Get Complete eBook Download By email at student.support@hotmail.com Exploring the Diversity of Life Fifth Canadian Edition Fenton • Maxwell • Haffie • Milsom • Nickle • Ellis • Riskin • Hertz • McMillan • Benington Get Complete eBook Download By emailRussell at student.support@hotmail.com Get Complete eBook Download By email at student.support@hotmail.com Powered by You. With engaging content to challenge you and build your confidence, MindTap™ gives you complete control over your coursework. Study with digital flashcards, listen to audio textbooks and take quizzes. Review your current course grade and stay on track with your progress. Get the free Cengage Mobile App and learn wherever you are. MindTap. Powered by You. Get Complete eBook Download By email at student.support@hotmail.com Get Complete eBook Download By email at student.support@hotmail.com Exploring the Diversity of Life Fifth Canadian Edition M. Brock Fenton Western University Bill Milsom University of British Columbia Denis Maxwell Western University Todd Nickle Mount Royal University Tom Haffie Western University Shona Ellis University of British Columbia Shelby Riskin University of Toronto Peter J. Russell Paul E. Hertz Beverly McMillan Joel H. Benington With contributions by Ivona Mladenovic, Simon Fraser University, Jonathan Ferrier, Dalhousie University, Jeff Baker, University of Saskatchewan, Jean Becker, University of Waterloo, and Erin Hodson, Wilfrid Laurier University Australia • Brazil • Canada • Mexico • Singapore • United Kingdom • United States Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 1 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Biology: Exploring the Diversity of Life, Fifth Canadian Edition M. Brock Fenton, Denis Maxwell, Tom Haffie, Bill Milsom, Todd Nickle, Shona Ellis, Shelby Riskin, Peter J. Russell, Paul E. Hertz, Beverly McMillan, and Joel H. Benington Sr. Director, Product: Jackie Wood © 2023, 2019 Cengage Learning Canada, Inc. ALL RIGHTS RESERVED. Adapted from Biology: The Dynamic Science, Fifth Edition, by Peter J. Russell, Paul E. Hertz, Beverly McMillan, and Joel H. Benington. Copyright © Cengage Learning, Inc., 2021. No part of this work covered by the copyright herein may be reproduced or distributed in any form or by any means, except as permitted by Canadian copyright law, without the prior written permission of the copyright owner. Cognero and Full-Circle Assessment are registered trademarks of Madeira Station LLC. Portfolio Manager: Carmen Yu Product Marketing Manager: Scott Brayne For product information and technology assistance, contact us at Director, Content and Production: Toula DiLeo Cengage Customer & Sales Support, 1-800-354-9706 or support.cengage.com. Content Development Manager: Toni Chahley For permission to use material from this text or product, submit all Sr. Content Production Manager: Imoinda Romain requests online at www.copyright.com. IP Analyst: Christine Myaskovsky IP Project Manager: Betsy Hathaway Production Service: MPS Limited Copy Editor: Frances Robinson Library and Archives Canada Cataloguing in Publication Title: Biology : exploring the diversity of life / M. Brock Fenton (Western University), Denis Maxwell (Western University), Tom Haffie (Western University), Bill Milsom (University of British Columbia), Todd Nickle (Mount Royal University), Shona Ellis (University of Compositor: MPS Limited British Columbia), Shelby Riskin (University of Toronto), Peter J. Russell, Paul E. Hertz, Art Director: Chris Doughman Beverly McMillan, Joel H. Benington ; with contributions by Ivona Mladenovic (Simon Illustrators: Dragonfly Media Group, MPS Limited Text Designer: Chris Doughman Fraser University) [and four others]. Names: Russell, Peter J., author. | Fenton, M. Brock (Melville Brockett), 1943– author. | Maxwell, Denis, author. | Haffie, Tom, author. | Milsom, Bill, 1947– author. | Nickle, Cover Designer: Courtney Hellam Cover Image: Shona Ellis Todd, 1967–2021 author. | Ellis, Shona, 1962– author. | Riskin, Shelby, author. Description: Fifth Canadian edition. | Issued also in 3 volumes. | Includes index. Identifiers: C anadiana (print) 20210378492 | Canadiana (ebook) 2021037862X | ISBN 9780176911140 (hardcover) | ISBN 9780176911225 (PDF) Subjects: LCSH: Biology—Textbooks. | LCGFT: Textbooks. Classification: LCC QH308.2 .R88 2022 | DDC 570—dc23 ISBN: 978-0-17-691114-0 Ebook ISBN: 978-0-17-691122-5 Cengage 200 Pier 4 Boulevard Boston, MA 02210 USA Cengage is a leading provider of customized learning solutions with employees residing in nearly 40 different countries and sales in more than 125 countries around the world. Find your local representative at: www.cengage.com. To learn more about Cengage platforms and services, register or access your online learning solution, or purchase materials for your course, visit www.cengage.com. Printed in the United States of America Print Number: 01 Print Year: 2022 Get Complete eBook Download By email at student.support@hotmail.com Get Complete eBook Download By email at student.support@hotmail.com For, and because of, our generations of students. Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 3 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Penny Nickle In Memoriam: Dr. Todd Nickle The entire Cengage Canada production team is saddened, yet honoured, to dedicate this fifth Canadian edition of Biology: Exploring the Diversity of Life to our friend, colleague, and coauthor Dr. Todd Nickle, as a celebration of his life. Before his death in August of 2021, Todd completed his revisions for this edition with characteristic passion, dedication, and enthusiasm. He was a particularly generous man, quick with praise and quicker with helpful support for colleagues and students. A very early adopter of bleeding-edge educational technologies for learning and assessment, Todd brought many innovative ideas to the table, while always keeping student learning at the centre of our discussions. If there was a new aspect of the project we wanted to explore, like The Purple Pages videos or the COVID-19 supplement, Todd was always happy to step up and mock up an example. He once apologized for the birdsong on the audio track of one of his draft video commentaries on research figures. He had been working on the piece at his cabin in the woods. Always the good-hearted and playful provocateur, Todd had a knack for engaging the author team in lively debate on important issues of student experience. While he did not live to see publication of this edition, his legacy and influence on this work will continue for many iterations to come. Todd received his PhD from Oklahoma State University in 1998 and taught biology at Mount Royal University, advocating active learning: students come to class prepared to work with material rather than just hear about it. Student preparation involves reading the text and applying the concepts to online exercises, the results of which inform what the next lecture will be about. Class time focuses on exploring connections between concepts and ideas in biology and how they relate to other disciplines. This inspired Todd to coauthor a handbook for first-year science students, Science3. A compelling candidate for the 3M National Fellowship, Todd’s work put him in the first cohort of full professors at Mount Royal University in 2012. He also garnered the 2015 ACIFA Innovation in Teaching Award and the 2016 Distinguished Faculty Award from MRU. Todd’s interest in promoting best teaching practices among educators beyond his home campus saw him expand and lead the Alberta Introductory Biology Association (AIBA) to official society status in Alberta as the Undergraduate Biology Educators of Alberta (UBEA). At the national level, Todd also leaves many close colleagues in the Open Consortium of Undergraduate Biology Educators (oCUBE). iv Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 4 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com About the Canadian Authors M. B. Fenton M. B. (Brock) Fenton received his PhD from the University of Toronto in 1969. Since then, he has been a faculty member in biology at Carleton University, then at York University, and then at Western University. In addition to teaching parts of first-year biology, he has also taught Vertebrate Biology, Animal Biology, and Conservation Biology, as well as field courses in the biology and behaviour of bats. Brock has received awards for his teaching (Carleton University Faculty of Science Teaching Award; Ontario Confederation of University Faculty Associations Teaching Award; and a 3M Teaching Fellowship, Society for Teaching and Learning in Higher Education) in addition to recognition of his work on public awareness of science (Gordin Kaplan Award from the Denis Maxwell Denis Maxwell received his PhD from the University of Western Ontario in 1995. His thesis focused on photosynthetic acclimation in green algae. Following his doctorate, he undertook postdoctoral training at the Department of Energy Plant Research Laboratory at Michigan State University, where he studied the function of the mitochondrial alternative oxidase. After taking up a faculty position at the University of New Brunswick in Mitch Zimmer Tom Haffie is a graduate of the University of Guelph and the University of Saskatchewan in the study of microbial genetics. Newly retired, he devoted his 33-year career at Western University to teaching large biology classes in lecture, laboratory, and tutorial settings. He led the development of the innovative core laboratory course in the Biology program; he was an early adopter of computer animation in lectures; and, most recently, he led a deep blended redevelopment of introductory biology informed by a students-as-partners approach to collaborative course design. Tom was a founding force in the Western Biology Undergraduate Society (BUGS), Bruce Moffat Bill Milsom received his PhD from the University of British Columbia and is a professor in UBC’s Department of Zoology, where he has taught a variety of courses, including first-year biology, for almost 40 years. His research interests include the evolutionary origins of respiratory processes and the adaptive changes in these processes that allow animals to exploit diverse environments. He examines respiratory and cardiovascular adaptations in vertebrate animals in rest, sleep, exercise, altitude, dormancy, hibernation, diving, and so on. This research contributes to our understanding of the mechanistic basis of biodiversity Canadian Federation of Biological Societies; Honorary Life Membership, Science North, Sudbury, Ontario; Canadian Council of University Biology Chairs Distinguished Canadian Biologist Award; The McNeil Medal for the Public Awareness of Science of the Royal Society of Canada; and the Sir Sandford Fleming Medal for Public Awareness of Science, the Royal Canadian Institute). He also received the C. Hart Merriam Award from the American Society of Mammalogists for excellence in scientific research. Bats and their biology, behaviour, evolution, and echolocation are the topics of his research, which has been funded by the Natural Sciences and Engineering Research Council of Canada (NSERC). In November 2014, Brock was inducted as a Fellow of the Royal Society of Canada. 2000, Denis moved in 2003 to the Department of Biology at Western University. He served as Associate Chair for Undergraduate Education for the Department of Biology from 2009 to 2016. Currently, he is Assistant Dean for the Faculty of Science, with a portfolio that includes Recruitment and First-Year Studies and outreach. Denis has taught first-year Biology to over 15 000 students, most of the time with coauthor Tom Haffie. the Open Consortium for Undergraduate Biology Educators (oCUBE), and the Western Conference on Science Education (WCSE). Tom’s educational practice was honoured with several awards, including a Western University Students’ Council Award for Excellence in Teaching, a Western University Edward G. Pleva Award for Excellence in Teaching, a Western University Fellowship in Teaching Innovation, a Western University Teaching Fellowship for Science, a Province of Ontario Award for Leadership in Faculty Teaching (LIFT), and a 3M National Teaching Fellowship for excellence in teaching. and the physiological costs of habitat selection. Bill’s research has been funded by NSERC, and he has received several academic awards and distinctions, including the Fry Medal of the Canadian Society of Zoologists, the August Krogh Distinguished Lectureship Award of the American Physiological Society, the Bidder Lecture of the Society for Experimental Biology, and the Izaak Walton Killam Award for Excellence in Mentoring. He has served as President of the Canadian Society of Zoologists and as President of the International Congress of Comparative Physiology and Biochemistry. v Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 5 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Shona Ellis received her MSc from the University Andy Cotton of British Columbia and is a professor of teaching in the Botany Department. She developed a keen interest in forests and oceans growing up on the central coast of British Columbia in Heiltsuk Territory. As an undergraduate, Shona pursued her interests in botany and entomology. Her MSc research incorporated tissue culture, phytochemistry, and plant anatomy. She realized a passion for teaching and joined the faculty at UBC in 1998. Shona teaches botany courses that include vascular plants, economic botany, bryology, and plant systematics, as well as Introductory Biology. She also currently teaches Shelby Riskin received her BA from Grinnell College Dan Riskin in Iowa, where she was first exposed to the wonderful world of biological research. She received her PhD from Brown University in a joint program with the Marine Biological Laboratory in Woods Hole, Massachusetts. Her dissertation focused on ecosystem-level biogeochemical consequences of conversion to agriculture in the Brazilian Amazon, the region of the world where deforestation and conversion to large-scale farming are happening most rapidly. Shelby then joined the University of Toronto as vi a course through the Haida Gwaii Institute that takes her and her class into the natural environment of Haida Territory. Shona teaches in a number of settings; in large and small lecture classes, in laboratories, and on field trips. While she feels the best classroom is outdoors, she integrates online technologies into all her courses; she is an early adopter of online teaching and learning resources. Shona has received two Killam Teaching Awards, a Dean of Science Service Award (UBC), UBC’s Margaret Fulton Award for student development, and the Charles Edwin Bessey Teaching Award from the Botanical Society of America. Assistant Professor in the teaching stream of the Ecology and Evolutionary Biology Department. She teaches a variety of undergraduate courses exploring ecosystem ecology and conservation biology and is Director of the U of T National Biology Competition, an international competition for high school students. Shelby is also passionate about mentoring undergraduates through independent research projects and about teaching biology and ecology to students outside the life sciences— understanding the diversity of life is for everyone. A B O U T T H E C A N A D I A N AU T H O R S Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 6 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com About the US Authors Courtesy of Peter J. Russell Peter J. Russell received his BSc in biology from the University of Sussex, England, in 1968 and his PhD in genetics from Cornell University in 1972. He has been a member of the Biology faculty of Reed College since 1972 and is currently Professor of Biology, Emeritus. Peter taught a section of the introductory biology course, a genetics course, and a research literature course on molecular virology. In 1987, he received the Burlington Northern Faculty Achievement Award from Reed College in recognition of his excellence in teaching. Since 1986, he has been the author of a successful genetics textbook; the current edition is iGenetics: A Molecular Approach. Peter’s research was in the area of molecular genetics, with a specific interest in characterizing the role of host genes in the replication of the RNA genome of a pathogenic plant virus and the expression of the genes of Courtesy of Aaron Kinard Paul E. Hertz was born and raised in New York City. He received a BA in biology from Stanford University in 1972, a master’s degree in biology from Harvard University in 1973, and a PhD in biology from Harvard University in 1977. While completing field research for his doctorate, he served on the Biology faculty of the University of Puerto Rico at Rio Piedras. After spending two years as an Isaac Walton Killam Postdoctoral Fellow at Dalhousie University, Paul accepted a teaching position at Barnard College, where he has taught since 1979. He was named Ann Whitney Olin Professor of Biology in 2000 and the Claire Tow Professor of Biology in 2016. He received The Barnard Award for Excellence in Teaching in 2007. In addition to serving on numerous college committees, Paul chaired Barnard’s Biology Department for eight years and served as Acting Provost and Dean of the Faculty from 2011 to 2012. He was also the founding Program Director of the Hughes Science Pipeline Project at Barnard, an undergraduate curriculum and research program funded continuously by the Howard Hughes Courtesy of Beverly McMillan Beverly McMillan holds undergraduate and graduate degrees from the University of California, Berkeley. She has worked extensively in educational and commercial publishing as an author, science writer, project manager, and multimedia content developer. In addition to her contributions to college textbooks, Beverly has written or coauthored multiple popular books on topics in natural the virus; yeast was used as the model host. His research has been funded by agencies such as the National Institutes of Health, the National Science Foundation, the American Cancer Society, the Department of Defense, the Medical Research Foundation of Oregon, and the Murdoch Foundation. He has published his research in a variety of journals, including Genetics, Journal of Bacteriology, Molecular and General Genetics, Nucleic Acids Research, Plasmid, and Molecular and Cellular Biology. Peter has a long history of encouraging faculty research involving undergraduates, including cofounding the biology division of the Council on Undergraduate Research in 1985. He was Principal Investigator/Program Director of a National Science Foundation Award for the Integration of Research and Education (NSF–AIRE) to Reed College, 1998 to 2002. Medical Institute, from 1992 to 2016. The Pipeline Project included the Intercollegiate Partnership, a program for local community-college students that facilitated their transfer to four-year colleges and universities. Since 2016, he has served as Director of the Science Pathways Scholars Program, which provides support and research opportunities to first-generation college students and students of colour at Barnard. He teaches one semester of the introductory sequence for biology majors and pre-professional students, lecture and laboratory courses in vertebrate zoology and ecology, and seminars that introduce first-year students to scientific research. Paul is an animal physiological ecologist with a specific research interest in the thermal biology of lizards. He has conducted fieldwork in the West Indies since the mid-1970s, most recently focusing on the lizards of Cuba and Puerto Rico. His work has been funded by the National Science Foundation, and he has published his research in such prestigious journals as The American Naturalist, Ecology, Nature, Oecologia, and The Proceedings of the Royal Society. history and human health and biology, as well as field guides to the flora and fauna of more than 20 US states. She has also created Web and print content for such clients as the US National Park Service, the Science Museum of Virginia, The Mariners’ Museum, the San Francisco Exploratorium, the University of California system, and the Virginia Institute of Marine Science/College of William and Mary. vii Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 7 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Joel H. Benington received his BA from St. John’s Courtesy of Joel H. Benington College in Annapolis, Maryland, in 1985 and his PhD in biology from Stanford University in 1992. He performed postdoctoral research at the University of Los Angeles and Stanford University until 1996. Since then, he has been a member of the Biology faculty of St. Bonaventure University, where he is currently Professor of Biology and Director of the Bioinformatics and Health and Society programs. He has twice served as Chair of the Department of Biology. During his entire time at St. Bonaventure University, he has taught one or both semesters of the general biology sequence for firstyear life science majors. He also teaches upper-level viii Neurobiology, Genomics, and Evolution courses and has led a variety of seminar courses in the university’s Honors Program. He has published his research in journals such as Progress in Neurobiology, Brain Research, The American Journal of Physiology, and The Scientist. In addition to laboratory research, he has published hypotheses concerning the role of sleep in brain energy metabolism, the functional relationship between REM sleep and non-REM sleep, and connections between sleep and learning. Joel’s research has been funded by the National Institutes of Health, and he has served as Principal Investigator of a National Grid grant to support K–12 STEM education in Cattaraugus County, New York. A B O U T T H E U S AU T H O R S Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 8 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Brief Contents VOLUME 1: BIOLOGY OF THE CELL 1 Defining Life and Its Origins 5 1 UNIT 1 SYSTEMS AND PROCESSES—THE CELL 2 The Cell: An Overview 31 3 Energy and Enzymes 59 4 Cell Membranes and Signalling 83 5 Cellular Respiration 109 6 Photosynthesis 135 UNIT 2 GENES 7 Cell Cycles 161 8 Genetic Recombination 185 9 The Chromosomal Basis of Inheritance 211 10 Genetic Linkage, Sex Linkage, and Other Extensions to Basic Inheritance Mechanisms UNIT 6 ECOLOGY AND BEHAVIOUR 26 Population Ecology 689 27 Species Interactions and Community Ecology 28 Ecosystems 753 29 Conservation of Biodiversity 779 THE CHEMICAL AND PHYSICAL FOUNDATIONS OF BIOLOGY (THE PURPLE PAGES) F-1 