Metabolism - wikipedia Metabolism `` Cell metabolism '' redirects here. For the journal, see Cell Metabolism. For the architectural movement, see Metabolism ( architecture ). Part of a series on Biochemistry Key components Biomolecules Metabolism Index Outline History and topics History Biochemistry Cell biology Bioinformatics Enzymology Genetics Immunology Molecular biology Plant biochemistry Structural biology Branches of biochemistry List of biochemists Portals : Biology, MCB Structure of adenosine triphosphate ( ATP ), a central intermediate in energy metabolism Metabolism ( from Greek : μεταβολή metabolē, `` change '' ) is the set of life - sustaining chemical transformations within the cells of organisms. The three main purposes of metabolism are the conversion of food / fuel to energy to run cellular processes, the conversion of food / fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme - catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism. Metabolism is usually divided into two categories : catabolism, the breaking down of organic matter for example, the breaking down of glucose to pyruvate, by cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell 's environment or to signals from other cells. The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food. A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy. Contents 1 Key biochemicals 1.1 Amino acids and proteins 1.2 Lipids 1.3 Carbohydrates 1.4 Nucleotides 1.5 Coenzymes 1.6 Minerals and cofactors 2 Catabolism 2.1 Digestion 2.2 Energy from organic compounds 3 Energy transformations 3.1 Oxidative phosphorylation 3.2 Energy from inorganic compounds 3.3 Energy from light 4 Anabolism 4.1 Carbon fixation 4.2 Carbohydrates and glycans 4.3 Fatty acids, isoprenoids and steroids 4.4 Proteins 4.5 Nucleotide synthesis and salvage 5 Xenobiotics and redox metabolism 6 Thermodynamics of living organisms 7 Regulation and control 8 Evolution 9 Investigation and manipulation 10 History 11 See also 12 References 13 Further reading 14 External links Key biochemicals Further information : Biomolecule, Cell ( biology ), and Biochemistry Structure of a triacylglycerol lipid This is a diagram depicting a large set of human metabolic pathways. Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule : amino acids, carbohydrates and lipids ( often called fats ). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. Type of molecule Name of monomer forms Name of polymer forms Examples of polymer forms Amino acids Amino acids Proteins ( made of polypeptides ) Fibrous proteins and globular proteins Carbohydrates Monosaccharides Polysaccharides Starch, glycogen and cellulose Nucleic acids Nucleotides Polynucleotides DNA and RNA Amino acids and proteins Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle ( tricarboxylic acid cycle ), especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress. Lipids Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform. The fats are a large group of compounds that contain fatty acids and glycerol ; a glycerol molecule attached to three fatty acid esters is called a triacylglyceride. Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids. Carbohydrates Glucose can exist in both a straight - chain and ring form. Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy ( starch, glycogen ) and structural components ( cellulose in plants, chitin in animals ). The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways. Nucleotides The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic - group - transfer reactions. Coenzymes Structure of the coenzyme acetyl - CoA. The transferable acetyl group is bonded to the sulfur atom at the extreme left. Main article : Coenzyme Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group - transfer intermediates are called coenzymes. Each class of group - transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled. One central coenzyme is adenosine triphosphate ( ATP ), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylation reactions. A vitamin is an organic compound needed in small quantities that can not be made in cells. In human nutrition, most vitamins function as coenzymes after modification ; for example, all water - soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide ( NAD ), a derivative of vitamin B ( niacin ), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD / NADH form is more important in catabolic reactions, while NADP / NADPH is used in anabolic reactions. Structure of hemoglobin. The protein subunits are in red and blue, and the iron - containing heme groups in green. From PDB : 1GZX ​. Minerals and cofactors Further information : Metal metabolism and Bioinorganic chemistry Inorganic elements play critical roles in metabolism ; some are abundant ( e.g. sodium and potassium ) while others function at minute concentrations. About 99 % of a mammal 's mass is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. Organic compounds ( proteins, lipids and carbohydrates ) contain the majority of the carbon and nitrogen ; most of the oxygen and hydrogen is present as water. The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell 's fluid, the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T - tubules. Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those. These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen - carrier proteins such as hemoglobin. Metal cofactors are bound tightly to specific sites in proteins ; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or metallothionein when not in use. Catabolism Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules. The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy and carbon ( their primary nutritional groups ), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates, and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals, these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms, such as plants and cyanobacteria, these electron - transfer reactions do not release energy but are used as a way of storing energy absorbed from sunlight. Classification of organisms based on their metabolism Energy source sunlight photo - - troph Preformed molecules chemo - Electron donor organic compound organo - inorganic compound litho - Carbon source organic compound hetero - inorganic compound auto - The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as proteins, polysaccharides or lipids, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually acetyl coenzyme A ( acetyl - CoA ), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide ( NAD ) into NADH. Digestion Further information : Digestion and Gastrointestinal tract Macromolecules such as starch, cellulose or proteins can not be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides. Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts, including the stomach and pancreas, and salivary glands. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins. A simplified outline of the catabolism of proteins, carbohydrates and fats Energy from organic compounds Further information : Cellular respiration, Fermentation ( biochemistry ), Carbohydrate catabolism, Fat catabolism, and Protein catabolism Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides. Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl - CoA through aerobic ( with oxygen ) glycolysis and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD as the acetyl - CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids. Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl - CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl - CoA, propionyl - CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol use pathway ( s ) have been validated as important during various stages of the infection lifecycle of M. tuberculosis. Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α - ketoglutarate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis ( discussed below ). Energy transformations Oxidative phosphorylation Further information : Oxidative phosphorylation, Chemiosmosis, and Mitochondrion In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell 's inner membrane. These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane. Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black. Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate -- turning it into ATP. Energy from inorganic compounds Further information : Microbial metabolism and Nitrogen cycle Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds ( such as sulfide, hydrogen sulfide and thiosulfate ), ferrous iron ( FeII ) or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility. Energy from light Further information : Phototroph, Photophosphorylation, and Chloroplast The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds. In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis. The electrons needed to drive this electron transport chain come from light - gathering proteins called photosynthetic reaction centres or rhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two. In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation. Anabolism Further information : Anabolism Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step - by - step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids. Organisms differ according to the number of constructed molecules in their cells. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy : photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions. Carbon fixation Further information : Photosynthesis, Carbon fixation, and Chemosynthesis Plant cells ( bounded by purple walls ) filled with chloroplasts ( green ), which are the site of photosynthesis Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide ( CO ). