Voet & Voet, Biochemistry, 3rd Edition, Chapter 3 (especially p. 56-60); Chapter
16 (especially p. 566-571).
Note: More detail will be provided later relating to redox reactions and active transport.
Some recent articles
A. Kornberg, N. N. Rao, & D. Ault-Riché (1999) "Inorganic polyphosphate: A molecule of many functions," Annu. Rev. Biochem. 68: 89-125.
D. C. Rees & J. B. Howard (1999) "Structural bioenergetics and energy transduction mechanisms," J. Molec. Biol. 293: 343-350.
C. R. Bagshaw (2001) "ATP analogues at a glance," J. Cell Sci. 114: 459-460.
P. P. Dzeja & A. Terzic (2003) "Phosphotransfer networks and cellular energetics," J. Exptl. Biol. 206: 2039-2047.
K. N. Allen & D. Dunaway-Mariano (2004) "Phosphoryl group transfer: evolution of a catalytic scaffold," Trends in Biochem. Sci. 39: 495-503.
M. J. McLeish & G. L. Kenyon (2005) "Relating structure to mechanism in Creatine Kinase," Critical Rev. Biochem. Molec. Biol. 40: 1-20.
D. G. Hardie, S. A. Hawley & J. W. Scott (2006) "AMP-activated protein kinase - development of the energy sensor concept," J. Physiol. 574: 7-15.
P. G. Falkowski (2006) "Tracing oxygen's imprint on earth's metabolic evolution," Science 311: 1724-1725.
Potential Test Question:
1.a. Draw the complete structure of the molecule
ATP. How does the linkage between the terminal two phosphates differ from
that between the ribose and the first phosphate? How does the magnitude of the free energy
of phosphate hydrolysis from ATP compare to the free energy of phosphate hydrolysis
from other compounds
such as phosphoenolpyruvate and glucose-6-phosphate? Explain why this is important to the role of
ATP in metabolism.
b. What determines the rates of cleavage of "high energy bonds" of molecules such as ATP? How is this significant with regard to the roles of "high energy" compounds in metabolism?
2. Write out the reaction catalyzed by each of the following enzymes, listing substrates and products, and summarize briefly the role in metabolism of that enzyme: Adenylate Kinase, Phosphodiesterase, Creatine Kinase, Nucleoside Diphosphate Kinase, Protein Kinase. (Structures of reactants and products not required here.)
Problems: Please do these calculations before checking answers in the Tutorial.
1. A simple pathway has two steps: A « B « C
DGo' for A « B = +11.4 kJ/mol, and Keq is 10-2
DGo' for B « C = -22.8 kJ/mol, and Keq is 104
a. What is the standard free energy change for conversion of A to C? ________kJ/mol
b. Write an equation
specifying the free energy change (DG)
of the first reaction from A to B, taking into account concentrations of
reactant and product:
c. At equilibrium what are the concentration ratios B/A, C/B, and C/A? (Hint: Base your calculation on the equilibrium constants.) B/A = _____ C/B = _____ C/A = _____
d. If you start with 1 M each
of A, B, and C, what will be the concentration of each of these compounds at equilibrium? (Hint:
The total concentration of A + B + C = 3 M.)
A = ________M B = ________M C = ________M
2.a. Calculate the free energy per
mole of Na+ for transport of Na+ out of a cell. Assume that the
membrane potential is 50 mV negative inside (positive outside), that the Na+
concentration is 12 mM inside and 150 mM outside, and the temperature is 310 oK.
Gas Constant: R = 8.3145 J(oK-1)(mol-1) Faraday: F =
96,485 J( V-1)(mol-1)
DG = __________kJ/mol
b. Assuming that the concentrations of ATP, ADP, and
Pi in the cell are 4 mM, 0.1 mM, and 4 mM respectively, what is the free energy
change per mole of ATP hydrolyzed to ADP + Pi, in kJ/mol?
c. Assuming the above conditions, and assuming that
3 Na+ must be transported per ATP hydrolyzed in each reaction cycle, would the
ATP-linked transport of Na+ out of the cell be spontaneous? ____________
Is there enough energy available to transport 5 Na+ per ATP? ___________
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