1.
BRENDA
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BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is a resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction, kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a user interface that allows a convenient and sophisticated access to the data. BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology in Braunschweig and was published as a series of books. Its name was originally an acronym for the Braunschweig Enzyme Database, from 1996 to 2007, BRENDA was located at the University of Cologne. There, BRENDA developed into a publicly accessible enzyme information system, in 2007, BRENDA returned to Braunschweig. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics, a major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the interface are also incorporated into the BRENDA database. The latest update was performed in January 2015, Database, The database contains more than 40 data fields with enzyme-specific information on more than 7000 EC numbers that are classified according to the IUBMB. Currently, BRENDA contains manually annotated data from over 140,000 different scientific articles, each enzyme entry is clearly linked to at least one literature reference, to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 110,000 enzyme ligands, the term ligand is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors, the origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides. Furthermore, cross-references to external resources such as sequence and 3D-structure databases. Extensions, Since 2006, the data in BRENDA is supplemented with information extracted from the literature by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA, AMENDA, DRENDA and KENDA were introduced and these text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed. Data access, There are several tools to access to the data in BRENDA
2.
MetaCyc
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The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc is also used in engineering and metabolomics research. MetaCyc contains extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, MetaCyc data on reactions includes predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds. It also provides enzyme mini-reviews and literature references, MetaCyc data on metabolites includes chemical structures, predicted Gibbs free energies of formation, and links to external databases
3.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
4.
PubMed
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
5.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research
6.
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
7.
Fungus
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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
8.
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
9.
Protozoa
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In 21st-century systems of biological classification, the Protozoa are defined as a diverse group of unicellular eukaryotic organisms. Historically, protozoa were defined as single-celled animals or organisms with animal-like behaviors, such as motility, the group was regarded as the zoological counterpart to the protophyta, which were considered to be plant-like, as they are capable of photosynthesis. The terms protozoa and protozoans are now mostly used informally to designate single-celled, non-photosynthetic protists, such as the ciliates, amoebae and flagellates. The term Protozoa was introduced in 1818 for a taxonomic class, in several classification systems proposed by Thomas Cavalier-Smith and his collaborators since 1981, Protozoa is ranked as a kingdom. The seven-kingdom scheme proposed by Ruggiero et al. in 2015, places eight phyla under Protozoa, Euglenozoa, Amoebozoa, Metamonada, Choanozoa, Loukozoa, Percolozoa, Microsporidia and Sulcozoa. This kingdom does not form a clade, but an evolutionary grade or paraphyletic group, from which the fungi, for this reason, the terms protists, Protista or Protoctista are sometimes preferred for the high-level classification of eukaryotic microbes. In 2005, members of the Society of Protozoologists voted to change the name of organization to the International Society of Protistologists. The word protozoa was coined in 1818 by zoologist Georg August Goldfuss, as the Greek equivalent of the German Urthiere, meaning primitive, Goldfuss erected Protozoa as a class containing what he believed to be the simplest animals. Originally, the group included not only microbes, but also some lower animals, such as rotifers, corals, sponges, jellyfish, bryozoa. In 1848, in light of advancements in cell theory pioneered by Theodore Schwann and Matthias Schleiden, von Siebold redefined Protozoa to include only such unicellular forms, to the exclusion of all metazoa. At the same time, he raised the group to the level of a phylum containing two broad classes of microbes, Infusoria, and Rhizopoda. As a phylum under Animalia, the Protozoa were firmly rooted in the old two-kingdom classification of life, criticism of this system began in the latter half of the 19th century, with the realization that many organisms met the criteria for inclusion among both plants and animals. For example, the algae Euglena and Dinobryon have chloroplasts for photosynthesis, as an alternative, he proposed a new kingdom called Primigenum, consisting of both the protozoa and unicellular algae, which he combined together under the name Protoctista. In Hoggss conception, the animal and plant kingdoms were likened to two great pyramids blending at their bases in the Kingdom Primigenum, six years later, Ernst Haeckel also proposed a third kingdom of life, which he named Protista. Despite these proposals, Protozoa emerged as the taxonomic placement for heterotrophic microbes such as amoebae and ciliates. A variety of systems were proposed, and Kingdoms Protista and Protoctista became well established in biology texts. While many taxonomists have abandoned Protozoa as a group, Thomas Cavalier-Smith has retained it as a kingdom in the various classifications he has proposed. As of 2015, Cavalier-Smiths Protozoa excludes several major groups of organisms traditionally placed among the protozoa, including the ciliates, dinoflagellates, Protozoa, as traditionally defined, are mainly microscopic organisms, ranging in size from 10 to 52 micrometers
10.
Catalysis
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Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. In most cases, reactions occur faster with a catalyst because they require less activation energy, furthermore, since they are not consumed in the catalyzed reaction, catalysts can continue to act repeatedly. Often only tiny amounts are required in principle, in the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations, the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have an activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However, the mechanics of catalysis is complex. Usually, the catalyst participates in this slowest step, and rates are limited by amount of catalyst, in heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst, analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, in heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a system or sublimate in a solid–gas system. The production of most industrially important chemicals involves catalysis, similarly, most biochemically significant processes are catalysed. Research into catalysis is a field in applied science and involves many areas of chemistry, notably organometallic chemistry. Catalysis is relevant to aspects of environmental science, e. g. the catalytic converter in automobiles. Many transition metals and transition metal complexes are used in catalysis as well, Catalysts called enzymes are important in biology. A catalyst works by providing a reaction pathway to the reaction product. The rate of the reaction is increased as this route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates water and oxygen, as shown below,2 H2O2 →2 H2O + O2 This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow. In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available and this reaction is strongly affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms
11.
