1.
Lysosome
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A lysosome is a membrane-bound organelle found in nearly all animal cells. They are spherical vesicles which contain hydrolytic enzymes that can break down all kinds of biomolecules. Simply stated, a lysosome is a type of vesicle with specific composition, the lumens pH is optimal for the enzymes involved in hydrolysis, analogous to the activity of the stomach. Besides degradation of polymers, the lysosome is involved in cell processes, including secretion, plasma membrane repair, cell signaling. The lysosomes also act as the disposal system of the cell by digesting unwanted materials in the cytoplasm. Material from the outside of the cell is taken-up through endocytosis and their sizes can be very different—the biggest ones can be more than 10 times bigger than the smallest ones. They were discovered and named by Belgian biologist Christian de Duve, lysosomes are known to contain more than 60 different enzymes. Enzymes of the lysosomes are synthesised in the endoplasmic reticulum. The enzymes are imported from the Golgi apparatus in small vesicles, enzymes destined for a lysosome are specifically tagged with the molecule mannose 6-phosphate, so that they are properly sorted into acidified vesicles. Synthesis of lysosomal enzymes is controlled by nuclear genes, mutations in the genes for these enzymes are responsible for more than 30 different human genetic diseases, which are collectively known as lysosomal storage diseases. These diseases result from an accumulation of specific substrates, due to the inability to break them down and these genetic defects are related to several neurodegenerative disorders, cancer, cardiovascular diseases, and ageing-related diseases. By 1949, he and his team had focused on the enzyme called glucose 6-phosphatase, which is the first crucial enzyme in sugar metabolism and they already suspected that this enzyme played a key role in regulating blood sugar levels. However, even after a series of experiments, they failed to purify, therefore, they tried a more arduous procedure of cell fractionation, by which cellular components are separated based on their sizes using centrifugation. They succeeded in detecting the activity from the microsomal fraction. This was the step in the serendipitous discovery of lysosomes. To estimate this enzyme activity, they used that of standardised enzyme acid phosphatase, one day, the enzyme activity of purified cell fractions which had been refrigerated for five days was measured. Surprisingly, the activity was increased to normal of that of the fresh sample. They described this membrane-like barrier as a saclike structure surrounded by a membrane, Novikoff from the University of Vermont visited de Duve´s laboratory, and successfully obtained the first electron micrographs of the new organelle
2.
Methylene blue
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Methylene blue, also known as methylthioninium chloride, is a medication and dye. As a medication it is used to treat methemoglobinemia. Specifically it is used to treat methemoglobinemia levels that are greater than 30% or in which there are symptoms despite oxygen therapy and it has previously been used for cyanide poisoning and urinary tract infections but this use is no longer recommended. It is typically given by injection into a vein, common side effects include headache, vomiting, confusion, shortness of breath, and high blood pressure. Other side effects include serotonin syndrome, red blood cell breakdown, use often turns the urine, sweat, and stool blue to green in color. While use during pregnancy may harm the baby, not using in methemoglobinemia is likely more dangerous, Methylene blue is a thiazine dye. It works by converting the ferric iron in hemoglobin to ferrous iron, Methylene blue was first prepared in 1876 by Heinrich Caro. It is on the World Health Organizations List of Essential Medicines, in the United States a 50 mg vial costs about 191.40 USD. In the United Kingdom a 50 mg vial costs the NHS about 39.38 pounds, while many texts indicate that methylene blue has oxidizing agent properties, its effects as an oxidizing agent occur only at very high doses. At pharmacologic doses it has reducing agent properties and it is owing to this reason that methylene blue is employed as a medication for the treatment of methemoglobinemia. This can arise from ingestion of certain pharmaceuticals, toxins, or broad beans, normally, through the NADH or NADPH dependent methemoglobin reductase enzymes, methemoglobin is reduced back to hemoglobin. When large amounts of methemoglobin occur secondary to toxins, methemoglobin reductases are overwhelmed, Methylene blue, when injected intravenously as an antidote, is itself first reduced to leucomethylene blue, which then reduces the heme group from methemoglobin to hemoglobin. Methylene blue can reduce the life of methemoglobin from hours to minutes. At high doses, however, methylene blue actually induces methemoglobinemia, Matilda Moldenhauer Brooks in San Francisco, although first demonstrated by Bo Sahlin of Lund University, in 1926. Methylene blue is used in endoscopic polypectomy as an adjunct to saline or epinephrine, Methylene blue is also used as a dye in chromoendoscopy, and is sprayed onto the mucosa of the gastrointestinal tract in order to identify dysplasia, or pre-cancerous lesions. Intravenously injected methylene blue is readily released into the urine and thus can be used to test the urinary tract for leaks or fistulas, in surgeries such as sentinel lymph node dissections, methylene blue can be used to visually trace the lymphatic drainage of pertinent tissues. Similarly, methylene blue is added to bone cement in orthopedic operations to provide easy discrimination between native bone and cement, additionally, methylene blue accelerates the hardening of bone cement, increasing the speed at which bone cement can be effectively applied. Methylene blue is used as an aid to visualisation/orientation in a number of devices, including a Surgical sealant film
3.
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
4.
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
5.
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
6.
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
7.
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
8.
