Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online





Learning Goals/Objectives for Chapter 8C: 

After class and this reading, students will be able to

  • explain reasons for the strongly exergonic hydrolysis of carboxylic acid anhydrides, phosphoric acid anhydrides, mixed anhydrides, and analogous structures and give approximate  values for the ΔG0 of hydrolysis of them;
  • identify from Lewis structures molecules whose hydrolytic cleavage are strongly exergonic;
  • explain how the exergonic cleavage of phophoanhydride bonds in ATP can be coupled to the endergonic synthesis of macromolecules like proteins;
  • draw mechanisms to show how oxidation and phosphorylation reactions are coupled in anaerobic metabolism through the productions of a mixed anhydride catalyzed by the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase;
  • explain how arsenate can double oxidation and phosphorlyation reactions in glycolysis
  • explain how NAD+ can be regenerated from NADH in anaeroboic condition to allow glycolysis to continue;
  • explain the general flow of electrons from NADH to dioxgen through a series of mobile and membrane protein bound electron acceptors in electron transport in the mitochondria inner member.
  • explain with picture diagrams how oxidation and phosphorylation reactions (to produce ATP) are coupled in aerobic metabolism through the generation and collapse of a proton gradient in the mitochondria;
  • draw pictures diagrams explaining the structure of F1F0ATPase in the inner mitochondria member and explain using the picture how ATP synthesis is coupled to protein gradient collapse
  • write an equation for the electrochemical potential and use it to calculate the available ΔG0 for ATP production on proton gradient collapse, given typical values for ΔpH and ΔE across the membrane 

C14.  Links and References

  1. Nature 465 (2010) 441-447. doi:10.1038/nature09066 
  2. Nature  465 (2010) 428-429.
  3. Journal Biological Chemistry 284, (2009) 29773–29783.
  4.  Journal Biological Chemistry 286 (2011) 18056–18065
  5. Wantanbe, R. et al. Nature Chemical Biology, 6, 814-820 (2010)
  6. Vander Heiden, M. et al. Understanding the Warburg Effect: The metabolic requirements of cell proliferation.  Science 234, pg 1029 (2009).
  7. Kersten, S. et al. Roles of PPARs in health and disease.  Nature. 405, pg 421 (2000)
  8. Yankovskaya, V. et al. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science. 299, pg 700, 671 (2003)
  9. Oliver, S. Demand Management in Cells.  Nature. 48, pg 33 (2002)
  10. Rastogi and Girvin. Structural changes linked to proton translocation by subunit c of the ATP synthase.  Nature. 402, pg 263 (1999)
  11. Larsen et al.  Dietary Advice on Q and Extension of Life-Span in C. Elegans by a Diet Lacking Coenzyme Q (free radicals and aging?). Science. 295, pg 54, 120 (2002)
  12. Lower et al. How Bacteria Respire minerals.  Science. 292. pg 1312, 1360 (2001)
  13. Echtay et. al. Coenzyme Q is an obligatory cofactor for uncoupling protein function.  Nature 408, pg 609 (2000)
  14. Chen et al. Atomically defined mechanism for proton transfer to a buried redox center in a protein. Nature. 405, pg 814 (2000)
  15. Echtay et al. Superoxide activates mitochondrial uncoupling proteins. Nature. 415. pg 96 (2002)


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Archived version of full Chapter 8C:  ATP and Oxidative Phosphorylation


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