Subcellular Biochemistry - Volume 6

This volume continues the tradition of SUBCELLULAR BIOCHEMISTRY of trying to break down interdisciplinary barriers in the study of cell function and of bringing the reader's attention to less well studied, but nevertheless useful, biological systems. We start with an extensive article by T. P. Karpetsky, M. S. Boguski and C. C. Levy on the structure, properties and possible functions of polyadenylic acid. Apart from revealing a general lack of appreciation of many important aspects of the chemical properties of poly adenylic acid, the literature also shows that there is a great gulf between those who study the biological role of polyadenylic acid. and those who study its physicochemi- cal properties. The article by Karpetsky and his colleagues is an attempt to overcome this lack of communication and to present an integrated view of the subject. The authors go into the subject in full detail and the more biologically inclined reader may on occasion have to reread his nucleic acid physical chemistry notes! However, the effort is worthwhile and the article is a timely reminder that we cannot treat nucleic acids as mere abstractions, but that they are complex organic macromolecules capable of equally complex, but nevertheless important, interactions. The next article is by J. Steensgaard and N. P. Hundahl M0ller and deals with computer simulation of density gradient centrifugation systems.

1 Structures, Properties, and Possible Biological Functions of Polyadenylic Acid.- 1. Introduction.- 2. Isolation and Detection of Poly(A).- 2.1. Methodology.- 2.2. Determination of the Size of Poly(A) Segments.- 3. Messenger RNA and the 3?-Terminal Poly(A) Sequence.- 3.1. Occurrence of Poly(A) in Living Organisms.- 3.2. Poly(A) Sequences in Prokaryotes.- 3.3. Messenger RNA Lacking Poly(A).- 3.4. Complexes of Poly(A) with Amino Acids and Proteins.- 4. Possible Biological Functions of Poly(A).- 4.1. Covalent Linkage of Poly(A) RNA.- 4.2. Transport of mRNA from the Nucleus to the Cytoplasm.- 4.3. Poly(A) and the Stability of mRNA.- 4.4. Poly(A) Involvement in the Binding of mRNA to Membranes.- 4.5. 3?-Terminal Poly(A) Sequences of mRNA and Protein Synthesis.- 4.6. Summary.- 5. Structure of Poly(A).- 5.1. Poly(A) at Neutral pH.- 5.2. Acidic Forms of Poly(A).- 5.3. Effect of Substituents on Poly(A) Structure.- 5.4. Synthesis of Analogues of Poly(A).- 5.5. Influence of Metal Ions on the Structure of Poly(A).- 6. Interaction of Poly(A) with Monomers and Polymers.- 6.1. Complexes of Low-Molecular-Weight Organic Compounds and Poly(A).- 6.2. Complexes of Poly(A) and Complementary Monomers.- 6.3. Interaction of Poly(A) with Poly(U) and Other Complementary Polynucleotides.- 7. Conclusions.- 8. References.- 2 Computer Simulation of Density-Gradient Centrifugation.- 1. Introduction.- 2. Some Aspects of the Basic Theory of Gradient Centrifugation.- 3. The Indirect Approach to Simulation of Gradient Centrifugation.- 4. The Compartmental Approach to Simulation of Gradient Centrifugation.- 5. The Analytical Approach to Simulation of Gradient Centrifugation.- 6. General Discussion.- 7. References.- 3 Crown-Gall and Agrobacterium tumefaciens: Survey of a Plant-Cell-Transformation System of Interest to Medicine and Agriculture.- 1. Introduction.- 2. Overview of the Process of Plant-Cell Transformation by Agrobacterium tumefaciens.- 3. Conditions for Plant-Cell Transformation by Agrobacterium tumefaciens.- 3.1. Dicotyledonous Host Plants or Gymnosperms.- 3.2. A Temperature below 30°C.- 3.3. A Wound or Wound Stimulus.- 4. Properties and Products of Agrobacterium tumefaciens.- 4.1. Induction of Crown-Galls.- 4.2. General Properties and Classification.- 4.3. Differential Ability to Use Unusual Amino Acids as Sole Nitrogen Source.- 4.4. Production of Plant Growth Substances.- 4.5. Production of Polysaccharides.- 4.6. Production of Vitamins.- 4.7. Production of Antibiotics.- 5. Molecular Components, Genetic Systems, and Search for the Tumor-Inducing Principle (TIP) of Agrobacterium tumefaciens.- 5.1. DNA and DNA Plasmids.- 5.2. An RNA Polymerase and Its Components.- 5.3. RNA.- 5.4. Ribosomes and Their Components.- 5.5. Bacteriophages and Their Components.- 6. Attempts to Define the Crown-Gall Tumor Cell.- 6.1. Transplantability.- 6.2. Presence of Unusual Amino Acids.- 6.3. Autonomy.