Molecular Associations in Biology

Proceedings of the International Symposium Held in Celebration of the 40th Anniversary of the institute de Biology physico-Chimique (Foundation Edmond de Rothschild)

1st Edition - November 11, 2012
Editor: Bernard Pullman
Language: English
Paperback ISBN:
9 7 8 - 0 - 1 2 - 4 1 4 1 8 7 - 2
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 1 4 5 0 2 - 2

Molecular Associations in Biology provides information pertinent to molecular biology. This book discusses several topics, including DNA replication, calculation of intermolecular… Read more

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Molecular Associations in Biology provides information pertinent to molecular biology. This book discusses several topics, including DNA replication, calculation of intermolecular energies, and thermodynamic parameters of polynucleotides. Organized into 35 chapters, this book starts with an overview of the specific association of the purine and pyrimidine bases in the nucleic acids, which provides the basis for storage, expression, and transmission of genetic information. This text then explores the secondary structures, interactions, and replication processes of nucleic acids. Other chapters consider the complex biological process of protein synthesis. This book discusses as well the methods of photodynamic action, which is significant in detecting energy transfer from dye to the biomolecule and identifying the free radicals produced. The final chapter deals with the macroscopic properties of molecular systems, which refer to such concepts as volume, mass, pressure, temperature, and pH. This book is a valuable resource for biophysicists, organic chemists, biochemists, and biologists.

List of Contributors

Preface

Associations Moléculaires en Biologie: Théorie et Expérience. Propos d'Introduction

Text

Bibliographie

Hydrogen Bonding between Purines and Pyrimidines

I. Introduction

II. Base Pairs in the Crystalline State

III. Base Pairs in Solution

IV. Conclusion

References

The Physicochemical Basis of Interactions of Nucleic Acid

I. Association of Bases and Nucleosides in Aqueous Solutions

II. Specific and Cooperative Interaction of the Nucleosides with the Complementary Polynucleotides

III. Contribution of the 2'-Hydroxyl Group to the Conformation and Interaction of Nucleic Acids

IV. Final Remarks

References

Base-Base Interactions in Nucleic Acids

I. Components

II. Single-Strand Polynucleotides

III. Base Pairing

IV. Multistrand Regions in Polynucleotides

V. Conformation of Ribonucleic Acids

VI. Codon-Anticodon Recognition

References

Oligonucleotide Interactions

I. Hypochromicity

II. Optical Rotatory Dispersion

III. Circular Dichroism

IV. Energy Transfer

V. Effect of Chain Length

VI. Nature of the Forces Involved

VII. Hydrogen-Bonded Complexes

VIII. Thermodynamic Stability and Tm

IX. Ribosome-Messenger tRNA Interactions

References

Some Effects of Noncomplementary Bases on the Stability of Helical Complexes of Polyribonucleotides

Text

References

Some Practical Improvements in the Calculation of Intermolecular Energies

I. Introduction

II. The Long-Range Interaction Energy

III. The Interaction Energy at Short Distances

IV. Conclusion

References

Physics of Protein Synthesis

I. Introduction

II. Interactions between Nucleotide Bases

III. Unconstrained Case

IV. DNA Replication

V. DNA Replication in the Presence of Base Analogs

References

Kinetics of Helix Formation and Slippage of the dAT Copolymer

I. Introduction

II. Formation of Hairpin Helices

III. Branching

IV. Mechanism Proposed for Reiterative Synthesis

V. Possible Mechanisms of Slippage

VI. A System for Measuring the Rates of Elementary Processes in dAT Helix Formation

VII. A Possible Slippage Reaction Observed with dAT Oligomers

VIII. Conclusion

IX. Appendix

References

Some Aspects of RNA Transcription

I. Introduction—A Brief Review of RNA Transcription In Vitro

II. Selective Transcription of DNA Templates

References

Influence of the Structure of Transfer RNA on Its Interaction with Enzymes and Divalent Cations

I. Introduction

II. Reactivity and Specificity in Various Enzymatic Reactions

III. Measurement of Proton Relaxation Rates of Water at the Binding Sites of Manganese

References

The Interaction of Aromatic Hydrocarbons with Nucleic Acids and Their Constituents

