The altercation described above is responsible for the formation of what critical biological structure?

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1 LAUGH to release tension and get points!!!! Extra Bonus +2 The altercation described above is responsible for the formation of what critical biological structure? This hydrophobic interaction is the basis for the formation of cellular membranes (phospholipid bilayers) (Note: Micelles are not biological structures

2 This Chem 315 Exam 1 -Fall 2017 Name Total points possible 117 graded out of 100 that s 17 bonus built in (12pts) 1. The hydration of fumarte (C 4 H 2 O 4-2 ) to malate (C 4 H 4 O 5-2 ) is part of the TCA cycle and catalyzed by the enzyme fumarase. The energy associated with the oxidation is 32.5 kj/mol. a) Write this reaction correctly showing reactants and products, appropriately including energy as reactant or product kj/mol + C 4 H 2 O H 2 O < == > C 4 H 4 O 5-2 b) Is this reaction thermodynamically favorable? Yes or No c) Is this reaction spontaneous? Yes or No d) Can this reaction proceed as written? Yes or No Note: AS WRITTEN the reaction is thermodynamically impossible as DG>O If no write the reaction that will proceed. If yes leave bl0nk The reaction that will proceed is the reverse reaction C 4 H 4 O 5-2 < == > 32.5 kj/mol + C 4 H 2 O H 2 O e) Will this reaction (as written in a ) be observed? Yes or No (explain) Thermodynamically impossible reactions will never be observed as written. f) Will the reaction in d) (if different than in a) proceed as written? Yes or No (explain) If a) and d) are the same leave blank. The reverse reaction is spontaneous DG<0 f) If appropriate, which of the following reactions from the table would most efficiently (with the least energy loss to the surroundings) drive the reaction in a) the forward direction. If chemical coupling is not required for a) write not needed. Data table (last page) may be useful. Since this reaction requires 32.5 kj/mol to proceed PPi + H 2 O < == > 2Pi + H + would provide kj/mol enough energy to drive the unfavorable reaction if coupled

3 (6pts) 2. Draw a reaction coordinate diagram (free energy on the y axis and reaction progress on the x-axis) for the reaction in question 1.a). Label all reactants with appropriate formulas, and show energies on the graph. You may assume a one step reaction. (4 pts) 3. For the reaction in problems 1a and 1d (if 1d is different from 1a) comment quantitatively on the efficiency of coupling ATP hydroylsis or fixation (production) to the reactions. Data table (last page) may be useful. ATP hydrolysis to ADP produces kj/mol This would not be sufficient energy to drive fumarate to malate conversion (32.5 kj/mol required) ATP hydrolysis to AMP produces kj/mol this would be sufficient There are a number of ways to discuss this quantitatively (using numbers!). For ATP to ADP coupling 2 ATP would be required kj/mol * 2 = -61 kj/mol kj/mol = kj/ mol energy not utilized or 32.5 kj/mol / 61 kj/mol *100 = 53% of the energy utilized or 47% wasted A similar analysis can be done for ATP to AMP but only one molecule would be required. (10pts) 4. The standard state entropy of hydrogenation of linoleic acid at ph 7 is 4200 J/molK. The enthalpy under like conditions is kj/mol. a) Determine the free energy of the reaction under biological standard conditions (at ph 7) DG = DH TDS kj/mol (298K * 4.2 kj/molk) = kj/mol b) Determine the equilibrium constant for the reaction under biological standard state conditions DG = -RT lnkeq = kj/mol = kj/mol K * 298K ln Keq Keq = Very large number! (depending on your calculator you may get an error) this is because the DG is so large the Keq is HUGE. In other words the reaction is highly favorable!

4 c) Does this value indicate a higher concentration of products or of reactants at equilibrium? Products (see b) d) If the concentration of hydrogen gas were to be increased how would the position of the equilibrium position be affected? Hydrogen gas is a reactant (linoleic acid is having hydrogen added). Therefore according to Le Chatlier increasing the concentration of reactant increases the production of product. Moreproduct shifts the reaction to the RIGHT (4 pts) 5. What is the difference between equilibrium and steady state? Explain briefly. Equilibrium is a condition where the rate of the forward and reverse reactions are the same. NOT where the amount of product and reactant are the same. At equilibrium each step forward results in a step in reverse and there is no net change observed. There is also no net energy produced DG = 0. Steady state can also appear to have no net change in concentrations so it appears as if the system is at equilibrium. However, energy is being exchanged (and is required) to maintain that steady state so the system is NOT at equilibrium. (12pts) 6. The peptide lys-gly undergoes hydrolysis in acidic aqueous solution. hydrolysis is -8.6 kj/mol. The free energy of a) Write the reaction (you do not have to draw the structure, you may abbreviate the amino acids using the three letter codes. lys-gly + H 3 O + < == > lys + gly ( kj/mol) c) Briefly discuss the driving force of the reaction is this reaction entropically or enthalpically driven or both? This reaction is entropically driven. Two polar amino acids are more effectively solubilized by water than the dipeptide.

