1.
Protein Data Bank
–
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
Protein Data Bank
–
Examples of protein structures from the PDB (created with UCSF Chimera)
2.
GeneCards
–
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
GeneCards
–
Expression profile of FAM214A found in normal human tissue, as shown in GeneCards.
3.
Chromosome
–
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
Chromosome
–
Walter Sutton (left) and
Theodor Boveri (right) independently developed the chromosome theory of inheritance in 1902.
Chromosome
–
Diagram of a replicated and condensed
metaphase eukaryotic chromosome. (1)
Chromatid – one of the two identical parts of the chromosome after
S phase. (2)
Centromere – the point where the two chromatids touch. (3) Short arm. (4) Long arm.
Chromosome
Chromosome
–
Human chromosomes during
metaphase
4.
Chromosome 22 (human)
–
Chromosome 22 is one of the 23 pairs of chromosomes in human cells. Humans normally have two copies of chromosome 22 in each cell, Chromosome 22 is the second smallest human chromosome, spanning about 49 million DNA base pairs and representing between 1.5 and 2% of the total DNA in cells. In 1999, researchers working on the Human Genome Project announced they had determined the sequence of pairs that make up this chromosome. Chromosome 22 was the first human chromosome to be fully sequenced, identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies, in January 2017, two estimates differed by 33%, with one estimate giving 956 genes, and the other estimate giving 1,110 genes. Chromosome 22 was originally identified as the smallest chromosome, after extensive research, however, researchers concluded that chromosome 21 was smaller. The deletion occurs near the middle of the chromosome at a designated as q11.2. This region contains about 30 genes, but many of these genes have not been well characterized, a small percentage of affected individuals have shorter deletions in the same region. A loss of this gene does not appear to cause learning disabilities, other genes in the deleted region are also likely to contribute to the signs and symptoms of 22q11.2 deletion syndrome. Cat-eye syndrome is a rare disorder most often caused by a change called an inverted duplicated 22. A small extra chromosome is made up of material from chromosome 22 that has been abnormally duplicated. A rearrangement of genetic material between chromosomes 9 and 22 is associated with types of blood cancer. This chromosomal abnormality, which is called the Philadelphia chromosome, is found only in cancer cells. The Philadelphia chromosome has been identified in most cases of a slowly progressing form of cancer called chronic myeloid leukemia. It also has found in some cases of more rapidly progressing blood cancers. The presence of the Philadelphia chromosome can help predict how the cancer will progress, emanuel Syndrome is a translocation of chromosomes 11 and 22. Originally known as Supernumerary der Syndrome, it occurs when an individual has an extra chromosome composed of pieces of the 11th and this is based on a physiological mechanism and is not pathogenetic for leukemias or lymphomas. However, the rearrangement of several lambda variable subgenes can activate expression of an overlapping miRNA gene, the DNA sequence of human chromosome 22
Chromosome 22 (human)
–
Pair of human chromosome 22 (after
G-banding). One is from mother, one is from father.
5.
Locus (genetics)
–
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
Locus (genetics)
–
Chromosome components: (1)
Chromatid (2)
Centromere (3) Short (p) arm (4) Long (q) arm
Locus (genetics)
–
Short and long arms
6.
Base pair
–
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
Base pair
–
Depiction of the
adenine -
thymine Watson-Crick base pair.
7.
Gene expression
–
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
Gene expression
–
The patchy colours of a
tortoiseshell cat are the result of different levels of expression of
pigmentation genes in different areas of the
skin.
Gene expression
–
Genes are expressed by being transcribed into RNA, and this transcript may then be translated into protein.
Gene expression
–
In situ-hybridization of
Drosophila embryos at different developmental stages for the mRNA responsible for the expression of
hunchback. High intensity of blue color marks places with high hunchback mRNA quantity.
8.
Entrez
–
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
Entrez
–
The NCBI Entrez CD-ROM c. 1996
Entrez
–
The Entrez logo
9.
Ensembl
–
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
Ensembl
–
Centres and institutes
Ensembl
–
The Ensembl genome database project.
10.
UniProt
–
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
UniProt
–
UniProt
11.
PubMed
–
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
PubMed
–
PubMed
12.
Wikidata
–
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
Wikidata
–
Wikidata
13.
Iron
–
Iron is a chemical element with symbol Fe and atomic number 26. It is a metal in the first transition series and it is by mass the most common element on Earth, forming much of Earths outer and inner core. It is the fourth most common element in the Earths crust, like the other group 8 elements, ruthenium and osmium, iron exists in a wide range of oxidation states, −2 to +6, although +2 and +3 are the most common. Elemental iron occurs in meteoroids and other low oxygen environments, but is reactive to oxygen, fresh iron surfaces appear lustrous silvery-gray, but oxidize in normal air to give hydrated iron oxides, commonly known as rust. Unlike the metals that form passivating oxide layers, iron oxides occupy more volume than the metal and thus flake off, Iron metal has been used since ancient times, although copper alloys, which have lower melting temperatures, were used even earlier in human history. Pure iron is soft, but is unobtainable by smelting because it is significantly hardened and strengthened by impurities, in particular carbon. A certain proportion of carbon steel, which may be up to 1000 times harder than pure iron. Crude iron metal is produced in blast furnaces, where ore is reduced by coke to pig iron, further refinement with oxygen reduces the carbon content to the correct proportion to make steel. Steels and iron alloys formed with metals are by far the most common industrial metals because they have a great range of desirable properties. Iron chemical compounds have many uses, Iron oxide mixed with aluminium powder can be ignited to create a thermite reaction, used in welding and purifying ores. Iron forms binary compounds with the halogens and the chalcogens, among its organometallic compounds is ferrocene, the first sandwich compound discovered. Iron plays an important role in biology, forming complexes with oxygen in hemoglobin and myoglobin. Iron is also the metal at the site of many important redox enzymes dealing with cellular respiration and oxidation and reduction in plants. A human male of average height has about 4 grams of iron in his body and this iron is distributed throughout the body in hemoglobin, tissues, muscles, bone marrow, blood proteins, enzymes, ferritin, hemosiderin, and transport in plasma. The mechanical properties of iron and its alloys can be evaluated using a variety of tests, including the Brinell test, Rockwell test, the data on iron is so consistent that it is often used to calibrate measurements or to compare tests. An increase in the content will cause a significant increase in the hardness. Maximum hardness of 65 Rc is achieved with a 0. 6% carbon content, because of the softness of iron, it is much easier to work with than its heavier congeners ruthenium and osmium. Because of its significance for planetary cores, the properties of iron at high pressures and temperatures have also been studied extensively
Iron
–
Iron, 26 Fe
Iron
–
Spectral lines of iron
Iron
–
Iron meteorites, similar in composition to the Earth's inner- and outer core
Iron
–
Hydrated
iron(III) chloride, also known as ferric chloride
14.
