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.
HK1
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Hexokinase-1 is an enzyme that in humans is encoded by the HK1 gene on chromosome 10. Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways and this gene encodes a ubiquitous form of hexokinase which localizes to the outer membrane of mitochondria. Mutations in this gene have been associated with anemia due to hexokinase deficiency. Alternative splicing of this results in five transcript variants which encode different isoforms. Each isoform has a distinct N-terminus, the remainder of the protein is identical among all the isoforms, a sixth transcript variant has been described, but due to the presence of several stop codons, it is not thought to encode a protein. HK1 is one of four highly homologous hexokinase isoforms in mammalian cells, the HK1 gene spans approximately 131 kb and consists of 25 exons.85 kb downstream of exon R, is the first 5’ exon for the ubiquitously expressed HK1 isoform. Moreover, exon 7 encodes the porin-binding domain conserved in mammalian HK1 genes, meanwhile, the remaining 17 exons are shared among all HK1 isoforms. In addition to exon R, a stretch of the promoter that contains a GATA element, an SP1 site, CCAAT. This gene encodes a 100 kDa homodimer with a regulatory N-terminal domain, catalytic C-terminal domain, both terminal domains are composed of a large subdomain and a small subdomain. The flexible region of the C-terminal large subdomain can adopt various positions and is proposed to interact with the base of ATP, moreover, glucose and G6P bind in close proximity at the N- and C-terminal domains and stabilize a common conformational state of the C-terminal domain. A second model posits that G6P acts as an inhibitor that stabilizes the closed conformation. Results from several studies suggest that the C-terminal is capable of catalytic and regulatory action. Physiological levels of G6P can regulate this process by inhibiting HK1 as negative feedback, however, unlike HK2 and HK3, HK1 itself is not directly regulated by Pi, which better suits its ubiquitous catabolic role. By phosphorylating glucose, HK1 effectively prevents glucose from leaving the cell and, thus, specifically, OMM-bound HK1 binds VDAC1 to trigger opening of the mitochondrial permeability transition pore and release mitochondrial ATP to further fuel the glycolytic process. Another critical function for OMM-bound HK1 is cell survival and protection against oxidative damage, furthermore, HK1 has demonstrated anti-apoptotic activity by antagonizing Bcl-2 proteins located at the OMM, which then inhibits TNF-induced apoptosis. It is also expressed in cells derived from stem cells, such as RBCs, leukocytes. In rats, it is also the predominant hexokinase in fetal tissues, mutations in this gene are associated with type 4H of Charcot–Marie–Tooth disease, also known as Russe-type hereditary motor and sensory neuropathy. Due to the role of HK1 in glycolysis, hexokinase deficiency has been identified as a cause of erythroenzymopathies associated with hereditary non-spherocytic hemolytic anemia
7.
Entrez
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The name Entrez was chosen to reflect the spirit of welcoming the public to search the content available from the NLM. Entrez Global Query is a search and retrieval system that provides access to all databases simultaneously with a single query string. Entrez can efficiently retrieve related sequences, structures, and references, the Entrez system can provide views of gene and protein sequences and chromosome maps. Some textbooks are available online through the Entrez system. The Entrez front page provides, by default, access to the global query, all databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to limit parts of the search statement to particular fields. This returns a unified results page, that shows the number of hits for the search in each of the databases, Entrez also provides a similar interface for searching each particular database and for refining search results. The Limits feature allows the user to narrow a search a web forms interface, the History feature gives a numbered list of recently performed queries. Results of previous queries can be referred to by number and combined via boolean operators, search results can be saved temporarily in a Clipboard. Users with a MyNCBI account can save queries indefinitely and also choose to have updates with new search results e-mailed for saved queries of most databases and it is widely used in the field of biotechnology as a reference tool for students and professionals alike. Entrez searches the following databases, PubMed, biomedical literature citations and abstracts, including Medline - articles from journals, in addition to using the search engine forms to query the data in Entrez, NCBI provides the Entrez Programming Utilities for more direct access to query results. The eUtils are accessed by posting specially formed URLs to the NCBI server, there was also an eUtils SOAP interface which was terminated on July 2015. In 1991, entrez was introduced in CD form, in 1993, a client-server version of the software provided connectivity with the internet. In 1994, NCBI established a website, and Entrez was a part of initial release. In 2001, Entrez bookshelf was released and in 2003, the Entrez Gene database was developed, Entrez search engine form Entrez Help
8.
