1.
Anaerobic digestion
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Anaerobic digestion is a collection of processes by which microorganisms break down biodegradable material in the absence of oxygen. The process is used for industrial or domestic purposes to waste or to produce fuels. Much of the fermentation used industrially to produce food and drink products, as well as home fermentation, anaerobic digestion occurs naturally in some soils and in lake and oceanic basin sediments, where it is usually referred to as anaerobic activity. This is the source of marsh gas methane as discovered by Volta in 1776, the digestion process begins with bacterial hydrolysis of the input materials. Insoluble organic polymers, such as carbohydrates, are broken down to soluble derivatives that become available for other bacteria, acidogenic bacteria then convert the sugars and amino acids into carbon dioxide, hydrogen, ammonia, and organic acids. These bacteria convert these resulting organic acids into acetic acid, along with ammonia, hydrogen. Finally, methanogens convert these products to methane and carbon dioxide, the methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Anaerobic digestion is used as part of the process to treat biodegradable waste, as part of an integrated waste management system, anaerobic digestion reduces the emission of landfill gas into the atmosphere. Anaerobic digesters can also be fed with energy crops, such as maize. Anaerobic digestion is used as a source of renewable energy. The process produces a biogas, consisting of methane, carbon dioxide and this biogas can be used directly as fuel, in combined heat and power gas engines or upgraded to natural gas-quality biomethane. The nutrient-rich digestate also produced can be used as fertilizer, many microorganisms affect anaerobic digestion, including acetic acid-forming bacteria and methane-forming archaea. These organisms promote a number of processes in converting the biomass to biogas. Gaseous oxygen is excluded from the reactions by physical containment, anaerobes utilize electron acceptors from sources other than oxygen gas. These acceptors can be the material itself or may be supplied by inorganic oxides from within the input material. When the oxygen source in a system is derived from the organic material itself, the intermediate end products are primarily alcohols, aldehydes. In the presence of specialised methanogens, the intermediates are converted to the end products of methane, carbon dioxide. In an anaerobic system, the majority of the energy contained within the starting material is released by methanogenic bacteria as methane
2.
Precipitation (chemistry)
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Precipitation is the creation of a solid from a solution. When the reaction occurs in a solution, the solid formed is called the precipitate. The chemical that causes the solid to form is called the precipitant, without sufficient force of gravity to bring the solid particles together, the precipitate remains in suspension. After sedimentation, especially when using a centrifuge to press it into a compact mass, Precipitation can be used as a medium. The precipitate-free liquid remaining above the solid is called the supernate or supernatant, powders derived from precipitation have also historically been known as flowers. When the solid appears in the form of fibers which have been through chemical processing. Sometimes the formation of a precipitate indicates the occurrence of a chemical reaction, if silver nitrate solution is poured into a solution of sodium chloride, a chemical reaction occurs forming a white precipitate of silver chloride. When potassium iodide solution reacts with lead nitrate solution, a precipitate of lead iodide is formed. Precipitation may occur if the concentration of a compound exceeds its solubility, Precipitation may occur rapidly from a supersaturated solution. Precipitation in solids is routinely used to synthesize nanoclusters, an important stage of the precipitation process is the onset of nucleation. The creation of a solid particle includes the formation of an interface, which requires some energy based on the relative surface energy of the solid. If this energy is not available, and no suitable nucleation surface is available, Precipitation reactions can be used for making pigments, removing salts from water in water treatment, and in classical qualitative inorganic analysis. Precipitation is also useful to isolate the products of a reaction during workup, ideally, the product of the reaction is insoluble in the reaction solvent. Thus, it precipitates as it is formed, preferably forming pure crystals, an example of this would be the synthesis of porphyrins in refluxing propionic acid. Thereafter, the precipitate may easily be separated by filtration, decanting, an example would be the synthesis of chromic tetraphenylporphyrin chloride, water is added to the DMF reaction solution, and the product precipitates. Precipitation is also useful in purifying products, crude bmim-Cl is taken up in acetonitrile, and dropped into ethyl acetate, another important application of an antisolvent is in ethanol precipitation of DNA. In metallurgy, precipitation from a solution is also a useful way to strengthen alloys. An example of a reaction, Aqueous silver nitrate is added to a solution containing potassium chloride
3.
Latin
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Latin is a classical language belonging to the Italic branch of the Indo-European languages. The Latin alphabet is derived from the Etruscan and Greek alphabets, Latin was originally spoken in Latium, in the Italian Peninsula. Through the power of the Roman Republic, it became the dominant language, Vulgar Latin developed into the Romance languages, such as Italian, Portuguese, Spanish, French, and Romanian. Latin, Italian and French have contributed many words to the English language, Latin and Ancient Greek roots are used in theology, biology, and medicine. By the late Roman Republic, Old Latin had been standardised into Classical Latin, Vulgar Latin was the colloquial form spoken during the same time and attested in inscriptions and the works of comic playwrights like Plautus and Terence. Late Latin is the language from the 3rd century. Later, Early Modern Latin and Modern Latin evolved, Latin was used as the language of international communication, scholarship, and science until well into the 18th century, when it began to be supplanted by vernaculars. Ecclesiastical Latin remains the language of the Holy See and the Roman Rite of the Catholic Church. Today, many students, scholars and members of the Catholic clergy speak Latin fluently and it is taught in primary, secondary and postsecondary educational institutions around the world. The language has been passed down through various forms, some inscriptions have been published in an internationally agreed, monumental, multivolume series, the Corpus Inscriptionum Latinarum. Authors and publishers vary, but the format is about the same, volumes detailing inscriptions with a critical apparatus stating the provenance, the reading and interpretation of these inscriptions is the subject matter of the field of epigraphy. The works of several hundred ancient authors who wrote in Latin have survived in whole or in part and they are in part the subject matter of the field of classics. The Cat in the Hat, and a book of fairy tales, additional resources include phrasebooks and resources for rendering everyday phrases and concepts into Latin, such as Meissners Latin Phrasebook. The Latin influence in English has been significant at all stages of its insular development. From the 16th to the 18th centuries, English writers cobbled together huge numbers of new words from Latin and Greek words, dubbed inkhorn terms, as if they had spilled from a pot of ink. Many of these words were used once by the author and then forgotten, many of the most common polysyllabic English words are of Latin origin through the medium of Old French. Romance words make respectively 59%, 20% and 14% of English, German and those figures can rise dramatically when only non-compound and non-derived words are included. Accordingly, Romance words make roughly 35% of the vocabulary of Dutch, Roman engineering had the same effect on scientific terminology as a whole
4.
Anatomical terminology
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Anatomical terminology is a form of scientific terminology used by anatomists, zoologists, and health professionals such as doctors. Anatomical terminology uses many terms, suffixes, and prefixes deriving from Ancient Greek. These terms can be confusing to those unfamiliar with them, but can be more precise reducing ambiguity, also, since these anatomical terms are not used in everyday conversation, their meanings are less likely to change, and less likely to be misinterpreted. By using precise anatomical terminology such ambiguity is eliminated, an international standard for anatomical terminology, Terminologia Anatomica has been created. Anatomical terminology has quite regular morphology, the prefixes and suffixes are used to add meanings to different roots. The root of a term refers to an organ, tissue. For example, in the disorder hypertension, the prefix hyper- means high or over, the roots, prefixes and suffixes are often derived from Greek or Latin, and often quite dissimilar from their English-language variants. Latin names of such as musculus biceps brachii can be split up and refer to, musculus for muscle, biceps for two-headed. The first word tells us what we are speaking about, the second describes it, when describing the position of anatomical structures, structures may be described according to the anatomical landmark they are near. These landmarks may include structures, such as the umbilicus or sternum, or anatomical lines, the cephalon or cephalic region refers to the head. This area is differentiated into the cranium, facies, frons, oculus, auris, bucca, nausus, oris. The neck area is called the cervicis or cervical region, examples of structures named according to this include the frontalis muscle, submental lymph nodes, buccal membrane and orbicularis oculi muscle. Sometimes, unique terminology is used to reduce confusion in different parts of the body, for example, different terms are used when it comes to the skull in compliance with its embryonic origin and its tilted position compared to in other animals. Here, Rostral refers to proximity to the front of the nose, similarly, in the arms, different terminology is often used in the arms, in part to reduce ambiguity as what is the front, back, inner and outer surfaces. For this reason, the terms below are used, Radial referring to the radius bone, ulnar referring to the ulna bone, medially positioned when in the standard anatomical position. Other terms are used to describe the movement and actions of the hands and feet. International morphological terminology is used by the colleges of medicine and dentistry and it facilitates communication and exchanges between scientists from different countries of the world and it is used daily in the fields of research, teaching and medical care. The international morphological terminology refers to morphological sciences as a biological sciences branch, in this field, the form and structure are examined as well as the changes or developments in the organism
5.
