Homework - I. Hand draw the structure of an eukaryotic cell with all organelles clearly drawn and describe the function of each organelle.

Transcription

1 Homework - I Hand draw the structure of an eukaryotic cell with all organelles clearly drawn and describe the function of each organelle. Please get a book and read the chapter related to cell structure!!!

2 Homework II Key 1. Calculate the thermal energy, 3/2 kt, at 300K in term of kcal/mol. Ans: E = 3/2 kt = 3/2 x 1.38 x x 300 x x = J/mol = 0.45 kcal/mol. 2. Calculate the probability of breaking (i) a covalent bond (100 kcal/mol) at 300K; (ii) a hydrogen bond (0.5 kcal/mol) Ans: (i) P = exp (- E/kT) = exp (-100/0.298x2) = exp(-166) ~ 0. (ii) P = exp (-0.5/0.298x2) = 0.43

3 Homework II Key 3. If the energy difference between a folded state and an unfolded state is 10 kcal/mol in favor of folded state what is the temperature at which the protein is equally likely to be in folded state and unfoled state? Ans: For the molecule to be equally likely to be in folded and unfolded state p = 1 or 1 = exp(-10/rt) T = -10/(-Rln0.5) = -10/[(-0.002)x(0)] = o K (Infinitely high temperature) But it did happen. Why? G = H - T S. What we measured above is H, not considering S.

4 Homework III 1. Calculate the ratio of [A - ]/[AH] for ph equals: (i) pk + 1; (ii) pk 1; (iii) pk + 2; (iv) pk 2. Ans.: PK = ph + Log([AH]/[A - ] (a) [A - ]/[AH] = 10 (ph pk) = 10 1 = 10 (b) 0.1; (c) 100; (d) Plot the net charge of the amino acid Histidine for the ph range of 2 to 10 (ph titration). You need to calculate the net charge at least every 0.2 units. You may also write a program to calcualte it. Assuming pk a s are 3.5, 6.5 and 8.5 for the carboxy, imidazole and the amino groups, respectively. Ans.: PK = ph + Log([AH]/[A - ] ; - COOH COO - + H + (pk = 2.5); His + His; (pk = 6.5) NH 4+ NH 3 + H + (pk = 8.5) Charge: ph = 2, Q = +2; ph = 10, Q = -1-1 Q ph

5 3. Calculate the net charge of the following peptide at ph 7.3 using the pk a table given in the lecture. MEGLSKHYFPQIDWCHVRNT Ans.: Net charge: -1, E (1), D (1) and C-terminus (1); +1, K (1), R (1)and N-terminus (0.92 for pk = 8.5) His (2) charge at ph 7.3 (assume pk = 6.0) = x 2 = , Total charge = = NH 3 -M--E-GLS-K---H-YFPQI D WC--H--V--R-NT-COO - pk At ph 7.0: X - X + - Net charge: (+3) + 2X + (-3) = 2X Calculate 2X ~ 0.2 Total charge: + 0.2

6 Homework IV. Bioenergetics 1. Calculate the G for ATP hydrolysis in a cell in which the [ATP]/[ADP] ratio had climbed to 100:1 while the P i concentration remained at10 mm. How does this compare to the ratio of [ATP]/[ADP] when the reaction is at equilibrium and P i concentration remains at 10 mm? What would be the value of G when the reactants and products were all at standard state conditions of 1 M? Ans.: (a) G = G o + RTlnK; K = [ADP] [P i ] / [ATP]; G o = kcal/mol G = x log( ) = kcal/mol (b) G = 0 at equilibrium. Larger than in equilibrium (More energy is released) (c) At standard state G = G o = - 7 kcal/more < under condition in (a). 2. Calculate the free energy released when FADH 2 is oxidized by molecular O 2 under standard conditions. Ans.: (a) FADH 2 FAD + 2H + + 2e - E o = V ½ O 2 + 2H + + 2e - H 2 O E o = V FADH 2 + ½ O 2 FAD + H 2 O E o = = V G = -nfe o = -2 x 23 x = kcal/mol

7 3. Of the following substances, ubiquinone, cytochrome c, NAD +, NADH, O 2, H 2 O, which is the strongest reducing agent? Which is the strongest oxidizing agent? Which has the greatest affinity for electrons? Ans.: Look up table 5.1. (a) The strongest reducing agent is NDAH (E o = V) (b) The strongest oxidizing agent is O 2 (E o = V) (c) The strongest oxidizing agent also has the highest electron affinity Thus, O 2 has the strongest electron affinity. 4. Suppose that you are able to manipulate the potential of the inner membrane of an mitochondrion. You measure the ph of the mitochondrial matrix and find it to be 8.0. You measure the bathing solution and find its ph to be 7.0. You clamp the inner membrane potential at +59 mv, i.e. you force the matrix to be 59 mv positive with respect to the bathing solution. Under these circumstances, can the mitochondrion use the proton gradient to drive the synthesis of ATP? Explain your answer. Ans.: Electromotive force: p = Ψ (RT/F) ph = Ψ - 59 ph (mv) If Ψ = 59 mv and ph = 8 7 = 1 Then p = 0 Proton gradient can not be used to drive ATP synthesis. _ + _ + _ + Outside: ph = 7.0 Ψ = 59 mm _ ph = 8.0