UniProt
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UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains an amount of information about the biological function of proteins derived from the research literature. The UniProt consortium comprises the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy servers that are a resource for proteomics tools. In 2002, EBI, SIB, and PIR joined forces as the UniProt consortium, each consortium member is heavily involved in protein database maintenance and annotation. Until recently, EBI and SIB together produced the Swiss-Prot and TrEMBL databases and these databases coexisted with differing protein sequence coverage and annotation priorities. Swiss-Prot aimed to provide reliable protein sequences associated with a level of annotation. Recognizing that sequence data were being generated at a pace exceeding Swiss-Prots ability to keep up, meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass, a database of protein sequences and curated families. The consortium members pooled their resources and expertise, and launched UniProt in December 2003. UniProt provides four core databases, UniProtKB, UniParc, UniRef, UniProt Knowledgebase is a protein database partially curated by experts, consisting of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. As of 19 March 2014, release 2014_03 of UniProtKB/Swiss-Prot contains 542,782 sequence entries, UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from literature and biocurator-evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to all known relevant information about a particular protein. Annotation is regularly reviewed to keep up with current scientific findings, the manual annotation of an entry involves detailed analysis of the protein sequence and of the scientific literature. Sequences from the gene and the same species are merged into the same database entry. Differences between sequences are identified, and their cause documented, a range of sequence analysis tools is used in the annotation of UniProtKB/Swiss-Prot entries. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry and these predictions include post-translational modifications, transmembrane domains and topology, signal peptides, domain identification, and protein family classification. Relevant publications are identified by searching databases such as PubMed, the full text of each paper is read, and information is extracted and added to the entry
9.
Locus (genetics)
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A locus in genetics is the position on a chromosome. Each chromosome carries many genes, humans estimated haploid protein coding genes are 19, 000-20,000, a variant of the similar DNA sequence located at a given locus is called an allele. The ordered list of known for a particular genome is called a gene map. Gene mapping is the process of determining the locus for a biological trait. The chromosomal locus of a gene might be written 3p22.1, here 3 means chromosome 3, p means p-arm. And 22 refers to region 2, band 2 and this is read as two two, not as twenty-two. So the entire locus is read as three P two two point one, the cytogenetic bands are counting from the centromere out toward the telomeres. A range of loci is specified in a similar way. For example, the locus of gene OCA1 may be written 11q1. 4-q2.1, meaning it is on the arm of chromosome 11. The ends of a chromosome are labeled pter and qter, a centisome is defined as 1% of a chromosome length. Chromosomal translocation Cytogenetic notation Karyotype Null allele Michael, R. Cummings, belmont, California, Brooks/Cole Overview at ornl. gov Chromosome Banding and Nomenclature from NCBI
10.
Chromosome 10 (human)
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Chromosome 10 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome, chromosome 10 spans about 133 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells. Identifying genes on each chromosome is an area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies, in January 2017, two estimates differed by 13%, with one estimate giving 2,174 genes, and the other estimate giving 1,899 genes
11.
HK2
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Hexokinase 2 also known as HK2 is an enzyme which in humans is encoded by the HK2 gene on chromosome 2. Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways and this gene encodes hexokinase 2, the predominant form found in skeletal muscle. It localizes to the membrane of mitochondria. Expression of this gene is insulin-responsive, and studies in rat suggest that it is involved in the rate of glycolysis seen in rapidly growing cancer cells. HK2 is one of four highly homologous hexokinase isoforms in mammalian cells, the HK2 gene spans approximately 50 kb and consists of 18 exons. There is also an HK2 pseudogene integrated into a long interspersed nuclear repetitive DNA element located on the X chromosome, though its DNA sequence is similar to the cDNA product of the actual HK2 mRNA transcript, it lacks an open reading frame for gene expression. This gene encodes a 100-kDa, 917-residue enzyme with highly similar N- and this high similarity, along with the existence of a 50-kDa hexokinase, suggests that the 100-kDa hexokinases originated from a 50-kDa precursor via gene duplication and tandem ligation. Despite there being two binding sites for glucose, it is proposed that glucose binding at one site induces a change which prevents a second glucose from binding the other site. Meanwhile, the first 12 amino acids of the highly hydrophobic N-terminal serve to bind the enzyme to the mitochondria, physiological levels of G6P can regulate this process by inhibiting HK2 as negative feedback, though inorganic phosphate can relieve G6P inhibition. Pi can also directly regulate HK2, and the double regulation may better suit its anabolic functions, by phosphorylating glucose, HK2 effectively prevents glucose from leaving the cell and, thus, commits glucose to energy metabolism. Specifically, HK2 binds VDAC to trigger opening of the channel, another critical function for OMM-bound HK2 is mediation of cell survival. Activation of Akt kinase maintains HK2-VDAC coupling, which subsequently prevents cytochrome c release and apoptosis, one model proposes that HK2 competes with the pro-apoptotic proteins BAX to bind VDAC, and in the absence of HK2, BAX induces cytochrome c release. In fact, there is evidence that HK2 restricts BAX and BAK oligomerization, in a similar mechanism, the pro-apoptotic creatine kinase binds and opens VDAC in the absence of HK2. An alternative model proposes the opposite, that HK2 regulates binding of the anti-apoptotic protein Bcl-Xl to VDAC, in particular, HK2 is ubiquitously expressed in tissues, though it is majorly found in muscle and adipose tissue. In cardiac and skeletal muscle, HK2 can be bound to both the mitochondrial and sarcoplasmic membrane. HK2 gene expression is regulated by a phosphatidylinositol 3-kinaselp70 S6 protein kinase-dependent pathway and can be induced by such as insulin, hypoxia, cold temperatures. Its inducible expression indicates its adaptive role in responses to changes in the cellular environment. HK2 is highly expressed in cancers, including breast cancer
12.
