1.
Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
2.
Sugar
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Sugar is the generic name for sweet, soluble carbohydrates, many of which are used in food. There are various types of derived from different sources. Simple sugars are called monosaccharides and include glucose, fructose, the table sugar or granulated sugar most customarily used as food is sucrose, a disaccharide of glucose and fructose. Sugar is used in prepared foods and it is added to some foods, in the body, sucrose is hydrolysed into the simple sugars fructose and glucose. Other disaccharides include maltose from malted grain, and lactose from milk, longer chains of sugars are called oligosaccharides or polysaccharides. Some other chemical substances, such as glycerol may also have a sweet taste, low-calorie food substitutes for sugar, described as artificial sweeteners, include aspartame and sucralose, a chlorinated derivative of sucrose. Sugars are found in the tissues of most plants and are present in sufficient concentrations for efficient commercial extraction in sugarcane, the world production of sugar in 2011 was about 168 million tonnes. The average person consumes about 24 kilograms of sugar each year, equivalent to over 260 food calories per person, since the latter part of the twentieth century, it has been questioned whether a diet high in sugars, especially refined sugars, is good for human health. Sugar has been linked to obesity, and suspected of, or fully implicated as a cause in the occurrence of diabetes, cardiovascular disease, dementia, macular degeneration, the etymology reflects the spread of the commodity. The English word sugar ultimately originates from the Sanskrit शर्करा, via Arabic سكر as granular or candied sugar, the contemporary Italian word is zucchero, whereas the Spanish and Portuguese words, azúcar and açúcar, respectively, have kept a trace of the Arabic definite article. The Old French word is zuchre and the contemporary French, sucre, the earliest Greek word attested is σάκχαρις. The English word jaggery, a brown sugar made from date palm sap or sugarcane juice, has a similar etymological origin – Portuguese jagara from the Sanskrit शर्करा. Sugar has been produced in the Indian subcontinent since ancient times and it was not plentiful or cheap in early times and honey was more often used for sweetening in most parts of the world. Originally, people chewed raw sugarcane to extract its sweetness, sugarcane was a native of tropical South Asia and Southeast Asia. Different species seem to have originated from different locations with Saccharum barberi originating in India and S. edule, one of the earliest historical references to sugarcane is in Chinese manuscripts dating back to 8th century BC that state that the use of sugarcane originated in India. Sugar was found in Europe by the 1st century AD, but only as an imported medicine and it is a kind of honey found in cane, white as gum, and it crunches between the teeth. It comes in lumps the size of a hazelnut, sugar is used only for medical purposes. Sugar remained relatively unimportant until the Indians discovered methods of turning sugarcane juice into granulated crystals that were easier to store, crystallized sugar was discovered by the time of the Imperial Guptas, around the 5th century AD
3.
Energy
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In physics, energy is the property that must be transferred to an object in order to perform work on – or to heat – the object, and can be converted in form, but not created or destroyed. The SI unit of energy is the joule, which is the transferred to an object by the mechanical work of moving it a distance of 1 metre against a force of 1 newton. Mass and energy are closely related, for example, with a sensitive enough scale, one could measure an increase in mass after heating an object. Living organisms require available energy to stay alive, such as the humans get from food. Civilisation gets the energy it needs from energy resources such as fuels, nuclear fuel. The processes of Earths climate and ecosystem are driven by the radiant energy Earth receives from the sun, the total energy of a system can be subdivided and classified in various ways. It may also be convenient to distinguish gravitational energy, thermal energy, several types of energy, electric energy. Many of these overlap, for instance, thermal energy usually consists partly of kinetic. Some types of energy are a mix of both potential and kinetic energy. An example is energy which is the sum of kinetic. Whenever physical scientists discover that a phenomenon appears to violate the law of energy conservation. Heat and work are special cases in that they are not properties of systems, in general we cannot measure how much heat or work are present in an object, but rather only how much energy is transferred among objects in certain ways during the occurrence of a given process. Heat and work are measured as positive or negative depending on which side of the transfer we view them from, the distinctions between different kinds of energy is not always clear-cut. In contrast to the definition, energeia was a qualitative philosophical concept, broad enough to include ideas such as happiness. The modern analog of this property, kinetic energy, differs from vis viva only by a factor of two, in 1807, Thomas Young was possibly the first to use the term energy instead of vis viva, in its modern sense. Gustave-Gaspard Coriolis described kinetic energy in 1829 in its modern sense, the law of conservation of energy was also first postulated in the early 19th century, and applies to any isolated system. It was argued for years whether heat was a physical substance, dubbed the caloric, or merely a physical quantity. In 1845 James Prescott Joule discovered the link between mechanical work and the generation of heat and these developments led to the theory of conservation of energy, formalized largely by William Thomson as the field of thermodynamics
4.