5 (10 pts)7. In the following molecule indicate the type of bond, bonding interaction, or bonding force indicated by dashed line (pointed to by the letter). A salt bridge D dipolar interaction B hydrogen bond E hydrophobic interaction C ionic bond (4 pts) 8. a) Write the reaction for the disassociation of water (don t cheat by using H+ like I do) and make Dr. Doherty happy by balancing and using all appropriate notations for state. 2H2O(l) < == > H3O+ (aq) + OH-(aq) b) Write the equilibrium expression for the reaction appropriately labeling the equilibrium constant. Keq = [H3O+][ OH-]/ [H2O]2 [H2O]2 *Keq = [H3O+][ OH-] = Kw

6 (16 pts) 9a) You are tasked with making 1 L of a 1 M citrate buffer at ph You have all appropriate potassium salts, mono-, di- and tribasic (K 3 C 6 H 5 O 7 (306.4g/mol), K 2 HC 6 H 5 O 7 (268.3g/mol), KH 2 C 6 H 5 O 7 (230.2 g/mol)), and solid citric acid (H 3 C 6 H 5 O 7 (192.1g/mol)) available. Explain how you will make the buffer. Show all work. If you recognize some short cuts use them and briefly explain. Looking up the pka on the last page you will note that one pka is That is the pka closest to the desired ph. You need to determine the acid and the base. The acid is NOT always the one with the most protons! At ph 4.77 the equilibrium occurring is the second KH 2 C 6 H 5 O > K 2 HC 6 H 5 O 7 Acid Base You can use the Henderson Hasselbach equation and solve for the ratio of acid to base or simply realize that when the ph = pka the concentrations of acid and base are equal! (Remember rules of thumb in notes!) If you solve the H-H equation you will come up with that anyway. So if the concentrations are equal and the concentrations total 1 M each must be 0.5 M. So you have to make 1 L of a solution that is 0.5 M in KH 2 C 6 H 5 O 7 and 0.5 M in K 2 HC 6 H 5 O 7 1L * 0.5 M/L = 0.5 mol K 2 HC 6 H 5 O mol * g/mol = g and KH 2 C 6 H 5 O mol * g/mol = g Weigh grams of the base and g of the acid and dissolve in about 900 ml of water. Adjust the ph to 4.77 as needed and fill to the 1 L mark.

7 9b) Calculate the ionic strength of a 50 mm solution of MgFl 2. Show your work mu = 1/ sum (C i*( x i ) 2 for MgF 2 the Mg is divalent and the fluoride monovalent The concentration of Mg in a 50 mm solution is 0.05 M and the concentration of fluoride is 2* 0.05 M since there are two fluorides for each Mg. Mg +2 = (0.05) (2) 2 = 0.2 M F - = (0.05)(2)(-1) 2 = 0.1 M Sum 0.3M ½ * sum = 0.15 M

8 Fill in the Blank/circle answer 1 pt each 10. The class of biomolecules that least resemble a classical polymer are lipids. 11. The two most common biological redox pairs are NAD+ /_NADH_ and FAD / FADH 2. (in each pair you listed circle the oxidized form of the pair) These molecules are unique because reduction occurs via transfer of a (an) hydride under relatively mild physiological conditions. 12. In the TCA or Krebs cycle pyruvate is broken down in a sequence of enzymatically catalyzed steps to produce carbon dioxide and water (and a net production of ATP). This break down is an example of a metabolic catabolic anabolic reduction hydrolysis process. (circle correct italicized word) Multiple Guess Put the letter in the blank to the left of the number (2 points each) D_13) What ph range is generally considered to be the physiological ph range? A) B) C) D) E) B 14) The ph of a 6.0 x 10-9 M aqueous solution of HCl (pka, -7) is: (Please think carefully about this) A) 8.22 B) 6.99 C) 1.0 D) 7.5 E) The solution is too dilute to measure the ph _D 15) Which of the following is the conjugate base of hydrogen phosphate, H 2 PO 4 -? A) H 2 PO 3 - B) H 2 PO 4 - C) H 3 PO 4 D) HPO 4 2- E) none of the above _B 16) Which of the following represents the breaking of a noncovalent interaction? A) ionization of water B) dissolving of salt crystals C) hydrolysis of an ester D) decomposition of hydrogen peroxide E) none of the above _C 17) Match the correct symbol with the correct term A) S-enthalpy, G-free energy, H-entropy, q-heat, w-work B) S-entropy, G-internal energy, H-enthalpy, Q-heat, W-work C) S-entropy, G-free energy, H-enthalpy, q-heat, w-work D) S-enthalpy, G-free energy, H-entropy, Q-heat, W-work E) None of the above is a correct coupling of terms and symbols.

