Basic CMB 4e Cell and Molecular Biology What We Know & How We Found Out Gerald Bergtrom An Open Access, Open Education Resource (OER) interactive electronic textbook (iText) published under a Creative Commons (cc-by) License Image Adapted From: Microarray CMB3e i Cell and Molecular Biology What We Know & How We Found Out Annotated CMB 4e An Open Access, Open Education Resource (OER) interactive electronic textbook (iText) published under a Creative Commons (cc-by) license By Gerald Bergtrom, Ph.D. Revised January, 2020 ISBN# 978-0-9961502-5-5 New in CMB4e: ✓ Reformatting, including o An expanded ‘active’ Table of Contents (the original Table of Contents remains as the Table of Chapters) o numbered figures with figure legends o New List of Figures and sources (Appendix I; other appendices renumbered) o An epilog! ✓ Many content updates (new illustrations, figures, links) ✓ More than 50 pages of new and reformatted content, with new sections on: Viruses, Proprioreception, Schrödinger’s cat (!), history of CRISPR/Cas, ‘next gen’ DNA sequencing, directed evolution and more ✓ New Challenge boxes (Annotated & Instructors’ editions) Cover Microarray Image: From: A Microarray; the work of WikiPremed is published under a Creative Commons Attribution Share Alike (cc-by) 3.0 License. CMB4e i Dedicated to: Sydell, Aaron, Aviva, Edan, Oren and our extended family whose patience and encouragement made this work possible, my students from whose curiosity I received as much as I gave, and the memory of my mentor Herbert Oberlander, who gave me the time, opportunity and tools to do science. CMB4e ii Creative Commons Licensure and Permissions Written, Compiled and Curated Under (Creative Commons with Attribution) License and Fair Use Rules of Distribution* The following is a human-readable summary of (and not a substitute for) the cc-by 4.0 license. You are free to: • Share — copy and redistribute the material in any medium or format • Adapt — remix, transform, and build upon the material for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. Under the following terms: • Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. • No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. Notices: • You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. • No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. 4th Edition, Published 2020 *At the author’s request, reviewed all externally sourced photographs and illustrations in CMB3e to verify that each is accompanied by an appropriate open access indication, i.e., public domain, GNU, specific Creative Commons license. Images created by Dr. Bergtrom or from his original research are so designated. By random spot-check, I further verified the licensure and attribution status of >20 iText images at random. I confirm to the best of my ability to make these determinations, that all images in CMB3e meet open access standards. I can further state with confidence that for this edition (CMB4e), Dr. Bergtrom revised or selected substitute photographs and illustrations to ensure that all images are licensed without restrictions on commercial use (e.g., CC-0 , CC-BY or CC-BY-SA). This effort anticipates the production of a commercial (albeit low cost) print version of CMB4e for which open access requirements are stricter than for the online iText. M.T. Bott, Senior Lecturer, Biological Sciences, University of Wisconsin-Milwaukee CMB4e iii Preface to CMB4e A grasp of the logic and practice of science is essential to understand the rest of the world around us. To that end, the CMB4e iText remains focused on experimental support for what we know about cell and molecular biology, and on showing students the relationship of cell structure and function. Rather than trying to be a comprehensive reference book, the Basic CMB4e itext selectively details investigative questions, methods and experiments that lead to our understanding of cell biology. This focus is nowhere more obvious than in the chapter learning objectives and in *web-links. In addition to external online resources, links to the author’s short YouTube voice-over PowerPoint (VOP) videos with optional closed captions are embedded near relevant text. Each video is identified by a play-video symbol and can be opened by clicking a descriptive title or using QR bar codes, such as the example below: 102 Golgi Vesicles & the Endomembrane System The Learning objectives align with content and ask students to use new knowledge to make connections and deepen their understanding of concept and experiment. All external links are intended to expand or explain textual content and concepts and to engage student curiosity. All images in the iText and just-in-time VOPs are by the author or are from public domain or Creative Commons (CC) licensed sources. Beyond the Basic CMB4e, a freely available Annotated version of the iText contains interactive links and formative assessments in the form of Challenge boxes. The Instructors CMB4e version models additional interactive features, including short 25 Words or Less writing assignments that can be incorporated into almost any course management system, many of which the author has assigned as homework in his flipped, blended course. These assessments