Oxygen
–
Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the group on the periodic table and is a highly reactive nonmetal. By mass, oxygen is the third-most abundant element in the universe, after hydrogen, at standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. This is an important part of the atmosphere and diatomic oxygen gas constitutes 20. 8% of the Earths atmosphere, additionally, as oxides the element makes up almost half of the Earths crust. Most of the mass of living organisms is oxygen as a component of water, conversely, oxygen is continuously replenished by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide. Oxygen is too reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone, strongly absorbs ultraviolet UVB radiation, but ozone is a pollutant near the surface where it is a by-product of smog. At low earth orbit altitudes, sufficient atomic oxygen is present to cause corrosion of spacecraft, the name oxygen was coined in 1777 by Antoine Lavoisier, whose experiments with oxygen helped to discredit the then-popular phlogiston theory of combustion and corrosion. One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle, Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries later Leonardo da Vinci built on Philos work by observing that a portion of air is consumed during combustion and respiration, Oxygen was discovered by the Polish alchemist Sendivogius, who considered it the philosophers stone. In the late 17th century, Robert Boyle proved that air is necessary for combustion, English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. From this he surmised that nitroaereus is consumed in both respiration and combustion, Mayow observed that antimony increased in weight when heated, and inferred that the nitroaereus must have combined with it. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract De respiratione. Robert Hooke, Ole Borch, Mikhail Lomonosov, and Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element. This may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, which was then the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, one part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. The fact that a substance like wood gains overall weight in burning was hidden by the buoyancy of the combustion products
Oxygen
–
Spectral lines of oxygen
Oxygen
Oxygen
–
A trickle of liquid oxygen is deflected by a magnetic field, illustrating its paramagnetic property
Oxygen
–
Oxygen discharge (spectrum) tube. The green color is similar to the color of an
"aurora borealis"
15.
Protein
–
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
Protein
–
Proteins in different
cellular compartments and structures tagged with
green fluorescent protein (here, white)
Protein
–
A representation of the 3D structure of the protein
myoglobin showing turquoise
alpha helices. This protein was the first to have its structure solved by
X-ray crystallography. Towards the right-center among the coils, a
prosthetic group called a
heme group (shown in gray) with a bound oxygen molecule (red).
Protein
–
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing
heme units
Protein
–
John Kendrew with model of myoglobin in progress
16.
Hemoglobin
–
Hemoglobin in the blood carries oxygen from the respiratory organs to the rest of the body. There it releases the oxygen to permit aerobic respiration to provide energy to power the functions of the organism in the process called metabolism, in mammals, the protein makes up about 96% of the red blood cells dry content, and around 35% of the total content. Hemoglobin has a capacity of 1.34 mL O2 per gram. The mammalian hemoglobin molecule can bind up to four oxygen molecules, Hemoglobin is involved in the transport of other gases, It carries some of the bodys respiratory carbon dioxide as carbaminohemoglobin, in which CO2 is bound to the globin protein. The molecule also carries the important regulatory molecule nitric oxide bound to a globin protein thiol group, Hemoglobin is also found outside red blood cells and their progenitor lines. Other cells that contain hemoglobin include the A9 dopaminergic neurons in the substantia nigra, macrophages, alveolar cells, in these tissues, hemoglobin has a non-oxygen-carrying function as an antioxidant and a regulator of iron metabolism. Hemoglobin and hemoglobin-like molecules are found in many invertebrates, fungi. In these organisms, hemoglobins may carry oxygen, or they may act to transport and regulate other small molecules and ions such as carbon dioxide, nitric oxide, hydrogen sulfide and sulfide. In 1825 J. F. Engelhard discovered that the ratio of Fe to protein is identical in the hemoglobins of several species, from the known atomic mass of iron he calculated the molecular mass of hemoglobin to n ×16000, the first determination of a proteins molecular mass. This hasty conclusion drew a lot of ridicule at the time from scientists who could not believe that any molecule could be that big, gilbert Smithson Adair confirmed Engelhards results in 1925 by measuring the osmotic pressure of hemoglobin solutions. The oxygen-carrying protein hemoglobin was discovered by Hünefeld in 1840, hemoglobins reversible oxygenation was described a few years later by Felix Hoppe-Seyler. In 1959, Max Perutz determined the structure of myoglobin by X-ray crystallography. This work resulted in his sharing with John Kendrew the 1962 Nobel Prize in Chemistry, the role of hemoglobin in the blood was elucidated by French physiologist Claude Bernard. The name hemoglobin is derived from the heme and globin. Each heme group contains one iron atom, that can bind one oxygen molecule through ion-induced dipole forces, the most common type of hemoglobin in mammals contains four such subunits. Hemoglobin consists of subunits, and these proteins, in turn, are folded chains of a large number of different amino acids called polypeptides. The amino acid sequence of any polypeptide created by a cell is in turn determined by the stretches of DNA called genes, in all proteins, it is the amino acid sequence that determines the proteins chemical properties and function. There is more than one gene, in humans, hemoglobin A is coded for by the genes, HBA1, HBA2
Hemoglobin
–
Max Perutz, one of the founding fathers of molecular biology
Hemoglobin
–
hemoglobin
Hemoglobin
–
A hemoglobin concentration measurement being administered before a blood donation at the
American Red Cross Boston Blood Donation Center.