9 _A 18) In thermodynamic terms which best describes an ideal (perfectly working) closed thermos of coffee A) isolated system B) closed system C) open system D) isolated surroundings E) none of the above describe the ideal thermos _C 19) In thermodynamic terms which best describes biological organism A) isolated system B) closed system C) open system D) isolated surroundings E) none of the above describe the ideal thermos _B 20) If the ΔG ʹ for ATP hydrolysis is 31 kj/mol and the ΔG ʹ for phosphoenolpyruvate hydrolysis is 62 kj/mol, what is the ΔG ʹ for the phosphorylation of ADP by phosphoenolpyruvate? A) 93 kj/mol B) 31 kj/mol C) +31 kj/mol D) +93 kj/mol E) none of the above _D 21) What functional groups are found in the following molecule? A) amine, aldehyde and amide B) amine, aldehyde and ketone C) amine, carboxylic acid and ketone D) amine, carboxylic acid and amide E) none of the above _E 22) If gastric juice has a ph of about 1.5, which of the following would be predominantly deprotonated in the stomach? A) phenol (pk a = 9.9) B) acetic acid (pk a = 4.7) C) lactic acid, (pk a = 3.9) D) phosphoric acid (pk a = 2.1) E) hydrochloric acid (pk a = -6) _A 23) The highly exergonic nature of ATP hydrolysis is explained by which of the following? A) the resulting orthophosphate is stabilized by resonance B) electrostatic repulsion occurs between phosphate groups and the adenine base of ATP C) the resulting product undergoes tautomerization to the keto form of ADP D) the bond that is hydrolyzed is considered an ester of phosphoric acid, making it highly unstable E) all of the above 24) Which of the following is a characteristic of living organism circle all that apply a) Organisms are randomly organized maximizing entropy b) Living organisms have the ability to adapt to changing surroundings (to a limited extent; individual level and evolutionary level) c) Living organisms contain biological structures serve functional purposes d) Living systems are actively engaged in energy transformations e) Living systems maintain boundries (compartmentalization) f) Living systems are not able to operate systems in seclusion g) Living systems cannot self-replicate

10 25) True or False (6 pts) T The density of liquid water is higher than solid water (ice) F Water forms a meniscus because water is repelled by the surface of the glass tube or cylinder T Water s boiling point is 200 o C higher than expected given the boiling points of H 2 S,H 2 Se, and H 2 Te. _T Water has the largest surface tension of any common liquid except liquid mercury. F Water has an unusually low viscosity. T_Water is an excellent solvent. It can dissolve compounds, such as NaCl, that are insoluble or only slightly soluble in other liquids. F_Water has an unusually low heat capacity. It takes little heat to raise the temperature of 1 g of water 1 C _F Steam is incredibly hot because more hydrogen bonds are formed in the vapor phase than the liquid phase T A clathrate structure is another name for the hydration shell formed as water solvates a molecule _T Lipid bilayers and micelles are examples of the hydrophobic effect F Water has a low dielectric constant _F The hydrogen bonds in water are so strong because they are static 26) Match the class of macromolecule with the correct description or characteristic (2 pts) nucleic acids proteins lipids polysaccharides polysaccharides linear or branched chains of simple sugars lipids fatty acids, glycerol, and other water insoluble molecules proteins polymers of amino acids nucleic acids monomer unit consists of a sugar, a base and phosphate

11 Potentially Useless information pka of common biologically relevant acids Acid pka1 pka2 pka3 Citric acid Acetic acid 4.75 Phosphoric acid Ascorbic acid Carbonic