GeneCards
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GeneCards is a database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. It is being developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science and this database aims at providing a quick overview of the current available biomedical information about the searched gene, including the human genes, the encoded proteins, and the relevant diseases. The GeneCards database provides access to free Web resources about more than 7000 all known human genes that integrated from >90 data resources, such as HGNC, Ensembl, the core gene list is based on approved gene symbols published by the HUGO Gene Nomenclature Committee. The information are carefully gathered and selected from these databases by the powerful, over time, the GeneCards database has developed a suite of tools that has more specialised capability. Since 1998, the GeneCards database has been used by bioinformatics, genomics. Since the 1980s, sequence information has become abundant, many laboratories realized this. However, the information provided by the sequence databases focus on different aspect. To gather these scattered data, The Weizmann Institute of Science Crown Human Genome Centre developed a database called ‘GeneCards’ in 1997 and this database mainly deals with the human genome information, human genes, the encoded proteins’ functions, and the related diseases. At first, it includes two main features, the function to get integrated biomedical information about certain gene in ‘card’ format. Currently, the version 3 gather information from more than 90 database resources based on a consolidated gene list and it has developed a set of GeneCards suit, which are focus one more specific purposes. Nearly every 3 years life cycle, a new planning phase for subsequent revision will start, including implementation, development and semi-automated quality assurance, and deployment. Technologies used include Eclipse, Apache, Perl, XML, PHP, Propel, Java, R and MySQL. genecards. org/, annotation combinatory, Using GeneDecks, one can get a set of similar genes for a particular gene with a selected combinatorial annotation. The summary table result in ranking the different level of similarity between the genes and the probe gene. Annotation unification, Different data source often offer annotations with heterogeneous naming system, annotation unification of GeneDecks is based on the similarity in GeneCards gene-content space detection algorithms. Partner hunting, In GeneDecks’s Partner Hunter, users give a query gene, Set distillation, In Set distiller, users give a set of genes, and the system ranks attributes by their degree of sharing within a given gene set. GeneALaCart is a gene-set-orientated batch-querying engine based on the popular GeneCards database and it allows retrieval of information about multiple genes in a batch query. The GeneLoc suit member presents a human chromosome map, which is very important for designing a custom-made capture chip. GeneLoc includes further links to GeneCards, NCBIs Human Genome Sequencing, UniGene, firstly, enter what you want to search into the blank on the homepages
9.
Chromosome
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A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
10.
Chromosome 12 (human)
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Chromosome 12 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome, chromosome 12 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 66%, with one estimate giving 2,521 genes, and the other estimate giving 1,676 genes. Chromosome 12 contains the Homeobox C gene cluster
11.
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
12.
Base pair
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A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
13.
Gene expression
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Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are proteins, but in non-protein coding genes such as transfer RNA or small nuclear RNA genes. The process of gene expression is used by all known life—eukaryotes, prokaryotes, several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for differentiation, morphogenesis. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, the genetic code stored in DNA is interpreted by gene expression, and the properties of the expression give rise to the organisms phenotype. Such phenotypes are expressed by the synthesis of proteins that control the organisms shape. Regulation of gene expression is critical to an organisms development. A gene is a stretch of DNA that encodes information, genomic DNA consists of two antiparallel and reverse complementary strands, each having 5 and 3 ends. This RNA is complementary to the template 3 →5 DNA strand, therefore, the resulting 5 →3 RNA strand is identical to the coding DNA strand with the exception that thymines are replaced with uracils in the RNA. A coding DNA strand reading ATG is indirectly transcribed through the non-coding strand as AUG in RNA, in prokaryotes, transcription is carried out by a single type of RNA polymerase, which needs a DNA sequence called a Pribnow box as well as a sigma factor to start transcription. RNA polymerase I is responsible for transcription of ribosomal RNA genes, RNA polymerase II transcribes all protein-coding genes but also some non-coding RNAs. Pol II includes a C-terminal domain that is rich in serine residues, when these residues are phosphorylated, the CTD binds to various protein factors that promote transcript maturation and modification. RNA polymerase III transcribes 5S rRNA, transfer RNA genes, transcription ends when the polymerase encounters a sequence called the terminator. These include 5 capping, which is set of reactions that add 7-methylguanosine to the 5 end of pre-mRNA. The m7G cap is then bound by cap binding complex heterodimer, another modification is 3 cleavage and polyadenylation. They occur if polyadenylation signal sequence is present in pre-mRNA, which is usually between protein-coding sequence and terminator, the pre-mRNA is first cleaved and then a series of ~200 adenines are added to form poly tail, which protects the RNA from degradation. Poly tail is bound by multiple poly-binding proteins necessary for mRNA export, a very important modification of eukaryotic pre-mRNA is RNA splicing. The majority of eukaryotic pre-mRNAs consist of alternating segments called exons and introns, in certain cases, some introns or exons can be either removed or retained in mature mRNA
14.
Homology (biology)
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In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor, examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Sequence homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either an event or a duplication event. Homology among proteins or DNA is inferred from their sequence similarity, significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions, the word homology, coined in about 1656, derives from the Greek ὁμόλογος homologos from ὁμός homos same and λόγος logos relation. Homology is the relationship between biological structures or sequences that are derived from a common ancestor, for example, many insects possess two pairs of flying wings. In beetles, the first pair of wings has evolved into a pair of hard wing covers, the same major forearm bones are found in fossils of lobe-finned fish such as Eusthenopteron. The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not present in their last common ancestor but rather evolved separately. For example, the wings of insects and birds evolved independently in widely separated groups, similarly, the wings of a sycamore maple seed and the wings of a bird are analogous but not homologous, as they develop from quite different structures. A structure can be homologous at one level, but only analogous at another, for example, in the pterosaurs, the wing involves both the forelimb and the hindlimb. Analogy is called homoplasy in cladistics, and convergent or parallel evolution in evolutionary biology, specialised terms are used in taxonomic research. Primary homology is that initially conjectured by a researcher based on similar structure or anatomical connections, secondary homology is implied by parsimony analysis, where a character that only occurs once on a tree is taken to be homologous. As implied in this definition, many cladists consider homology to be synonymous with synapomorphy, homologies provide the fundamental basis for all biological classification, although some may be highly counter-intuitive. The homologies between these have been discovered by comparing genes in evolutionary developmental biology, among insects, the stinger of the female honey bee is a modified ovipositor, homologous with ovipositors in other insects such as the Orthoptera, Hemiptera, and those Hymenoptera without stingers. The three small bones in the ear of mammals including humans, the malleus, incus. The malleus and incus develop in the embryo from structures that form jaw bones in lizards, both lines of evidence show that these bones are homologous, sharing a common ancestor. Among the many homologies in mammal reproductive systems, ovaries and testicles are homologous, in many plants, defensive or storage structures are made by modifications of the development of primary leaves, stems, and roots
15.
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
16.
