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.
Pfam
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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017, the general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of families has been widely adopted by biologists because of its wide coverage of proteins. Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data, the Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database. If DNA is submitted, a translation is performed, then each frame is searched. Family is the class, which simply indicates that members are related. Domains are defined as a structural unit or reusable sequence unit that can be found in multiple protein contexts. Repeats are not usually stable in isolation, but rather are required to form tandem repeats in order to form a domain or extended structure. Motifs are usually shorter sequence units found outside of globular domains, the descriptions of Pfam families are managed by the general public using Wikipedia. As of release 29.0,76. 1% of protein sequences in UniprotKB matched to at least one Pfam domain, new families come from a range of sources, primarily the PDB and analysis of complete proteomes to find genes with no Pfam hit. For each family, a subset of sequences are aligned into a high-quality seed alignment. Sequences for the alignment are taken primarily from pfamseq with some supplementation from UniprotKB. This seed alignment is used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that reach a curated gathering threshold are classified as members of the protein family, the resulting collection of members is then aligned to the profile HMM to generate a full alignment. For each family, a curated gathering threshold is assigned that maximises the number of true matches to the family while excluding any false positive matches. False positives are estimated by observing overlaps between Pfam family hits that are not from the same clan and this threshold is used to assess whether a match to a family HMM should be included in the protein family. Upon each update of Pfam, gathering thresholds are reassessed to prevent overlaps between new and existing families, domains of Unknown Function represent a growing fraction of the Pfam database
7.
InterPro
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The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models which describe protein families, domains or sites, models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences in order to classify them. Each of the databases of InterPro contribute towards a different niche, from very high-level. InterPros intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry, additional information such as a description, consistent names and Gene Ontology terms are associated with each entry, where possible. InterPro contains three main entities, proteins, signatures and entries, the proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB, only signatures deemed to be of sufficient quality are integrated into InterPro. InterPro also includes data for splice variants and the contained in the UniParc. The signatures from InterPro come from 11 member databases, which are listed below, cATH-Gene3D describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity, mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources, functional prediction and analysis of domain architectures is available from the Gene3D website. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes, HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. PANTHER is a collection of protein families that have been subdivided into functionally related subfamilies. Hidden Markov models are built for each family and subfamily for classifying additional protein sequences, Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. The primary PIRSF classification unit is the family, whose members are both homologous and homeomorphic. PRINTS is a compendium of protein fingerprints, a fingerprint is a group of conserved motifs used to characterise a protein family, its diagnostic power is refined by iterative scanning of UniProt. Usually the motifs do not overlap, but are separated along a sequence, ProDom domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a procedure based on recursive PSI-BLAST searches
8.
PROSITE
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It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics, PROSITE was created in 1988 by Amos Bairoch, who directed the group for more than 20 years. Since July 2009, the director of the PROSITE, Swiss-Prot, pROSITEs uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. Properties from well-studied genes can be propagated to biologically related organisms, PROSITE offers tools for protein sequence analysis and motif detection. It is part of the ExPASy proteomics analysis servers, the database ProRule builds on the domain descriptions of PROSITE. It provides additional information about functionally or structurally critical amino acids and these can automatically generate annotation based on PROSITE motifs. As of 29 June 2016, release 20.128 has 1,762 documentation entries,1,309 patterns,1,161 profiles, uniprot — the universal protein database, a central resource on protein information - PROSITE adds data to it. InterPro — a centralized database, grouping data from databases of protein families, domains, protein subcellular localization prediction — another example of use of PROSITE. Official website ProRule — database of rules based on PROSITE predictors
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.
