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.
Xanthine dehydrogenase
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Xanthine dehydrogenase, also known as XDH, is a protein that, in humans, is encoded by the XDH gene. Xanthine dehydrogenase belongs to the group of molybdenum-containing hydroxylases involved in the metabolism of purines. Xanthine dehydrogenase can be converted to xanthine oxidase by reversible sulfhydryl oxidation or by irreversible proteolytic modification, xanthine dehydrogenase catalyzes the following chemical reaction, The three substrates of this enzyme are xanthine, NAD+, and H2O, whereas its three products are urate, NADH, and H+. This enzyme participates in purine metabolism and this enzyme belongs to the family of oxidoreductases, to be specific, those acting on CH or CH2 groups with NAD+ or NADP+ as acceptor. The systematic name of this class is xanthine, NAD+ oxidoreductase. Other names in use include NAD+-xanthine dehydrogenase, xanthine-NAD+ oxidoreductase, xanthine/NAD+ oxidoreductase. Defects in xanthine dehydrogenase cause xanthinuria, may contribute to respiratory stress syndrome. Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain MOCOS xanthine oxidase
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 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
11.
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
12.
Reactive oxygen species
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Reactive oxygen species are chemically reactive chemical species containing oxygen. Examples include peroxides, superoxide, hydroxyl radical, and singlet oxygen, in a biological context, ROS are formed as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling and homeostasis. However, during times of stress, ROS levels can increase dramatically. This may result in significant damage to cell structures, cumulatively, this is known as oxidative stress. ROS are also generated by sources such as ionizing radiation. Ionizing radiation can generate damaging intermediates through the interaction with water, since water comprises 55–60% of the human body, the probability of radiolysis is quite high under the presence of ionizing radiation. In the process, water loses an electron and becomes highly reactive, then through a three-step chain reaction, water is sequentially converted to hydroxyl radical, hydrogen peroxide, superoxide radical and ultimately oxygen. The hydroxyl radical is extremely reactive and immediately removes electrons from any molecule in its path, turning that molecule into a free radical, mitochondria convert energy for the cell into a usable form, adenosine triphosphate. The process in which ATP is produced, called oxidative phosphorylation, the last destination for an electron along this chain is an oxygen molecule. Superoxide is not particularly reactive by itself, but can inactivate specific enzymes or initiate lipid peroxidation in its protonated form, the pKa of hydroperoxyl is 4.8. Thus, at physiological pH, the majority will exist as superoxide anion, if too much damage is present in mitochondria, a cell undergoes apoptosis or programmed cell death. This cytochrome C binds to Apaf-1, or apoptotic protease activating factor-1, using energy from the ATPs in the mitochondrion, the Apaf-1 and cytochrome C bind together to form apoptosomes. The apoptosomes bind to and activate caspase-9, another free-floating protein, the caspase-9 then cleaves the proteins of the mitochondrial membrane, causing it to break down and start a chain reaction of protein denaturation and eventually phagocytosis of the cell. Superoxide dismutases are a class of enzymes catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in all cells exposed to oxygen. In mammals and most chordates, three forms of superoxide dismutase are present, sOD1 is located primarily in the cytoplasm, SOD2 in the mitochondria and SOD3 is extracellular. The first is a dimer, while the others are tetramers, sOD1 and SOD3 contain copper and zinc ions, while SOD2 has a manganese ion in its reactive centre. The genes are located on chromosomes 21,6, and 4, respectively
13.
Redox
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Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions in which atoms have their oxidation state changed, in general, the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in terms, Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom. Reduction is the gain of electrons or a decrease in state by a molecule, atom. As an example, during the combustion of wood, oxygen from the air is reduced, the reaction can occur relatively slowly, as in the case of rust, or more quickly, as in the case of fire. Redox is a portmanteau of reduction and oxidation, the word oxidation originally implied reaction with oxygen to form an oxide, since dioxygen was historically the first recognized oxidizing agent. Later, the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions, ultimately, the meaning was generalized to include all processes involving loss of electrons. The word reduction originally referred to the loss in weight upon heating a metallic ore such as an oxide to extract the metal. In other words, ore was reduced to metal, antoine Lavoisier showed that this loss of weight was due to the loss of oxygen as a gas. Later, scientists realized that the atom gains electrons in this process. The meaning of reduction then became generalized to all processes involving gain of electrons. Even though reduction seems counter-intuitive when speaking of the gain of electrons, it help to think of reduction as the loss of oxygen. Since electrons are charged, it is also helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes respectively when they occur at electrodes and these words are analogous to protonation and deprotonation, but they have not been widely adopted by chemists. The term hydrogenation could be used instead of reduction, since hydrogen is the agent in a large number of reactions. But, unlike oxidation, which has been generalized beyond its root element, the word redox was first used in 1928. The processes of oxidation and reduction occur simultaneously and cannot happen independently of one another, the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction
14.