Ensembl genome database project
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Ensembl is one of several well known genome browsers for the retrieval of genomic information. Similar databases and browsers are found at NCBI and the University of California, the human genome consists of three billion base pairs, which code for approximately 20, 000–25,000 genes. However the genome alone is of use, unless the locations. One option is manual annotation, whereby a team of scientists tries to locate genes using experimental data from scientific journals, however this is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers to do the complex pattern-matching of protein to DNA. In the Ensembl project, sequence data are fed into the gene annotation system which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis, Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, in addition, the Ensembl website provides computer-generated visual displays of much of the data. Over time the project has expanded to additional species as well as a wider range of genomic data, including genetic variations. Central to the Ensembl concept is the ability to automatically generate graphical views of the alignment of genes and these are shown as data tracks, and individual tracks can be turned on and off, allowing the user to customise the display to suit their research interests. The interface also enables the user to zoom in to a region or move along the genome in either direction, the graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA. Externally produced data can also be added to the display, either via a DAS server on the internet, or by uploading a file in one of the supported formats, such as BAM, BED. Graphics are generated using a suite of custom Perl modules based on GD, in addition to its website, Ensembl provides a Perl API that models biological objects such as genes and proteins, allowing simple scripts to be written to retrieve data of interest. The same API is used internally by the web interface to display the data and it is divided in sections like the core API, the compara API, the variation API, and the functional genomics API. The Ensembl website provides information on how to install and use the API. This software can be used to access the public MySQL database, the users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema. Large datasets can be retrieved using the BioMart data-mining tool and it provides a web interface for downloading datasets using complex queries. Last, there is an FTP server which can be used to download entire MySQL databases as some selected data sets in other formats. The annotated genomes include most fully sequenced vertebrates and selected model organisms, all of them are eukaryotes, there are no prokaryotes
17.
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
18.
Wikidata
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Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a source of data which can be used by Wikimedia projects such as Wikipedia. This is similar to the way Wikimedia Commons provides storage for files and access to those files for all Wikimedia projects. Wikidata is powered by the software Wikibase, Wikidata is a document-oriented database, focused on items. Each item represents a topic and is identified by a number, prefixed with the letter Q—for example. This enables the basic information required to identify the topic the item covers to be translated without favouring any language, information is added to items by creating statements. Statements take the form of pairs, with each statement consisting of a property. The creation of the project was funded by donations from the Allen Institute for Artificial Intelligence, the Gordon and Betty Moore Foundation, at this time, only the first phase was available. Historically, a Wikipedia article would include a list of links, being links to articles on the same topic in other editions of Wikipedia. Initially, Wikidata was a repository of interlanguage links. No Wikipedia language editions were able to access Wikidata, so they needed to continue to maintain their own lists of interlanguage links, on 14 January 2013, the Hungarian Wikipedia became the first to enable the provision of interlanguage links via Wikidata. This functionality was extended to the Hebrew and Italian Wikipedias on 30 January, to the English Wikipedia on 13 February, on 23 September 2013, phase 1 went live on Wikimedia Commons. The first aspects of the second phase were deployed on 4 February 2013, the values were initially limited to two data types, with more data types to follow later. The first new type, string, was deployed on 6 March, the ability of the various language editions of Wikipedia to access data added to Wikidata as part of phase two was rolled out progressively between 27 March and 25 April 2013. On 16 September 2015, Wikidata began allowing so-called arbitrary access, for example, in the past the article about Berlin you could not access data about Germany, but with arbitrary access it could. On 27 April 2016 arbitrary access was activated on Wikimedia Commons, phase 3 will involve database querying and the creation of lists based on data stored on Wikidata. As of October 2016 two tools for querying Wikidata were available, AutoList and PetScan, additionally to a public SPARQL endpoint, there is concern that the project is being influenced by lobbying companies, PR professionals and search engine optimizers. As of December 2015, according to Wikimedia statistics, half of the information in Wikidata is unsourced, another 30% is labeled as having come from Wikipedia, but with no indication as to which article
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Antimicrobial
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An antimicrobial is an agent that kills microorganisms or stop their growth. Antimicrobial medicines can be grouped according to the microorganisms they act primarily against, for example, antibiotics are used against bacteria and antifungals are used against fungi. They can also be classified according to their function, agents that kill microbes are called microbicidal, while those that merely inhibit their growth are called biostatic. The use of medicines to treat infection is known as antimicrobial chemotherapy. The main classes of agents are disinfectants, which kill a wide range of microbes on non-living surfaces to prevent the spread of illness, antiseptics. The term antibiotic originally described only those formulations derived from living organisms but is now applied to synthetic antimicrobials, such as the sulphonamides. The term also used to be restricted to antibacterials, but its context has broadened to include all antimicrobials, antibacterial agents can be further subdivided into bactericidal agents, which kill bacteria, and bacteriostatic agents, which slow down or stall bacterial growth. In response, further advancements in technologies have resulted in solutions that can go beyond simply inhibiting microbial growth. Instead, certain types of media have been developed to kill microbes on contact. Use of substances with antimicrobial properties is known to have been common practice for at least 2000 years, ancient Egyptians and ancient Greeks used specific molds and plant extracts to treat infection. More recently, microbiologists such as Louis Pasteur and Jules Francois Joubert observed antagonism between some bacteria and discussed the merits of controlling these interactions in medicine, in 1928, Alexander Fleming became the first to discover a natural antimicrobial fungus known as Penicillium rubens. The substance extracted from the fungus he named penicillin and in 1942 it was used to treat a Streptococcus infection. Penicillin also proved successful in the treatment of other infectious diseases such as gonorrhea, strep throat and pneumonia. Many antimicrobial agents exist, for use against a range of infectious diseases. Antibacterials are used to treat bacterial infections, the toxicity to humans and other animals from antibacterials is generally considered low. However, prolonged use of certain antibacterials can decrease the number of gut flora, after prolonged antibacterial use consumption of probiotics and reasonable eating can help to replace destroyed gut flora. Stool transplants may be considered for patients who are having difficulty recovering from prolonged antibiotic treatment, the discovery, development and clinical use of antibacterials during the 20th century has substantially reduced mortality from bacterial infections. However, since 1980 the introduction of new agents for clinical use has declined
20.