Chromosome 2 (human)
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Chromosome 2 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome, chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs and representing almost 8% of the total DNA in human cells. Identifying genes on each chromosome is an area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies, in January 2017, two estimates differed by 12%, with one estimate giving 3,862 genes, and the other estimate giving 3,399 genes. Chromosome had the HOXD homeobox gene cluster, all members of Hominidae except humans, Neanderthals, and Denisovans have 24 pairs of chromosomes. Humans have only 23 pairs of chromosomes, human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes. The evidence for this includes, The correspondence of chromosome 2 to two ape chromosomes, the closest human relative, the chimpanzee, has near-identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan, the presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere in the q21. 3–q22.1 region. These are normally only at the ends of a chromosome
13.
HK3
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Hexokinase 3 also known as HK3 is an enzyme which in humans is encoded by the HK2 gene on chromosome 5. Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways, similar to hexokinases 1 and 2, this allosteric enzyme is inhibited by its product glucose-6-phosphate. HK3 is one of four highly homologous hexokinase isoforms in mammalian cells and this protein has a molecular weight of 100 kDa and is composed of two highly similar 50-kDa domains at its N- and C-terminals. This high similarity, along with the and the existence of a 50-kDa hexokinase, suggests that the 100-kDa hexokinases originated from a 50-kDa precursor via gene duplication, moreover, the catalytic activity depends on the interaction between the two terminal domains. Unlike HK1 and HK2, HK3 lacks a mitochondrial binding sequence at its N-terminal, physiological levels of G6P can regulate this process by inhibiting HK3 as negative feedback, though inorganic phosphate can relieve G6P inhibition. Inorganic phosphate can also directly regulate HK3, and the double regulation may better suit its anabolic functions, by phosphorylating glucose, HK3 effectively prevents glucose from leaving the cell and, thus, commits glucose to energy metabolism. Compared to HK1 and HK2, HK3 possesses an affinity for glucose and will bind the substrate even at physiological levels. Uniquely, HK3 can be inhibited by glucose at high concentrations, HK3 is also less sensitive to G6P inhibition. Despite its lack of association, HK3 also functions to protect the cell against apoptosis. Overall, HK3 may promote cell survival by controlling ROS levels, currently, only hypoxia is known to induce HK3 expression through a HIF-dependent pathway. The inducible expression of HK3 indicates its adaptive role in responses to changes in the cellular environment. In particular, HK3 is ubiquitously expressed in tissues, albeit at low abundance. Higher abundance levels have been cited in lung, kidney, within cells, HK3 localizes to the cytoplasm and putatively binds the perinuclear envelope. HK3 is the predominant hexokinase in myeloid cells, particularly granulocytes, HK3 is found to be overexpressed in malignant follicular thyroid nodules. In conjunction with cyclin A and galectin-3, HK3 could be used as biomarker to screen for malignancy in patients. Meanwhile, HK3 was found to be repressed in acute myeloid leukemia blast cells, regulators repressing HK3 expression in AML include PML-RARA and CEBPA. Regarding acute lymphoblastic leukemia, functional enrichment analysis revealed HK3 as a key gene and suggests that HK3 shares antiapoptotic function with HK1, the HK3 promoter is known to interact with PU.1, PML-RARA, and CEBPA. Click on genes, proteins and metabolites below to link to respective articles, hexokinase HK1 HK2 Glucokinase This article incorporates text from the United States National Library of Medicine, which is in the public domain
14.
Chromosome 5 (human)
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Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome, chromosome 5 spans about 181 million base pairs and represents almost 6% of the total DNA in cells. Chromosome 5 is the 5th largest human chromosomes, yet has one of the lowest gene densities, identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies, in January 2017, two estimates differed by 3%, with one estimate giving 2,578 genes, and the other estimate giving 2,505 genes. Because chromosome 5 is responsible for forms of growth and development changes may cause cancers. One example would be acute myeloid leukemia and this chromosomal change is written as 5p-. The signs and symptoms of cri-du-chat syndrome are related to the loss of multiple genes in this region. Researchers have not identified all of these genes or determined how their loss leads to the features of the disorder and they have discovered, however, that a larger deletion tends to result in more severe mental retardation and developmental delays in people with cri-du-chat syndrome. Researchers have defined narrow regions of the arm of chromosome 5 that are associated with particular features of cri-du-chat syndrome. A specific region designated 5p15.3 is associated with a cry, and a nearby region called 5p15.2 is associated with mental retardation, small head. Familial Adenomatous Polyposis is caused by a deletion of the APC tumor suppressor gene on the arm of chromosome 5. This chromosomal change results in thousands of polyps which gives the patient a 100% risk of colon cancer if total colectomy is not done. Chromosome 5q deletion syndrome is caused by the deletion of the q arm of chromosome 5 and this deletion has been linked to several blood related disorders including Myelodysplastic syndrome and Erythroblastopenia. This is a different condition than Cri-du-chat which was mentioned above, a ring chromosome occurs when both ends of a broken chromosome are reunited
15.
