Respiration

From EvoWiki

In its most general sense, respiration refers to the release of energy from food. That is, it is the process by which the chemical energy of molecules ingested by an organism is converted into a form that is readily usable to power cellular processes.

Because it plays such a fundamental role in sustaining life, it occurs in all organisms except viruses, viroids and prions, which may not be considered living, depending on the definition of life one chooses to adopt. Some definitions of life include respiration as a necessary —though usually not sufficient— criterion.

Respiration encompasses several different biochemical processes. These processes are broadly classed into one of two types. Anaerobic respiration refers to respiratory processes that can occur in the absence of oxygen. Aerobic respiration refers to those that require oxygen to occur. Because of the importance of aerobic respiration in most multicellular organisms, the word "respiration" is often used to refer to the process by which these organisms exchange oxygen and the respiratory waste gas carbon dioxide with the environment.

Contents 1 Cellular respiration 1.1 Anaerobic respiration 1.2 Aerobic respiration 2 Respiratory systems 2.1 Types of respiratory system 2.2 The human respiratory system 2.3 The avian respiratory system 3 Evolution of Respiration 4 References

Cellular respiration

Some form of respiration is carried out in all cells. During respiration, a cell transfers the chemical energy of carbohydrates, lipids and sometimes proteins into the a carrier molecule. The most important such molecule is adenosine triphosphate or ATP.

Energy is extracted from ATP by hydrolytic dephosphorylation, or the removal of a phosphate group, leaving behind a molecule of adenosine diphosphate or ADP. This process, which breaks the phophoanhydride bond connecting the last two phosphate groups together has a Gibbs free energy of about -7.3 kcal/mol. This strongly exergonic or energetically favorable reaction can be coupled by proteins to many endergonic or energetically unfavorable reactions in the cell.

One of the most important food molecules is the sugar glucose because many more complex carbohydrates like polysacharrides are broken down to glucose by digestion before respiration, and because it is a common food molecule in its own right.

The aerobic respiration of glucose can be summarized as

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

or equivalently

(glucose) + 6(oxygen) → 6(carbon dioxide) +6(water).

It is worth noting that this is exactly the reverse of photosynthesis, another important biological reaction that occurs in many autotrophs and is necessary to support most life on Earth.

Also note that there is a net gain in water as a result of respiration. This is important to some organisms, such as the kangaroo rat, which are able to live their entire lives solely on water produced by processes like respiration and anabolism.

Anaerobic respiration

Anaerobic respiration consists of those respiratory processes that occur in the absence of oxygen. As its products are required for aerobic respiration to occur, this process takes place in all cells that respire. The anaerobic breakdown of glucose into pyruvate is called glycolysis. Though it releases only a relatively small proportion of the chemical energy stored in food molecules —its net product is 2 moles ATP per mole glucose broken down compared to up to 34 ATP/glucose for aerobic respiration—, many bacteria, yeast, and even some annelids are able to utilize this method by itself of respiration to survive in an anaerobic environment. When glycolysis occurs in such environments, its byproducts are transformed into lactate or ethanol (drinking alcohol) and excreted. This entire process is known as fermentation.

Because of its role in the production of ethanol, the study of fermentation was of great interest to chemists and biologists of the late nineteenth and early twentieth centuries, and much study was devoted to it. This was one of the major driving forces that led to the creation of the field of biochemistry, and as a result, glycolysis is now one of the best understood of biological processes.

Glycolysis takes place in a ten-stage reaction that usually occurs in the cytosol. Each stage is catalyzed by a different enzyme. The stages are outlined in the table below:

