of years later. This early life did, somehow, find how to use the energy of sunlight to fuel metabolism, and how to extract carbon from CO2 to make the chemicals they needed. Today, photosynthesis does this in one process. Some of the details of photosynthesis are probably of great antiquity. We have no contact with the earliest days of life, but have the results of those times.
The oxygen released by photosynthesis changed the nature of the atmosphere from a soothing, inert mixture of carbon dioxide and nitrogen into a viciously oxidizing medium, even with only a few percent of oxygen. The early life was probably not able to handle this, as the oxygen diffused into their protoplasm, destroying it. Even so, using this oxygen to oxidize the carbohydrate products of photosynthesis had been discovered by some of the early life forms, and the benefits of oxidation were extremely great--up to 18 times as much energy could be extracted from carbohydrates by oxidation as from nonoxidizing processes. Life resistant to oxygen developed in response to the new atmosphere, and some of this life enclosed the earlier forms that could carry out photosynthesis and oxygen respiration, protecting them from the oxygen while milking them for food and energy. The steadily increasing oxygen in the atmosphere and dissolved in the sea eventually killed all the older life that was not symbiotically protected in this way. Present life is all descended from the oxygen-resistant life that included the photosynthetic and respiratory bodies inherited from the first life. The photosynthetic bodies are called chloroplasts, and the respiratory bodies are called mitochondria.
By 500 million years ago, the oxygen had oxidized all the ferrous iron it could get to, and was increasing in the atmosphere, supporting a wide variety of life, both plant and animal, in the sea, whose saltiness was steadily increasing. About this time, the evolution of animal predators had favored the development of protective shells made of thick layers of calcium carbonate, using the calcium in the brackish seas and the carbon dioxide from the air. This led to the further depletion of atmospheric carbon dioxide and the deposition of thick beds of carbonate rocks. Finally, the atmosphere approached its present composition of 70 N2, 30 O2, and the sea its present saltiness. Also, most of the carbon dioxide has always been dissolved in the sea, much more than was ever in the atmosphere. The oceans used to be soda water. Carbon dioxide is now present in the atmosphere only to the amount of 0.03% - 0.04%, but plants have adapted to this low concentration. Life could not begin under these conditions.
Much the same probably happened on Mars--the origin of life, the oxygen that made its red ferric surface--but the lighter gravity allowed the water to escape, the life died, and now Mars will be lifeless forever. Venus, closer to the Sun than Earth, was too extreme for life to develop (perhaps it had no areas of chemical disequilibrium because of smaller volcanic activity, or too little water), and is still enveloped by hot clouds of sulphuric acid in a carbon dioxide atmosphere. Only our planet is lucky enough to have spoiled and become covered with mold.
A uniform feature of current life, and probably all past life as well, is its division into colloidal cells. A colloid is a substance whose surface to volume ratio is large; any part of the body is close to a surface. Colloids can be sheets, filaments or granules. Cells make great use of membranes, which are sheet colloids, to control the diffusion of molecules, but they themselves are granules surrounded by membranes that define their volume. For most of its history, life has been single cells, surrounded by a liquid, from which molecules dissolved in the liquid arrive, and into which waste products, and other products, of metabolism diffuse. Metabolism is the sum of the chemical reactions of the contents of the cell. These reactions are catalyzed and controlled by enzymes. Most enzymes are now proteins, but these very effective catalysts are a late development.
Multicellular organisms can be much larger than single cells, but are still constructed of colloidal cells and must arrange for them to be bathed in suitable fluids, fed properly, and their wastes carried away. Metabolism in the cells of multicellular organisms is the same as in single-celled organisms.
Cells that contain chloroplasts are called plants, and cells that actively move are called animals. As can be supposed, there are many organisms whose classification is doubtful. There are actively moving cells that contain chloroplasts (like Euglena), and cells that do not move that do not (like yeast). Generally, however, the distinction is a useful one, and arguments are useless. Clearly, it is possible to distinguish between cells that obtain their energy from photosynthesis and those that obtain it from food that they eat. Plants are stiffened with cellulose, animals with collagen. Plants have no nervous systems, though they can respond to their environment, while animals possess nervous systems to meet the challenges of motion. Life does not develop to suit artificial classifications, which is all that an imperfect science can conceive. The fundamental metabolic processes in a plant cell are the same as in an animal cell. Most human genes are the same as those in maize, or yeast, or a mouse.