Food
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Food is any substance consumed to provide nutritional support for an organism. It is usually of plant or animal origin, and contains essential nutrients, such as carbohydrates, fats, proteins, vitamins, the substance is ingested by an organism and assimilated by the organisms cells to provide energy, maintain life, or stimulate growth. Historically, humans secured food through two methods, hunting and gathering and agriculture, today, the majority of the food energy required by the ever increasing population of the world is supplied by the food industry. They address issues such as sustainability, biological diversity, climate change, nutritional economics, population growth, water supply, most food has its origin in plants. Some food is obtained directly from plants, but even animals that are used as sources are raised by feeding them food derived from plants. Cereal grain is a food that provides more food energy worldwide than any other type of crop. Corn, wheat, and rice – in all of their varieties – account for 87% of all grain production worldwide, most of the grain that is produced worldwide is fed to livestock. Some foods not from animal or plant sources include various edible fungi, fungi and ambient bacteria are used in the preparation of fermented and pickled foods like leavened bread, alcoholic drinks, cheese, pickles, kombucha, and yogurt. Another example is blue-green algae such as Spirulina, inorganic substances such as salt, baking soda and cream of tartar are used to preserve or chemically alter an ingredient. Many plants and plant parts are eaten as food and around 2,000 plant species are cultivated for food, many of these plant species have several distinct cultivars. Seeds of plants are a source of food for animals, including humans, because they contain the nutrients necessary for the plants initial growth, including many healthful fats. In fact, the majority of food consumed by human beings are seed-based foods, edible seeds include cereals, legumes, and nuts. Oilseeds are often pressed to produce rich oils - sunflower, flaxseed, rapeseed, sesame, seeds are typically high in unsaturated fats and, in moderation, are considered a health food, although not all seeds are edible. Large seeds, such as those from a lemon, pose a choking hazard, fruits are the ripened ovaries of plants, including the seeds within. Many plants and animals have coevolved such that the fruits of the former are a food source to the latter. Fruits, therefore, make up a significant part of the diets of most cultures, some botanical fruits, such as tomatoes, pumpkins, and eggplants, are eaten as vegetables. Vegetables are a type of plant matter that is commonly eaten as food. These include root vegetables, bulbs, leaf vegetables, stem vegetables, animals are used as food either directly or indirectly by the products they produce
6.
Blood plasma
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Blood plasma is a straw coloured liquid component of blood that normally holds the blood cells in whole blood in suspension, this makes plasma the extracellular matrix of blood cells. It makes up about 55% of the total blood volume. It is the fluid part of extracellular fluid. It is mostly water, and contains dissolved proteins, glucose, clotting factors, electrolytes, hormones, carbon dioxide, Plasma also serves as the protein reserve of the human body. It plays a role in an intravascular osmotic effect that keeps electrolytes in balanced form and protects the body from infection. Blood plasma is prepared by spinning a tube of fresh blood containing an anticoagulant in a centrifuge until the blood fall to the bottom of the tube. The blood plasma is then poured or drawn off, Blood plasma has a density of approximately 1025 kg/m3, or 1.025 g/ml. Blood serum is blood plasma without clotting factors, in other words, plasmapheresis is a medical therapy that involves blood plasma extraction, treatment, and reintegration. Fresh frozen plasma is on the WHO Model List of Essential Medicines, Blood plasma volume may be expanded by or drained to extravascular fluid when there are changes in Starling forces across capillary walls. For example, when blood pressure drops in circulatory shock, Starling forces drive fluid into the interstitium, standing still for a prolonged period will cause an increase in transcapillary hydrostatic pressure. As a result, approximately 12% of blood plasma volume will cross into the extravascular compartment and this causes an increase in hematocrit, serum total protein, blood viscosity and, as a result of increased concentration of coagulation factors, it causes orthostatic hypercoagulability. The use of plasma as a substitute for whole blood and for transfusion purposes was proposed in March 1918, in the correspondence columns of the British Medical Journal. Dried plasmas in powder or strips of material format were developed, prior to the United States involvement in the war, liquid plasma and whole blood were used. The Blood for Britain program during the early 1940s was quite successful based on Charles Drews contribution, a large project began in August 1940 to collect blood in New York City hospitals for the export of plasma to Britain. Drew was appointed supervisor of the Plasma for Britain project. His notable contribution at this time was to transform the test tube methods of many blood researchers into the first successful mass production techniques. Nonetheless, the decision was made to develop a dried plasma package for the forces as it would reduce breakage and make the transportation, packaging. The resulting dried plasma package came in two tin cans containing 400 cc bottles, one bottle contained enough distilled water to reconstitute the dried plasma contained within the other bottle
7.
Blood stream
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The study of the blood flow is called hemodynamics. The study of the properties of the flow is called hemorheology. The circulatory system is seen to comprise two separate systems, the cardiovascular system, which distributes blood, and the lymphatic system. The passage of lymph for example takes much longer than that of blood, lymph is essentially recycled excess blood plasma after it has been filtered from the interstitial fluid and returned to the lymphatic system. The cardiovascular system comprises the blood, heart, and blood vessels, the lymph, lymph nodes, and lymph vessels form the lymphatic system, which returns filtered blood plasma from the interstitial fluid as lymph. While humans, as well as vertebrates, have a closed cardiovascular system. The lymphatic system, on the hand, is an open system providing an accessory route for excess interstitial fluid to be returned to the blood. The more primitive, diploblastic animal phyla lack circulatory systems, the essential components of the human cardiovascular system are the heart, blood and blood vessels. It includes the circulation, a loop through the lungs where blood is oxygenated, and the systemic circulation. The systemic circulation can also be seen to function in two parts–a macrocirculation and a microcirculation, an average adult contains five to six quarts of blood, accounting for approximately 7% of their total body weight. Blood consists of plasma, red cells, white blood cells. Also, the system works with the circulatory system to provide the nutrients the system needs to keep the heart pumping. The cardiovascular systems of humans are closed, meaning that the blood never leaves the network of blood vessels, the other component of the circulatory system, the lymphatic system, is open. Oxygenated blood enters the circulation when leaving the left ventricle. The first part of the circulation is the aorta, a massive. The aorta arches and gives branches supplying the upper part of the body, after passing through the aortic opening of the diaphragm at the level of thoracic ten vertebra, it enters the abdomen. Later it descends down and supplies branches to abdomen, pelvis, perineum, according to Difores Atlas of Histology the walls of aorta are elastic. This elasticity helps to maintain the pressure throughout the body
8.
Catabolism
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Catabolism is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks down molecules into smaller units. Cells use the monomers released from breaking down polymers to construct new polymer molecules, or degrade the monomers further to simple waste products. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia and this molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up anabolism. Catabolism therefore provides the energy necessary for the maintenance and growth of cells. There are many signals that control catabolism, most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, the so-called classic catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline. In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin, many of these catabolic hormones express an anti-catabolic effect in muscle tissue. One study found that the administration of epinephrine had an anti-proteolytic effect, another study found that catecholamines in general, greatly decreased the rate of muscle catabolism. Autophagy Dehydration synthesis Hydrolysis Nocturnal post absorptive catabolism Psilacetin § Pharmacology Sarcopenia Media related to Catabolism at Wikimedia Commons
9.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and 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. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
10.
Mastication
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Mastication or chewing is the process by which food is crushed and ground by teeth. It is the first step of digestion, and it increases the area of foods to allow more efficient break down by enzymes. During the mastication process, the food is positioned by the cheek, the muscles of mastication move the jaws to bring the teeth into intermittent contact, repeatedly occluding and opening. As chewing continues, the food is made softer and warmer, after chewing, the food is swallowed. It enters the esophagus and via peristalsis continues on to the stomach, premastication is sometimes performed by human parents for infants who are unable to do so for themselves. The food is masticated in the mouth of the parent into a bolus, cattle and some other animals, called ruminants, chew food more than once to extract more nutrients. After the first round of chewing, this food is called cud, mastication is primarily an unconscious act, but can be mediated by higher conscious input. The motor program for mastication is a central nervous system function by which the complex patterns governing mastication are created and controlled. This motor program continuously adapts to changes in type or occlusion. This adaptation is a skill that may sometimes require relearning to adapt to loss of teeth or to dental appliances such as dentures. It is also theorized that excessive input to the program from myofascial pain or occlusal imbalance can contribute to parafunctional habits. A study found that meat and vegetables were not digested, while tallow, cheese, fish, eggs. Mastication stimulates saliva production and increases sensory perception of the food being eaten, avoiding mastication, by choice or due to medical reasons as tooth loss, is known as a soft diet. Such a diet may lead to inadequate nutrition due to a reduction in fruit, mastication also stimulates the hippocampus and is necessary to maintain its normal function. Chewing is largely an adaptation for mammalian herbivory, carnivores generally chew very little or swallow their food whole or in chunks. This act of gulping food without chewing has inspired the English idiom wolfing it down and this may have given them the advantage needed to usurp the formidable sauropods, who depended on gastroliths for grinding food, from their ecological niches. They eventually became some of the most successful animals on the planet until the Cretaceous–Paleogene extinction event wiped them out, the process of mastication has, by analogy, been applied to machinery. The U. S. Forest Service uses a machine called a masticator to chew through brush, gnathology Muscles of mastication Horace Fletcher Chewing Gum MeSH A02.633.567.600
11.