Dihydroxyacetone phosphate
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Dihydroxyacetone phosphate is a biochemical compound involved in many metabolic pathways, including the Calvin cycle in plants and glycolysis. Dihydroxyacetone phosphate lies in the metabolic pathway, and is one of the two products of breakdown of fructose 1, 6-bisphosphate, along with glyceraldehyde 3-phosphate. It is rapidly and reversibly isomerised to glyceraldehyde 3-phosphate, Compound C05378 at KEGG Pathway Database. Enzyme 4.1.2.13 at KEGG Pathway Database, Compound C00111 at KEGG Pathway Database. Compound C00118 at KEGG Pathway Database, the numbering of the carbon atoms indicates the fate of the carbons according to their position in fructose 6-phosphate. Compound C00111 at KEGG Pathway Database. Enzyme 5.3.1.1 at KEGG Pathway Database. Compound C00118 at KEGG Pathway Database, click on genes, proteins and metabolites below to link to respective articles. In the Calvin cycle, DHAP is one of the products of the reduction of 1. It is also used in the synthesis of sedoheptulose 1, 7-bisphosphate and fructose 1, 6-bisphosphate, DHAP is also the product of the dehydrogenation of L-glycerol-3-phosphate, which is part of the entry of glycerol into the glycolytic pathway. Conversely, reduction of glycolysis-derived DHAP to L-glycerol-3-phosphate provides adipose cells with the glycerol backbone they require to synthesize new triglycerides. Both reactions are catalyzed by the enzyme glycerol 3-phosphate dehydrogenase with NAD+/NADH as cofactor, DHAP also has a role in the ether-lipid biosynthesis process in the protozoan parasite Leishmania mexicana
11.
Ketose
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A ketose is a monosaccharide containing one ketone group per molecule. With three carbon atoms, dihydroxyacetone is the simplest of all ketoses and is the one having no optical activity. Ketoses can isomerize into an aldose when the group is located at the end of the molecule
12.
Sedoheptulose-bisphosphatase
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Sedoheptulose-bisphosphatase is an enzyme that catalyzes the removal of a phosphate group from sedoheptulose 1, 7-bisphosphate to produce sedoheptulose 7-phosphate. SBPase is an example of a phosphatase, or, more generally and this enzyme participates in the Calvin cycle. SBPase is a protein, meaning that it is made up of two identical subunits. The size of this varies between species, but is about 92,000 Da in cucumber plant leaves. The key functional domain controlling SBPase function involves a disulfide bond between two cysteine residues, additionally, SBPase requires the presence of magnesium to be functionally active. SBPase is bound to the side of the thylakoid membrane in the chloroplast in a plant. Some studies have suggested the SBPase may be part of a large multi-enzyme complex along with a number of other photosynthetic enzymes, SBPase is involved in the regeneration of 5-carbon sugars during the Calvin cycle. Although SBPase has not been emphasized as an important control point in the Calvin cycle historically, additionally, SBPase activity has been found to have a strong correlation with the amount of photosynthetic carbon fixation. Like many Calvin cycle enzymes, SBPase is activated in the presence of light through a ferredoxin/thioredoxin system, in the light reactions of photosynthesis, light energy powers the transport of electrons to eventually reduce ferredoxin. The enzyme ferredoxin-thioredoxin reductase uses reduced ferredoxin to reduce thioredoxin from the form to the dithiol. Finally, the reduced thioredoxin is used to reduced a cysteine-cysteine disulfide bond in SBPase to a dithiol, SBPase has additional levels of regulation beyond the ferredoxin/thioredoxin system. Mg2+ concentration has a significant impact on the activity of SBPase, SBPase is inhibited by acidic conditions. This is a contributor to the overall inhibition of carbon fixation when the pH is low inside the stroma of the chloroplast. Finally, SBPase is subject to feedback regulation by sedoheptulose-7-phosphate and inorganic phosphate. SBPase and FBPase are both phosphatases that catalyze similar during the Calvin cycle, the genes for SBPase and FBPase are related. Both genes are found in the nucleus in plants, and have bacterial ancestry, SBPase is found across many species. In addition to being present in photosynthetic organism, SBPase is found in a number of evolutionarily-related. SBPase likely originated in red algae
13.