A typical plant cell is shown at the right. The cell wall is of cellulose, and is made porous so that substances can easily pass through it. Its inner surface is a semipermeable cell membrane. The living matter of the cell is protoplasm, consisting of the nucleus and the cytoplasm. The nucleus contains the genetic material, and the control mechanisms for much of the cell metabolism. The cytoplasm contains the chloroplasts and mitochondria, which are too small to be represented. Energy is stored by means of insoluble starch grains in the cytoplasm. The vacuole contains a concentrated solution (the sap) and is usually kept turgid by osmotic pressure, since the surrounding fluids are less concentrated.
A typical animal cell is shown at the right. It is surrounded by a flexible membrane, that some single-celled animals can extend to form pseudopoda for locomotion and for enveloping food. A particle of food is shown that has been ingested by this process, and the membrane has closed behind it, so it is inside the cell but not inside the cytoplasm, in a food vacuole. The leftovers can be expelled again when the vacuole goes to the cell membrane. The nucleus contains the genetic and control mechanisms, as in the plant cell. A flagellum is shown that can be used for driving the cell through water. The flagellum can actually rotate by means of a molecular motor. Single cells do not have muscles. Some cells have cilia that oscillate. The most elaborate of the protozoa, like Paramecium, are covered with them. The cells of multicellular animals, metazoa, may have similar features, such as the cilia of cells of the breathing passages, but most do not. A glycogen grain is shown. Animal cells store energy in this form rather than as starch. Glycogen is also insoluble, and is easily reconverted to glucose.
Both the cells represented are eucaryotic, having distinct nuclei. A cell without a nucleus is called procaryotic. Most early life was procaryotic. Today, bacteria and blue-green algae are the most numerous procaryotes, both plants. Bacteria do not contain chloroplasts, and also are not motile. Biologists once fought bitterly over whether they were plants or animals, as if it mattered a damn. They are bacteria. Algae are made up of single cells containing chloroplasts, and can associate into quite macroscopic seaweeds. Stromatolites are ancient algal colonies that probably made most of the oxygen in the atmosphere. Today, single-celled diatoms are the grass of the sea. For the diatom story, see Silicon. They protect themselves by transparent silica shells, and support most of the life in the oceans. All these small plants and creatures are curious and fascinating, and often very beautiful.
It has been fashionable to call single-celled organisms "primitive" and to speak of evolution to "higher" forms of life. This is simply the old illusion of progress that is such a sterile mode of thought and encouraged by hypocritical superstition. Evolution simply tries what it can, and what survives, survives, and what does not, does not. Excellent animals, like the trilobite and the ammonite, flourished and then disappeared, not because they were in any way "lower" that what succeeded them. Horseshoe crabs, an unprepossessing "lower" form, swam with both trilobites and ammonites and still visits beaches to reproduce. In fact, the single-celled organisms that thrive today have proved conclusively that they are equal to the challenge, and represent excellent designs. Anything that can do all it needs in a single cell and survive is certainly not simple. "Higher" forms often show structures and behavior that are clearly not optimum. For example, Humans cannot control their reproduction any more successfully than yeast, and press their resources until they eventually fail.
The living cell can get the energy it needs to survive by absorbing energy from light to produce carbohydrates, or by eating carbohydrates that it find in its environment, and then burning the carbohydrates using atmospheric O2 to CO2 and H2O. This process, called respiration, is very complicated, but also very efficient. About 38% of the free energy in the nutrients can be utilized by the organism.
When fuels are burned to produce heat, and the heat is used to produce mechanical power, the efficiency is limited by the requirement that the overall entropy change caused by the heat transfers must not be negative. The most efficient engine possible is one operating reversibly between a hot temperature T and a cold temperature T'. Heat Q is absorbed at T, heat Q' is rejected at T', and the difference Q - Q' is available as work (ordered energy). The entropy principle requires that Q/T - Q'/T' = 0 if the engine is perfect, so the thermal efficiency is η = 1 - T'/T, which is always less than unity if T' > 0.
In respiration, we are not limited by this condition, and can extract all the free energy if we do it reversibly. The reactions of respiration cannot be reversible, because they must be spontaneous. Body warmth represents an irreversibility as well. This increase in entropy causes a decrease in the free energy F = U - TS, so not all the free energy in food can be realized. Nevertheless, respiration is very efficient, and this efficiency means that it must be broken up into a long chain of small steps. This chain has the same end effect as burning in air, but is extremely involved.