Saliva
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Saliva is a watery substance formed in the mouths of animals, secreted by the salivary glands. Human saliva comprises 99. 5% water, plus electrolytes, mucus, white cells, epithelial cells, glycoproteins, enzymes, antimicrobial agents such as secretory IgA. The enzymes found in saliva are essential in beginning the process of digestion of dietary starches and these enzymes also play a role in breaking down food particles entrapped within dental crevices, thus protecting teeth from bacterial decay. Furthermore, saliva serves a function, wetting food and permitting the initiation of swallowing. Various animal species have uses for saliva that go beyond pre-digestion. Some swifts use their saliva to build nests. Aerodramus nests form the basis of birds nest soup, cobras, vipers, and certain other members of the venom clade hunt with venomous saliva injected by fangs. Some arthropods, such as spiders and caterpillars, produce thread from salivary glands, produced in salivary glands, human saliva is 99. 5% water, but it contains many important substances, including electrolytes, mucus, antibacterial compounds and various enzymes. In humans, the submandibular gland contributes around 70–75% of secretion, while the parotid gland secretes about 20–25%, saliva contributes to the digestion of food and to the maintenance of oral hygiene. Without normal salivary function the frequency of caries, gum disease. Saliva coats the oral mucosa, mechanically protecting it from trauma during eating, swallowing and speaking, in people with little saliva, soreness of the mouth is very common, and the food sticks to the inside of the mouth. The digestive functions of saliva include moistening food and helping to create a food bolus and this lubricative function of saliva allows the food bolus to be passed easily from the mouth into the esophagus. Only about 30% starch digestion takes place in the mouth cavity, Salivary glands also secrete salivary lipase to begin fat digestion. Salivary lipase plays a role in fat digestion in newborn infants as their pancreatic lipase still needs some time to develop. Saliva is very important in the sense of taste and it is the liquid medium in which chemicals are carried to taste receptor cells. Persons with little saliva often complain of dysgeusia, saliva maintains the pH of the mouth. Saliva is supersaturated with various ions, certain salivary proteins prevent precipitation, which would form salts. These ions act as a buffer, keeping the acidity of the mouth within a certain range and this prevents minerals in the dental hard tissues from dissolving
12.
Salivary glands
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In humans and some other mammals the secretion is alpha-amylase also known as ptyalin. The salivary glands are detailed below, The two parotid glands are major salivary glands wrapped around the mandibular ramus in humans, the largest of the salivary glands, they secrete saliva to facilitate mastication and swallowing, and amylase to begin the digestion of starches. It is the type of gland which secretes the ptyalin. It enters the cavity via the parotid duct or Stensen duct. The glands are located posterior to the mandibular ramus and anterior to the process of the temporal bone. They produce 20% of the total salivary content in the oral cavity, the submandibular glands are a pair of major salivary glands located beneath the lower jaws, superior to the digastric muscles. The secretion produced is a mixture of both fluid and mucus, and enters the oral cavity via the submandibular duct or Wharton duct. It is located two fingers above the Adams apple and about two inches apart under the chin. The sublingual glands are a pair of salivary glands located inferior to the tongue. The secretion produced is mainly mucous in nature, however, it is categorized as a mixed gland, approximately 5% of saliva entering the oral cavity comes from these glands. They are 1-2mm in diameter and unlike the major glands, they are not encapsulated by connective tissue, the gland has usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland and their secretion is mainly mucous in nature and have many functions such as coating the oral cavity with saliva. Problems with dentures are sometimes associated with salivary glands if there is dry mouth present. The minor salivary glands are innervated by the seventh cranial or facial nerve, von Ebners glands are glands found in a trough circling the circumvallate papillae on the dorsal surface of the tongue near the terminal sulcus. They secrete a purely serous fluid that begins lipid hydrolysis and they also facilitate the perception of taste through secretion of digestive enzymes and proteins. The arrangement of these glands around the circumvallate papillae provides a flow of fluid over great number of taste bud along the sides of the papillae. It is important for dissolving the food particles to be tested, Salivary glands are innervated, either directly or indirectly, by the parasympathetic and sympathetic arms of the autonomic nervous system. Parasympathetic stimulation evokes a copious flow of saliva, in contrast, sympathetic stimulation produces either a small flow, which is rich in protein, or no flow at all
13.
Salivary amylase
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α-Amylase is a protein enzyme EC3.2.1.1 that hydrolyses alpha bonds of large, alpha-linked polysaccharides, such as starch and glycogen, yielding glucose and maltose. It is the form of amylase found in humans and other mammals. It is also present in seeds containing starch as a food reserve, although found in many tissues, amylase is most prominent in pancreatic juice and saliva, each of which has its own isoform of human α-amylase. They behave differently on isoelectric focusing, and can also be separated in testing by using specific monoclonal antibodies, in humans, all amylase isoforms link to chromosome 1p21. Amylase is found in saliva and breaks starch into maltose and dextrin and this form of amylase is also called ptyalin /ˈtaɪəlɪn/ It will break large, insoluble starch molecules into soluble starches producing successively smaller starches and ultimately maltose. Ptyalin acts on linear α glycosidic linkages, but compound hydrolysis requires an enzyme that acts on branched products, salivary amylase is inactivated in the stomach by gastric acid. In gastric juice adjusted to pH3.3, ptyalin was totally inactivated in 20 minutes at 37 °C, in contrast, 50% of amylase activity remained after 150 minutes of exposure to gastric juice at pH4.3. Both starch, the substrate for ptyalin, and the product are able to protect it against inactivation by gastric acid. The number of gene copies correlates with the levels of salivary amylase, gene copy number is associated with apparent evolutionary exposure to high-starch diets. For example, a Japanese individual had 14 copies of the amylase gene, the Japanese diet has traditionally contained large amounts of rice starch. In contrast, a Biaka individual carried six copies, the Biaka are rainforest hunter-gatherers who have traditionally consumed a low-starch diet. Perry and colleagues speculated the increased number of the salivary amylase gene may have enhanced survival coincident to a shift to a starchy diet during human evolution. Pancreatic α-amylase randomly cleaves the α glycosidic linkages of amylose to yield dextrin, maltose and it adopts a double displacement mechanism with retention of anomeric configuration. The test for amylase is easier to perform than that for lipase, making it the primary test used to detect, medical laboratories will usually measure either pancreatic amylase or total amylase. If only pancreatic amylase is measured, an increase will not be noted with mumps or other salivary gland trauma, however, because of the small amount present, timing is critical when sampling blood for this measurement. Blood should be taken soon after a bout of pancreatitis pain, salivary α-amylase has been used as a biomarker for stress that does not require a blood draw. Five to 10 times the ULN may indicate ileus or duodenal disease or renal failure, α-Amylase is used in ethanol production to break starches in grains into fermentable sugars. The first step in the production of corn syrup is the treatment of cornstarch with α-amylase
14.
Mucus
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In vertebrates, mucus is a slippery secretion produced by, and covering, mucous membranes. Mucous fluid is rich in glycoproteins and water and is produced from cells found in mucous glands. Mucous fluid may also originate from mixed glands, which contain both serous and mucous cells and this mucus serves to protect epithelial cells in the respiratory, gastrointestinal, urogenital, visual, and auditory systems, the epidermis in amphibians, and the gills in fish. A major function of mucus is to protect against infectious agents such as fungi, bacteria. The average human nose produces about a liter of mucus per day, most of the mucus produced is in the gastrointestinal tract. Bony fish, hagfish, snails, slugs, and some other invertebrates also produce external mucus, the rest of this article deals with the production and function of mucus in humans. In the human system, mucus aids in the protection of the lungs by trapping foreign particles that enter them, in particular, through the nose. Phlegm is a term for mucus that is restricted to the respiratory tract. Nasal mucus is produced by the mucosa, and mucosal tissues lining the airways is produced by specialized airway epithelial cells. Small particles such as dust, particulate pollutants, and allergens, as well as agents and bacteria are caught in the viscous nasal or airway mucus. This event along with the movement of the respiratory mucus layer toward the oropharynx. This explains why coughing often occurs in those who smoke cigarettes, the bodys natural reaction is to increase mucus production. In addition, mucus aids in moisturizing the inhaled air and prevents tissues such as the nasal, nasal and airway mucus is produced continuously, with most of it swallowed subconsciously, even when it is dried. Increased mucus production in the tract is a symptom of many common illnesses, such as the common cold. Hypersecretion of mucus can occur in respiratory diseases such as respiratory allergies, asthma. The presence of mucus in the nose and throat is normal, in general, nasal mucus is clear and thin, serving to filter air during inhalation. During times of infection, mucus can change color to yellow or green either as a result of trapped bacteria or due to the reaction to viral infection. The green color of mucus comes from the group in the iron-containing enzyme myeloperoxidase secreted by white blood cells as a cytotoxic defense during a respiratory burst
15.
