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A superhydrophobic coating is a thin surface layer that repels water. It is made from superhydrophobic (ultrahydrophobicity) materials. Droplets hitting this kind of coating can fully rebound. Generally speaking, superhydrophobic coatings are made from composite materials where one component provides the roughness and the other provides low surface energy. | 7 | Physical Chemistry |
During a meeting of the New York Academy of Sciences Section of Geology and Mineralogy in 1903, geologist Amadeus William Grabau proposed a new rock classification system in his paper Discussion of and Suggestions Regarding a New Classification of Rocks'. Within the primary subdivision of "Endogenetic rocks" – rocks formed through chemical processes – was a category termed "Biogenic rocks", which was used synonymously with "Organic rocks". Other secondary categories were "Igneous" and "Hydrogenic" rocks.
In the 1930s German chemist Alfred E. Treibs first detected biogenic substances in petroleum as part of his studies of porphyrins. Based on this research, there was a later increase in the 1970s in the investigation of biogenic substances in sedimentary rocks as part of the study of geology. This was facilitated by the development of more advanced analytical methods, and led to greater collaboration between geologists and organic chemists in order to research the biogenic compounds in sediments.
Researchers additionally began to investigate the production of compounds by microorganisms in the marine environment during the early 1960s. By 1975, different research areas had developed in the study of marine biochemistry. These were "marine toxins, marine bioproducts and marine chemical ecology". Following this in 1994, Teuscher and Lindequist defined biogenic substances as "chemical compounds which are synthesised by living organisms and which, if they exceed certain concentrations, cause temporary or permanent damage or even death of other organisms by chemical or physicochemical effects" in their book, Biogene Gifte. This emphasis in research and classification on the toxicity of biogenic substances was partly due to the cytotoxicity-directed screening assays that were used to detect the biologically active compounds. The diversity of biogenic products has since been expanded from cytotoxic substances through the use of alternative pharmaceutical and industrial assays. | 0 | Organic Chemistry |
Austenite, also known as gamma-phase iron (γ-Fe), is a metallic, non-magnetic allotrope of iron or a solid solution of iron with an alloying element. In plain-carbon steel, austenite exists above the critical eutectoid temperature of 1000 K (727 °C); other alloys of steel have different eutectoid temperatures. The austenite allotrope is named after Sir William Chandler Roberts-Austen (1843–1902). It exists at room temperature in some stainless steels due to the presence of nickel stabilizing the austenite at lower temperatures. | 8 | Metallurgy |
In 2005, British researchers noticed that the net flow of the northern Gulf Stream had decreased by about 30% since 1957. Coincidentally, scientists at Woods Hole had been measuring the freshening of the North Atlantic as Earth becomes warmer. Their findings suggested that precipitation increases in the high northern latitudes, and polar ice melts as a consequence. By flooding the northern seas with excessive fresh water, global warming could, in theory, divert the Gulf Stream waters that usually flow northward, past the British Isles and Norway, and cause them to instead circulate toward the equator. Were this to happen, Europe's climate would be seriously impacted.
Don Chambers from the USF College of Marine Science mentioned, "The major effect of a slowing AMOC is expected to be cooler winters and summers around the North Atlantic, and small regional increases in sea level on the North American coast." James Hansen and Makiko Sato stated, "AMOC slowdown that causes cooling ~1°C and perhaps affects weather patterns is very different from an AMOC shutdown that cools the North Atlantic several degrees Celsius; the latter would have dramatic effects on storms and be irreversible on the century time scale." Downturn of the Atlantic meridional overturning circulation, has been tied to extreme regional sea level rise. | 9 | Geochemistry |
Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U).
Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), Valine (Val, V). | 1 | Biochemistry |
Generally, it is not easy to achieve pure organic phosphorescence, partly because of the instability of the triplet state (easily be quenched by moisture, oxygen, etc). Host-guest structures can provide a rigid matrix, which protects the triplet state from being quenched. In this circumstance, α-CD and CB could be used, in which the phosphor is served as a guest to interact with the host. For example, 4-phenylpyridium derivatives interacted with CB, and copolymerize with acrylamide. The resulting polymer yielded ~2 s of phosphorescence lifetime. Additionally, Zhu et al used crown ether and potassium ion to modify the polymer, and enhance the emission of phosphorescence. | 6 | Supramolecular Chemistry |
As shown in Eq. 2, the neutral pathway of the Heck reaction begins with the oxidative addition of the aryl or alkenyl halide into a coordinatively unsaturated palladium(0) complex (typically bound to two phosphine ligands) to give complex I. Dissociation of a phosphine ligand followed by association of the alkene yields complex II, and migratory insertion of the alkene into the carbon-palladium bond establishes the key carbon-carbon bond.
Insertion takes place in a suprafacial fashion, but the dihedral angle between the alkene and palladium-carbon bond during insertion can vary from 0° to ~90°. After insertion, β-hydride elimination affords the product and a palladium(II)-hydrido complex IV, which is reduced by base back to palladium(0). | 0 | Organic Chemistry |
Decreased oxygen availability results in decreases in many zooplankton species’ egg production, food intake, respiration, and metabolic rates. Temperature and salinity in areas of decreased oxygen concentrations also affect oxygen availability. Higher temperatures and salinity lower oxygen solubility decrease the partial pressure of oxygen. This decreased partial pressure increases organisms’ respiration rates, causing the oxygen demand of the organism to increase.
In addition to affecting their vital functions, zooplankton alter their distribution in response to hypoxic or anoxic zones. Many species actively avoid low oxygen zones, while others take advantage of their predators’ low tolerance for hypoxia and use these areas as a refuge. Zooplankton that exhibit daily vertical migrations to avoid predation and low oxygen conditions also excrete ammonium near the oxycline and contribute to increased anaerobic ammonium oxidation (anammox, which produces N gas. As hypoxic regions expand vertically and horizontally, the habitable ranges for phytoplankton, zooplankton, and nekton increasingly overlap, increasing their susceptibility to predation and human exploitation. | 9 | Geochemistry |
Recognition of its prevalence and consequences has led to governments and non-government organizations promoting vitamin A fortification of foods and creating programs that administer large bolus-size oral doses of vitamin A to young children every four to six months. In 2008, the World Health Organization estimated that vitamin A supplementation over a decade in 40 countries averted 1.25 million deaths due to vitamin A deficiency. A Cochrane review reported that vitamin A supplementation is associated with a clinically meaningful reduction in morbidity and mortality in children ages six month to five years of age. All-cause mortality was reduced by 14%, and incidences of diarrhea by 12%. However, a Cochrane review by the same group concluded there was insufficient evidence to recommend blanket vitamin A supplementation for infants one to six months of age, as it did not reduce infant mortality or morbidity. | 1 | Biochemistry |
Neutron stars form as remnants of massive stars after a supernova event. Unlike their progenitor star, neutron stars do not consist of a gaseous plasma. Rather, the intense gravitational attraction of the compact mass overcomes the electron degeneracy pressure and causes electron capture to occur within the star. The result is a compact ball of nearly pure neutron matter with sparse protons and electrons interspersed, filling a space several thousand times smaller than the progenitor star.
At the surface, the pressure is low enough that conventional nuclei, such as helium and iron, can exist independently of one another and are not crushed together due to the mutual Coulomb repulsion of their nuclei. At the core, the pressure is so great that this Coulomb repulsion cannot support individual nuclei, and some form of ultra-dense matter, such as the theorized quark–gluon plasma, should exist.
The presence of a small population of protons is essential to the formation of nuclear pasta. The nuclear attraction between protons and neutrons is greater than the nuclear attraction of two protons or two neutrons. Similar to how neutrons act to stabilize heavy nuclei of conventional atoms against the electric repulsion of the protons, the protons act to stabilize the pasta phases. The competition between the electric repulsion of the protons, the attractive force between nuclei, and the pressure at different depths in the star lead to the formation of nuclear pasta. | 7 | Physical Chemistry |
Many electrophilic oxides insert into metal carbon bonds; these include sulfur dioxide, carbon dioxide, and nitric oxide. These reactions have limited practical significance, but are of historic interest. With transition metal alkyls, these oxides behave as electrophiles and insert into the bond between metals and their relatively nucleophilic alkyl ligands. As discussed in the article on Metal sulfur dioxide complexes, the insertion of SO has been examined in particular detail. | 0 | Organic Chemistry |
Information about the mechanism of a reaction is often provided by the use of chemical kinetics to determine the rate equation and the reaction order in each reactant.
Consider the following reaction for example:
:CO + NO → CO + NO
In this case, experiments have determined that this reaction takes place according to the rate law . This form suggests that the rate-determining step is a reaction between two molecules of NO. A possible mechanism for the overall reaction that explains the rate law is:
:2 NO → NO + NO (slow)
:NO + CO → NO + CO (fast)
Each step is called an elementary step, and each has its own rate law and molecularity. The elementary steps should add up to the original reaction. (Meaning, if we were to cancel out all the molecules that appear on both sides of the reaction, we would be left with the original reaction.)
When determining the overall rate law for a reaction, the slowest step is the step that determines the reaction rate. Because the first step (in the above reaction) is the slowest step, it is the rate-determining step. Because it involves the collision of two NO molecules, it is a bimolecular reaction with a rate which obeys the rate law .
Other reactions may have mechanisms of several consecutive steps. In organic chemistry, the reaction mechanism for the benzoin condensation, put forward in 1903 by A. J. Lapworth, was one of the first proposed reaction mechanisms.
A chain reaction is an example of a complex mechanism, in which the propagation steps form a closed cycle.
In a chain reaction, the intermediate produced in one step generates an intermediate in another step.
Intermediates are called chain carriers. Sometimes, the chain carriers are radicals, they can be ions as well. In nuclear fission they are neutrons.
Chain reactions have several steps, which may include:
# Chain initiation: this can be by thermolysis (heating the molecules) or photolysis (absorption of light) leading to the breakage of a bond.
# Propagation: a chain carrier makes another carrier.
# Branching: one carrier makes more than one carrier.
# Retardation: a chain carrier may react with a product reducing the rate of formation of the product. It makes another chain carrier, but the product concentration is reduced.
# Chain termination: radicals combine and the chain carriers are lost.
# Inhibition: chain carriers are removed by processes other than termination, such as by forming radicals.
Even though all these steps can appear in one chain reaction, the minimum necessary ones are Initiation, propagation, and termination.
An example of a simple chain reaction is the thermal decomposition of acetaldehyde (CHCHO) to methane (CH) and carbon monoxide (CO). The experimental reaction order is 3/2, which can be explained by a Rice-Herzfeld mechanism.
This reaction mechanism for acetaldehyde has 4 steps with rate equations for each step :
# Initiation : CHCHO → •CH + •CHO (Rate=k [CHCHO])
# Propagation: CHCHO + •CH → CH + CHCO• (Rate=k [CHCHO][•CH])
# Propagation: CHCO• → •CH + CO (Rate=k [CHCO•])
# Termination: •CH + •CH → CHCH (Rate=k [•CH])
For the overall reaction, the rates of change of the concentration of the intermediates •CH and CHCO• are zero, according to the steady-state approximation, which is used to account for the rate laws of chain reactions.
d[•CH]/dt = k[CHCHO] – k[•CH][CHCHO] + k[CHCO•] - 2k[•CH] = 0
and d[CHCO•]/dt = k[•CH][CHCHO] – k[CHCO•] = 0
The sum of these two equations is k[CHCHO] – 2 k[•CH] = 0. This may be solved to find the steady-state concentration of •CH radicals as [•CH] = (k / 2k) [CHCHO].