Nutrients can usefully be assigned to three classes. Fats are esters of fatty acids, carboxylic acids with long hydrocarbon chains, and alcohols. Esters with glycerol produce triglycerides, since glycerol has three OH groups. The hydrocarbon chains may be saturated, monounsaturated or polyunsaturated, and so are the fats they make. Fats are as close to fuels like petroleum as they can get, and provide 9.3 kcal/gm of energy. Fats are insoluble, and so can be stored safely in the body for times of need. The second class is protein, made up of 20 different kinds of amino acids. Amino acids have the COOH (carboxyl) group on one end, and the NH2 (amide) group on the other. A carboxyl on one acid and an amide group on another can fuse to make a peptide link, and proteins are long chains of amino acids. Most proteins are catalysts for reactions, or enzymes. The amino acids contain nitrogen and sulphur, making up a tool kit for the reactions of life. Protein supplies 4.1 kcal/g when it is burned, and the leftover N and S are very valuable. A kilocalorie, kcal or Cal, is the heat required to warm 1 kg (1 litre) of water by 1 °C. It is the usual calorie in diet books.
The third class is polysaccharides, which are carbohydrates with formulas Cn(H2O)m, composed of a great variety of sugars. Sugars are the raw materials for metabolism, the principal fuels of the fires of life. DNA and RNA, the molecules of heredity, are chains of sugar molecules. The core of the ATP molecule, the energy carrier of life, is a sugar. Sugars are soluble, and easy to transport. Plants assemble sugars into cellulose for structural purposes, and into starch for energy storage. Cellulose and starch are insoluble, staying where they are put. Animals store sugars as insoluble glycogen, which the liver can also manufacture from fat, and which is stored in the liver and in muscle tissue. Carbohydrates provide 4.3 kcal/g of energy, the same as proteins. In calculating the calorie content of foods, remember that foods usually contain much water. The figures above are for actual fat, protein or carbohydrate mass. A person under normal conditions cannot survive on a diet of less than 1500 kcal daily, and gains weight morbidly on more than 2500 kcal. The natural tendency is to overeat to build up reserves of fat for coming lean times. Since there are no longer any lean times, diet should be restricted accordingly.
Foods that we eat are very complex, but are broken down to simpler components for absorption, usually by means of enzymes in the digestive juices. Fats are broken down into their constituent fatty acids and glycerol by the enzyme lipase, secreted by the liver in bile. If lipase can't faze them, they simply pass through. Proteins are broken down into their amino acids by pepsin in the acid environment of the stomace, and by trypsin and peptidase in the alkaline environment of the small intestine. Protein is difficult to digest because of the variety of the amino acids. Digestion of carbohydrates begins in the mouth, since saliva contains amylase that breaks down starches into sugars, such as maltose. The enzymes maltase, sucrase and lactase split maltose, sucrose and lactose into the simple sugar glucose. Only fatty acids, glycerol, amino acids, sucrose and inorganic ions are absorbed across the wall of the ileum. A few other large molecules necessary to life, such as the vitamins, are helped across by various means.
Small molecules, such as inorganic salts, can easily enter the body in stomach and intestines. Alcohol is absorbed in the stomach, which makes alcoholic drinks absorbed quickly enough to be fun. Waiting several hours for a drink to take effect would make a bar a gloomy place. The absorption seems to be helped by carbonic acid, as in scotch and soda.
Complex molecules do not get into the body. If one lacks lactase, then lactose simply passes through to be fermented in the colon to the distress of the owner of the colon. If you consume cholesterol, it is broken up into saturated fatty acids and glycerol, and they get into the body along with the products from other fats. Only simple medicines that survive stomach acidity and are small enough to be absorbed can be taken orally. Insulin, if taken by mouth, would simply be digested like any other protein. So long as a diet is varied, the proper nutrients will be absorbed; there is no benefit in selecting this or that special food. There may be important effects of unbalance, or of excess or scarcity, or of poisoning by small molecules, but there can be no special virtue in specific foods, as so many vainly believe, to the detriment of their healths and wallets. Many organisms make a life in your colon off of things that were not absorbed, and the byproducts of these organisms (many, if not most, of which are beneficial) may be as important as what you eat. Vitamins D and K, as well as B12, seem to come from the intestinal flora. Grazing animals use bacteria in various parts of their digestive systems to break down cellulose so they can make a meal of it. We are all in this together.