Hydrogencarbonate
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In inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid. It is an anion with the chemical formula HCO−3. Bicarbonate serves a crucial role in the physiological pH buffering system. The term bicarbonate was coined in 1814 by the English chemist William Hyde Wollaston, the name lives on as a trivial name. It is isoelectronic with nitric acid HNO3, a bicarbonate salt forms when a positively charged ion attaches to the negatively charged oxygen atoms of the ion, forming an ionic compound. Many bicarbonates are soluble in water at temperature and pressure, in particular, sodium bicarbonate contributes to total dissolved solids. Bicarbonate is alkaline, and a component of the pH buffering system of the human body. 70–75% of CO2 in the body is converted into carbonic acid and this is especially important for protecting tissues of the central nervous system, where pH changes too far outside of the normal range in either direction could prove disastrous. Bicarbonate also acts to regulate pH in the small intestine and it is released from the pancreas in response to the hormone secretin to neutralize the acidic chyme entering the duodenum from the stomach. In freshwater ecology, strong photosynthetic activity by freshwater plants in daylight releases gaseous oxygen into the water and these shift the pH upward until in certain circumstances the degree of alkalinity can become toxic to some organisms or can make other chemical constituents such as ammonia toxic. In darkness, when no photosynthesis occurs, respiration processes release carbon dioxide, the most common salt of the bicarbonate ion is sodium bicarbonate, NaHCO3, which is commonly known as baking soda. When heated or exposed to a such as acetic acid. This is used as an agent in baking. The flow of ions from rocks weathered by the carbonic acid in rainwater is an important part of the carbon cycle. Bicarbonate also serves much in the digestive system and it raises the internal pH of the stomach, after highly acidic digestive juices have finished in their digestion of food. Ammonium bicarbonate is used in digestive biscuit manufacture, in diagnostic medicine, the blood value of bicarbonate is one of several indicators of the state of acid–base physiology in the body. It is measured, along with carbon dioxide, chloride, potassium, the parameter standard bicarbonate concentration is the bicarbonate concentration in the blood at a PaCO2 of 40 mmHg, full oxygen saturation and 36 °C
16.
Alkaline
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Alkalinity is the name given to the quantitative capacity of an aqueous solution to neutralize an acid. Measuring alkalinity is important in determining a streams ability to neutralize acidic pollution from rainfall or wastewater and it is one of the best measures of the sensitivity of the stream to acid inputs. There can be changes in the alkalinity of streams and rivers in response to human disturbances. Alkalinity is related to the pH of a solution, but measures a different property, roughly, the alkalinity of a solution is a measure of how strong the bases are in a solution, whereas the pH measures the amount of chemical bases. A good example is a solution, which can have many available bases despite having only a moderate pH level. Alkalinity roughly refers to the amount of bases in a solution that can be converted to uncharged species by a strong acid. The cited author, James Drever, provides an equation expressed in terms of molar equivalents, which means the number of moles of each ion type multiplied by the charge of the ion. For example,1 mole of HCO31− in solution represents 1 molar equivalent, the total charge of a solution always equals zero. On the left-hand side of the equation is the sum of conservative cations minus the sum of conservative anions, balancing this on the right side is the sum of the anions that could be neutralized by added H+ ions minus H+ ions already present, as indicated by the pH. This right side term is called total alkalinity and it is, quoting Drever, formally defined as the equivalent sum of the bases that are titratable with strong acid. The listing of ions shown on the right in Drever was mHCO3− + 2mCO32− + mB4− + mH34− + mHS− + morganic anions + mOH− - mH+, total alkalinity is measured by adding a strong acid until all the anions listed above are converted to uncharged species. The total alkalinity is not affected by temperature, pressure, or pH, though the values of individual constituents are, Drever further notes that in most natural waters, all ions except HCO3− and CO3−2 have low concentrations. Thus carbonate alkalinity, which is equal to mHCO3− + 2mCO3−2 is also equal to the total alkalinity. Alkalinity or AT measures the ability of a solution to neutralize acids to the point of carbonate or bicarbonate. The alkalinity is equal to the sum of the bases in solution. Other common natural components that can contribute to alkalinity include borate, hydroxide, phosphate, silicate, dissolved ammonia, the bases of some organic acids. Solutions produced in a laboratory may contain a virtually limitless number of bases that contribute to alkalinity, Alkalinity is usually given in the unit mEq/L. Commercially, as in the pool industry, alkalinity might also be given in parts per million of equivalent calcium carbonate
17.
Peristalsis
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Peristalsis is a radially symmetrical contraction and relaxation of muscles that propagates in a wave down a tube, in an anterograde direction. In much of a digestive tract such as the human gastrointestinal tract, smooth muscle contracts in sequence to produce a peristaltic wave. Earthworms use a mechanism to drive their locomotion, and some modern machinery imitates this design. The word comes from New Latin and is derived from the Greek peristellein, to wrap around, from peri-, around + stellein, draw in, bring together, after food is chewed into a bolus, it is swallowed and moved through the esophagus. Smooth muscles contract behind the bolus to prevent it from being squeezed back into the mouth, then rhythmic, unidirectional waves of contractions work to rapidly force the food into the stomach. The migrating motor complex helps trigger peristaltic waves and this process works in one direction only and its sole esophageal function is to move food from the mouth into the stomach. In the esophagus, two types of peristalsis occur, First, there is a primary peristaltic wave, which occurs when the bolus enters the esophagus during swallowing, the primary peristaltic wave forces the bolus down the esophagus and into the stomach in a wave lasting about 8–9 seconds. The wave travels down to the even if the bolus of food descends at a greater rate than the wave itself. The process of peristalsis is controlled by medulla oblongata, esophageal peristalsis is typically assessed by performing an esophageal motility study. During vomiting, the propulsion of food up the oesophagus and out the mouth comes from contraction of the abdominal muscles, once processed and digested by the stomach, the milky chyme is squeezed through the pyloric sphincter into the small intestine. Once past the stomach, a typical peristaltic wave only lasts for a few seconds and its primary purpose is to mix the chyme in the intestine rather than to move it forward in the intestine. Through this process of mixing and continued digestion and absorption of nutrients, in contrast to peristalsis, segmentation contractions result in that churning and mixing without pushing materials further down the digestive tract. Although the large intestine has peristalsis of the type that the small intestine uses, instead, general contractions called mass movements occur one to three times per day in the large intestine, propelling the chyme toward the rectum. Mass movements often tend to be triggered by meals, as the presence of chyme in the stomach, the human lymphatic system has no central pump. Instead, lymph circulates through peristalsis in the capillaries, as well as valves in the capillaries, compression during contraction of adjacent skeletal muscle. During ejaculation, the muscle in the walls of the vas deferens contracts reflexively in peristalsis. The earthworm is an annelid worm with a hydrostatic skeleton that moves by peristalsis. Its hydrostatic skeleton consists of a body cavity surrounded by an extensible body wall
18.
Gastric juice
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Gastric acid, gastric juice or stomach acid, is a digestive fluid, formed in the stomach and is composed of hydrochloric acid. 05–0.1 M, potassium chloride and sodium chloride. The acid plays a key role in digestion of proteins, by activating digestive enzymes, gastric acid is produced by cells in the lining of the stomach, which are coupled in feedback systems to increase acid production when needed. Other cells in the stomach produce bicarbonate, a base, to buffer the fluid and these cells also produce mucus, which forms a viscous physical barrier to prevent gastric acid from damaging the stomach. Cells in the beginning of the intestine, or duodenum. The main constituent of acid is hydrochloric acid which is produced by parietal cells in the gastric glands in the stomach. Its secretion is a complex and relatively expensive process. Parietal cells contain an extensive secretory network from which the acid is secreted into the lumen of the stomach. The pH of gastric acid is 1.5 to 3.5 in the stomach lumen. The parietal cell releases bicarbonate into the bloodstream in the process, the highly acidic environment in the stomach lumen causes proteins from food to lose their characteristic folded structure. This exposes the proteins peptide bonds, the gastric chief cells of the stomach secrete enzymes for protein breakdown. Hydrochloric acid activates pepsinogen into the enzyme pepsin, which helps digestion by breaking the bonds linking amino acids. In addition, many microorganisms have their growth inhibited by such an acidic environment, a typical adult human stomach will secrete about 1.5 liters of gastric acid daily. Gastric acid secretion happens in several steps, chloride and hydrogen ions are secreted separately from the cytoplasm of parietal cells and mixed in the canaliculi. Gastric acid is secreted into the lumen of the gastric gland. The exact manner in which the secreted acid reaches the stomach lumen is controversial, chloride and sodium ions are secreted actively from the cytoplasm of the parietal cell into the lumen of the canaliculus. The enzyme carbonic anhydrase catalyses the reaction between carbon dioxide and water to carbonic acid. This acid immediately dissociates into hydrogen and bicarbonate ions, the hydrogen ions leave the cell through H+/K+ ATPase antiporter pumps. At the same time, sodium ions are actively reabsorbed and this means that the majority of secreted K+ and Na+ ions return to the cytoplasm
19.