Cellulose
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Cellulose is an organic compound with the formula n, a polysaccharide consisting of a linear chain of several hundred to many thousands of β linked D-glucose units. Cellulose is an important structural component of the cell wall of green plants, many forms of algae. Some species of bacteria secrete it to form biofilms, Cellulose is the most abundant organic polymer on Earth. The cellulose content of cotton fiber is 90%, that of wood is 40–50%, Cellulose is mainly used to produce paperboard and paper. Smaller quantities are converted into a variety of derivative products such as cellophane. Conversion of cellulose from energy crops into biofuels such as ethanol is under investigation as an alternative fuel source. Cellulose for industrial use is mainly obtained from wood pulp and cotton, some animals, particularly ruminants and termites, can digest cellulose with the help of symbiotic micro-organisms that live in their guts, such as Trichonympha. In humans, cellulose acts as a bulking agent for feces and is often referred to as a dietary fiber. Cellulose was discovered in 1838 by the French chemist Anselme Payen, Cellulose was used to produce the first successful thermoplastic polymer, celluloid, by Hyatt Manufacturing Company in 1870. Production of rayon from cellulose began in the 1890s and cellophane was invented in 1912, hermann Staudinger determined the polymer structure of cellulose in 1920. The compound was first chemically synthesized in 1992, by Kobayashi, Cellulose has no taste, is odorless, is hydrophilic with the contact angle of 20–30 degrees, is insoluble in water and most organic solvents, is chiral and is biodegradable. It was shown to melt at 467 °C in 2016 and it can be broken down chemically into its glucose units by treating it with concentrated mineral acids at high temperature. Cellulose is derived from D-glucose units, which condense through β-glycosidic bonds and this linkage motif contrasts with that for α-glycosidic bonds present in starch and glycogen. This confers tensile strength in cell walls, where cellulose microfibrils are meshed into a polysaccharide matrix, compared to starch, cellulose is also much more crystalline. Whereas starch undergoes a crystalline to amorphous transition when heated beyond 60–70 °C in water, cellulose requires a temperature of 320 °C, several different crystalline structures of cellulose are known, corresponding to the location of hydrogen bonds between and within strands. Natural cellulose is cellulose I, with structures Iα and Iβ, Cellulose produced by bacteria and algae is enriched in Iα while cellulose of higher plants consists mainly of Iβ. Cellulose in regenerated cellulose fibers is cellulose II, the conversion of cellulose I to cellulose II is irreversible, suggesting that cellulose I is metastable and cellulose II is stable. With various chemical treatments it is possible to produce the structures cellulose III, many properties of cellulose depend on its chain length or degree of polymerization, the number of glucose units that make up one polymer molecule
12.
Polysaccharide
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They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose, polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their building blocks. They may be amorphous or even insoluble in water, natural saccharides are generally of simple carbohydrates called monosaccharides with general formula n where n is three or more. Examples of monosaccharides are glucose, fructose, and glyceraldehyde, polysaccharides, meanwhile, have a general formula of Cxy where x is usually a large number between 200 and 2500. When the repeating units in the backbone are six-carbon monosaccharides, as is often the case, the general formula simplifies to n. Polysaccharides are an important class of biological polymers and their function in living organisms is usually either structure- or storage-related. Starch is used as a polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the structurally similar glucose polymer is the more densely branched glycogen, glycogens properties allow it to be metabolized more quickly, which suits the active lives of moving animals. Cellulose and chitin are examples of structural polysaccharides, cellulose is used in the cell walls of plants and other organisms, and is said to be the most abundant organic molecule on Earth. It has many such as a significant role in the paper and textile industries, and is used as a feedstock for the production of rayon, cellulose acetate, celluloid. Chitin has a structure, but has nitrogen-containing side branches. It is found in arthropod exoskeletons and in the walls of some fungi. It also has multiple uses, including surgical threads, polysaccharides also include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan and galactomannan. Nutrition polysaccharides are common sources of energy, many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrate types can be metabolized by bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose, even though these complex carbohydrates are not very digestible, they provide important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits, the main action of dietary fiber is to change the nature of the contents of the gastrointestinal tract, and to change how other nutrients and chemicals are absorbed
13.
Monosaccharide
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Monosaccharides, also called simple sugars, are the most basic units of carbohydrates. They are fundamental units of carbohydrates and cannot be hydrolyzed to simpler compounds. The general formula is CnH 2nOn and they are the simplest form of sugar and are usually colorless, water-soluble, and crystalline solids. Some monosaccharides have a sweet taste, examples of monosaccharides include glucose, fructose and galactose. Monosaccharides are the blocks of disaccharides and polysaccharides. Further, each carbon atom that supports a group is chiral, giving rise to a number of isomeric forms. For instance, galactose and glucose are both aldohexoses, but have different physical structures and chemical properties, with few exceptions, monosaccharides have this chemical formula, Cxy, where conventionally x ≥3. Monosaccharides can be classified by the x of carbon atoms they contain, triose tetrose, pentose, hexose, heptose. The most important monosaccharide, glucose, is a hexose, examples of heptoses include the ketoses mannoheptulose and sedoheptulose. Monosaccharides with eight or more carbons are rarely observed as they are quite unstable, in aqueous solutions monosaccharides exist as rings. Simple monosaccharides have a linear and unbranched carbon skeleton with one carbonyl functional group, therefore, the molecular structure of a simple monosaccharide can be written as HnmH, where n +1 + m = x, so that its elemental formula is CxH2xOx. By convention, the atoms are numbered from 1 to x along the backbone. If the carbonyl is at position 1, the molecule begins with a formyl group H− and is technically an aldehyde, in that case, the compound is termed an aldose. Otherwise, the molecule has a group, a carbonyl −− between two carbons, then it is formally a ketone, and is termed a ketose. Ketoses of biological interest usually have the carbonyl at position 2, the various classifications above can be combined, resulting in names such as aldohexose and ketotriose. A more general nomenclature for open-chain monosaccharides combines a Greek prefix to indicate the number of carbons with the suffixes -ose for aldoses, in the latter case, if the carbonyl is not at position 2, its position is then indicated by a numeric infix. So, for example, H4H is pentose, H3H is pentulose, two monosaccharides with equivalent molecular graphs may still be distinct stereoisomers, whose molecules differ in the three-dimensional arrangement of the bonds of certain atoms. This happens only if the molecule contains a center, specifically a carbon atom that is chiral
14.
