1.
Green fluorescent protein
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The green fluorescent protein is a protein composed of 238 amino acid residues that exhibits bright green fluorescence when exposed to light in the blue to ultraviolet range. Although many other organisms have similar green fluorescent proteins, GFP traditionally refers to the protein first isolated from the jellyfish Aequorea victoria. The GFP from A. victoria has an excitation peak at a wavelength of 395 nm. Its emission peak is at 509 nm, which is in the green portion of the visible spectrum. The fluorescence quantum yield of GFP is 0.79, the GFP from the sea pansy has a single major excitation peak at 498 nm. In cell and molecular biology, the GFP gene is used as a reporter of expression. GFP can be introduced into animals or other species through transgenic techniques, and maintained in their genome, to date, GFP has been expressed in many species, including bacteria, yeasts, fungi, fish and mammals, including in human cells. Tsien, Osamu Shimomura, and Martin Chalfie were awarded the 2008 Nobel Prize in Chemistry on 10 October 2008 for their discovery and development of the green fluorescent protein. In the 1960s and 1970s, GFP, along with the separate luminescent protein aequorin, was first purified from Aequorea victoria, in A. victoria, GFP fluorescence occurs when aequorin interacts with Ca2+ ions, inducing a blue glow. Some of this luminescent energy is transferred to the GFP, shifting the overall color towards green, however, its utility as a tool for molecular biologists did not begin to be realized until 1992 when Douglas Prasher reported the cloning and nucleotide sequence of wtGFP in Gene. The funding for this project had run out, so Prasher sent cDNA samples to several labs. The lab of Martin Chalfie expressed the coding sequence of wtGFP, with the first few amino acids deleted, in cells of E. coli and C. elegans. Frederick Tsujis lab independently reported the expression of the recombinant protein one month later, remarkably, the GFP molecule folded and was fluorescent at room temperature, without the need for exogenous cofactors specific to the jellyfish. The first reported crystal structure of a GFP was that of the S65T mutant by the Remington group in Science in 1996, one month later, the Phillips group independently reported the wild-type GFP structure in Nature Biotechnology. These crystal structures provided vital background on chromophore formation and neighboring residue interactions, researchers have modified these residues by directed and random mutagenesis to produce the wide variety of GFP derivatives in use today. Due to the potential for widespread usage and the needs of researchers. The first major improvement was a point mutation reported in 1995 in Nature by Roger Tsien. This matched the spectral characteristics of commonly available FITC filter sets, a 37 °C folding efficiency point mutant to this scaffold, yielding enhanced GFP, was discovered in 1995 by the laboratories of Thastrup and Falkow
2.
Carbonate minerals
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IMA-CNMNC proposes a new hierarchical scheme. This list uses the Classification of Nickel–Strunz
3.
Crystal habit
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In mineralogy, crystal habit is the characteristic external shape of an individual crystal or crystal group. A single crystals habit is a description of its shape and its crystallographic forms. Recognizing the habit may help in identifying a mineral, when the faces are well-developed due to uncrowded growth a crystal is called euhedral, one with partially developed faces is subhedral, and one with undeveloped crystal faces is called anhedral. The long axis of a quartz crystal typically has a six-sided prismatic habit with parallel opposite faces. Aggregates can be formed of individual crystals with euhedral to anhedral grains, the arrangement of crystals within the aggregate can be characteristic of certain minerals. For example, minerals used for asbestos insulation often grow in a fibrous habit, the terms used by mineralogists to report crystal habits describe the typical appearance of an ideal mineral. Recognizing the habit can aid in identification as some habits are characteristic, most minerals, however, do not display ideal habits due to conditions during crystallization. Minerals belonging to the crystal system do not necessarily exhibit the same habit. Some habits of a mineral are unique to its variety and locality, For example, while most sapphires form elongate barrel-shaped crystals, ordinarily, the latter habit is seen only in ruby. Sapphire and ruby are both varieties of the mineral, corundum. Some minerals may replace other existing minerals while preserving the originals habit, a classic example is tigers eye quartz, crocidolite asbestos replaced by silica. While quartz typically forms prismatic crystals, in tigers eye the original fibrous habit of crocidolite is preserved, the names of crystal habits are derived from, Predominant crystal faces. Abnormal grain growth Grain growth Crystallization
4.