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO into glycerate 3 - phosphate, which can then be converted into glucose. This carbon - fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin -- Benson cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO directly, while C4 and CAM photosynthesis incorporate the CO into other compounds first, as adaptations to deal with intense sunlight and dry conditions. In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin -- Benson cycle, a reversed citric acid cycle, or the carboxylation of acetyl - CoA. Prokaryotic chemoautotrophs also fix CO through the Calvin -- Benson cycle, but use energy from inorganic compounds to drive the reaction. Carbohydrates and glycans Further information : Gluconeogenesis, Glyoxylate cycle, Glycogenesis, and Glycosylation In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3 - phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose - 6 - phosphate through a series of intermediates, many of which are shared with glycolysis. However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle. Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores can not be converted to glucose through gluconeogenesis as these organisms can not convert acetyl - CoA into pyruvate ; plants do, but animals do not, have the necessary enzymatic machinery. As a result, after long - term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that can not metabolize fatty acids. In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl - CoA to oxaloacetate, where it can be used for the production of glucose. Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar - phosphate donor such as uridine diphosphate glucose ( UDP - glucose ) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases. Fatty acids, isoprenoids and steroids Further information : Fatty acid synthesis and Steroid metabolism Simplified version of the steroid synthesis pathway with the intermediates isopentenyl pyrophosphate ( IPP ), dimethylallyl pyrophosphate ( DMAPP ), geranyl pyrophosphate ( GPP ) and squalene shown. Some intermediates are omitted for clarity. Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl - CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups : in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway. Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl - CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3 - phosphate as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other steroids such as cholesterol and ergosterol. Proteins Further information : Protein biosynthesis and Amino acid synthesis Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha - keto acid, which is then transaminated to form an amino acid. Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues : this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl - tRNA precursor is produced in an ATP - dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl - tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA. Nucleotide synthesis and salvage Further information : Nucleotide salvage, Pyrimidine biosynthesis, and Purine § Metabolism Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides ( bases attached to ribose ). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate. Xenobiotics and redox metabolism Further information : Xenobiotic metabolism, Drug metabolism, Alcohol metabolism, and Antioxidant All organisms are constantly exposed to compounds that they can not use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics. Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic - metabolizing enzymes. In humans, these include cytochrome P450 oxidases, UDP - glucuronosyltransferases, and glutathione S - transferases. This system of enzymes acts in three stages to firstly oxidize the xenobiotic ( phase I ) and then conjugate water - soluble groups onto the molecule ( phase II ). The modified water - soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted ( phase III ). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills. Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds. A related problem for aerobic organisms is oxidative stress. Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases. Thermodynamics of living organisms Further information : Biological thermodynamics Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy ( disorder ) can not decrease. Although living organisms ' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder. Regulation and control Further information : Metabolic pathway, Metabolic control analysis, Hormone, Regulatory enzymes, and Cell signaling As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway ( the flux through the pathway ). For example, an enzyme may show large changes in activity ( i.e. it is highly regulated ) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway. Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor ( 1 ), which in turn starts many protein activation cascades ( 2 ). These include : translocation of Glut - 4 transporter to the plasma membrane and influx of glucose ( 3 ), glycogen synthesis ( 4 ), glycolysis ( 5 ) and fatty acid synthesis ( 6 ). There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self - regulates to respond to changes in the levels of substrates or products ; for example, a decrease in the amount of product can increase the flux through the pathway to compensate. This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface. These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins. A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and glycogen. The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes. Evolution Further information : Molecular evolution and Phylogenetics Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of some of the phyla included are shown around the tree. The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal common ancestor. This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps. The first pathways of enzyme - based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world. Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step - by - step fashion with novel functions created from pre-existing steps in the pathway. An alternative model comes from studies that trace the evolution of proteins ' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways ( evident in the MANET database ) These recruitment processes result in an evolutionary enzymatic mosaic. A third possibility is that some parts of metabolism might exist as `` modules '' that can be reused in different pathways and perform similar functions on different molecules. As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host. Similar reduced metabolic capabilities are seen in endosymbiotic organisms. Investigation and manipulation Further information : Protein methods, Proteomics, Metabolomics, and Metabolic network modelling Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines. Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole - organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue ; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell. An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right : the sequences of genomes provide lists containing anything up to 45,000 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites. Bacterial metabolic networks are a striking example of bow - tie organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1, 3 - propanediol and shikimic acid. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes. History Further information : History of biochemistry and History of molecular biology The term metabolism is derived from the Greek Μεταβολισμός -- `` Metabolismos '' for `` change '', or `` overthrow ''. Aristotle 's metabolism as an open flow model Aristotle 's The Parts of Animals sets out enough details of his views on metabolism for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the classical element of fire, and residual materials being excreted as urine, bile, or faeces. Ibn al - Nafis described metabolism in his 1260 AD work titled Al - Risalah al - Kamiliyyah fil Siera al - Nabawiyyah ( The Treatise of Kamil on the Prophet 's Biography ) which included the following phrase `` Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change. '' The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina. He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called `` insensible perspiration ''. Santorio Santorio in his steelyard balance, from Ars de statica medicina, first published 1614 In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called `` ferments ''. He wrote that `` alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. '' This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells. See also Metabolism portal Underwater diving portal Anthropogenic metabolism Antimetabolite Basal metabolic rate Calorimetry Isothermal microcalorimetry Inborn error of metabolism Iron - sulfur world theory, a `` metabolism first '' theory of the origin of life Metabolic disorder Primary nutritional groups Respirometry Stream metabolism Sulfur metabolism Thermic effect of food Urban metabolism Water metabolism Overflow metabolism References ^ Jump up to : Friedrich C ( 1998 ). `` Physiology and genetics of sulfur - oxidizing bacteria ''. Adv Microb Physiol. Advances in Microbial Physiology. 39 : 235 -- 89. doi : 10.1016 / S0065 - 2911 ( 08 ) 60018 - 1. ISBN 978 - 0 - 12 - 027739 - 1. PMID 9328649. Jump up ^ Pace NR ( January 2001 ). `` The universal nature of biochemistry ''. Proc. Natl. Acad. Sci. U.S.A. 98 ( 3 ) : 805 -- 8. Bibcode : 2001PNAS... 98... 805P. doi : 10.1073 / pnas. 98.3. 