The restriction endonuclease Fok 1 , naturally found in Flavobacterium okeanokoites , is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non sequence-specific DNA cleavage domain at the C-terminal . Once the protein is bound to duplex DNA via its DNA-binding domain at the 5'-GGATG-3' recognition site , the DNA cleavage domain is activated and cleaves the DNA at two locations, regardless of the nucleotide sequence at the cut site. The DNA is cut 9 nucleotides downstream of the motif on the forward strand, and 13 nucleotides downstream of the motif on the reverse strand, producing two sticky ends with 4-bp overhangs.
39-463: Its molecular mass is 65.4 kDa, being composed of 587 amino acids. The recognition domain contains three subdomains (D1, D2 and D3) that are evolutionarily related to the DNA-binding domain of the catabolite gene activator protein which contains a helix-turn-helix. DNA cleavage is mediated through the non-specific cleavage domain which also includes the dimerisation surface. The dimer interface
78-442: A conversion factor, describing the shape of a particular molecule. This allows the apparent molecular mass to be described from a range of techniques sensitive to hydrodynamic effects, including DLS , SEC (also known as GPC when the eluent is an organic solvent), viscometry , and diffusion ordered nuclear magnetic resonance spectroscopy (DOSY). The apparent hydrodynamic size can then be used to approximate molecular mass using
117-468: A nonoptimal number of neutrons or protons decay by beta decay (including positron decay), electron capture or more exotic means, such as spontaneous fission and cluster decay . The majority of stable nuclides are even-proton–even-neutron, where all numbers Z , N , and A are even. The odd- A stable nuclides are divided (roughly evenly) into odd-proton–even-neutron, and even-proton–odd-neutron nuclides. Odd-proton–odd-neutron nuclides (and nuclei) are
156-533: A series of macromolecule-specific standards. As this requires calibration, it's frequently described as a "relative" molecular mass determination method. It is also possible to determine absolute molecular mass directly from light scattering, traditionally using the Zimm method . This can be accomplished either via classical static light scattering or via multi-angle light scattering detectors. Molecular masses determined by this method do not require calibration, hence
195-555: A set of nuclides with equal proton number and equal mass number (thus making them by definition the same isotope), but different states of excitation. An example is the two states of the single isotope 43 Tc shown among the decay schemes . Each of these two states (technetium-99m and technetium-99) qualifies as a different nuclide, illustrating one way that nuclides may differ from isotopes (an isotope may consist of several different nuclides of different excitation states). The longest-lived non- ground state nuclear isomer
234-514: A stable nucleus (see graph). For example, although the neutron–proton ratio of 2 He is 1:2, the neutron–proton ratio of 92 U is greater than 3:2. A number of lighter elements have stable nuclides with the ratio 1:1 ( Z = N ). The nuclide 20 Ca (calcium-40) is observationally the heaviest stable nuclide with the same number of neutrons and protons. All stable nuclides heavier than calcium-40 contain more neutrons than protons. The proton–neutron ratio
273-419: A wide range of molecular masses (40 kDa – 5 MDa). To a first approximation, the basis for determination of molecular mass according to Mark–Houwink relations is the fact that the intrinsic viscosity of solutions (or suspensions ) of macromolecules depends on volumetric proportion of the dispersed particles in a particular solvent. Specifically, the hydrodynamic size as related to molecular mass depends on
312-790: Is 138 times rarer. About 34 of these nuclides have been discovered (see List of nuclides and Primordial nuclide for details). The second group of radionuclides that exist naturally consists of radiogenic nuclides such as Ra (t 1/2 = 1602 years ), an isotope of radium , which are formed by radioactive decay . They occur in the decay chains of primordial isotopes of uranium or thorium. Some of these nuclides are very short-lived, such as isotopes of francium . There exist about 51 of these daughter nuclides that have half-lives too short to be primordial, and which exist in nature solely due to decay from longer lived radioactive primordial nuclides. The third group consists of nuclides that are continuously being made in another fashion that