Fracture (mineralogy)
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In the field of mineralogy, fracture is the texture and shape of a rocks surface formed when a mineral is fractured. Minerals often have a highly distinctive fracture, making it a feature used in their identification. Fracture differs from cleavage in that the latter involves clean splitting along the planes of the minerals crystal structure. All minerals exhibit fracture, but when very strong cleavage is present, conchoidal fracture breakage that resembles the concentric ripples of a mussel shell. It often occurs in amorphous or fine-grained minerals such as flint, opal or obsidian, subconchoidal fracture is similar to conchoidal fracture, but with less significant curvature. Earthy fracture is reminiscent of freshly broken soil and it is frequently seen in relatively soft, loosely bound minerals, such as limonite, kaolinite and aluminite. Hackly fracture is jagged, sharp and not even and it occurs when metals are torn, and so is often encountered in native metals such as copper and silver. Splintery fracture comprises sharp elongated points and it is particularly seen in fibrous minerals such as chrysotile, but may also occur in non-fibrous minerals such as kyanite. Uneven fracture is a surface or one with random irregularities. It occurs in a range of minerals including arsenopyrite, pyrite and magnetite. Rudolf Duda and Lubos Rejl, Minerals of the World http, //www. galleries. com/minerals/property/fracture. htm
5.
Mohs scale of mineral hardness
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The Mohs scale of mineral hardness is a qualitative ordinal scale characterizing scratch resistance of various minerals through the ability of harder material to scratch softer material. Created in 1812 by German geologist and mineralogist Friedrich Mohs, it is one of several definitions of hardness in materials science, while greatly facilitating the identification of minerals in the field, the Mohs scale does not show how well hard materials perform in an industrial setting. Despite its lack of precision, the Mohs scale is highly relevant for field geologists, the Mohs scale hardness of minerals can be commonly found in reference sheets. Reference materials may be expected to have a uniform Mohs hardness, the Mohs scale of mineral hardness is based on the ability of one natural sample of mineral to scratch another mineral visibly. The samples of matter used by Mohs are all different minerals, Minerals are pure substances found in nature. Rocks are made up of one or more minerals, as the hardest known naturally occurring substance when the scale was designed, diamonds are at the top of the scale. The hardness of a material is measured against the scale by finding the hardest material that the material can scratch. For example, if material is scratched by apatite but not by fluorite. Scratching a material for the purposes of the Mohs scale means creating non-elastic dislocations visible to the naked eye, frequently, materials that are lower on the Mohs scale can create microscopic, non-elastic dislocations on materials that have a higher Mohs number. The Mohs scale is an ordinal scale. For example, corundum is twice as hard as topaz, the table below shows the comparison with the absolute hardness measured by a sclerometer, with pictorial examples. On the Mohs scale, a streak plate has a hardness of 7.0, using these ordinary materials of known hardness can be a simple way to approximate the position of a mineral on the scale. The table below incorporates additional substances that may fall between levels, Comparison between Hardness and Hardness, Mohs hardness of elements is taken from G. V, samsonov in Handbook of the physicochemical properties of the elements, IFI-Plenum, New York, USA,1968. The Hardness of Minerals and Rocks
6.
Lustre (mineralogy)
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Lustre or luster is the way light interacts with the surface of a crystal, rock, or mineral. The word traces its origins back to the latin lux, meaning light, a range of terms are used to describe lustre, such as earthy, metallic, greasy, and silky. Similarly, the term refers to a glassy lustre. A list of terms is given below. Lustre varies over a continuum, and so there are no rigid boundaries between the different types of lustre. The terms are frequently combined to describe types of lustre. Some minerals exhibit unusual optical phenomena, such as asterism or chatoyancy, a list of such phenomena is given below. Adamantine minerals possess a superlative lustre, which is most notably seen in diamond, such minerals are transparent or translucent, and have a high refractive index. Minerals with an adamantine lustre are uncommon, with examples being cerussite. Minerals with a degree of lustre are referred to as subadamantine, with some examples being garnet. Dull minerals exhibit little to no lustre, due to coarse granulations which scatter light in all directions, a distinction is sometimes drawn between dull minerals and earthy minerals, with the latter being coarser, and having even less lustre. Greasy minerals resemble fat or grease, a greasy lustre often occurs in minerals containing a great abundance of microscopic inclusions, with examples including opal and cordierite. Many minerals with a greasy lustre also feel greasy to the touch, metallic minerals have the lustre of polished metal, and with ideal surfaces will work as a reflective surface. Examples include galena, pyrite and magnetite, pearly minerals consist of thin transparent co-planar sheets. Light reflecting from these layers give them a lustre reminiscent of pearls, such minerals possess perfect cleavage, with examples including muscovite and stilbite. Resinous minerals have the appearance of resin, chewing gum or plastic, a principal example is amber, which is a form of fossilized resin. Silky minerals have an arrangement of extremely fine fibres, giving them a lustre reminiscent of silk. Examples include asbestos, ulexite and the satin spar variety of gypsum, a fibrous lustre is similar, but has a coarser texture
7.