VOLUME 3: SYSTEMS AND PROCESSES 33 34 VOLUME 2: EVOLUTION, ECOLOGY, AND THE DIVERSITY OF LIFE 403 UNIT 4 EVOLUTION AND CLASSIFICATION 16 Evolution: The Development of the Theory 407 17 Microevolution: Changes within Populations 429 18 Speciation and Macroevolution 451 19 Systematics and Phylogenetics: Revealing the Tree 40 41 42 43 44 471 UNIT 5 THE DIVERSITY OF LIFE 20 Bacteria and Archaea 497 21 Protists 519 22 Fungi 547 23 Plants 571 24 Animals 603 25 Viruses, Viroids, and Prions: Infectious Biological Particles Plants 853 Plant Nutrition 875 Plant Signals and Responses to the Environment 895 UNIT 8 SYSTEMS AND PROCESSES—ANIMALS 35 Introduction to Animal Organization and 36 37 38 39 of Life 801 UNIT 7 SYSTEMS AND PROCESSES—PLANTS 30 Organization of the Plant Body 805 31 Transport in Plants 833 32 Reproduction and Development in Flowering 237 UNIT 3 DNA AND GENE EXPRESSION 11 DNA Structure, Replication, and Repair 265 12 Gene Structure, Expression, and Mutation 291 13 Regulation of Gene Expression 321 14 DNA Technologies 347 15 Genomes 375 717 45 Physiology 925 Animal Nutrition 947 Gas Exchange: The Respiratory System 977 Internal Transport: The Circulatory System 1001 Regulation of the Internal Environment: Water, Solutes, and Temperature 1027 Control of Animal Processes: Endocrine Control 1059 Animal Reproduction and Development 1085 Control of Animal Processes: Neural Control 1123 Muscles, Skeletons, and Body Movements 1179 Animal Behaviour and Responses to the Environment 1201 Defences against Disease 1237 APPENDIX A: ANSWERS TO SELF-TEST QUESTIONS A-1 GLOSSARY G-1 INDEX I-1 671 ix Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 9 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Contents 4 Cell Membranes and Signalling 4.1 An Overview of the Structure of Membranes 84 83 Figure 4.2 Experimental Research The Frye–Edidin Experiment Demonstrating That the Phospholipid Bilayer Is Fluid 85 In Memoriam: Dr. Todd Nickle About the Canadian Authors About the US Authors Letter to Students xvii New to This Edition xxi Figure 4.3 Research Method Freeze Fracture 86 iv v vii Welcome to Biology: Exploring the Diversity of Life, 5Ce xxiv Active Learning 4.2 The Lipid Fabric of a Membrane 86 4.3 Membrane Proteins 89 4.4 Passive Membrane Transport 91 4.5 Active Membrane Transport 95 4.6 Exocytosis and Endocytosis 98 4.7 The Role of Membranes in Cell Signalling 100 SUMMARY ILLUSTRATION FOR CHAPTER 4 104 xxvi Student and Instructor Resources xxx Acknowledgments xxxi VOLUME 1: BIOLOGY OF THE CELL 1 5 Cellular Respiration 109 5.1 The Chemical Basis of Cellular Respiration 110 5.2 Cellular Respiration: An Overview 112 5.3 Glycolysis: The Splitting of Glucose 113 5.4 Pyruvate Oxidation and the Citric Acid Cycle 116 5.5 Oxidative Phosphorylation: Electron Transport and Chemiosmosis 119 5.6 The Efficiency and Regulation of Cellular Respiration 122 5.7 Oxygen and Cellular Respiration 125 1 Defining Life and Its Origins 1.1 What Is Life? 6 1.2 The Chemical Origins of Life 8 1.3 The Evolution of Information Flow: RNA, DNA, Protein 11 1.4. The Development of Metabolism and the First Cells 13 1.5 The Tree of Life 16 1.6 Eukaryotes and the Rise of Multicellularity 19 6 Photosynthesis 1.7 The Fossil Record 24 6.1 The Physical Nature of Light 136 6.2 Photosynthesis: An Overview 138 5 UNIT 1 SYSTEMS AND PROCESSES—THE CELL SUMMARY ILLUSTRATION FOR CHAPTER 6 130 135 6.3 The Photosynthetic Apparatus 140 6.4 The Light Reactions 144 Basic Features of Cell Structure and Function 32 6.5 The Calvin Cycle 146 2.2 Prokaryotic Cells 36 6.6 Photorespiration and CO2-Concentrating Mechanisms 149 2.3 Eukaryotic Cells 37 6.7 Photosynthesis and Cellular Respiration Compared 154 2 The Cell: An Overview 2.1 31 Figure 2.8 Research Method Cell Fractionation 38 SUMMARY ILLUSTRATION FOR CHAPTER 5 156 2.4 Specialized Structures of Plant Cells 49 2.5 The Animal Cell Surface 51 UNIT 2 GENES SUMMARY ILLUSTRATION FOR CHAPTER 2 54 3 Energy and Enzymes 3.1 Energy and the Laws of Thermodynamics 60 3.2 Free Energy and Spontaneous Processes 63 3.3 Thermodynamics and Life 66 3.4 Overview of Metabolism 67 3.5 The Role of Enzymes in Biological Reactions 70 3.6 Factors That Affect Enzyme Activity 74 59 SUMMARY ILLUSTRATION FOR CHAPTER 3 78 7 Cell Cycles 7.1 The Cycle of Cell Growth and Division: An Overview 162 7.2 The Cell Cycle in Prokaryotic Organisms 163 7.3 Mitosis and the Eukaryotic Cell Cycle 164 7.4 Formation and Action of the Mitotic Spindle 172 7.5 Cell Cycle Regulation 174 161 Figure 7.19 Experimental Research Movement of Chromosomes during Anaphase of Mitosis 176 SUMMARY ILLUSTRATION FOR CHAPTER 7 180 x Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 10 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com 8 Genetic Recombination 8.1 Mechanism of Genetic Recombination 186 Figure 11.2 Experimental Research The Hershey and Chase Experiment Demonstrating That DNA Is the Hereditary Molecule 268 8.2 Genetic Recombination in Bacteria 187 11.2 DNA Structure 269 Figure 8.2 Research Method Replica Plating 188 11.3 DNA Replication 272 Figure 8.3 Experimental Research Genetic Recombination in Bacteria 189 Figure 11.9 Experimental Research The Meselson and Stahl Experiment Demonstrating the Semiconservative Model for DNA Replication to Be Correct 274 8.3 185 Genetic Recombination Occurs in Eukaryotes during Meiosis 195 9.1 The Chromosomal Basis of Inheritance Repair of Damage in DNA 283 SUMMARY ILLUSTRATION FOR CHAPTER 11 286 SUMMARY ILLUSTRATION FOR CHAPTER 8 206 9 11.4 211 Mendel’s Experiments with Garden Peas 212 12 Gene Structure, Expression, and Mutation 12.1 The Connection between DNA, RNA, and Protein 292 291 Figure 9.2 Research Method Making a Genetic Cross between Two Pea Plants 213 Figure 12.2 Experimental Research The Gene–Enzyme Relationship 294 Figure 9.4 Experimental Research The Principle of Segregation: Inheritance of Flower Colour in Garden Peas 216 12.2 Transcription: DNA-Directed RNA Synthesis 297 12.3 Processing of mRNAs in Eukaryotes 299 12.4 Translation: mRNA-Directed Polypeptide Synthesis 303 12.5 Mutations Can Affect Protein Structure and Function 313 Figure 9.7 Experimental Research Testing the Predicted Outcomes of Genetic Crosses 220 Figure 9.8 Experimental Research The Principle of Independent Assortment 221 9.2 Later Modifications and Additions to Mendel’s Hypotheses 224 Figure 9.12 Experimental Research Experiment Showing Incomplete Dominance of a Trait 225 SUMMARY ILLUSTRATION FOR CHAPTER 9 232 10 Genetic Linkage, Sex Linkage, and Other Extensions to Basic Inheritance Mechanisms 237 10.1 Genetic Linkage and Recombination 238 Figure 10.2 Experimental Research Evidence for Gene Linkage 240 10.2 Sex-Linked Genes 243 SUMMARY ILLUSTRATION FOR CHAPTER 12 316 13 Regulation of Gene Expression 13.1 Regulation of Gene Expression in Prokaryotic Cells 322 13.2 Regulation of Transcription in Eukaryotes 328 13.3 Posttranscriptional, Translational, and Posttranslational Regulation 335 13.4 The Loss of Regulatory Controls in Cancer 339 321 SUMMARY ILLUSTRATION FOR CHAPTER 13 342 14 DNA Technologies 14.1 DNA Cloning 348 347 Figure 14.3 Research Method Identifying a Recombinant Plasmid Containing a Gene of Interest 351 Figure 10.8 Experimental Research Evidence for Sex-Linked Genes 246 Figure 14.4 Research Method Synthesis of DNA from mRNA Using Reverse Transcriptase 352 10.3 Chromosomal Mutations That Affect Inheritance 248 10.4 Human Genetic Traits, Pedigree Analysis, and Genetic Counselling 252 Figure 14.5 Research Method The Polymerase Chain Reaction (PCR) 353 10.5 Additional Patterns of Inheritance 256 Figure 14.6 Research Method Separation of DNA Fragments by Agarose Gel Electrophoresis 354 SUMMARY ILLUSTRATION FOR CHAPTER 10 260 14.2 Applications of DNA Technologies 355 Figure 14.8 Research Method Southern Blot Analysis 357 UNIT 3 DNA AND GENE EXPRESSION Figure 14.11 Research Method Making a Knockout Mouse 361 11 DNA Structure, Replication, and Repair 11.1 Establishing DNA as the Hereditary Molecule 266 265 Figure 11.1 Experimental Research Griffith’s Experiment with Virulent and Nonvirulent Strains of Streptococcus pneumoniae 267 Figure 14.14 Experimental Research The First Cloning of a Mammal 364 Figure 14.16 Research Method Using the Ti Plasmid of Rhizobium radiobacter to Produce Transgenic Plants 366 CONTENTS xi Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 11 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com SUMMARY ILLUSTRATION FOR CHAPTER 14 370 18.4 15 Genomes 15.1 Genomics: An Overview 376 Figure 18.16 Observational Research Chromosomal Similarities and Differences among Humans and the Great Apes 465 15.2 Genome Sequencing 377 375 SUMMARY ILLUSTRATION FOR CHAPTER 18 466 Figure 15.1 Research Method Sanger Sequencing 378 Figure 15.2 Research Method Pyrosequencing 382 15.3 Genetic Mechanisms of Speciation 461 Annotation Identifies Genes 385 19 Systematics and Phylogenetics: Revealing the Tree of Life 471 19.1 Nomenclature and Classification 472 19.2 Phylogenetic Trees 474 Figure 15.8 Research Method Analysis of Gene Expression Levels using RNA-seq 390 19.3 Sources of Data for Phylogenetic Analyses 477 19.4 Traditional Classification and Paraphyletic Groups 480 15.4 19.5 The Cladistic Revolution 481 Comparative Genomics Can Reveal How Genes and Genomes Evolved 391 Figure 19.11 Research Method Using Cladistics to Construct a Phylogenetic Tree 483 SUMMARY ILLUSTRATION FOR CHAPTER 15 400 19.6 Phylogenetic Trees as Research Tools 486 VOLUME 2: EVOLUTION, ECOLOGY, AND THE DIVERSITY OF LIFE 403 UNIT 4 EVOLUTION AND CLASSIFICATION Figure 19.13 Research Method Using Genetic Distances to Construct a Phylogenetic Tree 487 16 Evolution: The Development of the Theory SUMMARY ILLUSTRATION FOR CHAPTER 19 490 16.1 What Is Evolution through Natural Selection? 408 16.2 Evidence for Evolution through Natural Selection 411 16.3 Development of the Theory of Evolution 414 19.7 407 UNIT 5 THE DIVERSITY OF LIFE Figure 16.9 Experimental Research Adaptation of E. coli to a Change in Temperature 415 16.4 Molecular Phylogenetic Analyses 489 Evolutionary Theory since Darwin 421 20 Bacteria and Archaea 20.1 The Full Extent of the Diversity of Bacteria and Archaea Is Unknown 498 20.2 Prokaryotic Structure and Function 498 497 Figure 20.5 Experimental Research Genetic Recombination in Bacteria 501 SUMMARY ILLUSTRATION FOR CHAPTER 16 424 17 Microevolution: Changes within Populations 17.1 Variation in Natural Populations 430 20.4 The Domain Archaea 510 17.2 Population Genetics 432 SUMMARY ILLUSTRATION FOR CHAPTER 20 514 17.3 The Agents of Microevolution 434 429 Figure 17.8 Research Method Using the Hardy–Weinberg Principle 435 Figure 17.13 Experimental Research Do Humans Experience Stabilizing Selection? 440 17.4 Non-random Mating 441 Figure 17.16 Experimental Research Sexual Selection in Action 443 17.5 Maintaining Genetic and Phenotypic Variation 444 SUMMARY ILLUSTRATION FOR CHAPTER 17 446 20.3 The Domain Bacteria 508 21 Protists 21.1 The Vast Majority of Eukaryotes Are Protists 520 21.2 Characteristics of Protists 521 21.3 Protists’ Diversity Is Reflected in Their Habitats, Structure, Metabolism, and Reproduction 522 21.4 Eukaryotic Supergroups and Key Protist Lineages 523 519 Figure 21.8 Observational Research Isolation and Identification of Marine Diplonemids, Potentially the Most Abundant Marine Organism 525 21.5 Some Protist Lineages Arose from Primary Endosymbiosis and Others from Secondary Endosymbiosis 539 18 Speciation and Macroevolution 18.1 What Is a Species? 452 18.2 Maintaining Reproductive Isolation 455 22 Fungi 18.3 The Geography of Speciation 458 22.1 General Characteristics of Fungi 548 xii 451 SUMMARY ILLUSTRATION FOR CHAPTER 21 542 547 CONTENTS Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 12 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com 22.2 Evolution and Diversity of Fungi 550 26.5 Models of Population Growth 697 22.3 Fungal Life Styles 561 26.6 Population Regulation 702 Figure 22.20 Experimental Research Hidden Third Partner in Lichen Symbiosis 562 Figure 26.16 Experimental Research Evaluating Density-Dependent Interactions between Species 704 SUMMARY ILLUSTRATION FOR CHAPTER 22 566 26.7 Human Population Growth 707 SUMMARY ILLUSTRATION FOR CHAPTER 26 712 23 Plants 23.1 Defining Characteristics of Land Plants 572 27 Species Interactions and Community Ecology 23.2 The Transition to Life on Land 573 27.1 Population Interactions Shape Communities 718 571 23.3 Bryophytes: Nonvascular Land Plants 579 27.2 Symbioses: Close Associations 719 23.4 Seedless Vascular Plants 583 27.3 Energy Intake and Exchange 721 23.5 Gymnosperms: The First Seed Plants 588 27.4 Defence 723 23.6 Angiosperms: Flowering Plants 593 27.5 Competition 727 Figure 23.30 Experimental Research Exploring a Possible Early Angiosperm Adaptation for Efficient Photosynthesis in Dim Environments 595 SUMMARY ILLUSTRATION FOR CHAPTER 23 598 Figure 27.15 Experimental Research Gause’s Experiments on Interspecific Competition in Paramecium 728 Figure 27.18 Experimental Research Demonstration of Competition between Two Species of Barnacles 730 Figure 27.19 Experimental Research The Complex Effects of a Herbivorous Snail on Algal Species Richness 731 24 Animals 24.1 What Are Animals? 604 24.2 Animal Origins: Animals Probably Arose from a Colonial Flagellate 605 24.3 Key Features Used to Classify Animals 606 24.4 Basal Phyla 611 24.5 The Protostomes 619 24.6 The Deuterostomes 638 603 SUMMARY ILLUSTRATION FOR CHAPTER 24 666 25 Viruses, Viroids, and Prions: Infectious Biological Particles 671 25.1 What Is a Virus? Characteristics of Viruses 672 25.2 Viruses Infect Bacterial, Animal, and Plant Cells by Similar Pathways 675 27.6 The Nature of Ecological Communities 732 27.7 Community Characteristics 734 27.8 Effects of Population Interactions on Community Structure 738 27.9 Succession 740 27.10 Variations in Species Richness among Communities 743 SUMMARY ILLUSTRATION FOR CHAPTER 27 748 28 Ecosystems 28.1 Ecosystems and Energy 754 753 Figure 28.12 Experimental Research A Trophic Cascade in Salt Marshes 763 28.2 Nutrient Cycling in Ecosystems 764 Anthropogenic Global Change 771 25.3 Treating and Preventing Viral Infections 680 28.3 25.4 Virotherapy: Using Viruses to Cure Disease 681 SUMMARY ILLUSTRATION FOR CHAPTER 28 774 25.5 Viruses May Have Evolved from Fragments of Cellular DNA or RNA 681 29 Conservation of Biodiversity 29.1 The Anthropocene 780 29.2 Threats to Biodiversity 781 25.6 717 Viroids and Prions Are Infective Agents Even Simpler in Structure than Viruses 682 SUMMARY ILLUSTRATION FOR CHAPTER 25 684 UNIT 6 ECOLOGY AND BEHAVIOUR Figure 29.3 Observational Research Near-Complete Extinction of Small Mammals in Tropical Forest Fragments 783 29.3 26 Population Ecology 26.1 Introduction 690 26.2 Population Characteristics 690 26.3 Demography 693 689 26.4 Evolution of Life Histories 695 779 Ecosystem Services Highlight the Benefits of Ecosystems 787 29.4 Conservation Biology: Principles and Theory 789 Figure 29.16 Experimental Research Effect of Landscape Corridors on Plant Species Richness in Habitat Fragments 793 29.5 Assessing Threatened Species and Prioritizing Efforts 793 CONTENTS xiii Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 13 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com 29.6 Protecting Biodiversity Requires a Diversity of Solutions 794 34 Plant Signals and Responses to the Environment SUMMARY ILLUSTRATION FOR CHAPTER 29 798 34.1 Plant Hormones 896 THE CHEMICAL AND PHYSICAL FOUNDATIONS OF BIOLOGY (THE PURPLE PAGES) F-1 VOLUME 3: SYSTEMS AND PROCESSES 801 UNIT 7 SYSTEMS AND PROCESSES—PLANTS 30 Organization of the Plant Body 30.1 Plant Structure and Growth: An Overview 806 30.2 The Three Plant Tissue Systems 810 805 Figure 34.3 Experimental Research The Darwins’ Experiments on Phototropism 899 Figure 34.4 Experimental Research Two Experiments by Frits Went Demonstrating the Effect of Indoleacetic Acid (IAA) on an Oat Coleoptile 900 34.2 Plant Chemical Defences 907 34.3 Plant Movements 911 34.4 Plant Biological Clocks 915 34.5 Learned Behaviour in Plants 919 SUMMARY ILLUSTRATION FOR CHAPTER 34 920 Figure 30.9 Experimental Research Networking the Secondary Cell Wall 813 UNIT 8 SYSTEMS AND PROCESSES—ANIMALS 30.3 35 Introduction to Animal Organization and Physiology 925 35.1 Organization of the Animal Body 926 Primary Shoot Structure 815 30.4 Primary Root Structure 820 30.5 Secondary Growth 823 SUMMARY ILLUSTRATION FOR CHAPTER 30 828 895 35.2 Animal Tissues 928 35.3 Coordination of Tissues in Organs and Organ Systems 935 31 Transport in Plants 31.1 Principles of Water and Solute Movement in Plants 834 31.2 Uptake and Transport of Water and Solutes by Roots 837 Figure 35.12 Experimental Research Demonstration of the Use of the Bill for Thermoregulation in Birds 939 31.3 Long-Distance Transport of Water and Minerals in the Xylem 839 SUMMARY ILLUSTRATION FOR CHAPTER 35 942 31.4 Transport of Organic Substances in the Phloem 844 36 Animal Nutrition Figure 31.12 Experimental Research Translocation Pressure 845 36.1 Nutrients Are Essential Components of Any Diet 948 SUMMARY ILLUSTRATION FOR CHAPTER 31 848 36.2 Feeding to Obtain Nutrients 952 36.3 Digestive Processes 954 833 32 Reproduction and Development in Flowering Plants 853 32.1 Overview of Flowering Plant Reproduction 854 32.2 Flower Structure and Formation of Gametes 856 32.3 Pollination, Fertilization, and Germination 860 32.4 Asexual Reproduction in Flowering Plants 866 Figure 32.16 Research Method Plant Tissue Culture Protocol 868 35.4 Homeostasis 935 947 36.4 Structure and Function of the Mammalian Digestive System 957 36.5 Regulation of Digestive Processes 967 Figure 36.20 Experimental Research Association of Bacterial Populations in the Gut Microbiome with Obesity in Humans 969 36.6 Reflections on the Chapter 971 SUMMARY ILLUSTRATION FOR CHAPTER 36 972 37 Gas Exchange: The Respiratory System 37.1 General Principles 979 37.2 Ventilation of the Gas-Exchange Organs 983 37.3 The Mammalian Respiratory System 987 37.4 Exchange of Gas with Blood 989 Figure 33.2 Research Method Hydroponic Culture 877 37.5 Transport of Gases in Blood 990 33.2 Soil 880 37.6 Reflections on the Chapter 994 33.3 Root Adaptations for Obtaining and Absorbing Nutrients 883 Figure 37.21 Experimental Research Demonstration of a Molecular Basis for High-Altitude Adaptation in Deer Mice 995 32.5 Early Development of Plant Form and Function 868 SUMMARY ILLUSTRATION FOR CHAPTER 32 870 33 Plant Nutrition 33.1 Plant Nutritional Requirements 876 875 SUMMARY ILLUSTRATION FOR CHAPTER 33 890 977 SUMMARY ILLUSTRATION FOR CHAPTER 37 996 xiv CONTENTS Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 14 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com 38 Internal Transport: The Circulatory System 38.1 Animal Circulatory Systems: An Introduction 1003 Figure 41.12 Experimental Research Vocal Cues to Ovulation in Human Females 1097 38.2 Blood and Its Components 1006 41.5 38.3 The Heart 1009 SUMMARY ILLUSTRATION FOR CHAPTER 41 1118 1001 Development 1104 38.4 Blood Vessels of the Circulatory System 1013 38.5 Maintaining Blood Flow and Pressure 1017 Figure 38.19 Experimental Research Demonstration of a Vasodilatory Signalling Molecule 1019 Reflections on the Chapter 1021 39 Regulation of the Internal Environment: Water, Solutes, and Temperature 1027 39.1 Introduction to Osmoregulation and Excretion 1028 39.2 Osmoregulation and Excretion in Invertebrates 1032 39.3 Osmoregulation and Excretion in Non-mammalian Vertebrates 1034 39.4 Osmoregulation and Excretion in Mammals 1036 The Basis of Information Flow in Nervous Systems: An Overview 1124 1123 Sensory Inputs: Reception 1137 Figure 42.25 Experimental Research How Do Sea Urchins Detect Light? 