Xanthine
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Xanthine, is a purine base found in most human body tissues and fluids and in other organisms. A number of stimulants are derived from xanthine, including caffeine and theobromine, xanthine is a product on the pathway of purine degradation. It is created from guanine by guanine deaminase and it is created from hypoxanthine by xanthine oxidoreductase. It is also created from xanthosine by purine nucleoside phosphorylase, xanthine is subsequently converted to uric acid by the action of the xanthine oxidase enzyme. People with the genetic disorder xanthinuria lack sufficient xanthine oxidase. Derivatives of xanthine are a group of alkaloids commonly used for their effects as mild stimulants and as bronchodilators and they also stimulate the respiratory centre, and are used for treatment of infantile apnea. Due to widespread effects, the range of xanthines is narrow. The therapeutic level is 10-20 micrograms/mL blood, signs of toxicity include tremor, nausea, nervousness, in high doses they can lead to convulsions that are resistant to anticonvulsants. Methylxanthines induce acid and pepsin secretions in the GI tract, methylxanthines are metabolized by cytochrome P450 in the liver. Xanthines are also very rarely as constituents of nucleic acids. Non-specific LC-MS UV Spectroscopy Fourier transform infrared spectrometry Murchison meteorite Xanthene Xanthydrol Xanthone Theobromine poisoning DMPX
15.
HUGO Gene Nomenclature Committee
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The HUGO Gene Nomenclature Committee is a committee of the Human Genome Organisation that sets the standards for human gene nomenclature. The HGNC approves a unique and meaningful name for every known human gene, in addition to the name, which is usually 1 to 10 words long, the HGNC also assigns a symbol to every gene. As with an SI symbol, a symbol is like an abbreviation but is more than that. It may not necessarily stand for the initials of the name, especially gene abbreviations/symbols but also full gene names are often not specific for a single gene. A marked example is CAP which can refer to any of 6 different genes, the HGNC short gene names, or gene symbols, unlike previously used or published symbols, are specifically assigned to one gene only. This can result in less common abbreviations being selected but reduces confusion as to which gene is referred to. e, h/h for human The full description of HGNCs nomenclature guidelines can be found on their web site. HGNC advocates the appendices _v1, _v2. to distinguish between different splice variants and _pr1, _pr2. for promoter variants of a single gene. HGNC also states that gene nomenclature should evolve with new technology rather than be restrictive as sometimes occurs when historical, HGNC also coordinates with the related Mouse and Rat Genomic Nomenclature Committees, other database curators, and experts for given specific gene families or sets of genes. For this reason the HGNC aims to change a name only if agreement for that change can be reached among a majority of researchers working on that gene. Human Genome Organisation Human Genome Project Human genome Gene Gene nomenclature HGNC homepage HUGO homepage
16.
