User:Ssilverman00/sandbox/trace metal biogeochemistry/old

Stable isotopes and natural abundances
Copper has two naturally occurring stable isotopes: 63Cu and 65Cu, which exist in natural abundances of 69.17 and 30.83%, respectively. The isotopic composition of Cu is reported in delta notation (in ‰) relative to a NIST SRM 976 standard:

$$\delta^{65}Cu = \left [ \frac{(^{65}Cu/^{63}Cu)_{sample}}{(^{65}Cu/^{63}Cu)_{NIST976}} \right ]$$

Chemistry
Copper has two redox states: Cu1+ and Cu2+. The coordination chemistries conferred by its electronic configurations enable Cu to participate in many biological and chemical reactions. In its atomic state, Cu has an electronic configuration of [Ar]3d10 4s1. Upon oxidation to Cu1+, one electron is removed from the 4s shell, giving an electronic configuration of [Ar]3d104s0. Upon further oxidation to Cu2+, an electron is removed from the 3d shell, giving an electronic configuration of [Ar]3d94s0. Due to its full d-orbital, Cu1+ has diamagnetic resonance. In contrast, Cu2+ has one unpaired electron in its d-orbital, giving it paramagnetic resonance.

Equilibrium isotope fractionation
Redox speciation of Cu1+ and Cu2+ fractionates Cu isotopes. 63Cu2+ is preferentially reduced over 65Cu2+, leaving the residual Cu2+ enriched in 65Cu. The equilibrium fractionation factor for speciation between Cu2+ and Cu1+ (αCu(II)-Cu(I)) is 1.00403 [Zhu et al., 2002].

Biology
Copper can be found in the active sites of most enzymes that catalyze redox reactions (i.e., oxidoreductases), as it facilitates single electron transfers while reversibly oscillating between the Cu1+ and Cu2+ redox states. Enzymes typically contain between one (mononuclear) to four (tetranuclear) copper centers, which enable enzymes to catalyze different reactions. These copper centers are generally coordinated to N-, O- and S-containing groups, including histidine, aspartic acid, glutamic acid, cysteine and methionine. Copper's powerful redox capability makes it critically important for biology, but comes at a cost: Cu1+ is a highly toxic metal to cells because it readily abstracts single electrons from organic compounds and cellular material, leading to production of free radicals. Thus, cells have evolved specific strategies for carefully controlling the activity of Cu1+ while exploiting its redox behavior.

Examples of copper-based enzymes
Copper proteins function as electron or oxygen carriers, oxidases, mono- and dioxygenases, superoxide dismutases (SOD) and nitrogen oxide (NOx) reductases. In mollusks, copper-containing hemocyanins bind and transport O2 through the blood, much like hemoglobin in humans. One of the three major families of SOD contains Cu and Zn as its metal cofactors. In E. coli, the copper protein multicopper oxidase CueO oxidizes toxic Cu1+ to Cu2+ to regulate copper homeostasis. Particulate methane monooxygenase (pMMO) is a copper-containing protein in methanotrophs that oxidizes methane to methanol for both energy and carbon acquisition. Methane oxidation by pMMO is kinetically faster than by soluble methane monooxygenase (sMMO), the iron-containing counterpart to pMMO.

Biological fractionation
The natural 65Cu/63Cu varies according to copper's redox form and the ligand to which copper binds. Oxidized Cu2+ preferentially coordinates with hard donor ligands (e.g., N- or O-containing ligands), while reduced Cu(I) preferentially coordinates with soft donor ligands (e.g., S-containing ligands) [Fujii et al., 2013]. As 65Cu is preferentially oxidized over 63Cu, these isotopes tend to coordinate with hard and soft donor ligands, respectively [Fujii et al., 2013]. Cu isotopes can fractionate upon Cu-bacteria interactions from processes that include Cu adsorption to cells, intracellular uptake, metabolic regulation and redox speciation [Zhu et al., 2002; Navarrete et al., 2011]. Fractionation of Cu isotopes upon adsorption to cellular walls appears to depend on the surface functional groups that Cu complexes with, and can span positive and negative values [Navarrete et al., 2011]. Furthermore, bacteria preferentially incorporate the lighter Cu isotope intracellularly and into proteins. For example, E. coli, B. subtilis and a natural consortia of microbes sequestered Cu with apparent fractionations (ε65Cu) ranging from ~-1.0 to -4.4‰ [Navarrete et al., 2011]. Additionally, fractionation of Cu upon incorporation into the apoprotein of azurin was -9.8‰ in P. aeruginosa, and -15.3‰ in E. coli, while ε65Cu values of Cu incorporation into Cu-metallothionein and Cu-Zn-SOD in yeast were -17.1 and -11.8‰, respectively [Zhu et al., 2002].

