Mitochondria

In writing this book, I found the choice of a suitable title to be a most vexing problem. Lehninger's excellent earlier monograph The Mitochondrion had already appropriated in the domain of library cards what appeared to be the most fitting description of the subject matter. Once the text was completed, however, it became obvious that pluralization was the simplest solution to this dilemma. Variations in the structure and function of this organelle and recent discoveries of the phylogenetic diversity in the organization and genetic con- tent of its DNA all seemed to justify the idea that there are as many different mitochondria as there are mitochondriologists. Even though my initial intention was to provide advanced undergraduate and graduate students of cell biology with supplemental reading material on topics usually dealt with in a cursory manner by most standard texts, inevitably the scope was broadened to attract the interest of more seasoned readers who might be familiar with some but not other areas of mitochondrial studies. Con- sistent with the original aim, literature citations have been kept to a minimum and are avoided in the main body of the text for purposes of readability.

Table of Contents:
1 Evolution of Mitochondrial Studies.- I. Early Cytological Studies (1850-1900).- II. Early Studies of Biological Oxidation Reactions (1900-1940).- III. Identification of Mitochondria as Centers of Energy Metabolism (1940-1950).- IV. Gross and Fine Structure of Mitochondria.- V. Electron Transfer.- VI. Oxidative Phosphorylation.- VII. Biogenesis and Genetics of Mitochondria.- Selected Readings.- 2 Mitochondrial Structure and Compartmentalization.- I. Gross Morphology of Mitochondria.- A. Fixed and Stained Thin Sections.- B. Orthodox versus Condensed Conformations.- C. Mitochondria as Seen in Live Cells.- D. Mitochondria with Unusual Morphologies.- II. Subfractionation of Mitochondria.- A. Osmotic Method.- B. Digitonin Method.- C. Fractionation of Mitochondria into Soluble and Membrane Components.- III. Distribution of Mitochondrial Enzymes.- A. Outer Membrane.- B. Inner Membrane.- C. Intermembrane Space.- D. Matrix.- IV. Composition of the Inner and Outer Membranes.- A. Lipid Constituents.- B. Protein Constituents.- V. Current Views on the Structure of Biological Membranes.- VI. Fine Structure of Mitochondrial Membranes.- A. Ultrastructure in Thin Sections.- B. Ultrastructure in Negative Staining.- C. Ultrastructure in Freeze-Etching.- Selected Readings.- 3 Oxidative Pathways of Mitochondria.- I. Conversion of Pyruvic Acid to Acetyl-CoA.- A. Structure of the Pyruvate Dehydrogenase Complex.- B. Regulation of the Mammalian Pyruvate Dehydrogenase Complex.- II. ?-Oxidation of Fatty Acids.- A. Entry of Fatty Acids into the Mitochondrion.- B. Enzymes of ?-Oxidation.- C. Ancillary Enzymes of ?-Oxidation.- III. Utilization of Ketone Bodies.- IV. Metabolism of Amino Acids.- A. Amino Acids as a Source of Acetyl-CoA.- B. Amino Acids as a Source of Tricarboxylic Acid Cycle Intermediates.- C. The Glutamate Cycle.- V. Tricarboxylic Acid Cycle.- A. Enzymes of the Tricarboxylic Acid Cycle.- B. Regulation of the Tricarboxylic Acid Cycle.- VI. Yield of ATP from the Aerobic Oxidation of Glucose.- A. Free Energy Change of ATP Hydrolysis.- B. ATP Yield from Glucose.- Selected Readings.- 4 The Electron Transfer Chain.- I. Carriers of the Electron Transfer Chain.- A. Flavoenzymes.- B. Cytochromes.- C. Metalloproteins.- D. Low-Molecular-Weight Carriers.- II. Redox Potentials of the Electron Transfer Chain Carriers.- III. Sequence of Electron Transfer Carriers Based on their Rates of Oxidation and Reduction.- A. Cytochrome Chain.- B. Placement of the Iron-Sulfur Centers.- C. Placement of Copper.- D. Placement of Coenzyme Q.- E. Deduced Sequence of Electron Transfer Carriers Based on their Kinetic Properties.- IV. Inhibitors of Electron Transfer.- A. Cyanide and Carbon Monoxide.- B. Antimycin A.- C. Rotenone, Piericidin, Amobarbital.- V. Properties of the Respiratory Complexes.- A. Purification of Respiratory Complexes.- B. Compositions and Enzymatic Properties of the Respiratory Complexes.- VI. Stoichiometry of the Electron Transfer Carriers.- VII. Other Respiratory Chain-Linked Dehydrogenases.- Selected Readings.- 5 Cytochrome Oxidase: Model of a Membrane Enzyme.- I. Purification and Assay of Cytochrome Oxidase.- II. Structure of Cytochrome Oxidase.- A. Subunit Composition.- B. Purification of Subunits and Identity with Known Carriers.- C. Quaternary Structure.- III. Formation of Cytochrome Oxidase Membranes.- IV. Shape of Cytochrome Oxidase.- V. Phospholipid Activation of Enzymatic Activity.- VI. Mechanism of Catalysis.- Selected Readings.- 6 Oxidative Phosphorylation.- I. The Concept of Coupling.