1147 Figure 42.42 Experimental Research Magnetic Sense in Sea Turtles 1158 42.3 The Central Nervous System: Integration 1159 42.4 The Peripheral Nervous System: Transmission and Response 1171 SUMMARY ILLUSTRATION FOR CHAPTER 42 1174 Figure 39.15 Experimental Research ADH-Stimulated Water Reabsorption in the Kidney Collecting Duct 1042 Introduction to Thermoregulation 1043 43 Muscles, Skeletons, and Body Movements 43.1 Vertebrate Skeletal Muscle: Structure and Function 1180 1179 Figure 43.5 Experimental Research The Sliding Filament Model of Muscle Contraction 1183 39.6 Ectothermy 1045 39.7 42.1 42.2 SUMMARY ILLUSTRATION FOR CHAPTER 38 1022 39.5 Control of Animal Processes: Neural Control Figure 42.13 Experimental Research Demonstration of Chemical Transmission of Nerve Impulses at Synapses 1136 38.6 The Lymphatic System 1019 38.7 42 Endothermy 1048 39.8 Reflections on the Chapter 1053 43.2 Skeletal Systems 1189 SUMMARY ILLUSTRATION FOR CHAPTER 39 1054 43.3 Vertebrate Movement: The Interactions between Muscles and Bones 1193 40 Control of Animal Processes: Endocrine Control 40.1 Hormones and Their Secretion 1060 1059 40.2 Mechanisms of Hormone Action 1063 Figure 40.6 Experimental Research Demonstration That Epinephrine Acts by Binding to a Plasma Membrane Receptor 1066 40.3 The Hypothalamus and Pituitary 1068 40.4 Other Major Endocrine Glands of Vertebrates 1071 40.5 Endocrine Systems in Invertebrates 1076 Figure 40.16 Experimental Research Demonstration That Growth and Moulting in Insects Is Hormonally Controlled 1078 SUMMARY ILLUSTRATION FOR CHAPTER 43 1196 44 Animal Behaviour and Responses to the Environment 1201 44.1 Introduction 1203 Figure 44.3 Experimental Research The Role of Sign Stimuli in Parent–Offspring Interactions 1204 44.2 Genes and Behaviour: Nature or Instinct 1204 44.3 Environment and Behaviour: Learning or Nurture 1206 44.4 Hormones and Behaviour 1207 44.5 Neurophysiology and Behaviour 1209 44.6 Finding Food/Defences against Predation 1211 40.6 Reflections on the Chapter 1079 44.7 SUMMARY ILLUSTRATION FOR CHAPTER 40 1080 Communication 1212 44.8 Choice of Habitat 1216 41.1 The Drive to Reproduce 1086 Figure 44.28 Experimental Research Experimental Analysis of the Indigo Bunting’s Star Compass 1221 41.2 Asexual and Sexual Reproduction 1086 44.9 Mating 1224 41.3 Mechanisms of Sexual Reproduction 1088 44.10 Social Behaviour 1226 41.4 Sexual Reproduction in Mammals 1095 SUMMARY ILLUSTRATION FOR CHAPTER 44 1232 41 Animal Reproduction and Development 1085 CONTENTS xv Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 15 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com 45 Defences against Disease 45.1 Three Lines of Defence against Invasion 1238 45.5 45.2 Innate Immunity: Nonspecific Defence 1239 SUMMARY ILLUSTRATION FOR CHAPTER 45 1256 45.3 Adaptive Immunity: Specific Defences 1242 1237 Figure 45.10 Research Method Production of Monoclonal Antibodies 1248 xvi 45.4 Impairment and Peculiarities of the Immune System 1251 Immune Systems in Other Organisms 1254 Appendix A: Answers to Self-Test Questions Glossary G-1 Index I-1 A-1 CONTENTS Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 16 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Letter to Students As you take another step toward increasing your understanding of the biological world, we welcome you to this exploration of the diversity of life. The main goal of this textbook is to guide you on a journey of discovery about life’s diversity across interconnected levels of organization, ranging from molecules to genes, from cells to organs, and from species to ecosystems. Along the way, we will explore many questions about the mechanisms underlying diversity as well as the importance of maintaining diversity for all species, including our own. Diverse perspectives… With this edition of Biology: Exploring the Diversity of Life, we have been deliberate in beginning an ongoing process of opening this resource to a wider range of sources, voices, and perspectives devoted to a more fulsome understanding of the interconnected biological world. In particular, we offer this edition as a first step in responding to the Truth and Reconciliation Commission of Canada’s (TRC) Calls to Action and to the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP). The truth of the relationship between science and Indigenous Peoples in Canada has often, unfortunately, been one of oppression and exploitation. The racism that fuelled the colonization of the land that is now Canada influenced all aspects of social life, including the delivery of education and the conduct of science. The residential school system used education as a tool of cultural assimilation, with tragic effects on Indigenous communities that continue to play out today. Science education was rarely provided in these schools, thus limiting the capacity for Indigenous peoples to effectively interact with scientists representing government, industry, or academia. A significant underrepresentation of Indigenous peoples in Canadian science- and technology-related careers continues to this day. In many Indigenous communities, science and research have been viewed fearfully as tools of oppression. Some scientists have engaged in unethical practices in Indigenous communities that have resulted in deliberate harm to people and/or their environment. Indigenous Traditional Knowledge and technologies have been taken, and sometimes commercialized, without consent from or benefit to the original KnowledgeKeeping Elders and their communities. Part of the work of reconciliation in this edition is a contribution to the ongoing shift in perspectives of science from those of Eurocentrism (i.e., science as emanating from, and largely exclusive to, European nations and their current or former colonies) to a more open, decolonized, “multi-science” perspective that acknowledges all Indigenous Peoples as having scientific knowledge of the natural world, albeit through their own cultural lenses. One such perspective is Indigenous Science, the accumulated empirical knowledge that has been generated by thriving and prosperous Indigenous peoples through their observations of and relationships with natural phenomena over millennia. This book is one result of deepening relationships among the primary authors and their professional colleagues, the editorial and production teams at Cengage Canada, students of biology, Indigenous Elders and scholars, as well as members of our Indigenous Advisory Board. The author team participated in Ceremony with Indigenous advisors, experiencing firsthand Indigenous cultural practices to acknowledge the collective desire for the success of this project as an example of and inspiration for reconciliatory learning. With open minds and hearts, we are committed to creating a meeting place where scientists of all backgrounds can tell their stories. As an author, advisory, and production team including both settlers and Indigenous People of Turtle Island, we want our work to contribute to reconciliation and improved relations among settlers and First Nations, Inuit, and Métis Peoples. As educators, we want our classes to be widely accessible. We understand that this means making efforts to increase the level of safety felt by Indigenous students and others who have been excluded in our science education system. As authors of educational resources, we want to promote innovative, wholistic, effective andragogy that supports teaching and learning by all students and instructors. As global citizens, we want to promote collaboration in harnessing the creative power of a wide variety of perspectives in the face of global challenges. An emphasis on the diversity of life… At first glance, the riot of life that animates the biosphere overwhelms our minds. One way to begin to make sense of this diversity in a textbook is to divide it into manageable sections on the basis of either similarities or differences. We examine how different organisms solve the common problems of finding nutrients, energy, and mates on the third rock from our Sun. Evolution provides a powerful conceptual lens for viewing and understanding the roots and history of the diversity of living things. What basic evolutionary principles inform the relationships among life forms regardless of their different body plans, habitats, or life histories? We will demonstrate how knowledge of evolution helps us appreciate the changes we observe in organisms. Whether the focus is the conversion of free-living prokaryotic organisms into mitochondria and chloroplasts or the loss of eyes in cave fish, selection for particular traits over time can explain the current observations. Examining how biological systems work is another theme pervading this text and underlying the idea of diversity. We have intentionally tried to include examples that will tax your imaginaxvii Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 17 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com tion, from sea slugs that steal chloroplasts for use as solar panels, to the molecular basis of high-altitude adaptations in deer mice, to adaptive radiation of viruses. In each situation, we examine how biologists have explored and assessed the inner workings of organisms, from gene regulation to the challenges of digesting cellulose. Solving problems is another theme that runs throughout the book. Whether the topic is gene therapy to treat a disease in people, preventing harmful algal blooms, or reducing the incidence of human cancer, both the problem and the solution lie in biology. We will explore large problems facing planet Earth and the social implications that arise from them. Emphasizing the big picture… While many biology textbooks use the first few chapters to review fundamentals of chemistry and biochemistry as well as information on the scientific method, this book immediately engages in some of the excitement, mystery and controversy that is modern biology right up front in Chapter 1. Important background information appears in the centre of the book as a distinct reference section entitled The Chemical and Physical Foundations of Biology. With their purple borders, these pages are distinct and easy to find, and have become affectionately known as The Purple Pages. These pages enable information to be readily identifiable and accessible to you as you move through the textbook rather than it being tied to a particular chapter. The concepts of atoms, molecules, and macromolecules are connected through the theme of “emergent properties.” By considering how the “stuff of life” interrelates as a function of increasing complexity rather than just memorizing the attributes of individual items, you can better grasp why biology works the way it does rather than be awed by how much information we know about it. Throughout this book, we have highlighted the work of Indigenous and non-Indigenous scientists in Canada and elsewhere, and we present many examples and biological concepts in Canadian contexts. We hope that you, as a student studying in Canada, will find this context accessible and engaging. Focusing on research to engage the living world through a scientific lens… A primary goal of this book is to evoke and sustain your curiosity about biology, rather than dulling it with a mountain of disconnected facts. We can help you develop the mental habits of scientists and a fascination with the living world by conveying our passion for biological research. We want to excite you not only with what biologists know about the living world but also with how they know it and what they still need to learn. In doing so, we can encourage some of you to accept the challenge and become biologists, posing and answering important new questions through your own innovative research. For those of you who pursue other careers, we hope that you will leave your introductory—and perhaps only—biology course armed with intellectual skills that will enable you to evaluate future knowledge with a critical eye. xviii In this book, we introduce you to a biologist’s “way of learning.” Research biologists constantly integrate new observations, hypotheses, questions, experiments, and insights with existing knowledge and ideas. To help you engage the world as biologists do, we must not simply introduce you to the current state of knowledge, we must also foster an appreciation of the historical context within which those ideas developed and identify the future directions that biological research is likely to take. Because advances in science occur against a background of research, we also give you a feel for how biologists of the past formulated basic knowledge in the field. By fostering an appreciation of such discoveries, given the information and theories available to scientists in their own time, we can help you understand the successes and limitations of what we consider cutting-edge today. This historical perspective also encourages you to view biology as a dynamic intellectual enterprise, not just a collection of facts and generalities to be memorized. We have endeavoured to make the science of biology come alive by describing how biologists formulate hypotheses and evaluate them using hard-won data, how data sometimes tell only part of a story, and how the results of studies often end up posing more questions than they answer. Our exploration of the Tully Monster in Chapter 23 is a case in point. Since its fossil discovery and description, this mainly soft-bodied animal has been tentatively classified with species in five different groups of animals. Through this example and throughout Chapter 23, we explore the current recognition that the historical and traditional grouping of animals into protostomes and deuterostomes is more artificial than real. Although you might prefer simply to learn the right answer to a question, we encourage you to embrace the unknown— those gaps in knowledge that create opportunities for further research. An appreciation of what biologists do not yet know may draw you into the field. And by defining why scientists do not understand interesting phenomena, we encourage you to think critically about possible solutions and to follow paths dictated by your own curiosity. We hope that this approach will encourage you to make biology a part of your daily life by having informal discussions and debates about new scientific discoveries with members of your personal and academic communities. This textbook is a toolbox… You may see your professor as primarily a teacher, but as practicing scientists, professors are always learning from colleagues, from the scientific literature, from their research programs, and from their students. You may see yourself as primarily a learner, but as a member of a social network, you are very likely to find yourself explaining biological concepts to your friends, family members, and the general public. Recognizing that we are all lifelong learners and teachers may help you to see how each part of your learning, both in and out of class, fits into the continuously developing picture of your life. L E T T E R TO S T U D E N T S Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 18 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Although it’s usual to think of this resource as merely a book, it may be more helpful to imagine it as a toolbox containing various interrelated components carefully designed to inspire, inform, structure, connect, and confirm your learning. Modern science courses are often blended and/or flipped. That is, you will likely be assigned an online learning component to complement subsequent face-to-face classroom interaction. Professors will often assign textbook readings in advance of class. If, for example, you are assigned to read Sections 14.2 to 14.4 of the text, be aware that educational research has identified specific strategies for approaching this reading that are more likely to result in durable learning. The least-effective strategy is to go directly to the assigned material and simply read it as you would read a novel or social media post. Learning is more durable if new concepts can be connected to ideas that are already known or relevant to you. This means that the structure and context for new learning is important. Assume that you are responsible for reading certain sections of a chapter. Begin with the brief Why It Matters section at the opening of the chapter. This will help you to see the relevance of the material and, hopefully, allow you to make some personal connection to the concepts. Check the chapter-opening Roadmap to see how the assigned topics are related to other ideas within the chapter and also to material in other chapters. Then look over the Summary Illustration at the end of the chapter to get a broad visual sense of the scope of the material. What do you recognize from previous learning? What looks new? What looks especially interesting? Then, go to the assigned sections of the chapter with the awareness of how they fit into the bigger picture of the chapter and to the concepts that are already known or interesting to you. Even then, don’t just start reading at the first word. Instead, continue the exercise of noting the structure of the material by just noticing the main headings and perusing the figures. Once you begin to read, create your own organization of the material by making your own notes, highlights, etc. Learning science requires that you understand new vocabulary; consult the Glossary to confirm the meaning of unfamiliar terms (or look up elsewhere terms not included in the Glossary—get comfortable with all of the vocabulary). Use the embedded Study Break questions as an opportunity to pause and help confirm that you have identified and understood the major ideas. If you don’t know the answer to a Study Break question, this is a sign that you should go back and read more carefully and/or seek additional help. Pay particular attention to the Concept Fix feature as well. These brief sections identify and clarify many misconceptions that biology students are prone to experience as they are learning. As your notes develop, notice any connections that arise to what you have already learned in previous classes and other courses. Highlighting such relationships will help you to retain your new knowledge. As you read, use the complementary photos and illustrations to supplement and confirm your understanding. Notice that graphs and anatomical drawings are annotated with interpretive explanations that lead you step by step through the major points they convey. Science is a progressive enterprise in which answers open new questions for consideration. As you read a chapter, watch for the underlying thread of the research process that gave rise to the information you are learning. Notice the three types of specially designed research figures providing more detailed information about how biologists formulate specific hypotheses and test them by gathering and interpreting data. Experimental Research figures describe specific studies in which researchers used both experimental and control treatments, either in the laboratory or in the field, to test hypotheses or Why It Matters will help you see the relevance of the material and allow you to make some personal connections to the concepts. Study Break Questions provide an opportunity to pause and help confirm that you have identified and understood the major ideas. Assigned Readings The Summary Illustration will give you a broad, visual sense of the scope of the material. • What do you recognize from previous learning? • What looks new? • What looks especially interesting? The Chapter Roadmap will show you how each of the chapters’ topics are related to other ideas within the chapter and to the material in other chapters. L E T T E R TO S T U D E N T S xix Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 19 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com answer research questions by manipulating the system they studied. Observational Research figures describe specific studies in which biologists have tested hypotheses by comparing systems under varying natural circumstances. Research Method figures provide examples of important techniques, such as light and electron microscopy, the polymerase chain reaction, making a knockout mouse, DNA microarray analysis, plant cell culture, producing monoclonal antibodies, radiometric dating, and cladistic analysis. Each Research Method figure leads you through the purpose of the technique and protocol and describes how scientists interpret the data it generates. To complement the textbook material relating to research, we encourage you to take any opportunity to participate in hands-on laboratory or field investigations. Such first-hand experiences can help you to see how the theoretical knowledge in the book relates to your life and the aspects of biology that interest you most. As a final check of your learning, you might address selected Self-Test Questions at the end of the chapter. These chapterreview questions are organized according to Bloom’s Taxonomy into three sections: Recall/Understand, Apply/Analyze, and Create/Evaluate. This structure allows you to review the material in a sequence that moves from the basic knowledge of factual material to more challenging and sophisticated applications of that knowledge to novel situations. Although answers to the xx Self-Test Questions are found in an appendix at the back of the book, looking at answers before generating your own can lead to hindsight bias and misplaced confidence. Working through the questions before consulting the answers will give you a more accurate assessment of your understanding of the material before you are faced with high-stakes exam questions. In summary, we have applied our collective experience as teachers, researchers, and writers to create text and complementary visuals that provide accessible explanations of fundamental concepts from an evolutionary perspective that binds all the biological sciences. We hope that you are as captivated by the biological world as we are and are drawn from one chapter to another. But don’t stop there; use MindTap and other resources to broaden your search for understanding and, most importantly, observe and enjoy the diversity of life around you. M. Brock Fenton Denis Maxwell Tom Haffie Bill Milsom Todd Nickle Shona Ellis Shelby Riskin London, Toronto, Calgary, and Vancouver January 2022 L E T T E R TO S T U D E N T S Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 20 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com New to This Edition This section highlights the changes we made to enhance the effectiveness of Biology: Exploring the Diversity of Life, Fifth Canadian Edition. Every chapter has been updated to ensure currency of information. We made organizational changes to more closely link related topics and preferred teaching sequences. Key chapters have been extensively revised to provide a full treatment of the subject matter that reflects new developments in these specialized fields. Organization We begin the fifth Canadian edition with the question “What is life?” Chapter 1: Defining Life and Its Origins starts with the recognition that the origin and definition of life are widely considered to be one of the great mysteries and challenges in science. It explores how we define the characteristics of life, why scientists cannot agree on a universal definition of life, and how the way a discipline defines life is intimately connected to the questions it explores. This opening chapter situates biology as a method of inquiry that has at its core curiosity and a sense of awe. This sense of wonderment is once again brought to the fore in Unit 5: The Diversity of Life, which features a two-page spread introducing students to the Tree of Life. The starburst tree presents students with a perspective on the truly astounding organismal diversity on the planet, the relative place of humans within it, and the equally astounding amount of biological diversity that remains unknown. This unit has been reorganized so that Bacteria and Archaea (Chapter 20) now precedes Protists (Chapter 21), followed by Fungi (Chapter 22), Plants (Chapter 23), Animals (Chapter 24), and Viruses, Viroids, and Prions (Chapter 25). Conservation of Biodiversity (Chapter 29) was moved from this unit to the end of Unit 6: Ecology and Behaviour. Plant Signals and Responses to the Environment (Chapter 34) and Animal Behaviour and Responses to the Environment (Chapter 44) have been moved to their respective units covering the systems and processes of plants and animals. And finally, the fifth Canadian edition concludes with a new and timely Chapter 45: Defences against Disease. Reintroduced into the book by popular demand, this chapter covers innate and adaptive immunity, vaccines, convalescent plasma and antibody therapies, malfunction and failures of the immune system, and defence systems in other organisms. Indigenous Ways of Knowing and Learning in the Why It Matters sections. We have included specific examples from First Nations, Inuit, and Métis communities, using the traditional names of Indigenous Nations and the traditional languages of Indigenous groups. We have attempted to cite research from Indigenous researchers; research where Indigenous communities have partnered with the researchers; and research where Indigenous knowledge has informed, enhanced, or changed our understanding of a particular phenomenon. To authentically represent concepts and stories that we have been given