Innate immune system
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The cells of the innate system recognize and respond to pathogens in a generic way, but, unlike the adaptive immune system, the system does not provide long-lasting immunity to the host. Innate immune systems provide immediate defense against infection, and are found in all classes of plant, the innate immune system is an evolutionarily older defense strategy, and is the dominant immune system found in plants, fungi, insects, and primitive multicellular organisms. Anatomical barriers include physical, chemical and biological barriers, the epithelial surfaces form a physical barrier that is impermeable to most infectious agents, acting as the first line of defense against invading organisms. Desquamation of skin also helps remove bacteria and other infectious agents that have adhered to the epithelial surfaces. Lack of blood vessels and inability of the epidermis to retain moisture, in the gastrointestinal and respiratory tract, movement due to peristalsis or cilia, respectively, helps remove infectious agents. The gut flora can prevent the colonization of pathogenic bacteria by secreting toxic substances or by competing with pathogenic bacteria for nutrients or attachment to cell surfaces, the flushing action of tears and saliva helps prevent infection of the eyes and mouth. Inflammation is one of the first responses of the system to infection or irritation. The process of inflammation is initiated by cells already present in all tissues, mainly resident macrophages, dendritic cells, histiocytes, Kupffer cells. At the onset of an infection, burn, or other injuries, chemical factors produced during inflammation sensitize pain receptors, cause local vasodilation of the blood vessels, and attract phagocytes, especially neutrophils. Neutrophils then trigger other parts of the system by releasing factors that summon additional leukocytes and lymphocytes. Cytokines produced by macrophages and other cells of the immune system mediate the inflammatory response. These cytokines include TNF, HMGB1, and IL-1, the complement system is a biochemical cascade of the immune system that helps, or “complements”, the ability of antibodies to clear pathogens or mark them for destruction by other cells. The cascade is composed of plasma proteins, synthesized in the liver. Elements of the complement cascade can be found in many species including plants, birds, fish. All white blood cells are known as leukocytes, leukocytes are able to move freely and interact with and capture cellular debris, foreign particles, and invading microorganisms. Unlike many other cells in the body, most innate immune leukocytes cannot divide or reproduce on their own, mast cells are a type of innate immune cell that reside in connective tissue and in the mucous membranes. They are intimately associated with healing and defense against pathogens. When activated, mast cells rapidly release characteristic granules, rich in histamine and heparin, along with various hormonal mediators and chemokines, histamine dilates blood vessels, causing the characteristic signs of inflammation, and recruits neutrophils and macrophages
21.
Glycoside hydrolase
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Glycoside hydrolases assist in the hydrolysis of glycosidic bonds in complex sugars. Together with glycosyltransferases, glycosidases form the catalytic machinery for the synthesis. Glycoside hydrolases are found in all domains of life. In prokaryotes, they are both as intracellular and extracellular enzymes that are largely involved in nutrient acquisition. One of the important occurrences of glycoside hydrolases in bacteria is the enzyme beta-galactosidase, deficiency in specific lysosomal glycoside hydrolases can lead to a range of lysosomal storage disorders that result in developmental problems or death. Glycoside hydrolases are found in the tract and in saliva where they degrade complex carbohydrates such as lactose, starch. In the gut they are found as glycosylphosphatidyl anchored enzymes on endothelial cells, the enzyme O-GlcNAcase is involved in removal of N-acetylglucosamine groups from serine and threonine residues in the cytoplasm and nucleus of the cell. The glycoside hydrolases are involved in the biosynthesis and degradation of glycogen in the body, glycoside hydrolases are classified into EC3.2.1 as enzymes catalyzing the hydrolysis of O- or S-glycosides. Glycoside hydrolases can also be classified according to the outcome of the hydrolysis reaction. Glycoside hydrolases can also be classified as exo or endo acting, dependent upon whether they act at the end or in the middle, respectively, glycoside hydrolases may also be classified by sequence or structure based methods. Sequence-based classifications are among the most powerful method for suggesting function for newly sequenced enzymes for which function has not been biochemically demonstrated. A classification system for glycosyl hydrolases, based on similarity, has led to the definition of more than 100 different families. This classification is available on the CAZy web site, the database provides a series of regularly updated sequence based classification that allow reliable prediction of mechanism, active site residues and possible substrates. The online database is supported by CAZypedia, an encyclopedia of carbohydrate active enzymes. Based on three-dimensional structural similarities, the families have been classified into clans of related structure. Recent progress in glycosidase sequence analysis and 3D structure comparison has allowed the proposal of a hierarchical classification of the glycoside hydrolases. Again, two residues are involved, which are usually enzyme-borne carboxylates, one acts as a nucleophile and the other as an acid/base. In the first step the nucleophile attacks the centre, resulting in the formation of a glycosyl enzyme intermediate
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Hydrolysis
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Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, generally, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt also dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid. In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households. In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
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N-Acetylmuramic acid
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N-Acetylmuramic acid, or MurNAc, is the ether of lactic acid and N-acetylglucosamine with a chemical formula of C11H19NO8. This layered structure is called peptidoglycan, MurNAc is a monosaccharide derivative of N-acetylglucosamine. N-Acetylmuramic acid is part of the polymer of Gram-positive bacterial cell walls. MURNAc is covalently linked to N-acetylglucosamine and may also be linked through the hydroxyl on carbon number 4 to the carbon of L-alanine, a pentapeptide composed of L-alanyl-d--isoglutaminyl-L-lysyl-D-alanine-D-alanine is added to the MURNAc in the process of making the peptidoglycan strands of the cell wall
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N-Acetylglucosamine
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N-Acetylglucosamine is a monosaccharide and a derivative of glucose. It is an amide between glucosamine and acetic acid and it has a molecular formula of C8H15NO6, a molar mass of 221.21 g/mol, and it is significant in several biological systems. It is part of a biopolymer in the cell wall, built from alternating units of GlcNAc and N-acetylmuramic acid. This layered structure is called peptidoglycan, GlcNAc is the monomeric unit of the polymer chitin, which forms the outer coverings of insects and crustaceans. It is the component of the radulas of mollusks, the beaks of cephalopods. Polymerized with glucuronic acid, it forms hyaluronan, GlcNAc has been reported to be an inhibitor of elastase release from human polymorphonuclear leukocytes, however this is much weaker than the inhibition seen with N-acetylgalactosamine. It has been proposed as a treatment for diseases. Keratan sulfate Chitin N-Acetyllactosamine synthase N-Acetylgalactosamine Wheat germ agglutinin, a plant lectin that binds to this substrate Re Multiple Sclerosis
25.
