PROBLEM SET 6. Energetics

1. Draw an energy diagram that shows the progress of A→B when

a. There is no unstable intermediate.
b. There is an unstable intermediate.
Assume the energy of A>B.
Label both axes. Show ΔG and ΔG*.

2. How does a transition state differ from an unstable intermediate?

3. Define the Principle of Microscopic Reversibility

4. What does the following equation tell us?

ΔG = ΔGº + RT ln[P]/[R]
where
R = 1.986 cal/molºK = 8.314 joules/molºK
T = ºK
[P] = molar concentration of the product(s)
[R] = molar concentration of the reactants
[By convention, the energy level of the reactants is subtracted from the energy level of the products].

5. What is the difference between ΔG, ΔGº, ΔG’ and ΔGº’?

6. Define standard thermodynamic conditions.

7. How many cal/mol are available when [H+] is diluted from 1 M to 10-7 M at 25ºC?

8. Explain why ATP has such a high ΔGº’ (- 7,300 cal/mol) of hydrolysis.

9. Explain why phosphoenol pyruvate has such a high ΔGº’ (-13,800 cal/mol) of hydrolysis.

10. Write a mechanism for the formation of glucose 6-phosphate from glucose and ATP.

11. Define a coupled reaction and give an example.

12. What is the difference between a “closed system” and an “open system”?

13. Assume the pathway A→ B→C→D occurs in an open system at steady state at 37º C where

KM (mM)      Vmax (arbitrary units)       ΔGº’ (cal/mol)

A→B      5                     90                                         – 1,000
B→C    10                     80                                         +1,500
C→D      1                   100                                            – 500

a. From these data, what can you conclude about the pathway under standard conditions at pH 7?
b. Calculate ΔG’ for each reaction at 37ºC if the steady state concentrations of [A] = 6 mM and [D] = 0.1 mM.
[Remember all concentrations must be M; T is in ºK and R = 1.986 cal/molºK

14. The Nomenclature Committee of the International Union of Biochemistry has defined ligases as “—enzymes catalyzing the joining of two molecules coupled with the hydrolysis of a pyrophosphate bond in ATP or a similar triphosphate. The bonds formed are often “high-energy bonds”.
What is wrong with this definition?

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