Potential energy
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In physics, potential energy is energy possessed by a body by virtue of its position relative to others, stresses within itself, electric charge, and other factors. The unit for energy in the International System of Units is the joule, the term potential energy was introduced by the 19th century Scottish engineer and physicist William Rankine, although it has links to Greek philosopher Aristotles concept of potentiality. Potential energy is associated with forces that act on a body in a way that the work done by these forces on the body depends only on the initial and final positions of the body in space. These forces, that are called potential forces, can be represented at every point in space by vectors expressed as gradients of a scalar function called potential. Potential energy is the energy of an object. It is the energy by virtue of a position relative to other objects. Potential energy is associated with restoring forces such as a spring or the force of gravity. The action of stretching the spring or lifting the mass is performed by a force that works against the force field of the potential. This work is stored in the field, which is said to be stored as potential energy. If the external force is removed the field acts on the body to perform the work as it moves the body back to the initial position. Suppose a ball which mass is m, and it is in h position in height, if the acceleration of free fall is g, the weight of the ball is mg. There are various types of energy, each associated with a particular type of force. Chemical potential energy, such as the energy stored in fossil fuels, is the work of the Coulomb force during rearrangement of mutual positions of electrons and nuclei in atoms and molecules. Thermal energy usually has two components, the energy of random motions of particles and the potential energy of their mutual positions. Forces derivable from a potential are also called conservative forces, the work done by a conservative force is W = − Δ U where Δ U is the change in the potential energy associated with the force. The negative sign provides the convention that work done against a force field increases potential energy, common notations for potential energy are U, V, also Ep. Potential energy is closely linked with forces, in this case, the force can be defined as the negative of the vector gradient of the potential field. If the work for a force is independent of the path, then the work done by the force is evaluated at the start
5.
Actin
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Actin is a family of globular multi-functional proteins that form microfilaments. It is found in all eukaryotic cells, where it may be present at a concentration of over 100 μM. Many of these processes are mediated by extensive and intimate interactions of actin with cellular membranes, in vertebrates, three main groups of actin isoforms, alpha, beta, and gamma have been identified. The alpha actins, found in tissues, are a major constituent of the contractile apparatus. The beta and gamma actins coexist in most cell types as components of the cytoskeleton and it is believed that the diverse range of structures formed by actin enabling it to fulfill such a large range of functions is regulated through the binding of tropomyosin along the filaments. Other enzymes or organelles such as cilia can be anchored to this scaffolding in order to control the deformation of the cell membrane. It can also produce movement either by itself or with the help of molecular motors, Actin therefore contributes to processes such as the intracellular transport of vesicles and organelles as well as muscular contraction and cellular migration. It therefore plays an important role in embryogenesis, the healing of wounds, the evolutionary origin of actin can be traced to prokaryotic cells, which have equivalent proteins. Actin homologs from prokaryotes and archaea polymerize into different helical or linear filaments consisting of one or multiple strands, however the in-strand contacts and nucleotide binding sites are preserved in prokaryotes and in archaea. Lastly, actin plays an important role in the control of gene expression, a large number of illnesses and diseases are caused by mutations in alleles of the genes that regulate the production of actin or of its associated proteins. The production of actin is also key to the process of infection by some pathogenic microorganisms, mutations in the different genes that regulate actin production in humans can cause muscular diseases, variations in the size and function of the heart as well as deafness. The make-up of the cytoskeleton is also related to the pathogenicity of bacteria and viruses. Actin was first observed experimentally in 1887 by W. D. Halliburton, in 1942, Straub developed a novel technique for extracting muscle protein that allowed him to isolate substantial amounts of relatively pure actin. Straubs method is essentially the same as used in laboratories today. Adding ATP to a mixture of both proteins causes a decrease in viscosity, the hostilities of World War II meant Szent-Gyorgyi and Straub were unable to publish the work in Western scientific journals. Actin therefore only became known in the West in 1945. Straub suggested that the transformation of ATP-bound actin to ADP-bound actin played a role in muscular contraction, in fact, this is true only in smooth muscle, and was not supported through experimentation until 2001. The amino acid sequencing of actin was completed by M. Elzinga, the crystal structure of G-actin was solved in 1990 by Kabsch and colleagues
6.