Hemoglobin
–
The giant tube worm
Riftia pachyptila showing red hemoglobin-containing plumes
17.
Red blood cell
–
RBCs take up oxygen in the lungs, or gills of fish, and release it into tissues while squeezing through the bodys capillaries. The cytoplasm of erythrocytes is rich in hemoglobin, a biomolecule that can bind oxygen and is responsible for the red color of the cells. In humans, mature red cells are flexible and oval biconcave disks. They lack a nucleus and most organelles, in order to accommodate maximum space for hemoglobin, they can be viewed as sacks of hemoglobin. Approximately 2.4 million new erythrocytes are produced per second in human adults, the cells develop in the bone marrow and circulate for about 100–120 days in the body before their components are recycled by macrophages. Each circulation takes about 60 seconds, approximately a quarter of the cells in the human body are red blood cells. Nearly half of the volume is red blood cells. Red blood cells are known as RBCs, red cells, red blood corpuscles, haematids. Packed red blood cells are red blood cells that have donated, processed. Almost all vertebrates, including all mammals and humans, have red blood cells, red blood cells are cells present in blood in order to transport oxygen. The only known vertebrates without red blood cells are the crocodile icefish, they live in very cold water. While they no longer use hemoglobin, remnants of hemoglobin genes can be found in their genome, oxygen can easily diffuse through the red blood cells cell membrane. Myoglobin, a related to hemoglobin, acts to store oxygen in muscle cells. The color of red cells is due to the heme group of hemoglobin. However, blood can appear bluish when seen through the vessel wall, pulse oximetry takes advantage of the hemoglobin color change to directly measure the arterial blood oxygen saturation using colorimetric techniques. Hemoglobin also has a high affinity for carbon monoxide, forming carboxyhemoglobin which is a very bright red in color. Flushed, confused patients with a reading of 100% on pulse oximetry are sometimes found to be suffering from carbon monoxide poisoning. The red blood cells of mammals are typically shaped as disks, flattened and depressed in the center, with a dumbbell-shaped cross section
Red blood cell
–
Scanning electron micrograph of
human red blood cells (ca. 6–8 μm in diameter)
Red blood cell
–
There is an immense size variation in vertebrate erythrocytes, as well as a correlation between cell and nucleus size. Mammalian erythrocytes, which do not contain nuclei, are considerably smaller than those of most other vertebrates.
Red blood cell
–
Mature erythrocytes of birds have a nucleus, however in the blood of adult females of penguin
Pygoscelis papua enucleated red blood cells (B) have been observed, but with very low frequency.
Red blood cell
–
Scanning electron micrograph of blood cells. From left to right: human erythrocyte,
thrombocyte (platelet),
leukocyte.
18.
Biological pigment
–
Biological pigments, also known simply as pigments or biochromes, are substances produced by living organisms that have a color resulting from selective color absorption. Biological pigments include plant pigments and flower pigments, many biological structures, such as skin, eyes, feathers, fur and hair contain pigments such as melanin in specialized cells called chromatophores. For example, butterfly wings typically contain structural color, although many butterflies have cells that contain pigment as well, see conjugated systems for electron bond chemistry that causes these molecules to have pigment. Other functions of pigments in plants include attracting insects to flowers to encourage pollination, plant pigments include a variety of different kinds of molecule, including porphyrins, carotenoids, anthocyanins and betalains. All biological pigments selectively absorb certain wavelengths of light while reflecting others, the principal pigments responsible are, Chlorophyll is the primary pigment in plants, it is a chlorin that absorbs yellow and blue wavelengths of light while reflecting green. It is the presence and relative abundance of chlorophyll that gives plants their green color, all land plants and green algae possess two forms of this pigment, chlorophyll a and chlorophyll b. Kelps, diatoms, and other photosynthetic heterokonts contain chlorophyll c instead of b, all chlorophylls serve as the primary means plants use to intercept light in order to fuel photosynthesis. Carotenoids are red, orange, or yellow tetraterpenoids, during the process of photosynthesis, they have functions in light-harvesting, in photoprotection, and also serve as protein structural elements. In higher plants, they serve as precursors to the plant hormone abscisic acid. Plants, in general, contain six ubiquitous carotenoids, neoxanthin, violaxanthin, antheraxanthin, zeaxanthin, lutein, lutein is a yellow pigment found in fruits and vegetables and is the most abundant carotenoid in plants. Lycopene is the red pigment responsible for the color of tomatoes, other less common carotenoids in plants include lutein epoxide, lactucaxanthin, and alpha carotene. In cyanobacteria, many other carotenoids exist such as canthaxanthin, myxoxanthophyll, synechoxanthin, algal phototrophs such as dinoflagellates use peridinin as a light harvesting pigment. Anthocyanins are water-soluble flavonoid pigments that appear red to blue, according to pH and they occur in all tissues of higher plants, providing color in leaves, plant stem, roots, flowers, and fruits, though not always in sufficient quantities to be noticeable. Anthocyanins are most visible in the petals of flowers of many species, betalains are red or yellow pigments. Like anthocyanins they are water-soluble, but unlike anthocyanins they are synthesized from tyrosine and this class of pigments is found only in the Caryophyllales, and never co-occur in plants with anthocyanins. Betalains are responsible for the red color of beets. Chlorophylls degrade into colorless tetrapyrroles known as nonfluorescent chlorophyll catabolites, as the predominant chlorophylls degrade, the hidden pigments of yellow xanthophylls and orange beta-carotene are revealed. These pigments are present throughout the year, but the red pigments, pigmentation is used by many animals for protection, by means of camouflage, mimicry, or warning coloration
Biological pigment
–
The
budgerigar gets its yellow color from a
psittacofulvin pigment and its green color from a combination of the same yellow pigment and blue
structural color. The blue and white bird in the background lacks the yellow pigment. The dark markings on both birds are due to the black pigment
eumelanin.
