108-499: Celestichthys margaritatus Roberts, 2007 Danio margaritatus , the celestial pearl danio , often referred to in the aquarium trade as galaxy rasbora or Microrasbora sp. 'Galaxy' , is a small cyprinid from Myanmar and Northern Thailand (in Salween basin). It has so far been found only in a very small area near Hopong east of Inle Lake , at an elevation of over 1,000 m (3,400 ft). Its habitat
216-520: A carboxyl group, and a variable side chain are bonded . Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids , have a great variety of chemical structures and properties; it is the combined effect of all of
324-470: A gene may be duplicated before it can mutate freely. However, this can also lead to complete loss of gene function and thus pseudo-genes . More commonly, single amino acid changes have limited consequences although some can change protein function substantially, especially in enzymes . For instance, many enzymes can change their substrate specificity by one or a few mutations. Changes in substrate specificity are facilitated by substrate promiscuity , i.e.
432-484: A chewing plate formed by a bony process of the skull . The pharyngeal teeth are unique to each species and are used by scientists to identify species. Strong pharyngeal teeth allow fish such as the common carp and ide to eat hard baits such as snails and bivalves . Hearing is a well-developed sense in the cyprinids since they have the Weberian organ , three specialized vertebral processes that transfer motion of
540-552: A combination of sequence, structure and function, and they can be combined in many different ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more than 5 domains). 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,
648-403: A defined conformation . Proteins can interact with many types of molecules, including with other proteins , with lipids , with carbohydrates , and with DNA . It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. E. coli and Staphylococcus aureus ). Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on
756-851: A detailed review of the vegetable proteins at the Connecticut Agricultural Experiment Station . Then, working with Lafayette Mendel and applying Liebig's law of the minimum , which states that growth is limited by the scarcest resource, to the feeding of laboratory rats, the nutritionally essential amino acids were established. The work was continued and communicated by William Cumming Rose . The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, including those of blood, egg whites, and various toxins, as well as digestive and metabolic enzymes obtained from slaughterhouses. In
864-478: A little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation , whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of
972-548: A management tool to control various factors in the aquatic environment, such as aquatic vegetation and diseases transmitted by snails. Unlike most fish species, cyprinids generally increase in abundance in eutrophic lakes. Here, they contribute towards positive feedback as they are efficient at eating the zooplankton that would otherwise graze on the algae, reducing its abundance. Cyprinids are highly important food fish; they are fished and farmed across Eurasia . In land-locked countries in particular, cyprinids are often
1080-410: A particular cell or cell type is known as its proteome . The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by
1188-500: A protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism . In silico studies use computational methods to study proteins. Proteins may be purified from other cellular components using
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#17327766283391296-411: A protein is defined by the sequence of a gene, which is encoded in the genetic code . In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea — pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters
1404-542: A protein that fold into distinct structural units. Domains usually also have specific functions, such as enzymatic activities (e.g. kinase ) or they serve as binding modules (e.g. the SH3 domain binds to proline-rich sequences in other proteins). Short amino acid sequences within proteins often act as recognition sites for other proteins. For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated by two unspecified amino acids [x], although
1512-509: A radical move, though reasonable, is probably premature. The tench ( Tinca tinca ), a significant food species farmed in western Eurasia in large numbers, is unusual. It is most often grouped with the Leuciscinae, but even when these were rather loosely circumscribed, it always stood apart. A cladistic analysis of DNA sequence data of the S7 ribosomal protein intron 1 supports
1620-486: A role in biological recognition phenomena involving cells and proteins. Receptors and hormones are highly specific binding proteins. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse . Membrane proteins contain internal channels that allow such molecules to enter and exit
1728-406: A series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a " His-tag "),
1836-454: A small tank, a group of six individuals—half males, half females—will do well and exhibit natural behavior. They tend to be rather stationary, hovering in a peculiar position in favorite spots; males and females tend to keep separate when at rest. Altogether, their behavior again resembles Danio erythromicron more than other fish. Tanks for the celestial pearl danio should be well-planted and direct daylight may be favorable (the natural habitat
