The Evolution of Molecular Biology The Search for the Secrets of Life FIRST EDITION Kensal E van Holde Oregon State University, Department of Biochemistry and Biophysics, Corvallis, OR, USA Jordanka Zlatanova University of Wyoming, Department of Molecular Biology, Laramie, WY, USA Table of Contents Cover image Title page Copyright Preface Chapter 1: Beginnings Abstract Prologue Some Ancient Intuitions Spontaneous Generation Vitalism The Demise of Vitalism The Rise of Modern Biology The Microscope Opens a New World Epilogue Chapter 2: The Origins of Biochemistry Abstract Prologue Recognition of Proteins Some Proteins Are Catalysts: Enzymes What Enzymes Do, and Why It Is so Important How Do Enzymes Work? Proteins Fulfill Many Roles What Are Proteins Made of? Epilogue Chapter 3: The Chemical Structure of Proteins Abstract Prologue The Peptide Hypothesis Colloid or Macromolecule? Some Unexpected Results Proteins as Homogeneous Polypeptides Fred Sanger and the Sequence of Insulin Epilogue Chapter 4: Proteins in Three Dimensions Abstract Prologue Fibers Globules The First Globular Protein Structures Epilogue Chapter 5: The Origins of Genetics Abstract Prologue Classical Genetics and the Rules of Trait Inheritance Friar Gregor Mendel Plants Some Peas Mendel Formulates the two Laws of Inheritance Mendel's Laws have Extensions and Exceptions Mendel Was Long Ignored Darwin, Mendelism, and Mutations Genes Are Arranged Linearly on Chromosomes and Can be Mapped What Do Genes Do, and What Are They Made of? Epilogue Chapter 6: Nucleic Acids Abstract Prologue Miescher's Mysteries The Chemical Structures of Nucleic Acids “What is Life?” DNA Carries Genetic Information Mysterious Numbers Epilogue Chapter 7: The Great Synthesis Abstract Prologue Do Bacteria and Bacteriophage Have Genetics? The Watson-Crick Model of DNA Structure Provided the Final Key to Molecular Genetics Epilogue Chapter 8: How DNA is Replicated Abstract Prologue What Is the Mode of Replication? How Does Replication Proceed? The Lagging-Strand Problem Epilogue Chapter 9: The Central Dogma Abstract Prologue Speaking in Different Languages Intuiting a Dogma Who Is the Messenger? The Great Decade: 1952–62 Epilogue Chapter 10: The Genetic Code Abstract Prologue How Might a Code Function? What Kind of Code? What Were the Code Words? The Code Epilogue Chapter 11: Gene to Protein: The Whole Path Abstract Prologue What Was Known in 1960? Breakthrough The Rest of the Story Regulation of Transcription in Bacteria Overview Epilogue Chapter 12: Eukaryotes Pose New Problems Abstract Prologue What Is a Eukaryote? The Origins of Eukaryotes The Three Domains of Life Interrupted Messages and Splicing Every Cell Type Has Special Needs and Functions Multiple Levels of Control Chromatin and Nucleosomes Too Much DNA? Junk DNA? Epilogue Chapter 13: Development and Differentiation Abstract Prologue Two Ideas About Development Dominated Thinking in Ancient Times The Introduction of Scientific Approaches to the Field of Development An Opportunity Missed? What Do We Know About Development and Differentiation at Present? ESC Serve as a Model for Pluripotency The Molecular Basis of Differentiation and Development Insights From a Simple Worm Nuclear Transfer Experiments and the Principle of Genetic Equivalence Genome Reprogramming Toward Earlier Phases of Development is Possible Epilogue Chapter 14: Recombinant DNA: The Next Revolution Abstract Prologue The Power of DNA Recombination How to Clone DNA Construction of Recombinant DNA Molecules Needs Restriction Endonucleases and Ligases The First Recombinant DNA Molecules Polymerase Chain Reaction and Site-Directed Mutagenesis Manipulating the Genetic Content of Eukaryotic Organisms CRISPR, the Gene-Editing Technology of Today and Tomorrow Epilogue Chapter 15: Understanding Whole Genomes: Creating New Paradigms Abstract Prologue The Evolution of Sequencing Methodology Genomic Libraries Contain the Entire Genome of an Organism as a Collection of Recombinant DNA Molecules There are Two Classic Approaches for Sequencing Large Genomes Ultrafast Sequencing Allows Deep Analysis of Genomes Whole Genomes The Human Genome Project ENCODE Results Raise Question Whence biology? So, What Was Learned From ENCODE? TFs Interact in a Huge Network Where Is ENCODE Leading? Attempts at a Contemporary Definition of a Gene Epilogue Chapter 16: Whole Genomes and Evolution Abstract Prologue Evolutionary Theory: From Darwin to the Present Day Classifying Organisms: Phylogenetics Phylogenetics Goes Molecular The Comparative Genomics Revolution Tracing Human Evolution Epilogue Chapter 17: Practical Applications