Biological pigment
–
Anthocyanin gives these
pansies their purple pigmentation.
Biological pigment
–
Bougainvillea bracts get their color from
betalains
19.
Smooth muscle tissue
–
Smooth muscle is an involuntary non-striated muscle. It is divided into two subgroups, the single-unit and multiunit smooth muscle, within single-unit cells, the whole bundle or sheet contracts as a syncytium. Single unit smooth muscle, however, is most common and lines blood vessels, the tract. Smooth muscle is different from skeletal muscle and cardiac muscle in terms of structure, function, regulation of contraction. Smooth muscle cells known as myocytes, have a shape and, like striated muscle, can tense. However, smooth muscle tissue tends to demonstrate greater elasticity and function within a larger length-tension curve than striated muscle and this ability to stretch and still maintain contractility is important in organs like the intestines and urinary bladder. In the relaxed state, each cell is spindle-shaped, 20-500 micrometers in length, the smooth muscle is the only type of muscle without the ability to be voluntarily controlled in stressful situations. Myosin is primarily class II in smooth muscle, myosin II contains two heavy chains which constitute the head and tail domains. Each of these heavy chains contains the N-terminal head domain, while the C-terminal tails take on a coiled-coil morphology, thus, myosin II has two heads. In smooth muscle, there is a gene that codes for the heavy chains myosin II. Also, smooth muscle may contain MHC that is not involved in contraction, myosin II also contains 4 light chains, resulting in 2 per head, weighing 20 and 17 kDa. These bind the chains in the neck region between the head and tail. The MLC20 is also known as the light chain and actively participates in muscle contraction. Two MLC20 isoforms are found in muscle, and they are encoded by different genes. The MLC17 is also known as the light chain. Its exact function is unclear, but its believed that it contributes to the stability of the myosin head along with MLC20. Two variants of MLC17 exist as a result of alternate splicing at the MLC17 gene, in the uterus, a shift in myosin expression has been hypothesized to avail for changes in the directions of uterine contractions that are seen during the menstrual cycle. The thin filaments that form part of the machinery are predominantly composed of α-
Smooth muscle tissue
–
Layers of Esophageal Wall: 1.
Mucosa 2.
Submucosa 3.
Muscularis 4.
Adventitia 5.
Striated muscle 6. Striated and smooth 7. Smooth muscle 8. Lamina
muscularis mucosae 9.
Esophageal glands
Smooth muscle tissue
–
The dense bodies and intermediate filaments are networked through the sarcoplasm, which cause the muscle fiber to contract.
Smooth muscle tissue
–
A series of axon-like swelling, called varicosities or “boutons,” from autonomic neurons form motor units through the smooth muscle.
20.
X-ray crystallography
–
By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder. The method also revealed the structure and function of biological molecules, including vitamins, drugs, proteins. X-ray crystallography is still the method for characterizing the atomic structure of new materials. In a single-crystal X-ray diffraction measurement, a crystal is mounted on a goniometer, the goniometer is used to position the crystal at selected orientations. The crystal is illuminated with a finely focused monochromatic beam of X-rays, poor resolution or even errors may result if the crystals are too small, or not uniform enough in their internal makeup. X-ray crystallography is related to other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or neutrons, for all above mentioned X-ray diffraction methods, the scattering is elastic, the scattered X-rays have the same wavelength as the incoming X-ray. By contrast, inelastic X-ray scattering methods are useful in studying excitations of the sample, Crystals, though long admired for their regularity and symmetry, were not investigated scientifically until the 17th century. Johannes Kepler hypothesized in his work Strena seu de Nive Sexangula that the symmetry of snowflake crystals was due to a regular packing of spherical water particles. The Danish scientist Nicolas Steno pioneered experimental investigations of crystal symmetry, hence, William Hallowes Miller in 1839 was able to give each face a unique label of three small integers, the Miller indices which remain in use today for identifying crystal faces. In the 19th century, a catalog of the possible symmetries of a crystal was worked out by Johan Hessel, Auguste Bravais, Evgraf Fedorov, Arthur Schönflies. Wilhelm Röntgen discovered X-rays in 1895, just as the studies of crystal symmetry were being concluded, physicists were initially uncertain of the nature of X-rays, but soon suspected that they were waves of electromagnetic radiation, in other words, another form of light. Single-slit experiments in the laboratory of Arnold Sommerfeld suggested that X-rays had a wavelength of about 1 angstrom, however, X-rays are composed of photons, and thus are not only waves of electromagnetic radiation but also exhibit particle-like properties. Albert Einstein introduced the concept in 1905, but it was not broadly accepted until 1922. Therefore, these properties of X-rays, such as their ionization of gases. Nevertheless, Braggs view was not broadly accepted and the observation of X-ray diffraction by Max von Laue in 1912 confirmed for most scientists that X-rays were a form of electromagnetic radiation, Crystals are regular arrays of atoms, and X-rays can be considered waves of electromagnetic radiation. Atoms scatter X-ray waves, primarily through the atoms electrons and this phenomenon is known as elastic scattering, and the electron is known as the scatterer
X-ray crystallography
–
Drawing of square (Figure A, above) and hexagonal (Figure B, below) packing from
Kepler's work, Strena seu de Nive Sexangula.
X-ray crystallography
–
X-ray crystallography can locate every atom in a
zeolite, an
aluminosilicate.
X-ray crystallography
X-ray crystallography
–
First X-ray diffraction view of
Martian soil -
CheMin analysis reveals
feldspar,
pyroxenes,
olivine and more (
Curiosity rover at "
Rocknest ", October 17, 2012).