1944-432: A solution known as a crude lysate . The resulting mixture can be purified using ultracentrifugation , which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles , and nucleic acids . Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate
2052-451: A specific 3D structure that determines its activity. 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 . The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in
2160-441: A variety of techniques such as ultracentrifugation , precipitation , electrophoresis , and chromatography ; the advent of genetic engineering has made possible a number of methods to facilitate purification. To perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis , in which a cell's membrane is disrupted and its internal contents released into
2268-432: A vast array of functions within organisms, including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes , and which usually results in protein folding into
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#17327766283392376-511: A very few fish species: a Microrasbora similar to M. rubescens , a rosy loach ( Yunnanilus , possibly a new species, and the dwarf snakehead Channa harcourtbutleri . The latter species presumably is the only known significant predator of D. margaritatus . The species is locally fished for food to some extent; it is dried and bought as a protein source by poor people. A can of some 500 D. margaritatus sold for food fetched about 25 kyat (about 2 UK pounds/3.9 US$ /2.7 EUR) before
2484-500: A year after the discovery of the celestial pearl danio, it was scientifically described and given the genus name Celestichthys . In 2008, a more comprehensive study showed the celestial pearl danio was a member of the genus Danio , with Danio erythromicron and Danio choprae as its closest relatives. The fish lives in small ponds created by seeping groundwater or overflow from small brooks or springs. Water temperature in January
2592-408: Is Paedocypris progenetica , reaching 10.3 mm (0.41 in) at the longest. All fish in this family are egg-layers and most do not guard their eggs; however, a few species build nests and/or guard the eggs. The bitterlings of subfamily Acheilognathinae are notable for depositing their eggs in bivalve molluscs , where the young develop until able to fend for themselves. Cyprinids contain
2700-573: Is a major pest species in Australia impacting freshwater environments, amenity, and the agricultural economy, devastating biodiversity by decimating native fish populations where they first became established as a major pest in the wild in the 1960s. In the major river system of eastern Australia, the Murray-Darling Basin , they constitute 80–90 per cent of fish biomass. In 2016 the federal government announced A$ 15.2 million to fund
2808-406: Is bronzy green, and the belly in females is yellowish-white. The gill covers are transparent, letting the blood-red gills shine through. The males will prominently display their unpaired fins to conspecifics. All fins, save the pectoral fins , show two parallel black lines with a bright red area in between; on the tail fin, this pattern is present twice (once on each lobe) and the outer black band
2916-428: Is captive-bred worldwide commercially and by hobbyists, pushing the price down from its initial high of $ 20 or more per fish to around $ 4 each. The celestial pearl danio is a rather undemanding fish if its basic requirements are being met. It does not require much space, as it is not a very active swimmer, and is not a true shoaling fish, meaning it does not require large numbers of conspecifics for its well-being. In
3024-479: Is discovered, for example: Psilorhynchus Probarbinae Parapsilorhynchini Labeonini Garrini Torinae Smiliogastrinae Cyprinini Rohteichthyini Acrossocheilini Spinibarbini Schizothoracini Schizopygopsini Barbini Protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues . Proteins perform
3132-628: Is found in hard or filamentous structures such as hair , nails , feathers , hooves , and some animal shells . Some globular proteins can also play structural functions, for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton , which allows the cell to maintain its shape and size. Other proteins that serve structural functions are motor proteins such as myosin , kinesin , and dynein , which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and
3240-402: Is high. In general shape, it resembles Danio erythromicron more than any other known species. This species shows some sexual dimorphism : males have a bright-blue background color (dull blue-green in females), and their fins are more brightly colored. The tail end of their bodies (the caudal peduncle) is also higher than in females. The body is sprinkled with small, pearly dots. The back
3348-469: Is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. The process of synthesizing a protein from an mRNA template is known as translation . The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges"
Danio margaritatus - Misplaced Pages Continue
3456-461: Is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure . Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation . Although many proteins can fold unassisted, simply through
3564-404: Is often enormous—as much as 10 -fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme). The molecules bound and acted upon by enzymes are called substrates . Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with