It follows that the rate of formation of CH is d[CH]/dt = k[•CH][CHCHO] = k (k / 2k) [CHCHO]
Thus the mechanism explains the observed rate expression, for the principal products CH and CO. The exact rate law may be even more complicated, there are also minor products such as acetone (CHCOCH) and propanal (CHCHCHO). | 7 | Physical Chemistry |
A disproportionation reaction is one in which a single substance is both oxidized and reduced. For example, thiosulfate ion with sulfur in oxidation state +2 can react in the presence of acid to form elemental sulfur (oxidation state 0) and sulfur dioxide (oxidation state +4).
Thus one sulfur atom is reduced from +2 to 0, while the other is oxidized from +2 to +4. | 9 | Geochemistry |
The compound 2-chlorobenzalmalononitrile (also called o-chlorobenzylidene malononitrile; chemical formula: CHClN), a cyanocarbon, is the defining component of tear gas commonly referred to as CS gas, which is used as a riot control agent.
Exposure causes a burning sensation and tearing of the eyes to the extent that the subject cannot keep their eyes open, and a burning irritation of the mucous membranes of the nose, mouth and throat, resulting in profuse coughing, nasal mucus discharge, disorientation, and difficulty breathing, partially incapacitating the subject. CS gas is an aerosol of a volatile solvent (a substance that dissolves other active substances and that easily evaporates) and 2-chlorobenzalmalononitrile, which is a solid compound at room temperature. CS gas is generally accepted as being non-lethal. It was first synthesized by two Americans, Ben Corson and Roger Stoughton, at Middlebury College in 1928, and the chemicals name is derived from the first letters of the scientists surnames.
CS was developed and tested secretly at Porton Down in Wiltshire, UK, in the 1950s and '60s. CS was used first on animals, then subsequently on British Army servicemen volunteers. CS has less effect on animals because they have different tear ducts and, in the case of non-human mammals, their fur inhibits the free entry of the gas. | 1 | Biochemistry |
All data in BacMap is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. BacMap data is available through a public web interface and downloads. | 1 | Biochemistry |
The five atoms bonded to the central atom are not all equivalent, and two different types of position are defined. For phosphorus pentachloride as an example, the phosphorus atom shares a plane with three chlorine atoms at 120° angles to each other in equatorial positions, and two more chlorine atoms above and below the plane (axial or apical positions).
According to the VSEPR theory of molecular geometry, an axial position is more crowded because an axial atom has three neighboring equatorial atoms (on the same central atom) at a 90° bond angle, whereas an equatorial atom has only two neighboring axial atoms at a 90° bond angle. For molecules with five identical ligands, the axial bond lengths tend to be longer because the ligand atom cannot approach the central atom as closely. As examples, in PF the axial P−F bond length is 158 pm and the equatorial is 152 pm, and in PCl the axial and equatorial are 214 and 202 pm respectively.
In the mixed halide PFCl the chlorines occupy two of the equatorial positions, indicating that fluorine has a greater apicophilicity or tendency to occupy an axial position. In general ligand apicophilicity increases with electronegativity and also with pi-electron withdrawing ability, as in the sequence Cl < F < CN. Both factors decrease electron density in the bonding region near the central atom so that crowding in the axial position is less important. | 4 | Stereochemistry |
Using the dynamic partitioning capabilities employed in dPCR, improved NGS sequencing can be achieved by partitioning of complex PCR reactions prior to amplification to give more uniform amplification across many distinct amplicons for NGS analysis. Additionally, the improved specificity of complex PCR amplification reactions in droplets has been shown to greatly reduce the number of iterations required to select for high affinity aptamers in the SELEX method. Partitioning can also allow for more robust measurements of telomerase activity from cell lysates. dPCR’s dynamic partitioning capabilities can also be used to partition thousands of nuclei or whole cells into individual droplets to facilitate library preparation for a single cell assay for transposase-accessible chromatin using sequencing (scATAC-seq). | 1 | Biochemistry |
In cases where the diameter of a trapped particle is significantly smaller than the wavelength of light, the conditions for Rayleigh scattering are satisfied and the particle can be treated as a point dipole in an inhomogeneous electromagnetic field. The force applied on a single charge in an electromagnetic field is known as the Lorentz force,
The force on the dipole can be calculated by substituting two terms for the electric field in the equation above, one for each charge. The polarization of a dipole is where is the distance between the two charges. For a point dipole, the distance is infinitesimal, Taking into account that the two charges have opposite signs, the force takes the form
Notice that the cancel out. Multiplying through by the charge, , converts position, , into polarization, ,
where in the second equality, it has been assumed that the dielectric particle is linear (i.e. ).
In the final steps, two equalities will be used: (1) a vector analysis equality, (2) Faraday's law of induction.
First, the vector equality will be inserted for the first term in the force equation above. Maxwell's equation will be substituted in for the second term in the vector equality. Then the two terms which contain time derivatives can be combined into a single term.
The second term in the last equality is the time derivative of a quantity that is related through a multiplicative constant to the Poynting vector, which describes the power per unit area passing through a surface. Since the power of the laser is constant when sampling over frequencies much longer than the frequency of the laser's light ~10 Hz, the derivative of this term averages to zero and the force can be written as
where in the second part we have included the induced dipole moment (in MKS units) of a spherical dielectric particle: , where is the particle radius, is the index of refraction of the particle and is the relative refractive index between the particle and the medium. The square of the magnitude of the electric field is equal to the intensity of the beam as a function of position. Therefore, the result indicates that the force on the dielectric particle, when treated as a point dipole, is proportional to the gradient along the intensity of the beam. In other words, the gradient force described here tends to attract the particle to the region of highest intensity. In reality, the scattering force of the light works against the gradient force in the axial direction of the trap, resulting in an equilibrium position that is displaced slightly downstream of the intensity maximum. Under the Rayleigh approximation, we can also write the scattering force as
Since the scattering is isotropic, the net momentum is transferred in the forward direction. On the quantum level, we picture the gradient force as forward Rayleigh scattering in which identical photons are created and annihilated concurrently, while in the scattering (radiation) force the incident photons travel in the same direction and ‘scatter’ isotropically. By conservation of momentum, the particle must accumulate the photons' original momenta, causing a forward force in the latter. | 1 | Biochemistry |
All microbial metabolisms can be arranged according to three principles:
1. How the organism obtains carbon for synthesizing cell mass:
* autotrophic – carbon is obtained from carbon dioxide ()
* heterotrophic – carbon is obtained from organic compounds
* mixotrophic – carbon is obtained from both organic compounds and by fixing carbon dioxide
2. How the organism obtains reducing equivalents (hydrogen atoms or electrons) used either in energy conservation or in biosynthetic reactions:
* lithotrophic – reducing equivalents are obtained from inorganic compounds
* organotrophic – reducing equivalents are obtained from organic compounds
3. How the organism obtains energy for living and growing:
* phototrophic – energy is obtained from light
* chemotrophic – energy is obtained from external chemical compounds
In practice, these terms are almost freely combined. Typical examples are as follows:
* chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. Examples: Nitrifying bacteria, sulfur-oxidizing bacteria, iron-oxidizing bacteria, Knallgas-bacteria
* photolithoautotrophs obtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds. Examples: Cyanobacteria (water () as reducing equivalent = hydrogen donor), Chlorobiaceae, Chromatiaceae (hydrogen sulfide () as hydrogen donor), Chloroflexus (hydrogen () as reducing equivalent donor)
* chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (). Examples: some Thiobacilus, some Beggiatoa, some Nitrobacter spp., Wolinella (with as reducing equivalent donor), some Knallgas-bacteria, some sulfate-reducing bacteria
* chemoorganoheterotrophs obtain energy, carbon, and hydrogen for biosynthetic reactions from organic compounds. Examples: most bacteria, e. g. Escherichia coli, Bacillus spp., Actinomycetota
* photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples: Rhodobacter, Rhodopseudomonas, Rhodospirillum, Rhodomicrobium, Rhodocyclus, Heliobacterium, Chloroflexus (alternatively to photolithoautotrophy with hydrogen) | 1 | Biochemistry |
Despite their modern abundance, due to their small size and fragility, copepods are extremely rare in the fossil record. The oldest known fossils of copepods are from the late Carboniferous (Pennsylvanian) of Oman, around 303 million years old, which were found in a clast of bitumen from a glacial diamictite. The copepods present in the bitumen clast were likely residents of a subglacial lake which the bitumen had seeped upwards through while still liquid, before the clast subsequently solidified and was deposited by glaciers. Though most of the remains were undiagnostic, at least some likely belonged to the extant harpacticoid family Canthocamptidae, suggesting that copepods had already substantially diversified by this time. Possible microfossils of copepods are known from the Cambrian of North America. Transitions to parasitism have occurred within copepods independently at least 14 different times, with the oldest record of this being from damage to fossil echinoids done by cyclopoids from the Middle Jurassic of France, around 168 million years old. | 2 | Environmental Chemistry |
The analysis of ratios of carbon-13 to carbon-12 along the length of a single elephant hair led Cerling and his crew to understand the elephants' diet. During the wet season, after the grass had grown long enough for elephants to grab with their trunks, their tail hair showed the presence of different form of carbon, indicating a high amount of high-protein grass. On the other hand, during the dry season, the results obtained by the analysis of the hair pointed out how elephants had switched over to shrubs and trees. | 9 | Geochemistry |
Palmitoylcarnitine is an ester derivative of carnitine involved in the metabolism of fatty acids. During the tricarboxylic acid cycle (TCA), fatty acids undergo a process known as β-oxidation to produce energy in the form of ATP. β-oxidation occurs primarily within mitochondria, however the mitochondrial membrane prevents the entry of long chain fatty acids (>C10), so the conversion of fatty acids such as palmitic acid is key. Palmitic acid is brought to the cell and once inside the cytoplasm is first converted to Palmitoyl-CoA. Palmitoyl-CoA has the ability to freely pass the outer mitochondrial membrane, but the inner membrane is impermeable to the Acyl-CoA and thioester forms of various long-chain fatty acids such as palmitic acid. The palmitoyl-CoA is then enzymatically transformed into palmitoylcarnitine via the Carnitine O-palmitoyltransferase family. The palmitoylcarnitine is then actively transferred into the inner membrane of the mitochondria via the carnitine-acylcarnitine translocase. Once inside the inner mitochondrial membrane, the same Carnitine O-palmitoyltransferase family is then responsible for transforming the palmitoylcarnitine back to the palmitoyl-CoA form. | 1 | Biochemistry |
Common side effects associated with the administration of piperacillin-tazobactam include:
* Gastrointestinal: constipation, diarrhea, nausea, vomiting
* Dermatologic: erythema, pain, phlebitis, rash
* Neurologic: headaches, insomnia
Prolonged periods of piperacillin-tazobactam therapy have been associated with the potential development of hematologic adversities such as leukopenia (16.3%), neutropenia (10%), and eosinophilia (10%) in adult patients. The combination of piperacillin-tazobactam with other antibiotics was found to be a major risk factor for leukopenia as well. Additionally, the chances of developing these illnesses increases in younger patients with fewer conditions, prolonging their time to recover.