Gluconeogenesis
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Gluconeogenesis is a metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates. From breakdown of proteins, these substrates include glucogenic amino acids, from breakdown of lipids, they include glycerol, gluconeogenesis is one of several main mechanisms used by humans and many other animals to maintain blood glucose levels, avoiding low levels. Other means include the degradation of glycogen, fatty acid breakdown, gluconeogenesis is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms. In vertebrates, gluconeogenesis takes place mainly in the liver and, to a lesser extent, in ruminants, this tends to be a continuous process. In many other animals, the process occurs during periods of fasting, starvation, low-carbohydrate diets, the process is highly endergonic until it is coupled to the hydrolysis of ATP or GTP, effectively making the process exergonic. For example, the leading from pyruvate to glucose-6-phosphate requires 4 molecules of ATP and 2 molecules of GTP to proceed spontaneously. Gluconeogenesis is often associated with ketosis, gluconeogenesis is also a target of therapy for type 2 diabetes, such as the antidiabetic drug, metformin, which inhibits glucose formation and stimulates glucose uptake by cells. In ruminants, because dietary carbohydrates tend to be metabolized by rumen organisms, gluconeogenesis occurs regardless of fasting, low-carbohydrate diets, exercise, in humans the main gluconeogenic precursors are lactate, glycerol, alanine and glutamine. Altogether, they account for over 90% of the overall gluconeogenesis, other glucogenic amino acids as well as all citric acid cycle intermediates, the latter through conversion to oxaloacetate, can also function as substrates for gluconeogenesis. In ruminants, propionate is the principal gluconeogenic substrate, lactate is transported back to the liver where it is converted into pyruvate by the Cori cycle using the enzyme lactate dehydrogenase. Pyruvate, the first designated substrate of the pathway, can then be used to generate glucose. Transamination or deamination of amino acids facilitates entering of their carbon skeleton into the cycle directly, whether even-chain fatty acids can be converted into glucose in animals has been a longstanding question in biochemistry. It is known that odd-chain fatty acids can be oxidized to yield propionyl-CoA, a precursor for succinyl-CoA, in plants, specifically seedlings, the glyoxylate cycle can be used to convert fatty acids into the primary carbon source of the organism. The glyoxylate cycle produces four-carbon dicarboxylic acids that can enter gluconeogenesis, in 1995, researchers identified the glyoxylate cycle in nematodes. In addition, the glyoxylate enzymes malate synthase and isocitrate lyase have been found in animal tissues, genes coding for malate synthase have been identified in other metazoans including arthropods, echinoderms, and even some vertebrates. Mammals found to possess these genes include monotremes and marsupials but not placental mammals, genes for isocitrate lyase are found only in nematodes, in which, it is apparent, they originated in horizontal gene transfer from bacteria. The existence of cycles in humans has not been established. However, carbon-14 has been shown to end up in glucose when it is supplied in fatty acids
14.
Light-independent reactions
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The Carbon reactions of photosynthesis are chemical reactions that convert carbon dioxide and other compounds into glucose. These reactions occur in the stroma, the area of a chloroplast outside of the thylakoid membranes. These reactions take the products of light-dependent reactions and perform further chemical processes on them, there are three phases to the light-independent reactions, collectively called the Calvin cycle, carbon fixation, reduction reactions, and ribulose 1, 5-bisphosphate regeneration. This process occurs only when light is available, plants do not carry out the Calvin cycle during nighttime. They instead release sucrose into the phloem from their starch reserves. They are also known as dark reactions and these reactions are closely coupled to the thylakoid electron transport chain as reducing power provided by NADPH produced in the photosystem I is actively needed. The cycle was discovered by Melvin Calvin, James Bassham, and Andrew Benson at the University of California, photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport molecules ATP, the Calvin cycle uses the energy from short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism. This set of reactions is called carbon fixation. The key enzyme of the cycle is called RuBisCO, in the following biochemical equations, the chemical species exist in equilibria among their various ionized states as governed by the pH. They are activated in the light, and also by products of the light-dependent reaction and these regulatory functions prevent the Calvin cycle from being respired to carbon dioxide. Energy would be wasted in carrying out these reactions that have no net productivity, although many texts list a product of photosynthesis as C 6H 12O6, this is mainly a convenience to counter the equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin cycle are three-carbon sugar phosphate molecules, or triose phosphates, namely, the three steps involved are, The enzyme RuBisCO catalyses the carboxylation of ribulose-1, 5-bisphosphate, RuBP, a 5-carbon compound, by carbon dioxide in a two-step reaction. The product of the first step is enediol-enzyme complex that can capture CO2 or O2, thus, enediol-enzyme complex is the real carboxylase/oxygenase. The enzyme phosphoglycerate kinase catalyses the phosphorylation of 3-PGA by ATP,1, 3-Bisphosphoglycerate and ADP are the products. The enzyme glyceraldehyde 3-phosphate dehydrogenase catalyses the reduction of 1, 3BPGA by NADPH, glyceraldehyde 3-phosphate is produced, and the NADPH itself is oxidized and becomes NADP+. Again, two NADPH are utilized per CO2 fixed, the next stage in the Calvin cycle is to regenerate RuBP. Five G3P molecules produce three RuBP molecules, using up three molecules of ATP, the regeneration stage can be broken down into steps. Triose phosphate isomerase converts all of the G3P reversibly into dihydroxyacetone phosphate, aldolase and fructose-1, 6-bisphosphatase convert a G3P and a DHAP into fructose 6-phosphate