3672-464: Is part of the Salween basin, namely the Nam Lang and Nam Pawn Rivers. Discovered in 2006, the species quickly appeared in the aquarium trade , where its small size and bright colours made it an instant hit. This is a small, plump danionin with a markedly blunt snout, measuring 2–2.5 cm standard length ,a few individuals can able to reach 3 cm. The body is about three times as long as it
3780-462: Is prolific, spawning "almost every day", causing ponds that were thought to be empty to be fully restocked a few months later as fry hatched, grew, and reproduced quickly. The government of Myanmar banned exports of the fish in February 2007. However, an inquest into the species by Myanmar officials discovered populations of the fish in at least "five locations around Hopong ". Currently, the fish
3888-401: Is so shallow as to be well lit throughout). Water weed and similar plants should be abundant, and stones and wood to create hiding spots should be provided. It is advisable to supply the fish with a spawning mop or a dense growth of suitable plants ( java moss has been successfully used). A dense tangle of natural plants for spawning has the additional advantage of harboring protists on which
3996-584: Is the giant barb ( Catlocarpio siamensis ), which may grow up to 3 m (9.8 ft) in length and 300 kg (660 lb) in weight. Other very large species that can surpass 2 m (6.6 ft) are the golden mahseer ( Tor putitora ) and mangar ( Luciobarbus esocinus ). The largest North American species is the Colorado pikeminnow ( Ptychocheilus lucius ), which can reach up to 1.8 m (5.9 ft) in length. Conversely, many species are smaller than 5 cm (2 in). The smallest known fish
4104-535: Is the code for methionine . Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. Genes encoded in DNA are first transcribed into pre- messenger RNA (mRNA) by proteins such as RNA polymerase . Most organisms then process the pre-mRNA (also known as a primary transcript ) using various forms of post-transcriptional modification to form
4212-413: Is unknown at present. Eggs are not strewn freely into the water, but they are not deposited in clutches to a prepared surface either; rather, it seems, that they are hidden away in vegetation as a loose batch. Courting males will seek out and try to defend a patch of dense vegetation. While pursuit swimming has been observed, it does not seem to be connected directly to the actual act of reproduction in which
4320-399: Is vestigial. Females have a weaker version of the pattern in the tail and dorsal fins only, sometimes in the anal fin, too. A courting male develops a red belly and the flanks brighten and darken, making the pearly spots stand out even more, with the back appearing paler than the flanks and also standing out. A female in reproductive age can be recognized by a black anal spot which separates
4428-557: The Cultrinae and Leuciscinae, regardless of their exact delimitation, are rather close relatives and stand apart from Cyprininae – but the overall systematics and taxonomy of the Cyprinidae remain a subject of considerable debate. A large number of genera are incertae sedis , too equivocal in their traits and/or too little-studied to permit assignment to a particular subfamily with any certainty. Part of
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4536-530: The Labeoninae or Squaliobarbinae also remain doubtful, although the latter do appear to correspond to a distinct lineage. The sometimes-seen grouping of the large-headed carps ( Hypophthalmichthyinae ) with Xenocypris , though, seems quite in error. More likely, the latter are part of the Cultrinae. The entirely paraphyletic "Barbinae" and the disputed Labeoninae might be better treated as part of
4644-492: The amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da . Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh." Around 1862, Karl Heinrich Ritthausen isolated the amino acid glutamic acid . Thomas Burr Osborne compiled
4752-874: The aquarium and fishpond hobbies, most famously the goldfish , which was bred in China from the Prussian carp ( Carassius (auratus) gibelio ). First imported into Europe around 1728, it was originally much-fancied by the Chinese nobility as early as 1150 AD and, after it arrived there in 1502, also in Japan . In addition to the goldfish, the common carp was bred in Japan into the colorful ornamental variety known as koi — or more accurately nishikigoi ( 錦鯉 ) , as koi ( 鯉 ) simply means "common carp" in Japanese — from
4860-413: The barbs and barbels , among others. Cyprinidae is the largest and most diverse fish family, and the largest vertebrate animal family overall, with about 3,000 species ; only 1,270 of these remain extant, divided into about 200 valid genera . Cyprinids range from about 12 mm (0.5 in) in size to the 3 m (9.8 ft) giant barb ( Catlocarpio siamensis ). By genus and species count,
4968-454: The fry feed initially. The celestial pearl danio seems overall quite peaceful, though some fin-nipping occurs. Consequently, it cannot be kept with large or "bully" fish. Small, swarming danionins which require similar water conditions would be a natural choice for company, as such more active species provide nice contrast behaviorally and, being available in a wide range of colors and patterns, also make it possible to choose fish that complement
5076-555: The gas bladder to the inner ear. The vertebral processes of the Weberian organ also permit a cyprinid to detect changes in motion of the gas bladder due to atmospheric conditions or depth changes. The cyprinids are considered physostomes because the pneumatic duct is retained in adult stages and the fish are able to gulp air to fill the gas bladder, or they can dispose of excess gas to the gut. Cyprinids are native to North America , Africa , and Eurasia . The largest known cyprinid