Other cases of adverse effects include instances of renal dysfunction, hepatitis, hyperactivity, anemia, abnormalities in coagulation, and hypokalemia. Allergic reactions can be induced from the side chains of β-lactam antibiotics such as amoxicillin, or antibodies surrounding the nucleus of penicillin. | 4 | Stereochemistry |
NPP3 is probably a major contributor to nucleotide metabolism in the intestine and liver.
Intestinal NPP3 would be involved in hydrolyzing food-derived nucleotides.
The liver releases ATP and ADP into the bile to regulate bile secretion. It subsequently reclaims adenosine via a pathway that probably contains NPP3. | 1 | Biochemistry |
The reaction catalyzed is:
ATP + AMP ⇔ 2 ADP
The equilibrium constant varies with condition, but it is close to 1. Thus, ΔG for this reaction is close to zero. In muscle from a variety of species of vertebrates and invertebrates, the concentration of ATP is typically 7-10 times that of ADP, and usually greater than 100 times that of AMP. The rate of oxidative phosphorylation is controlled by the availability of ADP. Thus, the mitochondrion attempts to keep ATP levels high due to the combined action of adenylate kinase and the controls on oxidative phosphorylation. | 1 | Biochemistry |
For an odd-numbered saturated fat (C), 0.5 * n - 1.5 oxidations are necessary, and the final process yields 8 acetyl CoA and 1 propionyl CoA. It is then converted to a succinyl CoA by a carboxylation reaction and generates additional 5 ATP (1 ATP is consumed in carboxylation process generating a net of 4 ATP). In addition, two equivalents of ATP are lost during the activation of the fatty acid. Therefore, the total ATP yield can be stated as:
or
For instance, the ATP yield of Nonadecylic acid (C, n = 19) is:
Represented in table form: | 1 | Biochemistry |
One DNA or RNA molecule differs from another primarily in the sequence of nucleotides. Nucleotide sequences are of great importance in biology since they carry the ultimate instructions that encode all biological molecules, molecular assemblies, subcellular and cellular structures, organs, and organisms, and directly enable cognition, memory, and behavior. Enormous efforts have gone into the development of experimental methods to determine the nucleotide sequence of biological DNA and RNA molecules, and today hundreds of millions of nucleotides are sequenced daily at genome centers and smaller laboratories worldwide. In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. | 1 | Biochemistry |
Cyclohexane conformations are any of several three-dimensional shapes adopted by molecules of cyclohexane. Because many compounds feature structurally similar six-membered rings, the structure and dynamics of cyclohexane are important prototypes of a wide range of compounds.
The internal angles of a regular, flat hexagon are 120°, while the preferred angle between successive bonds in a carbon chain is about 109.5°, the tetrahedral angle (the arc cosine of −). Therefore, the cyclohexane ring tends to assume non-planar (warped) conformations, which have all angles closer to 109.5° and therefore a lower strain energy than the flat hexagonal shape.
Consider the carbon atoms numbered from 1 to 6 around the ring. If we hold carbon atoms 1, 2, and 3 stationary, with the correct bond lengths and the tetrahedral angle between the two bonds, and then continue by adding carbon atoms 4, 5, and 6 with the correct bond length and the tetrahedral angle, we can vary the three dihedral angles for the sequences (2,3,4), (3,4,5), and (4,5,6). The next bond, from atom 6, is also oriented by a dihedral angle, so we have four degrees of freedom. But that last bond has to end at the position of atom 1, which imposes three conditions in three-dimensional space. If the bond angle in the chain (6,1,2) should also be the tetrahedral angle then we have four conditions. In principle this means that there are no degrees of freedom of conformation, assuming all the bond lengths are equal and all the angles between bonds are equal. It turns out that, with atoms 1, 2, and 3 fixed, there are two solutions called chair, depending on whether the dihedral angle for (1,2,3,4) is positive or negative, and these two solutions are the same under a rotation. But there is also a continuum of solutions, a topological circle where angle strain is zero, including the twist boat and the boat conformations. All the conformations on this continuum have a twofold axis of symmetry running through the ring, whereas the chair conformations do not (they have D symmetry, with a threefold axis running through the ring). It is because of the symmetry of the conformations on this continuum that it is possible to satisfy all four constraints with a range of dihedral angles at (1,2,3,4). On this continuum the energy varies because of Pitzer strain related to the dihedral angles. The twist boat has a lower energy than the boat. In order to go from the chair conformation to a twist-boat conformation or the other chair conformation, bond angles have to be changed, leading to a high-energy half-chair conformation. So the relative stabilities are: . All relative conformational energies are shown below. At room temperature the molecule can easily move among these conformations, but only chair and twist-boat can be isolated in pure form, because the others are not at local energy minima.
The boat and twist-boat conformations, as said, lie along a continuum of zero angle strain. If there are substituents that allow the different carbon atoms to be distinguished, then this continuum is like a circle with six boat conformations and six twist-boat conformations between them, three "right-handed" and three "left-handed". (Which should be called right-handed is unimportant.) But if the carbon atoms are indistinguishable, as in cyclohexane itself, then moving along the continuum takes the molecule from the boat form to a "right-handed" twist-boat, and then back to the same boat form (with a permutation of the carbon atoms), then to a "left-handed" twist-boat, and then back again to the achiral boat. The passage boat⊣twist-boat⊣boat⊣twist-boat⊣boat constitutes a pseudorotation. | 4 | Stereochemistry |
Iminium cations are obtained by protonation and alkylation of imines:
They also are generated by the condensation of secondary amines with ketones or aldehydes:
This rapid, reversible reaction is one step in "iminium catalysis".
More exotic routes to iminium cations are known, e.g. from ring-opening reactions of pyridine. | 0 | Organic Chemistry |
Depending on the type of ligand a co-receptor binds, its location and function can vary. Various ligands include interleukins, neurotrophic factors, fibroblast growth factors, transforming growth factors, vascular endothelial growth factors and epidermal growth factors. Co-receptors prominent in embryonic tissue have an essential role in morphogen gradient formation or tissue differentiation. Co-receptors localized in endothelial cells function to enhance cell proliferation and cell migration.
With such variety in regards to location, co-receptors can participate in many different cellular activities. Co-receptors have been identified as participants in cell signalling cascades, embryonic development, cell adhesion regulation, gradient formation, tissue proliferation and migration. | 1 | Biochemistry |
The electron transport protein plastocyanin is present in the lumen and shuttles electrons from the cytochrome b6f protein complex to photosystem I. While plastoquinones are lipid-soluble and therefore move within the thylakoid membrane, plastocyanin moves through the thylakoid lumen.
The lumen of the thylakoids is also the site of water oxidation by the oxygen evolving complex associated with the lumenal side of photosystem II.
Lumenal proteins can be predicted computationally based on their targeting signals. In Arabidopsis, out of the predicted lumenal proteins possessing the Tat signal, the largest groups with known functions are 19% involved in protein processing (proteolysis and folding), 18% in photosynthesis, 11% in metabolism, and 7% redox carriers and defense. | 5 | Photochemistry |
* Termination: The TE-domain (thio-esterase domain) hydrolyzes the completed polypeptide chain from the PCP-domain of the previous module, thereby often forming cyclic amides (lactams) or cyclic esters (lactones).
* Also, the peptide can be released by an R-domain that reduces the thioester bond to terminal aldehyde or alcohol. | 1 | Biochemistry |
Iron was never smelted by Native Americans, thus the New World never entered a proper "Iron Age" before European discovery, and the term is not used of the Americas. But there was limited use of native (unsmelted) iron ore, from magnetite, iron pyrite and ilmenite (iron–titanium), especially in the Andes (Chavin and Moche cultures) and Mesoamerica, after 900 BCE and until . Various forms of iron ore were mined,
drilled and highly polished. There is considerable evidence that this technology, its raw materials and end products were widely traded in Mesoamerica throughout the Formative era (2000–200BCE).
Lumps of iron pyrite, magnetite, and other materials were mostly shaped into mirrors, pendants, medallions, and headdress ornaments for decorative and ceremonial effect.
However, concave iron ore mirrors were apparently used for firing and optical purposes by the Olmec (1500–400BCE) and Chavin (900–300BCE) cultures,
and ilmenite "beads" may have served as hammers for fine work.
The Olmec and Izapa (300BCE – 100CE) also seem to have used iron magnetism to align and position monuments.
They may have developed a zeroth-order compass using a magnetite bar.
Some Mesoamerican uses of native iron seem to have been military. Steven Jones proposed that the Olmec sewed ilmenite "beads" into protective mail armour or helmets. Iron pyrite mosaics and plates formed protective tezcacuitlapalli (mirrored back flap shields) and breastplate ornaments in the military attire of the Teotihuacan (100 BCE – 600 CE), Toltec (800–1150 CE) and Chichen Itza (800–1200 CE) cultures. | 8 | Metallurgy |
Adrenaline stimulates photocytes to emit light for many species of fish. It is believed that sympathetic nervous impulses provide the stimulus that causes photocytes to emit light. | 1 | Biochemistry |
The relative importance-measuring property of the PageRank link analysis algorithm could be used to identify new possible drug targets in proteins. A PageRank-based algorithm could identify important protein targets in the pathogen organism better than a method considering only the number of incoming edges (in-degree) of a node in the metabolic network. The reason for this is that some already known, important protein targets do not have a high degree (are not hubs) and also, perturbing some hubs could result in unwanted physiological effects. | 1 | Biochemistry |
The "A260 unit" is used as a quantity measure for nucleic acids. One A260 unit is the amount of nucleic acid contained in 1 mL and producing an OD of 1. The same conversion factors apply, and therefore, in such contexts:
:1 A260 unit dsDNA = 50 µg
:1 A260 unit ssDNA = 33 µg
:1 A260 unit ssRNA = 40 µg | 7 | Physical Chemistry |
For large base-sizes, some of the cyclobutanes can be fused anti to each other, giving a non-convex polygon base. These are geometric isomers of the prismanes. Two isomers of [12]prismane that have been studied computationally are named helvetane and israelane, based on the star-like shapes of the rings that form their bases. This was explored computationally after originally being proposed as an April fools joke. Their names refer to the shapes found on the flags of Switzerland and Israel, respectively. | 4 | Stereochemistry |
Sulfidation is relevant to the formation of sulfide minerals.
A large scale application of sulfidation is the conversion of molybdenum oxides to the corresponding sulfides. This conversion is a step in the preparation of catalysts for hydrodesulfurization wherein alumina impregnated with molybdate salts are converted to molybdenum disulfide by the action of hydrogen sulfide.