Stage No.	Description	Enzyme
1.	Glucose is phosphorylated.	hexokinase
2.	The hexagonal sugar glucose is isomerized into the pentagonal sugar fructose 6-phosphate	phosphoglucose isomerase
3.	Fructose 6-phosphate is phosphorylated into fructose 1,6-bisphosphate.	phosphofructokinase
4.	Fructose 1,6 bisphosphate is split into glyceraldehyde 3-phosphate and dihydroxyacetone. The glyceraldehyde 3-phosphate then proceeds directly to stage 6, while dihydroxyacetone goes to step 5.	aldolase
5.	Dihydroxyacetone is isomerized into a second molecule of glyceraldehyde 3-phosphate.	triose phosphate isomerase
6.	Each glyceraldehyde 3-phosphate is phosphorylated to 1,3 bisphosphoglycerate oxidized by a molecule of nicotinamide adenine dinucleotide or NAD+, which is converted to NADH.	glyceraldehyde 3-phosphate dehydrogenase
7.	Each 1,3 bisphosphoglycerate is de-phosphorylated to 3-phosphoglycerate and phosphorylates an ADP to produce ATP.	phosphoglycerate kinase
8.	Each 3-phosphoglycerate is isomerized to 2-phosphoglycerate.	phosphoglycerate mutase
9.	Each 2-phosphoglycerate is dehydrogenated to phosphoenol pyruvate.	enolase
10.	Each phosphoenol pyruvate donates a phosphate group to an ADP molecule.	Pyruvate kinase

The total reaction can be summarized as:

C₆H₁₂O₆ + 2NAD⁺ +2ADP +2P_i → 2C₃H₄O₃ + 2NADH 2ATP +2H⁺.

or

(glucose) + 2(NAD⁺) + 2ADP + 2(inorganic phosphate) → 2(pyruvate) + 2NADH + 2ATP.

Note that while the early stages of glycolysis require ATP to power them, the final product includes four molecules of ATP for a net gain of two ATPs. Fermentation of pyruvate to ethanol or lactic acid converts the NADH molecules back to NAD⁺ so that the cell's supply is not depleted by continued glycolysis.

Otherwise, the molecules of pyruvate that are left behind then enter into some other metabolic pathway such as biosynthesis or begin the process of aerobic respiration, and the NADH is utilized in aerobic processes to create more ATP.

Aerobic respiration

Aerobic respiration is the important process utilizing oxygen to release further chemical energy from the products of glycolysis. In eukaryotic aerobes these products —two molecules of pyruvate per molecule of glucose— are first transported to a mitochondrion, where the aerobic reactions take place. In prokaryotic aerobes the reactions take place in the cytosol, so no further transport is needed.

The pyruvate is then used to convert HS-Coenzyme A to acetyl-coenzyme A or acetyl-CoA, which passes through a series of 8 stages known as the citric acid cycle, the tricarboxylic acid cycle, or the Krebs cycle after the German biologist Sir Hans Adolf Krebs.

The acetyl-CoA is added to oxyloacetate to create citric acid and HS-CoA. The citric acid then proceeds through a series of steps in which it is converted back to oxyloacetate. In the process, the citric acid cycle produces three molecules of NADH, one of flavin adenine dinucleotide or FADH₂, one of guanosine triphosphate or GTP, two of carbon dioxide, and four protons. Energy is these products to produce ATP by the process of oxidative phosphorylation. This cycle produces up to 34 ATP molecules for each original molecule of glucose, thus making aerobic respiration 18 times more efficient than fermentation alone.

Oxidative phosphorylation is powered by the electron transport chain. This pathway occurs in the inner membrane of mitochondria in eukaryotes and on the plasma membrane of prokaryotes, and is a process by which the oxidizing agents of the previous reactions, NADH and FADH₂ are themselves oxidized by donating their electrons to proteins embedded in the membrane. The electrons are transported along a chain of molecules, each time going to a lower energy state. At the end of the chain, the electrons are accepted by molecular oxygen, which, now negatively charged, combines with the excess protons to produce water. The energy released by the electron transport chain is used to pump H⁺ across the membrane and create a proton gradient, the energy of which is used by other membrane proteins to phosphorylate ADP into ATP.

Oxidative phosphorylation is the only truly aerobic part of respiration, but it is the process that makes use of the products of the citric acid cycle, which would otherwise result in a depletion of a cell's supply of NAD⁺.

Respiratory systems

While single-celled organisms can directly procure and excrete the raw materials of respiration by diffusion across the plasma membrane, large muticellular organisms must develop some way to transport the oxygen needed for aerobic respiration and the waste gases it produces between its cells and the environment. In order to do this, the organism needs an organ system called a respiratory system. The respiratory systems of multicellular organisms allow for large-scale gas exchange, and are coupled to the circulatory system, which transports these raw materials throughout the organism.