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
16.
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
17.
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
18.
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
19.
Phosphorylation
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Phosphorylation is the addition of a phosphoryl group − to a molecule. In biology, phosphorylation and its counterpart, dephosphorylation, are critical for cellular processes. A large fraction of proteins are at least temporarily phosphorylated, as are many sugars, lipids, Phosphorylation is especially important for protein function as this modification activates many enzymes, thereby regulating their function. Protein phosphorylation is one type of post-translational modification, the prominent role of protein phosphorylation in biochemistry is illustrated by the huge body of studies published on the subject. Phosphorylation of sugars is often the first stage of their catabolism and it allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter. Phosphorylation of glucose is a key reaction in sugar metabolism because many sugars are first converted to glucose before they are metabolized further. The chemical equation for the conversion of D-glucose to D-glucose-6-phosphate in the first step of glycolysis is given by D-glucose + ATP -> D-glucose-6-phosphate + ADP ΔG° = -16.7 kJ/mol, the two enzymes have been identified as a specific glucokinase and non-specific hexokinase. Hepatic cell is freely permeable to glucose, and the rate of phosphorylation of glucose is the rate-limiting step in glucose metabolism by the liver. The role of glucose 6-phosphate in glycogen synthase, High blood glucose concentration causes an increase in levels of glucose 6 phosphate in liver, skeletal muscle. In liver, synthesis of glycogen is directly correlated by blood glucose concentration and in muscle and adipocytes. High blood glucose releases insulin, stimulating the trans location of specific glucose transporters to the cell membrane, the hexokinase enzyme has a low Km, indicating a high affinity for glucose, so this initial phosphorylation can proceed even when glucose levels at nanoscopic scale within the blood. The phosphorylation of glucose can be enhanced by the binding of Fructose-6-phosphate, fructose consumed in the diet is converted to F1P in the liver. This negates the action of F6P on glucokinase, which favors the forward reaction. The capacity of cells to phosphorylate fructose exceeds capacity of metabolize fructose-1-phosphate. Consuming excess fructose ultimately results in an imbalance in liver metabolism, Phosphorylation of glucose is imperative in processes within the body. For example, phosphorylating glucose is necessary for insulin-dependent mechanistic target of rapamycin pathway activity within the heart and this further suggests a link between intermediary metabolism and cardiac growth. Reversible phosphorylation of proteins is an important regulatory mechanism occurs in both prokaryotic and eukaryotic organisms. Kinases phosphorylate proteins and phosphatases dephosphorylate proteins, many enzymes and receptors are switched on or off by phosphorylation and dephosphorylation
20.
Hexose
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In bio-organic chemistry, a hexose is a monosaccharide with six carbon atoms, having the chemical formula C6H12O6. Hexoses are classified by functional group, with aldohexoses having an aldehyde at position 1, the aldohexoses have four chiral centres for a total of 16 possible aldohexose stereoisomers. The D/L configuration is based on the orientation of the hydroxyl at position 5, the eight D-aldohexoses are, Of these D-isomers, all except D-altrose are naturally occurring. L-Altrose, however, has been isolated from strains of the bacterium Butyrivibrio fibrisolvens, a mnemonic for the aldohexoses is All Altruists Gladly Make Gum in Gallon Tanks, allose, altrose, glucose, mannose, gulose, idose, galactose, talose. At carbon 3, the first two are on the right, the two are on the left, and so on. At carbon 4, the first four are on the right, at carbon 5, all eight D-aldohexoses have the hydroxyl group on the right. This can be seen as binary counting to seven, where 0 stands for hydroxyl and 1 for hydrogen and it has been known since 1926 that 6-carbon aldose sugars form cyclic hemiacetals. The diagram below shows the forms for D-glucose and D-mannose. The numbered carbons in the forms correspond to the same numbered carbons in the hemiacetal forms. The formation of the hemiacetal causes carbon number 1, which is symmetric in the open-chain form and this means that both glucose and mannose each have two cyclic forms. In solution, both of these exist in equilibrium with the open-chain form, the open-chain form, however, does not crystallize. Hence the two cyclic forms become separable when they are crystallized, the ketohexoses have 3 chiral centres and therefore eight possible stereoisomers. Of these, only the four D-isomers are known to naturally, Only the naturally occurring hexoses are capable of being fermented by yeasts. The aldehyde and ketone functional groups in these carbohydrates react with neighbouring hydroxyl groups to form intramolecular hemiacetals and hemiketals. The resulting ring structure is related to pyran, and is termed a pyranose, the ring spontaneously opens and closes, allowing rotation to occur about the bond between the carbonyl group and the neighbouring carbon atom, yielding two distinct configurations. Hexose sugars can form dihexose sugars with a reaction to form a 1
21.