In organosulfur chemistry, sulfiding is often called thiation. The preparation of thioamides from amides involves thiation. A typical reagent is phosphorus pentasulfide (PS). The idealized equation for this conversion is:
:RC(O)NH + 1/4 PS → RC(S)NH + 1/4 PSO
This conversion where an oxygen atom in the amide function is replaced by a sulfur atom involves no redox reaction. | 7 | Physical Chemistry |
Fluorinated gases (F-gases) are a group of gases containing fluorine. They are divided into several types, the main of those are hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), sulphur hexafluoride (SF6). They are used in refrigeration, air conditioning, heat pumps, fire suppression, electronics, aerospace, magnesium industry, foam and high voltage switchgear. As they are greenhouse gases with a strong global warming potential, their use is regulated. | 2 | Environmental Chemistry |
Jeewanu is derived from Sanskrit jeewa, meaning "life", and anu, meaning the "smallest part of something", or the "indivisible". In contemporary Hindi, jeewanu also means unicellular organisms such as bacteria. Bahadur specifically used the term to represent the Indian philosophical tradition not only through the use of Sanskrit but also by inferring ideas on the origin of life from the Vedas. Bahadur, while employing the traditional Hindu philosophy, attempted to incorporate the advances in cell biology to the concept of abiogenesis. | 9 | Geochemistry |
In solid-state physics and solid-state chemistry, a band gap, also called a bandgap or energy gap, is an energy range in a solid where no electronic states exist. In graphs of the electronic band structure of solids, the band gap refers to the energy difference (often expressed in electronvolts) between the top of the valence band and the bottom of the conduction band in insulators and semiconductors. It is the energy required to promote an electron from the valence band to the conduction band. The resulting conduction-band electron (and the electron hole in the valence band) are free to move within the crystal lattice and serve as charge carriers to conduct electric current. It is closely related to the HOMO/LUMO gap in chemistry. If the valence band is completely full and the conduction band is completely empty, then electrons cannot move within the solid because there are no available states. If the electrons are not free to move within the crystal lattice, then there is no generated current due to no net charge carrier mobility. However, if some electrons transfer from the valence band (mostly full) to the conduction band (mostly empty), then current can flow (see carrier generation and recombination). Therefore, the band gap is a major factor determining the electrical conductivity of a solid. Substances having large band gaps (also called "wide" band gaps) are generally insulators, those with small band gaps (also called "narrow" band gaps) are semiconductor, and conductors either have very small band gaps or none, because the valence and conduction bands overlap to form a continuous band. | 7 | Physical Chemistry |
It is based on the principle that the intensity of light received by the observer depends upon the distance of the observer from the source and the temperature of the distant source. A modern pyrometer has an optical system and a detector. The optical system focuses the thermal radiation onto the detector. The output signal of the detector (temperature T) is related to the thermal radiation or irradiance of the target object through the Stefan–Boltzmann law, the constant of proportionality σ, called the Stefan–Boltzmann constant and the emissivity ε of the object:
This output is used to infer the object's temperature from a distance, with no need for the pyrometer to be in thermal contact with the object; most other thermometers (e.g. thermocouples and resistance temperature detectors (RTDs)) are placed in thermal contact with the object and allowed to reach thermal equilibrium.
Pyrometry of gases presents difficulties. These are most commonly overcome by using thin-filament pyrometry or soot pyrometry. Both techniques involve small solids in contact with hot gases. | 8 | Metallurgy |
Toxicology refers to the science of the chemical and physical properties of toxic substances. Samples from a body are analyzed for drugs or other toxic substances. The concentrations are measured and the substance's contribution to a death can be determined. This is done by comparing concentrations to lethal limits. The most common samples analyzed are blood, urine, kidney, liver, and brain. The samples are usually put through various tests, but the most common instrument used to quantify and determine a substance is gas chromatography-mass spectrometry (GC-MS). These instruments produce chromatograms of the sample, which are then compared to a database of known substances. In blood samples, the substance can usually be found, but in the liver, kidneys, and urine the metabolite may be the only substance that can be found. A metabolite is the broken down version of the original substance after it has gone through digestion and/or other biological processes. Substances can take anywhere from hours to weeks to metabolize and leave the body and have different retention times in different parts of the body. For example, cocaine can be detected in the blood for two to ten days, while it can be detected in urine for two to five days.
The results of post-mortem toxicology testing are interpreted alongside the victim's history, a thorough investigation of the scene, and autopsy and ancillary study findings to determine the manner of death.
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The potential for transcription and translation to regulate each other was recognized by the team of Marshall Nirenberg, who discovered that the processes are physically connected through the formation of a DNA-ribosome complex. As part of the efforts of Nirenbergs group to determine the genetic code that underlies protein synthesis, they pioneered the use of cell-free in vitro protein synthesis reactions. Analysis of these reactions revealed that protein synthesis is mRNA-dependent, and that the sequence of the mRNA strictly defines the sequence of the protein product. For this work in breaking in the genetic code, Nirenberg was jointly awarded the Nobel Prize in Physiology or Medicine in 1968. Having established that transcription and translation are linked biochemically (translation depends on the product of transcription), an outstanding question remained whether they were linked physically - whether the newly synthesized mRNA released from the DNA before it is translated, or if can translation occur concurrently with transcription. Electron micrographs of stained cell-free protein synthesis reactions revealed branched assemblies in which strings of ribosomes are linked to a central DNA fibre. DNA isolated from bacterial cells co-sediment with ribosomes, further supporting the conclusion that transcription and translation occur together. Direct contact between ribosomes and RNA polymerase are observable within these early micrographs. The potential for simultaneous regulation of transcription and translation at this junction was noted in Nirenbergs work as early as 1964. | 1 | Biochemistry |
Butyryl phosphate is an intermediate in the fermentation of butyric acid. The glutamate oxidation of butyryl phosphate may provide the main source of energy for Clostridium tetanomorphum. | 1 | Biochemistry |
The International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB) is an international PhD program in molecular biology and cellular biology founded in 2006 by the Max Planck Institute of Immunobiology and Epigenetics and the University of Freiburg.
The Max Planck Society (MPG) started in 2000 an initiative to attract more international students to Germany to pursue their PhD studies. Therefore, International-Max-Planck-Research-Schools (IMPRS) were established. The number of IMPRS has ever been increasing since then in all three sections of research of the MPG. | 1 | Biochemistry |
The Krebs cycle, also known as the TCA cycle or Citric Acid cycle, is a biochemical pathway that facilitates the breakdown of glucose in a cell. Both citrate and malate involved in the citrate-malate shuttle are necessary intermediates of the Krebs cycle. Usually, oxaloacetate in the Krebs cycle is generated from the carboxylation of pyruvate in the mitochondrion; however, malate generated in the cytosol can also enter the mitochondrion through the transport protein located in the inner mitochondrial membrane to directly join the Krebs cycle.
The mitochondrial transport proteins are encoded by the SLC25 gene in humans and facilitate the transportation of various metabolites, including citrate and malate, in the Krebs cycle. These transport proteins control the flow of metabolites in and out of the inner mitochondrial membrane, which is impermeable to most molecules. They connect the carbohydrate metabolism of the Krebs cycle to fatty acid synthesis in lipogenesis by catalyzing the transportation of acetyl-CoA out of the mitochondrial matrix into the cytosol, which is done in the form of citrate export from the mitochondria to the cytosol. Cytosolic citrate, meaning citrate in the cytosol, is a key substrate for the generation of energy. It releases acetyl-CoA and provides NADPH for fatty acid synthesis, and, in subsequent pathways, generates NAD for glycolysis. Citrate also activates acetyl-CoA carboxylase, an enzyme that is essential in the fatty acid synthesis pathway.
Citrate-malate shuttle might partly or completely replace the function of the Krebs cycle in cancer cell metabolism. | 1 | Biochemistry |
Fluoroethyl fluoroacetate, or more accurately 2-fluoroethyl fluoroacetate, is an organic compound with the chemical formula . It is the fluoroacetate ester of 2-fluoroethanol, or in other words, the 2-fluoroethyl ester of fluoroacetic acid. 2-Fluoroethyl fluoroacetate is two times more toxic than methyl fluoroacetate. | 1 | Biochemistry |
Symbiosis in lichens is so well-balanced that lichens have been considered to be relatively self-contained miniature ecosystems in and of themselves. It is thought that lichens may be even more complex symbiotic systems that include non-photosynthetic bacterial communities performing other functions as partners in a holobiont.
Many lichens are very sensitive to environmental disturbances and can be used to cheaply assess air pollution, ozone depletion, and metal contamination. Lichens have been used in making dyes, perfumes (oakmoss), and in traditional medicines. A few lichen species are eaten by insects or larger animals, such as reindeer. Lichens are widely used as environmental indicators or bio-indicators. When air is very badly polluted with sulphur dioxide, there may be no lichens present; only some green algae can tolerate those conditions. If the air is clean, then shrubby, hairy and leafy lichens become abundant. A few lichen species can tolerate fairly high levels of pollution, and are commonly found in urban areas, on pavements, walls and tree bark. The most sensitive lichens are shrubby and leafy, while the most tolerant lichens are all crusty in appearance. Since industrialisation, many of the shrubby and leafy lichens such as Ramalina, Usnea and Lobaria species have very limited ranges, often being confined to the areas which have the cleanest air. | 2 | Environmental Chemistry |
Under certain hydrological parameters, some aquifers are more prone to contamination than other aquifers. The parameters that are taken into consideration when calculating the vulnerability of aquifers to contamination are: depth to water (factor d), net recharge (factor r), aquifer media (factor a), soil media (factor s), topography (factor t), impact of the vadose zone (factor i), and the hydraulic conductivity (factor c), which together spell out DRASTIC. Furthermore, there is a weighting factor associated with each of the parameters that can range from one to five. In addition, the lower the numbers for the DRASTIC index after the assessment of the aquifer, than the lower the risk of aquifer contamination in that area. These seven parameters derive DRASTIC summary index score, which determines which are more prone to contamination than other. The significance of the DRASTIC summary index score is that it shows areas that are more prone; as a result, the state or local authorities depending on the scale will place necessary measures in place that would prevent or mitigate contamination of the water supply.
Using GIS, a map was developed for the seven counties (Hillsborough, Polk, Manatee, Hardee, Sarasota, DeSoto, and Charlotte) in Florida, which shows the DRASTIC summary index score for the Floridan Aquifer System, Surficial Aquifer System, and Other Rocks aquifer. The developed map is a combination of multiple layers that are stacked on top of each other as shown in Figure 1. | 2 | Environmental Chemistry |
R-410A cannot be used in R-22 service equipment because of higher operating pressures (approximately 40 to 70% higher).
While R-410A has negligible fractionation potential, it cannot be ignored when charging. | 2 | Environmental Chemistry |
It is during encapsulation that the ZnS shell plays an especially important role, in that it helps prevent the agglomeration of CdSe particles that had no shell by occupying the previously mentioned bonds on the dot's surface; however, clumping can still occur through secondary forces that arise from common hydrophobicity. This can result in multiple particles within each micelle, which may negatively impact overall resolution. For this reason multiple combinations of PEG chain length and particle diameter are necessary to achieve optimal imaging properties. | 7 | Physical Chemistry |
Research on paracrine signaling through the JAK-STAT pathway revealed its potential in activating invasive behavior of ovarian epithelial cells. This epithelial to mesenchymal transition is highly evident in metastasis. Paracrine signaling through the JAK-STAT pathway is necessary in the transition from stationary epithelial cells to mobile mesenchymal cells, which are capable of invading surrounding tissue. Only the JAK-STAT pathway has been found to induce migratory cells. | 1 | Biochemistry |
Before the 2019 redefinition of the SI base units, the mole was defined as the amount of substance of a system that contains as many elementary entities as there are atoms in 12 grams of carbon-12 (the most common isotope of carbon).