Caffeine
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Caffeine is a central nervous system stimulant of the methylxanthine class. It is the worlds most widely consumed psychoactive drug, unlike many other psychoactive substances, it is legal and unregulated in nearly all parts of the world. There are several mechanisms of action to explain the effects of caffeine. The most prominent is that it blocks the action of adenosine on its receptor. Caffeine also stimulates certain portions of the nervous system. Caffeine is a bitter, white crystalline purine, a methylxanthine alkaloid and it is found in the seeds, nuts, or leaves of a number of plants native to South America and East Asia and helps to protect them against predator insects and prevent germination of nearby seeds. The most well known source of caffeine is the coffee bean, beverages containing caffeine are ingested to relieve or prevent drowsiness and to improve performance. To make these drinks, caffeine is extracted by steeping the plant product in water, caffeine-containing drinks, such as coffee, tea, and cola, are very popular, in 2005, 90% of North American adults consumed caffeine daily. Caffeine can have positive and negative health effects. It can treat and prevent the premature infant breathing disorders bronchopulmonary dysplasia of prematurity, Caffeine citrate is on the WHO Model List of Essential Medicines. It may confer a modest protective effect against some diseases, including Parkinsons disease, some people experience insomnia or sleep disruption if they consume caffeine, especially during the evening hours, but others show little disturbance. Evidence of a risk during pregnancy is equivocal, some authorities recommend that pregnant women limit consumption to the equivalent of two cups of coffee per day or less. Tolerance to the effects of increased blood pressure and heart rate. Caffeine is classified by the Food and Drug Administration as generally recognized as safe, toxic doses, over 10 grams per day for an adult, are much higher than typical doses of under 500 milligrams per day. A cup of coffee contains 80–175 mg of caffeine, depending on what bean is used, thus it requires roughly 50–100 ordinary cups of coffee to reach a lethal dose. However pure powdered caffeine, which is available as a dietary supplement, Caffeine is used in, Bronchopulmonary dysplasia in premature infants for both prevention and treatment. It may improve weight gain during therapy and reduce the incidence of cerebral palsy as well as reduce language, on the other hand, subtle long-term side effects are possible. Apnea of prematurity as a treatment, but not prevention
17.
Superoxide
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A superoxide, also known by the obsolete name hyperoxide, is a compound that contains the superoxide anion with the chemical formula O−2. The systematic name of the anion is dioxide, the reactive oxygen anion superoxide is particularly important as the product of the one-electron reduction of dioxygen O2, which occurs widely in nature. Both dioxygen and the anion are free radicals that exhibit paramagnetism. Superoxides are compounds in which the number of oxygen is − 1⁄2. The O–O bond distance in O−2 is 1.33 Å, the salts CsO2, RbO2, KO2, and NaO2 are prepared by the direct reaction of O2 with the respective alkali metal. The overall trend corresponds to a reduction in the order from 2, to 1.5. The alkali salts of O−2 are orange-yellow in color and quite stable, superoxides are also used in firefighters oxygen tanks in order to provide a readily available source of oxygen. In this process O−2 acts as a Brønsted base, initially forming the radical HO2·. But the pKa of its conjugate acid, hydrogen superoxide, is 4.88 so that at neutral pH7 all but 0. 3% of superoxide is in the anionic form, O−2. Potassium superoxide can be dissolved in dimethyl sulfoxide and is stable as long as protons are not available, superoxide can also be generated in aprotic solvents by cyclic voltammetry. Superoxide is biologically quite toxic and is deployed by the system to kill invading microorganisms. In phagocytes, superoxide is produced in quantities by the enzyme NADPH oxidase for use in oxygen-dependent killing mechanisms of invading pathogens. In turn, micro-organisms genetically engineered to lack superoxide dismutase lose virulence, superoxide is also deleterious when produced as a byproduct of mitochondrial respiration, as well as several other enzymes, for example xanthine oxidase. Because superoxide is toxic, nearly all living in the presence of oxygen contain isoforms of the superoxide-scavenging enzyme superoxide dismutase. SOD is an efficient enzyme, it catalyzes the neutralization of superoxide nearly as quickly as the two can diffuse together spontaneously in solution. Other proteins that can be oxidized and reduced by superoxide have weak SOD-like activity. Genetic inactivation of SOD produces deleterious phenotypes in organisms ranging from bacteria to mice and have provided important clues as to the mechanisms of toxicity of superoxide in vivo, yeast lacking both mitochondrial and cytosolic SOD grow very poorly in air, but quite well under anaerobic conditions. Absence of cytosolic SOD causes an increase in mutagenesis and genomic instability
18.