Proteolysis
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Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years, proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically and it is also important in the regulation of some physiological and cellular processes, as well as preventing the accumulation of unwanted or abnormal proteins in cells. Consequently, dis-regulation of proteolysis can cause diseases and is used in some venoms to damage their prey, proteolysis is important as an analytical tool for studying proteins in the laboratory, as well as industrially, for example in food processing and stain removal. Limited proteolysis of a polypeptide during or after translation in protein synthesis often occurs for many proteins and this may involve removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one. The precursor to the functional form of protein is termed proprotein. For example, albumin is first synthesized as preproalbumin and contains a signal peptide. This forms the proalbumin after the signal peptide is cleaved, the initiating methionine may be removed during translation of the nascent protein. For E. coli, fMet is efficiently removed if the second residue is small and uncharged, in both prokaryotes and eukaryotes, the exposed N-terminal residue may determine the half-life of the protein according to the N-end rule. Proteins that are to be targeted to a particular organelle or for secretion have an N-terminal signal peptide directs the protein to its final destination. This signal peptide is removed by proteolysis after their transport through a membrane, the polyprotein pro-opiomelanocortin contains many polypeptide hormones. The cleavage pattern of POMC, however, may vary between different tissues, yielding different sets of polypeptide hormones from the same polyprotein, many viruses also produce their proteins initially as a single polypeptide chain that were translated from a polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains, many proteins and hormones are synthesized in the form of their precursors - zymogens, proenzymes, and prehormones. These proteins are cleaved to form their final active structures, insulin, for example, is synthesized as preproinsulin, which yields proinsulin after the signal peptide has been cleaved. The proinsulin is then cleaved at two positions to yield two polypeptide chains linked by two disulfide bonds, removal of two C-terminal residues from the B-chain then yields the mature insulin. Proteases in particular are synthesized in the form so that they may be safely stored in cells. This is to ensure that the protease is activated only in the location or context. Proteolysis can, therefore, be a method of regulating biological processes by turning inactive proteins into active ones, a good example is the blood clotting cascade whereby an initial event triggers a cascade of sequential proteolytic activation of many specific proteases, resulting in blood coagulation
20.
Hydrochloric acid
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Hydrochloric acid is a corrosive, strong mineral acid with many industrial uses. A colorless, highly pungent solution of chloride in water. Free hydrochloric acid was first formally described in the 16th century by Libavius, later, it was used by chemists such as Glauber, Priestley, and Davy in their scientific research. It has numerous applications, including household cleaning, production of gelatin and other food additives, descaling. About 20 million tonnes of acid are produced worldwide annually. It is also found naturally in gastric acid, Hydrochloric acid was known to European alchemists as spirits of salt or acidum salis. Both names are used, especially in other languages, such as German, Salzsäure, Dutch, Zoutzuur, Swedish, Saltsyra, Turkish, Tuz Ruhu, Polish, kwas solny and Chinese. Gaseous HCl was called marine acid air, the old name muriatic acid has the same origin, and this name is still sometimes used. The name hydrochloric acid was coined by the French chemist Joseph Louis Gay-Lussac in 1814, aqua regia, a mixture consisting of hydrochloric and nitric acids, prepared by dissolving sal ammoniac in nitric acid, was described in the works of Pseudo-Geber, a 13th-century European alchemist. Other references suggest that the first mention of aqua regia is in Byzantine manuscripts dating to the end of the 13th century, free hydrochloric acid was first formally described in the 16th century by Libavius, who prepared it by heating salt in clay crucibles. Joseph Priestley of Leeds, England prepared pure hydrogen chloride in 1772, during the Industrial Revolution in Europe, demand for alkaline substances increased. A new industrial process developed by Nicolas Leblanc of Issoundun, France enabled cheap large-scale production of sodium carbonate, in this Leblanc process, common salt is converted to soda ash, using sulfuric acid, limestone, and coal, releasing hydrogen chloride as a by-product. Until the British Alkali Act 1863 and similar legislation in other countries, after the passage of the act, soda ash producers were obliged to absorb the waste gas in water, producing hydrochloric acid on an industrial scale. In the 20th century, the Leblanc process was replaced by the Solvay process without a hydrochloric acid by-product. Since hydrochloric acid was already settled as an important chemical in numerous applications. After the year 2000, hydrochloric acid is made by absorbing by-product hydrogen chloride from industrial organic compounds production. Hydrochloric acid is the salt of hydronium ion, H3O+ and chloride and it is usually prepared by treating HCl with water. H C l + H2 O ⟶ H3 O + + C l − Hydrochloric acid can therefore be used to prepare salts called chlorides, Hydrochloric acid is a strong acid, since it is completely dissociated in water
21.
Pepsin
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Pepsin is an enzyme that breaks down proteins into smaller peptides. It is produced in the stomach and is one of the digestive enzymes in the digestive systems of humans and many other animals. It is one of three principal proteases in the digestive system, the other two being chymotrypsin and trypsin. e. Peptides and amino acids, which can be absorbed by the small intestine. Pepsin is most efficient in cleaving peptide bonds between hydrophobic and preferably aromatic amino acids such as phenylalanine, tryptophan, and tyrosine. Pepsins proenzyme, pepsinogen, is released by the cells in the stomach wall. Pepsin is a protease, using a catalytic aspartate in its active site. Pepsin was one of the first enzymes to be discovered and it was discovered in 1836 by Theodor Schwann. Schwann coined its name from the Greek word πέψις pepsis, meaning digestion, scientists around this time began discovering many biochemical compounds that play a significant role in biological processes, and pepsin was one of them. An acidic substance that was able to convert nitrogen-based foods into water-soluble material was determined to be pepsin, in 1928, it became one of the first enzymes to be crystallized when John H. Northrop crystallized it using dialysis, filtration, and cooling. Pepsin is expressed as a zymogen called pepsinogen, whose structure has an additional 44 amino acids. In the stomach, chief cells release pepsinogen and this zymogen is activated by hydrochloric acid, which is released from parietal cells in the stomach lining. The hormone gastrin and the vagus nerve trigger the release of both pepsinogen and HCl from the stomach lining when food is ingested, hydrochloric acid creates an acidic environment, which allows pepsinogen to unfold and cleave itself in an autocatalytic fashion, thereby generating pepsin. Pepsin cleaves the 44 amino acids from pepsinogen to create more pepsin, pepsin is most active in acidic environments between 37 °C and 42 °C. Accordingly, its site of synthesis and activity is in the stomach. Pepsin will digest up to 20% of ingested amide bonds by cleaving preferentially at the N-terminal side of aromatic amino acids such as phenylalanine, tryptophan, pepsin exhibits preferential cleavage for hydrophobic, preferably aromatic, residues in P1 and P1 positions. Increased susceptibility to hydrolysis occurs if there is an amino acid close to the peptide bond. Pepsin cleaves Phe1Val, Gln4His, Glu13Ala, Ala14Leu, Leu15Tyr, Tyr16Leu, Gly23Phe, pepsin exhibits maximal activity at pH2.0 and is inactive at pH6.5 and above, however pepsin is not fully denatured or irreversibly inactivated until pH8.0
22.
Pylorus
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The pylorus, or pyloric part, connects the stomach to the duodenum. The pylorus is considered as having two parts, the pyloric antrum and the pyloric canal, the pyloric canal ends as the pyloric orifice, which marks the junction between the stomach and the duodenum. The orifice is surrounded by a sphincter, a band of muscle, the word pylorus comes from Greek πυλωρός, via Latin. The word pylorus in Greek means gatekeeper, related to gate and is linguistically related to the word pylon. The pylorus is the furthest part of the stomach that connects to the duodenum and it is divided into two parts, the antrum, which connects to the body of the stomach, and the pyloric canal, which connects to the duodenum. The pyloric antrum is the portion of the pylorus. It is near the bottom of the stomach, proximal to the sphincter, which separates the stomach. The canal is the opening between the stomach and the duodenum, the pyloric sphincter, or valve, is a strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It controls the outflow of gastric contents into the duodenum and it receives sympathetic innervation from the celiac ganglion. Under microscopy, the pylorus contains numerous glands, including gastric pits and they consist of two or three short closed tubes opening into a common duct or mouth. These tubes are wavy, and are about one-half the length of the duct, the duct is lined by columnar cells, continuous with the epithelium lining the surface of the mucous membrane of the stomach, the tubes by shorter and more cubical cell which are finely granular. The glands contain mucus cells and G cells that secrete gastrin, the pylorus also contains scattered parietal cells and neuroendocrine cells. These endocrine cells including D cells, which release somatostatin, the pylorus is one component of the gastrointestinal system. Food from the stomach, as chyme, passes through the pylorus to the duodenum, the pylorus, through the pyloric sphincter, regulates entry of food from the stomach into the duodenum. In such conditions as stomach cancer, tumours may partly block the pyloric canal, a special tube can be implanted surgically to connect the stomach to the duodenum so as to facilitate the passage of food from one to the other. This tube is called a gastroduodenostomy, pyloric stenosis refers to a pylorus that is narrow. This is due to congenital hypertrophy of the pyloric sphincter, the lumen of the pylorus is narrower, and less food is able to pass through. This problem is detected in the early weeks of life
23.