The term gram-molecule was formerly used to mean one mole of molecules, and gram-atom for one mole of atoms. For example, 1 mole of MgBr is 1 gram-molecule of MgBr but 3 gram-atoms of MgBr.
In 2011, the 24th meeting of the General Conference on Weights and Measures (CGPM) agreed to a plan for a possible revision of the SI base unit definitions at an undetermined date.
On 16 November 2018, after a meeting of scientists from more than 60 countries at the CGPM in Versailles, France, all SI base units were defined in terms of physical constants. This meant that each SI unit, including the mole, would not be defined in terms of any physical objects but rather they would be defined by physical constants that are, in their nature, exact.
Such changes officially came into effect on 20 May 2019. Following such changes, "one mole" of a substance was redefined as containing "exactly elementary entities" of that substance. | 3 | Analytical Chemistry |
Determining whether a potential biosignature is worth investigating is a fundamentally complicated process. Scientists must consider any and every possible alternate explanation before concluding that something is a true biosignature. Such consideration entails investigating the minute details that make other planets unique and understanding when there is a deviation from the expected non-biological processes present on a planet. In the case of a planet with life, these differences can be extremely small or not present at all, adding to the difficulties of discovering a biosignature. Years of scientific studies have culminated in three criteria that a potential biosignature must meet to be considered viable for further research: Reliability, survivability, and detectability. | 2 | Environmental Chemistry |
Exopolysaccharides can facilitate the attachment of nitrogen-fixing bacteria to plant roots and soil particles, which mediates a symbiotic relationship. This is important for colonization of roots and the rhizosphere, which is a key component of soil food webs and nutrient cycling in ecosystems. It also allows for successful invasion and infection of the host plant. Bacterial extracellular polymeric substances can aid in bioremediation of heavy metals as they have the capacity to adsorb metal cations, among other dissolved substances. This can be useful in the treatment of wastewater systems, as biofilms are able to bind to and remove metals such as copper, lead, nickel, and cadmium. The binding affinity and metal specificity of EPSs varies, depending on polymer composition as well as factors such as concentration and pH. In a geomicrobiological context, EPSs have been observed to affect precipitation of minerals, particularly carbonates. EPS may also bind to and trap particles in biofilm suspensions, which can restrict dispersion and element cycling. Sediment stability can be increased by EPS, as it influences cohesion, permeability, and erosion of the sediment. There is evidence that the adhesion and metal-binding ability of EPS affects mineral leaching rates in both environmental and industrial contexts. These interactions between EPS and the abiotic environment allow for EPS to have a large impact on biogeochemical cycling. Predator-prey interactions between biofilms and bacterivores, such as the soil-dwelling nematode Caenorhabditis elegans, had been extensively studied. Via the production of sticky matrix and formation of aggregates, Yersinia pestis biofilms can prevent feeding by obstructing the mouth of C. elegans. Moreover, Pseudomonas aeruginosa biofilms can impede the slithering motility of C. elegans, termed as quagmire phenotype, resulting in trapping of C. elegans within the biofilms and preventing the exploration of nematodes to feed on susceptible biofilms. This significantly reduced the ability of predator to feed and reproduce, thereby promoting the survival of biofilms. | 1 | Biochemistry |
The Prilezhaev reaction involves the conversion of an alkene to an epoxide using a peracid as the oxidant and was first reported in 1909. The reaction has been used as the final step of the synthesis of scopine, a tropane alkaloid. In this approach, a [4+3] cycloaddition mediated by diiron nonacarbonyl is used to construct the bicyclic skeleton, the hydroxyl functional group is then introduced by diastereoselective reduction of the ketone with diisobutylaluminum hydride, and the preparation completed with a Prilezhaev trifluoroperacetic acid epoxidation.
The high reactivity of trifluoroperacetic acid relative to other peroxy acids allows it to successfully oxidize relatively electron-poor alkenes such as 1-hexene and α,β-unsaturated esters such as methyl methacrylate, substrates that are generally resistant to peroxy-acid epoxidation. Including additional buffered trifluoroacetic acid in the mixture gives a vicinal hydroxy–trifluoroacetate structure instead of an epoxide, which can be converted to the diol by treatment with acidic methanol, such as in the following conversion of 1-dodecene to 1,2-dodecanediol.
In the case of an allyl alcohol compound with a proximate carbonyl functional group, the epoxide can undergo a ring-expansion reaction to form a dioxolane. The process below was used as part of the total synthesis of neosporol, a natural product:
The preparation of the isomeric compound sporol involved a similar dioxolane formation. In this case, the use of trifluoroperacetic acid derived from hydrogen peroxide, which therefore presumably contained traces of water, gave mostly a hemiacetal rather than the closed-ring dioxolane. The use of the urea complex, which gave a water-free material, successfully gave the dioxolane as the major product. The dioxolane is expanded to the 1,3-dioxane system found in sporol at a later step in the synthesis. | 0 | Organic Chemistry |
Metabolite damage can occur through enzyme promiscuity or spontaneous chemical reactions. Many metabolites are chemically reactive and unstable and can react with other cell components or undergo unwanted modifications. Enzymatically or chemically damaged metabolites are always useless and often toxic. To prevent toxicity that can occur from the accumulation of damaged metabolites, organisms have damage-control systems that:
# Reconvert damaged metabolites to their original, undamaged form (damage repair)
# Convert a potentially harmful metabolite to a benign one (damage pre-emption)
# Prevent damage from happening by limiting the build-up of reactive, but non-damaged metabolites that can lead to harmful products (directed overflow)
Damage-control systems can involve one or more specific enzymes. | 1 | Biochemistry |
Jordi Folch Pi (March 25, 1911October 3, 1979) was a Spanish biochemist at Harvard University (McLean Hospital) who was recognized universally as one of the founders of the field of structural chemistry of complex lipids and as a leader in the development of Neurochemistry , as a distinct discipline within the Neurosciences. | 1 | Biochemistry |
An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. The ability to exhibit aerobic respiration may yield benefits to the aerobic organism, as aerobic respiration yields more energy than anaerobic respiration. Energy production of the cell involves the synthesis of ATP by an enzyme called ATP synthase. In aerobic respiration, ATP synthase is coupled with an electron transport chain in which oxygen acts as a terminal electron acceptor. In July 2020, marine biologists reported that aerobic microorganisms (mainly), in "quasi-suspended animation", were found in organically poor sediments, up to 101.5 million years old, 250 feet below the seafloor in the South Pacific Gyre (SPG) ("the deadest spot in the ocean"), and could be the longest-living life forms ever found. | 1 | Biochemistry |
Source:
* Lomonosov Prize, 1974.
* Mendeleev Prize, 1979.
* Nesmeyanov Prize, 1991.
* Demidov Prize, 2003.
* State Prize, 2004.
* IUPAC 2013 Distinguished Women in Chemistry or Chemical Engineering Award, 2013. | 0 | Organic Chemistry |
EosFP was first discovered in 2005 during a large scale screen for PAFPs (photoactivatable fluorescent proteins) within the stony coral Lobophyllia hemprichii. It has since been successfully cloned in Escherichia coli and fusion constructs have been developed for use in human cells. Eos was named after the Greek goddess of dawn.
Unlike the tetrameric fluorescent proteins derived from anthozoan coral, which can interfere with normal cellular function due to interactions between protein subunits, EosFP has been broken up into dimeric and monomeric variants through the introduction of single point mutations. These variants have been successful in the tracking of cellular components without disturbing function in the host cell and maintain the same photophysical properties as wild-type Eos.
Since their discovery, monomeric Eos probes (mEos) have been shown to localize in the cytosol, plasma membrane, endosomes, prevacuolar vesicles, vacuoles, the endoplasmic reticulum, golgi bodies, peroxisomes, mitochondria, invaginations, filamentous actin and cortical microtubules. mEos fusion proteins allow for differential colour labelling in single cells, or groups of cells in developing organs. They can also be used for the understanding of spatial/ temporal interactions between organelles and vesicles. The two fluorescent forms of mEosFP (green and red) are compatible with CFP, GFP, YFP and RFP for multicolour labelling. | 1 | Biochemistry |
* Nearly all RAPD markers are dominant, i.e. it is not possible to distinguish whether a DNA segment is amplified from a locus that is heterozygous (1 copy) or homozygous (2 copies). Codominant RAPD markers, observed as different-sized DNA segments amplified from the same locus, are detected only rarely.
* PCR is an enzymatic reaction, therefore, the quality and concentration of template DNA, concentrations of PCR components, and the PCR cycling conditions may greatly influence the outcome. Thus, the RAPD technique is notoriously laboratory dependent and needs carefully developed laboratory protocols to be reproducible.
* Mismatches between the primer and the template may result in the total absence of PCR product as well as in a merely decreased amount of the product. Thus, the RAPD results can be difficult to interpret, unlike traditional PCR analysis. | 1 | Biochemistry |
Andrée Marquet and her collaborators have been interested in reaction mechanisms in organic chemistry, in particular those involving carbanions (enolates, alpha anions of sulfoxides), and have used the results of these studies in synthesis, for example for total synthesis of biotin.
She then turned to mechanistic enzymology, applying the approach used in organic chemistry to the functioning of enzymes.
The main areas covered are :
* steroid biochemistry: inhibition of the biosynthesis of aldosterone (among the various compounds synthesized and tested, 18-vinyl progesterone proved to be an excellent inhibitor of Cytochrome P450 involved in the last stage of this biosynthesis, making this molecule a potential hypotensor.
* the mechanism of action of vitamin K, an essential cofactor in the cascade of blood coagulation reactions.
* the biotin biosynthesis pathway: the mechanism of several of the enzymes involved has been deciphered and various inhibitors have been designed and synthesized. A particularly difficult problem to which Andrée Marquet and her team have made a decisive contribution is that of the mechanism of biotin synthase, which catalyses the final step.
They have shown that it belongs to the newly discovered family of proteins (Fe-S) dependent on S-Adenosylmethionine, catalysing radical reactions. This is a family that opens a new chapter in enzymology.
Another field of activity of the laboratory, the result of a collaboration with the neurobiology laboratory of the Collège de France (Prof. Jacques Glovinski) concerns the activity of a family of peptide neurotransmitters, the tachykinins. | 0 | Organic Chemistry |
Thigmonastic movements, those that occur in response to touch, are used as a defense in some plants. The leaves of the sensitive plant, Mimosa pudica, close up rapidly in response to direct touch, vibration, or even electrical and thermal stimuli. The proximate cause of this mechanical response is an abrupt change in the turgor pressure in the pulvini at the base of leaves resulting from osmotic phenomena. This is then spread via both electrical and chemical means through the plant; only a single leaflet need be disturbed. This response lowers the surface area available to herbivores, which are presented with the underside of each leaflet, and results in a wilted appearance. It may also physically dislodge small herbivores, such as insects. | 1 | Biochemistry |
Several protein members of the BRCA1-associated genome surveillance complex (BASC) associate with RNA polymerase II and play a role in transcription.