805. PMC 33372. PMID 11158550. ^ Jump up to : Smith E, Morowitz H ( 2004 ). `` Universality in intermediary metabolism ''. Proc Natl Acad Sci USA. 101 ( 36 ) : 13168 -- 73. Bibcode : 2004PNAS... 10113168S. doi : 10.1073 / pnas. 0404922101. PMC 516543. PMID 15340153. ^ Jump up to : Ebenhöh O, Heinrich R ( 2001 ). `` Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems ''. Bull Math Biol. 63 ( 1 ) : 21 -- 55. doi : 10.1006 / bulm. 2000.0197. PMID 11146883. ^ Jump up to : Meléndez - Hevia E, Waddell T, Cascante M ( 1996 ). `` The puzzle of the Krebs citric acid cycle : assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution ''. J Mol Evol. 43 ( 3 ) : 293 -- 303. doi : 10.1007 / BF02338838. PMID 8703096. Jump up ^ Michie K, Löwe J ( 2006 ). `` Dynamic filaments of the bacterial cytoskeleton ''. Annu Rev Biochem. 75 : 467 -- 92. doi : 10.1146 / annurev. biochem. 75.103004. 142452. PMID 16756499. ^ Jump up to : Nelson, David L. ; Michael M. Cox ( 2005 ). Lehninger Principles of Biochemistry. New York : W.H. Freeman and company. p. 841. ISBN 0 - 7167 - 4339 - 6. Jump up ^ Kelleher J, Bryan 3rd, B, Mallet R, Holleran A, Murphy A, and Fiskum G ( 1987 ). `` Analysis of tricarboxylic acid - cycle metabolism of hepatoma cells by comparison of CO ratios ''. Biochem J. 246 ( 3 ) : 633 -- 639. doi : 10.1042 / bj2460633. PMC 1148327. PMID 3120698. CS1 maint : Uses authors parameter ( link ) Jump up ^ Hothersall, J & Ahmed, A ( 2013 ). `` Metabolic fate of the increased yeast amino acid uptake subsequent to catabolite derepression ''. J Amino Acids. 2013 : e461901. doi : 10.1155 / 2013 / 461901. PMC 3575661. PMID 23431419. Jump up ^ Fahy E, Subramaniam S, Brown H, Glass C, Merrill A, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze M, White S, Witztum J, Dennis E ( 2005 ). `` A comprehensive classification system for lipids ''. J Lipid Res. 46 ( 5 ) : 839 -- 61. doi : 10.1194 / jlr. E400004 - JLR200. PMID 15722563. Jump up ^ `` Nomenclature of Lipids ''. IUPAC - IUB Commission on Biochemical Nomenclature ( CBN ). Retrieved 2007 - 03 - 08. Jump up ^ Hegardt F ( 1999 ). `` Mitochondrial 3 - hydroxy - 3 - methylglutaryl - CoA synthase : a control enzyme in ketogenesis ''. Biochem J. 338 ( Pt 3 ) : 569 -- 82. doi : 10.1042 / 0264 - 6021 : 3380569. PMC 1220089. PMID 10051425. Jump up ^ Raman R, Raguram S, Venkataraman G, Paulson J, Sasisekharan R ( 2005 ). `` Glycomics : an integrated systems approach to structure - function relationships of glycans ''. Nat Methods. 2 ( 11 ) : 817 -- 24. doi : 10.1038 / nmeth807. PMID 16278650. Jump up ^ Sierra S, Kupfer B, Kaiser R ( 2005 ). `` Basics of the virology of HIV - 1 and its replication ''. J Clin Virol. 34 ( 4 ) : 233 -- 44. doi : 10.1016 / j. jcv. 2005.09. 004. PMID 16198625. ^ Jump up to : Wimmer M, Rose I ( 1978 ). `` Mechanisms of enzyme - catalyzed group transfer reactions ''. Annu Rev Biochem. 47 : 1031 -- 78. doi : 10.1146 / annurev. bi. 47.070178. 005123. PMID 354490. Jump up ^ Mitchell P ( 1979 ). `` The Ninth Sir Hans Krebs Lecture. Compartmentation and communication in living systems. Ligand conduction : a general catalytic principle in chemical, osmotic and chemiosmotic reaction systems ''. Eur J Biochem. 95 ( 1 ) : 1 -- 20. doi : 10.1111 / j. 1432 - 1033.1979. tb12934. x. PMID 378655. ^ Jump up to : Dimroth P, von Ballmoos C, Meier T ( March 2006 ). `` Catalytic and mechanical cycles in F - ATP synthases : Fourth in the Cycles Review Series ''. EMBO Rep. 7 ( 3 ) : 276 -- 82. doi : 10.1038 / sj. embor. 7400646. PMC 1456893. PMID 16607397. Jump up ^ Coulston, Ann ; Kerner, John ; Hattner, JoAnn ; Srivastava, Ashini ( 2006 ). `` Nutrition Principles and Clinical Nutrition ''. Stanford School of Medicine Nutrition Courses. SUMMIT. Jump up ^ Pollak N, Dölle C, Ziegler M ( 2007 ). `` The power to reduce : pyridine nucleotides -- small molecules with a multitude of functions ''. Biochem J. 402 ( 2 ) : 205 -- 18. doi : 10.1042 / BJ20061638. PMC 1798440. PMID 17295611. ^ Jump up to : Heymsfield S, Waki M, Kehayias J, Lichtman S, Dilmanian F, Kamen Y, Wang J, Pierson R ( 1991 ). `` Chemical and elemental analysis of humans in vivo using improved body composition models ''. Am J Physiol. 261 ( 2 Pt 1 ) : E190 -- 8. PMID 1872381. Jump up ^ Sychrová H ( 2004 ). `` Yeast as a model organism to study transport and homeostasis of alkali metal cations '' ( PDF ). Physiol Res. 53 Suppl 1 : S91 -- 8. PMID 15119939. Jump up ^ Levitan I ( 1988 ). `` Modulation of ion channels in neurons and other cells ''. Annu Rev Neurosci. 11 : 119 -- 36. doi : 10.1146 / annurev. ne. 11.030188. 001003. PMID 2452594. Jump up ^ Dulhunty A ( 2006 ). `` Excitation - contraction coupling from the 1950s into the new millennium ''. Clin Exp Pharmacol Physiol. 33 ( 9 ) : 763 -- 72. doi : 10.1111 / j. 1440 - 1681.2006. 04441. x. PMID 16922804. Jump up ^ Mahan D, Shields R ( 1998 ). `` Macro - and micromineral composition of pigs from birth to 145 kilograms of body weight '' ( PDF ). J Anim Sci. 76 ( 2 ) : 506 -- 12. PMID 9498359. Jump up ^ Husted S, Mikkelsen B, Jensen J, Nielsen N ( 2004 ). `` Elemental fingerprint analysis of barley ( Hordeum vulgare ) using inductively coupled plasma mass spectrometry, isotope - ratio mass spectrometry, and multivariate statistics ''. Anal Bioanal Chem. 378 ( 1 ) : 171 -- 82. doi : 10.1007 / s00216 - 003 - 2219 - 0. PMID 14551660. Jump up ^ Finney L, O'Halloran T ( 2003 ). `` Transition metal speciation in the cell : insights from the chemistry of metal ion receptors ''. Science. 300 ( 5621 ) : 931 -- 6. Bibcode : 2003Sci... 300... 931F. doi : 10.1126 / science. 1085049. PMID 12738850. Jump up ^ Cousins R, Liuzzi J, Lichten L ( 2006 ). `` Mammalian zinc transport, trafficking, and signals ''. J Biol Chem. 281 ( 34 ) : 24085 -- 9. doi : 10.1074 / jbc. R600011200. PMID 16793761. Jump up ^ Dunn L, Rahmanto Y, Richardson D ( 2007 ). `` Iron uptake and metabolism in the new millennium ''. Trends Cell Biol. 17 ( 2 ) : 93 -- 100. doi : 10.1016 / j. tcb. 2006.12. 003. PMID 17194590. Jump up ^ Nealson K, Conrad P ( 1999 ). `` Life : past, present and future ''. Philos Trans R Soc Lond B Biol Sci. 354 ( 1392 ) : 1923 -- 39. doi : 10.1098 / rstb. 1999.0532. PMC 1692713. PMID 10670014. ^ Jump up to : Nelson N, Ben - Shem A ( 2004 ). `` The complex architecture of oxygenic photosynthesis ''. Nat Rev Mol Cell Biol. 5 ( 12 ) : 971 -- 82. doi : 10.1038 / nrm1525. PMID 15573135. Jump up ^ Häse C, Finkelstein R ( December 1993 ). `` Bacterial extracellular zinc - containing metalloproteases ''. Microbiol Rev. 57 ( 4 ) : 823 -- 37. PMC 372940. PMID 8302217. Jump up ^ Gupta R, Gupta N, Rathi P ( 2004 ). `` Bacterial lipases : an overview of production, purification and biochemical properties ''. Appl Microbiol Biotechnol. 64 ( 6 ) : 763 -- 81. doi : 10.1007 / s00253 - 004 - 1568 - 8. PMID 14966663. Jump up ^ Hoyle T ( 1997 ). `` The digestive system : linking theory and practice ''. Br J Nurs. 6 ( 22 ) : 1285 -- 91. PMID 9470654. Jump up ^ Souba W, Pacitti A ( 1992 ). `` How amino acids get into cells : mechanisms, models, menus, and mediators ''. JPEN J Parenter Enteral Nutr. 16 ( 6 ) : 569 -- 78. doi : 10.1177 / 0148607192016006569. PMID 1494216. Jump up ^ Barrett M, Walmsley A, Gould G ( 1999 ). `` Structure and function of facilitative sugar transporters ''. Curr Opin Cell Biol. 11 ( 4 ) : 496 -- 502. doi : 10.1016 / S0955 - 0674 ( 99 ) 80072 - 6. PMID 10449337. Jump up ^ Bell G, Burant C, Takeda J, Gould G ( 1993 ). `` Structure and function of mammalian facilitative sugar transporters ''. J Biol Chem. 268 ( 26 ) : 19161 -- 4. PMID 8366068. ^ Jump up to : Bouché C, Serdy S, Kahn C, Goldfine A ( 2004 ). `` The cellular fate of glucose and its relevance in type 2 diabetes ''. Endocr Rev. 25 ( 5 ) : 807 -- 30. doi : 10.1210 / er. 2003 - 0026. PMID 15466941. Jump up ^ Wipperman, Matthew, F. ; Thomas, Suzanne, T. ; Sampson, Nicole, S. ( 2014 ). `` Pathogen roid rage : Cholesterol utilization by Mycobacterium tuberculosis ''. Crit. Rev. Biochem. Mol. Biol. 49 ( 4 ) : 269 -- 93. doi : 10.3109 / 10409238.2014. 895700. PMC 4255906. PMID 24611808. Jump up ^ Sakami W, Harrington H ( 1963 ). `` Amino acid metabolism ''. Annu Rev Biochem. 32 : 355 -- 98. doi : 10.1146 / annurev. bi. 32.070163. 002035. PMID 14144484. Jump up ^ Brosnan J ( 2000 ). `` Glutamate, at the interface between amino acid and carbohydrate metabolism ''. J Nutr. 130 ( 4S Suppl ) : 988S -- 90S. PMID 10736367. Jump up ^ Young V, Ajami A ( 2001 ). `` Glutamine : the emperor or his clothes ? ''. J Nutr. 131 ( 9 Suppl ) : 2449S -- 59S ; discussion 2486S -- 7S. PMID 11533293. Jump up ^ Hosler J, Ferguson - Miller S, Mills D ( 2006 ). `` Energy Transduction : Proton Transfer Through the Respiratory Complexes ''. Annu Rev Biochem. 75 : 165 -- 87. doi : 10.1146 / annurev. biochem. 75.062003. 101730. PMC 2659341. PMID 16756489. Jump up ^ Schultz B, Chan S ( 2001 ). `` Structures and proton - pumping strategies of mitochondrial respiratory enzymes ''. Annu Rev Biophys Biomol Struct. 30 : 23 -- 65. doi : 10.1146 / annurev. biophys. 30.1. 23. PMID 11340051. Jump up ^ Capaldi R, Aggeler R ( 2002 ). `` Mechanism of the F ( 1 ) F ( 0 ) - type ATP synthase, a biological rotary motor ''. Trends Biochem Sci. 27 ( 3 ) : 154 -- 60. doi : 10.1016 / S0968 - 0004 ( 01 ) 02051 - 5. PMID 11893513. Jump up ^ Friedrich B, Schwartz E ( 1993 ). `` Molecular biology of hydrogen utilization in aerobic chemolithotrophs ''. Annu Rev Microbiol. 47 : 351 -- 83. doi : 10.1146 / annurev. mi. 47.100193. 002031. PMID 8257102. Jump up ^ Weber K, Achenbach L, Coates J ( 2006 ). `` Microorganisms pumping iron : anaerobic microbial iron oxidation and reduction ''. Nat Rev Microbiol. 