Colon (anatomy)
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The large intestine, or the large bowel, is the last part of the gastrointestinal tract and of the digestive system in vertebrates. Water is absorbed here and the waste material is stored as feces before being removed by defecation. Most sources define the large intestine as the combination of the cecum, colon, rectum, some other sources exclude the anal canal. In humans, the large intestine begins in the right region of the pelvis, just at or below the waist. It then continues as the colon ascending the abdomen, across the width of the cavity as the transverse colon. Overall, in humans, the intestine is about 1.5 metres long. The colon is the last part of the digestive system and it extracts water and salt from solid wastes before they are eliminated from the body and is the site in which flora-aided fermentation of unabsorbed material occurs. Unlike the small intestine, the colon does not play a role in absorption of foods. About 1.5 litres or 45 ounces of water arrives in the each day. The length of the human male colon is 166 cm, on average. In mammals, the colon consists of five sections, the cecum plus the colon, the transverse colon, the descending colon, the sigmoid colon. Retroperitoneal organs in general do not have a covering of peritoneum. Intraperitoneal organs are completely surrounded by peritoneum and are therefore mobile, of the colon, the ascending colon, descending colon and rectum are retroperitoneal, while the cecum, appendix, transverse colon and sigmoid colon are intraperitoneal. This is important as it affects which organs can be accessed during surgery. The ascending colon is the first of four sections of the large intestine and it is connected to the small intestine by a section of bowel called the cecum. The ascending colon runs upwards through the abdominal cavity toward the transverse colon for approximately eight inches, one of the main functions of the colon is to remove the water and other key nutrients from waste material and recycle it. As the waste material exits the small intestine through the valve, it will move into the cecum. The unwanted waste material is moved upwards toward the transverse colon by the action of peristalsis, the ascending colon is sometimes attached to the appendix via Gerlachs valve
24.
Biotin
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Biotin is a water-soluble B-vitamin, also called vitamin B7 and formerly known as vitamin H or coenzyme R. It is composed of a ureido ring fused with a tetrahydrothiophene ring, a valeric acid substituent is attached to one of the carbon atoms of the tetrahydrothiophene ring. Biotin is a coenzyme for carboxylase enzymes, involved in the synthesis of fatty acids, isoleucine, and valine, biotin deficiency can be caused by inadequate dietary intake or inheritance of one or more inborn genetic disorders that affect biotin metabolism. Subclinical deficiency can cause symptoms, such as hair thinning or skin rash typically on the face. Neonatal screening for biotinidase deficiency began in the United States in 1984, individuals born prior to 1984 are unlikely to have been screened, thus the true prevalence of the disorder is unknown. Biotin is necessary for growth, the production of fatty acids. Biotin assists in various metabolic reactions involving the transfer of carbon dioxide and it may also be helpful in maintaining a steady blood sugar level. Biotin is often recommended as a supplement for strengthening hair and nails. Nevertheless, biotin is found in cosmetics and health products for the hair. The amounts needed are small, a range of foods contain biotin, and intestinal bacteria synthesize biotin. For that reason, statutory agencies in countries, for example the USA. Instead, an Adequate Intake is identified based on the theory that average intake meets needs, future research could result in biotin AIs with EARs and RDAs. Biotin has a structure, with two rings fused together via one of their sides. The two rings are ureido and thiophene moieties, biotin is a heterocyclic, S-containing monocarboxylic acid. It is made from two precursors, alanine and pimeloyl-CoA via three enzymes, 8-Amino-7-oxopelargonic acid synthase is a pyridoxal 5-phosphate enzyme. The pimeloyl-CoA, could be produced by a fatty acid pathway involving a malonyl thioester as the starter. 7, 8Diaminopelargonic acid aminotransferase is unusual in using S-adenosyl methionine as the NH2 donor, dethiobiotin synthetase catalyzes the formation of the ureido ring via a DAPA carbamate activated with ATP. It covalently attaches to the group of specific lysine residues in these carboxylases
25.
Defecation
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Defecation is the final act of digestion, by which organisms eliminate solid, semisolid, or liquid waste material from the digestive tract via the anus. Humans expel feces with a frequency varying from a few times daily to a few times weekly, waves of muscular contraction in the walls of the colon move fecal matter through the digestive tract towards the rectum. Undigested food may also be expelled this way, in a process called egestion, as the waste fills the rectum and expands the rectal walls, nervous system stretch receptors in the rectal walls stimulate the desire to defecate. If defecation is delayed for a period the fecal matter may harden. If defecation occurs too fast, before liquid is absorbed. When the rectum is full, an increase in intra-rectal pressure forces apart the walls of the anal canal, the rectum shortens as material is forced into the anal canal and peristaltic waves push the feces out of the rectum. The internal and external anal sphincters along with the puborectalis muscle allow the feces to be passed by muscles pulling the anus up over the exiting feces, Defecation is normally assisted by taking a deep breath and trying to expel this air against a closed glottis. This contraction of expiratory chest muscles, diaphragm, abdominal wall muscles, ventilation at this point temporarily ceases as the lungs push the chest diaphragm down to exert the pressure. Thoracic blood pressure rises and as a response the amount of blood pumped by the heart decreases. Death has been known to occur in cases where defecation causes the pressure to rise enough to cause the rupture of an aneurysm or to dislodge blood clots. Also, in releasing the Valsalva maneuver blood pressure falls, this, coupled with standing up quickly to leave the toilet, during defecation, the external sphincter muscles relax. The anal and urethral sphincter muscles are closely linked, experiments by Harrison Weed at the Ohio State University Medical Center have shown they can only be contracted together, not individually, and that both show relaxation during urination. This explains why defecation is frequently accompanied by urination, Defecation may be involuntary or voluntary. Young children learn voluntary control through the process of toilet training, the anus and buttocks may be cleansed after defecation with toilet paper, similar paper products, or other absorbent material. In many cultures, such as Hindu and Muslim, water is used for cleansing after defecation. When water is used for cleansing after defecation, toilet paper may be used for drying the area afterwards. The positions and modalities of defecation are culture-dependent, squat toilets are used by the vast majority of the world, including most of Africa, Asia, and the Middle East. The use of sit-down toilets in the Western world is a recent development
26.
Fungi
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A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants, a characteristic that places fungi in a different kingdom from plants, bacteria and some protists, is chitin in their cell walls. Similar to animals, fungi are heterotrophs, they acquire their food by absorbing dissolved molecules, growth is their means of mobility, except for spores, which may travel through the air or water. Fungi are the principal decomposers in ecological systems and this fungal group is distinct from the structurally similar myxomycetes and oomycetes. The discipline of biology devoted to the study of fungi is known as mycology, in the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the size of their structures. Fungi include symbionts of plants, animals, or other fungi and they may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform a role in the decomposition of organic matter and have fundamental roles in nutrient cycling. Since the 1940s, fungi have been used for the production of antibiotics, Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, the fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans, losses of crops due to fungal diseases or food spoilage can have a large impact on human food supplies and local economies. The fungus kingdom encompasses a diversity of taxa with varied ecologies, life cycle strategies. However, little is known of the biodiversity of Kingdom Fungi. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla. The English word fungus is directly adopted from the Latin fungus, used in the writings of Horace, a group of all the fungi present in a particular area or geographic region is known as mycobiota, e. g. the mycobiota of Ireland. Like plants, fungi grow in soil and, in the case of mushrooms, form conspicuous fruit bodies. The fungi are now considered a kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes and they have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols, disaccharides, and polysaccharides
27.
Secretion
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Secretion is the movement of material from one point to another, e. g. secreted chemical substance from a cell or gland. In contrast, excretion, is the removal of certain substances or waste products from a cell or organism, the classical mechanism of cell secretion is via secretory portals at the cell plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structure at the plasma membrane. Secretion in bacterial species means the transport or translocation of molecules for example, proteins. Secretion is an important mechanism in bacterial functioning and operation in their natural surrounding environment for adaptation. Eukaryotic cells, including human cells, have a highly evolved process of secretion, proteins targeted for the outside are synthesized by ribosomes docked to the rough endoplasmic reticulum. As they are synthesized, these proteins translocate into the ER lumen, where they are glycosylated, misfolded proteins are usually identified here and retrotranslocated by ER-associated degradation to the cytosol, where they are degraded by a proteasome. The vesicles containing the properly folded proteins then enter the Golgi apparatus, in the Golgi apparatus, the glycosylation of the proteins is modified and further posttranslational modifications, including cleavage and functionalization, may occur. The proteins are then moved into secretory vesicles which travel along the cytoskeleton to the edge of the cell, more modification can occur in the secretory vesicles. Eventually, there is vesicle fusion with the membrane at a structure called the porosome, in a process called exocytosis. Strict biochemical control is maintained over this sequence by usage of a pH gradient, the pH of the cytosol is 7.4, the ERs pH is 7.0, and the cis-golgi has a pH of 6.5. Secretory vesicles have pHs ranging between 5.0 and 6.0, some secretory vesicles evolve into lysosomes, which have a pH of 4.8, there are many proteins like FGF1, FGF2, interleukin-1 etc. which do not have a signal sequence. They do not use the classical ER-golgi pathway and these are secreted through various nonclassical pathways. At least four nonclassical protein secretion pathways have been described, many human cell types have the ability to be secretory cells. They have a well-developed endoplasmic reticulum and Golgi apparatus to fulfill their function, meibomian glands in the eyelid secrete sebum to lubricate and protect the eye. Secretion is not unique to eukaryotes alone, it is present in bacteria, ATP binding cassette type transporters are common to all the three domains of life. Some secreted proteins are translocated across the membrane by the Sec translocon. Others are translocated across the membrane by the twin-arginine translocation pathway
28.