The transcription factor TFIIH is involved in transcription initiation and DNA repair. MAT1 (for ménage à trois-1) is involved in the assembly of the CAK complex. CAK is a multisubunit protein that includes CDK7, cyclin H (CCNH), and MAT1. CAK is an essential component of the transcription factor TFIIH that is involved in transcription initiation and DNA repair.
The nucleotide excision repair (NER) pathway is a mechanism to repair damage to DNA. ERCC2 is involved in transcription-coupled NER and is an integral member of the basal transcription factor BTF2/TFIIH complex. ERCC3 is an ATP-dependent DNA helicase that functions in NER. It also is a subunit of basal transcription factor 2 (TFIIH) and, thus, functions in class II transcription. XPG (ERCC5) forms a stable complex with TFIIH, which is active in transcription and NER. ERCC6 encodes a DNA-binding protein that is important in transcription-coupled excision repair. ERCC8 interacts with Cockayne syndrome type B (CSB) protein, with p44 (GTF2H2), a subunit of the RNA polymerase II transcription factor IIH, and ERCC6. It is involved in transcription-coupled excision repair.
Higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn compared to Mg. | 1 | Biochemistry |
Many important biological processes involve redox reactions. Before some of these processes can begin iron must be assimilated from the environment.
Cellular respiration, for instance, is the oxidation of glucose (CHO) to CO and the reduction of oxygen to water. The summary equation for cell respiration is:
The process of cell respiration also depends heavily on the reduction of NAD to NADH and the reverse reaction (the oxidation of NADH to NAD). Photosynthesis and cellular respiration are complementary, but photosynthesis is not the reverse of the redox reaction in cell respiration:
Biological energy is frequently stored and released by means of redox reactions. Photosynthesis involves the reduction of carbon dioxide into sugars and the oxidation of water into molecular oxygen. The reverse reaction, respiration, oxidizes sugars to produce carbon dioxide and water. As intermediate steps, the reduced carbon compounds are used to reduce nicotinamide adenine dinucleotide (NAD) to NADH, which then contributes to the creation of a proton gradient, which drives the synthesis of adenosine triphosphate (ATP) and is maintained by the reduction of oxygen. In animal cells, mitochondria perform similar functions.
Free radical reactions are redox reactions that occur as a part of homeostasis and killing microorganisms, where an electron detaches from a molecule and then reattaches almost instantaneously. Free radicals are a part of redox molecules and can become harmful to the human body if they do not reattach to the redox molecule or an antioxidant.
The term redox state is often used to describe the balance of GSH/GSSG, NAD/NADH and NADP/NADPH in a biological system such as a cell or organ. The redox state is reflected in the balance of several sets of metabolites (e.g., lactate and pyruvate, beta-hydroxybutyrate, and acetoacetate), whose interconversion is dependent on these ratios. Redox mechanisms also control some cellular processes. Redox proteins and their genes must be co-located for redox regulation according to the CoRR hypothesis for the function of DNA in mitochondria and chloroplasts. | 9 | Geochemistry |
There is no known antidote against MFA, but there are some suggestions regarding the treatment of MFA poisoning. Advised is to use an intravenous injection of fast-acting anesthetics directly after poisoning. The anesthetic should be pentothal sodium or evipan sodium followed by an intramuscular injection of long-acting cortical depressants like sodium phenobarbitone or rectal avertin. Afterward, careful supervision of oxygen supply is necessary together with a BLB mask and the use of artificial respiration. Possibly, the use of hypertonic glucose intravenously is required as in status epilepticus. At last, careful use of tubocurarine chloride should be applied to control any convulsions. If any vomiting occurs, lean the patient forward to maintain an open airway.
Alternatively, there is a therapy aimed at the prevention of fluorocitrate synthesis, the blocking of aconitase within the mitochondria, and to provide a citrate outflow from the mitochondria to keep the TCA cycle going. For now, ethanol has proven to be the most effective against FC formation. When ethanol is oxidized, it increases blood acetate levels which inhibits FC production. In humans, an oral dose of 40-60 mL 96% ethanol is advised followed by 1.0-1.5 g/kg of 5-10% ethanol intravenously during the first hour and 0.1 g/kg during the following 6–8 hours. This therapy is meant for fluoroacetate (FA) poisoning which is highly related MFA, so this therapy aimed at MFA may result in other outcomes.
Treatment with monoacetin (glycerol monoacetate) helped against FA poisoning. It aids in increasing acetate levels of the blood and it decreases citrate levels in the heart, brain, and kidneys. However, this is only tested experimentally. In monkeys, monoacetin even reverses the effects of FA: all biological effects normalized. As with ethanol, monoacetin is effective against FA poisoning.
There is up until now, no proven treatment against MFA. However, the beforementioned treatments can provide starting points for therapy aimed at MFA since FA and MFA are closely related compounds. | 1 | Biochemistry |
In real-life situations, particles in solution do not have a fixed size, resulting in the probability that a particle that would otherwise be hampered by a pore passing right by it. Also, the stationary-phase particles are not ideally defined; both particles and pores may vary in size. Elution curves, therefore, resemble Gaussian distributions. The stationary phase may also interact in undesirable ways with a particle and influence retention times, though great care is taken by column manufacturers to use stationary phases that are inert and minimize this issue.
Like other forms of chromatography, increasing the column length enhances resolution, and increasing the column diameter increases column capacity. Proper column packing is important for maximum resolution: An over-packed column can collapse the pores in the beads, resulting in a loss of resolution. An under-packed column can reduce the relative surface area of the stationary phase accessible to smaller species, resulting in those species spending less time trapped in pores. Unlike affinity chromatography techniques, a solvent head at the top of the column can drastically diminish resolution as the sample diffuses prior to loading, broadening the downstream elution. | 1 | Biochemistry |
Boats are traditionally piloted from starboard (the right-hand side) to facilitate priority to the right.
According to the International Regulations for Preventing Collisions at Sea, water traffic is effectively RHT: a vessel proceeding along a narrow channel must keep to starboard, and when two power-driven vessels are meeting head-on both must alter course to starboard also. | 4 | Stereochemistry |
The phrase originates from the French word espoilelier, a verb conveying the meaning: to seize by violence, to plunder, to take by force. | 8 | Metallurgy |
PDC electrolysis was first considered theoretically in 1952, and experimental research began as early as 1960 however it was originally focused on its technical applications to industry and the possibilities of improving the quality and rate of metal deposition. It partially succeeded, providing promising results its ability to create smoother, denser deposits, and reducing the amount of metal required in electroplating.
The first instance it was considered to initialise the electrolysis of water was from the perspective of magnetolysis in 1985, where high strength magnets, or in this case electromagnets, are used in conjunction with homopolar propellers. Ghoroghichian and Bockris conducted this experimental research to determine how a pulsed current can impact the rate of hydrogen production and provide economic advantages. A current density ratio of 2.07 was observed, demonstrating, for the first time, that a pulsed current can double the production of hydrogen, in comparison to a steady state current.
Since hydrogen gas cannot be collected in its free form, and it can be used to provide a source of renewable and clean energy through fuel cells, discovering an electrolysis method with the greatest efficiency is valued. With early experimental and theoretical success, many patents began to be developed until as recent as 2002, but since 1985, it has only been researched intermittently with varying levels of success. | 7 | Physical Chemistry |
It has been shown that in brain ThTP is synthesized in mitochondria by a chemiosmotic mechanism, perhaps similar to ATP synthase. In mammals, ThTP is hydrolyzed to thiamine pyrophosphate (ThDP) by a specific thiamine-triphosphatase. It can also be converted into ThDP by thiamine-diphosphate kinase. | 1 | Biochemistry |
Cell-penetrating peptides (CPPs), also known as peptide transduction domains (PTDs), are short peptides (< 40 amino acids) that efficiently pass through cell membranes while being covalently or non-covalently bound to various molecules, thus facilitating these molecules' entry into cells. Cell entry occurs primarily by endocytosis but other entry mechanisms also exist. Examples of cargo molecules of CPPs include nucleic acids, liposomes, and drugs of low molecular weight.
CPP cargo can be directed into specific cell organelles by incorporating localization sequences into CPP sequences. For example, nuclear localization sequences are commonly used to guide CPP cargo into the nucleus. For guidance into mitochondria, a mitochondrial targeting sequence can be used; this method is used in protofection (a technique that allows for foreign mitochondrial DNA to be inserted into cells' mitochondria). | 1 | Biochemistry |
Hyperpolarization-activated and cyclic nucleotide–gated (HCN) channels belong to the superfamily of voltage-gated K (Kv) and cyclic nucleotide–gated (CNG) channels. HCN channels are thought to consist of four either identical or non-identical subunits that are integrally embedded in the cell membrane to create an ion-conducting pore. Each subunit comprises six membrane-spanning (S1–6) domains which include a putative voltage sensor (S4) and a pore region between S5 and S6 carrying the GYG triplet signature of K-permeable channels, and a cyclic nucleotide-binding domain (CNBD) in the C-terminus. HCN isoforms are highly conserved in their core transmembrane regions and cyclic nucleotide binding domain (80–90% identical), but diverge in their amino- and carboxy-terminal cytoplasmic regions.
HCN channels are regulated by both intracellular and extracellular molecules, but most importantly, by cyclic nucleotides (cAMP, cGMP, cCMP). Binding of cyclic nucleotides lowers the threshold potential of HCN channels, thus activating them. cAMP is a primary agonist of HCN2 while cGMP and cCMP may also bind to it. All three, however, are potent agonists. | 1 | Biochemistry |
Collectin-10, also known as collectin liver 1, is a collectin protein that in humans is encoded by the COLEC10 gene. Its structure is similar to mannan-binding lectin (MBL).
Collectin liver 1 (CL-L1) show very similar carbohydrate selectivity as MBL. Two other discovered collectins include collectin placenta 1 (CL-P1) and collectin kidney 1 (CL-K1). CL-L1's location found to be on chromosome 8 q23-24.1. Research concluded CL-L1 to be a serum protein. | 1 | Biochemistry |
In molecular biology, a GC box, also known as a GSG box, is a distinct pattern of nucleotides found in the promoter region of some eukaryotic genes. The GC box is upstream of the TATA box, and approximately 110 bases upstream from the transcription initiation site. It has a consensus sequence GGGCGG which is position-dependent and orientation-independent. The GC elements are bound by transcription factors and have similar functions to enhancers. Some known GC box-binding proteins include Sp1, Krox/Egr, Wilms' tumor, MIGI, and CREA.