15.
Glycolysis
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Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy molecules ATP, glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis, for example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful, for example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat. Glycolysis is an oxygen independent metabolic pathway, meaning that it not use molecular oxygen for any of its reactions. However the products of glycolysis are sometimes metabolized using atmospheric oxygen, when molecular oxygen is used for the metabolism of the products of glycolysis the process is usually referred to as aerobic, whereas if no oxygen is used the process is said to be anaerobic. Thus, glycolysis occurs, with variations, in all organisms. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways, glycolysis could thus have originated from chemical constraints of the prebiotic world. Glycolysis occurs in most organisms in the cytosol of the cell, the most common type of glycolysis is the Embden–Meyerhof–Parnas, which was discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway, however, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway. The overall reaction of glycolysis is, The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. In the cellular environment, all three groups of ADP dissociate into −O− and H+, giving ADP3−, and this ion tends to exist in an ionic bond with Mg2+. ATP behaves identically except that it has four groups, giving ATPMg2−. When these differences along with the charges on the two phosphate groups are considered together, the net charges of −4 on each side are balanced. For simple fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP, most cells will then carry out further reactions to repay the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+, cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis, the pathway of glycolysis as it is known today took almost 100 years to fully discover. The combined results of many experiments were required in order to understand the pathway as a whole
16.
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
17.
Aldol reaction
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The aldol reaction is a means of forming carbon–carbon bonds in organic chemistry. These products are known as aldols, from the aldehyde + alcohol, Aldol structural units are found in many important molecules, whether naturally occurring or synthetic. For example, the reaction has been used in the large-scale production of the commodity chemical pentaerythritol. The aldol reaction unites two relatively simple molecules into a complex one. Increased complexity arises because up to two new stereogenic centers are formed, Modern methodology is capable of not only allowing aldol reactions to proceed in high yield but also controlling both the relative and absolute configuration of these stereocenters. This ability to synthesize a particular stereoisomer is significant because different stereoisomers can have very different chemical and biological properties. For example, stereogenic aldol units are common in polyketides. In nature, polyketides are synthesized by enzymes that effect iterative Claisen condensations, the 1, 3-dicarbonyl products of these reactions can then be variously derivatized to produce a wide variety of interesting structures. Often, such derivitization involves the reduction of one of the carbonyl groups, some of these structures have potent biological properties, the immunosuppressant FK506, the anti-tumor agent discodermolide, or the antifungal agent amphotericin B, for example. Although the synthesis of such compounds was once considered nearly impossible. A typical modern aldol addition reaction, shown above, might involve the addition of a ketone enolate to an aldehyde. Once formed, the product can sometimes lose a molecule of water to form an α. A variety of nucleophiles may be employed in the reaction, including the enols, enolates, and enol ethers of ketones, aldehydes. The electrophilic partner is usually an aldehyde or ketone, the aldol reaction may proceed via two fundamentally different mechanisms. Carbonyl compounds, such as aldehydes and ketones, can be converted to enols or enol ethers and these species, being nucleophilic at the α-carbon, can attack especially reactive protonated carbonyls such as protonated aldehydes. Carbonyl compounds, being carbon acids, can also be deprotonated to form enolates, the usual electrophile is an aldehyde, since ketones are much less reactive. If the conditions are harsh, condensation may occur, but this can usually be avoided with mild reagents. In contrast, retro-aldol condensations are rare, but possible, when an acid catalyst is used, the initial step in the reaction mechanism involves acid-catalyzed tautomerization of the carbonyl compound to the enol
18.