permission to share, we have committed to ensuring that any associated artwork is created by an Indigenous artist. Points of Interest in Each Chapter At the beginning of each chapter are redesigned Chapter Roadmaps. Instead of providing a visual representation of how the chapter is organized, we revisited this feature with an eye to providing a clear visual overview of how the major topic areas in the chapter relate to one another. In addition to showing how concepts relate to each other within the chapter, the roadmaps also show the connections between the topics in the chapter and the other chapters in the book. Chapter 1: Defining Life and Its Origins ● ● ● ● Chapter 5: Cellular Respiration ● The fifth Canadian edition constitutes a modest first step in our contribution to the ongoing shift in perspectives of science from Eurocentrism to a more open, decolonized, “multi-science” perspective that acknowledges all Indigenous Peoples as having scientific knowledge of the natural world through their own cultural lenses. Throughout the book, we have made connections to NEW Why It Matters exploring the role of mitochondria and cold tolerance in Inuit individuals Chapter 6: Photosynthesis ● Diversity in Ways of Knowing and Learning NEW. While we know so much about life, science struggles to arrive at a simple definition of what it means to be living. We discuss this interesting question. NEW. More robust discussion of the origins of metabolism and how it may have evolved in close association with alkaline hydrothermal vents. NEW discussion of how science has moved from a threedomain view of the tree of life to a two-domain view NEW exploration of the latest evidence showing that eukaryotes are descended from a lineage of the Archaea ● ● NEW section on the physical nature of light NEW Concept Fix—Why are there three membranes in chloroplasts and only two in mitochondria, both of which evolved through endosymbiosis? NEW section on electron transport Chapter 7: Cell Cycles ● NEW references to the fastest-growing prokaryotic cell, Bibrino natiegens xxi Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 21 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com ● ● Expanded relevance to cancer through reference to Peto’s Paradox as commentary on underlying genetics of low cancer incidence in large mammals NEW Summary Illustration Chapter 8: Genetic Recombination ● ● Reconstructed chapter to integrate sources of variability with the description of respective stages of meiosis NEW Summary Illustration Chapter 9: The Chromosomal Basis of Inheritance ● ● NEW Why It Matters begins the process of decolonization by acknowledging that people have applied their understanding of inheritance to purposefully increase desirable characteristics among successive generations of plants and animals for tens of thousands of years before Mendel NEW Summary Illustration Chapter 10: Genetic Linkage, Sex Linkage, and Other Extensions to Basic Inheritance Mechanisms ● ● ● ● NEW reference to Indigenous clan system and ethical, respectful efforts to address the lack of Indigenous sequences in DNA databases NEW discussion of the three-parent baby controversy NEW connection to epigenetics and the possibility of a role for epigenetics in multigenerational trauma NEW Summary Illustration Chapter 11: DNA Structure, Replication, and Repair ● ● Refined and clarified text descriptions of early experiments NEW Summary Illustration Chapter 12: Gene Structure, Expression, and Mutation ● NEW Summary Illustration Chapter 13: Regulation of Gene Expression ● ● ● Substantial update of the paradigm of the mechanism underlying diauxic growth with respect to the lac operon NEW material on cancer incidence in Canada NEW Summary Illustration Chapter 14: DNA Technologies Chapter 16: Evolution: The Development of the Theory ● Chapter 17: Microevolution: Changes within Populations ● ● ● ● xxii NEW Why It Matters discussing how the Golden State Killer was caught because a relative submitted their DNA to a public database NEW Why It Matters describing how Native Papuans and Ernst Mayr identified a nearly identical number of bird species using very different methods Chapter 19: Systematics and Phylogenetics: Revealing the Tree of Life ● Revised Summary Illustration Chapter 20: Bacteria and Archaea ● ● ● NEW discussion around Pseudomonas aeruginosa as common co-infecting pathogen in COVID-19 patients Discussion of how tuberculosis is a leading cause of death due to infectious disease throughout history and how Indigenous people have been disproportionately affected by this disease Revised Summary Illustration Chapter 21: Protists ● ● NEW Why It Matters about how the people of Haíl~zaqv, Heiltsuk Nation, collect, process, and use seaweeds from intertidal areas NEW Summary Illustration Chapter 22: Fungi ● ● NEW material on the four main invasive fungal co-infections with COVID-19 NEW discussion of Ch’ãłtthi (willow tinder fungus), used by the Denesuline (Chipewyan) people as tinder and packaging Chapter 23: Plants ● ● Updated discussion of CRISPR Chapter 15: Genomes Clarified discussion around the four key aspects of mutation Selected figures reviewed and revised for clarity Chapter 18: Speciation and Macroevolution ● ● Thoroughly revised and reorganized, bringing the theory of natural selection itself to the fore ● ● ● Reorganized for flow and clarity Updated and revised selected illustrations for clarity NEW discussion of the story behind the name of Indian pipe (Monotropa uniflora) NEW discussion of sk’in (“horsetails” in the Haida language) and how it was used NEW discussion of the pitch from species of the pine family, which has many traditional uses by Indigenous Peoples Revised Summary Illustration N E W TO T H I S E D I T I O N Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 22 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Chapter 24: Animals ● ● ● ● Completely reorganized and streamlined to shift the approach to understanding and recognizing patterns and variations Emphasis on key groups rather than a description of all groups More emphasis on concepts and less on details NEW figures providing an overview of the group of animals discussed in each section Chapter 25: Viruses, Viroids, and Prions: Infectious Biological Particles ● ● ● NEW Why It Matters discussing the impact of smallpox on Indigenous communities Thoroughly revised and updated, including material on SARS-CoV-2 NEW section on virotherapy Chapter 26: Population Ecology ● ● ● NEW Why It Matters discussing a collaboration between the University of Guelph and the Chippewa of Nawash Unceded First Nation identifying five general principles associated with Nawash harvesting Thoroughly revised, streamlined, and updated NEW definitions and discussion of semelparity and iteroparity Chapter 28: Ecosystems ● ● ● ● ● NEW Why It Matters about the impact of 19th-century colonial development along Lake Erie NEW discussion of Three Sisters crop complementarity Thoroughly revised, streamlined, and updated Updated discussion of climate change and disruption of the global carbon cycle NEW Summary Illustration Chapter 30: Organization of the Plant Body ● ● NEW Why It Matters featuring a discussion of culturally modified trees written by researcher and Heiltsuk archeologist Elroy White (Q̌íx̌ itasu) of central coast British Columbia Revised Summary Illustration Chapter 31: Transport in Plants ● Figures revised and updated for clarity Chapter 34: Plant Signals and Responses to the Environment ● ● ● Chapter 36: Animal Nutrition ● ● ● NEW Why It Matters about the role of the salmon cycle and plant growth, featuring original artwork by Indigenous artist Chester Lawson of the Haíłzaqv (Heiltsuk) Territory, Central Coast, British Columbia. NEW discussion of Palliser’s Triangle in Alberta/Saskatchewan, a hunting ground for Cree, Sioux, and Blackfoot NEW Why It Matters about dietary requirements in animals and across cultures, and how there are no “essential foods,” only essential nutrients NEW material on the human gut biome Chapter 37: Gas Exchange: The Respiratory System ● NEW Why It Matters featuring a discussion of the many roles that breathing plays across different cultures Chapter 38: Internal Transport: The Circulatory System ● ● ● NEW Why It Matters featuring the significance of the notion of the beating heart across different cultures NEW section—Heart Attacks and Strokes Arise from Poor Blood Flow to the Heart Muscle and Brain Revised Summary Illustration Chapter 40: Control of Animal Processes: Endocrine Control ● Revised Summary Illustration Chapter 41: Animal Reproduction and Development ● ● NEW Why It Matters featuring the reproductive process of Pacific herring off the coast of British Columbia Revised Summary Illustration Chapter 44: Animal Behaviour and Responses to the Environment ● Chapter 33: Plant Nutrition ● NEW Why It Matters about the observation of plant behaviour to predict the timing of other resources, such as the soapberry harvest of Nlaka’pamux First Nation of Thompson River, British Columbia, and the link between elderberry blooms and halibut fishing among the First Nations of Nuuchah-nulth on Vancouver Island NEW discussion of heliotropism Revised Summary Illustration ● NEW Why It Matters featuring a discussion of how Indigenous hunting societies around the globe have relied on knowledge of the behaviours of their food species for survival Thoroughly revised and streamlined NEW Chapter 45: Defences against Disease ● ● NEW chapter Why It Matters featuring a discussion of plagues, epidemics, and pandemics, including COVID-19 N E W TO T H I S E D I T I O N xxiii Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 23 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Welcome to Biology: Exploring the Diversity of Life, 5Ce Biology: Exploring the Diversity of Life and MindTap engage students so they learn not only WHAT scientists know, but HOW they know it and what they still need to learn. ◀ Each chapter begins with Why Does ___ Matter to Me?, an engaging reading that explores a real-life application of the chapter topic, providing students with context around the relevance of the material they are learning. ▲ Learn It! The Media Library, with its dynamic animations and videos, offers a different entry point into the content that helps students process and understand concepts in a different way. ▲ Study It! Exam Prep auto-graded questions have been carefully curated to replicate the type and level of questions that students will encounter in a testing scenario. Chapter Flashcards help students remember key term in each chapter. xxiv Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 24 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com ◀ Apply It! Think and Engage Like a Scientist by taking gradable short-answer quizzes: • • • Apply Evolutionary Thinking questions ask students to interpret a relevant topic in relation to the principles of evolutionary biology. Design an Experiment challenges students’ understanding of the chapter and helps them deepen their understanding of the scientific method as they consider how to develop and test hypotheses about a situation that relates to a main chapter topic. Interpret the Data questions help students develop analytical and quantitative skills by asking them to interpret graphical or tabular results of experimental or observational research experiments for which the hypotheses and methods of analysis are presented. Also available in MindTap for Biology are engaging and informative videos that accompany The Purple Pages. From matter to polypeptides, author Todd Nickle of Mount Royal University (pictured) will walk students through these foundational concepts, strengthening their understanding and helping them build a strong base of knowledge and understanding of biology. Test students’ mastery of concepts with Conceptual Learning Activities that complement the text and help them learn and understand key concepts through focused assignments, an engaging variety of problem types, exceptional text/art integration, and immediate feedback. xxv Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 25 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Active Learning Visually stunning features are provided engage your students in the process of learning because an engaged student is a successful student. Chapter Roadmap Plant Nutrition 33.1 From Chapter 30 to make connections between root structure and water/nutrient absorption Plant Nutritional Requirements Plants can make all the macromolecules, including their subunits. Plants supply macromolecules to other trophic levels. Nitrogen acquisition often limits plant growth. Symbiosis and predation on animals are adaptations to help plants thrive. © Chester Lawson To Chapter 6 for details about photosynthesis and how some plants are modified for hot and dry environments PT 33.2 Soil To Chapter 27 make connections between nutrients and organism interactions Plant health depends on soil for both texture and dissolved nutrients. Humus provides nutrition and also stores water, both of which are absorbed by roots. Soil acidity and ion content also affect availability of dissolved nutrients to the plant. Plant Nutrition 33.3 Root Adaptations for Obtaining and Absorbing Nutrients Microorganisms such as bacteria and fungi contribute to nutrient cycling. Symbiotic associations are important in making nutrients from the soil more available to the plant. Root adaptations encourage symbiotic interactions. Xylem carries dissolved materials to the shoots from the roots. To Chapter 31 to consider how nutrients are taken up and distributed in plants To Chapter 22 to consider how nutrients are taken up and distributed in plants To Chapter 28 to investigate how nutrients are cycled within an ecosystem Spawning Salmon by Chester Lawson To Chapter 34 to make connections between nutrients and auxin as well as other plant hormones Why it matters. . . Coastal British Columbia is known for its rugged mountains, rivers, and lush forests. The ocean is connected through the rivers to what have been termed the “salmon forests.” Salmon has sustained the peoples of these lands for thousands of years; First Nations fisheries were run sustainably, ensuring the returning runs of coho, pink, sockeye, chinook, and chum. Fishing technologies were designed so that only what was needed was taken. The migration runs occur at certain times of the year, when enough salmon would be collected and processed to provide food all year round. Drying and smoking were important forms of preservation; more recently, canning and freezing have become important. These salmon are on their migratory path to their place of birth in rivers, streams, and lakes, where they spawn and then die. What does this have to do with plant nutrition? Salmon are not only integral to the health and nutrition of First Nations, they are crucial to the health of the ecosystems of the coast as well as further inland as the fish venture up into the interior through the networks of waterways. Imagine thousands of fish making their way up rivers, with bears, otters, eagles, and ravens depending on their arrival. The salmon that make it to their spawning grounds lay their eggs, fertilize them, and then die. Bears in particular drag the fish carcasses up into the forest. They are selective eaters and often consume only particular portions of the fish, leaving the carcasses to provide food and nesting sites (e.g., for blowflies), and for decomposers to recycle their nutrient-rich bodies (Figure 33.1). There is a distinct fragrance that fills the air during these runs, the smell of decomposition, as you find carcasses along the riverside, the riparian areas, and deep in the forest. The nutrients within the fish, particularly nitrogen, are made available to other organisms. As we will see in this chapter, nitrogen is a limiting nutrient in plants, and a number of researchers have followed its path through coastal ecosystems. Nitrogen does not have a direct route into plants; microorganisms are instrumental in breaking down the carcasses, and important intermediaries make the nitrogen available for uptake by plants. Animals that consume the fish release nitrogen in their excrement and urine (urea), which get broken down by soil enzymes and microbes. Plants absorb nitrogen in the form of nitrate and ammonium, often facilitated by fungi through mycorrhizal associations or bacterial symbioses. Within the plants, this nitrogen is incorporated into organic molecules such as proteins and nucleic 33 875 ▲ Chapter Roadmaps The Chapter Roadmaps provide a visual overview of how the major topic areas in the chapter relate to one another and show the connections between the topics in the chapter and other chapters in the book. Why It Matters Why It Matters draws students in with an engaging vignette that is linked to the concepts discussed in the chapter. Concept Fix Concept Fix sections draw on the extensive research literature dealing with misconceptions commonly held by biology students. Strategically placed throughout the text, these short segments help students identify—and correct—a wide range of misunderstandings. ▼ ▲ Study Break The Study Break features fall at the end of each major section and encourage students to pause and review what they have learned before going on to the next topic within the chapter. xxvi Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 26 21/03/22 5:52 PM Get Complete eBook Download By email at student.support@hotmail.com ◀ Experimental Research Experimental Research Experimental Research FIGURE 10.2 Evidence for Gene Linkage Question: Do the purple-eye and vestigial-wing genes of Drosophila assort independently? Experiment: Morgan crossed true-breeding, wild-type flies having red eyes and normal wings with purple-eyed, vestigial-winged flies. The F 1 dihybrids were all wild type in phenotype. Next, he crossed the F1 dihybrid flies with purple-eyed, vestigial-winged flies (this is a testcross) and analyzed the phenotypes of the progeny. 1. P generation Wild-type female (red eyes, wild-type wings) 2. F1 generation Double mutant male (purple eyes, vestigial wings) pr + pr + vg + vg + pr pr vg vg F1 dihybrid (red eyes, wild-type wings) F1 dihybrid (red eyes, wild-type wings) 3. Testcross All F1 flies were wildtype in phenotype and were heterozygous for both pairs of alleles: pr+pr vg+vg. pr + pr vg + vg pr + pr vg + vg F1 dihybrid (red eyes, wild-type wings) Double mutant male (purple eyes, vestigial wings) Morgan next performed a testcross of F1 wild-type phenotype females with purple-eyed, vestigialwinged males; this is a testcross. pr + pr vg + vg 4. Progeny of testcross Gamete from male parent The wild-type parent is homozygous for the wild-type allele of each gene: pr+pr+ vg+vg+. The purple-eyed, vestigial-winged parent is homozygous for the recessive allele of each gene: prpr vgvg. figures describe specific studies in which research used both experimental and control treatments—either in the laboratory or in the field—to test hypotheses or answer research questions by manipulating the system they studied. pr pr vg vg Gametes from female parent pr+ vg+ pr vg pr+ vg pr vg+ Wild type, wild type Purple, vestigial Red, vestigial Purple, normal Fusion of the one type of sperm produced by the male, and the four types of eggs produced by the female, generates the progeny of the testcross. pr vg pr + pr vg + vg prpr vg vg pr + pr vg vg pr pr vg+ vg Observed 1339 1195 151 154 Expected, if assort independently Parental phenotypes Recombinant phenotypes ~710 ~710 ~710 ~710 = 2839 total progeny (709.75 each) = 2839 total progeny Results: 2534 of the testcross progeny flies were parental—wild type or purple, vestigial—while 305 of the progeny were recombinant—red, vestigial or purple, wild type. If the genes assorted independently, the expectation is for a 1:1:1:1 ratio for testcross progeny: approximately 1420 of both parental and recombinant progeny. Conclusion: The purple-eye and vestigial-wing genes do not assort independently. The simplest alternative is that the two genes are linked on the same chromosome. The small number of flies with recombinant phenotypes is explained by crossing-over. 240 UNIT 2 Research Method Research Method figures provide examples of important techniques, lead students through the purpose of the technique and protocol, and describe how scientists interpret the data generated. ▼ GENES FIGURE 14.3 FIGURE 18.16 Research Method Identifying a Recombinant Plasmid Containing a Gene of Interest Observational Research Chromosomal Similarities and Differences among Humans and the Great Apes Purpose: To identify a recombinant plasmid containing a gene of Protocol: Inserted DNA fragment with gene of interest (red) Question: Does chromosome structure differ between humans and their closest relatives among the apes? Hypothesis: Large-scale chromosome rearrangements contributed to the development of reproductive isolation between species within the Resealed plasmid cloning vector with no inserted DNA fragment interest from a ligation reaction mixture containing a bacterial cloning vector and a DNA fragment containing the gene of interest, each digested with the same restriction enzyme evolutionary lineage that includes humans and apes. 1. The ligation reaction produces recombinant plasmids (the only products that might contain the gene of interest), nonrecombinant plasmids, and joined pieces of genomic DNA (not shown). Prediction: Chromosome structure differs markedly between humans and their close relatives among the great apes: chimpanzees, gorillas, and orangutans. Method: Jorge J. Yunis and Om Prakash of the University of Minnesota Medical School used Giemsa stain to visualize the banding patterns on metaphase chromosome preparations from humans, chimpanzees, gorillas, and orangutans. They identified about 1000 bands that are present in humans and in the 3 ape species. By matching the banding patterns on the chromosomes, the researchers verified that they were comparing the same segments of the genomes in the four species. They then searched for similarities and differences in the structure of the chromosomes. Recombinant plasmid Nonrecombinant plasmid Results: Analysis of human chromosome 2 reveals that it was produced by the fusion of two smaller chromosomes that are still present in the other three species. Although the position of the centromere in human chromosome 2 matches that of the centromere in one of the chimpanzee chromosomes, in gorillas and orangutans it falls within an inverted segment of the chromosome. Human Bacteria transformed with plasmids Centromere position is similar in humans and chimpanzees Chimpanzee Selection: Bacteria transformed with plasmids grow on medium containing ampicillin because of ampR gene on plasmid. Untransformed bacteria or bacteria transformed with gene fragments cannot grow on medium containing ampicillin. Matching bands Screening: Gorilla Orangutan Compared to the chromosomes of humans and chimpanzees, the region that includes the centromere is inverted (its position is reversed) in both gorillas and orangutans. Blue colony contains bacteria with a nonrecombinant plasmid; that is, the lacZ + gene is intact. White colony contains bacteria with a recombinant plasmid, that is, the vector with an inserted DNA fragment, in this case the gene of interest. Conclusion: Differences in chromosome structure between humans and both gorillas and orangutans are more pronounced than they are Bacteria not transformed with a plasmid or transformed with gene fragments 3. Spread the bacterial cells on a plate of growth medium containing ampicillin and X-gal, and incubate the plate until colonies appear. Plate of growth medium containing ampicillin and X-gal between humans and chimpanzees. Structural differences in the chromosomes of these four species may contribute to their reproductive isolation. Source: Based on J. J. Yunis and O. Prakash. 