21.
John Kendrew
–
He was born in Oxford, son of Wilford George Kendrew, reader in climatology in the University of Oxford, and Evelyn May Graham Sandburg, art historian. After prep school at the Dragon School in Oxford, he was educated at Clifton College in Bristol and he attended Trinity College, Cambridge in 1936, as a Major Scholar, graduating in chemistry in 1939. He spent the months of World War II doing research on reaction kinetics. In 1940 he became engaged in research at the Royal Air Force headquarters. During the war years, he became interested in biochemical problems. In 1945 he approached Max Perutz in the Cavendish Laboratory in Cambridge, joseph Barcroft, a respiratory physiologist, suggested he might make a comparative protein crystallographic study of adult and fetal sheep hemoglobin, and he started that work. In 1954 he became a Reader at the Davy-Faraday Laboratory of the Royal Institution in London, Kendrew shared the 1962 Nobel Prize for chemistry with Max Perutz for determining the first atomic structures of proteins using X-ray crystallography. Their work was done at what is now the MRC Laboratory of Molecular Biology in Cambridge, Kendrew determined the structure of the protein myoglobin, which stores oxygen in muscle cells. In 1947 the MRC agreed to make a unit for the Study of the Molecular Structure of Biological Systems. His initial source of raw material was horse heart, but the crystals thus obtained were too small for X-ray analysis. Kendrew realized that the tissue of diving mammals could offer a better prospect. Whale myoglobin did give large crystals with clean X-ray diffraction patterns, an electron density map at 6 angstrom resolution was obtained by 1957, and by 1959 an atomic model could be built at 2 angstrom resolution. In 1963 Kendrew became one of the founders of the European Molecular Biology Organization, as well and he became Fellow of the American Society of Biological Chemists in 1967 and honorary member of the International Academy of Science. In 1974 he succeeded in persuading governments to establish the European Molecular Biology Laboratory in Heidelberg and became its first director. From 1974 to 1979 he was a Trustee of the British Museum, and from 1974 to 1988 he was successively Secretary General, Vice-President, and President of the International Council of Scientific Unions. After his retirement from the European Molecular Biology Laboratory, Kendrew became President of St Johns College at Oxford University, kendrews entry in Whos Who lists ten other important national and international committees on which he served as either member or chairman. The Kendrew Quadrangle at St Johns College in Oxford, officially opened on 16 October 2010, is named after him and his scientific biography is currently being written by Paul Wasserman. *John Finch, A Nobel Fellow On Every Floor, Medical Research Council 2008,381 pp, ISBN 978-1-84046-940-0, Nobel website biography The New York Times obituary of Kendrew
John Kendrew
–
John Kendrew
John Kendrew
–
John Kendrew with model of myoglobin in progress. Copyright by the Laboratory of Molecular Biology in Cambridge, England.
22.
Nobel Prize in chemistry
–
The Nobel Prize in Chemistry is awarded annually by the Royal Swedish Academy of Sciences to scientists in the various fields of chemistry. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in chemistry, physics, literature, peace, and physiology or medicine. This award is administered by the Nobel Foundation and awarded by Royal Swedish Academy of Sciences on proposal of the Nobel Committee for Chemistry which consists of five elected by Academy. The award is presented in Stockholm at a ceremony on December 10. The first Nobel Prize in Chemistry was awarded in 1901 to Jacobus Henricus van t Hoff, of the Netherlands, for his discovery of the laws of chemical dynamics and osmotic pressure in solutions. From 1901 to 2016, the award has been bestowed on a total of 174 individuals, though Nobel wrote several wills during his lifetime, the last was written a little over a year before he died, and signed at the Swedish-Norwegian Club in Paris on 27 November 1895. Nobel bequeathed 94% of his assets,31 million Swedish kronor, to establish. Due to the level of surrounding the will, it was not until April 26,1897 that it was approved by the Storting. The executors of his will were Ragnar Sohlman and Rudolf Lilljequist, the members of the Norwegian Nobel Committee that were to award the Peace Prize were appointed shortly after the will was approved. The prize-awarding organisations followed, the Karolinska Institutet on June 7, the Swedish Academy on June 9, the Nobel Foundation then reached an agreement on guidelines for how the Nobel Prize should be awarded. In 1900, the Nobel Foundations newly created statutes were promulgated by King Oscar II, according to Nobels will, The Royal Swedish Academy of Sciences were to award the Prize in Chemistry. The committee and institution serving as the board for the prize typically announce the names of the laureates in October. The prize is awarded at formal ceremonies held annually on December 10. The highlight of the Nobel Prize Award Ceremony in Stockholm is when each Nobel Laureate steps forward to receive the prize from the hands of His Majesty the King of Sweden, the Nobel Laureate receives three things, a diploma, a medal and a document confirming the prize amount. Later the Nobel Banquet is held in Stockholm City Hall, a maximum of three laureates and two different works may be selected. The award can be given to a maximum of three recipients per year and it consists of a gold medal, a diploma, and a cash grant. The Nobel Laureates in chemistry are selected by a committee that consists of five elected by the Royal Swedish Academy of Sciences. In its first stage, several people are asked to nominate candidates
Nobel Prize in chemistry
–
Jacobus Henricus van 't Hoff (1852–1911) was the first person to receive the Nobel Prize in Chemistry, for his discovery of the laws of chemical dynamics and
osmotic pressure in solutions.
Nobel Prize in chemistry
–
The Nobel Prize in Chemistry
23.
