Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria

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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. Monosaccharides can be linked together to form polysaccharides in almost limitless ways. 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. 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. 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. 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. 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 cannot 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.

This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Inorganic elements play critical roles in metabolism; some are abundant e. 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.

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. 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 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.

Mammalian Sirtuins and Energy Metabolism

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. 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.

Macromolecules such as starch, cellulose or proteins cannot 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, [31] [32] while animals only secrete these enzymes from specialized cells in their guts , including the stomach and pancreas , and salivary glands. Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides. This oxidation releases carbon dioxide as a waste product.

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. Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. The amino group is fed into the urea cycle , leaving a deaminated carbon skeleton in the form of a keto acid. 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. Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen , [45] reduced sulfur compounds such as sulfide , hydrogen sulfide and thiosulfate , [1] ferrous iron FeII [46] or ammonia [47] as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite.

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. 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. 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.

3. Mitochondria

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.

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide CO 2. 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 2 into glycerate 3-phosphate , which can then be converted into glucose. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO 2 directly, while C4 and CAM photosynthesis incorporate the CO 2 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. 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 glucosephosphate through a series of intermediates, many of which are shared with glycolysis.

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 cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate ; plants do, but animals do not, have the necessary enzymatic machinery.

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. 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, [69] 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. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, [74] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.

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. 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. Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy.

Pyrimidines , on the other hand, are synthesized from the base orotate , which is formed from glutamine and aspartate. All organisms are constantly exposed to compounds that they cannot 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.

In humans, these include cytochrome P oxidases , [87] UDP-glucuronosyltransferases , [88] and glutathione S -transferases. 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. A related problem for aerobic organisms is oxidative stress. 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 cannot 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. In thermodynamic terms, metabolism maintains order by creating disorder.

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. 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.

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. 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. A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin.

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.

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. 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.

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. 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.

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. 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, genes. 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. Aristotle 's The Parts of Animals sets out enough details of his views on metabolism for an open flow model to be made.

Steps of glycolysis - Cellular respiration - Biology - Khan Academy

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 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 in his book Ars de statica medicina. He found that most of the food he took in was lost through what he called "insensible perspiration".

In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. 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 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. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells. From Wikipedia, the free encyclopedia.

For the journal, see Cell Metabolism. For the architectural movement, see Metabolism architecture. The set of life-sustaining chemical transformations within the cells of organisms. Index Outline. Further information: Biomolecule , Cell biology , and Biochemistry.

Main article: Coenzyme. Further information: Metal metabolism and Bioinorganic chemistry. Further information: Digestion and Gastrointestinal tract. Further information: Cellular respiration , Fermentation biochemistry , Carbohydrate catabolism , Fat catabolism , and Protein catabolism. Further information: Oxidative phosphorylation , Chemiosmosis , and Mitochondrion.

Further information: Microbial metabolism and Nitrogen cycle. Further information: Phototroph , Photophosphorylation , and Chloroplast. Further information: Anabolism. Further information: Photosynthesis , Carbon fixation , and Chemosynthesis. Further information: Gluconeogenesis , Glyoxylate cycle , Glycogenesis , and Glycosylation. Exercise improves mitochondrial and redox-regulated stress responses in the elderly: better late than never! Biogerontology 16, — Conti, V. Sports Exerc. Cortassa, S. PLoS Comput. Csibi, A. Davila, A. Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.

Dean, D. Exercise diminishes the activity of acetyl-CoA carboxylase in human muscle. Diabetes 49, — Di Lisa, F. Du, J. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science , — Elkhwanky, M. Extranuclear sirtuins and metabolic stress. Redox Signal. Farris, W. Fedewa, M. Exercise and insulin resistance in youth: a meta-analysis. Pediatrics , e—e Frye, R.

