Evolving Genes and Proteins (eBook)

Front Cover 1
Evolving Genes and Proteins: A Symposium 4
Copyright Page 5
Table of Contents 20
Dedication 6
List of Participants 8
Preface 18
Introductory Remarks 26
Opening Address: Evolution and Molecular Biology 28
PART I: EVOLUTION OF PATHWAYS I 36
Chairman's Remarks 38
Chapter 1. The Evolution of Biochemical Syntheses – Retrospect and 
40 
THE GARDEN OF EDEN 40
THE 
41 
THE EVOLUTION OF "OPERONS" 42
THE SCATTERING OF FUNCTIONALLY RELATED GENES IN Neurospora 45
CONCLUSION 47
ACKNOWLEDGMENTS 47
REFERENCES 47
Chapter 2. Lysine Biosynthesis and Evolution 50
DIAGNOSTIC RADIOCARBON TRACERS 50
DISTRIBUTION OF THE Two LYSINE PATHS 56
ON THE DESCENT OF THE LYSINE PATHS 62
CONCLUSION 64
ACKNOWLEDGMENTS 64
REFERENCES 64
Discussion of Part I 66
PART II: EVOLUTION OF PATHWAYS II 74
Chairman's Remarks 76
Chapter 3. Lipid Patterns in the Evolution of 
78 
STEROLS IN BACTERIA AND BLUE-GREEN ALGAE 79
POLYUNSATURATED FATTY ACIDS 82
POLYUNSATURATED FATTY ACIDS IN PLANTS AND ANIMALS 84
REFERENCES 89
Chapter 4. Evolution of Heme and Chlorophyll 92
INTRODUCTION 92
THE Two FUNCTIONS OF THE PORPHYRIN BIOSYNTHETIC CHAIN 92
POSSIBLE STARTING CONDITIONS FOR LIFE ON EARTH 94
A PHOTOVOLTAIC MINERAL UNIT AS THE POWERHOUSE UNIT 
96 
ELABORATION OF THE PHOTOCHEMICAL FUNCTION 99
ELABORATION OF THE REDOX FUNCTION 105
SOME PROPERTIES OF EVOLVING GENES 106
EVOLUTION OF GENES OF THE PORPHYRIN BIOSYNTHETIC CHAIN 107
DNA IN CYTOPLASMIC ORGANELLES 110
AN EXAMPLE OF THE RECENT EVOLUTION OF A HEME ENZYME 
110 
SUMMARY AND CONCLUSIONS 111
ACKNOWLEDGMENTS 112
REFERENCES 112
Discussion of Part II 114
PART III: EVOLUTION OF PROTEINS I 118
Chairman's Remarks 120
Chapter 5. Evolutionary Divergence and 
122 
I. THE MOLECULAR APPROACH TO THE ANALYSIS OF 
122 
II. PATTERNS OF AMINO ACID SUBSTITUTION 127
III. THE TIME DEPENDENCE OF EVOLUTIONARY TRANSFORMATIONS AT 
162 
IV. GENE DUPLICATION IN GLOBINS 177
V. EVOLUTIONARY CONVERGENCE AND COINCIDENCE IN PROTEIN MOLECULES 184
ACKNOWLEDGMENT 189
REFERENCES 189
Chapter 6. Evolution of Hemoglobin in Primates 192
INTRODUCTION 192
PRIMATE PHYLOGENY 193
HEMOGLOBINS AND EVOLUTION 196
SUMMARY 205
REFERENCES 205
Chapter 7. Constancy and Variability of Protein Structure in Respiratory and Viral 
208 
ACKNOWLEDGMENTS 216
REFERENCES 217
Discussion of Part III 218
PART IV: EVOLUTION OF PROTEINS II 228
Chairman's Remarks 230
Chapter 8. Comparative Aspects of the Structure and Function 
232 
Glucose 
232 
EXPERIMENTAL PROCEDURE AND RESULTS 233
SUMMARY 243
REFERENCES 244
Chapter 9. Structural and Functional Aspects of 
246 
INTRODUCTION 246
CONSTANT FEATURES OF CYTOCHROME C STRUCTURE—EVOLUTIONARY 
248 
VARIABLE FEATURES OF CYTOCHROME C STRUCTURE—PHYLOGENETIC 
255 
EVOLUTIONARY ASPECTS OF STRUCTURE-FUNCTION RELATIONS 
260 
CONCLUSIONS 264
ACKNOWLEDGMENT 265
REFERENCES 265
Chapter 10. Evolution of Dehydrogenases 268
COENZYME-ENZAYME 
268 
SIZE OF THE DEHYDROGENASES 270
ACTIVE SITE OF DEHYDROGENASES 275
AMINO ACID COMPOSITIONS 
280 
USE OF CATALYTIC CHARACTERIZATIONS IN EVOLUTIONARY STUDIES 282
IMMUNOLOGICAL CHARACTERIZATIONS 286
SIGNIFICANCE OF EVOLUTIONARY CHANGES IN ENZYMES 295
ACKNOWLEDGMENTS 301
REFERENCES 301
Chapter 11. Enzymatic Homology and Analogy 
304 
ANALOGOUS 
305 
Two HOMOLOGOUS SERIES OF CLASS I ALDOLASES 308
POSSIBLE EVOLUTIONARY RELATIONSHIPS WITH OTHERS ALDOLASES 309
OTHER ANALOGOUS AND HOMOLOGOUS RELATIONSHIPS 313
ACKNOWLEDGMENTS 314
REFERENCES 314
Discussion of Part IV 318
PART V: EVOLUTION OF PROTEINS III 324