Hydrolysis
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Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, generally, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt also dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid. In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households. In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
15.
Glycosidic bond
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In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide and the group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside, glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one also considers S-glycosidic bonds, where the oxygen of the bond is replaced with a sulfur atom. In the same way, N-glycosidic bonds, have the glycosidic oxygen replaced with nitrogen. Substances containing N-glycosidic bonds are known as glycosylamines. C-glycosyl bonds have the oxygen replaced by a carbon, the term C-glycoside is considered a misnomer by IUPAC and is discouraged. All of these modified glycosidic bonds have different susceptibility to hydrolysis, one distinguishes between α- and β-glycosidic bonds based on the relative stereochemistry of the anomeric position and the stereocenter furthest from C1 in the saccharide. An α-glycosidic bond is formed when both carbons have the same stereochemistry, whereas a β-glycosidic bond occurs when the two carbons have different stereochemistry. One complicating issue is that the alpha and beta conformations were originally defined based on the orientation of the major constituents in a Haworth projection. In this case, for D-sugars, a beta conformation would see the major constituent at each carbon drawn above the plane of the ring, for L-sugars, the definitions would then, necessarily, reverse. This is worth noting as these older definitions still permeate the literature, pharmacologists often join substances to glucuronic acid via glycosidic bonds in order to increase their water solubility, this is known as glucuronidation. Many other glycosides have important physiological functions, Nüchter et al. have shown a new approach to Fischer Glycosylation. Employing a microwave oven equipped with refluxing apparatus in a reactor with pressure bombs, Nüchter et al. were able to achieve 100% yield of α-. This method can be performed on a multi-kilogram scale, ondruschka, and W. Lautenschläger, Synthetic Communications 31,1277. Vishal Y Joshis method Joshi et al, d-glucose is first protected by forming the peracetate by addition of acetic anhydride in acetic acid, and then addition of hydrogen bromide which brominates at the 5-position. On addition of the alcohol ROH and lithium carbonate, the OR replaces the bromine and it was suggested by Joshi et al. that lithium acts as the nucleophile that attacks the carbon at the 5-position and through a transition state the alcohol is substituted for the bromine group. Glycoside hydrolases, are enzymes that break glycosidic bonds, glycoside hydrolases typically can act either on α- or on β-glycosidic bonds, but not on both
16.
Hemicellulose
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A hemicellulose is any of several heteropolymers, such as arabinoxylans, present along with cellulose in almost all plant cell walls. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicellulose has a random and it is easily hydrolyzed by dilute acid or base as well as myriad hemicellulase enzymes. Hemicelluloses include xylan, glucuronoxylan, arabinoxylan, glucomannan, and xyloglucan and these polysaccharides contain many different sugar monomers. In contrast, cellulose contains only anhydrous glucose, for instance, besides glucose, sugar monomers in hemicellulose can include xylose, mannose, galactose, rhamnose, and arabinose. Hemicelluloses contain most of the D-pentose sugars, and occasionally small amounts of L-sugars as well, xylose is in most cases the sugar monomer present in the largest amount, although in softwoods mannose can be the most abundant sugar. Not only regular sugars can be found in hemicellulose, but also their acidified form, for instance glucuronic acid, Hemicellulose is often associated with cellulose, but it has different composition. Unlike cellulose, hemicellulose consists of shorter chains – 500–3,000 sugar units as opposed to 7, 000–15,000 glucose molecules per polymer, in addition, hemicellulose is a branched polymer, while cellulose is unbranched. Hemicelluloses are embedded in the walls of plants, sometimes in chains that form a ground - they bind with pectin to cellulose to form a network of cross-linked fibres. Hemicelluloses are synthesised from sugar nucleotides in the cells Golgi apparatus, after synthesis, hemicelluloses are transported to the plasma membrane via Golgi vesicles. As percent content of hemicellulose increases in animal feed, the voluntary feed intake decreases, Hemicellulose is represented by the difference between neutral detergent fiber and acid detergent fiber. Microfibrils are cross-linked together by hemicellulose homopolymers, lignins assist and strengthen the attachment of hemicelluloses to microfibrils. Hemicellulose found in trees is predominantly xylan with some glucomannan, while in softwoods it is mainly rich in galactoglucomannan. The average molecular weight is lower than that of cellulose at less than 30,000, cellulose Lignin Pectin Structure and Properties of Hemicellulose /David Wang’s Wood Chemistry Class
17.
Lichenin
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Lichenin, also known as lichenan or moss starch, is a complex glucan occurring in certain species of lichens. It can be extracted from Cetraria islandica and it has been studied since about 1957. Chemically, lichenin consists of repeating units linked by β-1,3. It is an important carbohydrate for reindeers and northern flying squirrels and it can be extracted by digesting Iceland moss in a cold, weak solution of carbonate of soda for some time, and then boiling. By this process the lichenin is dissolved and on cooling separates as a colorless jelly, iodine imparts no color to it. In his 1960 novel Trouble with Lichen, John Wyndham gives the name Lichenin to an extract of lichen used to extend life expectancy beyond 300 years
18.