Cytochrome c
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The cytochrome complex, or cyt c is a small hemeprotein found loosely associated with the inner membrane of the mitochondrion. It belongs to the cytochrome c family of proteins, cytochrome c is highly water-soluble, unlike other cytochromes, and is an essential component of the electron transport chain, where it carries one electron. It is capable of undergoing oxidation and reduction, but does not bind oxygen and it transfers electrons between Complexes III and IV. In humans, cytochrome c is encoded by the CYCS gene, cytochrome c is a highly conserved protein across the spectrum of species, found in plants, animals, and many unicellular organisms. This, along with its size, makes it useful in studies of cladistics. The cytochrome c molecule has been studied for the glimpse it gives into evolutionary biology and its primary structure consists of a chain of about 100 amino acids. Many higher-order organisms possess a chain of 104 amino acids, the sequences of cytochrome c in humans is identical to that of chimpanzees, but differs more from that of horses. Its amino acid sequence is conserved in eukaryotes, differing by only a few residues. In more than thirty species,34 of the 104 amino acids are conserved, for example, human cytochrome oxidase reacts with wheat cytochrome c, in vitro, this is true for all pairs of species tested. In addition the redox potential of +0.25 volts is the same in all cytochrome c molecules studied, all cytochrome c proteins contain a characteristic CXXCH amino acid motif that binds heme. However, there are four classes of cytochrome c, each possessing a different fold, in 1991 R. P. Ambler recognized four classes of cytochrome c, Class I includes the lowspin soluble cytochrome c of mitochondria and bacteria. It has the heme-attachment site towards the N terminus of histidine, Class II includes the highspin cytochrome c. It has the heme-attachment site closed to the N terminus of histidine, Class III comprises the low redox potential multiple-heme cytochromes. The heme c groups are structurally and functionally nonequivalent and present different redox potentials in the range 0 to −400 mV, Class IV was originally created to hold the complex proteins that have other prosthetic groups as well as heme c. One of the properties of heme c, which allows cytochrome c to have variety of functions, is its ability to have different reduction potentials in nature. This property determines the kinetics and thermodynamics of a transfer reaction. The dipole moment has an important role in orienting proteins to the proper directions, the dipole moment of cytochrome c is a result from a cluster of negatively charged amino acid side chains at the back of the enzyme. Despite variations in the number of bound heme groups and variations in sequence, for examples, vertebrate cytochromes c all have dipole moment of approximately 320 debye while cytochromes c of plants and insects have dipole moment of approximately 340 debye
19.
Carbonic anhydrase
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The active site of most carbonic anhydrases contains a zinc ion, they are therefore classified as metalloenzymes. Typical catalytic rates of the different forms of this enzyme ranging between 104 and 106 reactions per second, the reverse reaction is relatively slow in the absence of a catalyst. H C O3 − + H + → H2 C O3 → C O2 + H2 O A zinc prosthetic group in the enzyme is coordinated in three positions by histidine side-chains, the fourth coordination position is occupied by water. This causes polarisation of the bond, making the oxygen slightly more positive. A fourth histidine is placed close to the substrate of water and accepts a proton and this leaves a hydroxide attached to the zinc. The active site contains a specificity pocket for carbon dioxide. This allows the electron-rich hydroxide to attack the carbon dioxide, forming bicarbonate, there are at least five distinct CA families. These families have no significant amino acid sequence similarity and in most cases are thought to be an example of convergent evolution, the α-CAs are found in humans. Vertebrates, algae and some bacteria have this family of CAs, most prokaryotic and plant chloroplast CAs belong to the beta family. Two signature patterns for this family have been identified, C--D-S-R--x- --A--x--x--x-G-H-x-C-G The gamma class of CAs come from methanogens, the delta class of CAs has been described in diatoms. The distinction of class of CA has recently come into question. The zeta class of CAs occurs exclusively in bacteria in a few chemolithotrophs, recent 3-dimensional analyses suggest that ζ-CA bears some structural resemblance to β-CA, particularly near the metal ion site. Thus, the two forms may be related, even though the underlying amino acid sequence has since diverged considerably. The eta family of CAs was recently found in organisms of the genus Plasmodium and these are a group of enzymes previously thought to belong to the alpha family of CAs, however it has been demonstrated that η-CAs have unique features, such as their metal ion coordination pattern. Several forms of carbonic anhydrase occur in nature, in the best-studied α-carbonic anhydrase form present in animals, the zinc ion is coordinated by the imidazole rings of 3 histidine residues, His94, His96, and His119. There are at least 14 different isoforms in mammals, in plants, carbonic anhydrase helps raise the concentration of CO2 within the chloroplast in order to increase the carboxylation rate of the enzyme RuBisCO. This is the reaction that integrates CO2 into organic carbon sugars during photosynthesis, marine diatoms have been found to express a new form of ζ carbonic anhydrase. T. weissflogii, a species of phytoplankton common to marine ecosystems, was found to contain carbonic anhydrase with a cadmium ion in place of zinc
20.