Max Perutz
–
He went on to win the Royal Medal of the Royal Society in 1971 and the Copley Medal in 1979. At Cambridge he founded and chaired The Medical Research Council Laboratory of Molecular Biology, Perutzs contributions to molecular biology in Cambridge are documented in The History of the University of Cambridge, Volume 4 published by the Cambridge University Press in 1992. Perutz was born in Vienna, the son of Adele Dely and Hugo Perutz and his parents were Jewish by ancestry, but had baptised Perutz in the Catholic religion. Although Perutz rejected religion and was an atheist in his later years and his parents hoped that he would become a lawyer, but he became interested in chemistry while at school. Overcoming his parents objections he enrolled as an undergraduate at the University of Vienna. However he had visited J. D. Bernal, who was looking for a student to assist him with studies into X-ray crystallography. Perutz was dismayed as he knew nothing about the subject, marks countered by saying that he would soon learn. Bernal accepted him as a student in his crystallography research group at the Cavendish Laboratory. His father had deposited £500 with his London agent to support him, Bernal encouraged him to use the X-ray diffraction method to study the structure of proteins. As protein crystals were difficult to obtain he used horse haemoglobin crystals, Haemoglobin was a subject which was to occupy him for most of his professional career. He completed his Ph. D. under William Lawrence Bragg, rejected by Kings and St Johns colleges he applied to and became a member of Peterhouse, on the basis that it served the best food. He was elected an Honorary Fellow of Peterhouse in 1962 and he took a keen interest in the Junior Members, and was a regular and popular speaker at the Kelvin Club, the Colleges scientific society. When Hitler took over Austria in 1938 Perutzs parents managed to escape to Switzerland, as a result, Perutz lost their financial support. His resulting article for the Proceedings of the Royal Society made him known as an expert on glaciers, the application was accepted in January 1939 and with the money Perutz was able to bring his parents from Switzerland in March 1939 to England. On the outbreak of World War II Perutz was rounded up along with persons of German or Austrian background. After being interned for several months he returned to Cambridge and his knowledge on the subject of ice then lead to him in 1942 being recruited for Project Habakkuk. This was a project to build an ice platform in mid-Atlantic. To that end he investigated the recently invented mixture of ice and he carried out early experiments on pykrete in a secret location underneath Smithfield Meat Market in the City of London
Max Perutz
–
Perutz in 1962
Max Perutz
–
Perutz with his wife Gisela at the 1962 Nobel ball
24.
Reactive oxygen species
–
Reactive oxygen species are chemically reactive chemical species containing oxygen. Examples include peroxides, superoxide, hydroxyl radical, and singlet oxygen, in a biological context, ROS are formed as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling and homeostasis. However, during times of stress, ROS levels can increase dramatically. This may result in significant damage to cell structures, cumulatively, this is known as oxidative stress. ROS are also generated by sources such as ionizing radiation. Ionizing radiation can generate damaging intermediates through the interaction with water, since water comprises 55–60% of the human body, the probability of radiolysis is quite high under the presence of ionizing radiation. In the process, water loses an electron and becomes highly reactive, then through a three-step chain reaction, water is sequentially converted to hydroxyl radical, hydrogen peroxide, superoxide radical and ultimately oxygen. The hydroxyl radical is extremely reactive and immediately removes electrons from any molecule in its path, turning that molecule into a free radical, mitochondria convert energy for the cell into a usable form, adenosine triphosphate. The process in which ATP is produced, called oxidative phosphorylation, the last destination for an electron along this chain is an oxygen molecule. Superoxide is not particularly reactive by itself, but can inactivate specific enzymes or initiate lipid peroxidation in its protonated form, the pKa of hydroperoxyl is 4.8. Thus, at physiological pH, the majority will exist as superoxide anion, if too much damage is present in mitochondria, a cell undergoes apoptosis or programmed cell death. This cytochrome C binds to Apaf-1, or apoptotic protease activating factor-1, using energy from the ATPs in the mitochondrion, the Apaf-1 and cytochrome C bind together to form apoptosomes. The apoptosomes bind to and activate caspase-9, another free-floating protein, the caspase-9 then cleaves the proteins of the mitochondrial membrane, causing it to break down and start a chain reaction of protein denaturation and eventually phagocytosis of the cell. Superoxide dismutases are a class of enzymes catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in all cells exposed to oxygen. In mammals and most chordates, three forms of superoxide dismutase are present, sOD1 is located primarily in the cytoplasm, SOD2 in the mitochondria and SOD3 is extracellular. The first is a dimer, while the others are tetramers, sOD1 and SOD3 contain copper and zinc ions, while SOD2 has a manganese ion in its reactive centre. The genes are located on chromosomes 21,6, and 4, respectively
Reactive oxygen species
–
Major cellular sources of ROS in living non-
photosynthetic cells. From a review by Novo and Parola, 2008.
25.
Carboxyhemoglobin
–
Carboxyhemoglobin or carboxyhaemoglobin is a stable complex of carbon monoxide and hemoglobin that forms in red blood cells upon contact with carbon monoxide. Exposure to small concentrations of CO hinder the ability of Hb to deliver oxygen to the body, CO is produced in normal metabolism and is also a common chemical. Tobacco smoking raises the levels of COHb by a factor of several times from its normal concentrations. Hemoglobin contains four groups each capable of reversibly binding to one oxygen molecule. Oxygen binding to any of these causes an conformational change in the protein. Carbon monoxide binds to hemoglobin at the sites as oxygen. Normally, oxygen would bind to hemoglobin in the lungs and be released in areas with low oxygen partial pressure, when carbon monoxide binds to hemoglobin, it cannot be released as easily as oxygen. The slow release rate of carbon monoxide causes an accumulation of CO-bound hemoglobin molecules as exposure to carbon monoxide continues, because of this, fewer hemoglobin particles are available to bind and deliver oxygen, thus causing the gradual suffocation associated with carbon monoxide poisoning. Since COHb releases carbon monoxide slowly, less hemoglobin will be available to transport oxygen from the lungs to the rest of the body, conversion of most Hb to COHb results in death - known medically as carboxyhemoglobinemia or carbon monoxide poisoning. Smaller amounts COHb lead to deprivation of the body causing tiredness, dizziness. COHb has a half-life in the blood of 4 to 6 hours and this time can be reduced to 70 to 35 minutes with administration of pure oxygen. Additionally, treatment in a Hyperbaric Chamber is an effective manner of reducing the half-life of COHb than administering oxygen alone. In effect, the need for hemoglobin in the blood is bypassed, COHb increases risk of blood clot. It is thought that through this mechanism, smoking increases the risk of having thromboembolic disease, pregnant smokers may give birth to babies of a lower birth mass. In biology, carbon monoxide is produced by the action of heme oxygenase 1 and 2 on the heme from hemoglobin breakdown. This process produces an amount of carboxyhemoglobin in normal persons. In many tissues, all three gases are known to act as anti-inflammatories, vasodilators and encouragers of neovascular growth, studies involving carbon monoxide have been conducted in many laboratories throughout the world for its anti-inflammatory and cytoprotective properties. Clinical tests involving humans have been performed, as of 2009, however, the results had not yet been released
Carboxyhemoglobin
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A heme unit of human carboxyhaemoglobin, showing the cacarboy ligand at thre apical position, trans to the histidine residue.