Beta-glucan
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Various studies have examined the potential health effects of β-glucan. Oat fiber β-glucan at intake levels of at least 3 g per day can decrease the levels of saturated fats in the blood, some studies have suggested that cereal-derived β-glucan may also have immunomodulatory properties. Yeast- and medicinal mushroom-derived β-glucans have been investigated for their ability to modulate the immune system, β-glucans are further used in various nutraceutical and cosmetic products, as texturing agents, and as soluble fiber supplements, but can be problematic in the process of brewing. Cereal and fungal products have been used for centuries for medicinal and cosmetic purposes, however, β-glucans were first discovered in lichens, and shortly thereafter in barley. A particular interest in oat β-glucan arose after their cholesterol lowering effect was reported in 1984, in 1997, the FDA approved of a claim that intake of at least 3 g of β-glucan from oats per day decreased saturated fats and reduced the risk of heart disease. Although technically β-glucans are chains of D-glucose polysaccharides linked by glycosidic bonds. Cellulose is not typically considered a β-glucan, as it is insoluble, some β-glucan molecules have branching glucose side-chains attached to other positions on the main D-glucose chain, which branch off the β-glucan backbone. In addition, these side-chains can be attached to other types of molecules, like proteins, the most common forms of β-glucans are those comprising D-glucose units with β-1,3 links. Yeast and fungal β-glucans contain 1-6 side branches, while cereal β-glucans contain both β-1,3 and β-1,4 backbone bonds, the frequency, location, and length of the side-chains may play a role in immunomodulation. Differences in molecular weight, shape, and structure of β-glucans dictate the differences in biological activity, β-glucans form a natural component of the cell walls of bacteria, fungi, yeast, and cereals such as oat and barley. Each type of beta-glucan comprises a different molecular backbone, level of branching, one of the most common sources of βD-glucan for supplement use is derived from the cell wall of baker’s yeast. The βD-glucans from yeast are often insoluble, however, β-glucans are also extracted from the bran of some grains, such as oats and barley, and to a much lesser degree in rye and wheat. Other sources include some types of seaweed, and various species of mushrooms, such as reishi, Ganoderma applanatum, shiitake, Chaga, cereal β-glucans from oat, barley, wheat, and rye induce a variety of physiological effects that positively impact health. Barley and oat β-glucans have been studied for their effects on blood glucose regulation in test subjects with hypercholesterolemia, oats and barley differ in the ratio of trimer and tetramer 1-4 linkages. Barley has more 1-4 linkages with a degree of higher than 4. However, the majority of barley blocks remain trimers and tetramers, in oats, β-glucan is found mainly in the endosperm of the oat kernel, especially in the outer layers of that endosperm. β-D-Glucan forms part of the wall of certain medically important fungi. Mushroom beta-glucans are linked by 1,3 glycosidic bonds with 1,6 branches, an assay to detect its presence in blood is marketed as a means of diagnosing invasive fungal infection in patients
19.
Ruminant
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Ruminants are mammals that are able to acquire nutrients from plant-based food by fermenting it in a specialized stomach prior to digestion, principally through microbial actions. The process typically requires the fermented ingesta to be regurgitated and chewed again, the process of rechewing the cud to further break down plant matter and stimulate digestion is called rumination. The word ruminant comes from the Latin ruminare, which means to chew over again, the roughly 150 species of ruminants includes both domestic and wild species. Ruminating mammals include cattle, goats, sheep, giraffes, yaks, deer, antelope and it has also been suggested that notoungulates also relied on rumination, as opposed to other antlantogenates that relied on the more typical hindgut fermentation, though this is not entirely certain. Taxonomically, the suborder Ruminantia is a lineage of herbivorous artiodactyls that includes the most advanced, the term ruminant is not synonymous with Ruminantia. The suborder Ruminantia includes many ruminant species, but does not include tylopods, the primary difference between a ruminant and nonruminant is that ruminants have a four-compartment stomach. The four parts are the rumen, reticulum, omasum, in the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material. Solids clump together to form the cud or bolus, the cud is then regurgitated and chewed to completely mix it with saliva and to break down the particle size. Fiber, especially cellulose and hemicellulose, is broken down in these chambers by microbes into the three volatile fatty acids, acetic acid, propionic acid, and butyric acid. Protein and nonstructural carbohydrate are also fermented, though the rumen and reticulum have different names, they represent the same functional space as digesta can move back and forth between them. Together, these chambers are called the reticulorumen, after this, the digesta is moved to the true stomach, the abomasum. The abomasum is the equivalent of the monogastric stomach. Digesta is finally moved into the intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulorumen are also digested in the small intestine, fermentation continues in the large intestine in the same way as in the reticulorumen. Only small amounts of glucose are absorbed from dietary carbohydrates, most dietary carbohydrates are fermented into VFAs in the rumen. The VFA propionate is used for around 70% of the glucose and glycogen produced, also, some mammals are pseudoruminants, which have a three-compartment stomach instead of four like ruminants. Pseudoruminants, like traditional ruminants, are foregut fermentors and most ruminate or chew cud, however, their anatomy and method of digestion differs significantly from that of a four-chambered ruminant. Monogastric herbivores, such as rhinoceroses, horses, and rabbits, are not ruminants and these hindgut fermenters digest cellulose in an enlarged cecum through the reingestion of the cecotrope
20.
Symbiosis
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Symbiosis is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as the living together of unlike organisms, Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative when they can generally live independently. When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals. In 1877, Albert Bernhard Frank used the term symbiosis which previously had used to depict people living together in community to describe the mutualistic relationship in lichens. In 1879, the German mycologist Heinrich Anton de Bary defined it as the living together of unlike organisms, symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative. Endosymbiosis is any relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit, in general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both, a large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines, coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water, an example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators, a special mucus on the clownfish protects it from the stinging tentacles. A further example is the fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow, in case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow, different species of gobies also exhibit mutualistic behavior through cleaning up ectoparasites in other fish. Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs, the bryozoan colony develops a cirumrotatory growth and offers the crab a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell. A spectacular examples of mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps
21.
