Prostaglandin H Synthase PathwayEicosanoids are molecules that regulate inflammation, pain, sensitivity, swelling, and reproductive processes. Pain medications such as aspirin target eicosanoids. In an eicosanoid pathway a precursor fatty acid, arachidonate, is converted into a prostaglandin by a cyclization reaction. This prostaglandin can be converted into a variety of bioactive structures. The prostaglandin H synthase pathway is responsiblefor producing this variety of prostaglandins as well as prostacyclin and thromboxaneA2. In this pathway arachidonate is oxidized to form prostaglandin H2 (PGH2), which is converted to the other parts. The prostaglandin H synthase pathway includes the enzyme prostaglandin H synthase cyclooxygenase (COX-1), which can be inhibited by aspirin (acetylsalicylic acid). Pharmaceuticals such as aspirin are called COX inhibitors or NSAIDS. Aspirin inhibits COX-1 by acetylating a serine hydroxyl near the active site, which irreversibility prevents arachidonate binding. As a result, subsequent reactions in the eicosanoid pathway cannot occur. The enzyme COX-1 is expressed constitutively at low levels in a variety of cell types. It regulates mucin secretion in the stomach, thereby protecting the gastric wall. The result is that pain, inflammation, and stomach health are related. The connection depends on how onesstomach feels. CholesterolCholesterol is an example of a steroid, and we need cholesterol to live. Therefore, cholesterol is much needed in small doses in our body. However, in to large of doses cholesterol can form plaques, which can be very harmful to us. A stroke is one outcome that can result from excess cholesterol. A stroke can occur if one of the plaques detaches from a membrane and travels through the blood stream to the brain. Cholesterol is responsible for making membranes more rigid, modulating there pliability. Cholesterol is incorporated into chylomicrons in the gut after ingestion. It is stored within the cells in plasma lipoproteins. Cholesterol can suppress transcription of specific genes. By decreasing serum cholesterol levels, one can decrease their risk of coronary heart disease. The statin drugs are often used to treat excessive serum cholesterol levels, called hypercholesterolemia. Vitamin K and Blood Clotting Vitamin K is required to convert glutamates into -carboxy-glutamateγ in several blood clotting factors. These modified amino acids line Ca2+ -binding grooves that bind a set of Ca2+ to create a positive site, which binds strongly to electronegative proteins such as Fibrinogen.Nucleic Acids Lipids- UV absorption of bases: light is absorbed strongest at 260nm- Absorption occurs with large molar extinction coefficient (high sensitivity)- Absorbtion provides a convient way to measure and study the equilibrium poise between single and double bonded nucleic acids (double-to-single stranded equilibrium)- FIGURE- Duplex formation = annealing- Duplex disassociation = denaturation - Beer-Lambert Law:- Allow to convert measured A260 values to molar nucleic acid concentrations- A260= ε260 b c- A260= absorbance- ε260= ‘molar extinction coefficient’ - b= cuvette pathlength- c= molar concentration- Duplex Stability Measurement:- Used to study denaturation of double helix - Can determine equilibrium association constants (Ka)- By measuring Ka at a series of temps and DNA concentrations can determine ΔG, ΔH, ΔS values for duplex denaturation- Stability:- More stable with more G-C bonds- Calculated in terms of Tm (denaturation-renaturation midpoint)- Tm = 69.3C + 0.41 (%G+C)- Larger G-C -> higher temp- Cooperative Melting:- When duplex dissociates, the loss of the 1st base pair makes the next one dissociate moreeasily- Makes dissociation events very rapid- Duplex formation is also a cooperative process1. (a) Assuming equal length, do saturated or unsaturated fatty acids have a lower melting temperature (Tm)?- Longer chain= more stableo Because because the longer the chain the more van der waals interactions are present, thus it takes more energy to disrupt it.- Double bonds = less stableo w/o DB= saturatedo w/ DB= unsaturatedo Double bonds bend the chain, which prevents it from forming strong suface-surface interactions, or van der waals interactions, with neighboring lipids (b) What is the nature of the reaction/equilibrium one measures? What molecular property causes the differences in Tm values?- Longer chains- Double bonds- Doubles bonds produce bends which prevents close packing, van der waal interactions, and disorder the stacking/aggregation tendencies and thereby reduce their stabilities in liquid crystal structures 2. Compare and contrast the thermal denaturation curves for a lipid liquid crystal and a nucleic acid double helix. Show and explain the equilibrium thatis studied in each situation. Explain (1) what is measured and (2) two things that one might study in each case.3. A comparison was made between two different solutions that contained an equal large percentage of ether a saturated 18-carbon fatty acid solution or a Δ9-monounstaturated C18 fatty acid.(a) Does the solution containing the saturated or unsaturated lipid look more congealed/cloudy at room temperature? Explain your answer with reference to structural differences and resulting properties expected for the two types of molecules.(b) Provide a graph that shows the results from two experiments that would conform your conclusion. Explain how the experiment works, what is measured and what it means. 4. Explain how and why the absorption at 260nm (A260) can be used to determine if a double helix forms from 2 single strands of DNA or RNA.5. (a) The double helical structure of DNA is intrinsically unstable and easily dissociates to form two separate strands. Why? How does this affect the two key biological functions of chromosomal DNA? What would happen if the DNA helices were too stable?(b) How can one measure the stability of a particular duplex DNA? Which molecular properties affect the stability?6. (a)Explain how hydrophobicity of an amino acid is measured and quantified.(b) Show what the hydrophobicity plot measured with bacteriorhodopsin would look like. Explain how the plot is interpreted in terms of structural details of the protein in its native