aim to reinforce writing as well as critical thinking skills. As a Sample Chapter, Chapter 1 of the Instructors version of CMB4e is freely available for download; the complete Instructors version is available on request. My goal in writing and updating this iText is to make the content engaging, free and comparable in accuracy and currency to commercial textbooks. I encourage instructors to use the interactive features of the iText (critical thought questions, YouTube videos, etc.) to challenge their students. *Note: Web links to the author’s own resources may occasionally be updated, but should remain active. Links to resources selected (but not created) by the author were live at the time of publication of the iText, but may disappear without notice! CMB4e iv With all of these enhancements, I encourage students to think about • how good and great experiments were inspired and designed, • how alternative experimental results were predicted, • how data was interpreted and finally, • how investigators (and we!) arrive at the most interesting “next questions”. • The online iText is the most efficient way to access links and complete online assignments. Nevertheless, you can download, read, study, and access many links with a smart phone or tablet. And you can add your own annotations digitally or write in the margins of a printout the old-fashioned way! Your instructor may provide additional instructions for using your iText. Special to Instructors from the Author All versions of the Basic and Annotated versions of CMB4e are freely available as pdf files to you and your students. To get the Instructors version you will need to fill out a short form identifying yourself as an instructor. When you submit the form, you will get pdf as well as MS-Word files for the Basic, Annotated and Instructor’s CMB4e. Once you download the CMB4e iText(s) of your choice, you should find it an easy matter to use the MS-Word file to add, subtract, modify or embellish any parts of it to suit your purposes (in accordance with the Creative Commons CC-BY license under which it is published). Common modifications are adding content of your own, or even that students uncover as part of their studies (or as an assignment!). A useful enhancement of the iText is to add links to your own assessments (quizzes, writing assignments) that take students directly to a Quiz, Discussion Forum, DropBox, etc. in your Learning Management System, e.g., D2L, BlackBoard, Canvas, etc.) course site. This is seamless if students open the iText from within your course site, but also works as long as both the iText and course site are open at the same time. You can provide a customized version of the iText to your students as a smaller pdf file (recommended) or as an MS-Word document. As implied above, you ask your students participate in the improvement of the iText (for fun or for credit!) and to share the results with others! One final caveat: whereas I provide content updates, that have significant potential subject to confirmation, very current research is not necessarily definitive. I hope that you (and perhaps your students!) will enjoy creating and customizing interactive elements and digging in to some of the most recent research included in the iText. Above all, I hope that your students will achieve a better understanding of how scientists use skills of inductive and inferential logic to ask questions and formulate hypotheses…, and how they apply concept and method to testing those hypotheses. CMB4e v Acknowledgements Many thanks go to my erstwhile LTC (now CETL) colleagues Matthew Russell, Megan Haak, Melissa Davey Castillo, Jessica Hutchings and Dylan Barth for inspiration in suggesting ways to model how open course content can be made interactive and engaging. I also thank my colleagues Kristin Woodward and Ann Hanlon in the Golda Meir Library for their help in publishing the various online editions and versions of CMB on the University of Wisconsin-Milwaukee Digital Commons open access platform (http://dc.uwm.edu). I am most grateful to Ms. M. Terry Bott for reviewing and vetting the images used in this iText as either in the public domain or designated with a Creative Commons (CC) license as an open resource (see Creative Commons License page, above). Most recently, I owe a debt of gratitude to our departmental lab manager (and just down the hall neighbor) Jordan Gonnering for lots of hardware and software assistance during the preparation of CMB4e. Last but not least I must acknowledge the opportunity I was given at the University of Wisconsin-Milwaukee to teach, study and do research in science and interactive pedagogy for more than 35 years. My research and collegial experience at UW-M have left their mark on the content, concept and purpose of this digital Open Education Resource (OER). CMB4e vi About the Author Dr. Bergtrom is Professor (Emeritus) of Biological Sciences and a former Learning Technology Consultant in the UW-Milwaukee Center for Excellence in Teaching and Learning. Scientific interests include cell and molecular biology and evolution. Pedagogic interests are blended and online instruction and the use of technology to serve more active and engaged teaching and learning. He