Flavin group
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Flavin is the common name for a group of organic compounds based on pteridine, formed by the tricyclic heterocycle isoalloxazine. The biochemical source is the vitamin riboflavin and it is in one or the other of these forms that flavin is present as a prosthetic group in flavoproteins. The flavin group is capable of undergoing oxidation-reduction reactions, and can accept one electron in a two-step process or two electrons at once. In the form of FADH2, it is one of the cofactors that can transfer electrons to the electron transfer chain, FADH and FADH2 are reduced forms of FAD. FADH2 is produced as a group in succinate dehydrogenase, an enzyme involved in the citric acid cycle. In oxidative phosphorylation, two molecules of FADH2 typically yield 1.5 ATP each, or three ATP combined, flavin mononucleotide is a prosthetic group found in, among other proteins, NADH dehydrogenase, E. coli nitroreductase and old yellow enzyme. Pteridine Pterin Deazaflavin Voet, D. Voet, J. G
21.
Molybdenum
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Molybdenum is a chemical element with symbol Mo and atomic number 42. The name is from Neo-Latin molybdaenum, from Ancient Greek Μόλυβδος molybdos, meaning lead, molybdenum minerals have been known throughout history, but the element was discovered in 1778 by Carl Wilhelm Scheele. The metal was first isolated in 1781 by Peter Jacob Hjelm, molybdenum does not occur naturally as a free metal on Earth, it is found only in various oxidation states in minerals. The free element, a metal with a gray cast, has the sixth-highest melting point of any element. It readily forms hard, stable carbides in alloys, and for this reason most of production of the element is used in steel alloys. Most molybdenum compounds have low solubility in water, but when molybdenum-bearing minerals contact oxygen and water, industrially, molybdenum compounds are used in high-pressure and high-temperature applications as pigments and catalysts. Molybdenum-bearing enzymes are by far the most common catalysts for breaking the chemical bond in atmospheric molecular nitrogen in the process of biological nitrogen fixation. At least 50 molybdenum enzymes are now known in bacteria and animals and these nitrogenases contain molybdenum in a form different from other molybdenum enzymes, which all contain fully oxidized molybdenum in a molybdenum cofactor. These various molybdenum cofactor enzymes are vital to the organisms, and molybdenum is an element for life in all higher eukaryote organisms. In its pure form, molybdenum is a metal with a Mohs hardness of 5.5. It has a point of 2,623 °C, of the naturally occurring elements, only tantalum, osmium, rhenium, tungsten. Weak oxidation of molybdenum starts at 300 °C and it has one of the lowest coefficients of thermal expansion among commercially used metals. The tensile strength of molybdenum wires increases about 3 times, from about 10 to 30 GPa, there are 35 known isotopes of molybdenum, ranging in atomic mass from 83 to 117, as well as four metastable nuclear isomers. Seven isotopes occur naturally, with masses of 92,94,95,96,97,98. Of these naturally occurring isotopes, only molybdenum-100 is unstable, molybdenum-98 is the most abundant isotope, comprising 24. 14% of all molybdenum. Molybdenum-100 has a half-life of about 1019 y and undergoes double beta decay into ruthenium-100, molybdenum isotopes with mass numbers from 111 to 117 all have half-lives of approximately 150 ns. All unstable isotopes of molybdenum decay into isotopes of niobium, technetium, as also noted below, the most common isotopic molybdenum application involves molybdenum-99, which is a fission product. It is a parent radioisotope to the short-lived gamma-emitting daughter radioisotope technetium-99m, in 2008, the Delft University of Technology applied for a patent on the molybdenum-98-based production of molybdenum-99
22.