4 ( 10 ) : 752 -- 64. doi : 10.1038 / nrmicro1490. PMID 16980937. Jump up ^ Jetten M, Strous M, van de Pas - Schoonen K, Schalk J, van Dongen U, van de Graaf A, Logemann S, Muyzer G, van Loosdrecht M, Kuenen J ( 1998 ). `` The anaerobic oxidation of ammonium ''. FEMS Microbiol Rev. 22 ( 5 ) : 421 -- 37. doi : 10.1111 / j. 1574 - 6976.1998. tb00379. x. PMID 9990725. Jump up ^ Simon J ( 2002 ). `` Enzymology and bioenergetics of respiratory nitrite ammonification ''. FEMS Microbiol Rev. 26 ( 3 ) : 285 -- 309. doi : 10.1111 / j. 1574 - 6976.2002. tb00616. x. PMID 12165429. Jump up ^ Conrad R ( 1996 ). `` Soil microorganisms as controllers of atmospheric trace gases ( H2, CO, CH4, OCS, N2O, and NO ) ''. Microbiol Rev. 60 ( 4 ) : 609 -- 40. PMC 239458. PMID 8987358. Jump up ^ Barea J, Pozo M, Azcón R, Azcón - Aguilar C ( 2005 ). `` Microbial co-operation in the rhizosphere ''. J Exp Bot. 56 ( 417 ) : 1761 -- 78. doi : 10.1093 / jxb / eri197. PMID 15911555. Jump up ^ van der Meer M, Schouten S, Bateson M, Nübel U, Wieland A, Kühl M, de Leeuw J, Sinninghe Damsté J, Ward D ( July 2005 ). `` Diel Variations in Carbon Metabolism by Green Nonsulfur - Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park ''. Appl Environ Microbiol. 71 ( 7 ) : 3978 -- 86. doi : 10.1128 / AEM. 71.7. 3978 - 3986.2005. PMC 1168979. PMID 16000812. Jump up ^ Tichi M, Tabita F ( 2001 ). `` Interactive Control of Rhodobacter capsulatus Redox - Balancing Systems during Phototrophic Metabolism ''. J Bacteriol. 183 ( 21 ) : 6344 -- 54. doi : 10.1128 / JB. 183.21. 6344 - 6354.2001. PMC 100130. PMID 11591679. Jump up ^ Allen J, Williams J ( 1998 ). `` Photosynthetic reaction centers ''. FEBS Lett. 438 ( 1 -- 2 ) : 5 -- 9. doi : 10.1016 / S0014 - 5793 ( 98 ) 01245 - 9. PMID 9821949. Jump up ^ Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M, Shikanai T ( 2004 ). `` Cyclic electron flow around photosystem I is essential for photosynthesis ''. Nature. 429 ( 6991 ) : 579 -- 82. Bibcode : 2004Natur. 429... 579M. doi : 10.1038 / nature02598. PMID 15175756. Jump up ^ Miziorko H, Lorimer G ( 1983 ). `` Ribulose - 1, 5 - bisphosphate carboxylase - oxygenase ''. Annu Rev Biochem. 52 : 507 -- 35. doi : 10.1146 / annurev. bi. 52.070183. 002451. PMID 6351728. Jump up ^ Dodd A, Borland A, Haslam R, Griffiths H, Maxwell K ( 2002 ). `` Crassulacean acid metabolism : plastic, fantastic ''. J Exp Bot. 53 ( 369 ) : 569 -- 80. doi : 10.1093 / jexbot / 53.369. 569. PMID 11886877. Jump up ^ Hügler M, Wirsen C, Fuchs G, Taylor C, Sievert S ( May 2005 ). `` Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the ɛ Subdivision of Proteobacteria ''. J Bacteriol. 187 ( 9 ) : 3020 -- 7. doi : 10.1128 / JB. 187.9. 3020 - 3027.2005. PMC 1082812. PMID 15838028. Jump up ^ Strauss G, Fuchs G ( 1993 ). `` Enzymes of a novel autotrophic CO fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3 - hydroxypropionate cycle ''. Eur J Biochem. 215 ( 3 ) : 633 -- 43. doi : 10.1111 / j. 1432 - 1033.1993. tb18074. x. PMID 8354269. Jump up ^ Wood H ( 1991 ). `` Life with CO or CO and H as a source of carbon and energy ''. FASEB J. 5 ( 2 ) : 156 -- 63. PMID 1900793. Jump up ^ Shively J, van Keulen G, Meijer W ( 1998 ). `` Something from almost nothing : carbon dioxide fixation in chemoautotrophs ''. Annu Rev Microbiol. 52 : 191 -- 230. doi : 10.1146 / annurev. micro. 52.1. 191. PMID 9891798. Jump up ^ Boiteux A, Hess B ( 1981 ). `` Design of glycolysis ''. Philos Trans R Soc Lond B Biol Sci. 293 ( 1063 ) : 5 -- 22. Bibcode : 1981RSPTB. 293... 5B. doi : 10.1098 / rstb. 1981.0056. PMID 6115423. Jump up ^ Pilkis S, el - Maghrabi M, Claus T ( 1990 ). `` Fructose - 2, 6 - bisphosphate in control of hepatic gluconeogenesis. From metabolites to molecular genetics ''. Diabetes Care. 13 ( 6 ) : 582 -- 99. doi : 10.2337 / diacare. 13.6. 582. PMID 2162755. ^ Jump up to : Ensign S ( 2006 ). `` Revisiting the glyoxylate cycle : alternate pathways for microbial acetate assimilation ''. Mol Microbiol. 61 ( 2 ) : 274 -- 6. doi : 10.1111 / j. 1365 - 2958.2006. 05247. x. PMID 16856935. Jump up ^ Finn P, Dice J ( 2006 ). `` Proteolytic and lipolytic responses to starvation ''. Nutrition. 22 ( 7 -- 8 ) : 830 -- 44. doi : 10.1016 / j. nut. 2006.04. 008. PMID 16815497. ^ Jump up to : Kornberg H, Krebs H ( 1957 ). `` Synthesis of cell constituents from C2 - units by a modified tricarboxylic acid cycle ''. Nature. 179 ( 4568 ) : 988 -- 91. Bibcode : 1957Natur. 179... 988K. doi : 10.1038 / 179988a0. PMID 13430766. Jump up ^ Rademacher T, Parekh R, Dwek R ( 1988 ). `` Glycobiology ''. Annu Rev Biochem. 57 : 785 -- 838. doi : 10.1146 / annurev. bi. 57.070188. 004033. PMID 3052290. Jump up ^ Opdenakker G, Rudd P, Ponting C, Dwek R ( 1993 ). `` Concepts and principles of glycobiology ''. FASEB J. 7 ( 14 ) : 1330 -- 7. PMID 8224606. Jump up ^ McConville M, Menon A ( 2000 ). `` Recent developments in the cell biology and biochemistry of glycosylphosphatidylinositol lipids ( review ) ''. Mol Membr Biol. 17 ( 1 ) : 1 -- 16. doi : 10.1080 / 096876800294443. PMID 10824734. Jump up ^ Chirala S, Wakil S ( 2004 ). `` Structure and function of animal fatty acid synthase ''. Lipids. 39 ( 11 ) : 1045 -- 53. doi : 10.1007 / s11745 - 004 - 1329 - 9. PMID 15726818. Jump up ^ White S, Zheng J, Zhang Y ( 2005 ). `` The structural biology of type II fatty acid biosynthesis ''. Annu Rev Biochem. 74 : 791 -- 831. doi : 10.1146 / annurev. biochem. 74.082803. 133524. PMID 15952903. Jump up ^ Ohlrogge J, Jaworski J ( 1997 ). `` Regulation of fatty acid synthesis ''. Annu Rev Plant Physiol Plant Mol Biol. 48 : 109 -- 136. doi : 10.1146 / annurev. arplant. 48.1. 109. PMID 15012259. Jump up ^ Dubey V, Bhalla R, Luthra R ( 2003 ). `` An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants '' ( PDF ). J Biosci. 28 ( 5 ) : 637 -- 46. doi : 10.1007 / BF02703339. PMID 14517367. Archived from the original ( PDF ) on 2007 - 04 - 15. ^ Jump up to : Kuzuyama T, Seto H ( 2003 ). `` Diversity of the biosynthesis of the isoprene units ''. Nat Prod Rep. 20 ( 2 ) : 171 -- 83. doi : 10.1039 / b109860h. PMID 12735695. Jump up ^ Grochowski L, Xu H, White R ( May 2006 ). `` Methanocaldococcus jannaschii Uses a Modified Mevalonate Pathway for Biosynthesis of Isopentenyl Diphosphate ''. J Bacteriol. 188 ( 9 ) : 3192 -- 8. doi : 10.1128 / JB. 188.9. 3192 - 3198.2006. PMC 1447442. PMID 16621811. Jump up ^ Lichtenthaler H ( 1999 ). `` The 1 - Ddeoxy - D - xylulose - 5 - phosphate pathway of isoprenoid biosynthesis in plants ''. Annu Rev Plant Physiol Plant Mol Biol. 50 : 47 -- 65. doi : 10.1146 / annurev. arplant. 50.1. 47. PMID 15012203. ^ Jump up to : Schroepfer G ( 1981 ). `` Sterol biosynthesis ''. Annu Rev Biochem. 50 : 585 -- 621. doi : 10.1146 / annurev. bi. 50.070181. 003101. PMID 7023367. Jump up ^ Lees N, Skaggs B, Kirsch D, Bard M ( 1995 ). `` Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae -- a review ''. Lipids. 30 ( 3 ) : 221 -- 6. doi : 10.1007 / BF02537824. PMID 7791529. Jump up ^ Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R ( November 1996 ). `` Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae ''. Nucleic Acids Res. 24 ( 22 ) : 4420 -- 49. doi : 10.1093 / nar / 24.22. 4420. PMC 146264. PMID 8948633. Jump up ^ Guyton, Arthur C. ; John E. Hall ( 2006 ). Textbook of Medical Physiology. Philadelphia : Elsevier. pp. 855 -- 6. ISBN 0 - 7216 - 0240 - 1. Jump up ^ Ibba M, Söll D ( 2001 ). `` The renaissance of aminoacyl - tRNA synthesis ''. EMBO Rep. 2 ( 5 ) : 382 -- 7. doi : 10.1093 / embo - reports / kve095. PMC 1083889. PMID 11375928. Archived from the original on 2011 - 05 - 01. Jump up ^ Lengyel P, Söll D ( 1969 ). `` Mechanism of protein biosynthesis ''. Bacteriol Rev. 33 ( 2 ) : 264 -- 301. PMC 378322. PMID 4896351. ^ Jump up to : Rudolph F ( 1994 ). `` The biochemistry and physiology of nucleotides ''. J Nutr. 124 ( 1 Suppl ) : 124S -- 127S. PMID 8283301. Zrenner R, Stitt M, Sonnewald U, Boldt R ( 2006 ). `` Pyrimidine and purine biosynthesis and degradation in plants ''. Annu Rev Plant Biol. 57 : 805 -- 36. doi : 10.1146 / annurev. arplant. 57.032905. 105421. PMID 16669783. Jump up ^ Stasolla C, Katahira R, Thorpe T, Ashihara H ( 2003 ). `` Purine and pyrimidine nucleotide metabolism in higher plants ''. J Plant Physiol. 160 ( 11 ) : 1271 -- 95. doi : 10.1078 / 0176 - 1617 - 01169. PMID 14658380. Jump up ^ Davies O, Mendes P, Smallbone K, Malys N ( 2012 ). `` Characterisation of multiple substrate - specific ( d ) ITP / ( d ) XTPase and modelling of deaminated purine nucleotide metabolism ''. BMB Reports. 45 ( 4 ) : 259 -- 64. doi : 10.5483 / BMBRep. 2012.45. 4.259. PMID 22531138. Jump up ^ Smith J ( 1995 ). `` Enzymes of nucleotide synthesis ''. Curr Opin Struct Biol. 5 ( 6 ) : 752 -- 7. doi : 10.1016 / 0959 - 440X ( 95 ) 80007 - 7. PMID 8749362. Jump up ^ Testa B, Krämer S ( 2006 ). `` The biochemistry of drug metabolism -- an introduction : part 1. Principles and overview ''. Chem Biodivers. 3 ( 10 ) : 1053 -- 101. doi : 10.1002 / cbdv. 200690111. PMID 17193224. Jump up ^ Danielson P ( 2002 ). `` The cytochrome P450 superfamily : biochemistry, evolution and drug metabolism in humans ''. Curr Drug Metab. 3 ( 6 ) : 561 -- 97. doi : 10.2174 / 1389200023337054. PMID 12369887. Jump up ^ King C, Rios G, Green M, Tephly T ( 2000 ). `` UDP - glucuronosyltransferases ''. Curr Drug Metab. 1 ( 2 ) : 143 -- 61. doi : 10.2174 / 1389200003339171. PMID 11465080. Jump up ^ Sheehan D, Meade G, Foley V, Dowd C ( November 2001 ). `` Structure, function and evolution of glutathione transferases : implications for classification of non-mammalian members of an ancient enzyme superfamily ''. Biochem J. 360 ( Pt 1 ) : 1 -- 16. doi : 10.1042 / 0264 - 6021 : 3600001. PMC 1222196. PMID 11695986. Jump up ^ Galvão T, Mohn W, de Lorenzo V ( 2005 ). `` Exploring the microbial biodegradation and biotransformation gene pool ''. Trends Biotechnol. 23 ( 10 ) : 497 -- 506. doi : 10.1016 / j. tibtech. 2005.08. 002. PMID 16125262. Jump up ^ Janssen D, Dinkla I, Poelarends G, Terpstra P ( 2005 ). `` Bacterial degradation of xenobiotic compounds : evolution and distribution of novel enzyme activities ''. Environ Microbiol. 7 ( 12 ) : 1868 -- 82. doi : 10.1111 / j. 1462 - 2920.2005. 00966. x. PMID 16309386. Jump up ^ Davies K ( 1995 ). `` Oxidative stress : the paradox of aerobic life ''. Biochem Soc Symp. 61 : 1 -- 31. doi : 10.1042 / bss0610001. PMID 8660387. Jump up ^ Tu B, Weissman J ( 2004 ). `` Oxidative protein folding in eukaryotes : mechanisms and consequences ''. J Cell Biol. 164 ( 3 ) : 341 -- 6. doi : 10.1083 / jcb. 200311055. PMC 2172237. PMID 14757749. Jump up ^ Sies H ( 1997 ). `` Oxidative stress : oxidants and antioxidants '' ( PDF ). Exp Physiol. 