Types of respiratory system

Animals have evolved a variety of ways of exchanging gases with their environment.

Many annelids, amphibians, some mollusks, and other animals exchange gas with the air directly through their skin, which must be kept moist at all times. The moist skin is highly vascularized to allow as much exchange of gases as is possible. However, this is an extremely inefficient method for gas exchange, and severely limits the metabolic rate and/or size of an organism (as surface area to volume ratio decreases with size). Organisms dependent on this method of respiration also have the disadvantage of being limited to a moist environment. In larger organisms, like most amphibians and some land snails, this process is supplemented by the use of lungs.

Gills are an adaptation of many acquatic organisms including fish, some mollusks, echinoderms, arthropods and amphibians in their early stage of life. These external respiratory organs allow them to extract dissolved oxygen from their environment, and to remove carbon dioxide. Gills are flaps of delicate, highly vascular, folded tissue that are usually protected by flaps of skin. Gill slits are openings that allow water to pass through them and over the gills. Because the gills are folded, they have a large surface area, and are hence able to exchange relatively large amounts of O₂ and CO₂. This is especially important as water tends to dissolve only low concentrations of O₂ and CO₂. In order to further increase the efficiency of gills, blood flows through them from the anterior to the posterior side so that it flows in the opposite direction of water creating a countercurrent exchange system, which is a highly efficient method of exchange. Some fish, like the lungfish supplement this gas exchange system by breathing air. The gills of vertebrates are homologous to the feeding tubes of hemichordates.

Lungs are an internal respiratory organ found in many terrestrial organisms. They are used by most vertebrates, and some mollusks and arthropods, like spiders. They are hollow, often branched sacs and tubes into which air is drawn, and where it is exchanged with the circulatory system. They tend to have a surface area directly related to the metabolic needs of their owners. Amphibians, for example, which get some oxygen directly through their skin, have simple, saclike lungs with little surface area, while reptiles and mammals have extremely complex, branched lungs. Air is pumped into and out of lungs by an animal's muscles. Because air can hold more oxygen than water, lungs are much more efficient than gills for gas exchange.

Tracheae (sing. trachea) are hollow tubes used by many terrestrial arthropods (especially insects) to transport air throughout their body. The systems of tubes are connected to the atmosphere through holes found in the abdomen called spiracles. After the air enters the spiracles, it is often held in reservoirs called air sacs. From the air sacs, the systems of tracheae branch into many smaller trachea, and eventually into tiny tracheoles or "air capillaries". Tracheoles are often filled with fluid through which gas must dissolve to be exchanged. During periods of greater activity, however, increased metabolism causes a surplus of water solutes in the organism's body, causing the water to leave the tracheoles by osmosis, and hence allowing an increased respiration rate. Tracheae may also be pumped by the muscles of arthropods to push air through them and ensure that there is a thorough exchange with the environment.

In photosynthetic autotrophs like plants, an excess of molecular oxygen is produced by photosynthesis of which carbon dioxide is a raw material, so exchange often proceeds in the opposite direction as normal. In vascular plants, openings in leaves known as stomata allow the exchange of gases between the leaf and the atmosphere.

The human respiratory system

The human respiratory system is built around a pair of lungs found in the thoracic cavity and connected to the atmosphere through a trachea —not homologous to the tracheae of arthropods—, pharynx, mouth and nose, collectively called the respiratory tract. There are two phases, known as inhalation and exhalation, during which air is pulled in and expelled, respectively. Inhaled air is rich in O₂ while exhaled air has a depleted oxygen supply and is rich in CO₂. Inhaled and exhaled air follow exactly opposite paths through the respiratory tract.

Inhaled air first passes through the mouth or nose into the pharynx. When passing through the nostrils, tiny hairs help to filter out the larger particles. Air passes through the nostrils into the nasal cavity where a layer of epithelial cells secrete mucous to capture remaining particles. These cells have cilia which then push the mucous containing the trapped particles out the nose or toward the back of the throat. These safeguards ensure that harmful particles do not reach the delicate lungs during inhalation.