of Recombinant DNA Technologies Abstract Prologue Catching Criminals and Freeing the Innocent Production of Pharmaceutical Compounds in Recombinant Bacteria or Yeast Genetic Engineering of Plants Gene Therapy A CRISPR Revolution? Cloning of Whole Animals Jurassic Park or Deextinction Epilogue Glossary Appendix: Nobel Prize Laureates That Have Contributed to the Development of Molecular Biology Index Copyright Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom © 2018 Elsevier Inc All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein) Notices Knowledge and best practice in this field are constantly changing As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein Library of Congress Cataloging-in-Publication Data Induced pluripotent stem cells (iPSC) 145–146 Inducers 111 Insulin bovine 30f chromatography 29 Sanger’s work 29–30 Iron supplementation project, golden rice production 198, 198f Isoelectric focusing 24 Isoelectric point 23 J Jeffreys, A 193 Junk DNA 129 K Keratin 33 Knockdowns 160 Knockin organisms 160 Knockout mouse 160f Kornberg, A 80 Koshland, D 13 Kossel, A 13 L Lac operon 112f Lagging strand 82–83 Lamarck, J.-B 181 Law of independent assortment 49 Law of segregation 48 Leading strand 82–83 Leonardo’s anatomical studies 2–3, 4f Lock-and-key model 13, 15f Long noncoding RNAs (lncRNAs) 130 Lysogenic cycle 71–72 Lytic cycle 71–72 M Mammuthus primigenius 201–202 Margulis’s endosymbiotic theory 118–120 Maternal-zygotic transition 138 Matthaei, H 97–99 Meiosis 47–48 Mendelian inheritance garden pea experiments inheritance pattern 46f phenotype selection 46 self-fertilization 46 units of heredity 46–47 law of independent assortment 49 law of segregation 48 multifactorial inheritance group 49–50 phenocopying 50 single-gene inheritance group 49 Meselson, M 79–80 Messenger RNA (mRNA) ovalbumin gene 123f pre-mRNA 124–125 splicing process 124 Miescher, F 13 Mitosis 47 Modern biology 5–6 Molecular biology history of 1, 2f nobel prize laureates 217 Molecules Monoclonal antibody 144–145 Morphogens 141–142 Multipotency 136–137 Mus musculus 70 Myoglobin 37f, 40–41, 41f N Narcissus pseudonarcissus 197 Next-generation sequencing (NGS) Giraffa camelopardalis genomes 167–168 Mola mola 168 Ramazzottius varieornatus 168–169 sequenced genomes 174–175t Tarsius syricht 169 technical developments 167 Nirenberg, M 97–99 Nonoverlapping code 96f Nonpunctuated code 96f Nonviral vectors 199 Nuclear magnetic resonance (NMR) 43 Nuclease 11–12 Nucleic acids 57 See also Deoxyribonucleic acid chemical structures 57–58 deoxyribonucleic acid A/T and G/C ratios 61–62 deoxyribose sugar 57–58 fundamental structure 59f genetic information 60–61 Griffith experiment 60, 61f purine and pyrimidine base 57–58 hybridization 104f, 152f Miescher’s research 57 ribonucleic acid 57–58, 59f tetranucleotide hypothesis 58 Nucleosomes 126–129 O Okazaki fragments 82–83 One-gene, one-protein rule 176 Operator 111 Operon 111 Overlapping code 96f P PaJaMo experiment 92f Pauling, L 33–37 Peptide hypothesis amino acids and peptide bond 20f long polypeptide molecules 20 small peptides 19–20 Permease 111 Perutz, M 40 Phenocopying 50 Phylogenetics DNA sequences 185 Linnaeus hierarchy 185 protein sequences 185 RNA molecules 186 taxonomic schemes 185 Plant genetic engineering Bacillus toxin gene 197 biofactories 197 crop yields 197 golden rice production 197–198 herbicide resistant crops 197 insect resistant crops 197 Plasmid cloning vectors 152f, 153 Plasmids 152 Pleiotropy 49 Pluripotency embryonic stem cells 138, 140f experimental strategies 144f Polymerase chain reaction (PCR) 157, 158f Polymers 20 Polytene chromosomes 53–54, 54f Preformation model 135 Preyer, W 11 Primase 82–84 Proflavin 97 Prokaryotes 120f Promoter 153 Protein albumins amino acids 15–17, 16f cells and tissue structure maintainance 13 chromatography 22–23 colloidal aggregates 20–21 denaturation and renaturation 43 developments 10f electrophoresis 23–24 elemental composition 9–10 enzymes catalyst 10–11 crystallization 11 functions 12t hydrolytic splitting of sucrose 11, 12f induced-fit model 13, 15f lock-and-key model 13, 15f metabolic pathway regulation 12–13, 14f nuclease 11–12 Fischer-Hofmeister hypothesis 19–20 gluten hemoglobin 9, 25 immunological methods 26b insulin 29–30 molecular structure 11 nuclear magnetic resonance 43 one-dimensional amino acid sequence 89 posttranslational modifications 176 sedimentation 21–22 splicing 176 trans-splicing 176 x-ray diffraction crystals 35–37 domains 42–43 globular protein 40–43 α-helix and β-sheet 39f keratin 33, 38f polymer fiber 35 principle 34, 34f Proteomics 43 Pseudogenes 