Peptidoglycan
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Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine, attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a role in the bacterial cell wall, giving structural strength. Peptidoglycan is also involved in binary fission during bacterial cell reproduction, the peptidoglycan layer is substantially thicker in gram-positive bacteria than in gram-negative bacteria, with the attachment of the S-layer. Peptidoglycan forms around 90% of the dry weight of gram-positive bacteria, thus, presence of high levels of peptidoglycan is the primary determinant of the characterisation of bacteria as gram-positive. In gram-positive strains, it is important in attachment roles and serotyping purposes, for both gram-positive and gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. The peptidoglycan layer in the cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine and N-acetylmuramic acid. The alternating sugars are connected by a β--glycosidic bond, peptidoglycan is one of the most important sources of D-amino acids in nature. Cross-linking between amino acids in different linear amino sugar chains occurs with the help of the enzyme DD-transpeptidase and results in a 3-dimensional structure that is strong, the specific amino acid sequence and molecular structure vary with the bacterial species. The peptidoglycan monomers are synthesized in the cytosol and are attached to a membrane carrier bactoprenol. Bactoprenol transports peptidoglycan monomers across the membrane where they are inserted into the existing peptidoglycan. In the first step of peptidoglycan synthesis, the glutamine, which is an acid, donates an amino group to a sugar. This turns fructose 6-phosphate into glucosamine-6-phosphate, in step two, an acetyl group is transferred from acetyl CoA to the amino group on the glucosamine-6-phosphate creating N-acetyl-glucosamine-6-phosphate. In step three of the process, the N-acetyl-glucosamine-6-phosphate is isomerized, which will change N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate. In step 4, the N-acetyl-glucosamine-1-phosphate, which is now a monophosphate, uridine triphosphate, which is a pyrimidine nucleotide, has the ability to act as an energy source. In this particular reaction, after the monophosphate has attacked the UTP and this initial stage, is used to create the precursor for the NAG in peptidoglycan. In step 5, some of the UDP-N-acetylglucosamine is converted to UDP-MurNAc by the addition of a group to the glucosamine
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Gram-positive bacteria
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Gram-positive bacteria are bacteria that give a positive result in the Gram stain test. Gram-positive bacteria take up the crystal violet stain used in the test and this is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test. Their peptidoglycan layer is thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain. Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to antibiotics than gram-negative, peptidoglycan chains are cross-linked to form rigid cell walls by a bacterial enzyme DD-transpeptidase. A much smaller volume of periplasm than that in gram-negative bacteria, only some species have a capsule usually consisting of polysaccharides. Also only some species are flagellates, and when they do have flagella they only have two basal body rings to support them, both gram-positive and gram-negative bacteria commonly have a surface layer called an S-layer. In gram-positive bacteria, the S-layer is attached to the peptidoglycan layer, specific to gram-positive bacteria is the presence of teichoic acids in the cell wall. Some of these are lipoteichoic acids, which have a component in the cell membrane that can assist in anchoring the peptidoglycan. Along with cell shape, Gram staining is a method used to differentiate bacterial species. Historically, the kingdom Monera was divided into four divisions based primarily on Gram staining, based on molecular studies of the 16S sequences, Woese recognised twelve bacterial phyla. Two of these were both gram-positive and were divided on the proportion of the guanine and cytosine content in their DNA, the high G + C phylum was made up of the Actinobacteria and the low G + C phylum contained the Firmicutes. The Actinobacteria include the Corynebacterium, Mycobacterium, Nocardia and Streptomyces genera, the Firmicutes, have a 45–60% GC content, but this is lower than that of the Actinobacteria. The gram-positive and gram-negative staining response is not a reliable characteristic as these two kinds of bacteria do not form phylogenetic coherent groups. All gram-positive bacteria are bounded by a lipid membrane, and, in general. For the bacterial cells bounded by a cell membrane, the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes defines a new compartment in these cells and these bacteria have been designated as diderm bacteria. The distinction between the monoderm and diderm bacteria is supported by conserved signature indels in a number of important proteins, of these two structurally distinct groups of bacteria, monoderms are indicated to be ancestral. In general, gram-positive bacteria are monoderms and have a lipid bilayer whereas gram-negative bacteria are diderms and have two bilayers
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Secretion
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Secretion is the movement of material from one point to another, e. g. secreted chemical substance from a cell or gland. In contrast, excretion, is the removal of certain substances or waste products from a cell or organism, the classical mechanism of cell secretion is via secretory portals at the cell plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structure at the plasma membrane. Secretion in bacterial species means the transport or translocation of molecules for example, proteins. Secretion is an important mechanism in bacterial functioning and operation in their natural surrounding environment for adaptation. Eukaryotic cells, including human cells, have a highly evolved process of secretion, proteins targeted for the outside are synthesized by ribosomes docked to the rough endoplasmic reticulum. As they are synthesized, these proteins translocate into the ER lumen, where they are glycosylated, misfolded proteins are usually identified here and retrotranslocated by ER-associated degradation to the cytosol, where they are degraded by a proteasome. The vesicles containing the properly folded proteins then enter the Golgi apparatus, in the Golgi apparatus, the glycosylation of the proteins is modified and further posttranslational modifications, including cleavage and functionalization, may occur. The proteins are then moved into secretory vesicles which travel along the cytoskeleton to the edge of the cell, more modification can occur in the secretory vesicles. Eventually, there is vesicle fusion with the membrane at a structure called the porosome, in a process called exocytosis. Strict biochemical control is maintained over this sequence by usage of a pH gradient, the pH of the cytosol is 7.4, the ERs pH is 7.0, and the cis-golgi has a pH of 6.5. Secretory vesicles have pHs ranging between 5.0 and 6.0, some secretory vesicles evolve into lysosomes, which have a pH of 4.8, there are many proteins like FGF1, FGF2, interleukin-1 etc. which do not have a signal sequence. They do not use the classical ER-golgi pathway and these are secreted through various nonclassical pathways. At least four nonclassical protein secretion pathways have been described, many human cell types have the ability to be secretory cells. They have a well-developed endoplasmic reticulum and Golgi apparatus to fulfill their function, meibomian glands in the eyelid secrete sebum to lubricate and protect the eye. Secretion is not unique to eukaryotes alone, it is present in bacteria, ATP binding cassette type transporters are common to all the three domains of life. Some secreted proteins are translocated across the membrane by the Sec translocon. Others are translocated across the membrane by the twin-arginine translocation pathway
