Molecular Biochemistry I

Biochemical Energetics


Textbook Reading: 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 (optional reading): 
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 =


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?  
DG = __________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? 


Copyright © 1998-2007 by Joyce J. Diwan. All rights reserved.

Lecture notes on
Biochemical Energetics

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