5184-436: The moderlieschen , are opportunistic predators that will eat larvae of the common frog in artificial circumstances. Some cyprinids, such as the grass carp , are specialized herbivores; others, such as the common nase , eat algae and biofilms , while others, such as the black carp , specialize in snails, and some, such as the silver carp , are specialized filter feeders . For this reason, cyprinids are often introduced as
5292-644: The muscle sarcomere , with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids. Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis , which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains. These methods are useful in laboratory biochemistry and cell biology , though generally not for commercial applications. Chemical synthesis
5400-645: The sperm of many multicellular organisms which reproduce sexually . They also generate the forces exerted by contracting muscles and play essential roles in intracellular transport. A key question in molecular biology is how proteins evolve, i.e. how can mutations (or rather changes in amino acid sequence) lead to new structures and functions? Most amino acids in a protein can be changed without disrupting activity or function, as can be seen from numerous homologous proteins across species (as collected in specialized databases for protein families , e.g. PFAM ). In order to prevent dramatic consequences of mutations,
5508-497: The 1700s by Antoine Fourcroy and others, who often collectively called them " albumins ", or "albuminous materials" ( Eiweisskörper , in German). Gluten , for example, was first separated from wheat in published research around 1747, and later determined to exist in many plants. In 1789, Antoine Fourcroy recognized three distinct varieties of animal proteins: albumin , fibrin , and gelatin . Vegetable (plant) proteins studied in
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#17327766283395616-517: The 18th century until today. Other popular aquarium cyprinids include danionins , rasborines and true barbs . Larger species are bred by the thousands in outdoor ponds, particularly in Southeast Asia , and trade in these aquarium fishes is of considerable commercial importance. The small rasborines and danionines are perhaps only rivalled by characids (tetras) and poecilid livebearers in their popularity for community aquaria . Some of
5724-572: The 1950s, the Armour Hot Dog Company purified 1 kg of pure bovine pancreatic ribonuclease A and made it freely available to scientists; this gesture helped ribonuclease A become a major target for biochemical study for the following decades. The understanding of proteins as polypeptides , or chains of amino acids, came through the work of Franz Hofmeister and Hermann Emil Fischer in 1902. The central role of proteins as enzymes in living organisms that catalyzed reactions
5832-498: The 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG ( adenine – uracil – guanine )
5940-707: The Cyprininae, forming a close-knit group whose internal relationships are still little known. The small African " barbs " do not belong in Barbus sensu stricto – indeed, they are as distant from the typical barbels and the typical carps ( Cyprinus ) as these are from Garra (which is placed in the Labeoninae by most who accept the latter as distinct) and thus might form another as yet unnamed subfamily. However, as noted above, how various minor lineages tie into this has not yet been resolved; therefore, such
6048-519: The EC number system provides a functional classification scheme. Similarly, the gene ontology classifies both genes and proteins by their biological and biochemical function, but also by their intracellular location. Sequence similarity is used to classify proteins both in terms of evolutionary and functional similarity. This may use either whole proteins or protein domains , especially in multi-domain proteins . Protein domains allow protein classification by
6156-486: The National Carp Control Plan to investigate using Cyprinid herpesvirus 3 (carp virus) as a biological control agent while minimising impacts on industry and environment should a carp virus release go ahead. Despite initial, favourable assessment, in 2020 this plan was found to be unlikely to work due to the high fecundity of the fish. Numerous cyprinids have become popular and important within
6264-571: The Rasborinae as the basal lineage with the Cyprininae as a sister clade to the Leuciscinae. The subfamilies Acheilognathinae , Gobioninae , and Leuciscinae are monophyletic. The 5th Edition of Fishes of the World sets out the following subfamilies: With such a large and diverse family the taxonomy and phylogenies are always being worked on so alternative classifications are being created as new information
6372-709: The ability of many enzymes to bind and process multiple substrates . When mutations occur, the specificity of an enzyme can increase (or decrease) and thus its enzymatic activity. Thus, bacteria (or other organisms) can adapt to different food sources, including unnatural substrates such as plastic. Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . The activities and structures of proteins may be examined in vitro , in vivo , and in silico . In vitro studies of purified proteins in controlled environments are useful for learning how
6480-405: The addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine . Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of