Muscle contraction
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Muscle contraction is the activation of tension-generating sites within muscle fibers. The termination of muscle contraction is followed by muscle relaxation, which is a return of the fibers to their low tension-generating state. Muscle contractions can be described based on two variables, length and tension, a muscle contraction is described as isometric if the muscle tension changes but the muscle length remains the same. In contrast, a muscle contraction is isotonic if muscle length changes, if the muscle length shortens, the contraction is concentric, if the muscle length lengthens, the contraction is eccentric. In natural movements that underlie locomotor activity, muscle contractions are multifaceted as they are able to produce changes in length, therefore, neither length nor tension is likely to remain the same in muscles that contract during locomotor activity. In vertebrates, skeletal muscle contractions are neurogenic as they require synaptic input from neurons to produce muscle contractions. A single motor neuron is able to innervate multiple muscle fibers, once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, in skeletal muscles, muscle tension is at its greatest when the muscle is stretched to an intermediate length as described by the length-tension relationship. Unlike skeletal muscle, the contractions of smooth and cardiac muscles are myogenic, the mechanisms of contraction in these muscle tissues are similar to those in skeletal muscle tissues. Muscle contractions can be described based on two variables, force and length, force itself can be differentiated as either tension or load. Muscle tension is the force exerted by the muscle on an object whereas a load is the force exerted by an object on the muscle, when muscle tension changes without any corresponding changes in muscle length, the muscle contraction is described as isometric. If the muscle length changes while muscle tension remains the same, in an isotonic contraction, the muscle length can either shorten to produce a concentric contraction or lengthen to produce an eccentric contraction. Furthermore, if the muscle length shortens, the contraction is concentric, but if the muscle length lengthens, then the contraction is eccentric. In natural movements that underlie locomotor activity, muscle contractions are multifaceted as they are able to produce changes in length, therefore, neither length nor tension is likely to remain constant when the muscle is active during locomotor activity. An isometric contraction of a muscle generates tension without changing length, an example can be found when the muscles of the hand and forearm grip an object, the joints of the hand do not move, but muscles generate sufficient force to prevent the object from being dropped. In isotonic contraction, the tension in the muscle remains constant despite a change in muscle length and this occurs when a muscles force of contraction matches the total load on the muscle. In concentric contraction, muscle tension is sufficient to overcome the load, and this occurs when the force generated by the muscle exceeds the load opposing its contraction. During a concentric contraction, a muscle is stimulated to contract according to the sliding filament theory and this occurs throughout the length of the muscle, generating a force at the origin and insertion, causing the muscle to shorten and changing the angle of the joint
7.
Photosynthesis
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Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms activities. In most cases, oxygen is released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, such organisms are called photoautotrophs, in plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, in the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate. Using the ATP and NADPH produced by the light-dependent reactions, the compounds are then reduced and removed to form further carbohydrates. Cyanobacteria appeared later, the oxygen they produced contributed directly to the oxygenation of the Earth. Today, the rate of energy capture by photosynthesis globally is approximately 130 terawatts. Photosynthetic organisms also convert around 100–115 thousand million tonnes of carbon into biomass per year. Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide, however, not all organisms that use light as a source of energy carry out photosynthesis, photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen and this is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria. Carbon dioxide is converted into sugars in a process called carbon fixation, photosynthesis provides the energy in the form of free electrons that are used to split carbon from carbon dioxide that is then used to fix that carbon once again as carbohydrate. Carbon fixation is a redox reaction, so photosynthesis supplies the energy that drives both process. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP, during the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, some organisms employ even more radical variants of photosynthesis. Some archea use a method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump and this produces a proton gradient more directly, which is then converted to chemical energy
8.
