CHEM  30 B   Dr. R. Rinehart  
Chapters 21.1-21.3 and 22.1-22.6

ENERGY PRODUCTION I: AEROBIC METABOLISM

 The bottom-up order in which I cover the critically-important subject of cellular energy production is much different from the sequence in which it is done in most textbooks, so you’ll need to skip back and forth between parts of several chapters to develop a working picture. We’ll begin with a general introduction to what metabolism is, cellular organization, and the importance of energy in the overall scheme of things and the role of the magical compound ATP in cellular energy. ATP is primarily produced by a process called oxidative phosphorylation, so we’ll next dissect this process into its components and examine their operation individually.  Finally, we’ll look at the metabolic pathway called the Krebs Cycle, which is the major feeder pathway to oxidative phosphorylation.

You will [should] love Microbial Metabolism: Energetics by Thomas Terry at the University of Connecticut
http://www.sp.uconn.edu/~terry/229sp03/lectures/catabolism.html

Metabolism Overview by Charles Ophardt at Elmhurst College, IL
http://www.elmhurst.edu/~chm/vchembook/5900verviewmet.html

 I.  METABOLISM: the sum total of all the chemical reactions taking place in an organism at any
    given time

           
A. Anabolism: conversion of small simple molecules to large complex molecules;
                     requires input of chemical energy

           
B. Catabolism: breakdown of molecules with liberation of energy
                        1.  Stage I:  digestion = hydrolysis;  macromolecules à monomers
                        2.  Stage II:  “simplification”:  formation of Acetyl-Coenzyme A
                                        carbohydrates:  glycolysis
                                        fatty acids:  b-oxidation
                                        amino acids:  transamination, deamination, C-skeleton “trimming”
                        3.  Stage III:  “common pathway”
                                         Krebs cycle: complete (but indirect) oxidation of Acetyl-CoA

  
                                     oxidative phosphorylation: electron flow & ATP production

Diagram of the three stages of catabolism
by Robert J Hussey at the University of Virginia
http://www.people.virginia.edu/~rjh9u/metabolism2a.html

            C. Metabolic pathway
                       
1.  Series of linked chemical reactions where product of one reaction becomes
                              substrate for next reaction

                       
2.  Starting and ending points chosen for our convenience
                       
3.  Each and every reaction in a pathway is catalyzed by an enzyme
                                    reasons: speed, specificity, and control

                       
4.  Four major patterns of pathways
                       
            • linear:  glycolysis
                       
            • branched: pyrimidine synthesis
                       
            • cyclic: Krebs cycle, urea cycle, b-oxidation
                       
            • cascade [tiered]:  blood coagulation, hormonal activation of glycogenolysis
                       
5.  Control of  pathways can be exercised by:
                       
            • regulation of one or more key enzymes in pathway
                       
            • cellular compartmentation, which can control delivery of substrates,
                                                local pH, etc.

           
D.   Mitochondrial structure, organization, and function
                       
outer membrane: “leaky,” contains enzymes
           
            intermembrane space: contains enzymes, including
creatine kinase
                       
inner membrane: contains the electron transport system and many “translocases”
                                    or shuttle systems
                        matrix: a soup of enzymes, location of: the Krebs cycle,  fatty acid b-oxidation,
                                  amino acid oxidation, mtDNA, mt tRNA,  mt ribosomes

Mitochondrial Structure and Function by Morgan R. McKeller, student of  
John C. Pérez at Texas A&M's Natural Toxins Research Center, Kingsville
 http://ntri.tamuk.edu/cell/mitochondrion.html 

Mitochondrial Structure and Function Animations by John Kyrk
http://www.johnkyrk.com/mitochondrion.html
also has goodies on the Krebs cycle and electron transport

II.  ENERGY: the basics

A. The ability to do work
                        1.  Forms of energy: light, kinetic, potential, chemical, electrical, heat
                        2.  Energy flow in the biosphere
                        3.  The need for energy in living systems

  
                                 biosynthesis
                                    active transport
  
                                   
motility

            B.  ATP and “Free Energy” 

                       
1.  “Free energy” from chemical reactions  [it ain’t free] 
                       
2.  The ATP/ADP cycle
  
                    
3.  High-energy bonds

View ATP with Chime  

An overview of this whole subject area by James B. Blair at Oklahoma State is at
 http://opbs.okstate.edu/~Blair/Bioch2344/Chapter9/Chapter9.htm 