6588-607: The alpha carbons are roughly coplanar . The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. The end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of the protein is written from N-terminus to C-terminus, from left to right). The words protein , polypeptide, and peptide are
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#17327766283396696-531: The amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. The amino acids in a polypeptide chain are linked by peptide bonds . Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that
6804-442: The belly color from the uniformly reddish base of the anal fin . The male has a small black pad at the edges of the lower jaw, which is absent or reduced in females. Immature fish show some indication of a striped pattern, which eventually decomposes into the pearly dots. Initially, the celestial pearl danio was assumed to be a member of the genus Microrasbora , due to its similarity to "Microrasbora" erythromicron . Less than
6912-574: The binding of a substrate molecule to an enzyme's active site , or the physical region of the protein that participates in chemical catalysis. In solution, proteins also undergo variation in structure through thermal vibration and the collision with other molecules. Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins , fibrous proteins , and membrane proteins . Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, such as collagen ,
7020-570: The body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is haemoglobin , which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom . Lectins are sugar-binding proteins which are highly specific for their sugar moieties. Lectins typically play
7128-476: The brilliant colors of D. margaritatus . Many danionins prefer slightly acidic water, however, and maintaining the rather high pH found across the Inle basin seems a necessary condition to keep fish from there successfully. Cyprinid and see text Cyprinidae is a family of freshwater fish commonly called the carp or minnow family , including the carps , the true minnows , and their relatives
7236-558: The cell is as enzymes , which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism , as well as manipulating DNA in processes such as DNA replication , DNA repair , and transcription . Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis
7344-436: The cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell. Antibodies are protein components of an adaptive immune system whose main function is to bind antigens , or foreign substances in the body, and target them for destruction. Antibodies can be secreted into the extracellular environment or anchored in
7452-752: The cell's machinery through the process of protein turnover . A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either 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 and participate in virtually every process within cells . 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
7560-450: The cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins ; for example, collagen and elastin are critical components of connective tissue such as cartilage , and keratin
7668-621: The chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as " conformations ", and transitions between them are called conformational changes. Such changes are often induced by
7776-441: The chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. With the exception of certain types of RNA , most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively. The set of proteins expressed in
7884-409: The color pattern starts to appear from week 12 onwards. Within six months of its appearance in the aquarium trade, the species was falsely reported as having become so rare, collectors were obtaining only a "few dozen fish per day". Initially, only a small number of aquarists managed to breed the fish successfully, while nearly all the fish offered for sale were wild-caught. The (unfounded) concern over
7992-490: The construction of enormously complex signaling networks. As interactions between proteins are reversible, and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types. The best-known role of proteins in
8100-408: The derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respectively) due to a bigger number of protein domains constituting proteins in higher organisms. For instance, yeast proteins are on average 466 amino acids long and 53 kDa in mass. The largest known proteins are the titins , a component of
8208-451: The erroneous conclusion that they might be composed of a single type of (very large) molecule. The term "protein" to describe these molecules was proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος ( proteios ), meaning "primary", "in the lead", or "standing in front", + -in . Mulder went on to identify the products of protein degradation such as
8316-463: The family makes up more than two-thirds of the ostariophysian order Cypriniformes . The family name is derived from the Greek word kyprînos ( κυπρῖνος 'carp'). Cyprinids are stomachless, or agastric , fish with toothless jaws. Even so, food can be effectively chewed by the gill rakers of the specialized last gill bow. These pharyngeal teeth allow the fish to make chewing motions against
8424-509: The first and only known example of androgenesis in a vertebrate, in the Squalius alburnoides allopolyploid complex. Most cyprinids feed mainly on invertebrates and vegetation , probably due to the lack of teeth and stomach; however, some species, like the asp , are predators that specialize in fish. Many species, such as the ide and the common rudd , prey on small fish when individuals become large enough. Even small species, such as