Glycolysis
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Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy molecules ATP, glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis, for example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful, for example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat. Glycolysis is an oxygen independent metabolic pathway, meaning that it not use molecular oxygen for any of its reactions. However the products of glycolysis are sometimes metabolized using atmospheric oxygen, when molecular oxygen is used for the metabolism of the products of glycolysis the process is usually referred to as aerobic, whereas if no oxygen is used the process is said to be anaerobic. Thus, glycolysis occurs, with variations, in all organisms. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways, glycolysis could thus have originated from chemical constraints of the prebiotic world. Glycolysis occurs in most organisms in the cytosol of the cell, the most common type of glycolysis is the Embden–Meyerhof–Parnas, which was discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway, however, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway. The overall reaction of glycolysis is, The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. In the cellular environment, all three groups of ADP dissociate into −O− and H+, giving ADP3−, and this ion tends to exist in an ionic bond with Mg2+. ATP behaves identically except that it has four groups, giving ATPMg2−. When these differences along with the charges on the two phosphate groups are considered together, the net charges of −4 on each side are balanced. For simple fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP, most cells will then carry out further reactions to repay the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+, cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis, the pathway of glycolysis as it is known today took almost 100 years to fully discover. The combined results of many experiments were required in order to understand the pathway as a whole
9.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
10.
ATP synthase
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ATP synthase is an important enzyme that creates the energy storage molecule adenosine triphosphate. ATP is the most commonly used energy currency of cells for most organisms and it is formed from adenosine diphosphate and inorganic phosphate, and needs energy for its formation. Located within the membrane and the inner mitochondrial membrane, ATP synthase consists of two regions the FO portion embedded within the membrane. The F1 portion of the ATP synthase is outside the membrane, the nomenclature of the enzyme has a long history. These functional regions consist of different protein subunits — refer to tables, the F1 particle is large and can be seen in the transmission electron microscope by negative staining. These are particles of 9 nm diameter that pepper the inner mitochondrial membrane and this ATPase activity was further associated with the creation of ATP by a long series of experiments in many laboratories. The FO region of ATP synthase is a pore that is embedded in the mitochondrial membrane. It consists of three main subunits A, B, and C, and six additional subunits, d, e, f, g, F6, and 8. The research group of John E. Walker, then at the MRC Laboratory of Molecular Biology in Cambridge, the structure, at the time the largest asymmetric protein structure known, indicated that Boyers rotary-catalysis model was, in essence, correct. For elucidating this, Boyer and Walker shared half of the 1997 Nobel Prize in Chemistry, the crystal structure of the F1 showed alternating alpha and beta subunits, arranged like segments of an orange around a rotating asymmetrical gamma subunit. A portion of the FO rotates as the pass through the membrane. The major F1 subunits are prevented from rotating in sympathy with the central stalk rotor by a stalk that joins the alpha3beta3 to the non-rotating portion of FO. The structure of the intact ATP synthase is currently known at low-resolution from electron cryo-microscopy studies of the complex, the cryo-EM model of ATP synthase suggests that the peripheral stalk is a flexible structure that wraps around the complex as it joins F1 to FO. Under the right conditions, the reaction can also be carried out in reverse. The binding change mechanism involves the active site of a β subunits cycling between three states, in the open state, ADP and phosphate enter the active site, in the adjacent diagram, this is shown in red. The protein then closes up around the molecules and binds them loosely — the loose state, finally, the active site cycles back to the open state, releasing ATP and binding more ADP and phosphate, ready for the next cycle of ATP production. Like other enzymes, the activity of F1FO ATP synthase is reversible, the overall process of creating energy in this fashion is termed oxidative phosphorylation. The same process takes place in the mitochondria, where ATP synthase is located in the mitochondrial membrane
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