26.
Methemoglobin
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Methemoglobin is a form of the oxygen-carrying metalloprotein hemoglobin, in which the iron in the heme group is in the Fe3+ state, not the Fe2+ of normal hemoglobin. Methemoglobin cannot bind oxygen, unlike oxyhemoglobin and it is bluish chocolate-brown in color. In human blood a trace amount of methemoglobin is normally produced spontaneously, the NADH-dependent enzyme methemoglobin reductase is responsible for converting methemoglobin back to hemoglobin. A higher level of methemoglobin will tend to cause a pulse oximeter to read closer to 85% regardless of the level of oxygen saturation. In cats Ingestion of Paracetamol Amyl nitrite is administered to treat cyanide poisoning and it works by converting hemoglobin to methemoglobin, which allows for the binding of cyanide and the formation of cyanomethemoglobin. The immediate goal of forming this cyanide adduct is to prevent the binding of cyanide to the cytochrome a3 group in cytochrome c oxidase. Methemoglobin saturation is expressed as the percentage of hemoglobin in the methemoglobin state, upon exiting the body, bloodstains transit from bright red to dark brown, which is attributed to oxidation of oxy-hemoglobin to methemoglobin and hemichrome. Methemoglobinemia Blue baby syndrome Methemoglobin at the US National Library of Medicine Medical Subject Headings MetHb Formation The Blue people of Troublesome Creek
Methemoglobin
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The structure of the enzyme that converts methemoglobin to hemoglobin
27.
Pigment
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A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, many materials selectively absorb certain wavelengths of light. Materials that humans have chosen and developed for use as pigments usually have properties that make them ideal for coloring other materials. A pigment must have a high tinting strength relative to the materials it colors and it must be stable in solid form at ambient temperatures. For industrial applications, as well as in the arts, permanence, pigments that are not permanent are called fugitive. Fugitive pigments fade over time, or with exposure to light, pigments are used for coloring paint, ink, plastic, fabric, cosmetics, food, and other materials. Most pigments used in manufacturing and the arts are dry colorants. This powder is added to a binder, a neutral or colorless material that suspends the pigment. A distinction is made between a pigment, which is insoluble in its vehicle, and a dye, which either is itself a liquid or is soluble in its vehicle. A colorant can act as either a pigment or a dye depending on the vehicle involved, in some cases, a pigment can be manufactured from a dye by precipitating a soluble dye with a metallic salt. The resulting pigment is called a lake pigment, the term biological pigment is used for all colored substances independent of their solubility. In 2006, around 7.4 million tons of inorganic, organic, asia has the highest rate on a quantity basis followed by Europe and North America. By 2020, revenues will have risen to approx, the global demand on pigments was roughly US$20.5 billion in 2009, around 1. 5-2% up from the previous year. It is predicted to increase in a growth rate in the coming years. The worldwide sales are said to increase up to US$24.5 billion in 2015, pigments appear the colors they are because they selectively reflect and absorb certain wavelengths of visible light. White light is an equal mixture of the entire spectrum of visible light with a wavelength in a range from about 375 or 400 nanometers to about 760 or 780 nm. When this light encounters a pigment, parts of the spectrum are absorbed by the molecules or ions of the pigment, in organic pigments such as diazo or phthalocyanine compounds the light is absorbed by the conjugated systems of double bonds in the molecule. Some of the inorganic pigments such as vermilion or cadmium yellow absorb light by transferring an electron from the ion to the positive ion
Pigment
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Natural
ultramarine pigment in powdered form
Pigment
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Synthetic ultramarine pigment is chemically identical to natural ultramarine
Pigment
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Miracle of the Slave by
Tintoretto (c. 1548). The son of a master
dyer, Tintoretto used Carmine Red Lake pigment, derived from the
cochineal insect, to achieve dramatic color effects.
Pigment
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Girl with a Pearl Earring by
Johannes Vermeer (c. 1665).
28.