- 6.4. Accelerated Growth Rate.- 6.5. Limited Capacity for Differentiation.- 7. On the Genetic Basis of the Formation of the Crown-Gall Tumor Cell.- 7.1. Experiments on the Reversion and Suppression of the Tumorous State.- 7.2. Experiments Directed to the Detection of Bacterial and Bacteriophage Genes and Gene Products in Crown-Gall Tumor Cells.- 8. Medical and Agricultural Interest in Crown-Gall/ Agrobacterium Research.- 9. References.- 4 The Petite Mutation in Yeast.- 1. Discovery and Initial Characterization.- 1.1. Introduction.- 1.2. Discovery.- 1.3. Genetic and Biochemical Characterization.- 2. Cytology and Ultrastructure of Petite Mutants.- 3. Mitochondrial DNA in Petite Mutants.- 3.1. Grande Yeast Mitochondrial DNA.- 3.2. Petite Yeast Mitochondrial DNA.- 3.3. Mitochondrial DNA Synthesis.- 4. Mitochondrial RNA in Petite Mutants.- 4.1. Grande Yeast Mitochondrial RNA.- 4.2. Petite Yeast Mitochondrial RNA.- 5. Mitochondrial Proteins in Petite Mutants.- 5.1. Synthesis of Mitochondrial Proteins.- 5.2. Tricarboxylic Acid Cycle and Other Enzymes.- 5.3. Respiratory-Chain Components.- 5.4. Mitochondrial Adenosine Triphosphatase.- 5.5. Mitochondrial Transport Systems.- 6. Induction of the Petite Mutation.- 6.1. Temperature and Nutritional Effects.- 6.2. Inhibitors of Mitochondrial Macromolecular Synthesis.- 6.3. Miscellaneous Chemical Mutagens.- 6.4. Additional Mutagenic Treatments.- 6.5. Spontaneous Mutation.- 6.6. Antagonists of Petite Mutation.- 7. Petite Mutants and Mitochondrial Genetics.- 7.1. Suppressiveness.- 7.2. Petite Deletion Analysis.- 7.3. Petite Marker Rescue.- 8. Petite-Negative Yeasts.- 9. The Petite Mutation: A Broader View.- 10. Appendix: Abbreviations and Terms.- 11. References.- 5 The Role of Lipids in the Structure and Function of Membranes.- 1. Introduction.- 2. Properties of the Lipid Bilayer.- 2.1. Lamellar Systems.- 2.2. Thermotropic Phase Changes and Phase Separations.- 2.3. Lipid Viscosity.- 2.4. Summarizing Concepts.- 3. Lipid-Protein Interactions and Lipid Organization in Membranes.- 3.1. Lipid-Protein Interactions.- 3.2. Asymmetry of Membrane Components.- 3.3. Protein Mobility.- 4. Effects of Lipids and Their Physical State on the Properties of Biomembranes.- 4.1. Means Employed to Investigate the Effects of Lipids in Membrane Functions.- 4.2. Permeability and Transport.- 4.3. Lipids and Enzyme Activity.- 4.4. Effects of Lipids on Hormonal Response.- 4.5. Lipids and Other Membrane Properties.- 4.6. Coenzymatic Function of Lipids.- 5. Roles of Lipids in Membrane Functions.- 5.1. Lipids Represent a Binding Surface for Proteins.- 5.2. Latency and Compartmentation.- 5.3. Lipids Provide a Hydrophobic Medium or a Binding Interface.- 5.4. Molecularization and Membrane Formation.- 5.5. Conformational Role of Lipids.- 6. Summary.- 7. References.- 6 Dehydrogenases of the Plasma Membrane.- 1. Introduction.- 2. Extrinsic Dehydrogenases.- 2.1. Glyceraldehyde-3-phosphate Dehydrogenase.- 2.2. Lactic Dehydrogenase.- 2.3. Other Dehydrogenases.- 3. Intrinsic Dehydrogenases.- 3.1. NADH Dehydrogenases.- 3.2. Selective Inhibition of Plasma Membrane NADH Dehydrogenase.- 3.3. NADPH Dehydrogenases.- 3.4. Xanthine Oxidase.- 3.5. Other Dehydrogenases.- 4. Relationship of Dehydrogenases to Membrane function.- 4.1. Energy-Linked Transport.- 4.2. Metabolic Conversions.- 4.3. Peroxide or Superoxide Generation.- 4.4. Redox Control of Plasma Membrane Functions.- 5. Conclusions.- 6. References.- 7 Transport Processes in Membranes: A Consideration of Membrane Potential across Thick and Thin Membranes.- 1. Introduction.- 2. Biological and Lipid Bilayer Membranes.- 2.1. Chemical Constituents and Physical Structure.- 2.2. Properties of “Undoped” Bilayer Membranes and Biomembranes.- 2.3. Properties of “Doped” Bilayer Membranes and Biomembranes.- 3. Membrane Potential.- 3.1. Donnan Potential.- 3.2. Diffusion Potential.- 3.3. Theories of Membrane Potential.- 3.4. Distribution, Surface, or Interfacial Potentials.- 3.5. Applications of the Gouy-Chapman Double-Layer Theory.- 3.6. Adsorption Approach to Membrane Potential.- 4. Summary.- 5. Appendix: Mathematical and Electrochemical Terms and Symbols.- 6. References.- Some Recent Books in Cell Biochemistry and Biology.- 1. Molecular Biology and Cell Organelles.- 2. Membrane Research.- 3. Plant Biochemistry and Morphology.- 4. Educational Texts.