177–178 R Radical “adaptor” hypothesis 89 Recombinant DNA technology applications 195–196 cloning vectors 152b CRISPR techniques 200 DNA cloning 150, 151f DNA ligases 155 DNA profiling 193–194 gene therapy 198–200 genetically modified crops 149–150 HIV infection detection 196–197 host-controlled variation 154 mutation 149 natural DNA modification 155–156 PCR amplification reaction 157, 158f peptide-coding gene 157 phage DNA degradation 154 plant genetic engineering 197–198 plasmids 156 restriction endonucleases 150–155 cleavages 154, 155f discovery 150 DNA protection 154 host restriction 154 restriction process 154 site-directed mutagenesis 157, 159f transgenic organisms 159–160 vaccine production, hepatitis B 195–196 whole-animal cloning 200–201 woolly mammoth project 201–202 Redi, F 3–4 Replication of DNA bidirectional 84–85, 85f chemistry 80, 82f conservative replication 79, 80f core proteins 84f density gradient centrifugation 79–80 dispersive replication 79, 80f E coli mutant 81 Kornberg enzyme 81 leading strand 82–83 Meselson Stahl experiment 79–80, 81f polymerization reaction 80–83 replisome 83, 84f semiconservative replication 79, 80f Replisome 83, 84f Repressor 111 Restriction fragment length polymorphism (RFLP) 194 Reverse transcriptase polymerase chain reaction (RT-PCR) 196–197 Ribonucleic acid (RNA) editing 176 genetic information transfer messenger RNA 91–92 ribosomal RNA 91 nucleosides 57–58, 59f polymerase 107 Ribosomal RNA 91 Ribosomes 104–105 S Saccharomyces cerevisiae 67 Satellite DNA 131 Schizosaccharomyces pombe 67 Schrödinger, Erwin 58–60 Sedimentation equilibrium method 21–22 Semiconservative DNA replication 79, 80f Single-strand DNA-binding (SSB) proteins 84 Site-directed mutagenesis amino acid modification 157 oligonucleotide-based 158 principle 159f Sodium dodecyl sulfate (SDS)-gel electrophoresis 24 Spliced genes 176 Spontaneous generation 3–4 Stahl, F 79–80 T Tandem chimerism 176 Temperate phage 71–72 Tertiary structure of protein denaturation and renaturation 43 nuclear magnetic resonance 43 x-ray diffraction crystals 35–37 domains 42–43 globular protein 40–43 α-helix and β-sheet 39f keratin 33, 38f polymer fiber 35 principle 34, 34f Tetranucleotide hypothesis 58 Thermus aquaticus, RNA polymerase 107, 108f Three domains of life 120–122, 121t Three-strand helix model 75 Totipotency 136–137 Transcription 110–111, 113f Transcription factor (TF) 172 Transcription-induced chimerism 176 Transfer RNA (tRNA) aminoacylation 107–108, 109f structure 110f Translation 114f Transposons 130–131, 177 Trans-splicing 176 Tree of Life 122f Tropomyosin gene splicing 124f Two-dimensional electrophoresis 24 U Unipotent 136–137 V Van Leeuwenhoek’s microscope 6–7 Variable number tandem repeats (VNTRs) 194, 195f Vectors 150 Vertical polyacrylamide gel electrophoresis 24f Viral vectors 199 Vitalism demise of Newton’s mathematical analysis renaissance 4–5 W Watson-Crick model of DNA backbone structure 74–75 base pairing 75 B-form 76f complementary chain structure 75–76 x-ray diffraction 74–75 Western blot 27f, 196–197, 196f Whole-animal cloning amphibian cloning 200–201 clone production 200 cow genome modification 200–201 genetic exchange 200 mammal cloning 200–201 pig models 201 Whole-genome sequencing hierarchical shotgun sequencing approach 166–167 Human Genome Project 169–170 next-generation sequencing Giraffa camelopardalis genomes 167–168 Mola mola 168 Ramazzottius varieornatus 168–169 sequenced genomes 174–175t Tarsius syricht 169 technical developments 167 whole-genome shotgun approach 166–167 Whole-genome shotgun approach 166–167 Wobble hypothesis 100, 101f Wohler, F Woolly mammoth project 201–202 X Xenopus laevis 70 Xenopus tropicalis 70 X-ray diffraction of proteins crystals Bragg angle 35, 36f globular protein 35f phase difference 33, 36 domains 42–43 globular protein hemoglobin molecule 42, 42f myoglobin 37f, 40–41, 41f phase problem 40 velocity of sedimentation 39–40 α-helix and β-sheet 39f keratin 33, 38f polymer fiber 35 principle 34, 34f Z Zamecnik, P 97–99 ... century Their demise, together with the development of the microscope and rational taxonomy, sets the stage for the flowering of biochemistry and genetics during the early years of the 20th century These,.. .The Evolution of Molecular Biology The Search for the Secrets of Life FIRST EDITION Kensal E van Holde Oregon State University, Department of Biochemistry and Biophysics,... was not until the 19th century that the detailed structure of the cell came under study N evertheless, the impact of the microscope is probably the first example, in the history of biology, when