Iron
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Iron is a chemical element with symbol Fe and atomic number 26. It is a metal in the first transition series and it is by mass the most common element on Earth, forming much of Earths outer and inner core. It is the fourth most common element in the Earths crust, like the other group 8 elements, ruthenium and osmium, iron exists in a wide range of oxidation states, −2 to +6, although +2 and +3 are the most common. Elemental iron occurs in meteoroids and other low oxygen environments, but is reactive to oxygen, fresh iron surfaces appear lustrous silvery-gray, but oxidize in normal air to give hydrated iron oxides, commonly known as rust. Unlike the metals that form passivating oxide layers, iron oxides occupy more volume than the metal and thus flake off, Iron metal has been used since ancient times, although copper alloys, which have lower melting temperatures, were used even earlier in human history. Pure iron is soft, but is unobtainable by smelting because it is significantly hardened and strengthened by impurities, in particular carbon. A certain proportion of carbon steel, which may be up to 1000 times harder than pure iron. Crude iron metal is produced in blast furnaces, where ore is reduced by coke to pig iron, further refinement with oxygen reduces the carbon content to the correct proportion to make steel. Steels and iron alloys formed with metals are by far the most common industrial metals because they have a great range of desirable properties. Iron chemical compounds have many uses, Iron oxide mixed with aluminium powder can be ignited to create a thermite reaction, used in welding and purifying ores. Iron forms binary compounds with the halogens and the chalcogens, among its organometallic compounds is ferrocene, the first sandwich compound discovered. Iron plays an important role in biology, forming complexes with oxygen in hemoglobin and myoglobin. Iron is also the metal at the site of many important redox enzymes dealing with cellular respiration and oxidation and reduction in plants. A human male of average height has about 4 grams of iron in his body and this iron is distributed throughout the body in hemoglobin, tissues, muscles, bone marrow, blood proteins, enzymes, ferritin, hemosiderin, and transport in plasma. The mechanical properties of iron and its alloys can be evaluated using a variety of tests, including the Brinell test, Rockwell test, the data on iron is so consistent that it is often used to calibrate measurements or to compare tests. An increase in the content will cause a significant increase in the hardness. Maximum hardness of 65 Rc is achieved with a 0. 6% carbon content, because of the softness of iron, it is much easier to work with than its heavier congeners ruthenium and osmium. Because of its significance for planetary cores, the properties of iron at high pressures and temperatures have also been studied extensively
23.
Ferredoxin
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Ferredoxins are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term ferredoxin was coined by D. C, wharton of the DuPont Co. and applied to the iron protein first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum. Another redox protein, isolated from spinach chloroplasts, was termed chloroplast ferredoxin, the chloroplast ferredoxin is involved in both cyclic and non-cyclic photophosphorylation reactions of photosynthesis. In non-cyclic photophosphorylation, ferredoxin is the last electron acceptor thus reducing the enzyme NADP+ reductase and it accepts electrons produced from sunlight-excited chlorophyll and transfers them to the enzyme ferredoxin, NADP+ oxidoreductase EC1.18.1.2. Ferredoxins are small proteins containing iron and sulfur atoms organized as iron-sulfur clusters and these biological capacitors can accept or discharge electrons, with the effect of a change in the oxidation state of the iron atoms between +2 and +3. In this way, ferredoxin acts as a transfer agent in biological redox reactions. Other bioinorganic electron transport systems include rubredoxins, cytochromes, blue copper proteins, ferredoxins can be classified according to the nature of their iron-sulfur clusters and by sequence similarity. Members of the 2Fe-2S ferredoxin family have a core structure consisting of beta-alpha-beta, which includes putidaredoxin, terpredoxin. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated, one group of ferredoxins, originally found in chloroplast membranes, has been termed chloroplast-type or plant-type. Its active center is a cluster, where the atoms are tetrahedrally coordinated both by inorganic sulfur atoms and by sulfurs of four conserved cysteine residues. In hydroxylating bacterial dioxygenase systems, they serve as intermediate electron-transfer carriers between reductase flavoproteins and oxygenase, although the physiological role of this ferredoxin remains unclear, a strong and specific interaction of Cp2FeFd with the molybdenum-iron protein of nitrogenase has been revealed. Homologous ferredoxins from Azotobacter vinelandii and Aquifex aeolicus have been characterized, the crystal structure of AaFd has been solved. The structure of AaFd monomer is different from other Fe2S2 ferredoxins, the fold belongs to the α+β class, with first four β-strands and two α-helices adopting a variant of the thioredoxin fold. Adrenodoxin is expressed in mammals including humans, the human variant of adrenodoxin is referred to as ferredoxin 1. Adrenodoxin, putidaredoxin, and terpredoxin are soluble Fe2S2 proteins that act as electron carriers. In mitochondrial monooxygenase systems, adrenodoxin transfers an electron from NADPH, in bacteria, putidaredoxin and terpredoxin serve as electron carriers between corresponding NADH-dependent ferredoxin reductases and soluble P450s. The exact functions of members of this family are not known. Despite low sequence similarity between adrenodoxin-type and plant-type ferredoxins, the two classes have a similar folding topology, ferredoxin-1 in humans participates in the synthesis of thyroid hormones
24.
