Chemistry Valinomycin - Essay Example

? CHEMISTRY: Question 1a Valinomycn utilizes passive type of transport as an antibiotic, metal ions occur as free ions in the blood stream, however valinomycin acts as a carrier for K+ (Potassium ion, it binds on potassium and facilitates their transfer lipid bi-layer since itself is a macro cyclic molecule, thus it’s a cat ion transporter. The main driving force lies on the structure of valinomycin, it’s made up of 12alternating amino acids and esters which form a macro cyclic molecule, the twelve carbonyl groups are essential for binding K+ Ions also responsible for solavation in polar solvents, the isopropyl and methyl group are responsible for solavation in non-polar solvents thus exhibiting molecular duality, k+(potassium ions are octahedral co-ordinated in a square bi-pyramidal geometry of six carbonyl bonds in space of 1.33Angstrom which makes it select k+ potassium ion ten thousand times over sodium, thus potassium gives it stability of 10(6) from the complex it forms. The molecule is "locked" into a conformation with the isopropyl groups on the exterior. It is not actually locked into configuration because the size of the molecule makes it highly flexible, but the potassium ion gives some degree of coordination to the macromolecule (Metzeler 2001) Question 1b Valinomycin is a dodecadepsipeptide, that is, it is made of twelve alternating amino acids and esters to form a macro cyclic molecule. The twelve carbonyl groups are essential for the binding of metal ions, and also for solvation in polar solvent. The isopropyl and methyl groups are responsible for solvation in nonpolar solvents. Along with its shape and size this molecular duality is the main reason for its binding properties. K+ ions are octahedral coordinated in a square bi-pyramidal geometry by 6 carbonyl bonds in this space of 1.33 Angstrom, leading to a 10,000x selectivity for K+ ions. For polar solvents, valinomycin will mainly expose the carbonyls to the solvent and in nonpolar solvents the isopropyl groups are located predominantly on the exterior of the molecule. This conformation changes when valinomycin is bound to a potassium ion. The molecule is "locked" into a conformation with the isopropyl groups on the exterior. It is not actually locked into configuration because the size of the molecule makes it highly flexible, but the potassium ion gives some degree of coordination to the macromolecule. Conformational and ionophoric properties of 3 valinomycin analogs cyclo n (n = 2, 3, 4) were studied by spectral and extraction methods. Conformations of dodeca- and hexadecaisoleucinomycins in nonpolar media practically do not differ from that of valinomycin, whereas for octaisoleucinomycin and octavalinomycin the conformations change significantly. Spatial structures of complexes of the investigated compounds are analogous to structures of complexes of valinomycin cyclopolymerhomologs (Metzeler 2001) The presence of isoleucine residues in dodeca- and hexadecaisoleucinomycins results in substantial increase in their ability of transfer the cat ions from aqueous to organic phase. Each complex has a characteristic spectrum which differs from that of uncomplexed valinomycin, suggesting several distinct structures for each of the metal-valinomycin complexes. The biologically active K complex shows the most significant changes in its spectrum, especially in the intensity of the symmetric C-H stretching vibration of CH3 and the convergence of the 2 ester carbonyl stretching vibration bands into 1 upon complex formation. These results are due to the unique orientation of the ester carbonyl groups toward the caged K ion and the resulting more free rotation of isopropyl side chains, thus they are poor cat ions transporters, assumptions made are that valinomycin has a complex structure as compared to octa-isoleucinomycin and hexadecaisoleucinomycin, differs in bonding in the methyl groups and the space in orientation make it superior in terms of bonding and having a chelate effect as compared to its analogues. Question 1c The equilibrium potential of a cell uses Nernst equation, in this case assuming the cell is only permeable to sodium (Na+ ions) the equation is as follows: E eq Na+ = ln Where Eeq, Na+ represents the equilibrium potential for sodium, which is measured in 68mv R stands for the gas constant, that equals 8.314 ·K?1·mol?1 T stands for the absolute temperature, that is measured in kelvins (= K degrees Celsius + 273.15)=(25+273=298k) z stands for the no of elementary charges of sodium=1 F stands for Faraday constant, that equals 96,485 J·V?1·mol?1 [Na+]o stands for external concentration of sodium, measured in mmol·l?1 [Na+]I stands for internal concentration of sodium, , measured in mmol·l?1 68mv Na+ =8.314 Jk mol x 298k ln (Na+)o 1x96485 coulombs mol (Na+)i 68mv Na+ = 0.0256 ln (Na+)0 (Na+)i 68mv Na+ = -3.6651 (Na+)o (Na+)i -18.553= (Na+)0 (Na+)i Therefore the ratio of: Internal sodium ions (Na+)I to External sodium ion(Na+)0 is (Na+) i: (Na+) o -1: 0.053 decimal rounds off to the nearest hundred -100: 5.3 Question 2a Iron seeding also means iron fertilization, this is the intentional introduction of iron to the upper surface of ocean to stimulate a phytoplankton bloom, and it enhances biological productivity thus benefiting marine food chain. Apart from intentional introduction, naturally when up swellings bring rich nutrients to the surface, it can also be as a result of blown dust carried over long distances or by glaciers. The chemistry behind iron in sea water revolves around its reaction as pertains to solubility, reactivity and ability of iron to form complexes. The inorganic speciation of Fe (III) in seawater is dominated by its hydrolysis behavior and ready tendency to nucleate to particulate Fe (III) hydroxides. In general iron in oxic seawater around pH 8 is present predominantly in the particulate iron oxyhydroxide, which has an extremely low solubility, and thermodynamically stable 3+ oxidation state. Recent studies of the Fe (III) hydroxide solubility in seawater suggest that the Fe (III) solubility is controlled by organic complexation, which, subsequently, regulates dissolved iron concentrations in sea water (Metzeler 2001) As studies have shown the dissolved Fe concentrations in the surface mixed layer were lower than those in mid-depth and deep waters and the values of Fe (III) solubility in the surface water, resulting from the active biological removal of dissolved Fe and excess concentration of Fe-binding organic ligands iron concentration in seawater is very low, roughly 5 ? 