Molecular diffusion
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Molecular diffusion, often simply called diffusion, is the thermal motion of all particles at temperatures above absolute zero. The rate of movement is a function of temperature, viscosity of the fluid. Diffusion explains the net flux of molecules from a region of higher concentration to one of lower concentration, the result of diffusion is a gradual mixing of material such that the distribution of molecules is uniform. Since the molecules are still in motion, but an equilibrium has been established, in a phase with uniform temperature, absent external net forces acting on the particles, the diffusion process will eventually result in complete mixing. Consider two systems, S1 and S2 at the temperature and capable of exchanging particles. If there is a change in the energy of a system, for example μ1>μ2 an energy flow will occur from S1 to S2, because nature always prefers low energy. Molecular diffusion is described mathematically using Ficks laws of diffusion. Diffusion is of importance in many disciplines of physics, chemistry. Diffusion is part of the transport phenomena, of mass transport mechanisms, molecular diffusion is known as a slower one. In cell biology, diffusion is a form of transport for necessary materials such as amino acids within cells. Diffusion of solvents, such as water, through a membrane is classified as osmosis. Metabolism and respiration rely in part upon diffusion in addition to bulk or active processes, for example, in the alveoli of mammalian lungs, due to differences in partial pressures across the alveolar-capillary membrane, oxygen diffuses into the blood and carbon dioxide diffuses out. Lungs contain a large area to facilitate this gas exchange process. Fundamentally, two types of diffusion are distinguished, Tracer diffusion and Self-diffusion, which is a mixing of molecules taking place in the absence of concentration gradient. This type of diffusion can be followed using isotopic tracers, hence the name, the tracer diffusion is usually assumed to be identical to self-diffusion. This diffusion can take place under equilibrium, an excellent method for the measurement of self-diffusion coefficients is pulsed field gradient NMR, where no isotopic tracers are needed. The self-diffusion coefficient of water has been determined with high accuracy. The self-diffusion coefficient of water is,2. 299·10−9 m²·s−1 at 25 °C and 1. 261·10−9 m²·s−1 at 4 °C
29.
Animal
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Animals are multicellular, eukaryotic organisms of the kingdom Animalia. The animal kingdom emerged as a clade within Apoikozoa as the group to the choanoflagellates. Animals are motile, meaning they can move spontaneously and independently at some point in their lives and their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later in their lives. All animals are heterotrophs, they must ingest other organisms or their products for sustenance, most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago. Animals can be divided broadly into vertebrates and invertebrates, vertebrates have a backbone or spine, and amount to less than five percent of all described animal species. They include fish, amphibians, reptiles, birds and mammals, the remaining animals are the invertebrates, which lack a backbone. These include molluscs, arthropods, annelids, nematodes, flatworms, cnidarians, ctenophores, the study of animals is called zoology. The word animal comes from the Latin animalis, meaning having breath, the biological definition of the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges, jellyfish, insects, and humans. Aristotle divided the world between animals and plants, and this was followed by Carl Linnaeus, in the first hierarchical classification. In Linnaeuss original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, in 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms, Metazoa and Protozoa. The protozoa were later moved to the kingdom Protista, leaving only the metazoa, thus Metazoa is now considered a synonym of Animalia. Animals have several characteristics that set apart from other living things. Animals are eukaryotic and multicellular, which separates them from bacteria and they are heterotrophic, generally digesting food in an internal chamber, which separates them from plants and algae. They are also distinguished from plants, algae, and fungi by lacking cell walls. All animals are motile, if only at life stages. In most animals, embryos pass through a stage, which is a characteristic exclusive to animals. With a few exceptions, most notably the sponges and Placozoa and these include muscles, which are able to contract and control locomotion, and nerve tissues, which send and process signals
30.
Gastrointestinal tract
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Gastrointestinal is an adjective meaning of or pertaining to the stomach and intestines. A tract is a collection of related anatomic structures or a series of connected body organs, the mouth, oesophagus, stomach, and intestines are part of the human alimentary canal. All bilaterians have a gastrointestinal tract, also called a gut or an alimentary canal and this is a tube that transfers food to the organs of digestion. In large bilaterians, the gastrointestinal tract generally also has an exit, some small bilaterians have no anus and dispose of solid wastes by other means. The gastrointestinal tract contains thousands of different bacteria in their gut flora, the human gastrointestinal tract consists of the esophagus, stomach, and intestines, and is divided into the upper and lower gastrointestinal tracts. In contrast, the digestive system comprises the gastrointestinal tract plus the accessory organs of digestion. The tract may also be divided into foregut, midgut, and hindgut, the whole human GI tract is about nine metres long at autopsy. The GI tract releases hormones from enzymes to help regulate the digestive process, the structure and function can be described both as gross anatomy and as microscopic anatomy or histology. The tract itself is divided into upper and lower tracts, the upper gastrointestinal tract consists of the buccal cavity, pharynx, esophagus, stomach, and duodenum. The exact demarcation between the upper and lower tracts is the muscle of the duodenum. Upon dissection, the duodenum may appear to be an organ, but it is divided into four segments based upon function, location. The four segments of the duodenum are as follows, bulb, descending, horizontal, the suspensory muscle attaches the superior border of the ascending duodenum to the diaphragm. The suspensory muscle is an important anatomical landmark which shows the division between the duodenum and the jejunum, the first and second parts of the small intestine. This is a muscle which is derived from the embryonic mesoderm. The lower gastrointestinal tract includes most of the intestine and all of the large intestine. In humans, the intestine is further subdivided into the duodenum, jejunum and ileum while the large intestine is subdivided into the cecum, colon, rectum. The small intestine begins at the duodenum, which receives food from the stomach and it is a tubular structure, usually between 6 and 7 m long. The area of the human, adult small intestinal mucosa is about 30 m2 and its main function is to absorb the products of digestion into the bloodstream
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Spiders
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Spiders are air-breathing arthropods that have eight legs and chelicerae with fangs that inject venom. They are the largest order of arachnids and rank seventh in total species diversity among all other orders of organisms, Spiders are found worldwide on every continent except for Antarctica, and have become established in nearly every habitat with the exceptions of air and sea colonization. As of November 2015, at least 45,700 spider species, anatomically, spiders differ from other arthropods in that the usual body segments are fused into two tagmata, the cephalothorax and abdomen, and joined by a small, cylindrical pedicel. Unlike insects, spiders do not have antennae, in all except the most primitive group, the Mesothelae, spiders have the most centralized nervous systems of all arthropods, as all their ganglia are fused into one mass in the cephalothorax. Unlike most arthropods, spiders have no extensor muscles in their limbs and their abdomens bear appendages that have been modified into spinnerets that extrude silk from up to six types of glands. Spider webs vary widely in size, shape and the amount of thread used. It now appears that the orb web may be one of the earliest forms. Spider-like arachnids with silk-producing spigots appeared in the Devonian period about 386 million years ago, true spiders have been found in Carboniferous rocks from 318 to 299 million years ago, and are very similar to the most primitive surviving suborder, the Mesothelae. The main groups of spiders, Mygalomorphae and Araneomorphae, first appeared in the Triassic period. It is estimated that 25 million tons of spiders kill 400–800 million tons of prey per year. Spiders use a range of strategies to capture prey, trapping it in sticky webs, lassoing it with sticky bolas, mimicking the prey to avoid detection. Spiders guts are too narrow to take solids, and they liquefy their food by flooding it with digestive enzymes and they also grind food with the bases of their pedipalps, as arachnids do not have the mandibles that crustaceans and insects have. Male spiders identify themselves by a variety of courtship rituals to avoid being eaten by the females. Males of most species survive a few matings, limited mainly by their life spans. Females weave silk egg-cases, each of which may contain hundreds of eggs, females of many species care for their young, for example by carrying them around or by sharing food with them. A minority of species are social, building communal webs that may house anywhere from a few to 50,000 individuals, social behavior ranges from precarious toleration, as in the widow spiders, to co-operative hunting and food-sharing. Although most spiders live for at most two years, tarantulas and other spiders can live up to 25 years in captivity. While the venom of a few species is dangerous to humans, scientists are now researching the use of venom in medicine
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Organism
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In biology, an organism is any contiguous living system, such as an animal, plant, fungus, protist, archaeon, or bacterium. All known types of organisms are capable of some degree of response to stimuli, reproduction, growth and development and homeostasis. An organism consists of one or more cells, when it has one cell it is known as an organism. Most unicellular organisms are of microscopic scale and are thus described as microorganisms. Humans are multicellular organisms composed of trillions of cells grouped into specialized tissues. An organism may be either a prokaryote or a eukaryote, prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a cell nucleus. Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes, estimates on the number of Earths current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to five billion species. In 2016, a set of 355 genes from the last universal ancestor of all living organisms living was identified. The term organism first appeared in the English language in 1703 and it is directly related to the term organization. There is a tradition of defining organisms as self-organizing beings. An organism may be defined as an assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Dictionary definitions can be broad, using such as any living structure, such as a plant, animal, fungus or bacterium, capable of growth. Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the machinery of a host cell for reproduction. A superorganism is an organism consisting of individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism, several contributions are responses to the suggestion that the category of organism may well not be adequate in biology. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction and this controversy is problematic because some cellular organisms are also incapable of independent survival and live as obligatory intracellular parasites