8532-405: The fish was discovered for the aquarium trade. The spawning behavior has significant consequences for captive breeding (see below ). The celestial pearl danio appears to be adapted to somewhat ephemeral habitats. It does not have a dedicated spawning season, nor do the females lay continuously. Rather, they produce small batches of around 30 eggs per spawning episode. The time between spawnings
8640-585: The grass carp ( Ctenopharyngodon idella ) are the most important of these, for example in Florida . Carp in particular can stir up sediment , reducing the clarity of the water and making plant growth difficult. In America and Australia, such as the Asian carp in the Mississippi Basin , they have become invasive species that compete with native fishes or disrupt the environment. Cyprinus carpio
8748-534: The late 1700s and early 1800s included gluten , plant albumin , gliadin , and legumin . Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula , C 400 H 620 N 100 O 120 P 1 S 1 . He came to
8856-478: The major component of connective tissue, or keratin , the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane . A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration , are called dehydrons . Many proteins are composed of several protein domains , i.e. segments of
8964-910: The major species of fish eaten because they make the largest part of biomass in most water types except for fast-flowing rivers. In Eastern Europe, they are often prepared with traditional methods such as drying and salting. The prevalence of inexpensive frozen fish products made this less important now than it was in earlier times. Nonetheless, in certain places, they remain popular for food, as well as recreational fishing , for ornamental use, and have been deliberately stocked in ponds and lakes for centuries for this reason. Cyprinids are popular for angling especially for match fishing (due to their dominance in biomass and numbers) and fishing for common carp because of its size and strength. Several cyprinids have been introduced to waters outside their natural ranges to provide food, sport, or biological control for some pest species. The common carp ( Cyprinus carpio ) and
9072-669: The male displays to a passing female, and tests her readiness with a brief chase. The pair then moves into the substrate and deposits the eggs. Other males noticing reproduction will try to follow the mating pair, either to try to fertilize the eggs with their own sperm or eat them. At 24–25 °C, the larvae hatch after 3–4 days. They are dark and cryptic initially and for about three days after hatching, they hide away between substrate and detritus and are very hard to see. They subsequently become lighter in color and start swimming freely and feeding on their own. At some 8–10 weeks after hatching, they undergo metamorphosis to adult form, and
9180-443: The mature mRNA, which is then used as a template for protein synthesis by the ribosome . In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid . In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm , where protein synthesis then takes place. The rate of protein synthesis
9288-405: The membranes of specialized B cells known as plasma cells . Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high. Many ligand transport proteins bind particular small biomolecules and transport them to other locations in
9396-556: The most popular cyprinids among aquarists , other than goldfish and koi, include the cherry barb , Harlequin rasbora , pearl danios , rainbow sharks , tiger barbs , and the White Cloud Mountain minnow . One particular species of these small and undemanding danionines is the zebrafish ( Danio rerio ). It has become the standard model species for studying developmental genetics of vertebrates , in particular fish. Habitat destruction and other causes have reduced
9504-496: The nobel prize in 1972, solidified the thermodynamic hypothesis of protein folding, according to which the folded form of a protein represents its free energy minimum. With the development of X-ray crystallography , it became possible to determine protein structures as well as their sequences. The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew , in 1958. The use of computers and increasing computing power also supported
9612-500: The order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion. The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of
9720-440: The physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some 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 certain period and are then degraded and recycled by
9828-424: The process of cell signaling and signal transduction . Some proteins, such as insulin , are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues . Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell. Many receptors have a binding site exposed on
9936-534: The protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity. The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according to their charge using electrofocusing . For natural proteins,
10044-427: The proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. 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 metabolic use. Proteins have been studied and recognized since
10152-582: The same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein–protein interactions also regulate enzymatic activity, control progression through the cell cycle , and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows
10260-581: The sample, allowing scientists to obtain more information and analyze larger structures. Computational protein structure prediction of small protein structural domains has also helped researchers to approach atomic-level resolution of protein structures. As of April 2024 , the Protein Data Bank contains 181,018 X-ray, 19,809 EM and 12,697 NMR protein structures. Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes
10368-430: The sequencing of complex proteins. In 1999, Roger Kornberg succeeded in sequencing the highly complex structure of RNA polymerase using high intensity X-rays from synchrotrons . Since then, cryo-electron microscopy (cryo-EM) of large macromolecular assemblies has been developed. Cryo-EM uses protein samples that are frozen rather than crystals, and beams of electrons rather than X-rays. It causes less damage to
10476-413: The solution seems that the delicate rasborines are the core group, consisting of minor lineages that have not shifted far from their evolutionary niche , or have coevolved for millions of years. These are among the most basal lineages of living cyprinids. Other "rasborines" are apparently distributed across the diverse lineages of the family. The validity and circumscription of proposed subfamilies like
10584-445: The stock in all pools at one location is entirely fished off, it is unclear in how far the fish would be able to recolonize them. Conversely, if only part of a local subpopulation is removed, pools from which all celestial pearl danios have been removed likely will be recolonized with a healthy population again after one year or so. The dire warnings reported by Clarke, later in 2007 were found to be unfounded. The celestial pearl danio
10692-405: The substrate, and an even smaller fraction—three to four residues on average—that are directly involved in catalysis. The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site . Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes. Many proteins are involved in
10800-716: The surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear Motif (ELM) database. Topology of a protein describes the entanglement of the backbone and the arrangement of contacts within the folded chain. Two theoretical frameworks of knot theory and Circuit topology have been applied to characterise protein topology. Being able to describe protein topology opens up new pathways for protein engineering and pharmaceutical development, and adds to our understanding of protein misfolding diseases such as neuromuscular disorders and cancer. Proteins are
10908-400: The tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain . Proteins are always biosynthesized from N-terminus to C-terminus . The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass , which is normally reported in units of daltons (synonymous with atomic mass units ), or
11016-472: The tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10 M) but does not bind at all to its amphibian homolog onconase (> 1 M). Extremely minor chemical changes such as
11124-542: The view that it is distinct enough to constitute a monotypic subfamily. It also suggests it may be closer to the small East Asian Aphyocypris , Hemigrammocypris , and Yaoshanicus . They would have diverged roughly at the same time from cyprinids of east-central Asia, perhaps as a result of the Alpide orogeny that vastly changed the topography of that region in the late Paleogene , when their divergence presumably occurred. A DNA-based analysis of these fish places
11232-482: The wild populations led British fishkeeping magazine Practical Fishkeeping to request that only aquarists prepared to breed the fish should buy any fish they see for sale, to reduce pressure on the wild stocks by diminishing the demand for them in the UK. As the species seems adapted to living in and colonizing small, possibly ephemeral pools , it seemed not very well able to withstand prolonged and intense exploitation—if
11340-670: The wild stocks of several cyprinids to dangerously low levels; some are already entirely extinct . In particular, the cyprinids of the subfamily Leuciscinae from southwestern North America have been hit hard by pollution and unsustainable water use in the early to mid-20th century; most globally extinct cypriniform species are in fact leuciscinid cyprinids from the southwestern United States and northern Mexico. The massive diversity of cyprinids has so far made it difficult to resolve their phylogeny in sufficient detail to make assignment to subfamilies more than tentative in many cases. Some distinct lineages obviously exist – for example,
11448-472: Was insulin , by Frederick Sanger , in 1949. Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids , or cyclols . He won the Nobel Prize for this achievement in 1958. Christian Anfinsen 's studies of the oxidative folding process of ribonuclease A, for which he won
11556-581: Was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein. Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding , an idea first put forth by William Astbury in 1933. Later work by Walter Kauzmann on denaturation , based partly on previous studies by Kaj Linderstrøm-Lang , contributed an understanding of protein folding and structure mediated by hydrophobic interactions . The first protein to have its amino acid chain sequenced
11664-408: Was rather low (22–24 °C), but as the habitat is very shallow, it would heat up quickly during hot spells, thus D. margaritatus is probably tolerant of temperatures above 26°C. As in most water bodies in the Inle drainage, the water is slightly alkaline . The habitat is heavily vegetated with Hydrocharitaceae similar to Elodea (water weed). The celestial pearl danio shares its habitat with
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