Sugar
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Sugar is the generic name for sweet, soluble carbohydrates, many of which are used in food. There are various types of derived from different sources. Simple sugars are called monosaccharides and include glucose, fructose, the table sugar or granulated sugar most customarily used as food is sucrose, a disaccharide of glucose and fructose. Sugar is used in prepared foods and it is added to some foods, in the body, sucrose is hydrolysed into the simple sugars fructose and glucose. Other disaccharides include maltose from malted grain, and lactose from milk, longer chains of sugars are called oligosaccharides or polysaccharides. Some other chemical substances, such as glycerol may also have a sweet taste, low-calorie food substitutes for sugar, described as artificial sweeteners, include aspartame and sucralose, a chlorinated derivative of sucrose. Sugars are found in the tissues of most plants and are present in sufficient concentrations for efficient commercial extraction in sugarcane, the world production of sugar in 2011 was about 168 million tonnes. The average person consumes about 24 kilograms of sugar each year, equivalent to over 260 food calories per person, since the latter part of the twentieth century, it has been questioned whether a diet high in sugars, especially refined sugars, is good for human health. Sugar has been linked to obesity, and suspected of, or fully implicated as a cause in the occurrence of diabetes, cardiovascular disease, dementia, macular degeneration, the etymology reflects the spread of the commodity. The English word sugar ultimately originates from the Sanskrit शर्करा, via Arabic سكر as granular or candied sugar, the contemporary Italian word is zucchero, whereas the Spanish and Portuguese words, azúcar and açúcar, respectively, have kept a trace of the Arabic definite article. The Old French word is zuchre and the contemporary French, sucre, the earliest Greek word attested is σάκχαρις. The English word jaggery, a brown sugar made from date palm sap or sugarcane juice, has a similar etymological origin – Portuguese jagara from the Sanskrit शर्करा. Sugar has been produced in the Indian subcontinent since ancient times and it was not plentiful or cheap in early times and honey was more often used for sweetening in most parts of the world. Originally, people chewed raw sugarcane to extract its sweetness, sugarcane was a native of tropical South Asia and Southeast Asia. Different species seem to have originated from different locations with Saccharum barberi originating in India and S. edule, one of the earliest historical references to sugarcane is in Chinese manuscripts dating back to 8th century BC that state that the use of sugarcane originated in India. Sugar was found in Europe by the 1st century AD, but only as an imported medicine and it is a kind of honey found in cane, white as gum, and it crunches between the teeth. It comes in lumps the size of a hazelnut, sugar is used only for medical purposes. Sugar remained relatively unimportant until the Indians discovered methods of turning sugarcane juice into granulated crystals that were easier to store, crystallized sugar was discovered by the time of the Imperial Guptas, around the 5th century AD
22.
Glucokinase
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Glucokinase is an enzyme that facilitates phosphorylation of glucose to glucose-6-phosphate. Glucokinase occurs in cells in the liver and pancreas of humans, mutations of the gene for this enzyme can cause unusual forms of diabetes or hypoglycemia. Glucokinase is a hexokinase isozyme, related homologously to at least three other hexokinases, all of the hexokinases can mediate phosphorylation of glucose to glucose-6-phosphate, which is the first step of both glycogen synthesis and glycolysis. However, glucokinase is coded by a gene and its distinctive kinetic properties allow it to serve a different set of functions. Because of this reduced affinity, the activity of glucokinase, under physiological conditions. Alternative names for this enzyme are, human hexokinase IV, hexokinase D, the common name, glucokinase, is derived from its relative specificity for glucose under physiologic conditions.7.1.2. Nevertheless, glucokinase remains the name preferred in the contexts of medicine, another mammalian glucose kinase, ADP-specific glucokinase, was discovered in 2004. The gene is distinct and similar to that of primitive organisms and it is dependent on ADP rather than ATP, and the metabolic role and importance remain to be elucidated. The principal substrate of physiologic importance of glucokinase is glucose, the other necessary substrate, from which the phosphate is derived, is adenosine triphosphate, which is converted to adenosine diphosphate when the phosphate is removed. The reaction catalyzed by glucokinase is, ATP participates in the reaction in a form complexed to magnesium as a cofactor, furthermore, under certain conditions, glucokinase, like other hexokinases, can induce phosphorylation of other hexoses and similar molecules. Two important kinetic properties distinguish glucokinase from the other hexokinases, allowing it to function in a role as glucose sensor. Glucokinase has an affinity for glucose than the other hexokinases. Glucokinase changes conformation and/or function in parallel with rising glucose concentrations in the physiologically important range of 4–10 mmol/L and it is half-saturated at a glucose concentration of about 8 mmol/L. Glucokinase is not inhibited by its product, glucose-6-phosphate and this allows continued signal output amid significant amounts of its product These two features allow it to regulate a supply-driven metabolic pathway. That is, the rate of reaction is driven by the supply of glucose, another distinctive property of glucokinase is its moderate cooperativity with glucose, with a Hill coefficient of about 1.7. Glucokinase has only a binding site for glucose and is the only monomeric regulatory enzyme known to display substrate cooperativity. The nature of the cooperativity has been postulated to involve a transition between two different enzyme states with different rates of activity. If the dominant state depends upon glucose concentration, it would produce an apparent cooperativity similar to that observed, because of this cooperativity, the kinetic interaction of glucokinase with glucose does not follow classical Michaelis-Menten kinetics
23.