Geochemistry
The concentration of Cu in Bulk Silicate Earth is ~30 ppm [McDonough and Sun, 1995], slightly less than its average concentration (~72 ppm) in fresh mid-oceanic ridge basalt glass [Albarede, 2004]. Cu1+ and Cu2+ form a variety of sulfides (often in association with Fe), as well as carbonates and hydroxides (e.g., chalcopyrite, chalcocite, cuprite and malachite). In mafic and ultramafic rocks, Cu tends to be concentrated in sulfidic materials [Albarede, 2004]. In freshwater, the predominant form of Cu is free Cu2+; in seawater, Cu complexes with carbonate ligands to form CuCO3 and Cu(CO3)2]2- [ref?].

Measurement
65Cu/63Cu ratios are measured via multi-conductor inductively coupled plasma mass spectrometry (MC-ICP-MS), which ionizes samples using inductively coupled plasma.

δ65Cu variations in organisms
To first order, δ65Cu values in organisms are driven by dietary Cu isotopic compositions. In plants, δ65Cu values vary between the different components (seeds, stem and leaves) from -1 to +0.4‰ [Weinstein et al., 2011; Jouvin et al., 2012]. In animals, δ65Cu values vary among the different organs. δ65Cu values of livers from sheep and mice fed a diet of δ65Cu = 0‰ were -1.5‰, while δ65Cu values of their kidneys were +1.5‰ [Balter and Zazzo, 2011]. Serum in human blood is typically 65Cu-depleted relative to erythrocytes, with these blood components having a range of Cu isotopic compositions from -0.7 to +0.9‰ [Albarede et al., 2011].

Environmental δ65Cu variations
Due to equilibrium and biological processes that fractionate Cu isotopes in the marine environment, the bulk isotopic composition of copper (δ65Cu = +0.6 to +1.5‰) is different from the δ65Cu values of the riverine input (δ65Cu = +0.02 to +1.45‰, with discharge-weighted average δ65Cu = +0.68‰) to the oceans [Vance et al., 2008; Boyle et al., 2012]. Equilibrium processes that fractionate Cu isotopes include high temperature ion exchange and redox speciation between mineral phases, and low temperature ion exchange between aqueous species or redox speciation between inorganic species [Zhu et al., 2002]. In riverine and marine environments, 65Cu/63Cu ratios are driven by preferential adsorption of 63Cu to particulate matter and preferential binding of 65Cu to organic complexes [Vance et al., 2008]. Additionally, Cu is strongly cycled in the surface and deep ocean. Cu concentrations are ~5 nM in the deep Pacific [Bruland, 1980] and ~1.5 nM in the deep Atlantic [Boyle et al., 2012]. The deep/surface ratio of Cu in the ocean is typically <10. Depth concentration profiles for Cu are roughly linear due to biological recycling and scavenging processes [Bruland and Lohan, 2003] in addition to adsorption to particles. Similarly, δ65Cu values in the Atlantic ocean do not markedly vary with depth [Boyle et al., 2012].

Applications to medicine
Copper isotopes in human plasma may serve as a marker for various types of cancer. In general, the serum of patients with colon, breast and liver cancer appear to be 65Cu-depleted relative to the serum of healthy patients, while liver tumors are 65Cu-enriched [Albarede et al., 2016]. In one study, the blood of patients with hepatocellular carcinomas was found to be depleted in 65Cu by 0.4‰ relative to the blood of non-cancer patients [Balter et al., 2015].

Stable isotopes and natural abundances
Zinc has five stable isotopes: 64Zn, 66Zn, 67Zn, 68Zn and 70Zn, with natural abundances of 48.63, 27.90, 4.10, 18.75, and 0.62%, respectively.

Chemistry
Zinc has only one redox state: Zn2+. In its atomic state, Zn has an electronic configuration of [Ar]3d104s2. Zn2+ has an electronic configuration of [Ar]3d104s0.

Geochemistry
The concentration of Zn in Bulk Silicate Earth is ~55 ppm [McDonough and Sun, 1995], while its average concentration in fresh mid-oceanic ridge basalt glass is ~87 ppm [Albarede, 2004]. Like Cu, Zn commonly associates with Fe to form a variety of zinc sulfide minerals such as sphalerite. Additionally, Zn associates with carbonates (e.g., to form smithsonite) and hydroxides. In mafic and ultramafic rocks, Zn tends to concentrate in oxides such as spinel and magnetite. In freshwater, Zn predominantly complexes with water to form an octahedrally coordinated aqua ion [Zn(H2O)6]2+. In seawater, Cl- ions replace up to four water molecules in the Zn aqua ion, forming [ZnCl(H2O)5]+, [ZnCl2(H2O)4]0 and [ZnCl4(H2O)2]- [Stanley and Byrne, 1990; Millero, 1996].