351-409: Is CH 4 , are calculated respectively as follows: The uncertainty in molecular mass reflects variance (error) in measurement not the natural variance in isotopic abundances across the globe. In high-resolution mass spectrometry the mass isotopomers C H 4 and C H 4 are observed as distinct molecules, with molecular masses of approximately 16.031 Da and 17.035 Da, respectively. The intensity of
390-507: Is a summary table for the 905 nuclides with half-lives longer than one hour, given in list of nuclides . Note that numbers are not exact, and may change slightly in the future, if some "stable" nuclides are observed to be radioactive with very long half-lives. Atomic nuclei other than hydrogen 1 H have protons and neutrons bound together by the residual strong force . Because protons are positively charged, they repel each other. Neutrons, which are electrically neutral, stabilize
429-424: Is defined in terms of the mass of the isotope C (carbon-12). However, the name unified atomic mass unit (u) is still used in common practice. Relative atomic and molecular masses as defined are dimensionless . Molar masses when expressed in g / mol have almost identical numerical values as relative atomic and molecular masses. For example, the molar mass and molecular mass of methane , whose molecular formula
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#1732798787571468-415: Is equal to one dalton). The molecular mass and relative molecular mass are distinct from but related to the molar mass . The molar mass is defined as the mass of a given substance divided by the amount of the substance , and is expressed in grams per mol (g/mol). That makes the molar mass an average of many particles or molecules (potentially containing different isotopes ), and the molecular mass
507-411: Is formed by the parallel helices α4 and α5 and two loops P1 and P2 of the cleavage domain. When the nuclease is unbound to DNA, the endonuclease domain is sequestered by the DNA-binding domain and is released through a conformational change in the DNA-binding domain upon binding to its recognition site. Cleavage only occurs upon dimerization, when the recognition domain is bound to its cognate site and in
546-442: Is frequently as a weighted average similar to the molar mass but with different units. In molecular biology, the mass of macromolecules is referred to as their molecular weight and is expressed in kDa, although the numerical value is often approximate and representative of an average. The terms "molecular mass", "molecular weight", and "molar mass" may be used interchangeably in less formal contexts where unit- and quantity-correctness
585-403: Is made by cosmic ray bombardment of other elements, and nucleogenic Pu which is still being created by neutron bombardment of natural U as a result of natural fission in uranium ores. Cosmogenic nuclides may be either stable or radioactive. If they are stable, their existence must be deduced against a background of stable nuclides, since every known stable nuclide
624-485: Is not needed. The molecular mass is more commonly used when referring to the mass of a single or specific well-defined molecule and less commonly than molecular weight when referring to a weighted average of a sample. Prior to the 2019 revision of the SI quantities expressed in daltons (Da) were by definition numerically equivalent to molar mass expressed in the units g/mol and were thus strictly numerically interchangeable. After
663-585: Is not simple spontaneous radioactive decay (i.e., only one atom involved with no incoming particle) but instead involves a natural nuclear reaction . These occur when atoms react with natural neutrons (from cosmic rays, spontaneous fission , or other sources), or are bombarded directly with cosmic rays . The latter, if non-primordial, are called cosmogenic nuclides . Other types of natural nuclear reactions produce nuclides that are said to be nucleogenic nuclides. An example of nuclides made by nuclear reactions, are cosmogenic C ( radiocarbon ) that
702-472: Is not the only factor affecting nuclear stability. It depends also on even or odd parity of its atomic number Z , neutron number N and, consequently, of their sum, the mass number A . Oddness of both Z and N tends to lower the nuclear binding energy , making odd nuclei, generally, less stable. This remarkable difference of nuclear binding energy between neighbouring nuclei, especially of odd- A isobars , has important consequences: unstable isotopes with
741-499: Is present on Earth primordially. Beyond the naturally occurring nuclides, more than 3000 radionuclides of varying half-lives have been artificially produced and characterized. The known nuclides are shown in Table of nuclides . A list of primordial nuclides is given sorted by element, at List of elements by stability of isotopes . List of nuclides is sorted by half-life, for the 905 nuclides with half-lives longer than one hour. This