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
24.
Yeast
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Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The yeast lineage originated hundreds of millions of years ago, and 1,500 species are currently identified and they are estimated to constitute 1% of all described fungal species. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. Yeasts, with their growth habit, can be contrasted with molds. Fungal species that can take both forms are called dimorphic fungi and it is also a centrally important model organism in modern cell biology research, and is one of the most thoroughly researched eukaryotic microorganisms. Researchers have used it to information about the biology of the eukaryotic cell. Other species of yeasts, such as Candida albicans, are opportunistic pathogens, yeasts have recently been used to generate electricity in microbial fuel cells, and produce ethanol for the biofuel industry. Yeasts do not form a taxonomic or phylogenetic grouping. The budding yeasts are classified in the order Saccharomycetales, within the phylum Ascomycota, the word yeast comes from Old English gist, gyst, and from the Indo-European root yes-, meaning boil, foam, or bubble. Yeast microbes are probably one of the earliest domesticated organisms, archaeologists digging in Egyptian ruins found early grinding stones and baking chambers for yeast-raised bread, as well as drawings of 4, 000-year-old bakeries and breweries. In 1680, Dutch naturalist Anton van Leeuwenhoek first microscopically observed yeast, but at the time did not consider them to be living organisms, researchers were doubtful whether yeasts were algae or fungi, but in 1837 Theodor Schwann recognized them as fungi. In 1857, French microbiologist Louis Pasteur proved in the paper Mémoire sur la fermentation alcoolique that alcoholic fermentation was conducted by living yeasts and not by a chemical catalyst. Pasteur showed that by bubbling oxygen into the yeast broth, cell growth could be increased, by the late 18th century, two yeast strains used in brewing had been identified, Saccharomyces cerevisiae and S. carlsbergensis. S. cerevisiae has been sold commercially by the Dutch for bread-making since 1780, while, around 1800, in 1825, a method was developed to remove the liquid so the yeast could be prepared as solid blocks. The industrial production of yeast blocks was enhanced by the introduction of the press in 1867. In 1872, Baron Max de Springer developed a process to create granulated yeast. Yeasts are chemoorganotrophs, as they use organic compounds as a source of energy, carbon is obtained mostly from hexose sugars, such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can metabolize pentose sugars such as ribose, alcohols, Yeast species either require oxygen for aerobic cellular respiration or are anaerobic, but also have aerobic methods of energy production
25.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
26.