82 ( 2 ) : 291 -- 5. doi : 10.1113 / expphysiol. 1997. sp004024. PMID 9129943. Jump up ^ Vertuani S, Angusti A, Manfredini S ( 2004 ). `` The antioxidants and pro-antioxidants network : an overview ''. Curr Pharm Des. 10 ( 14 ) : 1677 -- 94. doi : 10.2174 / 1381612043384655. PMID 15134565. Jump up ^ von Stockar U, Liu J ( 1999 ). `` Does microbial life always feed on negative entropy ? Thermodynamic analysis of microbial growth ''. Biochim Biophys Acta. 1412 ( 3 ) : 191 -- 211. doi : 10.1016 / S0005 - 2728 ( 99 ) 00065 - 1. PMID 10482783. Jump up ^ Demirel Y, Sandler S ( 2002 ). `` Thermodynamics and bioenergetics ''. Biophys Chem. 97 ( 2 -- 3 ) : 87 -- 111. doi : 10.1016 / S0301 - 4622 ( 02 ) 00069 - 8. PMID 12050002. Jump up ^ Albert R ( 2005 ). `` Scale - free networks in cell biology ''. J Cell Sci. 118 ( Pt 21 ) : 4947 -- 57. doi : 10.1242 / jcs. 02714. PMID 16254242. Jump up ^ Brand M ( 1997 ). `` Regulation analysis of energy metabolism ''. J Exp Biol. 200 ( Pt 2 ) : 193 -- 202. PMID 9050227. Jump up ^ Soyer O, Salathé M, Bonhoeffer S ( 2006 ). `` Signal transduction networks : topology, response and biochemical processes ''. J Theor Biol. 238 ( 2 ) : 416 -- 25. doi : 10.1016 / j. jtbi. 2005.05. 030. PMID 16045939. ^ Jump up to : Salter M, Knowles R, Pogson C ( 1994 ). `` Metabolic control ''. Essays Biochem. 28 : 1 -- 12. PMID 7925313. Jump up ^ Westerhoff H, Groen A, Wanders R ( 1984 ). `` Modern theories of metabolic control and their applications ( review ) ''. Biosci Rep. 4 ( 1 ) : 1 -- 22. doi : 10.1007 / BF01120819. PMID 6365197. Jump up ^ Fell D, Thomas S ( 1995 ). `` Physiological control of metabolic flux : the requirement for multisite modulation ''. Biochem J. 311 ( Pt 1 ) : 35 -- 9. PMC 1136115. PMID 7575476. Jump up ^ Hendrickson W ( 2005 ). `` Transduction of biochemical signals across cell membranes ''. Q Rev Biophys. 38 ( 4 ) : 321 -- 30. doi : 10.1017 / S0033583506004136. PMID 16600054. Jump up ^ Cohen P ( 2000 ). `` The regulation of protein function by multisite phosphorylation -- a 25 year update ''. Trends Biochem Sci. 25 ( 12 ) : 596 -- 601. doi : 10.1016 / S0968 - 0004 ( 00 ) 01712 - 6. PMID 11116185. Jump up ^ Lienhard G, Slot J, James D, Mueckler M ( 1992 ). `` How cells absorb glucose ''. Sci Am. 266 ( 1 ) : 86 -- 91. doi : 10.1038 / scientificamerican0192 - 86. PMID 1734513. Jump up ^ Roach P ( 2002 ). `` Glycogen and its metabolism ''. Curr Mol Med. 2 ( 2 ) : 101 -- 20. doi : 10.2174 / 1566524024605761. PMID 11949930. Jump up ^ Newgard C, Brady M, O'Doherty R, Saltiel A ( 2000 ). `` Organizing glucose disposal : emerging roles of the glycogen targeting subunits of protein phosphatase - 1 '' ( PDF ). Diabetes. 49 ( 12 ) : 1967 -- 77. doi : 10.2337 / diabetes. 49.12. 1967. PMID 11117996. Jump up ^ Romano A, Conway T ( 1996 ). `` Evolution of carbohydrate metabolic pathways ''. Res Microbiol. 147 ( 6 -- 7 ) : 448 -- 55. doi : 10.1016 / 0923 - 2508 ( 96 ) 83998 - 2. PMID 9084754. Jump up ^ Koch A ( 1998 ). `` How did bacteria come to be ? ''. Adv Microb Physiol. Advances in Microbial Physiology. 40 : 353 -- 99. doi : 10.1016 / S0065 - 2911 ( 08 ) 60135 - 6. ISBN 978 - 0 - 12 - 027740 - 7. PMID 9889982. Jump up ^ Ouzounis C, Kyrpides N ( 1996 ). `` The emergence of major cellular processes in evolution ''. FEBS Lett. 390 ( 2 ) : 119 -- 23. doi : 10.1016 / 0014 - 5793 ( 96 ) 00631 - X. PMID 8706840. Jump up ^ Caetano - Anolles G, Kim HS, Mittenthal JE ( 2007 ). `` The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture ''. Proc Natl Acad Sci USA. 104 ( 22 ) : 9358 -- 63. Bibcode : 2007PNAS... 104.9358 C. doi : 10.1073 / pnas. 0701214104. PMC 1890499. PMID 17517598. Jump up ^ Schmidt S, Sunyaev S, Bork P, Dandekar T ( 2003 ). `` Metabolites : a helping hand for pathway evolution ? ''. Trends Biochem Sci. 28 ( 6 ) : 336 -- 41. doi : 10.1016 / S0968 - 0004 ( 03 ) 00114 - 2. PMID 12826406. Jump up ^ Light S, Kraulis P ( 2004 ). `` Network analysis of metabolic enzyme evolution in Escherichia coli ''. BMC Bioinformatics. 5 : 15. doi : 10.1186 / 1471 - 2105 - 5 - 15. PMC 394313. PMID 15113413. Alves R, Chaleil R, Sternberg M ( 2002 ). `` Evolution of enzymes in metabolism : a network perspective ''. J Mol Biol. 320 ( 4 ) : 751 -- 70. doi : 10.1016 / S0022 - 2836 ( 02 ) 00546 - 6. PMID 12095253. Jump up ^ Kim HS, Mittenthal JE, Caetano - Anolles G ( 2006 ). `` MANET : tracing evolution of protein architecture in metabolic networks ''. BMC Bioinformatics. 7 : 351. doi : 10.1186 / 1471 - 2105 - 7 - 351. PMC 1559654. PMID 16854231. Jump up ^ Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C ( 2001 ). `` Small - molecule metabolsim : an enzyme mosaic ''. Trends Biotechnol. 19 ( 12 ) : 482 -- 6. doi : 10.1016 / S0167 - 7799 ( 01 ) 01813 - 3. PMID 11711174. Jump up ^ Spirin V, Gelfand M, Mironov A, Mirny L ( June 2006 ). `` A metabolic network in the evolutionary context : Multiscale structure and modularity ''. Proc Natl Acad Sci USA. 103 ( 23 ) : 8774 -- 9. Bibcode : 2006PNAS... 103.8774 S. doi : 10.1073 / pnas. 0510258103. PMC 1482654. PMID 16731630. Jump up ^ Lawrence J ( 2005 ). `` Common themes in the genome strategies of pathogens ''. Curr Opin Genet Dev. 15 ( 6 ) : 584 -- 8. doi : 10.1016 / j. gde. 2005.09. 007. PMID 16188434. Wernegreen J ( 2005 ). `` For better or worse : genomic consequences of intracellular mutualism and parasitism ''. Curr Opin Genet Dev. 15 ( 6 ) : 572 -- 83. doi : 10.1016 / j. gde. 2005.09. 013. PMID 16230003. Jump up ^ Pál C, Papp B, Lercher M, Csermely P, Oliver S, Hurst L ( 2006 ). `` Chance and necessity in the evolution of minimal metabolic networks ''. Nature. 440 ( 7084 ) : 667 -- 70. Bibcode : 2006Natur. 440... 667P. doi : 10.1038 / nature04568. PMID 16572170. Jump up ^ Rennie M ( 1999 ). `` An introduction to the use of tracers in nutrition and metabolism ''. Proc Nutr Soc. 58 ( 4 ) : 935 -- 44. doi : 10.1017 / S002966519900124X. PMID 10817161. Jump up ^ Phair R ( 1997 ). `` Development of kinetic models in the nonlinear world of molecular cell biology ''. Metabolism. 46 ( 12 ) : 1489 -- 95. doi : 10.1016 / S0026 - 0495 ( 97 ) 90154 - 2. PMID 9439549. Jump up ^ Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y ( 2007 ). `` How many genes are there in plants (... and why are they there ) ? ''. Curr Opin Plant Biol. 10 ( 2 ) : 199 -- 203. doi : 10.1016 / j. pbi. 2007.01. 004. PMID 17289424. Jump up ^ Borodina I, Nielsen J ( 2005 ). `` From genomes to in silico cells via metabolic networks ''. Curr Opin Biotechnol. 16 ( 3 ) : 350 -- 5. doi : 10.1016 / j. copbio. 2005.04. 008. PMID 15961036. Jump up ^ Gianchandani E, Brautigan D, Papin J ( 2006 ). `` Systems analyses characterize integrated functions of biochemical networks ''. Trends Biochem Sci. 31 ( 5 ) : 284 -- 91. doi : 10.1016 / j. tibs. 2006.03. 007. PMID 16616498. Jump up ^ Duarte NC, Becker SA, Jamshidi N, et al. ( February 2007 ). `` Global reconstruction of the human metabolic network based on genomic and bibliomic data ''. Proc. Natl. Acad. Sci. U.S.A. 104 ( 6 ) : 1777 -- 82. Bibcode : 2007PNAS... 104.1777 D. doi : 10.1073 / pnas. 0610772104. PMC 1794290. PMID 17267599. Jump up ^ Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL ( May 2007 ). `` The human disease network ''. Proc. Natl. Acad. Sci. U.S.A. 104 ( 21 ) : 8685 -- 90. Bibcode : 2007PNAS... 104.8685 G. doi : 10.1073 / pnas. 0701361104. PMC 1885563. PMID 17502601. Jump up ^ Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabási AL ( July 2008 ). `` The implications of human metabolic network topology for disease comorbidity ''. Proc. Natl. Acad. Sci. U.S.A. 105 ( 29 ) : 9880 -- 9885. Bibcode : 2008PNAS... 105.9880 L. doi : 10.1073 / pnas. 0802208105. PMC 2481357. PMID 18599447. Jump up ^ Csete M, Doyle J ( 2004 ). `` Bow ties, metabolism and disease ''. Trends Biotechnol. 22 ( 9 ) : 446 -- 50. doi : 10.1016 / j. tibtech. 2004.07. 007. PMID 15331224. Jump up ^ Ma HW, Zeng AP ( 2003 ). `` The connectivity structure, giant strong component and centrality of metabolic networks ''. Bioinformatics. 19 ( 11 ) : 1423 -- 30. CiteSeerX 10.1. 1.605. 8964. doi : 10.1093 / bioinformatics / btg177. PMID 12874056. Jump up ^ Zhao J, Yu H, Luo JH, Cao ZW, Li YX ( 2006 ). `` Hierarchical modularity of nested bow - ties in metabolic networks ''. BMC Bioinformatics. 7 : 386. doi : 10.1186 / 1471 - 2105 - 7 - 386. PMC 1560398. PMID 16916470. Jump up ^ Thykaer J, Nielsen J ( 2003 ). `` Metabolic engineering of beta - lactam production ''. Metab Eng. 5 ( 1 ) : 56 -- 69. doi : 10.1016 / S1096 - 7176 ( 03 ) 00003 - X. PMID 12749845. González - Pajuelo M, Meynial - Salles I, Mendes F, Andrade J, Vasconcelos I, Soucaille P ( 2005 ). `` Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1, 3 - propanediol from glycerol ''. Metab Eng. 7 ( 5 -- 6 ) : 329 -- 36. doi : 10.1016 / j. ymben. 2005.06. 001. PMID 16095939. Krämer M, Bongaerts J, Bovenberg R, Kremer S, Müller U, Orf S, Wubbolts M, Raeven L ( 2003 ). `` Metabolic engineering for microbial production of shikimic acid ''. Metab Eng. 5 ( 4 ) : 277 -- 83. doi : 10.1016 / j. ymben. 2003.09. 001. PMID 14642355. Jump up ^ Koffas M, Roberge C, Lee K, Stephanopoulos G ( 1999 ). `` Metabolic engineering ''. Annu Rev Biomed Eng. 1 : 535 -- 57. doi : 10.1146 / annurev. bioeng. 1.1. 535. PMID 11701499. Jump up ^ `` Metabolism ''. The Online Etymology Dictionary. Retrieved 2007 - 02 - 20. Jump up ^ Leroi, Armand Marie ( 2014 ). The Lagoon : How Aristotle Invented Science. Bloomsbury. pp. 400 -- 401. ISBN 978 - 1 - 4088 - 3622 - 4. Jump up ^ Dr. Abu Shadi Al - Roubi ( 1982 ), `` Ibn Al - Nafis as a philosopher '', Symposium on Ibn al - Nafis, Second International Conference on Islamic Medicine : Islamic Medical Organization, Kuwait ( cf. Ibn al - Nafis As a Philosopher, Encyclopedia of Islamic World ( 1 ) ) Jump up ^ Eknoyan G ( 1999 ). `` Santorio Sanctorius ( 1561 -- 1636 ) -- founding father of metabolic balance studies ''. Am J Nephrol. 