780-473: Is the nuclide tantalum-180m ( 73 Ta ), which has a half-life in excess of 1,000 trillion years. This nuclide occurs primordially, and has never been observed to decay to the ground state. (In contrast, the ground state nuclide tantalum-180 does not occur primordially, since it decays with a half life of only 8 hours to Hf (86%) or W (14%).) There are 251 nuclides in nature that have never been observed to decay. They occur among
819-650: The atomic masses of each nuclide present in the molecule, while molar masses and relative molecular masses (molecular weights) are calculated from the standard atomic weights of each element . The standard atomic weight takes into account the isotopic distribution of the element in a given sample (usually assumed to be "normal"). For example, water has a molar mass of 18.0153(3) g/mol, but individual water molecules have molecular masses which range between 18.010 564 6863(15) Da ( H 2 O) and 22.027 7364(9) Da ( H 2 O). Atomic and molecular masses are usually reported in daltons , which
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#1732798787571858-447: The isotope concept (grouping all atoms of each element) emphasizes chemical over nuclear. The neutron number has large effects on nuclear properties, but its effect on chemical reactions is negligible for most elements. Even in the case of the very lightest elements, where the ratio of neutron number to atomic number varies the most between isotopes, it usually has only a small effect, but it matters in some circumstances. For hydrogen,
897-601: The 2019 revision, this relationship is only nearly equivalent, although the difference is negligible for all practical purposes. The molecular mass of small to medium size molecules, measured by mass spectrometry, can be used to determine the composition of elements in the molecule. The molecular masses of macromolecules, such as proteins, can also be determined by mass spectrometry; however, methods based on viscosity and light-scattering are also used to determine molecular mass when crystallographic or mass spectrometric data are not available. Molecular masses are calculated from
936-400: The 80 different elements that have one or more stable isotopes. See stable nuclide and primordial nuclide . Unstable nuclides are radioactive and are called radionuclides . Their decay products ('daughter' products) are called radiogenic nuclides . Natural radionuclides may be conveniently subdivided into three types. First, those whose half-lives t 1/2 are at least 2% as long as
975-642: The age of the Earth (for practical purposes, these are difficult to detect with half-lives less than 10% of the age of the Earth) ( 4.6 × 10 years ). These are remnants of nucleosynthesis that occurred in stars before the formation of the Solar System . For example, the isotope U (t 1/2 = 4.5 × 10 years ) of uranium is still fairly abundant in nature, but the shorter-lived isotope U (t 1/2 = 0.7 × 10 years )
1014-409: The choice of isotopes is defined and thus is a single specific molecular mass out of the (perhaps many) possibilities. The masses used to compute the monoisotopic molecular mass are found in a table of isotopic masses and are not found in a typical periodic table. The average molecular mass is often used for larger molecules, since molecules with many atoms are often unlikely to be composed exclusively of
1053-412: The element. Particular nuclides are still often loosely called "isotopes", but the term "nuclide" is the correct one in general (i.e., when Z is not fixed). In similar manner, a set of nuclides with equal mass number A , but different atomic number , are called isobars (isobar = equal in weight), and isotones are nuclides of equal neutron number but different proton numbers. Likewise, nuclides with
1092-431: The lightest element, the isotope effect is large enough to affect biological systems strongly. In the case of helium, helium-4 obeys Bose–Einstein statistics , while helium-3 obeys Fermi–Dirac statistics . Since isotope is the older term, it is better known than nuclide , and is still occasionally used in contexts in which nuclide might be more appropriate, such as nuclear technology and nuclear medicine. Although
1131-405: The mass of one specific particle or molecule. The molar mass is usually the more appropriate quantity when dealing with macroscopic (weigh-able) quantities of a substance. The definition of molecular weight is most authoritatively synonymous with relative molecular mass; however, in common practice, use of this terminology is highly variable. When the molecular weight is given with the unit Da, it