Text

References

On the Solubilization of Aromatic Carcinogens by Purines and Pyrimidines

Text

References

The Interaction of Heterocyclic Compounds with DNA

I. Introduction

II. The Experimental Study of the Interaction of DNA and Heterocyclic Compounds

III. Models for the Complex Formed by the Binding of Heterocyclic Molecules and Ions to DNA

IV. Free Energy Calculations for Models Based on Intercalation and External, Edgewise Binding of Aminoacridines

V. Discussion

References

Recherches Théoriques sur l'Intercalement des Aminoacridines dans l'ADN

I. Introduction

II. Théorie

III. Les Interactions Verticales

IV. Les Interactions Ioniques

V. Conclusion

Bibliographie

Statistical Mechanical Analysis of Binding of Acridines to DNA

I. Introduction

II. General Procedure

III. Two-State Models

IV. Models of Competitive Modes of Binding

References

Alterations of T4 DNA Synthesis in the Presence of 9-Aminoacridine

I. Intercalation in Mutagenesis

II. Perturbation of DNA Synthesis

III. The Relief from Acridine Inhibition

IV. Discussion

V. Summary

References

Interaction of Antibiotics with Nucleic Acids

I. Daunomycin, Nogalamycin, and Cinerubin

II. Chromomycin and Mithramycin

III. Discussion

References

Effect of Light on Dyes and Photodynamic Action on Biomolecules

I. Introduction

II. Experimental Techniques

III. Production of Free Radicals in Irradiated Dyes

IV. Photodynamic Effects

V. General Conclusions

References

Charge-Transfer Complexes in Biological Oxidations

I. Introduction

II. Charge-Transfer Association

III. Discussion

IV. Concluding Remarks

References

Charge-Transfer Complexes in Enzyme-Coenzyme Models

I. Indole-Pyridinium Ion Interaction

II. Indole: 1,4-Dihydronicotinamide Interaction

III. Amino Acid-Pyridinium Interactions

IV. Amino Acid Side Chains—1,4-Dihydronicotinamide Interactions

V. Substituted Benzene-Pyridinium Interactions

VI. Purine-Nicotinamide Interactions

References

Charge-Transfer Interactions in Certain Physiological Processes

I. Introduction

II. Vitamin B12

III. Hematoporphyrin

IV. General Conclusions

References

Complexes between Indole and Imidazole Derivatives of the Charge-Transfer Type

I. Intermodular Indole-Imidazolium Complexes in Aqueous Solution

II. Intramolecular Indole-Imidazolium Complexes in Model Compounds

III. Fluorometric Detection of Histidine-Tryptophan Complexes in Proteins

IV. Discussion

References

Nature of the Intramolecular Complex of Flavine Adenine Dinucleotide

I. Introduction

II. Experimental Findings

III. Alterations in the Flavine Moiety

IV. Alterations in the Adenosine Moiety

V. Shape of Flavine Complexes

References

Molecular Complexes of Flavines

I. Introduction

II. pH Dependence of Complex Formation

III. Complex Stoichiometry

IV. Spectral Properties of Complexes

V. Thermodynamics of Complex Formation

VI. Solid-State Properties of Complexes

VII. Modification of Flavine Properties by Complex Formation

VIII. Biochemical Implications

References

Les Forces de Van der Waals-London dans les Complexes Dits de Transfert de Charge

I. Introduction

II. Expression de l'Énergie d'Interaction Intermoléculaire

III. Calcul des Interactions de Van der Waals-London

IV. Conclusion

Bibliographie

Solvent Effects on Molecular Associations

I. Introduction

II. Theory

III. The Solvophobic Force

IV. Discussion of some Applications

V. Conclusion

VI. Appendix. Nonpolar Part of the Van der Waals Potential between Two Molecular Groups Immersed in a Liquid

References

Solvent Polarity and Molecular Associations

I. Introduction

II. Experiments and Results

III. Discussion

IV. Conclusion

References

The Structure of Antibodies and the Antigen-Antibody Reaction

Text

References

A New Allosteric Effect in the Reaction Cycle of Liver Alcohol Dehydrogenase

Text

References

On the Mechanism of Binding Choline Derivatives to an Anticholine Antibody

I. Introduction

II. Materials and Methods

III. Results and Discussion

References

Energy Transfer Methods in the Study of Ligand-Protein Interactions

I. Introduction

II. The System Anilinonaphthalene Sulfonate (ANS)-Bovine Serum Albumin (BSA)

III. Ligand Distribution and Protein Fluorescence Yield

IV. Fluorescence Polarization Observations

V. Significance of Decrease of p0 with Number Bound

VI. The Increase in Relaxation Time with Number Bound

VII. Dependence of Energy Transfer with Excitation Wavelength in ANS

References

Optical Studies of Polypeptide-Solvent Interactions in Sulfuric Acid-Water Mixtures

I. Introduction

II. Experimental Findings

III. Discussion

References

Phospholipid Membranes Are Necessarily Bimolecular

I. Calculation of γo/r

II. Can a Lipid Membrane Be Thicker Than Bimolecular

III. Can a Lipid Membrane Be Thinner Than a Bilayer

IV. The Equilibrium between Bilayers and Droplets

V. Conclusion

References

Molecular Associations in Biology—A Brief Summary

Text

References

Author Index

Topical Subject Index

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Molecular Associations in Biology

Proceedings of the International Symposium Held in Celebration of the 40th Anniversary of the institute de Biology physico-Chimique (Foundation Edmond de Rothschild)

Purchase options

Institutional subscription on ScienceDirect