Transition metal oxo complex
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In coordination chemistry, an oxo ligand is an oxygen atom bound only to one or more metal centers. These ligands can exist as terminal or as bridging atom, oxo ligands stabilize high oxidation states of a metal. Oxo ligands are pervasive, comprising the majority of the Earths crust. This article concerns a subset of oxides, molecular derivatives and they are also found in several metalloenzymes, e. g. in the molybdenum cofactor and in many iron-containing enzymes. One of the earliest synthetic compounds to incorporate an oxo ligand is sodium ferrate circa 1702, common reactions affected by metal-oxo compounds is olation, the condensation process that converts low molecular weight oxides to polymeric materials, including minerals. Olation often begins with the deprotonation of a metal-hydroxo complex, oxygen-atom transfer is common reaction of particular interest in organic chemistry and biochemistry. Some metal-oxos are capable of transferring their oxo ligand to organic substrates, one such example of this type of reactivity is from and enzyme super-family Molybdenum oxotransferase. Transition metal-oxos are also capable of abstracting strong C–H, N–H, cytochrome P450 contains a high-valent iron-oxo which is capable of abstracting hydrogen atoms from strong C–H bonds. Some of the longest known and most widely used oxo compounds are oxidizing agents such as potassium permanganate, compounds such as these are widely used for converting alkenes to vicinal diols and alcohols to ketones or carboxylic acids. More selective or gentler oxidizing reagents include pyridinium chlorochromate and pyridinium dichromate, metal oxo species are capable of catalytic, including asymmetric oxidations of various types. Some metal-oxo complexes promote C-H bond activation, converting hydrocarbons to alcohols, iron-oxo compounds are intermediates in many oxidations catalysed by heme-containing enzymes. Similarly, methane monooxygenase oxidizes methane to methanol via oxygen atom transfer from an intermediate at its non-heme di-iron center. First, C-H bonds are resistant to oxidation and are generally unreactive at moderate temperatures. The oxidant used in these reactions is molecular oxygen in contrast with the harsh. As is generally the case with enzymatic reactions, these oxidations are chemically selective, much of the effort in producing synthetic C-H bond activation catalysts has been inspired by these well designed natural catalysts. The oxo ligand is nearly ubiquitous in molybdenum and tungsten chemistry, appearing in the ores containing these elements, throughout their synthetic chemistry, the biologically transported species and starting point for biosynthesis is generally accepted to be oxometallates MoO4−2 or WO4−2. All Mo/W enzymes, again except nitrogenase, are bound to one or more molybdopterin prosthetic group, the Mo/W centers generally cycle between hexavalent and tetravalent states. Although there is variation among these enzymes, members from all three families involve oxygen atom transfer between the Mo/W center and the substrate
25.