- II. Uncouplers and Inhibitors of Oxidative Phosphorylation.- III. Efficiency of Phosphorylation.- IV. Phosphorylation Sites.- A. Crossover Points.- B. Site-Specific Assays.- V. Evidence for the Existence of a Nonphosphorylated Intermediate.- VI. Partial Reactions of Oxidative Phosphorylation.- A. ATP-Pi Exchange.- B. ATP-ADP Exchange.- C. ATP-H218O Exchange.- D. Pi-H218O Exchange.- VII. Role of Structure in Oxidative Phosphorylation.- VIII. Current Theories of the Coupling Mechanism.- A. Chemical Hypothesis.- B. Chemiosmotic Hypothesis.- C. Conformational Hypothesis.- Selected Readings.- 7 The Mitochondrial Adenosine Triphosphatase.- I. Purification and Properties of the ATPase Complex.- A. Mammalian ATPase.- B. Yeast ATPase.- C. Enzymatic Properties of the Oligomycin-Sensitive ATPase.- D. Subunit Polypeptides of the Oligomycin-Sensitive ATPase.- II. Functional Components of the ATPase Complex.- A. F1 ATPase.- B. Membrane Factor.- C. Oligomycin-Sensitivity-Conferring Protein.- III. Ultrastructure of the ATPase.- IV. Catalytic Mechanism of the ATPase.- V. Coupling Factor Activity of ATPase Components.- A. F1.- B. Coupling Factors That Are Related to F1.- C. Oligomycin-Sensitivity-Conferring Protein.- D. F6.- E. Factor B.- F. Present Status of Coupling Factors.- Selected Readings.- 8 Resolution and Reconstitution of Electron Transport and Oxidative Phosphorylation.- I. Electron Transport Chain.- II. Reconstitution of the Electron Transfer Complexes.- III. Resolution of Oxidative Phosphorylation in Submitochondrial Particles.- IV. Reconstitution of a Coupled ATPase Membrane.- V. Reconstitution of Coupled Electron Transport Membranes.- VI. Reconstitution of Oxidative Phosphorylation.- Selected Readings.- 9 Mitochondrial Transport Systems.- I. Some General Considerations of How Molecules Cross Biological Membranes.- A. Facilitated Diffusion.- B. Active Transport.- C. Group Translocation.- II. Methodology for Studying Mitochondrial Transport.- A. Direct Measurements of Substrate Concentration.- B. Mitochondrial Swelling.- C. Oxidation of Substrates.- III. Passive Diffusion of Gases and Water.- A. Water.- B. Oxygen.- C. Carbon Dioxide.- IV. Mechanisms of Substrate Transport in Mitochondria.- A. Passive Diffusion.- B. Carrier-Mediated Transport.- C. Energy-Coupled Transport.- V. Transport of Specific Substrates.- A. Anions.- B. Amino Acids.- C. Fatty Acids.- VI. Substrate Transport and Coordination of Mitochondrial and Cytoplasmic Metabolism.- A. Shuttles that Oxidize External NADH.- B. Transport Systems that Function in Gluconeogenesis and Ureogenesis.- VII. Metal Transport.- A. Ionophores.- B. Mechanisms of Metal Transport.- Selected Readings.- 10 Mitochondrial Biogenesis.- I. Mitochondrial Continuity.- II. Components of the Mitochondrial Translation Machinery.- A. Mitochondrial Ribosomes.- B. Transfer RNAs.- C. Aminoacyl Synthetases.- III. Mitochondrial Protein Synthesis.- A. In Vitro.- B. in Vivo.- C. Number of Mitochondrial Products.- D. Identification of the Mitochondrial Translation Products.- E. Properties of Mitochondrially Synthesized Proteins.- IV. Phospholipid Biosynthesis.- V. Nuclear Gene Products.- A. Nuclear Structural Genes.- B. Nuclear Regulation of the Mitochondrial Genome.- VI. Transport of Proteins into Mitochondria.- A. Transport of Cytochrome c.- B. Internalization of Mitochondrial Proteins.- VII. Biosynthesis of Inner Membrane Enzymes.- A. Oligomycin-Sensitive ATPase.- B. Cytochrome Oxidase.- C. Other Membrane Constituents.- Selected Readings.- 11 Mitochondrial Genetics.- I. Mitochondrial DNA.- II. Life Cycle of Saccharomyces cerevisiae.- III. Genetic Criteria for Distinguishing Nuclear and Mitochondrial Mutations.- A. Restoration of Wild-Type Growth by a ?0 Tester.- B. Meiotic Segregation.- C. Mitotic Segregation.- IV. Mitochondrial Genes and Mutants.- A. Genes.- B. Mutants.- V. Genetic Methods for Mapping Mitochondrial Mutations.- A. Loci on Mitochondrial DNA.- B. Mapping of Mitochondrial Markers by Recombination.- C. Mapping of Mitochondrial Mutations with ?? Clones.- VI. Physical Mapping of Mitochondrial Genes.- A. Yeast Mitochondrial Genes.- B. Identity of Yeast Mitochondrial Genes.- C. Other Mitochondrial Genomes.- VII. Sequencing of Mitochondrial DNA.- A. Chemical Method of DNA Sequencing.- B. Sequencing Strategy for Yeast mtDNA.- C. Nucleotide Sequences of Mit Genes.- D. Sequences of Ribosomal and tRNA Genes of Yeast Mitochondria.- E. General Organizational Features of Yeast mtDNA.- F. Mammalian mtDNA.- VIII. Transcription of mtDNA and Processing of RNA.- A. Mammalian Mitochondria.- B. Yeast Mitochondria.- C. Processing Pathway of the Yeast Apocytochrome b Messenger.- D. RNA Splicing Mechanism.- IX. Evolution of Mitochondria.- Selected Readings.