Transparency and translucency
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In the field of optics, transparency is the physical property of allowing light to pass through the material without being scattered. On a macroscopic scale, the photons can be said to follow Snells Law, in other words, a translucent medium allows the transport of light while a transparent medium not only allows the transport of light but allows for image formation. The opposite property of translucency is opacity, transparent materials appear clear, with the overall appearance of one color, or any combination leading up to a brilliant spectrum of every color. When light encounters a material, it can interact with it in different ways. These interactions depend on the wavelength of the light and the nature of the material, photons interact with an object by some combination of reflection, absorption and transmission. Some materials, such as glass and clean water, transmit much of the light that falls on them and reflect little of it. Many liquids and aqueous solutions are highly transparent, absence of structural defects and molecular structure of most liquids are mostly responsible for excellent optical transmission. Materials which do not transmit light are called opaque, many such substances have a chemical composition which includes what are referred to as absorption centers. Many substances are selective in their absorption of light frequencies. They absorb certain portions of the spectrum while reflecting others. The frequencies of the spectrum which are not absorbed are either reflected or transmitted for our physical observation and this is what gives rise to color. The attenuation of light of all frequencies and wavelengths is due to the mechanisms of absorption. Transparency can provide almost perfect camouflage for animals able to achieve it and this is easier in dimly-lit or turbid seawater than in good illumination. Many marine animals such as jellyfish are highly transparent, at the atomic or molecular level, physical absorption in the infrared portion of the spectrum depends on the frequencies of atomic or molecular vibrations or chemical bonds, and on selection rules. Nitrogen and oxygen are not greenhouse gases because there is no absorption because there is no molecular dipole moment. With regard to the scattering of light, the most critical factor is the scale of any or all of these structural features relative to the wavelength of the light being scattered. Primary material considerations include, Crystalline structure, whether or not the atoms or molecules exhibit the long-range order evidenced in crystalline solids, glassy structure, scattering centers include fluctuations in density or composition. Microstructure, scattering centers include internal surfaces such as boundaries, crystallographic defects
8.
Birefringence
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Birefringence is the optical property of a material having a refractive index that depends on the polarization and propagation direction of light. These optically anisotropic materials are said to be birefringent, the birefringence is often quantified as the maximum difference between refractive indices exhibited by the material. Crystals with non-cubic crystal structures are often birefringent, as are plastics under mechanical stress and this effect was first described by the Danish scientist Rasmus Bartholin in 1669, who observed it in calcite, a crystal having one of the strongest birefringences. A mathematical description of wave propagation in a birefringent medium is presented below, following is a qualitative explanation of the phenomenon. Thus rotating the material around this axis does not change its optical behavior and this special direction is known as the optic axis of the material. Light whose polarization is perpendicular to the axis is governed by a refractive index no. Light whose polarization is in the direction of the optic axis sees an optical index ne, for any ray direction there is a linear polarization direction perpendicular to the optic axis, and this is called an ordinary ray. The magnitude of the difference is quantified by the birefringence, Δ n = n e − n o, the propagation of the ordinary ray is simply described by no as if there were no birefringence involved. However the extraordinary ray, as its name suggests, propagates unlike any wave in an optical material. Its refraction at a surface can be using the effective refractive index. However it is in fact an inhomogeneous wave whose power flow is not exactly in the direction of the wave vector and this causes an additional shift in that beam, even when launched at normal incidence, as is popularly observed using a crystal of calcite as photographed above. Rotating the calcite crystal will cause one of the two images, that of the ray, to rotate slightly around that of the ordinary ray. When the light propagates either along or orthogonal to the optic axis, in the first case, both polarizations see the same effective refractive index, so there is no extraordinary ray. In the second case the extraordinary ray propagates at a different phase velocity but is not an inhomogeneous wave, for instance, a quarter-wave plate is commonly used to create circular polarization from a linearly polarized source. The case of so-called biaxial crystals is substantially more complex and these are characterized by three refractive indices corresponding to three principal axes of the crystal. For most ray directions, both polarizations would be classified as extraordinary rays but with different effective refractive indices, being extraordinary waves, however, the direction of power flow is not identical to the direction of the wave vector in either case. The two refractive indices can be determined using the index ellipsoids for given directions of the polarization, note that for biaxial crystals the index ellipsoid will not be an ellipsoid of revolution but is described by three unequal principle refractive indices nα, nβ and nγ. Thus there is no axis around which a rotation leaves the optical properties invariant, for this reason, birefringent materials with three distinct refractive indices are called biaxial
9.