Hydroxide
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Hydroxide is a diatomic anion with chemical formula OH−. It consists of an oxygen and hydrogen atom held together by a covalent bond and it is an important but usually minor constituent of water. It functions as a base, a ligand, a nucleophile, the hydroxide ion forms salts, some of which dissociate in aqueous solution, liberating solvated hydroxide ions. Sodium hydroxide is a multi-million-ton per annum commodity chemical, a hydroxide attached to a strongly electropositive center may itself ionize, liberating a hydrogen cation, making the parent compound an acid. The corresponding electrically neutral compound •HO is the hydroxyl radical, the corresponding covalently-bound group –OH of atoms is the hydroxyl group. Hydroxide ion and hydroxyl group are nucleophiles and can act as a catalyst in organic chemistry, many inorganic substances which bear the word hydroxide in their names are not ionic compounds of the hydroxide ion, but covalent compounds which contain hydroxyl groups. The pH of a solution is equal to the decimal cologarithm of the cation concentration. The concentration of ions can be expressed in terms of pOH. Addition of a base to water will reduce the hydrogen cation concentration, POH can be kept at a nearly constant value with various buffer solutions. In aqueous solution the hydroxide ion is a base in the Brønsted–Lowry sense as it can accept a proton from a Brønsted–Lowry acid to form a water molecule and it can also act as a Lewis base by donating a pair of electrons to a Lewis acid. In aqueous solution both hydrogen and hydroxide ions are solvated, with hydrogen bonds between oxygen and hydrogen atoms. Indeed, the bihydroxide ion H 3O−2 has been characterized in the solid state and this compound is centrosymmetric and has a very short hydrogen bond that is similar to the length in the bifluoride ion HF−2. In aqueous solution the hydroxide ion forms strong bonds with water molecules. A consequence of this is that concentrated solutions of sodium hydroxide have high viscosity due to the formation of a network of hydrogen bonds as in hydrogen fluoride solutions. In solution, exposed to air, the ion reacts rapidly with atmospheric carbon dioxide, acting as an acid, to form, initially. OH− + CO2 ⇌ HCO−3 The equilibrium constant for this reaction can be specified either as a reaction with dissolved carbon dioxide or as a reaction with carbon dioxide gas. At neutral or acid pH, the reaction is slow, but is catalyzed by the carbonic anhydrase. Solutions containing the hydroxide ion attack glass, in this case, the silicates in glass are acting as acids
26.
Serum (blood)
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In blood, the serum is the component that is neither a blood cell nor a clotting factor, it is the blood plasma not including the fibrinogens. Serum includes all proteins not used in blood clotting and all the electrolytes, antibodies, antigens, hormones, the study of serum is serology, which may also include proteomics. Serum is used in diagnostic tests, as well as blood typing. Blood is centrifuged to remove cellular components, anti-coagulated blood yields plasma containing fibrinogen and clotting factors. Coagulated blood yields serum without fibrinogen, although some clotting factors remain, serum is an essential factor for the self-renewal of embryonic stem cells in combination with the cytokine leukemia inhibitory factor. Such convalescent serum is a form of immunotherapy, blood serum and plasma are one the largest source of biomarkers, whether for diagnostics or therapeutics. For analysis of biomarkers in blood samples, it is possible to do a pre-separation by free-flow electrophoresis that usually consists of a depletion of serum albumin protein. This method enables greater penetration of the proteome via separation of a variety of charged or chargeable analytes. Like many other nouns, the word serum can be pluralized when used in certain senses. To speak of multiple serum specimens from people, physicians sometimes speak of sera
27.
Metabolic pathway
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In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of a reaction are known as metabolites. In a metabolic pathway, the product of one acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function, different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the citric cycle, electron transport chain. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell, the two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the pathway, which can be either catabolic or anabolic based on the need for or the availability of energy. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use, metabolic pathways are often considered to flow in one direction. Although all chemical reactions are reversible, conditions in the cell are often such that it is thermodynamically more favorable for flux to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of an amino acid. One example of an exception to rule is the metabolism of glucose. Glycolysis results in the breakdown of glucose, but several reactions in the pathway are reversible. Glycolysis was the first metabolic pathway discovered, As glucose enters a cell, metabolic pathways are often regulated by feedback inhibition. Some metabolic pathways flow in a cycle wherein each component of the cycle is a substrate for the subsequent reaction in the cycle, the net reaction is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products. A catabolic pathway is a system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats. The end products are carbon dioxide, water, and ammonia. Coupled with an reaction of anabolism, the cell can synthesize new macromolecules using the original precursors of the anabolic pathway
. PMID 11005854.