Termite
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Termites are eusocial insects that are classified at the taxonomic rank of infraorder Isoptera, or as epifamily Termitoidae within the cockroach order Blattodea. Termites were once classified in an order from cockroaches. However, the first termites emerged during the Permian or even the Carboniferous. About 3,106 species are described, with a few hundred more left to be described. Although these insects are called white ants, they are not ants. Like ants and some bees and wasps from the separate order Hymenoptera, all colonies have fertile males called kings and one or more fertile females called queens. Termites mostly feed on plant material and cellulose, generally in the form of wood, leaf litter, soil. Termites are major detritivores, particularly in the subtropical and tropical regions, Termites are among the most successful groups of insects on Earth, colonising most landmasses except for Antarctica. Their colonies range in size from a few hundred individuals to enormous societies with several million individuals, Termite queens have the longest lifespan of any insect in the world, with some queens reportedly living up to 30 to 50 years. Unlike ants, which undergo a metamorphosis, each individual termite goes through an incomplete metamorphosis that proceeds through egg, nymph. Colonies are described as superorganisms because the termites form part of a self-regulating entity, Termites are a delicacy in the diet of some human cultures and are used in many traditional medicines. Several hundred species are significant as pests that can cause serious damage to buildings, crops. Some species, such as the West Indian drywood termite, are regarded as invasive species, the infraorder name Isoptera is derived from the Greek words iso and ptera, which refers to the nearly equal size of the fore and hind wings. Termite derives from the Latin and Late Latin word termes, altered by the influence of Latin terere from the earlier word tarmes, Termite nests were commonly known as terminarium or termitaria. In early English, termites were known as wood ants or white ants, the modern term was first used in 1781. DNA analysis from 16S rRNA sequences has supported a hypothesis, originally suggested by Cleveland and colleagues in 1934 and this earlier conclusion had been based on the similarity of the symbiotic gut flagellates in the wood-eating cockroaches to those in certain species of termites regarded as living fossils. In the 1960s additional evidence supporting that hypothesis emerged when F. A. McKittrick noted similar morphological characteristics between some termites and Cryptocercus nymphs. These similarities have led some authors to propose that termites be reclassified as a family, the Termitidae, within the order Blattodea
22.
Cellulase
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Cellulase is any of several enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis, the decomposition of cellulose and of some related polysaccharides. The name is used for any naturally occurring mixture or complex of various such enzymes. Cellulases break down the molecule into monosaccharides such as beta-glucose. Cellulose breakdown is of economic importance, because it makes a major constituent of plants available for consumption. The specific reaction involved is the hydrolysis of the 1, 4-beta-D-glycosidic linkages in cellulose, hemicellulose, lichenin, because cellulose molecules bind strongly to each other, cellulolysis is relatively difficult compared to the breakdown of other polysaccharides such as starch. Most mammals have very limited ability to digest dietary fibres such as cellulose by themselves. In many herbivorous animals such as ruminants like cattle and sheep, cellulases are produced by a few types of animals, such as some termites. Several different kinds of cellulases are known, which differ structurally and mechanistically.5 cellulase, enzymes that cleave lignin are occasionally called cellulases, but this is usually considered erroneous. Five general types of cellulases based on the type of reaction catalyzed, exocellulases or cellobiohydrolases cleave two to four units from the ends of the exposed chains produced by endocellulase, resulting in tetrasaccharides or disaccharides, such as cellobiose. Exocellulases are further classified into type I, that work processively from the end of the cellulose chain, and type II. Cellobiases or beta-glucosidases hydrolyse the product into individual monosaccharides. Oxidative cellulases depolymerize cellulose by radical reactions, as for instance cellobiose dehydrogenase, cellulose phosphorylases depolymerize cellulose using phosphates instead of water. Avicelase has almost exclusively exo-cellulase activity, since avicel is a highly micro-crystalline substrate, within the above types there are also progressive and nonprogressive types. Progressive cellulase will continue to interact with a single polysaccharide strand, cellulase action is considered to be synergistic as all three classes of cellulase can yield much more sugar than the addition of all three separately. Most fungal cellulases have a structure, with one catalytic domain and one cellulose binding domain. This structure is adapted for working on a substrate. However, there are also cellulases that lack cellulose binding domains and these enzymes might have a swelling function. In many bacteria, cellulases in-vivo are complex enzyme structures organized in supramolecular complexes, numerous signature sequences known as dockerins and cohesins have been identified in the genomes of bacteria that produce cellulosomes
23.
Lignin
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Lignin is a class of complex organic polymers that form important structural materials in the support tissues of vascular plants and some algae. Lignins are particularly important in the formation of walls, especially in wood and bark, because they lend rigidity. Chemically, lignins are cross-linked phenolic polymers and he named the substance “lignine”, which is derived from the Latin word lignum, meaning wood. It is one of the most abundant organic polymers on Earth, lignin constitutes 30% of non-fossil organic carbon and 20-35% of the dry mass of wood. The Carboniferous Period is in part defined by the evolution of lignin, the composition of lignin varies from species to species. An example of composition from a sample is 63. 4% carbon,5. 9% hydrogen,0. 7% ash. As a biopolymer, lignin is unusual because of its heterogeneity and its most commonly noted function is the support through strengthening of wood in vascular plants. Global commercial production of lignin is around 1.1 million metric tons per year and is used in a range of low volume, niche applications where the form. Lignin fills the spaces in the wall between cellulose, hemicellulose, and pectin components, especially in vascular and support tissues, xylem tracheids, vessel elements. It is covalently linked to hemicellulose and therefore cross-links different plant polysaccharides, conferring mechanical strength to the cell wall and it is particularly abundant in compression wood but scarce in tension wood, which are types of reaction wood. Lignin plays a part in conducting water in plant stems. The polysaccharide components of plant cell walls are highly hydrophilic and thus permeable to water, the crosslinking of polysaccharides by lignin is an obstacle for water absorption to the cell wall. Thus, lignin makes it possible for the vascular tissue to conduct water efficiently. Lignin is present in all plants, but not in bryophytes. However, it is present in red algae, which seems to suggest that the ancestor of plants. This would suggest that its function was structural, it plays this role in the red alga Calliarthron. Another possibility is that the lignins in red algae and in plants are result of convergent evolution, lignin plays a significant role in the carbon cycle, sequestering atmospheric carbon into the living tissues of woody perennial vegetation. Lignin is one of the most slowly decomposing components of dead vegetation, the resulting soil humus, in general, holds nutrients onto its surface, and hence increases its cation exchange capacity and moisture retention, hence it increases the productivity of soil
24.