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Tears
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Tearing, lacrimation, or lachrymation is the secretion of tears, which often serves to clean and lubricate the eyes in response to an irritation of the eyes. Tears formed through crying are associated with strong emotions, such as sorrow, elation, love, awe. Laughing or yawning may also lead to the production of tears, eyes with thin tear film will dry out while wearing contact lenses. Special eye drops are available for contact lens wearers, certain types of contact lenses are designed to let more oxygen through to the eye. The lacrimal glands secrete lacrimal fluid, which flows through the main excretory ducts into the space between the eyeball and lids, when the eyes blink, the lacrimal fluid is spread across the surface of the eye. An excess of tears, as with strong emotion, can cause the nose to run. There are three basic types of tears, The trigeminal V1 nerve bears the sensory pathway of the tear reflexes. When the trigeminal nerve is cut, tears from reflexes will stop, likewise, application of cocaine to the surface of the eye, due to its paralyzing effect on the sensory nerve endings, inhibits the reflex even under exposure to strong tear gases. The motor pathway is autonomic, and, in general, uses the pathway of the nerve in the parasympathetic division. In parasympathetic imitators, more tears are produced, and a drug like atropine inhibits tear production. A newborn infant has insufficient development of control, so s/he cries without weeping. If the lacrimal gland malfunctions or is damaged, but does not cause any severe drying of the cornea, it is not a serious matter, in reflex situations, copious tears are produced mainly in emergencies. Quality of vision is affected by the stability of the tear film and it is presumed that one would also salivate while crying due to the inverse improper connection of the lacrimal nucleus to the salivary glands, but this would be less noticeable. Keratoconjunctivitis sicca, known as dry eye, is a common disorder of the tear film. However, sufferers can experience watering of the eyes, which is in fact a response to irritation caused by the tear film deficiency. Lack of Meibomian gland secretion can mean the tears are not enveloped in a hydrophobic film coat, familial dysautonomia is a genetic condition that can be associated with a lack of overflow tears during emotional crying. Obstruction of the punctum, nasolacrimal canal, or nasolacrimal duct can cause even normal levels of basal tear to overflow onto the face and this can have significant social consequences. In nearly all cultures, crying is seen as a specific act associated with tears trickling down the cheeks and accompanied by characteristic sobbing sounds
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Saliva
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Saliva is a watery substance formed in the mouths of animals, secreted by the salivary glands. Human saliva comprises 99. 5% water, plus electrolytes, mucus, white cells, epithelial cells, glycoproteins, enzymes, antimicrobial agents such as secretory IgA. The enzymes found in saliva are essential in beginning the process of digestion of dietary starches and these enzymes also play a role in breaking down food particles entrapped within dental crevices, thus protecting teeth from bacterial decay. Furthermore, saliva serves a function, wetting food and permitting the initiation of swallowing. Various animal species have uses for saliva that go beyond pre-digestion. Some swifts use their saliva to build nests. Aerodramus nests form the basis of birds nest soup, cobras, vipers, and certain other members of the venom clade hunt with venomous saliva injected by fangs. Some arthropods, such as spiders and caterpillars, produce thread from salivary glands, produced in salivary glands, human saliva is 99. 5% water, but it contains many important substances, including electrolytes, mucus, antibacterial compounds and various enzymes. In humans, the submandibular gland contributes around 70–75% of secretion, while the parotid gland secretes about 20–25%, saliva contributes to the digestion of food and to the maintenance of oral hygiene. Without normal salivary function the frequency of caries, gum disease. Saliva coats the oral mucosa, mechanically protecting it from trauma during eating, swallowing and speaking, in people with little saliva, soreness of the mouth is very common, and the food sticks to the inside of the mouth. The digestive functions of saliva include moistening food and helping to create a food bolus and this lubricative function of saliva allows the food bolus to be passed easily from the mouth into the esophagus. Only about 30% starch digestion takes place in the mouth cavity, Salivary glands also secrete salivary lipase to begin fat digestion. Salivary lipase plays a role in fat digestion in newborn infants as their pancreatic lipase still needs some time to develop. Saliva is very important in the sense of taste and it is the liquid medium in which chemicals are carried to taste receptor cells. Persons with little saliva often complain of dysgeusia, saliva maintains the pH of the mouth. Saliva is supersaturated with various ions, certain salivary proteins prevent precipitation, which would form salts. These ions act as a buffer, keeping the acidity of the mouth within a certain range and this prevents minerals in the dental hard tissues from dissolving
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Human milk
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Breast milk is the milk produced by the breasts of a human female to feed a child. Breast milk can be supplied by an other than the babys mother, either via donated pumped milk, or when a woman nurses a child other than her own at her breast. The World Health Organization recommends exclusive breastfeeding for the first six months of life, supplemented breastfeeding is recommended until at least age two and then for as long as the mother and child wish. Breastfeeding offers health benefits to mother and child even after infancy, breastfeeding also provides health benefits for the mother. It assists the uterus in returning to its size and reduces post-partum bleeding. Breastfeeding also reduces the risk of breast cancer later in life, lactation protects both mother and infant from both types of diabetes. However, it is now recognized that there is no commercial formula that can equal breast milk. In addition to the amounts of carbohydrate, protein, and fat, breast milk provides vitamins, minerals, digestive enzymes. Breast milk also contains antibodies and lymphocytes from the mother help the baby resist infections. At around four to six months of age, the internal iron supplies of the infant, held in the cells of the liver, are exhausted. Breast milk contains less iron than formula, because it is more bioavailable as lactoferrin, under the influence of the hormones prolactin and oxytocin, women produce milk after childbirth to feed the baby. The initial milk produced is referred to as colostrum, which is high in the immunoglobulin IgA and this helps to protect the newborn until its own immune system is functioning properly. It also creates a mild effect, expelling meconium and helping to prevent the build-up of bilirubin. There are many reasons a mother may not produce enough breast milk, some of the most common reasons are an improper latch, not nursing or pumping enough to meet supply, certain medications, illness, and dehydration. A rarer reason is Sheehans syndrome, also known as postpartum hypopituitarism, the amount of milk produced depends on how often the mother is nursing and/or pumping, the more the mother nurses her baby or pumps, the more milk is produced. It is beneficial to nurse when the baby wants to rather than on a schedule. A greater volume of milk expressed can also be attributed to instances where the mother starts pumping milk sooner and this may be important for low birthweight infants. If pumping, it is helpful to have an electric, high-grade pump so that all of the ducts are stimulated
