Molecular Biochemistry I 

Pyruvate Dehydrogenase and Krebs Cycle

Reading:

Textbook Reading: Biochemistry, 3rd Edition, by Voet & Voet, Chapter 21.

Some recent articles (optional reading): 
L. J. Reed (2001) "A trail of research from lipoic acid to a-keto acid dehydrogenase complexes," J. Biol. Chem. 276: 38329-38336.
T. E. Roche, Y. Hiromasa, A. Turkan, X. Gong, T. Peng, X. Yan, S. A. Kasten, H. Bao & J. Dong (2003) "Essential roles of lipoyl domains in the activated function and control of pyruvate dehydrogenase kinases and phosphatase isoform 1," Eur. J. Biochem. 270: 1050-1056.
R. A. Harris, M. M. Bowker-Kinley, B. Hyang & P. Wu (2002) "Regulation of the activity of the pyruvate dehydrogenase complex," Advan. Enzyme Regul. 42: 249-259.
T. E. Roche, Y. Hiromasa, A. Turkan, X. Gong, T. Peng, X. Yan, S. A. Kasten, H. Bao & J. Dong (2003) "Essential roles of lipoyl domains in the activated function and control of pyruvate dehydrogenase kinases and phosphatase isoform 1," Eur. J. Biochem. 270: 1050-1056.
H.-S. Kwon & R. A. Harris (2004) "Mechanisms responsible for regulation of pyruvate dehydrogenase kinase 4 gene expression," Advan. Enzyme Regul. 44: 109-121.
V. I. Bunik (2003) "2-Oxo acid dehydrogenase complexes in redox regulation: Role of the lipoate residues and thioredoxin," Eur. J. Biochem. 270: 1036-1042.
S. J. Lloyd, H. Lauble, G. S. Prasad & C. D. Stout (1999) "The mechanism of aconitase: 1.8 A resolution crystal structure of the S642A:citrate complex," Protein Science 8: 2655-2662.
C. R. D. Lancaster (2002) "Succinate:quinone oxidoreductases: an overview," Biochimica et Biophysica Acta 1553: 1-6.
G. Cecchini (2003) "Function and structure of complex II of the respiratory chain," Annu. Rev. Biochem. 72: 77-109.
O. E. Owen, S. C. Kalhan & R. W. Hanson (2002) "The key role of anaplerosis and cataplerosis for citric acid cycle function," J. Biol. Chem. 277: 30409-30412.
J. L. S. Milne, X. Wu, M. J. Borgnia, J. S. Lengyel, B. R. Brooks, D. Shi, R. N. Perham & S. Subramaniam (2006) "Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy," J. Biol. Chem. 281: 4364-4370.
C. A. Brautigam, R. M. Wynn, J. L. Chuang, M. Machius, D. R. Tomchick & D. T. Chuang (2006) "Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex," Structure 14: 611-621.

Potential Test Questions:

1. Diagram the Krebs Citric Acid Cycle, beginning with pyruvate, giving structures and names of all enzyme substrates and products and names of enzymes (no abbreviations). Include on your diagram where NAD+ NADH, FAD FADH2 (coenzyme Q QH2), or GDP + Pi GTP, and where coenzyme A, H2O, or CO2 are substrates or products of reactions.

2. Describe the sequence of reactions catalyzed by the Pyruvate Dehydrogenase enzyme complex. Provide a diagram showing structures of the relevant portions of major intermediates at each step. Include the role of each of the various cofactors and prosthetic groups of E1, E2, and E3. What is the nature and the role of the "long swinging arm" that includes lipoamide and its attachment to the complex?

Group Presentations

On Thursday or Friday November 13 or 14 (depending on the section), each group of 3-4 students will make a 5 minute presentation on an assigned enzyme in the Krebs Citric Acid Cycle or a related topic. For each enzyme, the reaction mechanism should be briefly presented, along with any relevant information about enzyme structure, energetics, inhibitors, regulation, etc. At least one short answer question, suitable for including in a tutorial, should be posed to the class at the end of the presentation.
Students should minimally research material in Chapter 21 of the textbook and the interactive module embedded in the class notes. Additional information for some topics may be found in recent articles listed above (optional reading) or in other chapters of the textbook (e.g., 22 & 23). Advance preparation is expected.
The presentation, to be graded on a scale of one to five, will count as five points of the last quiz. In addition, there will be a small prize for best presentation. 

Krebs Cycle: Enzyme or Topic

Students: Section 1

Students: Section 2 Students: Section 3

Citrate Synthase

 

   

Aconitase

 

   

Isocitrate Dehydrogenase

 

   

a-Ketoglutarate Dehydrogenase

 

   

Succinyl CoA Synthetase

 

   

Succinate Dehydrogenase

 

   

Fumarase

 

   

Malate Dehydrogenase

 

   
Stereospecificity of reactions; tracing labeled atoms through Krebs Cycle.      

Net Inputs and Outputs; Relation to Other Pathways

 

   
Summary of Regulation of Citric Acid Cycle      

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

Lecture notes on
Pyruvate Dehydrogenase & Krebs Cycle

Interactive Quiz on    
Krebs Cycle        

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