Vertebrate
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Vertebrates /ˈvɜːrtᵻbrᵻts/ comprise all species of animals within the subphylum Vertebrata /-ɑː/. Vertebrates represent the majority of the phylum Chordata, with currently about 66,000 species described. Vertebrates include the fish and the jawed vertebrates, which include the cartilaginous fish. A bony fish known as the lobe-finned fishes is included with tetrapods, which are further divided into amphibians, reptiles, mammals. Extant vertebrates range in size from the frog species Paedophryne amauensis, at as little as 7.7 mm, to the blue whale, vertebrates make up less than five percent of all described animal species, the rest are invertebrates, which lack vertebral columns. The vertebrates traditionally include the hagfish, which do not have proper vertebrae due to their loss in evolution, though their closest living relatives, hagfish do, however, possess a cranium. For this reason, the vertebrate subphylum is sometimes referred to as Craniata when discussing morphology, molecular analysis since 1992 has suggested that hagfish are most closely related to lampreys, and so also are vertebrates in a monophyletic sense. Others consider them a group of vertebrates in the common taxon of craniata. The word origin of vertebrate derives from the Latin word vertebratus, the Proto-Indo-European language origins are still unclear. Vertebrate is derived from the vertebra, which refers to any of the bones or segments of the spinal column. All vertebrates are built along the basic body plan, a stiff rod running through the length of the animal, with a hollow tube of nervous tissue above it. In all vertebrates, the mouth is found at, or right below, the remaining part of the body continuing after the anus forms a tail with vertebrae and spinal cord, but no gut. However, a few vertebrates have secondarily lost this anatomy, retaining the notochord into adulthood, such as the sturgeon, jawed vertebrates are typified by paired appendages, but this trait is not required in order for an animal to be a vertebrate. All basal vertebrates breathe with gills, the gills are carried right behind the head, bordering the posterior margins of a series of openings from the pharynx to the exterior. Each gill is supported by a cartilagenous or bony gill arch, the bony fish have three pairs of arches, cartilaginous fish have five to seven pairs, while the primitive jawless fish have seven. The vertebrate ancestor no doubt had more arches than this, as some of their relatives have more than 50 pairs of gills. In amphibians and some primitive fishes, the larvae bear external gills. These are reduced in adulthood, their function taken over by the gills proper in fishes, some amphibians retain the external larval gills in adulthood, the complex internal gill system as seen in fish apparently being irrevocably lost very early in the evolution of tetrapods
27.
Adenosine triphosphate
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Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
28.
Isozyme
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Isozymes are enzymes that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different kinetic parameters, or different regulatory properties, the existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage. In biochemistry, isozymes are isoforms of enzymes, in many cases, they are coded for by homologous genes that have diverged over time. Isozymes were first described by R. L, hunter and Clement Markert who defined them as different variants of the same enzyme having identical functions and present in the same individual. This definition encompasses enzyme variants that are the product of different genes and thus represent different loci, isozymes are usually the result of gene duplication, but can also arise from polyploidisation or nucleic acid hybridization. Over evolutionary time, if the function of the new variant remains identical to the original, then it is likely one or the other will be lost as mutation accumulate. For example, they may be expressed at different stages of development or in different tissues, allozymes may result from point mutations or from insertion-deletion events that affect the DNA coding sequence of the gene. Alternatively, if the acid residue that is changed is in a relatively unimportant part of the enzyme, then the mutation may be selectively neutral. An example of an isozyme is glucokinase, a variant of hexokinase which is not inhibited by glucose 6-phosphate, both of these processes must only occur when glucose is abundant, or problems occur. Unless they are identical in terms of their properties, for example their substrates and enzyme kinetics. However, such differences are usually subtle and this subtlety is to be expected, because two enzymes that differ significantly in their function are unlikely to have been identified as isozymes. Whilst isozymes may be almost identical in function, they may differ in other ways, historically, this has usually been done using gels made from potato starch, but acrylamide gels provide better resolution. All the proteins from the tissue are present in the gel and this assay method requires that the enzymes are still functional after separation, and provides the greatest challenge to using isozymes as a laboratory technique. The cytochrome P450 isozymes play important roles in metabolism and steroidogenesis, the multiple forms of phosphodiesterase also play major roles in various biological processes. Although more than one form of enzymes have been found in individual cells. From the clinical standpoint they have found to be selectively activated and inhibited. Histochemical demonstration of enzymes separated by electrophoresis in starch gels. Science 125, 1294-1295 Weiss, B. and Hait, W. N, selective cyclic nucleotide phosphodiesterase inhibitors as potential therapeutic agents
29.
Species
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In biology, a species is the basic unit of biological classification and a taxonomic rank. A species is defined as the largest group of organisms in which two individuals can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, looked at more closely it is problematic, for example, with hybridisation, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Other ways of defining species include similarity of DNA, morphology, all species are given a two-part name, a binomial. The first part of a binomial is the genus to which the species belongs, the second part is called the specific name or the specific epithet. For example, Boa constrictor is one of four species of the Boa genus, Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time, Charles Darwins 1859 book The Origin of Species explained how species could arise by natural selection. Genes can sometimes be exchanged between species by horizontal transfer, and species may become extinct for a variety of reasons. In his biology, Aristotle used the term γένος to mean a kind, such as a bird or fish, a kind was distinguished by its attributes, for instance, a bird has feathers, a beak, wings, a hard-shelled egg, and warm blood. A form was distinguished by being shared by all its members, Aristotle believed all kinds and forms to be distinct and unchanging. His approach remained influential until the Renaissance, when observers in the Early Modern period began to develop systems of organization for living things, they placed each kind of animal or plant into a context. Many of these early delineation schemes would now be considered whimsical, animals likewise that differ specifically preserve their distinct species permanently, one species never springs from the seed of another nor vice versa. In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics and he established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was widely believed that there was no organic connection between species, no matter how similar they appeared. However, whether or not it was supposed to be fixed, by the 19th century, naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, described the transmutation of species, proposing that a species could change over time, in 1859, Charles Darwin and Alfred Russel Wallace provided a compelling account of evolution and the formation of new species. Darwin argued that it was populations that evolved, not individuals and this required a new definition of species. Darwin concluded that species are what appear to be, ideas
30.