1982. The origin of man: A chromosomal pictorial legacy. Science 215:1525–1530. ▲ Observational Research STUDY Observational Research chromosome rearrangement becomes established within a BREAK QUESTIONS population, that population will diverge more rapidly from figures describe specific studies in which biologists have populations lacking the rearrangement. The genetic divergence eventually causes reproductive isolation. tested hypotheses by comparing systems under varying natural circumstances. 1. How can natural selection promote reproductive isolation in allopatric populations? 2. How does polyploidy promote speciation in plants? CHAPTER 18 S P E C i AT i o n A n d M A C R o E v o lu T i o n 2. Transform ampicillin-sensitive, lacZ– E. coli (which cannot make β-galactosidase) with a sample of the ligation reaction. In this step, some bacteria will take up DNA, whereas others will not. KEY Restriction site lacZ+ gene ampR gene Origin of replication (ori) Plasmid cloning vector Interpreting the Results: All the colonies on the plate contain plasmids because the bacteria that form the colonies are resistant to the ampicillin present in the growth medium. Blue–white screening distinguishes bacterial colonies with nonrecombinant plasmids from those with recombinant plasmids. Bacteria making up blue colonies contain nonrecombinant plasmids. These plasmids have intact lacZ 1 genes and produce β-galactosidase, which changes X-gal to a blue product. Bacteria that form the white colonies contain recombinant plasmids. Each recombinant plasmid has a DNA fragment (in this example, the gene of interest) inserted into the lacZ1 gene, so β-galactosidase cannot be produced. As a result, bacteria with recombinant plasmids cannot convert X-gal to the blue product and the colonies are white. Culturing a white colony produces large quantities of the recombinant plasmid that can be isolated and purified for analysis and/or manipulation of the gene 5 “gene of interest.” 465 xxvii Get Complete eBook Download By email at student.support@hotmail.com C H A P T E R 14 11140_fm_ptg01.indd 27 D N A T E C H N O LO G I E S 351 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Summary Illustrations Vivid, engaging, and carefully developed Summary Illustrations appear at the end of each chapter and help students visualize the main concepts covered in the chapter. ▼ Summary Illustration Acetyl CoA C C – CoA Citric Acid Cycle CoA Six-carbon molecule formed from acetyl CoA + oxaloacetate Cellular respiration is a collection of reactions that converts the chemical energy present in carbohydrates, fats, and proteins into an energy currency, ATP, that is readily used by the cell. The phases of cellular respiration are (i) glycolysis, (ii) pyruvate oxidation and the citric acid cycle, and (iii) oxidative phosphorylation. The overall process is represented by the chemical equation for the oxidation of glucose. Four-carbon acceptor molecule (regenerated in each cycle) C C C C Oxaloacetate C C C C C C Citrate NAD+ NADH + CO2 NADH C C C C C NAD+ NAD+ Cellular respiration is a redox process. • The overall change in free energy (ΔG) is negative. C6H12O6 + 6O2 Reduced electron carrier similar to NADH Low [O2] FAD GTP Second carbon lost as CO2 i Energy-carrying molecule equivalent to ATP Pyruvate is transported into the mitochondrial matrix and converted to acetyl-CoA, which enters the citric acid cycle and is oxidized. Notice the products formed. Glycolysis Pyruvate GDP, P FADH2 • The goal is to couple the energy released to the synthesis of ATP! Glucose Glycolysis occurs in the cytosol and splits glucose into pyruvate, which yields ATP and NADH. The fate of pyruvate depends on the availability of oxygen. NADH + CO2 C C C C • Energy released during the formation of the bonds in CO2 and H2O is greater than the energy required to break the bonds in glucose and O2. 6CO2 + 6H2O One carbon lost as CO2 Oxidative Phosphorylation Lactate/ethanol Cytosol Fermentation Outer mitochondrial membrane High [O2] While prokaryotic cells lack mitochondria, many bacteria and archaea possess a complete respiratory pathway that is similar to eukaryotes. Citric Acid Cycle H+ + H+ H H+ H+ Intermembrane compartment H+ H+ H+ H+ H+ H+ H+ cyt c e– Inner mitochondrial membrane NADH , FADH2 Complex I UQ e– Oxidative Phosphorylation Complex e– II H+ ATP NADH H+ NAD+ FADH2 H+ H+ H+ H+ ATP synthase FAD e– Complex IV e– Complex III UQ H+ H+ H+ e– H+ 2e– + 2 H+ + 1/2 O2 H2O Mitochondrial matrix ADP + P Electron transport i H+ ATP Chemiosmosis Electrons from the oxidation of NADH and FADH2 produced by glycolysis and the citric acid cycle are passed along an electron transport chain. Electron transport and chemiosmotic synthesis of ATP are coupled by a proton gradient. 130 131 Self-Test Questions These chapter-review questions are organized according to Bloom’s Taxonomy into three sections: Recall/Understand, Apply/Analyze, and Create/Evaluate. This structure allows students to review the material in a sequence that moves from the basic knowledge of factual material to more challenging and sophisticated applications of that knowledge to novel situations. Answers to the Self-Test Questions are found in the appendix at the back of the book. ▼ self - test questions Recall/Understand 1. Which of these factors is found in organic molecules that are considered good fuels? a. many C—H bonds b. many C=C double bonds c. an abundance of oxygen d. a high molecular weight 2. What is one of the places in a cell where cellular respiration occurs? a. in plant mitochondria, but not in animal mitochondria b. in plant chloroplasts c. in the mitochondria of both animals and plants d. in animal mitochondria, but not in plant mitochondria 3. Which of these processes occurs during glycolysis? a. oxidation of pyruvate b. reduction of glucose c. oxidative phosphorylation d. substrate-level phosphorylation 4. Which of these processes feeds glycolysis products into the citric acid cycle? a. chemiosmosis b. formation of G3P c. reduction of NAD+ d. pyruvate oxidation Apply/Analyze 5. The breakdown of fats releases fatty acids. In what form do the carbon molecules enter the respiratory pathway? a. as NADH b. as acetyl-CoA c. a glucose d. as pyruvate 6. You are reading this text while breathing in oxygen and breathing out carbon dioxide. Which two processes are the sources of the carbon dioxide? a. glycolysis and pyruvate oxidation b. glycolysis and oxidative phosphorylation c. pyruvate oxidation and the citric acid cycle d. the citric acid cycle and oxidative phosphorylation 7. Under conditions of low oxygen, what key role is played by fermentation in overall metabolism? a. It regenerates the NAD+ required for glycolysis. b. It synthesizes additional NADH for the citric acid cycle. c. It allows for pyruvate to be oxidized in mitochondria. d. By activating oxidative phosphorylation, it allows for the synthesis of extra ATP. 8. Suppose you are a doctor and your patient complains of feeling hot all the time, even on the coldest winter days. The young man perspires constantly and his skin is always flushed. He also eats a lot but is rather thin. You perform some laboratory tests, and find that the patient consumes lots of oxygen in his metabolic pathways. What would you suspect this patient suffers from and why? Create/Evaluate 9. In cellular respiration, which of the following does the term uncoupled refer to, specifically? a. The two parts of glycolysis are running independently of each other. b. Respiratory electron transport is operating, but chemiosmosis is inhibited. c. Respiratory electron transport is operating, but proton pumping is inhibited. d. Oxidative phosphorylation is occurring, but the protonmotive force remains high. 10. Phosphofructokinase (PFK) is regulated by a number of metabolites. In addition to those mentioned in the text, which one of the following would also make sense? a. Pyruvate could function as an activator of PFK. b. Glucose could function as an inhibitor of PFK. c. ADP could function as an activator of PFK. d. Acetyl-CoA could act as an activator of PFK. 11. Which of these statements best describes the “paradox of aerobic life”? a. Humans are completely protected from the toxic effects of oxygen. b. Hydrogen peroxide is formed when a single electron is donated to O2. c. Cytochrome oxidase is a major source of reactive oxygen species. d. Strict anaerobes often lack the enzyme(s) superoxide dismutase and/or catalase. 12. Compare direct burning of glucose and cellular respiration with reference to their progression. 13. Distinguish between reduction and oxidation during redox reactions. 14. Explain what happens with hydrogen and its bonding electrons during cellular respiration. 15. Cyanide is a strong toxin that reacts with the final protein in the electron transport chain (ETC). Explain why it can kill a human within a few minutes. Appendix A: Answers to Self-Test Questions Chapter 1 1. c 2. b 3. a 4. a 5. d 6. d 7. b 8. c 9. d 10. b 11. b 12. d 13. To determine relative dates, scientists order fossils found in different strata in sequence from the lowest (oldest) to the highest (newest) strata. This sequencing reveals their relative ages. By using a technique called radiometric dating, scientists can estimate the age of a rock by noting how much of an unstable “parent” isotope has decayed to another form. By measuring the relative amounts of the parent radioisotope and its breakdown products, and comparing this ratio with the isotope’s half-life—the time it takes for half a given amount of radioisotope to decay—researchers can estimate the absolute age of the rock. 14. LUCA stands for Last Universal Common Ancestor. We know it existed because of the core similarities that all forms of life on Earth today possess. The likeliest explanation for these common traits is all organisms today are descended from a single ancestor that also possessed all those traits. 15. Bacteria and Archaea have circular chromosomes; eukaryotes have linear chromosomes. The location of DNA in prokaryotes is in the nucleoid region, and in eukaryotes it is in the nucleus. Chromosomes segregate by binary fission in prokaryotes, and by mitosis/meiosis in eukaryotes. Introns are rarely present in bacteria, but are common in archaea and eukaryotes. Chapter 2 1. d 2. c 3. c 4. a 5. a 6. b 7. b 8. a 9. d 10. a 11. d 12. d 13. c 14. ribosomes, rough ER, transport vesicle, Golgi complex, secretory vesicle, plasma membrane 15. Anchoring junctions function to reinforce cell-to-cell connections made by adhesion molecules. Tight junctions seal the spaces between cells. Gap junctions create direct channels for communicating between adjacent cells. Chapter 3 1. c 2. d 3. b 4. a 5. b 6. c 7. c 8. d 9. c 10. d 11. As they dissolve, the sugar molecules raise their entropy. However, the crystals re-form because the water decreases in its order, changing from compact liquid to disordered vapour. 12. Although sugar breakdown is an exergonic process, the activation energy required for the reaction to proceed is high, which makes sugar unreactive. The addition of heat or an enzyme can increase the rate of breakdown. 13. Any substance in an ordered state (minimum entropy) will contain molecules with maximum free energy. On the contrary, any substance in a disordered state (maximum entropy) will contain molecules with minimum free energy. The relationship is reversed. 14. In an exergonic reaction, reactants contain more free energy than the products; energy is released and the reaction is spontaneous. In an endergonic reaction, reactants contain less free energy than the products; energy is required and the reaction is not spontaneous. 15. At any time in a cell, there must be exergonic reactions happening to provide enough energy for endergonic reactions. In addition, the energy released by exergonic reactions must be higher than the energy needed for endergonic reactions because some energy is always transferred to heat (second law of thermodynamics). Chapter 4 1. a 2. c 3. b 4. c 5. Some proteins perform transport; others have enzymatic activities; some are a part of signal transduction process; and others are involved in attachment and/or recognition. 6. b 7. c 8. b 9. c 10. c 11. b 12. a 13. d 14. Passive transport occurs down the concentration gradient of the solute, and active transport occurs against the gradient of the transported solute. Active transport therefore requires a protein and energy to perform. 15. They are both a form of passive transport, but facilitated diffusion utilizes proteins to speed up the transport of solute across the membrane. Chapter 5 1. a 2. c 3. d 4. d 5. b 6. c 7. a 8. This patient might have defective mitochondria in his cells. This condition is common in a number of diseases. The reason why it was suspected is that, based on his symptoms, probably little ATP is synthesized, in spite of high oxygen consumption, since his cells dissipated a lot of heat (the patient was hot all the time). 9. b 10. c 11. d 12. Direct burning of glucose is an uncontrolled process; cellular respiration occurs in a series of steps and is therefore a form of controlled combustion. 13. Reduction is the acceptance of electrons during a redox reaction. Oxidation is the loss of electrons during a redox reaction. 14. Hydrogen and its electrons move from sugar to oxygen, forming water. 15. The process of oxidative phosphorylation produces the large number of ATP molecules needed for the endergonic reactions in the cell that we are so dependent on. One of the major A-1 xxviii Get Complete eBook Download By email at student.support@hotmail.com 132 11140_fm_ptg01.indd 28 UNIT 1 SYSTEMS AND PROCESSES—THE CELL 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com ◀ The Chemical and Physical Foundations of Biology (The Purple Pages) While many textbooks use the first few chapters to introduce and/or review, we believe that the first chapters should convey the excitement and interest of biology itself. We therefore placed important background information about biology and chemistry in a reference section entitled The Chemical and Physical Foundations of Biology in the centre of the book. With their purple borders, these pages are distinct and easy to find and have become affectionately known as The Purple Pages. References to material covered in The Purple Pages are set in purple in the Chapter Roadmaps and in the Index. The Green Pages—Unit 5: The Diversity of Life opens with the Tree of Life, emphasizing the richness and tremendous variability among living organisms explored in the chapters of The Green Pages. With their green borders, these pages identify chapters that introduce and explore the diversity of life. ▼ Staphylococcus Actinobacteria Armatimonadetes Zixibacteria Atribacteria Cloacimonetes Aqui cae Chloro exi Fibrobacteres Calescamantes Gemmatimonadetes Caldiserica WOR-3 Dictyoglomi TA06 Thermotogae Poribacteria Deinococcus-Therm. Latescibacteria Synergistetes BRC1 Fusobacteria Marinimicrobia Bacteroidetes Ignavibacteria Caldithrix Chlorobi UNIT 5 THE DIVERSITY OF LIFE (Tenericutes) Bacteria Firmicutes Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Cyanobacteria Cyanobacteria Giovannonibacteria Wolfebacteria Jorgensenbacteria Melainabacteria RBX1 WOR1 Azambacteria PVC superphylum Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Parcubacteria Yanofskybacteria Moranbacteria Elusimicrobia Magasanikbacteria Uhrbacteria Falkowbacteria Omnitrophica Candidate Phyla Radiation SM2F11 Aminicentantes Rokubacteria NC10 Acidobacteria Tectomicrobia, Modulibacteria Nitrospinae Nitrospirae Dadabacteria Deltaprotebacteria (Thermodesulfobacteria) Chrysiogenetes Deferribacteres Hydrogenedentes NKB19 Spirochaetes Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Saccharibacteria Berkelbacteria Woesebacteria Shapirobacteria Amesbacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Dojkabacteria WS6 Gottesmanbacteria CPR1 Levybacteria CPR3 Daviesbacteria Microgenomates Katanobacteria Curtissbacteria WWE3 Wirthbacteria TM6 Epsilonproteobacteria Alphaproteobacteria Zetaproteo. Acidithiobacillia Betaproteobacteria 0.4 Major lineages with isolated representative - italics Major lineage lacking isolated representative - Gammaproteobacteria E. coli Salmonella Micrarchaeota Diapherotrites Nanohaloarchaeota Aenigmarchaeota Parvarchaeota 0.4 Eukaryotes Loki. Thor. Tree of Life Researchers at the University of California, Berkeley, recently generated a Tree of Life (opposite) comprising 3083 species, representing the major lineages of life on Earth. The tree was constructed by comparing the DNA sequences of genes that code for specific ribosomal proteins. Organisms with fewer sequence differences were grouped more closely together than species where the sequences were more dissimilar. This tree is called a starburst tree. The distant past is at the centre and the outer edge represents today. This type of representation is called an un-rooted tree because, in the centre, you will notice there is no clear starting point. The research that produced the tree was not designed to provide clarity about the origin of life or how early lineages developed—questions related to the distant past are met with tremendous uncertainty. Instead, the research team was focused on looking at the relationships among the diversity of life that exists today. And this is the focus of the chapters that make up Unit 5. Of the 3083 DNA sequences used to build the tree, over 1000 represent different microbial species that scientists have never actually studied in a laboratory! Their DNA was discovered in various environmental samples (e.g., soil, water) and is represented on the tree by red dots. Several research groups are developing methods to try and isolate and grow these microbes in the laboratory, a critical step to linking an actual organism to the DNA sequences isolated from the environment. This includes members of a specific group of archaeans called Asgard, which is represented on this tree by Loki. As discussed in Chapter 1, evidence indicates that the Asgard are the closest prokaryotic relatives of eukaryotes. You will notice that some branches of the tree are longer than others. Branch length is related to the amount of evolutionary change. Along longer branches, more sequence change has occurred than along shorter branches. For example, the branch leading to eukaryotes is particularly long, meaning there are many genetic differences between the organisms in that group compared to other organisms on the tree. To figure out exactly how much genetic change has occurred you need to use the scale bar. The 0.4 on the scale means that, for that length on any branch of the tree, there have been 0.4 changes at each nucleotide position in the RNA genes used to produce the tree. Korarch. Crenarch. Bathyarc. Pacearchaeota YNPFFA Nanoarchaeota Aigarch. Opisthokonta Woesearchaeota Altiarchaeales Halobacteria Z7ME43 Methanopyri TACK Methanococci Excavata Hadesarchaea Animals Thaumarchaeota Archaeplastida Thermococci Methanobacteria and Thermoplasmata Chromalveolata fungi Archaeoglobi Methanomicrobia Amoebozoa DPANN Archaea Plants, red and green algae xxix Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 29 495 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Student and Instructor Resources Student Resources MindTap Modern students require modern solutions. MindTap is a flexible all-in-one teaching and learning platform that includes the full ebook, a customizable learning path, and various coursespecific activities that drive student engagement and critical thinking. Download the Cengage Mobile App Get access to a full, interactive ebook, readable online or off; study tools that empower anytime, anywhere learning; and 24/7 course access. The Cengage Mobile app keeps students focused and ready to study whenever it is convenient for them. TurningPoint® Another valuable resource for instructors is TurningPoint® classroom response software customized for Biology: Exploring the Diversity of Life, Fifth Canadian Edition. Now instructors can author, deliver, show, access, and grade, all in PowerPoint, with no toggling back and forth between screens! JoinIn on TurningPoint is the only classroom response software tool that gives instructors true PowerPoint integration. With JoinIn, instructors are no longer tied to their computers. Instructors can walk about the classroom as they lecture, showing slides and collecting and displaying responses with ease. There is simply no easier or more effective way to turn a lecture hall into a personal, fully interactive experience for students. If an instructor can use PowerPoint, they can use JoinIn on TurningPoint! It contains poll slides and pre- and post-test slides for each chapter in the text. Image Library Instructor Resources This resource consists of digital copies of figures, tables, and photographs used in the book. Instructors may use these JPEGs to customize the PowerPoint slides or create their own PowerPoint presentations. The Image Library Key describes the images and lists the codes under which the JPEGs are saved. Test Bank Instructor Guide The test bank is available on a cloud-based platform. Testing Powered by Cognero® is a secure online testing system that allows instructors to author, edit, and