Nevertheless, the main purpose of eating is to supply energy for keeping the body warm and moving, so we will concentrate here on carbohydrates as a source of energy. First of all, we have to see how energy is transported and used in the body. The central molecule in this is ATP, adenosine triphosphate, shown in the diagram at the left. Molecules like this are called nucleotides. ATP is made up of one molecule of ribose, a sugar like those linked up to form the backbone of the the long strings of RNA (ribonucleic acid), which is bonded at one end to adenine, one of the four bases of the RNA genetic code (the others are guanine, cytosine and uracil), and at the other to the curious and distinctive triphosphate chain. This consists only of phosphorus and oxygen, (PO4)(PO3)(PO3)----. The negative charges repel one another most vigorously in this O-P-O-P-O-P-O- chain, storing considerable energy electrostatically. ATP hydroyzes to split off an H2PO4- and form ADP, adenosine diphosphate. ADP can hydrolyze again to form AMP, adenosine monophosphate. A lot of energy is available in these hydrolyses, so if the hydrolysis of ATP is linked with some reaction that needs energy to go (like the contraction of a muscle) then the overall reaction will go. Contracting muscles use up ATP (anabolism) and metabolism must replenish it (catabolism). Therefore, the production of ATP is a principal aim of metabolism. An average human uses 40 kg of ATP a day (yes, 40 kg!) and it is produced on the spot, as it is needed. ATP is not stored in the body. This large amount is not all present at one time, of course, since the turnover is rapid. If the turnover time is 1 minute, then only 28g will be present at any instant.
If you put ATP into water, you will have to wait a long time for it to hydrolyze. When its energy is needed in the body, an enzyme is produced to catalyze the reaction. This permits the body to control the release of energy, and, therefore, the rate at which a reaction coupled to ATP proceeds. Control is of utmost importance in any life process.
The ATP mechanism gives clues to the development of life. The ribose and adenine look like part of an RNA molecule, which was probably the original molecule of life, before proteins and DNA, and had to perform all the tasks now performed by these molecules. Therefore, the use of ATP as an energy source predated the current metabolic pathways, but was retained since it did its job so well, and did not have to be changed. This indicates very clearly that all the mechanisms of life developed incrementally and painfully slowly, as this and that random modification proved either beneficial or fatal. We even have that some viral proteins are still produced from RNA patterns, that have to be made from DNA, which was developed subsequently. DNA proved a more stable genetic code, but this did not change the method of protein manufacture based on the older system, which made proteins from RNA. The sequence of the development of life technology is probably RNA, ATP, proteins, DNA.
An overall view of respiration is given in the diagram at the right. The original nutrients are shown at the top. Digestion produces the simple substances shown at the ends of vertical lines representing digestion. Then follow processes, different for each class of nutrient, that modify these substances into still simpler substances that can be used by the principal respiratory mechanism. Only the path for carbohydrates is shown. The names of some of the principal chemical participants are shown here and there. We note that intermediates are regenerated in a cyclic fashion. The overall result of respiration is the acceptance of food and oxygen, and the production of carbon dioxide and water, while ADP is changed into ATP.
Suppose, then, that the carbohydrates we have eaten have been broken down into glucose, a 6-carbon sugar. Glycolysis is the sequence of reactions that further break down glucose into two 3-carbon pyruvate molecules, with the production of some ATP. In the absence of oxygen, the pyruvate can be converted to alcohol or lactate by the process of fermentation, and more energy extracted from it. The enzyme zymase, produced by yeast, catalyzes alcoholic fermentation. In the presence of oxygen, much more energy can be obtained by burning it to CO2 and H2O. This is accomplished in organelles called mitochondria by the citric acid cycle, that accepts bites of 2 carbons as acetate and makes two molecules of CO2 and some molecules carrying 8 electrons, followed by oxidative phosphorylation that uses the electrons to turn O2 into H20 while converting ADP into ATP. The free energy in the food is now in the form of ATP, and CO2 is evolved. There is no need to get rid of the H2O, of course, since it is always needed around the body.
It looks very much as if a cell that originally got its energy from fermentation had enveloped some small cells (procaryotes) that had found the secret of getting energy from burning glucose in the newly-present oxygen of the atmosphere (from photosynthesis) and milked them of their ATP, while feeding them pyruvate from what it ate. All eukaryotic cells now get their energy in this way, and all contain mitochondria. A mitochondrion has an inner membrane surrounding the matrix where the important business occurs, and an outer membrane surrounding all. The inner membrane was probably the original cell membrane. The name comes from Greek mitos, "thread," and chondros, "grain," for the small, thread-like bodies. They are about 2 μm long and 0.5 μm in diameter.