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Vesicle (biology)
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In cell biology, a vesicle is a small structure within a cell, consisting of fluid enclosed by a lipid bilayer. Vesicles form naturally during the processes of secretion, uptake and transport of materials within the cytoplasm, alternatively, they may be prepared artificially, in which case they are called liposomes. If there is only one phospholipid bilayer, they are called unilamellar liposome vesicles, the membrane enclosing the vesicle is also a lamellar phase, similar to that of the plasma membrane and vesicles can fuse with the plasma membrane to release their contents outside the cell. Vesicles can also fuse with other organelles within the cell, vesicles perform a variety of functions. Because it is separated from the cytosol, the inside of the vesicle can be made to be different from the cytosolic environment, for this reason, vesicles are a basic tool used by the cell for organizing cellular substances. Vesicles are involved in metabolism, transport, buoyancy control, and temporary storage of food and they can also act as chemical reaction chambers. Vesicle dysfunction is thought to contribute to Alzheimers disease, diabetes, some cases of epilepsy, some cancers and immunological disorders. Vacuoles are vesicles which contain mostly water, plant cells have a large central vacuole in the center of the cell that is used for osmotic control and nutrient storage. Contractile vacuoles are found in protists, especially those in Phylum Ciliophora. These vacuoles take water from the cytoplasm and excrete it from the cell to avoid bursting due to osmotic pressure, lysosomes are involved in cellular digestion. Food can be taken from outside the cell into food vacuoles by a process called endocytosis and these food vacuoles fuse with lysosomes which break down the components so that they can be used in the cell. This form of eating is called phagocytosis. Lysosomes are also used to destroy defective or damaged organelles in a process called autophagy and they fuse with the membrane of the damaged organelle, digesting it. Transport vesicles can move molecules between locations inside the cell, e. g. proteins from the endoplasmic reticulum to the Golgi apparatus. Membrane-bound and secreted proteins are made on ribosomes found in the endoplasmic reticulum. Most of these proteins mature in the Golgi apparatus before going to their destination which may be to lysosomes, peroxisomes. These proteins travel within the cell inside of transport vesicles, secretory vesicles contain materials that are to be excreted from the cell. Cells have many reasons to excrete materials, one reason is to dispose of wastes
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Pilus
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A pilus is a hair-like appendage found on the surface of many bacteria. The terms pilus and fimbria can be used interchangeably, although some researchers reserve the term pilus for the appendage required for bacterial conjugation, all pili in the latter sense are primarily composed of pilin proteins, which are oligomeric. Dozens of these structures can exist on the bacteria, some bacterial viruses or bacteriophages attach to receptors on pili at the start of their reproductive cycle. They are also fragile and constantly replaced, sometimes with pili of different composition, specific host responses to old pili structure are not effective on the new structure. Recombination genes of pili code for variable and constant regions of the pili, conjugative pili allow for the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called sex pili, in analogy to sexual reproduction, perhaps the most well-studied is the F pilus of Escherichia coli, encoded by the F plasmid or fertility factor. A pilus is typically 6 to 7 nm in diameter, not all bacteria can make conjugative pili, but conjugation can occur between bacteria of different species. Some pili, called type IV pili, generate motile forces, movement produced by type IV pili is typically jerky, so it is called twitching motility, as distinct from other forms of bacterial motility, such as that produced by flagella. However, some bacteria, for example Myxococcus xanthus, exhibit gliding motility, Bacterial type IV pilins are similar in structure to the component flagellins of archaeal flagella. Genetic transformation is the process by which a recipient bacterial cell takes up DNA from a neighboring cell, in Neisseria meningitidis, DNA transformation requires the presence of short DNA uptake sequences which are 9-10 monomers residing in coding regions of the donor DNA. Specific recognition of DUSs is mediated by a type IV pilin, menningococcal type IV pili bind DNA through the minor pilin ComP via an electropositive stripe that is predicted to be exposed on the filaments surface. ComP displays an exquisite binding preference for selective DUSs, the distribution of DUSs within the N. meningitides genome favors certain genes, suggesting that there is a bias for genes involved in genomic maintenance and repair. Attachment of bacteria to host surfaces is required for colonization during infection or to formation of a biofilm. A fimbria is a short pilus that is used to attach the bacterium to a surface and they are sometimes called attachment pili. Fimbriae are either located at the poles of a cell, or are spread over its entire surface. Mutant bacteria that lack fimbriae cannot adhere to their usual target surfaces, the lectins are necessary to adhere to target cells because they can recognize oligosaccharide units on the surface of these target cells. Other fimbriae bind to components of the extracellular matrix, fimbriae are found in Gram-negative bacteria. In Gram-positive bacteria, the subunits are covalently linked
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Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
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ATP-binding cassette family
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ABC transporters often consist of multiple subunits, one or two of which are transmembrane proteins and one or two of which are membrane-associated ATPases. Most but not all uptake systems also have an extracytoplasmic receptor, some homologous ATPases function in non-transport-related processes such as translation of RNA and DNA repair. The integral membrane proteins of ABC exporters appear to have evolved independently at least three times, aBC1 exporters evolved by intragenic triplication of a 2 TMS precursor to give 6 TMS proteins. The 10 TMS proteins appear to have two extra TMSs between the two 4 TMS repeat units, like the ABC exporters, it is possible that the integral membrane proteins of ABC uptake systems also evolved at least 3 times independently, based on their high resolution 3-dimensional structures. Some of these exporters in humans are involved in resistance, cystic fibrosis. Hundreds of ABC transporters have been characterized from both prokaryotes and eukaryotes, ABC genes are essential for many processes in the cell, and mutations in human genes cause or contribute to several human genetic diseases. Forty eight ABC genes have been reported in humans, ABC transporters are also involved in multiple drug resistance, and this is how some of them were first identified. When the ABC transport proteins are overexpressed in cells, they can export anticancer drugs. ABC transporters utilize the energy of ATP binding and hydrolysis to transport various substrates across cellular membranes and they are divided into three main functional categories. In prokaryotes, importers mediate the uptake of nutrients into the cell, the substrates that can be transported include ions, amino acids, peptides, sugars, and other molecules that are mostly hydrophilic. The membrane-spanning region of the ABC transporter protects hydrophilic substrates from the lipids of the membrane bilayer thus providing a pathway across the cell membrane, eukaryotes do not possess any importers. Exporters or effluxers, which are present both in prokaryotes and eukaryotes, function as pumps that extrude toxins and drugs out of the cell, in gram-negative bacteria, exporters transport lipids and some polysaccharides from the cytoplasm to the periplasm. The third subgroup of ABC proteins do not function as transporters, bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity. Iron ABC uptake systems, for example, are important effectors of virulence, pathogens use siderophores, such as Enterobactin, to scavenge iron that is in complex with high-affinity iron-binding proteins or erythrocytes. These are high-affinity iron-chelating molecules that are secreted by bacteria and reabsorb iron into iron-siderophore complexes, the chvE-gguAB gene in Agrobacterium tumefaciens encodes glucose and galactose importers that are also associated with virulence. Transporters are extremely vital in cell survival such that they function as protein systems that counteract any undesirable change occurring in the cell, for instance, a potential lethal increase in osmotic strength is counterbalanced by activation of osmosensing ABC transporters that mediate uptake of solutes. Other than functioning in transport, some bacterial ABC proteins are involved in the regulation of several physiological processes. They also play important roles in biosynthetic pathways, including extracellular polysaccharide biosynthesis, although most eukaryotic ABC transporters are effluxers, some are not directly involved in transporting substrates
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Outer membrane protein
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Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion. This family consists of bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and it is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain. The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins, Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, Borrelia burgdorferi outer surface proteins play role in persistence within ticks, mammalian host transmission, host cell adhesion, and in evasion of the host immune system. OspC trigger innate immune system via signaling through TLR1, TLR2, members of this group include, PagC, required by Salmonella typhimurium for survival in macrophages and for virulence in mice Rck outer membrane protein of the S. typhimurium and S. It also has a role in the resistance against attack by the complement system a Bacteriophage lambda outer membrane protein. OspA OspC is a major surface lipoprotein produced by Borrelia burgdorferi when infected ticks feed, OspC is necessary for tick salivary gland invasion. OspC-deficient B. burgdorferi have a reduced capacity for successful transmission to mice. Its synthesis decreases after transmission to a mammalian host and this protein disappears from the bacterial surface around 2 weeks after infection. The crystal structure of OmpX from E. coli reveals that OmpX consists of an eight-stranded antiparallel all-next-neighbour beta barrel, the structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the consists of an extended hydrogen bonding network of highly conserved residues. OmpX thus resembles an inverse micelle, the OmpX structure shows that the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that type of binding promotes cell adhesion and invasion. OspA from Borrelia burgdorferi is an outer surface protein, it has two globular domains which are connected with a single-layer β-sheet. This protein is soluble, contains a large number of Lys
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. PMID 15035043. doi:10.1038/nrmicro753.