manage test-bank content from anywhere internet access is available. No special installations or downloads are needed, and the desktop-inspired interface, with its drop-down menus and familiar, intuitive tools, allows instructors to create and manage tests with ease. Multiple test versions can be created in an instant, and content can be imported or exported into other systems. Tests can be delivered from a learning management system, the classroom, or wherever an instructor chooses. Testing Powered by Cognero for Biology: Exploring the Diversity of Life, Fifth Canadian Edition, can be accessed through http://login.cengage.com. The Instructor Guide is organized according to the textbook chapters and addresses key educational concerns, such as typical stumbling blocks student face and how to address them. PowerPoint Microsoft PowerPoint® lectures have an average of 80 slides per chapter, many featuring key figures, tables, and photographs from Biology: Exploring the Diversity of Life, Fifth Canadian Edition. Instructor notes have been incorporated throughout, making it simple for instructors to customize the deck for their courses. The PowerPoint slides also feature “build slides”— selected illustrations with labels from the book that have been reworked to allow optimal display in PowerPoint. MindTap MindTap is the digital learning solution that powers students from memorization to mastery. It gives instructors complete control of their course—to provide engaging content, challenge every individual, and build student confidence. Instructors can customize interactive syllabi to emphasize priority topics as well as add their own material or notes to the ebook as desired. This outcomedriven application gives instructors the tools needed to empower students and boost both understanding and performance. xxx Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 30 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Acknowledgments We would like to begin by expressing our gratitude for the contribution of Jonathan Ferrier. Jonathan has been an important member of this team from the very beginning, and his passion, insight, and guidance have informed and grounded our ongoing journey to a more open, “multi-science” perspective that acknowledges all Indigenous Peoples as having scientific knowledge of the natural world that enriches more Eurocentric views. We are very grateful for the quiet wisdom of Jean Becker, the patient guidance and expertise of Jeff Baker, and the warmth and insight of Erin Hodson. The three of you have been a source of inspiration, guidance, and encouragement. With great appreciation we acknowledge the contributions of Chester Lawson and Elroy White of the Haíłzaqv (Heiltsuk) Territory, Central Coast, British Columbia. Chester (Q'vúmkviá) is Yím'ás (Haíɫzaqv hereditary chief). He is a community artist and retired teacher. Chester has been creating art for over 70 years in several traditional and western art forms. Elroy (Q'íxitasu) is Yím'ás, a potlatch historian, and an archaeologist (Central Coast Archeology). We are grateful for the cultural knowledge he generously shared about seaweed harvest and processing and his work on assessing culturally modified trees (CMTs). As an archeologist, Elroy approaches his research in a way that combines academia and oral history; he calls this approach Mnuxvit (to unite/become one). We are deeply appreciative of the willingness of Elders Dan Smoke and Mary Lou Smoke, Cliff Summers, John Brown, and others to facilitate the Pipe Ceremony expressing our collective desire for a positive and productive impact of this project through strengthened relationships and respectful collaborations. We are also grateful to the members of the fifth Canadian edition Editorial Advisory Board and Student Advisory Board, who provided us with valuable feedback and alternative perspectives (special acknowledgments to these individuals are listed below). We also thank Richard Walker at the University of Calgary and Ken Davey at York University, who began this journey with us but were unable to continue. We are very grateful to Heather Addy of the University of Calgary for her significant contributions to the first three editions. The authors are all indebted to Ivona Mladenovic of Simon Fraser University for her excellent work on the Self-Test Questions and to Johnston Miller, whose extensive background research anchored our Concept Fix feature in the education literature. We are profoundly grateful to Toni Chahley, Content Development Manager, who was an insightful and reliably cheerful constant on this project. We appreciate the warm professionalism of Carmen Yu, Portfolio Manager, and Imoinda Romain, Senior Content Production Manager. We thank Christine Myaskovsky, Senior Intellectual Property Analyst, and Betsy Hathaway, Senior Intellectual Property Project Manager, for their hard work with the numerous visuals in the book and Frances Robinson for her careful and thoughtful copyediting. Finally, we thank Scott Brayne, Marketing Manager, for making us look good. Paul Fam was a warm friend and a truly fearless leader through the previous four editions of this text. The direction and emphasis of this fifth Canadian edition was sparked by his energy and enthusiasm and carries his vision forward. It is never easy to be the family of an academic scientist. We are especially grateful to our families for their sustained support over the course of our careers, particularly during those times when our attentions were fully captivated by bacteria, algae, fungi, parasites, snakes, geese, or bats. Saying “yes” to a textbook project means saying “no” to a variety of other pursuits. We appreciate the patience and understanding of those closest to us that enabled the temporary reallocation of considerable time from other endeavours and relationships. Many of our colleagues have contributed to our development as teachers and scholars by acting as mentors, collaborators, and, on occasion, “worthy opponents.” Like all teachers, we owe particular gratitude to our students. They have gathered with us around the discipline of biology, sharing their potent blend of enthusiasm and curiosity, and leaving us energized and optimistic for the future. Indigenous Advisory Board Jonathan Ferrier, Assistant Professor, Department of Biology, Dalhousie University Jeff Baker, Assistant Professor and Chair in Indigenous Education, University of Saskatchewan Jean Becker, Associate Vice-President, Indigenous Relations, University of Waterloo Erin Hodson, Educational Developer, Wilfrid Laurier University Editorial and Student Advisory Boards We were very fortunate to have the assistance of some extraordinary students and instructors of biology across Canada who provided us with feedback that helped shape this textbook into what you see before you. As such, we would like to say a very special thank you to the following people: Editorial Advisory Board Dora Cavallo-Medved, University of Windsor Emma Despland, Concordia University Heidi Engelhardt, University of Waterloo Mark Fitzpatrick, University of Toronto William Huddleston, University of Calgary Sobia Iqbal, Wilfrid Laurier University Amy Jeon, Kwantlen Polytechnic University xxxi Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 31 21/03/22 4:13 PM Get Complete eBook Download By email at student.support@hotmail.com Ivona Mladenovic, Simon Fraser University Ken Otter, University of Northern British Columbia Melissa Perrault, University of Guelph Alexandra Pettit, University of Ottawa Roy Rea, University of Northern British Columbia Ross Shaw, MacEwan University Student Advisory Boards University of Calgary Brooklyn Mattila Korbin Nunez Gurleen Randhawa Yvaine Stelmack Rayyan Zuberi xxxii Western University Catherine Andary Deepshikha Tessa Fortnum Muhammad Hussain Jan Helen Jiang Edward Liu Maryam Oloriegbe Sofia Varon Jonathan Wei Michelle Yu ACKNOWLEDGMENTS Get Complete eBook Download By email at student.support@hotmail.com 11140_fm_ptg01.indd 32 21/03/22 4:13 PM Lebendkulturen.de/Shutterstock.com BIOLOGY OF THE CELL Volvox is a genus of green algae. As a photosynthetic eukaryote, Volvox is a simple multicellular organism that exists as spheres of two distinct cell types. Small non-reproductive cells surround an interior that contains six to eight much larger reproductive cells. VOLUME 1 Get Complete eBook Download By email at student.support@hotmail.com What is life? We can make a list of the characteristics of living things, but why is it difficult to simply define life? In the introductory chapter of this opening volume, we tackle this question before exploring hypotheses around how life evolved some 4 billion years ago. Today, Earth is teaming with life; some estimates peg the total number of species at over 1 billion (with most yet to be described!). Yet, what this volume of the textbook should covey to you is that underlying that diversity is a remarkable level of similarity. From monkeys to mycoplasma to monocots, everything that is alive on Earth employs a variation on that remarkable innovation: the cell. No matter whether that cell is communicating with other cells in the brain of a fruit fly, or capturing sunlight in a spruce needle, or driving the muscles of a sprinting cheetah, or thriving in the mineralrich water of deep-sea vents; no matter what their role or activity, all cells share a remarkably long list of common features. Volume 1 explores these common features in detail. Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 1 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com The invention of the microscope allowed scientists to finally understand how living organisms were built from cells, which to early scientists were astonishingly small. Further work clearly delineated two major divisions in cell types: those without a nucleus (prokaryotic) and those with a nucleus (eukaryotic). And within both these groups there are clear subdivisions: for example, plants, fungi, and animal cells, in eukaryotes. The chapters of Unit 1 talk a lot about energy because without it living cells would die. Like the non-living world, all forms of life abide by the foundational laws of thermodynamics and need to bring in energy and matter from the environment to maintain their highly ordered state. In part, energy is required to build complex things (e.g., proteins) out of simpler things (e.g., amino acids). In addition to energy, the evolution of life is tied to the development of a remarkable group of proteins called enzymes, which when they get tied to a biochemical reaction can increase its rate by 1010 times! Another remarkable feature of cells that we dedicate a chapter to in Unit 1 is membranes. These self-forming lipid bilayers act as the gatekeepers of the cell: they allow certain things in but keep other things out. How they do this is by acting in concert with membrane-specific proteins that shuttle molecules from one side to another. Membrane proteins also play a remarkable role in transducing signals from outside the cells and compartments to the inside. As we will see, the transduction of signals associated with hormones, for example, can profoundly affect cell function. What you may not realize is that virtually all the energy used by living systems comes ultimately from sunlight being harvested and converted into a useable chemical form through photosynthesis. This process evolved perhaps as early as 3.5 billion years ago and used photons of light energy to extract electrons from water, releasing oxygen as a by-product. The rise in oxygen in an atmosphere that previously had none led to an explosion of life as the mechanism of cellular respiration evolved that could use that oxygen and enabled cells to produce huge amounts of energy. The chapters of Units 2 and 3 are dedicated to molecular biology and genetics, the central player being the gene. All cells possess genes that are coded by the molecule DNA that, 2 V O LU M E 1 through the process of transcription, get copied into RNA. All cells contain ribosomes where some kinds of RNAs get translated into proteins, the fundamental structural, functional, and regulatory molecule of the cell. Genes are stretches of DNA sequence in an organism that collectively comprise a kind of library of information about how a cell functions. Recent advances in technology have made it relatively easy to determine the entire DNA sequence of an organism, including individual humans. As a result, modern biology is awash in the As, Ts, Gs, and Cs of DNA sequences revealed by thousands of sequencing projects. New insights into evolutionary history as well as gene structure and function are arising from bioinformatic analysis of such extensive data sets. The elegant double-strandedness of DNA, whereby two long strands of nucleotides are held together by hydrogen bonds formed between complementary base pairs, affords a straightforward mechanism for replication that was recognized early on by Watson and Crick. Although conceptually simple, the mechanism for unwinding the DNA double helix and polymerizing new complementary bases is rather complicated and managed by a suite of interacting enzymes. Again, we see that all DNA on the planet is replicated using variations on one underlying strategy. DNA genes provide the cell with needed RNA by transcription. One remarkable feature of all protein-coding genes is that, with minor exceptions, the information they carry is specified by a universal code. That is, a gene from one organism can be “understood” by any other organism, even if only distantly related: a gene from a spider can be expressed by a goat; a gene from a jellyfish can be expressed in a flower. The field of genetic engineering is devoted to developing the tools and applications of this technology for moving genes from one organism to another. In a story that is about to come full circle, synthetic biologists have extensively customized naturally occurring cells and have made important advances toward their ultimate goal of creating novel life forms artificially in the lab. As students of biology in the early 21st century, you can well expect to witness a momentous event in Earth’s history, the creation of one life form by another. B I O LO G Y O F T H E C E L L Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 2 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 3 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Chapter Roadmap Defining Life and Its Origins What is life, and what do we know about how it may have begun about 4 billion years ago? 1.1 1.2 What Is Life? The Chemical Origins of Life Biology is the study of life, but a simple definition of life is not easy to come up with. The conditions on early Earth allowed for the synthesis of key molecules essential for life. The Purple Pages provides an overview of the key molecules of life. 1.3 The Evolution of Information Flow: DNA, RNA, Protein RNA was likely the first of these three molecules to evolve. It could carry information and act as a catalyst. 1.4 The Development of Metabolism and the First Cells Life may have evolved in alkaline hydrothermal vents, an environment with a constant source of geothermal energy and mineral catalysts. The chapters of Unit 3 introduce major concepts related to DNA and gene expression. Chapter 4 provides more details on energy and metabolism. 1.5 The Tree of Life Recent research indicates that there are two primary domains of life: Bacteria and Archaea. Eukaryotes evolved from a lineage of Archaea. In Chapter 19, we discuss the tree of life and the discipline of phylogenetics in more detail. 1.6 Eukaryotes and the Rise of Multicellularity 1.7 The Fossil Record Much of our understanding of the history of life comes from the fossil record. However, the fossil record has a lot of gaps and does not provide a record of the earliest forms of life. Eukaryotic cells have structural and functional complexity not found in prokaryotic cells. In addition to the nucleus, this includes mitochondria and chloroplasts that are descended from bacteria. In Chapter 2, we provide an overview of both prokaryotic and eukaryotic cells. Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 4 20/03/22 12:27 PM Triff/Shutterstock.com Get Complete eBook Download By email at student.support@hotmail.com Perseverance landed on Mars on February 18, 2021, to search for signs of life. Defining Life and Its Origins Why it matters… Finding evidence of life somewhere else would be the most profound dis- covery in human history. On February 18, 2021, the NASA rover Perseverance landed on Mars and, along with characterizing the Martian climate and geology, it is looking for signs of life. The landing site of Perseverance is the 45-kilometre–wide Jezero Crater that a few billion years ago was the site of a large lake. As the rover slowly roams over the Jezero lakebed, it employs an instrument with the acronym SHERLOC that uses laser light to detect within the sediments the presence of organic molecules that, on Earth, we know are produced through biological activity. Detailed analysis of samples that Perseverance collects will have to wait until they are sent back to Earth as part of a later mission. A hope of many astrobiologists is that Perseverance comes across a surface feature that can’t be attributed to anything other than ancient microbial life. On Earth, a good example of that is stromatolites, which are sediment formations generated by the action of photosynthetic bacteria. But therein lies one of the problems with searching for life elsewhere: we only know about life on Earth, and maybe life on other planets is very different. And then, of course, what is life anyway? It is actually really hard to come up with even a simple definition. While we continue to search for life elsewhere, our understanding of life and how it may have developed is limited to understanding how life may have developed on Earth. The events we are going to discuss in this chapter may seem improbable: the synthesis of organic molecules; the development of the first cells; the evolution of DNA, RNA, and proteins; the building of metabolic pathways; and all the way to the evolution of multicellular eukaryotes. Improbable? Perhaps. But we must keep in mind that these events took place over hundreds of millions of years. As scientist and author George Wald of Harvard University put it, given so much time, “the impossible becomes possible, the possible probable, and the probable virtually certain.” 1 5 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 5 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com 1.1 What Is Life? Picture a frog sitting in a pond, slowly shifting its head to follow the movements of an insect flying nearby (Figure 1.1). Most of us instinctively know that the frog is alive and the water is not. Or is water alive? The atoms found in living and non-living entities are the same. The oxygen and hydrogen atoms, for example, aren’t any different within cells than they are in a pool of water or a rock. As well, living cells may be extraordinary things but they abide by the same fundamental laws of chemistry and physics as the abiotic (non-living) world. Before we embark on a discussion of how life may have developed billions of years ago and the characteristics that early forms of life must have possessed it would be helpful if we had a clear notion of what distinguishes something that is living from something that is not living. 