Red meat
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Commonly, especially in gastronomy, red meat or dark meat is red when raw and dark in color when cooked, in contrast to white meat, which is pale in color before and after cooking. This definition only refers to flesh from mammals or fowl, in nutritional science, red meat is defined as any meat that has more myoglobin than white meat, white meat being defined as non-dark meat from chicken, or fish. Some meat, such as pork, is red meat using the nutritional definition, according to the USDA, all meats obtained from mammals are red meats because they contain more myoglobin than fish or white meat from chicken. The culinary definition has many rules and exceptions, generally meat from mammals and meat from hunting excluding fish and insects are considered red meat. Although poultry is usually considered white, duck and goose are red, for some animals the culinary definition of red meat differs by cut, and sometimes by the age of the animal is when it was slaughtered. Pork is considered red if the animal is adult, but white if young, the same applies to young lamb and veal. Game is sometimes put in a separate category altogether, Pork is considered white under the culinary definition, but red in nutritional studies. The National Pork Board has positioned it as Pork, the Other White Meat, profiting from the ambiguity to suggest that pork has the nutritional properties of white meat, which is considered more healthful. Red meat contains large amounts of iron, creatine, minerals such as zinc and phosphorus, red meat is a source of lipoic acid. Red meat contains small amounts of vitamin D, the liver contains much higher quantities than other parts of the animal. In 2011, the USDA launched MyPlate, which didnt distinguish between kinds of meat, but did recommend eating at least 8 oz of fish each week. In 2011, the Harvard School of Public Health launched the Healthy Eating Plate because of the inadequacies of the USDAs recommendations. The Healthy Eating Plate encourages consumers to limit red meat and avoid processed meat and its website says, Eating a lot of red meat and processed meat has been linked to increased risk of heart disease, diabetes, and colon cancer. So it’s best to avoid processed meat, and to limit red meat to no more than twice a week. Switching to fish, chicken, nuts, or beans in place of red meat and processed meat can improve cholesterol levels and can lower the risk of heart disease and diabetes. Red meat is not a product, its health effects can vary based on fat content, processing. Processed red meat is linked to mortality, mainly due to cardiovascular diseases. There is some evidence too that the consumption of unprocessed red meat may have health effects in humans
Red meat
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Thinly sliced raw beef
Red meat
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Roast beef
Red meat
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Poultry and game
Red meat
29.
Transition metal dioxygen complex
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Dioxygen complexes are coordination compounds that contain O2 as a ligand. The study of compounds is inspired by oxygen-carrying proteins such as myoglobin, hemoglobin, hemerythrin. Several transition metals complexes with O2, and many of these complexes form reversibly. The binding of O2 is the first step in many important phenomena, such as respiration, corrosion. The first synthetic oxygen complex was demonstrated in 1938 with cobalt complex reversibly bound O2, O2 binds to a single metal center either “end-on” or “side-on”. O2 adducts derived from cobalt and iron complexes and related anionic ligands exhibit this bonding mode. Myoglobin and hemoglobin are famous examples, and many analogues have been described that behave similarly. Binding of O2 is usually described as proceeding via electron transfer from the center to give superoxide complexes of metal centers. η2-bonding is the most common motif seen in coordination chemistry of dioxygen, such complexes can generated by treating low-valent metal complexes with gaseous oxygen. For example, Vaskas complex reversibly binds O2, IrCl2 + O2 ⇌ IrCl2O2 The conversion is described as a 2 e− redox process, since O2 has a triplet ground state and Vaskas complex is a singlet, the reaction is slower than when singlet oxygen is used. Complexes containing η2-O2 ligands are common, but most are generated using hydrogen peroxide. Chromate ]2−) can for example be converted to the tetraperoxide 2−, the reaction of hydrogen peroxide with aqueous titanium gives a brightly colored peroxy complex that is a useful test for titanium as well as hydrogen peroxide. O2 can bind to one metal of a unit via the same modes discussed above for mononuclear complexes. A well-known example in nature is hemerythrin, which features a diiron carboxylate that binds O2 at one Fe center, dinuclear complexes can also cooperate in the binding, although the initial attack of O2 probably occurs at a single metal. These binding modes include μ2-η2, η2-, μ2-η1, η1-, depending on the degree of electron-transfer from the dimetal unit, these O2 ligands can again be described as peroxo or superoxo. In nature, such dinuclear dioxygen complexes often feature copper, dioxygen complexes are the precursors to other families of oxygenic ligands. Metal oxo compounds arise from the cleavage of the O–O bond after complexation, hydroperoxo complexes are generated in the course of the reduction of dioxygen by metals. The reduction of O2 by metal catalysts is a key half-reaction in fuel cells, metal-catalyzed oxidations with O2 proceed via the intermediacy of dioxygen complexes, although the actual oxidants are often oxo derivatives
Transition metal dioxygen complex
30.
Well done
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Doneness is a gauge of how thoroughly cooked a cut of meat is based on the color, juiciness and internal temperature when cooked. The gradations of cooking are most often used in reference to beef but are applicable to lamb, pork, poultry, veal. Gradations, their description, and the temperature ranges vary regionally from cuisine to cuisine and in local practice. For steaks, common gradations include rare, medium rare, medium, medium well and well done. In lieu of gradations and ranges, the United States Department of Agriculture recommends a temperature of at least 63 °C for beef, veal, lamb steaks, the table below is from an American reference book and pertains to beef and lamb. The interior of a cut of meat will still increase in temperature 3–5 °C after it is removed from an oven or other heat source, the whole meat and the center will also continue to cook slightly as the hot exterior continues to warm the comparatively cooler interior. The exception is if the meat has been prepared in a sous-vide process, the temperatures indicated above are the peak temperature in the cooking process, so the meat should be removed from the heat source a few degrees cooler. As meat is cooked, it turns red to pink to gray to brown to black, and the amount of red liquid, myoglobin. The color change is due to changes in the oxidation of the atom of the heme group in the myoglobin protein, raw meat is red due to myoglobin protein in the muscles. Prior to cooking, the atom is in a +2 oxidation state. As cooking proceeds, it loses an electron, moving to a +3 oxidation state, searing raises the meat’s surface temperature to 150 °C, yielding browning via different reactions, caramelization of sugars, and the Maillard reaction of amino acids. Raised to a high temperature, meat blackens from burning. Well done cuts, in addition to being brown, are drier, note that searing in no way seals in the juices – water evaporates at the same or higher rates as unseared meat. Searing does play an important role, however, in browning, a crucial contributor to flavor and texture
Well done
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Meat thermometer
Well done
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Entrecôte, medium rare
A picket-fence porphyrin complex of Fe, with axial coordination sites occupied by methylimidazole (green) and dioxygen. The R groups flank the O2-binding site.
. PMID 15774055. doi:10.1186/cc3034.