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
31.
Glycogen
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Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in humans, animals, and fungi. The polysaccharide structure represents the main form of glucose in the body. In humans, glycogen is made and stored primarily in the cells of the liver, glycogen functions as the secondary long-term energy storage, with the primary energy stores being fats held in adipose tissue. Muscle glycogen is converted into glucose by muscle cells, and liver glycogen converts to glucose for use throughout the body including the nervous system. Glycogen is the analogue of starch, a polymer that functions as energy storage in plants. It has a similar to amylopectin, but is more extensively branched. Both are white powders in their dry state, glycogen is found in the form of granules in the cytosol/cytoplasm in many cell types, and plays an important role in the glucose cycle. Glycogen forms a reserve that can be quickly mobilized to meet a sudden need for glucose. In the liver, glycogen can make up from 5–6% of the fresh weight. Only the glycogen stored in the liver can be accessible to other organs. In the muscles, glycogen is found in a low concentration, the amount of glycogen stored in the body—especially within the muscles, liver, and red blood cells—mostly depends on physical training, basal metabolic rate, and eating habits. Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain cells in the brain. The uterus also stores glycogen during pregnancy to nourish the embryo, glycogen is a branched biopolymer consisting of linear chains of glucose residues with further chains branching off every 8 to 12 glucoses or so. Glucoses are linked together linearly by α glycosidic bonds from one glucose to the next, branches are linked to the chains from which they are branching off by α glycosidic bonds between the first glucose of the new branch and a glucose on the stem chain. Due to the way glycogen is synthesised, every glycogen granule has at its core a glycogenin protein. Glycogen in muscle, liver, and fat cells is stored in a hydrated form, as a meal containing carbohydrates or protein is eaten and digested, blood glucose levels rise, and the pancreas secretes insulin. Blood glucose from the vein enters liver cells. Insulin acts on the hepatocytes to stimulate the action of several enzymes, glucose molecules are added to the chains of glycogen as long as both insulin and glucose remain plentiful
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Mammal
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Mammals are any vertebrates within the class Mammalia, a clade of endothermic amniotes distinguished from reptiles by the possession of a neocortex, hair, three middle ear bones and mammary glands. All female mammals nurse their young with milk, secreted from the mammary glands, Mammals include the largest animals on the planet, the great whales. The basic body type is a quadruped, but some mammals are adapted for life at sea, in the air, in trees. The largest group of mammals, the placentals, have a placenta, Mammals range in size from the 30–40 mm bumblebee bat to the 30-meter blue whale. With the exception of the five species of monotreme, all modern mammals give birth to live young, most mammals, including the six most species-rich orders, belong to the placental group. The largest orders are the rodents, bats and Soricomorpha, the next three biggest orders, depending on the biological classification scheme used, are the Primates, the Cetartiodactyla, and the Carnivora. Living mammals are divided into the Yinotheria and Theriiformes There are around 5450 species of mammal, in some classifications, extant mammals are divided into two subclasses, the Prototheria, that is, the order Monotremata, and the Theria, or the infraclasses Metatheria and Eutheria. The marsupials constitute the group of the Metatheria, and include all living metatherians as well as many extinct ones. Much of the changes reflect the advances of cladistic analysis and molecular genetics, findings from molecular genetics, for example, have prompted adopting new groups, such as the Afrotheria, and abandoning traditional groups, such as the Insectivora. The mammals represent the only living Synapsida, which together with the Sauropsida form the Amniota clade, the early synapsid mammalian ancestors were sphenacodont pelycosaurs, a group that produced the non-mammalian Dimetrodon. At the end of the Carboniferous period, this group diverged from the line that led to todays reptiles. Some mammals are intelligent, with some possessing large brains, self-awareness, Mammals can communicate and vocalize in several different ways, including the production of ultrasound, scent-marking, alarm signals, singing, and echolocation. Mammals can organize themselves into fission-fusion societies, harems, and hierarchies, most mammals are polygynous, but some can be monogamous or polyandrous. They provided, and continue to provide, power for transport and agriculture, as well as commodities such as meat, dairy products, wool. Mammals are hunted or raced for sport, and are used as model organisms in science, Mammals have been depicted in art since Palaeolithic times, and appear in literature, film, mythology, and religion. Defaunation of mammals is primarily driven by anthropogenic factors, such as poaching and habitat destruction, Mammal classification has been through several iterations since Carl Linnaeus initially defined the class. No classification system is accepted, McKenna & Bell and Wilson & Reader provide useful recent compendiums. Though field work gradually made Simpsons classification outdated, it remains the closest thing to a classification of mammals
. PMID 198801.