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Mucus
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In vertebrates, mucus is a slippery secretion produced by, and covering, mucous membranes. Mucous fluid is rich in glycoproteins and water and is produced from cells found in mucous glands. Mucous fluid may also originate from mixed glands, which contain both serous and mucous cells and this mucus serves to protect epithelial cells in the respiratory, gastrointestinal, urogenital, visual, and auditory systems, the epidermis in amphibians, and the gills in fish. A major function of mucus is to protect against infectious agents such as fungi, bacteria. The average human nose produces about a liter of mucus per day, most of the mucus produced is in the gastrointestinal tract. Bony fish, hagfish, snails, slugs, and some other invertebrates also produce external mucus, the rest of this article deals with the production and function of mucus in humans. In the human system, mucus aids in the protection of the lungs by trapping foreign particles that enter them, in particular, through the nose. Phlegm is a term for mucus that is restricted to the respiratory tract. Nasal mucus is produced by the mucosa, and mucosal tissues lining the airways is produced by specialized airway epithelial cells. Small particles such as dust, particulate pollutants, and allergens, as well as agents and bacteria are caught in the viscous nasal or airway mucus. This event along with the movement of the respiratory mucus layer toward the oropharynx. This explains why coughing often occurs in those who smoke cigarettes, the bodys natural reaction is to increase mucus production. In addition, mucus aids in moisturizing the inhaled air and prevents tissues such as the nasal, nasal and airway mucus is produced continuously, with most of it swallowed subconsciously, even when it is dried. Increased mucus production in the tract is a symptom of many common illnesses, such as the common cold. Hypersecretion of mucus can occur in respiratory diseases such as respiratory allergies, asthma. The presence of mucus in the nose and throat is normal, in general, nasal mucus is clear and thin, serving to filter air during inhalation. During times of infection, mucus can change color to yellow or green either as a result of trapped bacteria or due to the reaction to viral infection. The green color of mucus comes from the group in the iron-containing enzyme myeloperoxidase secreted by white blood cells as a cytotoxic defense during a respiratory burst
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Cytoplasm
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In cell biology, the cytoplasm is the material within a living cell, excluding the cell nucleus. It comprises cytosol and the organelles – the cells internal sub-structures, all of the contents of the cells of prokaryotic organisms are contained within the cytoplasm. Within the cells of organisms the contents of the cell nucleus are separated from the cytoplasm. The cytoplasm is about 80% water and usually colorless, the submicroscopic ground cell substance or cytoplasmatic matrix which remains after exclusion the cell organelles and particles is groundplasm. It is within the cytoplasm that most cellular activities occur, such as many metabolic pathways including glycolysis, the concentrated inner area is called the endoplasm and the outer layer is called the cell cortex or the ectoplasm. Movement of calcium ions in and out of the cytoplasm is an activity for metabolic processes. In plants, movement of the cytoplasm around vacuoles is known as cytoplasmic streaming, the term was introduced by Rudolf von Kölliker in 1863, originally as a synonym for protoplasm, but later it has come to mean the cell substance and organelles outside the nucleus. There has been disagreement on the definition of cytoplasm, as some authors prefer to exclude from it some organelles. The physical properties of the cytoplasm have been contested in recent years and it remains uncertain how the varied components of the cytoplasm interact to allow movement of particles and organelles while maintaining the cell’s structure. The flow of cytoplasmic components plays an important role in cellular functions which are dependent on the permeability of the cytoplasm. An example of function is cell signalling, a process which is dependent on the manner in which signaling molecules are allowed to diffuse across the cell. While small signaling molecules like calcium ions are able to diffuse with ease, larger molecules, the irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm. There has long been evidence that the cytoplasm behaves like a sol-gel and it is thought that the component molecules and structures of the cytoplasm behave at times like a disordered colloidal solution and at other times like an integrated network, forming a solid mass. Recently it has proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition. A cells ability to vitrify in the absence of activity, as in dormant periods. There has been examining the motion of cytoplasmic particles independent of the nature of the cytoplasm. In such an approach, the aggregate random forces within the cell caused by motor proteins explain the non-Brownian motion of cytoplasmic constituents. The three major elements of the cytoplasm are the cytosol, organelles and inclusions, the cytosol is the portion of the cytoplasm not contained within membrane-bound organelles
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Macrophage
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These large phagocytes are found in essentially all tissues, where they patrol for potential pathogens by amoeboid movement. They take various forms throughout the body, but all are part of the mononuclear phagocyte system, besides phagocytosis, they play a critical role in nonspecific defense and also help initiate specific defense mechanisms by recruiting other immune cells such as lymphocytes. For example, they are important as antigen presenters to T cells, in humans, dysfunctional macrophages cause severe diseases such as chronic granulomatous disease that result in frequent infections. Beyond increasing inflammation and stimulating the system, macrophages also play an important anti-inflammatory role. Macrophages that encourage inflammation are called M1 macrophages, whereas those that decrease inflammation, human macrophages are about 21 micrometres in diameter and are produced by the differentiation of monocytes in tissues. They can be identified using flow cytometry or immunohistochemical staining by their expression of proteins such as CD14, CD40, CD11b, CD64, F4/80 /EMR1, lysozyme M, MAC-1/MAC-3. Macrophages were first discovered by Élie Metchnikoff, a Russian zoologist, when a monocyte enters damaged tissue through the endothelium of a blood vessel, a process known as the leukocyte extravasation, it undergoes a series of changes to become a macrophage. At some sites such as the testis, macrophages have shown to populate the organ through proliferation. Unlike short-lived neutrophils, macrophages survive longer in the body up to a maximum of several months, macrophages are professional phagocytes and are highly specialized in removal of dying or dead cells and cellular debris. This role is important in inflammation, as the early stages of inflammation are dominated by neutrophils. The neutrophils are at first attracted to a site, where they proliferate, when a macrophage ingests a pathogen, the pathogen becomes trapped in a phagosome, which then fuses with a lysosome. Within the phagolysosome, enzymes and toxic peroxides digest the pathogen, however, some bacteria, such as Mycobacterium tuberculosis, have become resistant to these methods of digestion. Typhoidal Salmonellae too induce their own phagocytosis by host macrophages in vivo, macrophages can digest more than 100 bacteria before they finally die due to their own digestive compounds. Macrophages are versatile cells that play many roles, as scavengers, they rid the body of worn-out cells and other debris. Along with dendritic cells, they are foremost among the cells present antigens. At the same time, they carry receptors for lymphokines that allow them to be activated into single-minded pursuit of microbes, after digesting a pathogen, a macrophage will present the antigen of the pathogen to the corresponding helper T cell. In some cases, pathogens are very resistant to adhesion by the macrophages, the antigen presentation on the surface of infected macrophages in a lymph node stimulates TH1 to proliferate. When a B-cell in the lymph node recognizes the same unprocessed surface antigen on the bacterium with its surface bound antibody, the processed antigen is then presented in MHCII on the surface of the B-cell