19 ( 2 ) : 226 -- 33. doi : 10.1159 / 000013455. PMID 10213823. Jump up ^ Williams, H.S. ( 1904 ) A History of Science : in Five Volumes. Volume IV : Modern Development of the Chemical and Biological Sciences Harper and Brothers ( New York ) Retrieved on 2007 - 03 - 26 Jump up ^ Dubos J. ( 1951 ). `` Louis Pasteur : Free Lance of Science, Gollancz. Quoted in Manchester K.L. ( 1995 ) Louis Pasteur ( 1822 -- 1895 ) -- chance and the prepared mind ''. Trends Biotechnol. 13 ( 12 ) : 511 -- 515. doi : 10.1016 / S0167 - 7799 ( 00 ) 89014 - 9. PMID 8595136. Jump up ^ Kinne - Saffran E, Kinne R ( 1999 ). `` Vitalism and synthesis of urea. From Friedrich Wöhler to Hans A. Krebs ''. Am J Nephrol. 19 ( 2 ) : 290 -- 4. doi : 10.1159 / 000013463. PMID 10213830. Jump up ^ Eduard Buchner 's 1907 Nobel lecture at http://nobelprize.org Accessed 2007 - 03 - 20 Jump up ^ Kornberg H ( 2000 ). `` Krebs and his trinity of cycles ''. Nat Rev Mol Cell Biol. 1 ( 3 ) : 225 -- 8. doi : 10.1038 / 35043073. PMID 11252898. Jump up ^ Krebs HA, Henseleit K ( 1932 ). `` Untersuchungen über die Harnstoffbildung im tierkorper ''. Z. Physiol. Chem. 210 : 33 -- 66. doi : 10.1515 / bchm2. 1932.210. 1 - 2.33. Krebs H, Johnson W ( April 1937 ). `` Metabolism of ketonic acids in animal tissues ''. Biochem J. 31 ( 4 ) : 645 -- 60. doi : 10.1042 / bj0310645. PMC 1266984. PMID 16746382. Further reading Library resources about Metabolism Online books Resources in your library Resources in other libraries Introductory Rose, S. and Mileusnic, R., The Chemistry of Life. ( Penguin Press Science, 1999 ), ISBN 0 - 14 - 027273 - 9 Schneider, E.D. and Sagan, D., Into the Cool : Energy Flow, Thermodynamics, and Life. ( University Of Chicago Press, 2005 ), ISBN 0 - 226 - 73936 - 8 Lane, N., Oxygen : The Molecule that Made the World. ( Oxford University Press, USA, 2004 ), ISBN 0 - 19 - 860783 - 0 Advanced Price, N. and Stevens, L., Fundamentals of Enzymology : Cell and Molecular Biology of Catalytic Proteins. ( Oxford University Press, 1999 ), ISBN 0 - 19 - 850229 - X Berg, J. Tymoczko, J. and Stryer, L., Biochemistry. ( W.H. Freeman and Company, 2002 ), ISBN 0 - 7167 - 4955 - 6 Cox, M. and Nelson, D.L., Lehninger Principles of Biochemistry. ( Palgrave Macmillan, 2004 ), ISBN 0 - 7167 - 4339 - 6 Brock, T.D. Madigan, M.T. Martinko, J. and Parker J., Brock 's Biology of Microorganisms. ( Benjamin Cummings, 2002 ), ISBN 0 - 13 - 066271 - 2 Da Silva, J.J.R.F. and Williams, R.J.P., The Biological Chemistry of the Elements : The Inorganic Chemistry of Life. ( Clarendon Press, 1991 ), ISBN 0 - 19 - 855598 - 9 Nicholls, D.G. and Ferguson, S.J., Bioenergetics. ( Academic Press Inc., 2002 ), ISBN 0 - 12 - 518121 - 3 External links Wikiversity has learning resources about Topic : Biochemistry Wikibooks has more on the topic of : Metabolism Look up metabolism in Wiktionary, the free dictionary. General information The Biochemistry of Metabolism Sparknotes SAT biochemistry Overview of biochemistry. School level. MIT Biology Hypertextbook Undergraduate - level guide to molecular biology. Human metabolism Topics in Medical Biochemistry Guide to human metabolic pathways. School level. http://themedicalbiochemistrypage.org/ THE Medical Biochemistry Page ) Comprehensive resource on human metabolism. Databases Flow Chart of Metabolic Pathways at ExPASy IUBMB - Nicholson Metabolic Pathways Chart SuperCYP : Database for Drug - Cytochrome - Metabolism Metabolic pathways Metabolism reference Pathway The Nitrogen cycle and Nitrogen fixation at the Wayback Machine ( archive index ) Articles related to Metabolism Metabolism map Carbon Fixation Photo - respiration Pentose Phosphate Pathway Citric Acid Cycle Glyoxylate Cycle Urea Cycle Fatty Acid Synthesis Fatty Acid Elongation Beta Oxidation Peroxisomal Beta Oxidation Glyco - genolysis Glyco - genesis Glyco - lysis Gluconeo - genesis Decarb - oxylation Fermentation Keto - lysis Keto - genesis feeders to Gluconeo - genesis Direct / C4 / CAM Carbon Intake Light Reaction Oxidative Phosphorylation Amino Acid Deamination Citrate Shuttle Lipogenesis Lipolysis Steroidogenesis MVA Pathway MEP Pathway Shikimate Pathway Transcription & Replication Translation Proteolysis Glycosy - lation Sugar Acids Double / Multiple Sugars & Glycans Simple Sugars Inositol - P Amino Sugars & Sialic Acids Nucleotide Sugars Hexose - P Triose - P Glycerol P - glycerates Pentose - P Tetrose - P Propionyl - CoA Succinate Acetyl - CoA Pentose - P P - glycerates Glyoxylate Photosystems Pyruvate Lactate Acetyl - CoA Citrate Oxalo - acetate Malate Succinyl - CoA α - Keto - glutarate Ketone Bodies Respiratory Chain Serine Group Alanine Branched - chain Amino Acids Aspartate Group Homoserine Group & Lysine Glutamate Group & Proline Arginine Creatine & Polyamines Ketogenic & Glucogenic Amino Acids Amino Acids Shikimate Aromatic Amino Acids & Histidine Ascorbate ( Vitamin C ) δ - ALA Bile Pigments Hemes Cobalamins ( Vitamin B ) Various Vitamin B 's Calciferols ( Vitamin D ) Retinoids ( Vitamin A ) Quinones ( Vitamin K ) & Carotenoids ( Vitamin E ) Cofactors Vitamins & Minerals Antioxidants PRPP Nucleotides Nucleic Acids Proteins Glycoproteins & Proteoglycans Chlorophylls MEP MVA Acetyl - CoA Polyketides Terpenoid Backbones Terpenoids & Carotenoids ( Vitamin A ) Cholesterol Bile Acids Glycero - phospholipids Glycerolipids Acyl - CoA Fatty Acids Glyco - sphingolipids Sphingolipids Waxes Polyunsaturated Fatty Acids Neurotransmitters & Thyroid Hormones Steroids Endo - cannabinoids Eicosanoids Major metabolic pathways in metro - style map. Click any text ( name of pathway or metabolites ) to link to the corresponding article. Single lines : pathways common to most lifeforms. Double lines : pathways not in humans ( occurs in e.g. plants, fungi, prokaryotes ). Orange nodes : carbohydrate metabolism. Violet nodes : photosynthesis. Red nodes : cellular respiration. Pink nodes : cell signaling. Blue nodes : amino acid metabolism. Grey nodes : vitamin and cofactor metabolism. Brown nodes : nucleotide and protein metabolism. Green nodes : lipid metabolism. Metabolism, catabolism, anabolism General Metabolic pathway Metabolic network Primary nutritional groups Energy metabolism Aerobic respiration Glycolysis → Pyruvate decarboxylation → Citric acid cycle → Oxidative phosphorylation ( electron transport chain + ATP synthase ) Anaerobic respiration Electron acceptors are other than oxygen Fermentation Glycolysis → Substrate - level phosphorylation ABE Ethanol Lactic acid Specific paths Protein metabolism Protein synthesis Catabolism Carbohydrate metabolism ( carbohydrate catabolism and anabolism ) Human Glycolysis ⇄ Gluconeogenesis Glycogenolysis ⇄ Glycogenesis Pentose phosphate pathway Fructolysis Galactolysis Glycosylation N - linked O - linked Nonhuman Photosynthesis Anoxygenic photosynthesis Chemosynthesis Carbon fixation Xylose metabolism Radiotrophism Lipid metabolism ( lipolysis, lipogenesis ) Fatty acid metabolism Fatty acid degradation ( Beta oxidation ) Fatty acid synthesis Other Steroid metabolism Sphingolipid metabolism Eicosanoid metabolism Ketosis Reverse cholesterol transport Amino acid Amino acid synthesis Urea cycle Nucleotide metabolism Purine metabolism Nucleotide salvage Pyrimidine metabolism Other Metal metabolism Iron metabolism Ethanol metabolism Metabolism : carbohydrate metabolism : glycolysis / gluconeogenesis enzymes Glycolysis Hexokinase ( HK1, HK2, HK3, Glucokinase ) → / Glucose 6 - phosphatase ← Glucose isomerase Phosphofructokinase 1 ( Liver, Muscle, Platelet ) → / Fructose 1, 6 - bisphosphatase ← Fructose - bisphosphate aldolase ( Aldolase A, B, C ) Triosephosphate isomerase Glyceraldehyde 3 - phosphate dehydrogenase Phosphoglycerate kinase Phosphoglycerate mutase Enolase Pyruvate kinase ( PKLR, PKM2 ) Gluconeogenesis only to oxaloacetate : Pyruvate carboxylase Phosphoenolpyruvate carboxykinase from lactate ( Cori cycle ) : Lactate dehydrogenase from alanine ( Alanine cycle ) : Alanine transaminase from glycerol : Glycerol kinase Glycerol dehydrogenase Regulatory Fructose 6 - P, 2 - kinase : fructose 2, 6 - bisphosphatase PFKFB1, PFKFB2, PFKFB3, PFKFB4 Bisphosphoglycerate mutase Metabolism : carbohydrate metabolism fructose and galactose enzymes Fructose / Fructolysis Hepatic fructokinase Aldolase B Triokinase Sorbitol Sorbitol dehydrogenase Aldose reductase Galactose / Galactolysis Galactokinase Galactose - 1 - phosphate uridylyltransferase / UDP - glucose 4 - epimerase Aldose reductase Lactose Lactose synthase Lactase Mannose Mannose phosphate isomerase Metabolism : carbohydrate metabolism proteoglycan enzymes glycosaminoglycan anabolism L - xylulose reductase L - gulonolactone oxidase UDP - glucuronate 5 ' - epimerase Xylosyltransferase Sulfotransferase Heparan sulfate EXT1 EXT2 Chondroitin sulfate PAPSS1 PAPSS2 glycosaminoglycan catabolism Hunter, Hurler Iduronate - 2 - sulfatase Iduronidase Sanfilippo, Sly Heparan sulfamidase N - acetyltransferase Alpha - N - acetylglucosaminidase Glucuronidase N - acetylglucosamine - 6 - sulfatase Morquio / Maroteaux - Lamy Arylsulfatase B Galactosamine - 6 sulfatase Beta - galactosidase ( GLB1 ) Metabolism : carbohydrate metabolism glycoprotein enzymes Anabolism Dolichol kinase GCS1 Oligosaccharyltransferase Catabolism Neuraminidase Beta - galactosidase Hexosaminidase mannosidase alpha - Mannosidase beta - mannosidase Aspartylglucosaminidase Fucosidase NAGA Transport SLC17A5 M6P tagging N - acetylglucosamine - 1 - phosphate transferase Metabolism, lipid metabolism, glycolipid enzymes Sphingolipid To glycosphingolipid Glycosyltransferase Sulfotransferase To ceramide From ganglioside