Chairman's Remarks 326
Chapter 12. The Evolution of an Enzyme 330
REFERENCES 343
Chapter 13. Enzyme Catalysis and Color of Light 
344 
CATALYTIC PROPERTIES OF FIREFLY LUCIFERASE 344
FACTORS AFFECTING THE COLOR OF LIGHT 353
DISCUSSION 362
REFERENCES 364
Chapter 14. The Role of Mutations 
366 
A. EVIDENCE FOR THE EVOLUTION OF 
366 
B. ALTERATIONS OF 
367 
C. THE PREFERENTIAL DIRECTION OF BASE PAIR TRANSITIONS 
370 
D. NONRANDOMNESS OF MUTATIONS 372
E. EVOLUTION OF PROTEINS 373
F. DEDUCTION OF THE DNA SEQUENCE FROM THE AMINO ACID 
376 
SUMMARY 376
REFERENCES 378
Chapter 15. On the Evolution of the Lactose Utilization Gene System 
382 
REFERENCES 383
Chapter 16. Experiments Suggesting 
384 
ACKNOWLEDGMENT 392
REFERENCES 392
Discussion of Part V 396
PART VI: EVENING LECTURE 400
Chapter 17. Degeneracy of the Genetic Code: 
402 
SUMMARY 402
I. THE AMOUNT OF DEGENERACY IN THE CODE 403
I I . THE NATURE OF THE DEGENERACY OF THE CODE 410
III. CONSEQUENCES OF COMPLETE CONNECTEDNESS AMONG SYNONYMS 413
REFERENCES 421
PART VII: EVOLUTION OF GENES I 424
Chairman's Remarks 426
Chapter 18. Synthesis 
428 
De novo SYNTHESIS OF DNA-LIKE POLYMERS 429
PRIMING BY AT OLIGOMERS 432
INFLUENCE OF 
434 
PRIMING OF dAT SYNTHESIS BY DNA 436
SUMMARY 440
ACKNOWLEDGMENT 441
REFERENCES 441
Chapter 19. Evolutionary Aspects of the 
444 
INTRODUCTION 444
OLIGONUCLEOTIDE FREQUENCIES IN DIFFERENT TYPES OF RNA 446
HELIX STABDLITY: ITS POSSIBLE ROLE IN MUTATIONS AND 
450 
SUMMARY 457
ACKNOWLEDGMENT 458
REFERENCES 458
Chapter 20. Nature of Bacteriophages Induced 
460 
REFERENCES 470
Discussion of Part 
472 
PART VIII: EVOLUTION OF GENES II 474
Chairman's Remarks 476
Chapter 21. Evolutionary Problems in the 
478 
AN OUTLINE OF PROTEIN SYNTHESIS 479
UNIVERSALITY OF THE PROTEIN SYNTHETIC MECHANISM 485
EVOLUTION OF THE NUCLEIC ACIDS 486
PRIMITIVE SYSTEMS FOR PROTEIN SYNTHESIS 490
REFERENCES 492
Chapter 22. The Short-Lived RNA in the Cell 
494 
REFERENCES 501
Chapter 23. On the Evolution of 
504 
DISTRIBUTION OF DNA BASE COMPOSITION 504
COMPOSITIONAL CORRELATION BETWEEN DNA AND PROTEIN 511
SPECIFICITY BETWEEN sRNA AND AMINOACYL-SRNA SYNTHETASE 512
CONCLUSION 519
ACKNOWLEDGMENT 519
REFERENCES 519
Discussion of Part VIII 522
PART IX: EVOLUTION OF GENES III 526
Chairman's Remarks 528
Chapter 24. Homology and Divergence in Genetic Material of Salmonella typhimurium 
530 
SUMMARY 534
ACKNOWLEDGMENT 535
REFERENCES 535
Chapter 25. Molecular Regulation and Its 
536 
ACKNOWLEDGMENT 559
REFERENCES 560
Chapter 26. The Relation of Ribosomal RNA 
562 
INTRODUCTION 562
THE 
563 
THE LENGTH OF THE DNA SEGMENT COMPLEMENTARY TO RIBOSOMAL RNA 573
COMPETITIVE INTERACTION AS A TEST FOR SPECIFICITY OF HYBRID FORMATION 576
THE RELATION BETWEEN 
579 
METHODS OF DNA-RNA HYBRIDIZATION AND DETECTION 585
HYBRIDIZATION WITH MEMBRANE-IMMOBILIZED DNA 586
MODIFICATION OF THE NYGAARD-HALL TECHNIQUE TO LOWER NOISE LEVELS 588
SATURATION PLATEAUS ATTAINED WITH IMMOBILIZED DNA 588
A COMPARISON OF PLATEAU STABILITY IN LIQUID AND IMMOBILIZED 
589 
SOME GENERAL PRECAUTIONS IN HYBRIDIZATION EXPERIMENTS 592
METHODS OF HYBRID DETECTION AND ASSAY 593
THE PROBLEM OF LOCALIZATION OF THE RIBOSOMAL RNA CISTRONS 
595 
IMPLICATIONS AND CONCLUDING REMARKS 601
REFERENCES 602
Chapter 27. The Evolution of Polynucleotides 606
INTRODUCTION 606
METHODOLOGY 607
RESULTS AND DISCUSSION 609
ACKNOWLEDGMENTS 615
REFERENCES 615
Chapter 28. On the Evolution of Genetic Systems 616
ACKNOWLEDGMENTS 622
REFERENCES 622
Discussion of Part IX 624
Author Index 626
Subject Index 642