The GC box is commonly the binding site for zinc finger proteins. An alpha helix section of the protein corresponds with a major groove in the DNA. Zinc-fingers bind to triplet base pair sequences, with residue 21 binding to the first base pair, residue 18 binding to the second base pair, and residue 15 binding to the third base pair. The triplet base pairs can either be a GGG or a GCG. If residue 18 is a histidine, it will bind to a G, and if residue 18 is a glutamate, it will bind to a C. GC box-binding zinc fingers have between 2 and 4 fingers, making them interact with base pair sequences that are 6 to 8 base pairs in length. | 1 | Biochemistry |
Although the acid catalyzed and base catalyzed hydrolysis of esters gives transition states for the rate determining steps that have differing charge densities, their structures differ only by two hydrogen atoms. Taft thus assumed that steric effects would influence both reaction mechanisms equally. Due to this, the steric substituent constant E was determined from solely the acid catalyzed reaction, as this would not include polar effects. E was defined as:
where k is the rate of the studied reaction and is the rate of the reference reaction (R = methyl). δ is a reaction constant that describes the susceptibility of a reaction series to steric effects. For the definition reaction series δ was set to 1 and E for the reference reaction was set to zero. This equation is combined with the equation for σ* to give the full Taft equation.
From comparing the E values for methyl, ethyl, isopropyl, and tert-butyl, it is seen that the value increases with increasing steric bulk. However, because context will have an effect on steric interactions some E values can be larger or smaller than expected. For example, the value for phenyl is much larger than that for tert-butyl. When comparing these groups using another measure of steric bulk, axial strain values, the tert-butyl group is larger. | 7 | Physical Chemistry |
Plastic pipes under water or other fluids experience hydrodynamic forces that can result in fatigue. The pipes reach failure sooner as temperatures and exposure to aggressive substances increase. For static fatigue tests, rotating machines apply weight on the material under study causing it to bend in different directions, which weakens the material overtime. | 8 | Metallurgy |
The photosynthetic partner in a lichen is called a photobiont. The photobionts in lichens come from a variety of simple prokaryotic and eukaryotic organisms. In the majority of lichens the photobiont is a green alga (Chlorophyta) or a cyanobacterium. In some lichens both types are present; in such cases, the alga is typically the primary partner, with the cyanobacteria being located in cryptic pockets. Algal photobionts are called phycobionts, while cyanobacterial photobionts are called cyanobionts. About 90% of all known lichens have phycobionts, and about 10% have cyanobionts. Approximately 100 species of photosynthetic partners from 40 genera and five distinct classes (prokaryotic: Cyanophyceae; eukaryotic: Trebouxiophyceae, Phaeophyceae, Chlorophyceae) have been found to associate with the lichen-forming fungi.
Common algal photobionts are from the genera Trebouxia, Trentepohlia, Pseudotrebouxia, or Myrmecia. Trebouxia is the most common genus of green algae in lichens, occurring in about 40% of all lichens. "Trebouxioid" means either a photobiont that is in the genus Trebouxia, or resembles a member of that genus, and is therefore presumably a member of the class Trebouxiophyceae. The second most commonly represented green alga genus is Trentepohlia. Overall, about 100 species of eukaryotes are known to occur as photobionts in lichens. All the algae are probably able to exist independently in nature as well as in the lichen.
A "cyanolichen" is a lichen with a cyanobacterium as its main photosynthetic component (photobiont). Most cyanolichen are also ascolichens, but a few basidiolichen like Dictyonema and Acantholichen have cyanobacteria as their partner.
The most commonly occurring cyanobacterium genus is Nostoc. Other common cyanobacterium photobionts are from Scytonema. Many cyanolichens are small and black, and have limestone as the substrate. Another cyanolichen group, the jelly lichens of the genera Collema or Leptogium are gelatinous and live on moist soils. Another group of large and foliose species including Peltigera, Lobaria, and Degelia are grey-blue, especially when dampened or wet. Many of these characterize the Lobarion communities of higher rainfall areas in western Britain, e.g., in the Celtic rain forest. Strains of cyanobacteria found in various cyanolichens are often closely related to one another. They differ from the most closely related free-living strains.
The lichen association is a close symbiosis. It extends the ecological range of both partners but is not always obligatory for their growth and reproduction in natural environments, since many of the algal symbionts can live independently. A prominent example is the alga Trentepohlia, which forms orange-coloured populations on tree trunks and suitable rock faces. Lichen propagules (diaspores) typically contain cells from both partners, although the fungal components of so-called "fringe species" rely instead on algal cells dispersed by the "core species".
The same cyanobiont species can occur in association with different fungal species as lichen partners. The same phycobiont species can occur in association with different fungal species as lichen partners. More than one phycobiont may be present in a single thallus.
A single lichen may contain several algal genotypes. These multiple genotypes may better enable response to adaptation to environmental changes, and enable the lichen to inhabit a wider range of environments. | 2 | Environmental Chemistry |
The hardening of the protein component of insect cuticle has been shown to be due to the tanning action of an agent produced by oxidation of a phenolic substance forming sclerotin. In the analogous hardening of the cockroach ootheca, the phenolic substance concerned is 3:4-dihydroxybenzoic acid (protocatechuic acid).
Acetosyringone is produced by the male leaffooted bug (Leptoglossus phyllopus) and used in its communication system. Guaiacol is produced in the gut of Desert locusts, Schistocerca gregaria, by the breakdown of plant material. This process is undertaken by the gut bacterium Pantoea agglomerans. Guaiacol is one of the main components of the pheromones that cause locust swarming. Orcinol has been detected in the "toxic glue" of the ant species Camponotus saundersi. Rhynchophorus ferrugineus (red palm weevil) use 2-methoxy-4-vinylphenol for chemical signaling (pheromones). Other simple and complex phenols can be found in eusocial ants (such as Crematogaster) as components of venom. | 0 | Organic Chemistry |
The game of Tetris is a puzzle game in which blocks of 4 are adsorbed onto a surface during game play. Scientists have used Tetris blocks "as a proxy for molecules with a complex shape" and their "adsorption on a flat surface" for studying the thermodynamics of nanoparticles. | 7 | Physical Chemistry |
A cryoprotectant is a substance used to protect biological tissue from freezing damage (i.e. that due to ice formation). Arctic and Antarctic insects, fish and amphibians create cryoprotectants (antifreeze compounds and antifreeze proteins) in their bodies to minimize freezing damage during cold winter periods. Cryoprotectants are also used to preserve living materials in the study of biology and to preserve food products.
For years, glycerol has been used in cryobiology as a cryoprotectant for blood cells and bull sperm, allowing storage in liquid nitrogen at temperatures around −196 °C. However, glycerol cannot be used to protect whole organs from damage. Instead, many biotechnology companies are researching the development of other cryoprotectants more suitable for such uses. A successful discovery may eventually make possible the bulk cryogenic storage (or "banking") of transplantable human and xenobiotic organs. A substantial step in that direction has already occurred. Twenty-First Century Medicine has vitrified a rabbit kidney to -135 °C with their proprietary vitrification cocktail. Upon rewarming, the kidney was successfully transplanted into a rabbit, with complete functionality and viability, able to sustain the rabbit indefinitely as the sole functioning kidney. | 1 | Biochemistry |
The mechanism of the SHJ reaction begins with the formation of the key cyclic cation 1. Nucleophilic attack at the anomeric position by the most nucleophilic nitrogen (N) then occurs, yielding the desired β-nucleoside 2. A second reaction of this nucleoside with 1 generates bis(riboside) 3. Depending on the nature of the Lewis acid used, coordination of the nucleophile to the Lewis acid may be significant. Reaction of this "blocked" nucleophile with 1 results in undesired constitutional isomer 4, which may undergo further reaction to 3. Generally Lewis acid coordination is not a problem when a Lewis acid such as trimethylsilyl triflate is used; it is much more important when a stronger Lewis acid like tin(IV) chloride is employed.
2-Deoxysugars are unable to form the cyclic cation intermediate 1 because of their missing benzoyl group; instead, under Lewis acidic conditions they form a resonance-stabilized oxocarbenium ion. The diastereoselectivity of nucleophilic attack on this intermediate is much lower than the stereoselectivity of attack on cyclic cation 1. Because of this low stereoselectivity, deoxyribonucleosides are usually synthesized using methods other than the SHJ reaction. | 0 | Organic Chemistry |
A large number of researchers have dedicated and are dedicating their efforts to the study of the Warburg effect that is intimately associated with the Warburg hypothesis. In oncology, the Warburg effect is the observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria as in most normal cells. Interestingly, researchers found that under obesity, tumor cells invert the metabolic flow by producing glucose by gluconeogenesis using lactic acid and other metabolic sources as substrates. This process in known as Warburg effect inversion.
In particular, almost 18,000 publications have been published on the matter of ATP and the Warburg effect in the period 2000 to 2015. Most of the functions of the Warburg Effect have been the object of study. Thousands of publications claim to have determined its functions or causes.
Thomas N. Seyfried and Peter L. Pedersen are leading supporters of the Warburg hypothesis of the cause of cancer and consider experimental and other evidence to overwhelming favor it over the widely accepted somatic mutation theory. | 1 | Biochemistry |
Based on her extraction, Wright thinks the "glomalin molecule is a clump of small glycoproteins with iron and other ions attached... glomalin contains from 1 to 9% tightly bound iron.... We've seen glomalin on the outside of hyphae, and we believe this is how the hyphae seal themselves so they can carry water and nutrients. It may also be what gives them the rigidity they need to span the air spaces between soil particles."
There is other circumstantial evidence to show that glomalin is of AM fungal origin. When AM fungi are eliminated from soil through incubation of soil without host plants, the concentration of GRSP declines. A similar decline in GRSP has also been observed in incubated soils from forested, afforested, and agricultural land and grasslands treated with fungicide.
It is important to emphasize that glomalin is not synonym of GRSP. Glomalin is the protein that binds to the Mab32B11 antibody, while GRSP is a crude extract containing many substances, including humic acids.
The chemistry of GRSP is not yet fully understood, and the link between glomalin, GRSP, and AM fungi is not yet clear. The physiological function of glomalin in fungi is also a topic of current research. | 9 | Geochemistry |
The success and implications of xDNA prompted research to examine other factors which could alter B-DNAs chemical properties and create a new system for information storage with broader applications. yDNA also uses a benzene ring, similar to xDNA, with the only difference being the site of addition of the aromatic ring. The location of the benzene ring changes the preferred structure of the expanded helix. The altered conformation makes yDNA more similar to B-DNA in its orientation by changing the interstrand hydrogen bonds. Stability is highly dependent on the bases rotation about the link between the base and the sugar of the backbone. yDNAs altered preference for this orientation makes it more stable overall than xDNA. The location of the benzene spacer also affects the bases groove geometry, altering neighbour interactions. The base pairs between y-nucleotides and natural nucleotides is planar, rather than slightly twisted as with xDNA. This decreases the rise of the helix even further than achieved by xDNA.
While xDNA and yDNA are quite similar in most properties, including their increased stacking interactions, yDNA shows superior mismatch recognition. y-pyrimidines display slightly stronger stacking interactions than x-pyrimidines as a result of the distance between the two anomeric carbons, which is slightly larger in yDNA. xDNA still has stronger stacking interactions in model helices, but adding either x- or y-pyrimidines to a natural double helix strengthens the intra- and interstrand interactions, increasing overall helix stability. In the end, which of the two has the strongest overall stacking interactions is dependent on the sequence; xT and yT bind A with similar strength, but the stacking energy of yC bound to G is stronger than xC by 4kJ/mol. yDNA and other expanded bases are part of a very young field which is highly understudied. Research suggest that the ideal conformation still remains to be discovered, but knowing that the benzene location affects the orientation and structure of expanded nucleobases adds information to their future design. | 1 | Biochemistry |
The Trinder glucose activity test is a diagnostic test used in medicine to determine the presence of glucose or glucose oxidase. The test employs the Trinder reagent, and is a colour change test resulting from the Trinder reaction.