Beta - galactosidase Hexosaminidase A Neuraminidase Glucocerebrosidase From globoside Hexosaminidase B Alpha - galactosidase Beta - galactosidase Glucocerebrosidase From sphingomyelin Sphingomyelin phosphodiesterase Sphingomyelin phosphodiesterase 1 From sulfatide Arylsulfatase A Galactosylceramidase To sphingosine Ceramidase ACER1 ACER2 ACER3 ASAH1 ASAH2 ASAH2B ASAH2C Other Sphingosine kinase NCL Palmitoyl protein thioesterase Tripeptidyl peptidase I CLN3 CLN5 CLN6 CLN8 Ceramide synthesis Serine C - palmitoyltransferase ( SPTLC1 ) Ceramide glucosyltransferase ( UGCG ) Metabolism : lipid metabolism - eicosanoid metabolism enzymes Precursor Phospholipase A2 Phospholipase C Diacylglycerol lipase Prostanoids Cyclooxygenase PTGS1 PTGS2 PGD2 synthase PGE synthase Prostaglandin - E2 9 - reductase PGI2 synthase TXA synthase Leukotrienes 5 - Lipoxygenase activating protein / Arachidonate 5 - lipoxygenase LTA4 hydrolase ( B4 synthesis ) LTC4 synthase Gamma - glutamyl transpeptidase LTD4 hydrolase Ungrouped HPGD Metabolism : lipid metabolism / fatty acid metabolism, triglyceride and fatty acid enzymes Synthesis Malonyl - CoA synthesis ATP citrate lyase Acetyl - CoA carboxylase Fatty acid synthesis / Fatty acid synthase Beta - ketoacyl - ACP synthase Β - Ketoacyl ACP reductase 3 - Hydroxyacyl ACP dehydrase Enoyl ACP reductase Fatty acid desaturases Stearoyl - CoA desaturase - 1 Triacyl glycerol Glycerol - 3 - phosphate dehydrogenase Thiokinase Degradation Acyl transport Carnitine palmitoyltransferase I Carnitine - acylcarnitine translocase Carnitine palmitoyltransferase II Beta oxidation General Acyl CoA dehydrogenase ( ACADL ACADM ACADS ACADVL ACADSB ) Enoyl - CoA hydratase MTP : HADH HADHA HADHB Acetyl - CoA C - acyltransferase Unsaturated Enoyl CoA isomerase 2, 4 Dienoyl - CoA reductase Odd chain Propionyl - CoA carboxylase Other Hydroxyacyl - Coenzyme A dehydrogenase To acetyl - CoA Malonyl - CoA decarboxylase Aldehydes Long - chain - aldehyde dehydrogenase Metabolism : amino acid metabolism - urea cycle enzymes Main cycle mitochondrial matrix : Carbamoyl phosphate synthetase I Ornithine transcarbamylase cytosol : Argininosuccinate synthetase Argininosuccinate lyase Arginase Regulatory / transport N - Acetylglutamate synthase Ornithine translocase Enzymes involved in neurotransmission monoamine histidine → histamine anabolism : Histidine decarboxylase catabolism : Histamine N - methyltransferase Diamine oxidase tyrosine → dopamine → epinephrine anabolism : Tyrosine hydroxylase Aromatic L - amino acid decarboxylase Dopamine beta - hydroxylase Phenylethanolamine N - methyltransferase catabolism : Catechol - O - methyl transferase Monoamine oxidase glutamate → GABA anabolism : Glutamate decarboxylase catabolism : 4 - aminobutyrate transaminase tryptophan → serotonin → melatonin Tryptophan hydroxylase Aromatic L - amino acid decarboxylase Aralkylamine N - acetyltransferase Acetylserotonin O - methyltransferase arginine → NO Nitric oxide synthase ( NOS1, NOS2, NOS3 ) choline → Acetylcholine anabolism : Choline acetyltransferase catabolism : Cholinesterase ( Acetylcholinesterase, Butyrylcholinesterase ) Enzymes involved in the metabolism of heme and porphyrin Porphyrin biosynthesis early mitochondrial : Aminolevulinic acid synthase ALAS1 ALAS2 cytosolic : Porphobilinogen synthase Porphobilinogen deaminase Uroporphyrinogen III synthase Uroporphyrinogen III decarboxylase late mitochondrial : Coproporphyrinogen III oxidase Protoporphyrinogen oxidase Ferrochelatase Heme degradation to bile spleen : Heme oxygenase Biliverdin reductase liver : glucuronosyltransferase UGT1A1 Metabolism of vitamins, coenzymes, and cofactors Fat soluble vitamins Vitamin A Retinol binding protein Vitamin E Alpha - tocopherol transfer protein Vitamin D liver ( Sterol 27 - hydroxylase or CYP27A1 ) renal ( 25 - Hydroxyvitamin D 1 - alpha - hydroxylase or CYP27B1 ) degradation ( 1, 25 - Dihydroxyvitamin D 24 - hydroxylase or CYP24A1 ) Vitamin K Vitamin K epoxide reductase Water soluble vitamins Thiamine ( B ) Thiamine diphosphokinase Niacin ( B ) Indoleamine 2, 3 - dioxygenase Formamidase Pantothenic acid ( B ) Pantothenate kinase Folic acid ( B ) Dihydropteroate synthase Dihydrofolate reductase Serine hydroxymethyltransferase Methylenetetrahydrofolate reductase Vitamin B MMAA MMAB MMACHC MMADHC Vitamin C L - gulonolactone oxidase Riboflavin ( B ) Riboflavin kinase Nonvitamin cofactors Tetrahydrobiopterin GTP cyclohydrolase I 6 - pyruvoyltetrahydropterin synthase Sepiapterin reductase PCBD1 PTS QDPR Molybdenum cofactor MOCS1 MOCS2 MOCS3 Gephyrin Metabolism : Protein metabolism, synthesis and catabolism enzymes Essential amino acids are in Capitals K → acetyl - CoA LYSINE → Saccharopine dehydrogenase Glutaryl - CoA dehydrogenase LEUCINE → Branched - chain amino acid aminotransferase Branched - chain alpha - keto acid dehydrogenase complex Isovaleryl coenzyme A dehydrogenase Methylcrotonyl - CoA carboxylase Methylglutaconyl - CoA hydratase 3 - hydroxy - 3 - methylglutaryl - CoA lyase TRYPTOPHAN → Indoleamine 2, 3 - dioxygenase / Tryptophan 2, 3 - dioxygenase Arylformamidase Kynureninase 3 - hydroxyanthranilate oxidase Aminocarboxymuconate - semialdehyde decarboxylase Aminomuconate - semialdehyde dehydrogenase PHENYLALANINE → tyrosine → ( see below ) G → pyruvate → citrate glycine → serine → Serine hydroxymethyltransferase Serine dehydratase glycine → creatine : Guanidinoacetate N - methyltransferase Creatine kinase alanine → Alanine transaminase cysteine → D - cysteine desulfhydrase threonine → L - threonine dehydrogenase G → glutamate → α - ketoglutarate HISTIDINE → Histidine ammonia - lyase Urocanate hydratase Formiminotransferase cyclodeaminase proline → Proline oxidase Pyrroline - 5 - carboxylate reductase 1 - Pyrroline - 5 - carboxylate dehydrogenase / ALDH4A1 PYCR1 arginine → Ornithine aminotransferase Ornithine decarboxylase Agmatinase → alpha - ketoglutarate → TCA Glutamate dehydrogenase Other cysteine + glutamate → glutathione : Gamma - glutamylcysteine synthetase Glutathione synthetase Gamma - glutamyl transpeptidase glutamate → glutamine : Glutamine synthetase Glutaminase G → propionyl - CoA → succinyl - CoA VALINE → Branched - chain amino acid aminotransferase Branched - chain alpha - keto acid dehydrogenase complex Enoyl - CoA hydratase 3 - hydroxyisobutyryl - CoA hydrolase 3 - hydroxyisobutyrate dehydrogenase Methylmalonate semialdehyde dehydrogenase ISOLEUCINE → Branched - chain amino acid aminotransferase Branched - chain alpha - keto acid dehydrogenase complex 3 - hydroxy - 2 - methylbutyryl - CoA dehydrogenase METHIONINE → generation of homocysteine : Methionine adenosyltransferase Adenosylhomocysteinase regeneration of methionine : Methionine synthase / Homocysteine methyltransferase Betaine - homocysteine methyltransferase conversion to cysteine : Cystathionine beta synthase Cystathionine gamma - lyase THREONINE → Threonine aldolase → succinyl - CoA → TCA Propionyl - CoA carboxylase Methylmalonyl CoA epimerase Methylmalonyl - CoA mutase G → fumarate PHENYLALANINE → tyrosine → Phenylalanine hydroxylase Tyrosine aminotransferase 4 - Hydroxyphenylpyruvate dioxygenase Homogentisate 1, 2 - dioxygenase Fumarylacetoacetate hydrolase tyrosine → melanin : Tyrosinase G → oxaloacetate asparagine → aspartate → Asparaginase / Asparagine synthetase Aspartate transaminase Metabolism : amino acid metabolism nucleotide enzymes Purine metabolism Anabolism R5P → IMP : Ribose - phosphate diphosphokinase Amidophosphoribosyltransferase Phosphoribosylglycinamide formyltransferase AIR synthetase ( FGAM cyclase ) Phosphoribosylaminoimidazole carboxylase Phosphoribosylaminoimidazolesuccinocarboxamide synthase IMP synthase IMP → AMP : Adenylosuccinate synthase Adenylosuccinate lyase reverse AMP deaminase IMP → GMP : IMP dehydrogenase GMP synthase reverse GMP reductase Nucleotide salvage Hypoxanthine - guanine phosphoribosyltransferase Adenine phosphoribosyltransferase Catabolism Adenosine deaminase Purine nucleoside phosphorylase Guanine deaminase Xanthine oxidase Urate oxidase Pyrimidine metabolism Anabolism CAD Carbamoyl phosphate synthase II Aspartate carbamoyltransferase Dihydroorotase Dihydroorotate dehydrogenase Orotidine 5 ' - phosphate decarboxylase / Uridine monophosphate synthetase CTP synthetase Catabolism Dihydropyrimidine dehydrogenase Dihydropyrimidinase / DPYS Beta - ureidopropionase / UPB1 Deoxyribonucleotides Ribonucleotide reductase Nucleoside - diphosphate kinase DCMP deaminase Thymidylate synthase Dihydrofolate reductase Metabolism : lipid metabolism -- ketones / cholesterol synthesis enzymes / steroid metabolism Mevalonate pathway To HMG - CoA Acetyl - Coenzyme A acetyltransferase HMG - CoA synthase ( regulated step ) Ketogenesis HMG - CoA lyase 3 - hydroxybutyrate dehydrogenase Thiophorase To Mevalonic acid HMG - CoA reductase To DMAPP Mevalonate kinase Phosphomevalonate kinase Pyrophosphomevalonate decarboxylase Isopentenyl - diphosphate delta isomerase Geranyl - Dimethylallyltranstransferase Geranyl pyrophosphate To cholesterol To lanosterol Farnesyl - diphosphate farnesyltransferase Squalene monooxygenase Lanosterol synthase 7 - Dehydrocholesterol path Lanosterol 14α - demethylase Sterol - C5 - desaturase - like 7 - Dehydrocholesterol reductase Desmosterol path 24 - Dehydrocholesterol reductase To Bile acids Cholesterol 7α - hydroxylase Sterol 27 - hydroxylase Steroidogenesis To pregnenolone Cholesterol side - chain cleavage To corticosteroids aldosterone : 18 - Hydroxylase cortisol / cortisone : 17α - Hydroxylase 11β - HSD both : 3β - HSD 21 - Hydroxylase 11β - Hydroxylase To sex hormones To androgens 17α - Hydroxylase 17, 20 - Lyase 3β - HSD 17β - HSD 5α - Reductase To estrogens Aromatase 17β - HSD Other / ungrouped Steroid metabolism : sulfatase Steroid sulfatase sulfotransferase SULT1A1 SULT2A1 Steroidogenic acute regulatory protein Cholesterol