has taught face-to-face, fully online, blended and flipped classes at both undergraduate and graduate levels. He also developed and co-instructed Teaching with Technology, an interdisciplinary course aimed at graduate students that they might someday find themselves teaching. In his 40+ years of teaching and research experience, he has tested and incorporated pedagogically proven teaching technologies into his courses. His research papers have been supplemented with publications on active blended, online and flipped classroom methods1-3. The first edition of his Open Access/Creative Commons electronic iText, Cell and Molecular Biology–What We Know & How We Found Out first appeared in 20154. Subsequent editions and versions followed in 20165, 20186 and 20197. The latest editions are available at http://dc.uwm.edu/biosci_facbooks_bergtrom/. Older editions (and versions) will remain available by request to the author. 1. Bergtrom, G. (2006) Clicker Sets as Learning Objects. Int. J. Knowl. & Learn. Obj. 2:105-110. (http://www.ijello.org/Volume2/v2p105-110Bergtrom.pdf) 2. Bergtrom, G. (2009) On Offering a Blended Cell Biology Course. J. Res. Center Ed. Tech. 5(1) (http://www.rcetj.org/?type=art&id=91609&). 3. Bergtrom, G. (2011) Content vs. Learning: An Old Dichotomy in Science Courses. J. Asynchr. Learning Networks 15:33-44 (http://jaln_v15n1_bergtrom.pdf) 4. Bergtrom, G. (2015) Cell and Molecular Biology: What We Know & How We Found Out [CMB] (If necessary, please contact the author to access this edition) 5. Bergtrom, G. (2016) Cell and Molecular Biology: What We Know & How We Found Out [CMB2e] (If necessary, please contact the author to access this edition ) 6. Bergtrom, G. (2018) Cell and Molecular Biology: What We Know & How We Found Out [CMB3e] (If necessary, please contact the author to access this edition ) 7. Bergtrom, G. (2020) Cell and Molecular Biology: What We Know & How We Found Out [CMB4e] (http://dc.uwm.edu/biosci_facbooks_bergtrom/) CMB4e vii Table of Chapters (Click title to see first page of chapter) Preface Chapter 1: Cell Tour, Life’s Properties and Evolution, Studying Cells Chapter 2: Basic Chemistry, Organic Chemistry and Biochemistry Chapter 3: Details of Protein Structure Chapter 4: Bioenergetics Chapter 5: Enzyme Catalysis and Kinetics Chapter 6: Glycolysis, the Krebs Cycle and the Atkins Diet Chapter 7: Electron Transport, Oxidative Phosphorylation and Photosynthesis Chapter 8: DNA Structure, Chromosomes and Chromatin Chapter 9: Details of DNA Replication & DNA Repair Chapter 10: Transcription and RNA Processing Chapter 11: The Genetic Code and Translation Chapter 12: Regulation of Transcription and Epigenetic Inheritance Chapter 13: Post-Transcriptional Regulation of Gene Expression Chapter 14: Repetitive DNA, A Eukaryotic Genomic Phenomenon Chapter 15: DNA Technologies Chapter 16: Membrane Structure Chapter 17: Membrane Function Chapter 18: The Cytoskeleton and Cell Motility Chapter 19: Cell Division and the Cell Cycle Chapter 20: The Origins of Life Epilogue Appendix I: List of Illustrations & Sources Appendix II: Context-Embedded YouTube Videos Appendix III: Other Useful Links CMB4e viii Table of Contents (Click Chapter title or numbered sections to navigate this e-text) Preface Chapter 1: Cell Tour, Life’s Properties and Evolution, Studying Cells 1.1 Introduction 1.2 Scientific Method – The Practice of Science 1.2.1 The Method As It is Really Practiced 1.2.2 Logic and the Origins of the Scientific Method 1.3 Domains of Life 1.3.1 Viruses: Dead or Alive; Big and Small; A History of Surprises 1.3.2 The Prokaryotes (Eubacteria = Bacteria and Cyanobacteria) Bacterial Reproduction Cell Motility and the Possibility of a Prokaryotic Cytoskeleton Some Bacteria Have Internal Membranes Bacterial Ribosomes Do the Same Thing as Eukaryotic Ribosomes… and Look Like Them! 1.3.3 The Archaebacteria (Archaea) 1.3.4 The Eukaryotes 1.4 Tour of the Eukaryotic Cell 1.4.1 The Nucleus Structure of the Interphase Nucleus Every Cell (i.e., Nucleus) of an Organism Contains the Same Genes 1.4.2 Ribosomes 1.4.3 Internal Membranes and the Internal Membrane System 1.4.4 Mitochondria and Plastids 1.4.5 Cytoskeletal Structures 1.5 How We Know the Functions of Cellular Organelles and Structures: Cell Fractionation 1.6 The Origins, Evolution, Speciation, Diversity and Unity of Life 1.6.1 Random Acts of Genetic Variation, the Basis of Natural Selection 1.6.2 The Genome: An Organism’s Complete Genetic Instructions 1.6.3 Genomic ‘Fossils’ Can Confirm Evolutionary Relationships 1.7 Microscopy Reveals Life’s Diversity of Structure and Form 1.7.1 Light Microscopy 1.7.2 Electron Microscopy Chapter 2: Basic Chemistry, Organic Chemistry and Biochemistry 2.2 Introduction 2.2 Atoms and Basic Chemistry 2.2.1 Overview of Elements and Atoms 2.2.2 Electron Configuration – Shells and Subshells 2.3 Chemical Bonds 2.3.1 Covalent bonds 2.3.2 Ionic Bonds 2.3.3 Hydrogen Bonds 2.4 Water Chemistry 2.5 Some Basic Biochemistry: Carbon, Monomers, Polymers and the Synthesis and Degradation of Macromolecules 2.5.1 Isomerism in Organic Molecules and the Diversity of Shape 2.5.2 Monomers to Polymers and Back: Dehydration Synthesis and Hydrolysis 2.5.3 A Tale of Chirality Gone Awry CMB4e ix