Sialic acid
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Sialic acid is a generic term for the N- or O-substituted derivatives of neuraminic acid, a monosaccharide with a nine-carbon backbone. It is also the name for the most common member of this group, Sialic acids are found widely distributed in animal tissues and to a lesser extent in other organisms, ranging from plants and fungi to yeasts and bacteria, mostly in glycoproteins and gangliosides. That is because it seems to have appeared late in evolution, however, it has been observed in Drosophila embryos and other insects and in the capsular polysaccharides of certain strains of bacteria. In humans the brain has the highest sialic acid concentration, where these acids play an important role in neural transmission, in general, the amino group bears either an acetyl or a glycolyl group, but other modifications have been described. The hydroxyl substituents may vary considerably, acetyl, lactyl, methyl, sulfate, the term sialic acid was first introduced by Swedish biochemist Gunnar Blix in 1952. The sialic acid family includes 43 derivatives of the nine-carbon sugar neuraminic acid, the numbering of the sialic acid structure begins at the carboxylate carbon and continues around the chain. The configuration that places the carboxylate in the position is the alpha-anomer. The alpha-anomer is the form that is found when sialic acid is bound to glycans, however, in solution, it is mainly in the beta-anomeric form. Sialic acid is synthesized by glucosamine 6 phosphate and acetyl CoA through a transferase and this becomes N-acetylmannosamine-6-P through epimerization, which reacts with phosphoenolpyruvate producing N-acetylneuraminic-9-P. This compound is synthesized in the nucleus of the animal cell, in bacterial systems, sialic acids are biosynthesized by an aldolase enzyme. The enzyme uses a derivative as a substrate, inserting three carbons from pyruvate into the resulting sialic acid structure. These enzymes can be used for synthesis of sialic acid derivatives. Sialic acid-rich glycoproteins bind selectin in humans and other organisms, metastatic cancer cells often express a high density of sialic acid-rich glycoproteins. This overexpression of sialic acid on surfaces creates a charge on cell membranes. This creates repulsion between cells and helps these late-stage cancer cells enter the blood stream, many bacteria also use sialic acid in their biology, although this is usually limited to bacteria that live in association with higher animals. Many of these incorporate sialic acid into cell surface features like their lipopolysaccharide and capsule, other bacteria simply use sialic acid as a good nutrient source, as it contains both carbon and nitrogen and can be converted to fructose-6-phosphate, which can then enter central metabolism. Sialic acid-rich oligosaccharides on the glycoconjugates found on surface membranes help keep water at the surface of cells, the sialic acid-rich regions contribute to creating a negative charge on the cells surfaces. Since water is a molecule with partial positive charges on both hydrogen atoms, it is attracted to cell surfaces and membranes
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Schiff base
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A Schiff base is a compound with the general structure R2C=NR. They can be considered a sub-class of imines, being either secondary ketimines or secondary depending on their structure. The term is synonymous with azomethine which refers specifically to secondary aldimines. A number of naming systems exist for these compounds. For instance a Schiff base derived from an aniline, where R3 is a phenyl or a substituted phenyl, can be called an anil, the term Schiff base is normally applied to these compounds when they are being used as ligands to form coordination complexes with metal ions. Such complexes do occur naturally, for instance in Corrin, but the majority of Schiff bases are artificial and are used to form many important catalysts, such as Jacobsens catalyst. Schiff bases can be synthesized from an aliphatic or aromatic amine, the common enzyme cofactor PLP forms a Schiff base with a lysine residue and is transaldiminated to the substrate. Similarly, the cofactor retinal forms a Schiff base in rhodopsins, including human rhodopsin, an example where the substrate forms a Schiff base to the enzyme is in the fructose 1, 6-bisphosphate aldolase catalyzed reaction during glycolysis and in the metabolism of amino acids. Schiff bases are common ligands in coordination chemistry, the imine nitrogen is basic and exhibits pi-acceptor properties. The ligands are derived from alkyl diamines and aromatic aldehydes. Chiral Schiff bases were one of the first ligands used for asymmetric catalysis, in 1968 Ryōji Noyori developed a copper-Schiff base complex for the metal-carbenoid cyclopropanation of styrene. For this work he was awarded a share of the 2001 Nobel Prize in Chemistry. Their simple and clean chemistry make them a candidate as a low cost alternative to currently used conjugated materials. Schiff base chemistry is used to prepare covalent organic framework