PowerPoint on generation of biochemical energy by Warren Gallagher at UWEC
http://www.chem.uwec.edu/Chem150_S06/Pages/lecture-materials.html > Lectures 8 & 9
http://www.chem.uwec.edu/Chem150_S06/Pages/Lecture-slides/C150_lect08_slides.html

              4. The vast majority of ATP in most of our cells is generated by a complex
                                mitochondrial process called “oxidative phosphorylation,” in
                                which the formation of water from O2 and “H2” abstracted from
                                organic substrates [the oxidation] yields energy, which is used to
                                drive the formation of ATP from ADP + Pi [the phosphorylation]

C.  Energy production from redox reactions
  
                     1.  Oxidation and Reduction: definitions and examples [see table]
            D. Alternative forms of hydrogen that can be oxidized [see table]

                       
“H2” = 2H+ + 2 e- = 2H• = H• + H+ + e- = H:- + H+

E.  Redox Coenzymes [hydrogen or electron acceptors]  and prosthetic groups 
                       
1. NAD+  nicotinamide-adenine dinucleotide
                       
2. FAD and FMN   flavin-adenine dinucleotide and flavin mononucleotide
                       
3. CoQ  coenzyme Q10  
                        4. Hemin  ferriprotoporphyrin IX

 III. Oxidative phosphorylation
           
A.  Oxidation of “H2” by the electron transport system [ETS, “respiratory chain”]
                       
1.  ETS organization: in inner mitochondrial membrane
           
            2. Energy conservation in the form of a transmembrane electrochemical gradient of H+
                       
            [the “Mitchell hypothesis”]

            B.  Phosphorylation:  synthesis of ATP from ADP + Pi by the mitochondrial “ATPase”
                         using energy supplied by the transmembrane electrochemical gradient of H+
                        1. The ATPase has multiple subunits; the “F1” “head” contains a3b3gde and the

  
                            
“F0” membrane channel has multiple copies of a short hydrophobic peptide

                        2.  The F0 proton channel can be blocked by oligomycin and DCCD, while the

  
                             F1 activity can be blocked by aurovertin or rutamycin  

ATP yield from ETS and Krebs Cycle

substrate

your text says

other texts say

NADH + H+

3 ATP

2.5 ATP

FADH2

2 ATP

1.5 ATP

AcCoA total via Krebs

12 ATP [includes 1 GTP]

10 ATP [includes 1 GTP]

             C.  Oxidation and phosphorylation are normally “coupled” – if one process is blocked for
  
                 any reason, so is the other.  Certain compounds called “uncouplers” disconnect the
                     two processes by collapsing the transmembrane proton gradient. This causes 
                    respiration rate to maximize, while ATP synthesis ceases. Uncouplers include
                     2,4-dinitrophenol and pentachlorophenol.    

Virtual Cell animation of electron transport at North Dakota State University is at
  http://vcell.ndsu.nodak.edu/animations/etc/movie.htm

another animation of electron transport posted by megh2748
http://www.youtube.com/watch?v=3LGgVTeP7yg&NR=1

Virtual Cell animation of ATP synthesis at North Dakota State University is at
http://vcell.ndsu.nodak.edu/animations/atpgradient/movie.htm

Animated ATP synthase presentation by Donald Nicholson, University of Leeds, UK
http://www.tcd.ie/Biochemistry/IUBMB-Nicholson/animaps.html > ATP Synthase

Mitochondrial Membrane Transport and Electron Transfer by Charles Mallery at the University of Miami
http://fig.cox.miami.edu/~cmallery/255/255etc/255etc.htm
http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Metabolomics/Key_Resources.html

 

IV.  The Krebs Cycle [citric acid cycle, tricarboxylic acid cycle, TCA]
            A.  Acetyl CoA, the major product of Stage II catabolism
                    can be formed from sugars, fatty acids, amino acids

             B. Reactions of the cycle [see table with additional references]
  
                         Net reaction for the cycle:
                        Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi à 2CO2 + 3(NADH + H+) + FADH2 + GTP
                    ATP yield per AcCoA:  3NADH + 1 FADH2 + GTP = 3x3 + 1x2 +1 = 12 ATP
                                    (in some texts you will see 3x2.5 + 1x1.5 +1 = 10 ATP)
  

           
C. Control of Krebs Cycle activity
                       
1. Rate of reoxidation of NADH and FADH2 ß à rate of ETS
                       
2. Allosteric control of ICDH, aKGDH, and CitSyn

© Ronald W. Rinehart, 2002-2007