Copper
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Copper is a chemical element with symbol Cu and atomic number 29. It is a soft, malleable, and ductile metal with high thermal and electrical conductivity. A freshly exposed surface of copper has a reddish-orange color. Copper is one of the few metals that occur in nature in directly usable metallic form as opposed to needing extraction from an ore and this led to very early human use, from c.8000 BC. Copper used in buildings, usually for roofing, oxidizes to form a green verdigris, Copper is sometimes used in decorative art, both in its elemental metal form and in compounds as pigments. Copper compounds are used as agents, fungicides, and wood preservatives. Copper is essential to all living organisms as a trace dietary mineral because it is a key constituent of the enzyme complex cytochrome c oxidase. In molluscs and crustaceans, copper is a constituent of the blood pigment hemocyanin, replaced by the hemoglobin in fish. In humans, copper is found mainly in the liver, muscle, the adult body contains between 1.4 and 2.1 mg of copper per kilogram of body weight. The filled d-shells in these elements contribute little to interatomic interactions, unlike metals with incomplete d-shells, metallic bonds in copper are lacking a covalent character and are relatively weak. This observation explains the low hardness and high ductility of single crystals of copper, at the macroscopic scale, introduction of extended defects to the crystal lattice, such as grain boundaries, hinders flow of the material under applied stress, thereby increasing its hardness. For this reason, copper is supplied in a fine-grained polycrystalline form. The softness of copper partly explains its high conductivity and high thermal conductivity. The maximum permissible current density of copper in open air is approximately 3. 1×106 A/m2 of cross-sectional area, Copper is one of a few metallic elements with a natural color other than gray or silver. Pure copper is orange-red and acquires a reddish tarnish when exposed to air, as with other metals, if copper is put in contact with another metal, galvanic corrosion will occur. A green layer of verdigris can often be seen on old structures, such as the roofing of many older buildings. Copper tarnishes when exposed to sulfur compounds, with which it reacts to form various copper sulfides. There are 29 isotopes of copper, 63Cu and 65Cu are stable, with 63Cu comprising approximately 69% of naturally occurring copper, both have a spin of 3⁄2
10.
Mineral
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A mineral is a naturally occurring chemical compound, usually of crystalline form and abiogenic in origin. A mineral has one specific chemical composition, whereas a rock can be an aggregate of different minerals or mineraloids, the study of minerals is called mineralogy. There are over 5,300 known mineral species, over 5,070 of these have been approved by the International Mineralogical Association, the silicate minerals compose over 90% of the Earths crust. The diversity and abundance of species is controlled by the Earths chemistry. Silicon and oxygen constitute approximately 75% of the Earths crust, which translates directly into the predominance of silicate minerals, minerals are distinguished by various chemical and physical properties. Differences in chemical composition and crystal structure distinguish the various species, changes in the temperature, pressure, or bulk composition of a rock mass cause changes in its minerals. Minerals can be described by their various properties, which are related to their chemical structure. Common distinguishing characteristics include crystal structure and habit, hardness, lustre, diaphaneity, colour, streak, tenacity, cleavage, fracture, parting, more specific tests for describing minerals include magnetism, taste or smell, radioactivity and reaction to acid. Minerals are classified by key chemical constituents, the two dominant systems are the Dana classification and the Strunz classification, the silicate class of minerals is subdivided into six subclasses by the degree of polymerization in the chemical structure. All silicate minerals have a unit of a 4− silica tetrahedron—that is, a silicon cation coordinated by four oxygen anions. These tetrahedra can be polymerized to give the subclasses, orthosilicates, disilicates, cyclosilicates, inosilicates, phyllosilicates, other important mineral groups include the native elements, sulfides, oxides, halides, carbonates, sulfates, and phosphates. The first criterion means that a mineral has to form by a natural process, stability at room temperature, in the simplest sense, is synonymous to the mineral being solid. More specifically, a compound has to be stable or metastable at 25 °C, modern advances have included extensive study of liquid crystals, which also extensively involve mineralogy. Minerals are chemical compounds, and as such they can be described by fixed or a variable formula, many mineral groups and species are composed of a solid solution, pure substances are not usually found because of contamination or chemical substitution. Finally, the requirement of an ordered atomic arrangement is usually synonymous with crystallinity, however, crystals are also periodic, an ordered atomic arrangement gives rise to a variety of macroscopic physical properties, such as crystal form, hardness, and cleavage. There have been recent proposals to amend the definition to consider biogenic or amorphous substances as minerals. The formal definition of an approved by the IMA in 1995, A mineral is an element or chemical compound that is normally crystalline. However, if geological processes were involved in the genesis of the compound, Mineral classification schemes and their definitions are evolving to match recent advances in mineral science
Spencer, Leonard James (1911). "Azurite". Encyclopædia Britannica. 3 (11th ed.). p. 86.