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Active site
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In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of residues that form bonds with the substrate. The active site is usually a groove or pocket of the enzyme which can be located in a tunnel within the enzyme. An active site can catalyse a reaction repeatedly as its residues are not altered at the end of the reaction, usually, an enzyme molecule has only one active site, and the active site fits with one specific type of substrate. An active site contains a site that binds the substrate. Residues in the site form hydrogen bonds, hydrophobic interactions. In order to function, the site needs to be in a specific conformation. A tighter fit between a site and the substrate molecule is believed to increase efficiency of a reaction. Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels, there are two proposed models of how enzymes fit to their specific substrate, the lock and key model and the induced fit model. Emil Fischers lock and key model assumes that the site is a perfect fit for a specific substrate. Daniel Koshlands theory of enzyme-substrate binding is that the active site, the induced fit model is a development of the lock-and-key model and assumes that an active site is flexible and it changes shape until the substrate is completely bound. The substrate is thought to induce a change in the shape of the active site, the hypothesis also predicts that the presence of certain residues in the active site will encourage the enzyme to locate the correct substrate. Conformational changes may occur as the substrate is bound. After the products of the move away from the enzyme. Once the substrate is bound and oriented in the active site, the residues of the catalytic site are typically very close to the binding site, and some residues can have dual-roles in both binding and catalysis. Catalytic residues of the site interact with the substrate to lower the energy of a reaction. They do this by a number of different mechanisms, firstly, they can act as donors or acceptors of protons or other groups on the substrate to facilitate the reaction. They can also form electrostatic interactions to stabilise charge buildup on the state or leaving group
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Lysine
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Lysine, encoded by the codons AAA and AAG, is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, an α-carboxylic acid group. It is essential in humans, meaning the body cannot synthesize it, lysine is a base, as are arginine and histidine. The ε-amino group often participates in hydrogen bonding and as a base in catalysis. The ε-amino group is attached to the carbon from the α-carbon. O-Glycosylation of hydroxylysine residues in the endoplasmic reticulum or Golgi apparatus is used to mark certain proteins for secretion from the cell, deficiencies may cause blindness, as well as many other problems due to its ubiquitous presence in proteins. As an essential amino acid, lysine is not synthesized in animals, in plants and most bacteria, it is synthesized from aspartic acid, L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase. ATP is needed as a source for this step. β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde, energy from NADPH is used in this conversion. 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a molecule is removed. This causes cyclization and gives rise to -4-hydroxy-2,3,4 and this product is reduced to 2,3,4, 5-tetrahydrodipicolinate by 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a water molecule. Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate, two water molecules and one acyl-CoA enzyme are used in this reaction. This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase, a glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct. N-succinyl-LL-2, 6-diaminoheptanedionate is converted into LL-2, 6-diaminoheptanedionate by succinyl diaminopimelate desuccinylase, a water molecule is consumed in this reaction and a succinate is produced a byproduct. LL-2, 6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2, 6-diamino-heptanedionate, finally, meso-2, 6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase. It is worth noting, however, that in fungi, euglenoids, lysine is metabolised in mammals to give acetyl-CoA, via an initial transamination with α-ketoglutarate. The bacterial degradation of lysine yields cadaverine by decarboxylation, allysine is a derivative of lysine, used in the production of elastin and collagen