Gerhart-Hines, Z. EMBO J. Gertz, M. Using mitochondrial sirtuins as drug targets: disease implications and available compounds. Life Sci. Haigis, M. SIRT4 inhibits glutamate dehydrogenase and opposes the effects of calorie restriction in pancreatic beta cells. Hart, N. Resveratrol attenuates exercise-induced adaptive responses in rats selectively bred for low running performance. Dose-Response 12, 57— Resveratrol enhances exercise training responses in rats selectively bred for high running performance.

Food Chem. Herrero-Yraola, A. Regulation of glutamate dehydrogenase by reversible ADP-ribosylation in mitochondria. Hipkiss, A. Google Scholar. Hirschey, M. SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation.

Teaching the role of mitochondrial transport in energy metabolism

Nature , — Ho, L. Aging 5, — Holloway, G. Mitochondrial function and dysfunction in exercise and insulin resistance. Houtkooper, R.

The stages of biosynthesis

Sirtuins as regulators of metabolism and healthspan. Huang, J. Mitochondrial sirtuins. Acta , — Huang, G. Sirtuin-4 SIRT4 , a therapeutic target with oncogenic and tumor-suppressive activity in cancer. OncoTargets Ther. Jeong, S. SIRT4 regulates cancer cell survival and growth after stress. SIRT4 has tumor-suppressive activity and regulates the cellular metabolic response to DNA damage by inhibiting mitochondrial glutamine metabolism. Cancer Cell 23, — Karvinen, S. Effects of intrinsic aerobic capacity, aging and voluntary running on skeletal muscle sirtuins and heat shock proteins.

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A Biol. Miller, B. Min, J. Nasrin, N. SIRT4 regulates fatty acid oxidation and mitochondrial gene expression in liver and muscle cells. Navas Enamorado, I. Differential influence of anaerobic and aerobic exercises in aging. PhD thesis. Seville: Universidad Pablo de Olavide. Newgard, C. Metabolic coupling factors in pancreatic beta-cell signal transduction. Osborne, B. The role of mitochondrial sirtuins in health and disease. Free Radic. Palacios, O. Aging 1, — Parihar, P. Mitochondrial sirtuins: emerging roles in metabolic regulations, energy homeostasis and diseases.

Parik, S. Loss of mitochondrial SIRT4 shortens lifespan and leads to a decline in physical activity. Park, E. Cardioprotective effects of rhamnetin in H9c2 cardiomyoblast cells under H 2 O 2 -induced apoptosis. Park, S. Exercise training improves vascular mitochondrial function. Heart Circ. Acetylation of mitochondrial proteins in the heart: the role of SIRT3. Metabolic processes are usually classified as: catabolism - obtaining energy and reducing power from nutrients. There is a very large number of metabolic pathways.

In humans, the most important metabolic pathways are: glycolysis - glucose oxidation in order to obtain ATP citric acid cycle Krebs' cycle - acetyl-CoA oxidation in order to obtain GTP and valuable intermediates. Much of the energy released in this process can be stored as ATP.

Click on the picture to get information on each pathway. Metabolic pathways interact in a complex way in order to allow an adequate regulation. This interaction includes the enzymatic control of each pathway, each organ's metabolic profile and hormone control.

Flow is regulated in the gluconeogenesis-specific reactions. Pyruvate carboxilase is activated by acetyl-CoA, which signals the abundance of citric acid cycle intermediates, i. The citric acid cycle is regulated mostly by substrate availability, product inhibition and by some cycle intermediates. Carbamoyl-phosphate sinthetase is stimulated by N-acetylglutamine, which signals the presence of high amounts of nitrogen in the body.

Liver contains a hexokinase hexokinase D or glucokinase with low affinity for glucose which unlike "regular" hexokinase is not subject to product inhibition. Therefore, glucose is only phosphrylated in the liver when it is present in very high concentrations i.

In this way, the liver will not compete with other tissues for glucose when this sugar is scarce, but will accumulate high levels of glucose for glycogen synthesis right after a meal. Acyl-CoA movement into the mitochondrion is a crucial factor in regulation.