10?11 to 2 ? 10?8 mol dm?3. Iron (III) is a strong Lewis acid, and will react with water in the following series of hydrolysis reactions to give a mixture of highly insoluble Fe(OH)3 and Fe2O3.3H2O, which appear as a brown-colored precipitate: Fe3+(aq) + H2O (l) = [Fe(OH)]2+(aq) + H+(aq) [Fe(OH)]2+(aq) + H2O(l) = [Fe(OH)2]+(aq) + H+(aq) [Fe (OH) 2]+ (aq) + H2O (l) = Fe (OH) 3(s) + H+ (aq) 2Fe (OH) 3(s) = Fe2O3.3H2O(s) Iron seeding thus affects the atmospheric Carbon Dioxide greatly; its introduction in sea water is used as a trace element necessary for photosynthesis in all plants. It is highly insoluble in sea water and is often the limiting nutrient for phytoplankton growth. Large phytoplankton blooms can be created by supplying iron to iron-deficient ,it’s this bloom that contains diatoms, prior to ocean fertilization in presence of high silica locations have observed much higher carbon sequestration rates because of diatom growth, a bloom of diatoms a large portion then dies and sinks to the ocean floor when iron fertilization is discontinued, demonstrating Carbon capture in the Atmosphere and its Relation in the Sea Plants and the balances of the greenhouse gas. Question 2b Domoic is a small tricarboxylate amino acid whose structure resembles that of iron complexion agents produced by plants. Thus because of its structure which can be compared to phytosiderophores it can act as a metal chelation. Investigations done using high selective adsorptive cathodic stripping voltametric technique reveals it does form chelates with both iron and copper, this possibility of a complex will then increase its availability to an essential micronutrient or decrease the availability of potentially toxic trace metals, thus in coastal areas where iron is suspended they could easily form a soluble complex which later helps in fertilization of sea water. Question 2c Lohafex experiment was done in low silicic acid environment, silicic acid is an essential nutrients for diatom growth, thus when the Atlantic Ocean was fertilized with iron sulphate, a large phytoplankton bloom was triggered, however bloom did not contain diatoms because the fertilized location was depleted of the acid essential for bloom growth, thus a small amount of carbon was sequestered and thus other phytoplankton were vulnerable by zoo plankton and did not sink upon death, this therefore suggested high silica locations have a higher carbon sequestration because of diatom growth and upon death many sank down the ocean. Lohafex therefore confirms that carbon sequestration potentially depends on strongly upon location with high levels of silicon and will have large portion of bloom sinking to the ocean than when low levels are provided having low numbers of blooms sinking (Metzeler 2001) Question 3(i) Concentration of oxalate is; Ksp = (Ca2+) (Oxalate) Calcium oxalate Ksp for Calcium oxalate= 2.32x10-9 mol2 dm;-6 Ca2+ in children = 1.19mmol dm-3 Assumption: solution is ideal Therefore concentration for oxalate: 2.32x10-9 mol2 dm-6 1.19 mol dm-3 1.95x 10-9 mol dm-3 that is the concentration for oxalate needed for saturation to occur Question 3(ii) A solution in which the concentration(s) of dissolved substance(s) exceeds the values given by the solubility product is known as a supersaturated solution. Question 3(bi) Arginine structurally is a bidentate ligand, in that it has a conjugation between double bonds and a Nitrogen group that has lone pairs of electrons which easily bonds with Ca2+ of bivalent to form a co-ordinated complex, thus it’s a good ligand, arginine is also a chelating agent structurally. Question 3b (ii) Arginine structurally has a guanidinium group which is positive charged in neutral, acidic and even basic environments thus imparting chemical properties to arginine, it also has conjugation of bonds between double bonds and a nitrogen group of lone pairs. Structurally when it comes in contact with Hydroxyapatite its lone pair of electrons from the nitrogen group reacts by capturing the Ca2+ to form a ligand and a complex, this is then deposited in the dentine tubules as a dentine material and as a protective layer, in the second scenario its chelating effect and the hydrogen bonds can pick up a hydrogen bond from the amine group to eliminate ammonia from the body and finally its hydrogen bonds from arginine can easily accommodate extra bonds of hydroxyapatite thus a dentine acidic material causing erosion from the excess hydrogen. Question 3(iii) Arginine is introduced in dental products about 8% in toothpastes containing calcium and phosphates, it provides relief by depositing a dentine like mineral containing calcium and phosphate within the dentine tubules and in a protective layer on the dentine surface, this is achieved by presence of saliva which has a saturation of hydroxyapatite which the reacts with arginine, the lone pairs in the nitrogen group pick up calcium ion in hydroxyapatite to form a complex or ligand which in turn with phosphate is deposited in the tubules (Metzeler 2001) Bibliography David E. Metzler. Biochemistry, Second Edition: The Chemical Reactions of Living Cells. 2001 Read More