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Carbonyl group
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In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom, C=O. It is common to several classes of compounds, as part of many larger functional groups. A compound containing a group is often referred to as a carbonyl compound. The term carbonyl can also refer to carbon monoxide as a ligand in an inorganic or organometallic complex, the remainder of this article concerns itself with the organic chemistry definition of carbonyl, where carbon and oxygen share a double bond. A carbonyl group characterizes the types of compounds, Note that the most specific labels are usually employed. For example, ROR structures are known as acid anhydride rather than the more generic ester, other organic carbonyls are urea and the carbamates, the derivatives of acyl chlorides chloroformates and phosgene, carbonate esters, thioesters, lactones, lactams, hydroxamates, and isocyanates. Examples of inorganic compounds are carbon dioxide and carbonyl sulfide. A special group of compounds are 1, 3-dicarbonyl compounds that have acidic protons in the central methylene unit. Examples are Meldrums acid, diethyl malonate and acetylacetone, because oxygen is more electronegative than carbon, carbonyl compounds often have resonance structures which affect their reactivity. This relative electronegativity draws electron density away from carbon, increasing the bonds polarity, carbon can then be attacked by nucleophiles or a negatively charged part of another molecule. During the reaction, the double bond is broken. This reaction is known as addition-elimination or condensation, the electronegative oxygen also can react with an electrophile, for example a proton in an acidic solution or with Lewis acids to form an oxocarbenium ion. The polarity of oxygen also makes the alpha hydrogens of carbonyl compounds much more acidic than typical sp3 C-H bonds, for example, the pKa values of acetaldehyde and acetone are 16.7 and 19 respectively, while the pKa value of methane is extrapolated to be approximately 50. This is because a carbonyl is in resonance with an enol. The deprotonation of the enol with a base produces an enolate. Amides are the most stable of the carbonyl couplings due to their high resonance stabilization between the nitrogen-carbon and carbon-oxygen bonds, carbonyl groups can be reduced by reaction with hydride reagents such as NaBH4 and LiAlH4, with bakers yeast, or by catalytic hydrogenation. Ketones give secondary alcohols while aldehydes, esters and carboxylic acids give primary alcohols, carbonyls can be alkylated in nucleophilic addition reactions using organometallic compounds such as organolithium reagents, Grignard reagents, or acetylides. Carbonyls also may be alkylated by enolates as in aldol reactions, carbonyls are also the prototypical groups with vinylogous reactivity
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Zinc
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Zinc is a chemical element with the symbol Zn and atomic number 30. It is the first element in group 12 of the periodic table, in some respects zinc is chemically similar to magnesium, both elements exhibit only one normal oxidation state, and the Zn2+ and Mg2+ ions are of similar size. Zinc is the 24th most abundant element in Earths crust and has five stable isotopes, the most common zinc ore is sphalerite, a zinc sulfide mineral. The largest workable lodes are in Australia, Asia, and the United States, Zinc is refined by froth flotation of the ore, roasting, and final extraction using electricity. Zinc metal was not produced on a large scale until the 12th century in India and was unknown to Europe until the end of the 16th century, the mines of Rajasthan have given definite evidence of zinc production going back to the 6th century BC. To date, the oldest evidence of pure zinc comes from Zawar, in Rajasthan, alchemists burned zinc in air to form what they called philosophers wool or white snow. The element was named by the alchemist Paracelsus after the German word Zinke. German chemist Andreas Sigismund Marggraf is credited with discovering pure metallic zinc in 1746, work by Luigi Galvani and Alessandro Volta uncovered the electrochemical properties of zinc by 1800. Corrosion-resistant zinc plating of iron is the application for zinc. Other