The Trinder reagent, named after P. Trinder of the Biochemistry Department of the Royal Infirmary in Sunderland (see the article listed in further reading), comprises an aminoantipyrine (such as 4-aminoantipyrine) and phenol (p-hydroxybenzene).
The Trinder reaction is the reaction between hydrogen peroxide and the phenol and aminoantipyrine to form a quinone (quinoneimine), catalyzed by the presence of a peroxidase (such as horseradish peroxidase). The hydrogen peroxide is itself produced by an initial reaction where the glucose is oxidised in the presence of the glucose oxidase catalyst into HO and gluconic acid.
The quinone is red-violet in colour, with the intensity of the colour being in proportion to the glucose concentration. The colour is measured at 505 nm, 510 nm, or 540 nm.
Diagnostic kits containing the Trinder reagent are available, including one from Sigma-Aldrich.
The Stanbio Single Reagent Glucose Method is based upon the Trinder technique. | 1 | Biochemistry |
In this book Agricola provides a detailed account of beneficiation of different ores. He describes the processes involved in ore sorting, roasting and crushing. The use of water for washing ores is discussed in great detail, e.g. the use of launders and washing tables. Several different types of machinery for crushing ore and washing it are illustrated and different techniques for different metals and different regions are described. | 8 | Metallurgy |
In 1988, climatologist Stephen Schneider organised a conference of the American Geophysical Union. The first Chapman Conference on Gaia, was held in San Diego, California on March 7, 1988.
During the "philosophical foundations" session of the conference, David Abram spoke on the influence of metaphor in science, and of the Gaia hypothesis as offering a new and potentially game-changing metaphorics, while James Kirchner criticised the Gaia hypothesis for its imprecision. Kirchner claimed that Lovelock and Margulis had not presented one Gaia hypothesis, but four:
* CoEvolutionary Gaia: that life and the environment had evolved in a coupled way. Kirchner claimed that this was already accepted scientifically and was not new.
* Homeostatic Gaia: that life maintained the stability of the natural environment, and that this stability enabled life to continue to exist.
* Geophysical Gaia: that the Gaia hypothesis generated interest in geophysical cycles and therefore led to interesting new research in terrestrial geophysical dynamics.
* Optimising Gaia: that Gaia shaped the planet in a way that made it an optimal environment for life as a whole. Kirchner claimed that this was not testable and therefore was not scientific.
Of Homeostatic Gaia, Kirchner recognised two alternatives. "Weak Gaia" asserted that life tends to make the environment stable for the flourishing of all life. "Strong Gaia" according to Kirchner, asserted that life tends to make the environment stable, to enable the flourishing of all life. Strong Gaia, Kirchner claimed, was untestable and therefore not scientific.
Lovelock and other Gaia-supporting scientists, however, did attempt to disprove the claim that the hypothesis is not scientific because it is impossible to test it by controlled experiment. For example, against the charge that Gaia was teleological, Lovelock and Andrew Watson offered the Daisyworld Model (and its modifications, above) as evidence against most of these criticisms. Lovelock said that the Daisyworld model "demonstrates that self-regulation of the global environment can emerge from competition amongst types of life altering their local environment in different ways".
Lovelock was careful to present a version of the Gaia hypothesis that had no claim that Gaia intentionally or consciously maintained the complex balance in her environment that life needed to survive. It would appear that the claim that Gaia acts "intentionally" was a statement in his popular initial book and was not meant to be taken literally. This new statement of the Gaia hypothesis was more acceptable to the scientific community. Most accusations of teleologism ceased, following this conference. | 9 | Geochemistry |
The pyrogallolarene macrocycle is typically prepared by condensation of pyrogallol and an aldehyde in concentrated acid solution in the presence of an alcohol solvent, usually methanol or ethanol. The reaction conditions can usually be carefully adjusted to precipitate the pure product or the product may be purified by recrystallization.
Pyrogallol[4]arene is simply made by mixing a solvent-free dispersion of isovaleraldehyde with pyrogallol, and a catalytic amount of p-toluenesulfonic acid, in a mortar and pestle. | 6 | Supramolecular Chemistry |
There are (at least) 10 different ways to classify space groups into classes. The relations between some of these are described in the following table. Each classification system is a refinement of the ones below it. To understand an explanation given here it may be necessary to understand the next one down.
gave another classification of the space groups, called a fibrifold notation, according to the fibrifold structures on the corresponding orbifold. They divided the 219 affine space groups into reducible and irreducible groups. The reducible groups fall into 17 classes corresponding to the 17 wallpaper groups, and the remaining 35 irreducible groups are the same as the cubic groups and are classified separately. | 4 | Stereochemistry |
Thermodynamic power cycles are the basis for the operation of heat engines, which supply most of the world's electric power and run the vast majority of motor vehicles. Power cycles can be organized into two categories: real cycles and ideal cycles. Cycles encountered in real world devices (real cycles) are difficult to analyze because of the presence of complicating effects (friction), and the absence of sufficient time for the establishment of equilibrium conditions. For the purpose of analysis and design, idealized models (ideal cycles) are created; these ideal models allow engineers to study the effects of major parameters that dominate the cycle without having to spend significant time working out intricate details present in the real cycle model.
Power cycles can also be divided according to the type of heat engine they seek to model. The most common cycles used to model internal combustion engines are the Otto cycle, which models gasoline engines, and the Diesel cycle, which models diesel engines. Cycles that model external combustion engines include the Brayton cycle, which models gas turbines, the Rankine cycle, which models steam turbines, the Stirling cycle, which models hot air engines, and the Ericsson cycle, which also models hot air engines.
For example :--the pressure-volume mechanical work output from the ideal Stirling cycle (net work out), consisting of 4 thermodynamic processes, is:
For the ideal Stirling cycle, no volume change happens in process 4-1 and 2-3, thus equation (3) simplifies to: | 7 | Physical Chemistry |
In reality, this method is rarely used due to the difficulty of collecting and analysing the gas concentrations. However, by using an assumed value for oxygen consumption, cardiac output can be closely approximated without the cumbersome and time-consuming oxygen consumption measurement. This is sometimes called an assumed Fick determination.
A commonly used value for O consumption at rest is O per minute per square meter of body surface area. | 1 | Biochemistry |
For people who are alert and able to swallow, drinking warm (not hot) sweetened liquids can help raise the temperature. General medical consensus advises against alcohol and caffeinated drinks. As most hypothermic people are moderately dehydrated due to cold-induced diuresis, warmed intravenous fluids to a temperature of are often recommended. | 1 | Biochemistry |
Elsholz et al. (2012), showed that McsB and YwlE are a protein arginine kinase and phosphatase, rather than a tyrosine kinase and phosphatase because they observed only an McsB/YwlE-dependent detection of protein arginine phosphorylation or dephosphorylation in vivo. Specifically, they suggested that YwIE acts as a PAP in vivo.
McsB and YwlE were thought to be tyrosine kinases and phosphatases. However, in 2012, Elsholz et al. detected 121 arginine phosphorylation sites in 87 proteins in living Bacillus Subtilis (B.subtillis), a gram-positive bacterium present in soil and human gastrointestinal tract. Their observations led them to believe that protein arginine phosphorylation exists in vivo as a posttranslational modification in bacteria. The arginine-phosphorylated proteins they detected were distributed among "distinct physiological classes of proteins" such as regulators, metabolic enzymes, stress, and ribosomal proteins. This result suggested that YwlE acts as a protein arginine phosphatase that explicitly dephosphorylates arginine residues both in vitro and in vivo
Secondly, Elsholz et al. (2012) were only able to detect protein arginine phosphorylation in a YwIE mutant gene and not the wild-type strain. But protein phosphorylates on either serine, threonine, or tyrosine were detected in both wild-type and a YwIE mutant strain in equal amounts. Therefore, they thought that YwIE might solely act as a protein arginine phosphatase. That is, the detection of protein arginine phosphorylation depended on the presence of YwIE. They confirmed this hypothesis after failing to detect protein arginine phosphorylation after (1) analyzing a mutant extract treated in vitro with purified YwIE protein before conducting mass spectroscopy analysis; and (2) overexpressing the YwIE in trans in a YwIE mutant in-vivo. The close interaction of the arginine phosphorylated proteins with YwIE suggested that the stability of the modifications was indeed influenced by the YwIE protein. | 1 | Biochemistry |
In the first human genome draft the fraction of LINE elements of the human genome was given as 21% and their copy number as 850,000. Of these, L1, L2 and L3 elements made up 516,000, 315,000 and 37,000 copies, respectively. The non-autonomous SINE elements which depend on L1 elements for their proliferation make up 13% of the human genome and have a copy number of around 1.5 million. They probably originated from the RTE family of LINEs. Recent estimates show the typical human genome contains on average 100 L1 elements with potential for mobilization, however there is a fair amount of variation and some individuals may contain a larger number of active L1 elements, making these individuals more prone to L1-induced mutagenesis.
Increased L1 copy numbers have also been found in the brains of people with schizophrenia, indicating that LINE elements may play a role in some neuronal diseases. | 1 | Biochemistry |
Levetiracetam, sold under the brand name Keppra among others, is a medication used to treat epilepsy. It is used for partial-onset, myoclonic, or tonic–clonic seizures and is taken either by mouth as an immediate or extended release formulation or by injection into a vein.
Common side effects of levetiracetam include sleepiness, dizziness, feeling tired, and aggression. Severe side effects may include psychosis, suicide, and allergic reactions such as Stevens–Johnson syndrome or anaphylaxis. Levetiracetam is the S-enantiomer of etiracetam. Its mechanism of action is not yet clear.
Levetiracetam was approved for medical use in the United States in 1999 and is available as a generic medication. In 2021, it was the 101st most commonly prescribed medication in the United States, with more than 6million prescriptions. It is on the World Health Organization's List of Essential Medicines. | 4 | Stereochemistry |
One industrial application is the production of magnesium, which begins with production of magnesium chloride by chlorination of magnesium oxide:
Electrolysis of the resulting molten magnesium chloride is conducted at 700 °C:
Aluminium metal is produced from aluminium oxides by electrolysis of a molten mixture of sodium hexafluoroaluminate and alumina at 950 °C. This conversion is called the Hall-Haroult process. | 8 | Metallurgy |
The Carnot cycle is a cycle composed of the totally reversible processes of isentropic compression and expansion and isothermal heat addition and rejection. The thermal efficiency of a Carnot cycle depends only on the absolute temperatures of the two reservoirs in which heat transfer takes place, and for a power cycle is:
where is the lowest cycle temperature and the highest. For Carnot power cycles the coefficient of performance for a heat pump is:
and for a refrigerator the coefficient of performance is:
The second law of thermodynamics limits the efficiency and COP for all cyclic devices to levels at or below the Carnot efficiency. The Stirling cycle and Ericsson cycle are two other reversible cycles that use regeneration to obtain isothermal heat transfer. | 7 | Physical Chemistry |
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