total synthesis Reverse cholesterol transport Metabolism : carbohydrate metabolism pentose phosphate pathway enzymes oxidative Glucose - 6 - phosphate dehydrogenase 6 - phosphogluconolactonase Phosphogluconate dehydrogenase nonoxidative Phosphopentose isomerase Phosphopentose epimerase Transketolase Transaldolase Metabolism - non-mevalonate pathway enzymes DXP synthase DXP reductoisomerase 2 - C - methyl - D - erythritol 4 - phosphate cytidylyltransferase 2 - C - methyl - D - erythritol 2, 4 - cyclodiphosphate synthase 4 - ( cytidine 5 ' - diphospho ) - 2 - C - methyl - D - erythritol kinase 4 - hydroxy - 3 - methylbut - 2 - en - 1 - yl diphosphate synthase 4 - hydroxy - 3 - methylbut - 2 - enyl diphosphate reductase Food science General Allergy Engineering Microbiology Nutrition Diet clinical Processing Processing aids Quality Sensory analysis Discrimination testing Rheology Storage Technology Food chemistry Additives Carbohydrates Coloring Enzymes Essential fatty acids Flavors Fortification Lipids `` Minerals '' ( Chemical elements ) Proteins Vitamins Water Food preservation Biopreservation Canning Cold chain Curing Drying Fermentation Freeze - drying Freezing Hurdle technology Irradiation Jamming Jellying Jugging Modified atmosphere Pascalization Pickling Potting Confit Potjevleesch Salting Smoking Sugaring Tyndallization Vacuum packing Food industry Manufacturing Packaging Marketing Foodservice Fortification Food safety Adulterants, food contaminants 3 - MCPD Aldicarb Cyanide Formaldehyde Lead poisoning Melamine Mercury in fish Sudan I Flavorings Monosodium glutamate ( MSG ) Salt Sugar High - fructose corn syrup Microorganisms Botulism Campylobacter jejuni Clostridium perfringens Escherichia coli O104 : H4 Escherichia coli O157 : H7 Hepatitis A Hepatitis E Listeria Norovirus Rotavirus Salmonella Parasitic infections through food Amoebiasis Anisakiasis Cryptosporidiosis Cyclosporiasis Diphyllobothriasis Enterobiasis Fasciolopsiasis Fasciolosis Giardiasis Gnathostomiasis Paragonimiasis Toxoplasmosis Trichinosis Trichuriasis Pesticides Chlorpyrifos DDT Lindane Malathion Methamidophos Preservatives Benzoic acid Ethylenediaminetetraacetic acid ( EDTA ) Sodium benzoate Sugar substitutes Acesulfame potassium Aspartame Saccharin Sodium cyclamate Sorbitol Sucralose Toxins, poisons, environment pollution Aflatoxin Arsenic contamination of groundwater Benzene in soft drinks Bisphenol A Dieldrin Diethylstilbestrol Dioxin Mycotoxins Nonylphenol Shellfish poisoning Food contamination incidents Devon colic 1858 Bradford sweets poisoning 1989 Chilean grape scare 1993 Jack in the Box E. coli outbreak 1996 Odwalla E. coli outbreak 1999 Sun Orchard salmonellosis outbreak 2005 Indonesia food scare 2006 North American E. coli O157 : H7 outbreaks 2007 Vietnam food scare 2008 Canada listeriosis outbreak 2008 Chinese milk scandal 2008 Irish pork crisis 2008 United States salmonellosis outbreak 2011 Germany E. coli O104 : H4 outbreak 2011 Taiwan food scandal 2011 United States listeriosis outbreak 2013 European aflatoxin contamination 2013 horse meat scandal 2013 Taiwan food scandal 2014 Taiwan food scandal 2015 United States E. coli outbreak 2017 Brazil weak meat scandal Food safety incidents in China Foodborne illness outbreaks death toll United States ICA meat repackaging controversy Minamata disease StarLink corn recall Toxic oil syndrome Regulation, standards, watchdogs Acceptable daily intake E number Food labeling regulations Food libel laws International Food Safety Network ISO 22000 Quality Assurance International Institutions Centre for Food Safety European Food Safety Authority Institute for Food Safety and Health International Food Safety Network Ministry of Food and Drug Safety Food substitutes Artificial fat substitutes Olestra Trans fat Artificial protein substitutes Acid - hydrolyzed vegetable protein Artificial sugar substitutes Acesulfame potassium Alitame Aspartame Aspartame - acesulfame salt Dulcin Glucin Hydrogenated starch hydrolysates Neohesperidin dihydrochalcone Neotame NutraSweet Nutrinova Saccharin Sodium cyclamate Sucralose Natural food substitutes Cheese analogues Coffee substitutes Egg substitutes Meat analogues bacon list Milk substitutes Phyllodulcin Salt substitutes Food politics Food power Food security Famine Malnutrition Overnutrition Institutions International Association for Food Protection Food and Drug Administration Food and Agriculture Organization National Agriculture and Food Research Organization National Food and Drug Authority Diving medicine, physiology, physics and environment Diving medicine Injuries and disorders Pressure Oxygen Freediving blackout Hyperoxia Hypoxia ( medical ) Oxygen toxicity Inert gases Atrial septal defect Avascular necrosis Decompression sickness Dysbaric osteonecrosis High - pressure nervous syndrome Hydrogen narcosis Isobaric counterdiffusion Nitrogen narcosis Taravana Uncontrolled decompression Carbon dioxide Hypercapnia Hypocapnia Aerosinusitis Air embolism Alternobaric vertigo Barodontalgia Barostriction Barotrauma Compression arthralgia Decompression illness Dental barotrauma Dysbarism Ear clearing Frenzel maneuver Valsalva maneuver Immersion Asphyxia Drowning Hypothermia Immersion diuresis Instinctive drowning response Laryngospasm Salt water aspiration syndrome Swimming - induced pulmonary edema List of signs and symptoms of diving disorders Cramps Diving disorders Motion sickness Surfer 's ear Treatments Diving chamber Diving medicine Hyperbaric medicine Hyperbaric treatment schedules In - water recompression Oxygen therapy Fitness to dive Diving physiology Artificial gills ( human ) Blood -- air barrier Blood shift Breathing Circulatory system CO2 retention Cold shock response Dead space ( physiology ) Decompression ( diving ) Decompression theory Diving reflex Gas exchange History of decompression research and development Lipid Maximum operating depth Metabolism Normocapnia Oxygen window in diving decompression Perfusion Physiological response to water immersion Physiology of decompression Pulmonary circulation Respiratory exchange ratio Respiratory quotient Respiratory system Systemic circulation Tissue ( biology ) Diving physics Ambient pressure Amontons ' law Anti-fog Archimedes ' principle Atmospheric pressure Boyle 's law Breathing performance of regulators Buoyancy Charles 's law Combined gas law Dalton 's law Diffusion Force Gay - Lussac 's law Henry 's law Hydrophobe Hydrostatic pressure Ideal gas law Molecular diffusion Neutral buoyancy Oxygen fraction Partial pressure Permeation Pressure Psychrometric constant Snell 's law Solubility Solution Supersaturation Surface tension Surfactant Torricellian chamber Underwater vision Weight Diving environment Algal bloom Breaking wave Ocean current Current ( stream ) Ekman transport Halocline List of diving hazards and precautions Longshore drift Rip current Stratification Surf Surge ( wave action ) Thermocline Tides Turbidity Undertow ( water waves ) Upwelling Researchers in diving medicine and physiology Arthur J. Bachrach Albert R. Behnke Paul Bert George F. Bond Robert Boyle Albert A. Bühlmann John R Clarke William Paul Fife John Scott Haldane Robert William Hamilton Jr. Leonard Erskine Hill Brian Andrew Hills Felix Hoppe - Seyler Christian J. Lambertsen Simon Mitchell Charles Momsen John Rawlins R.N. Charles Wesley Shilling Edward D. Thalmann Jules Triger Diving medical research organisations Aerospace Medical Association Divers Alert Network ( DAN ) Diving Diseases Research Centre ( DDRC ) Diving Medical Advisory Council ( DMAC ) European Diving Technology Committee ( EDTC ) European Underwater and Baromedical Society ( EUBS ) National Board of Diving and Hyperbaric Medical Technology Naval Submarine Medical Research Laboratory Royal Australian Navy School of Underwater Medicine Rubicon Foundation South Pacific Underwater Medicine Society ( SPUMS ) Southern African Underwater and Hyperbaric Medical Association ( SAUHMA ) Undersea and Hyperbaric Medical Society ( UHMS ) United States Navy Experimental Diving Unit ( NEDU ) Categories : Diving medicine Underwater diving physiology Underwater diving physics Physical oceanography Glossary Portal GND : 4057699 - 1 Retrieved from `` https://en.wikipedia.org/w/index.php?title=Metabolism&oldid=819110824 '' Categories : Metabolism Underwater diving physiology Hidden categories : CS1 maint : Uses authors parameter Wikipedia indefinitely move - protected pages Articles containing Greek - language text Webarchive template wayback links Featured articles Wikipedia articles with GND identifiers Talk Contents About Wikipedia Alemannisch Aragonés অসমীয়া Asturianu Azərbaycanca বাংলা Bân - lâm - gú Башҡортса Беларуская Беларуская ( тарашкевіца ) ‎ Български Bosanski Brezhoneg Català Čeština Cymraeg Dansk Deutsch Eesti Ελληνικά Español Esperanto Euskara فارسی Fiji Hindi Français Furlan Gaeilge Galego ગુજરાતી 客家 語 / Hak - kâ - ngî 한국어 Հայերեն हिन्दी Hrvatski Ido Ilokano Bahasa Indonesia Íslenska Italiano עברית Basa Jawa Къарачай - малкъар ქართული Қазақша Kiswahili Kreyòl ayisyen Кыргызча Лезги Latina Latviešu Lëtzebuergesch Lietuvių Limburgs Magyar Македонски മലയാളം मराठी მარგალური Bahasa Melayu Монгол Nederlands नेपाल भाषा 日本 語 Nordfriisk Norsk Norsk nynorsk Occitan Oʻzbekcha / ўзбекча ਪੰਜਾਬੀ پنجابی پښتو Plattdüütsch Polski Português Qaraqalpaqsha Română Runa Simi Русиньскый Русский Саха тыла Scots Shqip Simple English Slovenčina Slovenščina کوردی Српски / srpski Srpskohrvatski / српскохрватски Basa Sunda Suomi Svenska Tagalog தமிழ் Татарча / tatarça ไทย Türkçe Українська اردو Tiếng Việt Winaray 吴语 ייִדיש 粵語 中文 Edit links This page was last edited on 7 January 2018, at 14 : 17. 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Question: what is the definition of metabolism in science
Answer: set of life-sustaining chemical transformations within the cells of organisms