Cellobiose
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Cellobiose is a disaccharide with the formula 2O. Cellobiose, a sugar, consists of two β-glucose molecules linked by a β bond. It can be hydrolyzed to glucose enzymatically or with acid, cellobiose has eight free alcohol groups, one acetal linkage and one hemiacetal linkage, which give rise to strong inter- and intramolecular hydrogen bonds. It can be obtained by enzymatic or acidic hydrolysis of cellulose and cellulose rich materials such as cotton, jute, treatment of cellulose with acetic anhydride and sulfuric acid, gives cellobiose octoacetate, which is no longer a hydrogen bond donor and is soluble in nonpolar organic solvents
25.
Beta-glucosidase
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Beta-glucosidase catalyzes the hydrolysis of the glycosidic bonds to terminal non-reducing residues in beta-D-glucosides and oligosaccharides, with release of glucose. Cellulose is a composed of beta-1, 4-linked glucosyl residues. Cellulases, cellobiosidases, and beta-glucosidases are required by organisms that can consume it and these enzymes are powerful tools for degradation of plant cell walls by pathogens and other organisms consuming plant biomass
26.
Food energy
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Food energy is chemical energy that animals derive from food and molecular oxygen through the process of cellular respiration. Humans and other animals need a minimum intake of energy to sustain their metabolism. Foods are composed chiefly of carbohydrates, fats, proteins, alcohol, water, vitamins, carbohydrates, fats, proteins, alcohol, and water represent virtually all the weight of food, with vitamins and minerals making up only a small percentage of the weight. Organisms derive food energy from carbohydrates, fats and proteins as well as organic acids, polyols. Some diet components that provide little or no energy, such as water, minerals, vitamins, cholesterol. Water, minerals, vitamins, and cholesterol are not broken down, fiber, a type of carbohydrate, cannot be completely digested by the human body. Ruminants can extract energy from the respiration of cellulose because of bacteria in their rumens. Using the International System of Units, researchers measure energy in joules or in its multiples, the kilojoule is most often used for food-related quantities. An older metric system unit of energy, still used in food-related contexts, is the calorie, more precisely. Within the European Union, both the kilocalorie and kilojoule appear on nutrition labels, in many countries, only one of the units is displayed, in the US and Canada labels spell out the unit as calorie or as Calorie. Fats and ethanol have the greatest amount of energy per gram,37 and 29 kJ/g. Proteins and most carbohydrates have about 17 kJ/g, carbohydrates that are not easily absorbed, such as fiber, or lactose in lactose-intolerant individuals, contribute less food energy. Polyols and organic acids contribute 10 kJ/g and 13 kJ/g respectively, the amount of water, fat, and fiber in foods determines those foods energy density. Theoretically, one could measure food energy in different ways, using the Gibbs free energy of combustion, however, the convention is to use the heat of the oxidation reaction, with the water substance produced being in the liquid phase. The American chemist Wilbur Atwater worked these corrections out in the late 19th century, based on the work of Atwater, it became common practice to calculate energy content of foods using 4 kcal/g for carbohydrates and proteins and 9 kcal/g for lipids. The system was improved by Annabel Merrill and Bernice Watt of the USDA. Many governments require food manufacturers to label the energy content of their products, in the European Union, manufacturers of packaged food must label the nutritional energy of their products in both kilocalories and kilojoules, when required. In Australia and New Zealand, the energy must be stated in kilojoules
27.
Protein folding
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It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. Each protein exists as a polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable three-dimensional structure, as the polypeptide chain is being synthesized by the ribosome, the linear chain begins to fold into its three dimensional structure. Folding begins to occur even during translation of the polypeptide chain, amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein, known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure, the energy landscape describes the folding pathways in which the unfolded protein is able to assume its native state. Experiments beginning in the 1980s indicate the codon for an acid can also influence protein structure. The correct three-dimensional structure is essential to function, although parts of functional proteins may remain unfolded. Failure to fold into native structure generally produces inactive proteins, several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by folding of some proteins, because the immune system does not produce antibodies for certain protein structures. The primary structure of a protein, its linear amino-acid sequence, the amino acid composition is not as important as the sequence. The essential fact of folding, however, remains that the amino acid sequence of protein contains the information that specifies both the native structure and the pathway to attain that state. This is not to say that nearly identical amino acid sequences always fold similarly, conformations differ based on environmental factors as well, similar proteins fold differently based on where they are found. Formation of a structure is the first step in the folding process that a protein takes to assume its native structure. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability, alpha helices are formed by hydrogen bonding of the backbone to form a spiral shape. The beta pleated sheet is a structure forms with the backbone bending over itself to form the hydrogen bonds. The hydrogen bonds are between the hydrogen and carbonyl carbon of the peptide bond. The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion, secondary structure hierarchically gives way to tertiary structure formation. Tertiary structure of a protein involves a single chain, however
28.