The air then passes through a chamber called the pharynx, and then through a valve called the epiglottis into the larynx or "voice box". The larynx contains two ligaments called vocal cords, the vibration of which allow vocalization of exhaled air. This sound may be modified in the supralaryngeal pharynx to create vowel sounds. Further modification of exhaled air flow occurs in the mouth and makes language possible.

After passing through the larynx, air reaches the trachea, which is lined with more ciliated epithelial cells. The trachea branches into the primary bronchi or "bronchial tubes" which are the first part of the lungs. These then branch into secondary bronchi and so forth until they become very narrow tubes known as bronchioles. The trachea and the bronchi are kept from collapsing by flexible disks of cartilage attached to the outside. At the end of each bronchiole is a tiny sac called an alveolus (pl. alveoli). This highly vascularized sac is where most gas exchange occurs. The lungs of the average adult have about 750 million of them, and their total surface area is in excess of 80 meters, thus allowing for very efficient exchange of gas.

Inhalation is powered by muscular contractions which decrease the pressure in the thoracic (chest) cavity, hence causing the expansion of the bronchi. Except in the case of strenuous activity, exhalation is largely passive, and results from the relaxation of the diaphragm and intercostal muscles, allowing thoracic pressure to return to normal.

The avian respiratory system

Birds have a highly specialized respiratory system that allow for the strenuous activity of flying often even at high altitudes where less oxygen is present. Like most vertebrates, they have a pair of lungs. However, their respiratory system is connected to a set of air sacs used to store air and more importantly for buoyancy.

Rather than the two-way system of bronchioles and alveoli found in humans, air passes in one direction in a circular path through the lungs of birds, though the rest of the respiratory tract is two-way with inhalation and exhalation. Air passes through a system of "air capillaries" in the lungs. These run parallel to blood vessels in the lung, allowing for a highly efficient crosscurrent exchange system.

Evolution of Respiration

Fermentation is probably the oldest existing method of cellular respiration. The fact that glycolysis occurs in all known cells supports this hypothesis. It is not known how glycolysis evolved, but it is unlikely that it was the first method of respiration, as it is complex and as it exists today is catalyzed by a large number of complex enzymes. Furthermore, it creates a chicken-egg problem in that these proteins require ATP for glycolysis to take place in the first place! This suggests that early respiration was either a less efficient form of glycolysis that did not require external energy input or operated by a different mechanism entirely.

Another consideration about early respiration is the type of food molecules it used as an energy source. Glucose and other sugars do not occur often in nature except in the presence of life, so there's good reason to believe that the most primitive forms of respiration did not depend on such chemicals, but more likely obtained energy from inorganic chemicals in the environment. Beyond this, however, we can do little more than venture guesses about how pre-glycolytic might have taken place, as no living organisms are known to carry them out.

Aerobic respiration, by contrast, is thought to be a much more recent evolutionary innovation. Geological evidence indicates that there was no molecular oxygen in the early atmosphere. This is hardly surprising, since oxygen is a highly reactive substance and would tend to combine with other, more abundant substances rather than remain free, and other planetary atmospheres lack oxygen. In order for O₂ to exist in the atmosphere for any period of time, there needed to be a constant process taking place to replenish it. The best candidate for such a process is photosynthesis.

Thus, the evolution of aerobic respiration is strongly tied to that of photosynthesis. Photosynthesis must have evolved beforehand, and must have had time to fill the atmosphere and oceans with O₂. This required the oxidation of all of the exposed layers of ferrous iron, aluminum, and other chemicals to occur since, until this point, they quickly depleted the available oxygen. Since the atmosphere first became oxygen rich about two billion years ago, this places an upper limit on the age of aerobic respiration.

References

1. Alberts, B; Johnson, A; Lewis, J; Raff, M; Roberts, K; Walter, P. Molecular Biology of the Cell Third Edition, Garland Science 2002
2. Lodish, H; Berk, A; Zipursky, S L; Matsudaira, P; Baltimore, D; Darnell, J E. Molecular cell Biology Fourth Edition, W.H. Freeman and Company 2000
3. Wessells, Norman K; Hopson, Janet L. Biology, Random House Inc. 1988