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Neutrophil
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Neutrophil are the most abundant type of granulocytes and the most abundant type of white blood cells in most mammals. They form a part of the innate immune system. Its functionality varies in different animals and they are formed from stem cells in the bone marrow. They are short-lived and highly motile, or mobile, as they can enter parts of tissue where other cells/molecules wouldnt be able to enter otherwise, neutrophils may be subdivided into segmented neutrophils and banded neutrophils. They form part of the polymorphonuclear cells family together with basophils and eosinophils, the name neutrophil derives from staining characteristics on hematoxylin and eosin histological or cytological preparations. Whereas basophilic white blood cells stain dark blue and eosinophilic white blood cells stain bright red, normally, neutrophils contain a nucleus divided into 2–5 lobes. Neutrophils are a type of phagocyte and are found in the bloodstream. They migrate through the vessels, then through interstitial tissue, following chemical signals such as Interleukin-8, C5a, fMLP, Leukotriene B4. They are the predominant cells in pus, accounting for its whitish/yellowish appearance, Neutrophil granulocytes have an average diameter of 12-15 micrometers in peripheral blood smears. When analyzing neutrophils in suspension, neutrophils have a diameter of 8.85 µm. With the eosinophil and the basophil, they form the class of polymorphonuclear cells, the nucleus has a characteristic lobed appearance, the separate lobes connected by chromatin. The nucleolus disappears as the neutrophil matures, which is something that happens in only a few types of nucleated cells. In the cytoplasm, the Golgi apparatus is small, mitochondria and ribosomes are sparse, the cytoplasm also contains about 200 granules, of which a third are azurophilic. Neutrophils from women exhibit a small additional X chromosome structure, known as a neutrophil drumstick, neutrophils will show increasing segmentation as they mature. A normal neutrophil should have 3-5 segments, hypersegmentation is not normal, and occurs in some disorders, most notably vitamin B12 deficiency. This is noted on a review of the blood smear. Neutrophils are the most abundant white blood cells in humans, they account for approximately 50-70% of all blood cells. The stated normal range for human blood counts varies between laboratories, but a count of 2. 5–7.5 x 109/L is a standard normal range
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Alpha-lactalbumin
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Lactalbumin, alpha-, also known as LALBA, is a protein that in humans is encoded by the LALBA gene. α-Lactalbumin is a present in the milk of almost all mammalian species. In primates, alpha-lactalbumin expression is upregulated in response to the hormone prolactin, α-Lactalbumin forms the regulatory subunit of the lactose synthase heterodimer and β-1, 4-galactosyltransferase forms the catalytic component. Together, these proteins enable LS to produce lactose by transferring galactose moieties to glucose, as a multimer, alpha-lactalbumin strongly binds calcium and zinc ions and may possess bactericidal or antitumor activity. A folding variant of human alpha-lactalbumin that may form in environments such as the stomach, called HAMLET, probably induces apoptosis in tumor. The corresponding folding dynamics of alpha-lactalbumin is thus highly unusual and this gives rise to a pathway for forming lactose by converting Gal-TI to Lactose synthase. The structure of alpha-lactalbumin is well known and is composed of 123 amino acids and 4 disulfide bridges, the molecular weight is 14178 Da, and the isoelectric point is between 4.2 and 4.5. One of the structural differences with beta-lactoglobulin is that it does not have any free thiol group that can serve as the starting-point for a covalent aggregation reaction. As a result, pure α-lactalbumin will not form gels upon denaturation and acidification, the sequence comparison of α-lactalbumin shows a strong similarity to that of lysozymes, specifically the Ca2+-binding c-lysozyme. So the expected evolutionary history is that gene duplication of the c-lysozyme was followed by mutation
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Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
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Isoelectric point
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The isoelectric point, is the pH at which a particular molecule carries no net electrical charge in the statistical mean. The standard nomenclature to represent the point is pH, although pI is also commonly seen. The net charge on the molecule is affected by pH of its environment and can become more positively or negatively charged due to the gain or loss, respectively. Surfaces naturally charge to form a double layer, in the common case when the surface charge-determining ions are H+/OH−, the net surface charge is affected by the pH of the liquid in which the solid is submerged. The pI value can affect the solubility of a molecule at a given pH, such molecules have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution. Biological amphoteric molecules such as proteins contain both acidic and basic functional groups, amino acids that make up proteins may be positive, negative, neutral, or polar in nature, and together give a protein its overall charge. At a pH below their pI, proteins carry a net positive charge, isoelectric focusing is also the first step in 2-D gel polyacrylamide gel electrophoresis. For an amino acid with one amine and one carboxyl group. P I = p K a 1 + p K a 22 The pH of a gel is determined by the buffer used for that gel. If the pH of the buffer is above the pI of the protein being run, if the pH of the buffer is below the pI of the protein being run, the protein will migrate to the negative pole of the gel. If the protein is run with a buffer pH that is equal to the pI and this is also true for individual amino acids. In the two examples the isoelectric point is shown by the vertical line. In glycine the pK values are separated by nearly 7 units so the concentration of the neutral species, glycine may exist as a zwitterion at the isoelectric point, but the equilibrium constant for the isomerization reaction in solution H2NCH2CO2H ⇌ H3N+CH2CO2− is not known. The other example, adenosine monophosphate is shown to illustrate the fact that a species may, in principle. In fact the concentration of H32+ is negligible at the point in this case. If the pI is greater than the pH, the molecule will have a positive charge, a number of algorithms for estimating isoelectric points of peptides and proteins have been developed. Most of them use Henderson–Hasselbalch equation with different pK values, for instance, within the model proposed by Bjellqvist and co-workers the pKs were determined between closely related immobilines, by focusing the same sample in overlapping pH gradients. Some improvements in the methodology have also proposed
. PMID 23833521.