Trichoderma reesei
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Trichoderma reesei is a mesophilic and filamentous fungus. It is an anamorph of the fungus Hypocrea jecorina, T. reesei has the capacity to secrete large amounts of cellulolytic enzymes. Microbial cellulases have industrial application in the conversion of cellulose, a component of plant biomass. T. reesei isolate QM6a was originally isolated from the Solomon Islands during World War II because of its degradation of canvas, all strains currently used in biotechnology and basic research were derived from this one isolate. Several industrially useful strains have developed and characterised, e. g. Rut-C30, RL-P37. The genome of this organism was released in 2008 and this organism also has a mating type dependent characterised sexual cycle. T. reesei QM6a has a MAT1-2 mating type locus, the opposite mating type MAT1-1, was recently found, thus proving that T. reesei is a heterothallic species. After being regarded as asexual since its more than 50 years ago, sexual reproduction can now be induced in T. reesei QM6a leading to formation of fertilized stromata. T. reesei is an important commercial and industrial micro-organism due to its production ability. Many strains of T. reesei have been developed since its discovery and these improvement programs originally consisted of classical mutagenesis, which led to strains capable of producing 20 times as much cellulase as the QM6a isolate. The ultimate aim in the creation of hypercellulolytic strains was to obtain a carbon catabolite derepressed strain and this derepression would allow the T. reesei strain to produce cellulases under any set of growth conditions, even in the presence of glucose. However, with the advent of genetic engineering tools such as targeted deletion, targeted knockout, and more. Some of the highest performing industrial strains produce up to 100 grams of cellulases per litre, more than 3 times as much as the RUT-C30 strain, cellobiohydrolase Cellulosic ethanol Endoglucanase Risk Assessment Summary, CEPA1999. Trichoderma reesei 1391A Risk Assessment Summary, CEPA1999, Trichoderma reesei P59G Risk Assessment Summary, CEPA1999. Trichoderma reesei P210A Risk Assessment Summary, CEPA1999, enhanced production of Trichoderma reesei endoglucanases and use of the new cellulase preparations in producing the stonewashed effect on denim fabric. Medve J, Ståhlberg J, Tjerneld F. Adsorption and synergism of cellobiohydrolase I and this article incorporates public domain material from websites or documents of the United States Department of Energy
29.
Dalton (unit)
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The unified atomic mass unit or dalton is a standard unit of mass that quantifies mass on an atomic or molecular scale. One unified atomic mass unit is approximately the mass of one nucleon and is equivalent to 1 g/mol. The CIPM has categorised it as a non-SI unit accepted for use with the SI, the amu without the unified prefix is technically an obsolete unit based on oxygen, which was replaced in 1961. However, many still use the term amu but now define it in the same way as u. In this sense, most uses of the atomic mass units. For standardization a specific atomic nucleus had to be chosen because the mass of a nucleon depends on the count of the nucleons in the atomic nucleus due to mass defect. This is also why the mass of a proton or neutron by itself is more than 1 u, the atomic mass unit is not the unit of mass in the atomic units system, which is rather the electron rest mass. The relative atomic mass scale has traditionally been a relative value and this evaluation was made prior to the discovery of the existence of elemental isotopes, which occurred in 1912. The divergence of these values could result in errors in computations, the chemistry amu, based on the relative atomic mass of natural oxygen, was about 1.000282 as massive as the physics amu, based on pure isotopic 16O. For these and other reasons, the standard for both physics and chemistry was changed to carbon-12 in 1961. The choice of carbon-12 was made to minimise further divergence with prior literature. The new and current unit was referred to as the atomic mass unit u. and given a new symbol, u. The Dalton is another name for the atomic mass unit. 1 u = m u =112 m Despite this change, modern sources often use the old term amu but define it as u. Therefore, in general, amu likely does not refer to the old oxygen standard unit, the unified atomic mass unit and the dalton are different names for the same unit of measure. As with other names such as watt and newton, dalton is not capitalized in English. In 2003 the Consultative Committee for Units, part of the CIPM, recommended a preference for the usage of the dalton over the atomic mass unit as it is shorter. In 2005, the International Union of Pure and Applied Physics endorsed the use of the dalton as an alternative to the atomic mass unit
30.
Dockerin
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Dockerin is a protein domain found in the cellulosome cellular structure of anaerobic bacteria. It is found on many endoglucanase enzymes, the dockerins binding partner is the cohesin domain, located on the scaffoldin protein. The Dockerin domain has two repeats of a non-EF hand calcium binding motif. Each motif is characterized by a loop-helix structure, the three-dimensional structure of dockerin has been determined in solution, as well as in complex with Cohesin. There are three types of Dockerin domains, I, II and III which bind to Cohesin Type I, Cohesin Type II, a type I dockerin domain is 65-70 residues long. The binding specificity of Type I interaction was well studied by structural, Type II interaction is less well characterized. EF hand cellulosome Protein Structure, Lytle BL, Volkman BF, Westler WM, Heckman MP, solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. Bayer EA, Shimon LJ, Shoham Y, Lamed R. Cellulosomes-structure and ultrastructure, specificity Characterization, Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA. Cohesin-dockerin microarray, Diverse specificities between two families of interacting protein modules. Adams JJ, Webb BA, Spencer HL, Smith SP, structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum, calcium-induced effects on conformation and target recognition
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Cohesin
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Cohesin is a protein complex that regulates the separation of sister chromatids during cell division, either mitosis or meiosis. Cohesins hold sister chromatids together after DNA replication until anaphase when removal of cohesin leads to separation of sister chromatids, Cohesin is a multi-subunit protein complex, made up of four core subunits, two SMC proteins, an alpha-kleisin, and an orthologue of the yeast Scc3 protein. Smc1 and Smc3 are members of the Structural Maintenance of Chromosomes family, SMC proteins have two main structural characteristics, an ATP-binding cassette-like head domain with ATPase activity and a hinge domain that allows dimerization of SMCs. The head and the domains are connected to each other via long anti-parallel coiled coils. The dimer is present in a V-shaped form, connected by the hinges, upon ATP binding, the two head domains in the dimer bind to each other, forming a ring structure. ATP hydrolysis can therefore trigger opening and closing of the ring, Scc1 and Scc3 bind the ATPase domains of Smc1 and Smc3 stabilizing the ring structure. The amino and carboxy terminus of Scc1 bind Smc1 and Smc3, once Scc1 binds the SMC proteins, Scc3 can also associate by binding with the C-terminal region of Scc1. When Scc1 binds on both Smc1 and Smc3, the complex forms a closed ring structure. When it binds to