1170-420: The mass-spectrometry peaks is proportional to the isotopic abundances in the molecular species. C H H 3 can also be observed with molecular mass of 17 Da. In mass spectrometry, the molecular mass of a small molecule is usually reported as the monoisotopic mass : that is, the mass of the molecule containing only the most common isotope of each element. This also differs subtly from the molecular mass in that
1209-664: The molecular mass of proteins, lipids, sugars and nucleic acids at the single-molecule level. The technique is based on interferometric scattered light microscopy. Contrast from scattered light by a single binding event at the interface between the protein solution and glass slide is detected and is linearly proportional to the mass of the molecule. This technique can also be used to measure sample homogeneity, to detect protein oligomerisation states, and to identify complex macromolecular assemblies ( ribosomes , GroEL , AAV ) and protein interactions such as protein-protein interactions. Mass photometry can accurately measure molecular mass over
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1248-449: The most abundant isotope of each element. A theoretical average molecular mass can be calculated using the standard atomic weights found in a typical periodic table. The average molecular mass of a very small sample, however, might differ substantially from this since a single sample average is not the same as the average of many geographically distributed samples. Mass photometry (MP) is a rapid, in-solution, label-free method of obtaining
1287-405: The nucleus in two ways. Their copresence pushes protons slightly apart, reducing the electrostatic repulsion between the protons, and they exert the attractive nuclear force on each other and on protons. For this reason, one or more neutrons are necessary for two or more protons to be bound into a nucleus. As the number of protons increases, so does the ratio of neutrons to protons necessary to ensure
1326-404: The presence of magnesium ions. The endonuclease domain of Fok1 has been used in several studies, after combination with a variety of DNA-binding domains such as the zinc finger (see zinc finger nuclease ), or inactive Cas9 One of several human vitamin D receptor gene variants is caused by a single nucleotide polymorphism in the start codon of the gene which can be distinguished through
1365-415: The same neutron excess ( N − Z ) are called isodiaphers. The name isoto n e was derived from the name isoto p e to emphasize that in the first group of nuclides it is the number of neutrons (n) that is constant, whereas in the second the number of protons (p). See Isotope#Notation for an explanation of the notation used for different nuclide or isotope types. Nuclear isomers are members of
1404-411: The term "absolute". The only external measurement required is refractive index increment , which describes the change in refractive index with concentration. Nuclide Nuclides (or nucleides , from nucleus , also known as nuclear species) are a class of atoms characterized by their number of protons , Z , their number of neutrons , N , and their nuclear energy state . The word nuclide
1443-478: The use of the Fok1 enzyme. Molecular mass The molecular mass ( m ) is the mass of a given molecule . Units of daltons (Da) are often used. Different molecules of the same compound may have different molecular masses because they contain different isotopes of an element. The derived quantity relative molecular mass is the unitless ratio of the mass of a molecule to the atomic mass constant (which
1482-468: The words nuclide and isotope are often used interchangeably, being isotopes is actually only one relation between nuclides. The following table names some other relations. A nuclide and its alpha decay product are isodiaphers. (Z 1 = N 2 and Z 2 = N 1 ) but with different energy states A set of nuclides with equal proton number ( atomic number ), i.e., of the same chemical element but different neutron numbers , are called isotopes of
1521-605: Was coined by the American nuclear physicist Truman P. Kohman in 1947. Kohman defined nuclide as a "species of atom characterized by the constitution of its nucleus" containing a certain number of neutrons and protons. The term thus originally focused on the nucleus. A nuclide is a species of an atom with a specific number of protons and neutrons in the nucleus, for example carbon-13 with 6 protons and 7 neutrons. The nuclide concept (referring to individual nuclear species) emphasizes nuclear properties over chemical properties, while
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