applications are in batteries, small non-structural castings. A variety of compounds are commonly used, such as zinc carbonate and zinc gluconate, zinc chloride, zinc pyrithione, zinc sulfide. Zinc is an essential mineral perceived by the public today as being of exceptional biologic and public health importance, Zinc deficiency affects about two billion people in the developing world and is associated with many diseases. In children, deficiency causes growth retardation, delayed sexual maturation, infection susceptibility, enzymes with a zinc atom in the reactive center are widespread in biochemistry, such as alcohol dehydrogenase in humans. Consumption of excess zinc can cause ataxia, lethargy and copper deficiency, Zinc is a bluish-white, lustrous, diamagnetic metal, though most common commercial grades of the metal have a dull finish.6 pm. The metal is hard and brittle at most temperatures but becomes malleable between 100 and 150 °C, above 210 °C, the metal becomes brittle again and can be pulverized by beating. Zinc is a conductor of electricity. For a metal, zinc has relatively low melting and boiling points, the melting point is the lowest of all the transition metals aside from mercury and cadmium. Many alloys contain zinc, including brass, Other metals long known to form binary alloys with zinc are aluminium, antimony, bismuth, gold, iron, lead, mercury, silver, tin, magnesium, cobalt, nickel, tellurium, and sodium
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Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
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Operon
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In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter. The result of this is that the contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon, in general, expression of prokaryotic operons leads to the generation of polycistronic mRNAs, while eukaryotic operons lead to monocistronic mRNAs. Operons are also found in such as bacteriophages. For example, T7 phages have two operons, the first operon codes for various products, including a special T7 RNA polymerase which can bind to and transcribe the second operon. The second operon includes a lysis gene meant to cause the host cell to burst, the term operon was first proposed in a short paper in the Proceedings of the French Academy of Science in 1960. From this paper, the general theory of the operon was developed. This theory suggested that in all cases, genes within an operon are negatively controlled by a repressor acting at a single operator located before the first gene, later, it was discovered that genes could be positively regulated and also regulated at steps that follow transcription initiation. Therefore, it is not possible to talk of a regulatory mechanism. Today, the operon is simply defined as a cluster of genes transcribed into a single mRNA molecule, nevertheless, the development of the concept is considered a landmark event in the history of molecular biology. The first operon to be described was the lac operon in E. coli, the 1965 Nobel Prize in Physiology and Medicine was awarded to François Jacob, André Michel Lwoff and Jacques Monod for their discoveries concerning the operon and virus synthesis. Operons occur primarily in prokaryotes but also in some eukaryotes, including such as C. elegans. RRNA genes often exist in operons that have found in a range of eukaryotes including chordates. An operon is made up of structural genes arranged under a common promoter. The location and condition of the regulators, promoter, operator, according to its authors, the term operon means to operate. An operon contains one or more genes which are generally transcribed into one polycistronic mRNA. However, the definition of an operon does not require the mRNA to be polycistronic, though in practice, upstream of the structural genes lies a promoter sequence which provides a site for RNA polymerase to bind and initiate transcription. Close to the promoter lies a section of DNA called an operator, all the structural genes of an operon are turned ON or OFF together, due to a single promoter and operator upstream to them, but sometimes more control over the gene expression is needed
26.
N-acetyl galactosamine
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N-Acetylgalactosamine, is an amino sugar derivative of galactose. In humans it is the terminal forming the antigen of blood group A. It is typically the first monosaccharide that connects serine or threonine in particular forms of protein O-glycosylation, n-Acetylgalactosamine is necessary for intercellular communication, and is concentrated in sensory nerve structures of both humans and animals
. PMID 15470245.