one of the SMC proteins, the complex forms an open ring. While some studies support the idea of a model, the model is inconsistent with a number of experimental observations. The cohesin ring has many functions,1 and it is used to keep the sister chromatids connected with each other during metaphase ensuring that during mitosis, each sister chromatid segregates to opposite poles. It facilitates spindle attachment onto chromosomes and it facilitates DNA repair by recombination. Recently many novel functions of cohesin have been discovered in different cellular processes. The anaphase promoting complex associated to Cdc20 cleaves the securin, which holds the sister chromatids together, securin is cleaved at anaphase, following APC/C-cdc20 mediated degradation, and it renders separase to cleave the kleisin subunit. Dissociation of sister chromatids cohesion defines anaphase onset, which two sets of identical chromosomes at each pole of the cell. Then the two daughter cells separate, and a new round of the cell cycle starts in each one. Therefore, when the division process will end, each daughter cell will receive a complete set of organelles. At the same time, during S phase all cells must duplicate their DNA very precisely and it is not clear how the cohesion ring links sister chromatids together
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Genome
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In modern molecular biology and genetics, a genome is the genetic material of an organism. The genome includes both the genes, the noncoding DNA and the material of the mitochondria and chloroplasts. The term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, the Oxford Dictionary suggests the name is a blend of the words gene and chromosome. However, see omics for a thorough discussion. A few related -ome words already existed—such as biome, rhizome, Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism the gamete has half the number of chromosomes of the somatic cell, the halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis. Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, even in species that exist in only one sex, what is described as a genome sequence may be a composite read from the chromosomes of various individuals. Colloquially, the genetic makeup is sometimes used to signify the genome of a particular individual or organism. Both the number of pairs and the number of genes vary widely from one species to another. The only exception in humans is found in red blood cells which become enucleated during development. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete sequence of a viral RNA-genome. The next year Fred Sanger completed the first DNA-genome sequence, Phage Φ-X174, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made it easier and cheaper to do sequencing. The US National Institutes of Health maintains one of several databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the fish. In December 2013, scientists first sequenced the genome of a Neanderthal. The genome was extracted from the toe bone of a 130, new sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the genome of James D. Watson
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Protein primary structure
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Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the structure of a protein is reported starting from the amino-terminal end to the carboxyl-terminal end. Protein biosynthesis is most commonly performed by ribosomes in cells, peptides can also be synthesised in the laboratory. Protein primary structures can be sequenced, or inferred from DNA sequences. Amino acids are polymerised via peptide bonds to form a long backbone, in biological systems, proteins are produced during translation by a cells ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise peptides in the order to biological protein synthesis. Protein sequence is typically notated as a string of letters, listing the amino acids starting at the end through to the carboxyl-terminal end. Either a three letter code or single letter code can be used to represent the 20 naturally occurring amino acids, peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known protein sequences, in general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. The chiral centers of a chain can undergo racemization. Although it does not change the sequence, it affect the chemical properties of the sequence. In particular, the L-amino acids normally found in proteins can spontaneously isomerize at the C α atom to form D-amino acids, additionally, proline can form stable trans-isomers at the peptide bond. Finally, the protein can undergo a variety of posttranslational modifications, formylation − C H The N-terminal methionine usually found after translation has an N-terminus blocked with a formyl group. This formyl group is removed by the enzyme deformylase, pyroglutamate An N-terminal glutamine can attack itself, forming a cyclic pyroglutamate group. Myristoylation − C −12 − C H3 Similar to acetylation, instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes. The C-terminal carboxylate group of a polypeptide can also be modified, Glycosyl phosphatidylinositol attachment Glycosyl phosphatidylinositol is a large, hydrophobic phospholipid prosthetic group that achors proteins to cellular membranes. It is attached to the polypeptide C-terminus through a linkage that then connects to ethanolamine, thence to sundry sugars
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Biomolecular structure
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Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels, primary, secondary, tertiary, the scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecules various hydrogen bonds. The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University, the primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms. For a typical unbranched, un-crosslinked biopolymer, the structure is equivalent to specifying the sequence of its monomeric subunits. Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, the primary structure of a nucleic acid molecule refers to the exact sequence of nucleotides that comprise the whole molecule. Often, the primary structure encodes motifs that are of functional importance. The secondary structure is the pattern of hydrogen bonds in a biopolymer, secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the structure is defined by patterns of hydrogen bonds between backbone amide and carboxyl groups, where the DSSP definition of a hydrogen bond is used. In nucleic acids, the structure is defined by the hydrogen bonding between the nitrogenous bases. For proteins, however, the bonding is correlated with other structural features. Many other less formal definitions have been proposed, often applying concepts from the geometry of curves, such as curvature. Structural biologists solving a new structure will sometimes assign its secondary structure by eye. The secondary structure of an acid molecule refers to the base pairing interactions within one molecule or set of interacting molecules. The secondary structure of biological RNAs can often be uniquely decomposed into stems, often, these elements or combinations of them can be further classified, e. g. tetraloops, pseudoknots and stem-loops. There are many secondary structure elements of importance to biological RNAs. Famous examples include the Rho-independent terminator stem-loops and the transfer RNA cloverleaf, there is a minor industry of researchers attempting to determine the secondary structure of RNA molecules. Approaches include both experimental and computational methods, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates
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