The first thing a mitochondrion does is to convert the 3-carbon pyruvate into 2-carbon acetate and stick it on the protein coenzyme A (CoA) to form acetyl CoA (acCoA). The other carbon becomes CO2, and ATP is produced, together with a molecule called NADH, which carries an electron to oxidize oxygen. The acetyl CoA then adds the 2-carbon acetyl to 4-carbon oxaloacetate to make 6-carbon citrate, and regenerates the CoA. An H and an OH on the citrate are interchanged by the enzyme aconitase. Now this molecule can react with NAD+ to produce NADH and CO2, resulting in α-Ketoglutarate with 5 carbons. NAD+ comes from NADH that has done its work, and is being recycled. Now more NAD+ comes in with CoA, and makes succinyl CoA (sucCoA), CO2 and NADH. The 4-carbon succinate is now oxidized by the molecule FAD into FADH2, which is similar to NADH, more NAD+ comes in and is converted into NADH, a molecule of GTP, which is like ATP, is created, and the result is the 4-carbon oxaloacetate we started with, ready to carry another acetyl around the cycle. We have made 2CO2, 3NADH, and one each of FADH2 and GTP. All of the reactions are catalyzed by their specific enzymes, which coordinate everything into a smooth machine. We know the mechanisms, but the method of control is still foggy. Hans Krebs discovered the citric acid cycle in 1932-1937.
Together with the acetylation, the citric acid cycle has taken one 3-carbon pyruvate and made 3CO2, 4NADH, FADH2, ATP and GTP. The electron carriers now take part in a process called oxidative phosphorylation to regenerate the NAD+ and FAD that has been used by turning O2 into H2O, and in the process squeezing the energy out as ATP. This is the reason it can only operate in aerobic conditions. The citric acid cycle is about twice as efficient as any direct way to oxidize pyruvate, getting 10ATP for each acetate oxidized. The CoA is a ribonucleotide, recalling early RNA days of life, so part of the cycle at least must be very old. It was so efficient, it was never changed. When a molecule of glucose is oxidized, 36 ATP are formed. Of these, 32 come from oxidative phosphorylation (the other 4 are the ATP and GTP mentioned above). The reaction takes place on the inner membrane of the mitochondrion, while the citric acid cycle takes place in the matrix.
The oxidation of glucose according to glucose + 6H2O → 6CO2 + 6H2O yields 686 kcal/mol. The 36 ATP produced by the acetylation, citric acid cycle and oxidative phosphorylation give 263 kcal/mol. The thermodynamic efficiency of the process is, therefore, 38%, a rather high value for a system operating at room temperature. It is similar to the efficiency of a dual-cycle mercury/steam turbine power plant, no mean achievement for such a small and modest system.
This has been a condensation of a complex story that, I hope, explains the essence of glucose metabolism. The full story is told in Stryer, pp. 315-516, including what is done with fatty acids and amino acids. It is one of the most interesting stories in science, and the work of brilliant intellects. Although the body of knowledge is impressively large and satisfying, it is still incomplete and partial, especially in the area of control. The uncertainties still give ample scope for the superstitions and mumbo-jumbo of dieticians and medical practitioners.
To sum up, it is clear that you are not what you eat. What you are is made in your body from a small set of standard ingredients that are the same no matter whence they come. The problem in diet is amount and balance. There are no magic ingredients. Special diets can do damage, very seldom any good. Variety insures that all the basic substances required for nutrition are present in the diet. Natural sources will seldom provide a plethora (unhealthy excess) of any nutrient. Copper and zinc and selenium are necessary in the diet, in very small amounts. Too much copper or zinc or selenium are poisonous, never beneficial. Vitamins are required in small amounts; too much is toxic. More than the minimum amount necessary is not beneficial. Good advice is to select a diet that pleases you the most, is reasonable in amount, and is colorful, tasty and derived from many sources. Vegetables come from so many different places today that any deficiency of trace elements is very unlikely. Milk does not contain iron; maize does not contain an essential amino acid; white rice lacks B vitamins. A diet that contains all three will have all that is needed for health; a diet with just one will cause serious disease.
L. Stryer, Biochemistry, 3rd ed. (New York: W. H. Freeman, 1988).
D. G. Mackean, Introduction to Biology, 4th ed. (London: John Murray, 1969). A superior reference text for schools, and an excellent introduction to the subject, with good illustrations. The selection of material to illustrate fundamentals is excellent. It is not encyclopedic..
Composed by J. B. Calvert
Created 14 December 2002
Last revised 17 December 2002