1.1a Why It’s Hard to Define Life Alexander Sviridov/Shutterstock.com Biology is the study of life, and the purpose of Biology: Exploring the Diversity of Life is to provide you with an introduction to many aspects of living things: from the unique features of biological molecules, reaching outward to cells, organisms, and the interconnectedness that defines ecosystems. It may surprise you that, while we can describe in considerable detail the features that one organism has compared to another, and certainly we can think about the things that living things can do that non-living things can’t do, we struggle to come up with a clear definition of what life actually is. Doesn’t that seem a little odd? If you think about the other core disciplines often taught in first year, chemistry and physics, most of the concepts in those disciplines are pretty easy to define, even if they may not necessarily be easy to learn. A major hurdle in coming up with a definition for life is the pursuit of something that is universal. Ideally, the definition of life should be acceptable to scientists and non-scientists alike, and be useful and applicable across disciplines. As you will see, the way a discipline defines life is intimately connected to the questions that it explores. Let’s consider at three disciplines FIGURE 1.1 Northern leopard frog resting in a pond 6 CHAPTER 1 where defining life seems to be of fundamental importance. First, let’s think about evolutionary biology, the study of how life on Earth changes over time through processes such as natural selection and speciation. Second, there is the growing science of astrobiology, which considers questions related to the possibility of life beyond Earth and the factors necessary to support life on other planets. Any definition of life that we can come up with would need to apply to entities we may discover (or meet) on other worlds. Third, there is the field of artificial life, which uses computer simulations, robotics, and synthetic biochemistry to simulate many of the attributes of life. As shown in Figure 1.2, part of the problem with defining life is that each of these groups of researchers approach life from a slightly different perspective, and what one group thinks is an essential aspect of life, another group may not. One of the first people to take a crack at defining life was Aristotle, who mentioned that it is something that “grows, is selfsustaining and reproduces.” This seems like a pretty solid start; the ability to make more of itself seems a central feature of all forms of life. Another central feature seems to be the cell. Peering into the primitive light microscopes in the 17th century, it soon became obvious that all living things were formed of cells. As we will discuss in detail in the next chapter, this became part of cell theory: The cell was defined as the smallest unit of life and new cells were derived only when old cells divided. So, for a long time, if we couldn’t strictly define life, at least everyone could agree on one universally accepted characteristic: the cell. We will see later in this section how the discovery of viruses has muddled this cell-centric view of life. An entity is alive for evolutionary biologists only if it has properties A, B, and C. An entity is alive for astrobiologists only if it has properties B, D, and F. An entity is alive for artificial-life researchers only if it has properties A, D, and E. FIGURE 1.2 One of the issues with defining life is that, depending upon the branch of biology where it is important, the properties of life don’t completely match. For example, does life have to be composed of cells, evolve, contain DNA, undergo metabolism, reproduce? Some of these properties are important to some researchers and not important to others. We have yet to arrive at a definition of life that is universally accepted. DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 6 20/03/22 12:27 PM 1.1b Viruses Complicate Our Idea of Life Whether or not viruses should be considered life has been an argument that goes back to when they were first visualized early in the 20th century, after the advent of the electron microscope. Viruses, which we will discuss in detail in Chapter 25, don’t have their own metabolism; they don’t respire or carry out photosynthesis. But, like traditional forms of cellular life, they do contain nucleic acid and replicate, and they can evolve rapidly by natural selection. But they can’t complete their lifecycle without invading living cells, whether that be a bacterium or a human (Figure 1.3). Taking up residence within living cells is required for a virus because it does not have its own protein-making factories—ribosomes and key enzymes required for it to replicate. Because of this last fact, many put viruses clearly in the “not life” camp. But if viruses are not considered life because they are parasitic, what about Rickettsia? This bacterium is considered to be alive despite its inability to live outside a host cell. Things became more complicated on the virus front in 1992 with the discovery of a virus initially thought to be a bacterium. Named mimivirus for “mimicking microbe,” no one had ever observed a virus that was so large you could visualize it using conventional light microscopy. Its genome, at 1.2 million base pairs, far exceeds the size of any other known virus Image courtesy of John Wertz, Yale University Get Complete eBook Download By email at student.support@hotmail.com In 1992, the NASA exobiology advisory board put forward a working definition of life as being “a self-sustaining system capable of Darwinian evolution.” As we will see in Chapter 16, “Darwinian evolution” means the system can undergo the process of natural selection. While this definition was not formally adopted by NASA, it did help to define what types of chemistry would constitute life on another planet. The problem with the NASA definition is that there are many exceptions to it. There are many clearly living entities that are unable to reproduce. Think of a mule, which is the sterile hybrid offspring of a horse and a donkey. There are also entities that science deems “non-living” that possess qualities of life such as reproduction, evolution, or something else. For example, fire can certainly make more of itself (reproduce) and it can grow and consume matter. For decades, it has been known that mineral crystals can grow and maintain a highly ordered structure not unlike an organism. It was the physicist Erwin Schrödinger in 1945 who saw the maintenance of order as one key defining property of life. As we will see in Chapter 3, maintaining order (or low entropy) is a central reason for why life undergoes energy-requiring metabolism. Yet, within the past few years, researchers have shown that energy from light can be used to drive lifelike, selforganizing behaviours (think schooling fish or flocking birds) in particles. Published in the prestigious journal Science, the authors made reference to these as “living crystals.” As well, many computer viruses can reproduce and change over time (e.g., evolve), which, as we will see, are two key attribues. FIGURE 1.3 Bacteriophage infecting a bacterium. Notice the bacteriophages on the cell surface as well as inside the bacterium. A bacteriophage is a type of virus, and most scientists do not consider viruses to be alive. and is larger than many bacteria. Its genome has been predicted to encode over 900 proteins, many of them associated with functions never before seen in a virus. This includes proteins central to protein synthesis and metabolism, two hallmarks of life. However, like other viruses, mimivirus is still dependent upon host cell ribosome for protein synthesis. Clearly, if mimivirus is not allowed to be a member of the life “club,” it stands right outside the door. 1.1c Seven Characteristics Shared by All Cellular Life Forms From the above discussion it is pretty clear that we don’t have a universally accepted definition of life. In fact, a growing number of researchers reject the need for a common definition. Many want a “theory of living systems” that can fully describe life (its origins and characteristics) without forcing a strict definition. Others argue that, since we are constantly discovering new species and have yet to detect evidence of life on another planet, trying to strictly define it is silly because we simply don’t understand enough about it. For now, we need to make a compromise. While we can use the word entity to include a wide range of self-replicating and evolving systems, we are going to reserve the word organism for forms of life that are made of cells. It is cellular life that is going to hold our attention through the next 44 chapters of this textbook. Without a strict definition of life, organisms on Earth all possess a key list of attributes. As detailed in Figure 1.4, all life displays order, harnesses and utilizes energy, reproduces, responds to stimuli, exhibits homeostasis, grows and develops, and evolves. STUDY BREAK QUESTIONS 1. Why is it difficult to arrive at a definition for life? 2. Why is a virus often considered not to be alive? CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 7 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 7 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com SCIMAT/Science Source f. Grow and develop g. Evolve Stanislav Duben/Shutterstock.com Uwe Krejci/Stone/Getty Images Dr. Jeremy Burgess/Science Source e. Exhibit homeostasis Karin Duthie/Alamy Stock Photo d. Respond to stimuli c. Reproduce Steve Byland/Shutterstock.com b. Harness and utilize energy harmeet/StockXchng a. Display order FIGURE 1.4 Although it is hard to strictly define life, all cellular forms of life on Earth display these seven characteristics. (a) Display order. All forms of life, including this flower, are arranged in a highly ordered manner, with the cell being the fundamental unit that exhibits all properties of life. (b) Harness and utilize energy. Like this hummingbird, all forms of life acquire energy from the environment and use it to maintain their highly ordered state. (c) Reproduce. All organisms have the ability to make more of their own kind. Here, some of the bacteria have just divided into two daughter cells. (d) Respond to stimuli. Organisms can make adjustments to their structure, function, and behaviour in response to changes to the external environment. A plant can adjust the size of the pores (stomata) on the surface of its leaves to regulate gas exchange. (e) Exhibit homeostasis. Organisms are able to regulate their internal environment such that conditions remain relatively constant. Sweating is one way in which the human body attempts to remove heat and thereby maintain a constant temperature. (f) Grow and develop. All organisms increase their size and/or number of cells. Many organisms also change over time. (g) Evolve. Populations of living organisms change over the course of generations to become better adapted to their environment. The snowy owl illustrates this perfectly. 1.2 The Chemical Origins of Life One of the tenets of cell theory states that cells arise only from the growth and division of preexisting cells. This tenet, which we will discuss in detail in the next chapter, has probably been true for a few billion years, yet there must have been a time when this was not the case. There must have been a time when no cells existed, when there was no life. It is thought that, over the course of millions of years, cells with the characteristics of Oxygen produced by photosynthetic bacteria January 1 Earth forms Earliest life First eukaryotes January February March April Ma y First animals Jun e July Aug ust Septemb er FIGURE 1.5 The history of Earth condensed into one year 8 CHAPTER 1 life arose out of a mixture of molecules that existed on early Earth. In this section, we present hypotheses for how biologically important molecules could have been synthesized on early Earth in the absence of life. 1.2a Earth Is 4 600 000 000 Years Old Earth was formed about 4.6 billion years ago, at the same time as the rest of the planets in the solar system. The age of our planet has been arrived at using the technique of radiometric dating, which looks at specific isotopic ratios in rocks and knowledge of their rate of decay. December 31, The decay of uranium to lead, in 11:43 p.m. particular, has been used to age Modern Earth. To give us some sense of humans just how long 4.6 billion years is, appear Earliest as well as the relative timing of land some major events in the hisplants tory of life on Earth, Figure 1.5 condenses the entire history of Earth into a unit of time that we er b are more familiar with: 1 year. em Dec r With 4.6 billion years cone b m Nove densed into a single year, each October day represents an interval of 12.6 million years! DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 8 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Using our condensed version of the history of Earth, we set the date of the formation of Earth as January 1 at 12:00 a.m. We will discuss this in detail later but, based on chemical evidence, life may have started as early as 4 billion years ago. This translates to mid-March in our one-year calendar. The first clear fossil evidence of prokaryotic cells occurs in late March, or about 3.5 billion years ago. Fossil evidence of eukaryotes has been dated to about 2 billion years ago, which is not until early July using our 1-year analogy. Perhaps surprisingly, animals do not make an appearance until mid-October (about 525 million years ago) and land plants until the following month. The extinction of dinosaurs, which was completed by about 65 million years ago, does not occur until late December. What about humans? We may think humans, Homo sapiens, have been around a long time but, relative to other forms of life, the roughly 150 000 years that modern humans have existed is a very short period of time—a blip on our time scale. Using our year analogy, modern humans have existed only since December 31; more precisely, since December 31 at 11:43 p.m.! 1.2b Biologically Important Molecules Can Be Synthesized outside Living Cells In comparison to the proposed reducing atmosphere of early Earth, today’s atmosphere is classified as an oxidizing atmosphere. The presence of high levels of oxygen prevents complex, electron-rich molecules from being formed because oxygen is a particularly strong oxidizing molecule and would itself accept the electrons from organic molecules and be reduced to water. Apart from allowing for the buildup of electron-rich molecules, the lack of oxygen in the young atmosphere also meant that there was no ozone (O3) layer, which only developed after oxygen levels in the atmosphere began to increase. Both Oparin and Haldane hypothesized that, without the ozone layer, energetic ultraviolet light was able to reach the lower atmosphere and, along with abundant lightning, provided the energy needed to drive the formation of biologically important molecules. Experimental evidence in support of the Oparin–Haldane hypothesis came in 1953, when Stanley Miller, a graduate student in the lab of Harold Urey at the University of Chicago, created a laboratory simulation of a reducing atmosphere. Miller mixed the gasses hydrogen, methane, and ammonia in a closed apparatus and exposed the gases to an energy source in the form of continuously sparking electrodes (Figure 1.6). Water vapour was added to the “atmosphere” in one part of the apparatus and subsequently condensed back into water by cooling in another part. After running the experiment for one week, Miller found a large assortment of organic compounds, including urea; amino acids; and lactic, formic, and acetic acids in the condensed water. In fact, as much as 15% of the carbon that was originally in the methane at the start of the experiment ended up in molecules that are common in living organisms. All organisms are composed of four classes of essential macromolecules: nucleic acids, proteins, lipids, and polysaccharides (see The Purple Pages for an overview of these molecules). These molecules are constantly being synthesized within cells by various biochemical pathways and metabolic processes. If at least some of these molecules are an absolute requirement for life, then simple forms of them must have come before the first cells; they must have been produced in the absence of life, what is referred to as abiotic synthesis. When the earliest forms of life developed about ∼4.5 billion years ago 4 billion years ago, Earth was vastly different from Electrodes what it is today. The atmosphere probably conSpark tained an abundance of water vapour from the Simulated early discharge Earth’s atmosphere evaporation of water at the hot surface, as well as Inorganic molecules large quantities of hydrogen (H2), carbon dioxide CH4 simulating NH3 (CO2), ammonia (NH3), and methane (CH4). You early Earth’s Gases H 2O might be surprised to know there was an almost atmosphere H2 complete absence of oxygen (O2) in the early atmoWater out sphere. In the 1920s, two scientists, Aleksandr Condenser Oparin and John Haldane, independently proposed Boiling water to produce Water in that organic molecules, essential to the formation of water vapour, and using a Water life, could have formed in the atmosphere of early condenser to form water droplets droplets, simulates the Earth. A critical aspect of what is known as the Water containing water cycle on early Earth. Oparin–Haldane hypothesis is that the early atmoorganic compounds sphere was a reducing atmosphere because of the Liquid water in trap presence of large concentrations of molecules such Boiling water as hydrogen, methane, and ammonia. These moleFIGURE 1.6 The Miller–Urey experiment. Using this apparatus, Stanley Miller, a cules possess chemical bonds that allow them to graduate student, demonstrated that organic molecules can be synthesized under enter into reactions with one another that would conditions simulating primordial Earth. Source: Based on S. L. Miller, 1955 yield larger and more complex organic molecules. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 9 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 9 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Andrew Swift Other chemicals have been tested in the Miller–Urey apparatus, including hydrogen cyanide (HCN) and formaldehyde (CH 2O), which are also considered to have been among the substances formed in the primitive atmosphere. Microscopic When cyanide and formaldehyde were added to layers of clay the simulated atmosphere in the apparatus, all the building blocks of complex biological molecules were produced: amino acids; fatty acids; the purine and pyrimidine components of nucleic acids; sugars such as glyceraldehyde, ribose, glucose, and fructose; and phospholipids, which form the lipid bilayers of biological membranes. In the decades since the first Miller–Urey Nucleotides undergoing experiment, considerable debate has developed in polymerization the scientific community over whether Earth’s atmosphere held enough methane and ammonia FIGURE 1.7 Clay surfaces catalyze polymerization. The charged, microscopic, for it to be considered a reducing atmosphere. layered structure of clay allows for the formation of relatively short polymers of proteins Some geologists have suggested that, based on and nucleic acids. analysis of volcanic activity, primitive Earth contained other gases that made it probably someA working hypothesis to address this question needs to be what less reactive. And as we will see that, later in this built from the notion that the very earliest forms of life must chapter, many scientists have looked to the oceans as the have been very simple, far simpler than a modern bacterium, most likely place where abiotic synthesis took place and life for example. Scientists hypothesize that a polymer that conmost likely started. Regardless of these lingering debates, sists of even 10 to 50 monomers may have been of sufficient the significance of the Miller–Urey experiment cannot be length to impart a specific function (like a protein) or store overstated. It was the first experiment to demonstrate the sufficient information (like a nucleic acid) to make their forabiotic formation of molecules critical to life, such as amino mation advantageous to an organism. It is, however, doubtful acids, nucleotides, and simple sugars, and it showed that that polymerization could have occurred in the aqueous envithey could be produced relatively easily. This remarkable ronment of early Earth, as it would be very rare for monofinding laid the groundwork for further research into the mers to interact precisely enough with one another to origins of life. polymerize. It is more likely that solid surfaces, especially clays, could have provided the type of environment necessary 1.2c Life Requires Polymers for polymerization to occur (Figure 1.7). Clays consist of very Primordial Earth contained very little oxygen and, because of thin layers of minerals separated by layers of water only a few this, complex organic molecules could have existed for much nanometres thick. The layered structure of clay is also longer than would be possible in today’s oxidizing world. Even if charged, allowing for molecular adhesion forces to bring they did accumulate on early Earth, molecules such as amino monomers together in precise orientations that could more acids and nucleotides are monomers, which are simpler and readily lead to polymer formation. Clays can also store the easier to synthesize than the key chemical components of life, potential energy that may have been used for energy-requiring such as nucleic acids and proteins, which are polymers—macropolymerization reactions. This clay hypothesis is supported molecules formed from the bonding together of individual by laboratory experiments that demonstrate that the formamonomers. Nucleic acids are polymers of nucleotides, proteins tion of short nucleic acid chains and polypeptides can be synare polymers of amino acids, and polysaccharides (starch, celthesized on a clay surface. lulose) are polymers of simple sugars. Polymers are synthesized by dehydration synthesis, which is discussed in The Purple Pages. STUDY BREAK QUESTIONS Today, the synthesis of proteins and nucleic acids requires 1. For understanding the origins of life, what was the significance protein-based catalysts called enzymes and results in macroof the Miller–Urey experiment? molecules that often consist of hundreds to many thousands 2. What is the difference between a reducing atmosphere and an of monomers linked together. So, how do you make the polyoxidizing atmosphere? mers that are required for life without sophisticated enzymes? 10 CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 10 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com 1.3 The Evolution of Information Flow: RNA, DNA, Protein DNA RNA Protein In the previous section, we discussed how processes present on early Earth could have generated macromolecules crucial to the development of life. However, if we are to develop a comprehensive model for the origin of life, we need to explain the evolution of three key properties of a cell that go well beyond the synthesis of macromolecules. First, a mechanism to store information that can be replicated and passed on to daughter cells must have developed. Second, Information is The information The information in energy-transforming chemical reactions stored in DNA. in DNA is copied RNA guides the into RNA. production of proteins. must have evolved that would have enabled primitive cells to capture energy from their FIGURE 1.8 The central dogma. Information in DNA is used to synthesize proteins through an surroundings and use it to do work. Third, RNA intermediate. How did such a system evolve when the product, proteins, is required in these processes would need to take place modern-day cells to catalyze each step? within defined compartments (e.g., cells) that are distinct and separate from the our understanding of how such a system may have evolved environment. came in the early 1980s when Thomas Cech and Sidney Altman, In this section, we discuss the first of these: the developworking independently, discovered a group of RNA molecules ment of a genetics system that would allow the passing of inforthat could themselves act as catalysts. This group of RNA catamation to new cells following cell division. lysts, called ribozymes, are found in all types of cells. They are not as common as enzymes, but they carry out critical reactions related to the control of gene expression. One type of ribo1.3a RNA Can Carry Information zyme, for example, catalyzes the removal of introns from newly and Catalyze Reactions synthesized RNA molecules; other ribozymes can cleave speAs we will discuss in detail in Chapter 11, DNA (deoxyribose cific messenger RNA (mRNA) molecules, causing their degranucleic acid) is the molecule that provides every cell with the dation. The precise catalytic property of a ribozyme is instructions necessary to function. The information contained determined by its shape, which is based on the hydrogen in a sequence of nucleotides in DNA, called a gene, is copied bonding between specific nucleotides of the RNA molecule. into a unique molecule of RNA. Some of these RNA molecules The link between nucleotide sequence, shape, and thus funcprovide information for the synthesis of specific proteins. Even tion is analogous to an enzyme. The specific reaction catalyzed the simplest bacterium today contains thousands of genes, RNA by an enzyme is dependent on its precise three-dimensional molecules, and proteins. The flow of information from DNA to shape, which is the result of its unique amino acid sequence. All RNA to protein is common to all forms of life and is referred to ribozymes recognize their target by specific base pairing as the central dogma (Figure 1.8). Each step of the information between the ribozyme nucleotide sequence and the nucleotide flow requires the involvement of enzymes that catalyze the sequence of the target molecule (Figure 1.9). transcription of DNA into Ribozyme RNA, and the translation of the RNA into protein. A fundamental question about the flow of information from DNA to RNA to protein is How did such a system evolve when the final prodMessenger RNA Ribozyme-mediated cut Cut (cleaved) messenger introduced into RNA message RNA molecules ucts, proteins, are required to catalyze each step (e.g., tran- FIGURE 1.9 Ribozyme. An example of a ribozyme binding to an RNA molecule and catalyzing its breakage. Within scription, translation) of the a modern-day cell, such reactions help control gene expression by altering the abundance of functional messenger process? A breakthrough in RNA (mRNA) molecules. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 11 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 11 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com The discovery of ribozymes revolutionized our thinking about the origin of life. Instead of the contemporary system that requires all three molecules—DNA, RNA, and protein— early life may have existed in an “RNA world.” RNA could have served both as a carrier of information, by virtue of its nucleotide sequence, and as a structural/catalytic molecule due to its ability to fold on itself and form unique threedimensional shapes. Before the discovery of ribozymes, enzymes were the only known biological catalysts. For their remarkable discovery of RNA catalysts, Sidney Altman and Thomas Cech shared the Nobel Prize in Chemistry in 1989. 1.3b RNA Is Replaced by DNA for Information Storage and Proteins for Catalysis If life developed in an environment where RNA served as both an information carrier and a catalyst, why is it that, in all modern organisms, genetic information is stored in DNA, and why do a class of proteins (e.g., enzymes) catalyze the vast majority of biological reactions? The simple answer is that they do the respective jobs of information storage (DNA) and catalysis (protein) far better than RNA does by itself. The evolution of these other molecules would have given organisms that developed them a distinct advantage over others that relied solely on RNA. A possible scenario for the development of today’s system of information transfer is shown in Figure 1.10. The first cells may have contained only RNA, which could make copies of itself (self-replicating) and could catalyze a small number of reactions critical for survival. It is hypothesized that a small population of RNA molecules then evolved that could catalyze the formation of very short proteins before the development of ribosomes. Recall that, in modern cells, the ribosome is the site RNA of protein synthesis: it binds mRNA molecules and uses the information in the nucleotide sequence to generate a protein built from a pool of amino acids. It is interesting to note that the catalytic component of the ribosome that joins individual amino acids is itself an RNA molecule. So, in fact, the ribosome is a type of ribozyme. Cells that evolved the ability to use the information present in RNA to direct the synthesis of even small proteins would be at a tremendous advantage because proteins are far more versatile than RNA molecules for three reasons. First, the catalytic power of most enzymes is much greater than that of a ribozyme. A typical enzyme can catalyze the same reaction using a pool of substrate molecules many thousands of times a second. By comparison, the rate of catalysis of most ribozymes is one-tenth to one-hundredth that of enzymes. Second, while the number of ribozymes is very small, a typical cell synthesizes a huge array of different proteins. Twenty different kinds of amino acids, in different arrangements, can be incorporated into a protein, whereas an RNA molecule is composed of different combinations of only four nucleotides. Third, amino acids can interact chemically with each other in more complex and varied bonding arrangements not possible between nucleotides. For these reasons, proteins are the dominant structural and functional molecule of a modern cell. Continuing with the possible scenario shown in Figure 1.10, the evolution of DNA would have followed that of proteins. Compared with RNA, molecules of DNA are more structurally complex. Not only is DNA double stranded, but it also contains the sugar deoxyribose, which is more difficult to synthesize than the ribose found in molecules of RNA. A possible sequence begins with DNA nucleotides being produced by random removal of an oxygen atom from the ribose subunits of RNA nucleotides. At some point, the DNA nucleotides paired with the RNA informational molecules and were assembled into complementary copies of the RNA sequences. Some modernday viruses carry out this RNA-to-DNA reaction using enzyme reverse transcriptase (see Chapter 25). Once the DNA copies were made, selection may have favoured DNA, as it is a much better way to store information than RNA, for three main reasons: ● RNA Protein ● ● DNA RNA Protein FIGURE 1.10 Possible scenario for the evolution of the flow of information from DNA to RNA to protein 12 CHAPTER 1 ● Each strand of DNA is chemically more stable, and less likely to degrade, than a strand of RNA. The base uracil found in RNA is not found in DNA; it has been replaced by thymine. This may be because the conversion of cytosine to uracil is a common mutation in DNA. By utilizing thymine in DNA, any uracil is easily recognized as a damaged cytosine that needs to be repaired. DNA is double stranded, so in the case of a mutation to one of the strands, the information contained on the complementary strand can be used to correctly repair the damaged strand. The stability of DNA is illustrated by the fact that intact DNA can be successfully extracted from tissues that are many DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 12 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com thousands of years old. The well-known novel and movie Jurassic Park are based on this demonstrated ability. By comparison, RNA needs to be isolated quickly, even from freshly isolated cells, using a strict protocol to prevent its degradation. STUDY BREAK QUESTIONS 1. In what ways are ribozymes similar and different from enzymes? 2. RNA may have been the first information-carrying molecule, but it was replaced by DNA. Why? 1.4. The Development of Metabolism and the First Cells One of the seven characteristics of life as outlined in Figure 1.4 is the ability to harness and utilize energy. All life can bring in energy from its surroundings and use it to transform simple molecules into a range of complex compounds and structures that make up cells. To do this required the evolution of ordered chemical reactions and, while these must have started out very simple, they evolved into interlocked networks of metabolism that increased in sophistication over time. While simple chemical reactions important to life could have developed outside cells, even basic metabolic pathways would have had to be restricted to compartments (e.g., cells) where concentrations of molecules and conditions could be distinct from the external environment. While there remain a lot more questions than answers about how this all came about, what has been found is a habitat with a unique combination of characteristics that could have nurtured the earliest forms of life. Acidic ocean water H2S Fe2+ FeS Alkaline vent water Ni CO2 1.4a Alkaline Hydrothermal Vents May Have Led to the First Cells Over the past few decades, many scientists testing hypotheses related to the origin of life have come to agree that complex molecules necessary for life as well as life itself may have originated on the ocean floor at the sites of hydrothermal vents. These cracks are found around the globe near sites of volcanic or tectonic activity. Most hydrothermal vents release superheated, nutrient-rich water at temperatures in excess of 3008C. It’s because of these high temperatures that hydrothermal vents were largely dismissed as the site of where early life developed. More recently, however, researchers have discovered a different type of vent called an alkaline hydrothermal vent. Not only do these release water that is much cooler (1008C–1508C), the water is strongly alkaline (pH 9–11) and rich in a range of molecules, including H2, H2S, and NH3 (Figure 1.11). Chemical reactions that take place where the vent water encounters ocean water cause calcium carbonate to precipitate out of the water, forming chimneys that are honeycombed with microscopic pores that the water percolates through. Within these porous chimneys, the two different chemical environments of the vent water and the ocean water encounter each other. Because a fresh supply of alkaline water is constantly released from the vent, the interface between vent water and ocean water never reaches thermodynamic equilibrium, which, as we will see in Chapter 3, is a key feature of life. H2, H2S, NH3 100°C, pH 9–11 FIGURE 1.11 Alkaline hydrothermal vent. When water is released from a vent in the ocean floor and encounters ocean water, calcium carbonate precipitates out of the water, forming chimneys. The vent water is alkaline and carries hydrogen, hydrogen sulfide, and ammonia to the surface. The surrounding ocean water is cool and contains CO2 and a wide range of trace metals. Reactions among these various molecules could have produced the first metabolic reactions within cells. 1.4b Evolution of Metabolism To think about how life started, it’s helpful to consider the fundamentals of metabolism that we find in organisms today. The foundation of the biosphere includes microbes and plants that synthesize organic compounds (e.g., carbohydrates) by combining hydrogen (H2) with carbon dioxide (CO2) like this: 2H2 1 CO2 (CH2O)n 1 H2O where (CH2O)n is the general formula for a sugar. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 13 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 13 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com The most common process that drives this reaction today is photosynthesis, which uses light energy to extract hydrogen atoms and electrons from molecules of water and use them to convert carbon dioxide into organic compounds (carbon fixation). Because photosynthesis is quite sophisticated, it likely did not evolve for some time after life had become well established. But, there is a much simpler set of reactions that can fix carbon dioxide that is related to a metabolic process you’ve probably heard of: the citric acid cycle (or Krebs cycle). As we will discuss in Chapter 5, the citric acid cycle is a key component of cellular respiration and serves to oxidize organic molecules (e.g., acetate), releasing CO2 and water. The electrons released by the oxidation are in turn used further along in the respiratory pathway to generate ATP. In addition to its role in synthesis ATP, a second critical function of the citric acid cycle is that it synthesizes important precursor molecules, including those needed for the synthesis of amino acids and fatty acids. What is really interesting about the citric acid cycle is that, in addition to working in what is called the “oxidative mode,” as described above, in some bacteria it can actually run in reverse, in a “reductive mode” (Figure 1.12). It can take in energy in the form of high energy electrons from, for example, hydrogen gas (H2), and use those electrons to reduce carbon dioxide into more complex organic molecules, including the important metabolic intermediates pyruvate and acetate. So, in the oxidative mode, the input is complex organic molecules and the output is chemical energy; in the reductive mode, the input is chemical energy and carbon dioxide and the output is larger, more complex molecules. By operating the reverse citric acid cycle and harnessing the energy in the H2 released from the alkaline vents, the earliest forms of life would have been able to generate complex organic molecules, the sugars, amino acids, nucleotides, and fatty acids that are the building blocks of cells. FIGURE 1.13 FeS protein consists of an FeS cluster bound precisely to a peptide chain. The FeS cluster shown here consists of four Fe atoms and four S atoms (Fe4S4) that form a cube. FeS proteins play key roles in enzyme catalysis as well as in transferring electrons in electron transport chains. Like all metabolic pathways, the reverse citric acid cycle found in bacteria today requires enzymes to catalyze the conversion of one intermediate of the cycle into the next. Could the pathway have operated in very primitive cells in the absence of enzymes? Laboratory experiments have shown that the rate of these chemical reactions can be sped up without enzymes by the presence of certain metal-mineral complexes. One particular complex that could have served as a catalyst before enzymes is iron–sulfur (Fe–S) clusters that are produced by alkaline hydrothermal vents in a reaction between hydrogen sulfide (H2S) and iron (Fe) (look back at Figure 1.11). What is really exciting about this hypothesis is Fe–S clusters are essential to life today. They are key cofactors in what are referred to as FeS proteins (Figure 1.13), which play critical roles in enzyme a. Forward citric acid cycle: oxidative Acetate b. Reverse citric acid cycle: reductive KEY H2O CO2 H2 Carbon Oxygen Hydrogen Transfer of highenergy electrons to energy-harvesting pathways CO2 waste product Geologically produced, highenergy electrons surrender energy to reductive cycle Acetate product enters biosynthetic pathways FIGURE 1.12 Forward and reverse citric acid cycle. (a) The reactions and molecules of the citric acid cycle are found in all modern organisms. (b) In some microbes, the cycle runs in reverse. Instead of oxidizing a fuel molecule (e.g., acetate) and releasing CO2 as waste, the reverse cycle incorporates CO2 in organic molecules by using geologically produced molecules such as H2, which represent a rich source of usable electrons. The reverse citric acid cycle may have been the mechanism that early organisms used to generate complex molecules. Source: https://www.slideserve.com/isanne/origins-and-early-evolution-of-life 14 CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 14 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com catalysis, as well as in electron transfer, as components of both photosynthetic and respiratory electron transport chains. In addition to iron, many other metals (zinc, copper, nickel, molybdenum, etc.) are required in trace amounts for the function of many proteins, and thus are essential for life. The reliance of all organisms on these metals may reflect how modern biochemistry is linked to the geochemistry of the hydrothermal vents where life may have started. STUDY BREAK QUESTIONS 1. What are the characteristics of an alkaline hydrothermal vent? 2. Explain the difference between the forward citric acid cycle and the reverse citric acid cycle. 1.4c First Cells One of the key features that makes alkaline vents a promising site for the development of life is that the calcium carbonate chimneys (Figure 1.11) are honeycombed with microscopic pores that water can move through. These pores are only micrometres in diameter, which makes them comparable in size to a modern cell and provide a promising model for how the earliest cells could have evolved. One hypothesis suggests that the very first cells were not bound by lipid membranes but rather an inorganic casing composed of metal sulfides (NiS, FeS). Laboratory experiments have shown that these metal sulfides produce bubbles when they precipitate that could have served as the first cell membranes. Such a primitive membrane would have allowed an important attribute of life to develop— compartmentalization. These early inorganic membranes would have trapped and concentrated organic molecules, allowing for more complex chemical reactions to take place, driven at first by a mineral catalyst that would have produced products that could have accumulated to high concentrations. Such an environment would have been conducive to the evolution of the early metabolic processes (e.g., reverse citric acid cycle) as well as the synthesis of the first replicating molecules (RNA) (Figure 1.14). One common source of energy that relies on a cell membrane is chemiosmosis: using the difference in proton (H1) concentration across a membrane to do work. Since membranes are impermeable to protons, having more protons on one side than the other produces an electrochemical gradient that can be harnessed to do energy-requiring processes, including generating ATP from ADP and phosphate (PO432, abbreviated Pi). In organisms today, cells need to expend energy to pump protons out of the cell and generate proton gradients, but if the earliest cells evolved in the environment of alkaline hydrothermal vents, the gradient would be generated by geological processes. Recall that the water coming out of these vents has a low concentration of protons (they are alkaline). By comparison, the surrounding ocean water has a proton concentration that is estimated to be about 1000-fold greater (Figure 1.14). Today, the chemiosmotic synthesis of ATP from ADP and Pi is a reaction that is catalyzed by a sophisticated membranelocalized enzyme system ATP synthase that harnesses the energy present in the proton gradient. Being a key component of both photosynthesis and cellular respiration, ATP synthase is found across all life today, suggesting that ATP synthase evolved very early in the development of life. It’s hard to explain how such an elaborate enzyme complex could have evolved so early but it is worth reminding ourselves that even the earliest forms of life must have been quite sophisticated. It’s not just ATP synthase, the ribosome is another key feature of all cells that is very complex. The evolution of these cellular machines must have relied on two key features: easy access to a supply of usable energy and an environment where molecules could have been synthesized in a confined space. The alkaline vent system of 4 billion years ago may very well have supplied both of those features. At some point the inorganic nature of the first membrane would have been replaced by one dominated by lipid molecules produced by reaction pathways within the cell. The earliest lipid membranes could have been similar to a liposome, which is a lipid vesicle in which the lipid molecules form a bilayer very similar to a cell membrane (Figure 1.15). Given a mixture of lipid Microscopic compartments Acidic ocean water H+ ATP H+ H+ ADP + Pi H+ H+ David Mccarthy/Science Source Alkaline vent water High H+ H+ Low H+ a. FIGURE 1.14 The earliest cells may have been formed within the microscopic pores of the vent system. They would have had a cell membrane composed of geologically produced minerals. b. FIGURE 1.15 Liposome. (a) An artist’s rendition of a liposome, which is composed of a lipid bilayer. Liposomes can assemble spontaneously under simulated primordial conditions. (b) SEM image of lipid vesicles assembled CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 15 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 15 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com molecules, liposomes can form spontaneously (without the need for energy) and would be selectively permeable—allowing only some molecules to move in and out. As well, liposomes have been shown to swell and contract depending on the osmotic conditions of their environment. The key attributes of life including rudimentary metabolism and genetics could have developed relatively rapidly within the safe confines of the alkaline vent system and its constant supply of usable energy. The development of more varied metabolic pathways must have been essential to early life forms being able to leave the vent system, as was the development of a lipid membrane. STUDY BREAK QUESTIONS 1. Define chemiosmosis. 2. How was the proton gradient within the earliest cells produced? 3. Why was a cell membrane essential to the development of life? As we saw in the previous section, the alkaline hydrothermal vent system is a very promising geological feature where early life may have developed. Along with looking at the physical features present on Earth, insights into early life can come from studying the huge diversity of life that we find on Earth today and developing hypotheses around how different organisms may be related. To trace the evolutionary history of organisms, what is referred to as phylogeny, researchers build branching diagrams called trees that show the relationship among different groups of species. The construction of evolutionary (also called phylogenetic) trees has been a central feature of evolutionary biology since the time of Charles Darwin. In fact, Darwin sketched an early phylogenetic tree (Figure 1.16) in his notebook in 1837, 20 years before the publication of On the Origin of Species. Considering that life has existed for about 4 billion years and species change over time, building a reasonably accurate evolutionary tree that includes all major groups of organisms, a so-called tree of life, seems like a daunting task. And it shouldn’t surprise you that, as the research tools and techniques used to assess relatedness among organisms have improved, so have the evolutionary trees that are built as a result of that research. We will see in this section that through the use of modern molecular techniques we are able to infer a great deal about what our most ancient ancestors might have been like. 1.5a Analyses of Gene Sequences Have Revealed the Branching Pattern of the Entire Tree of Life When it comes to looking at the relationships among the major groups of organisms, the way we understood things about 50 years ago made everything seem so simple. All life could be divided into two clear camps: eukaryotes and prokaryotes. The eukaryotes were the organisms that we were most familiar with—the animals, plants, and fungi—each defined their own kingdom but were united into a single larger group by having cells that contained membrane-bound organelles, most importantly, the nucleus. Fifty years ago, prokaryotes meant only one thing—bacteria. Single-celled, structurally and metabolically simple, bacteria were largely hidden from our everyday world 16 CHAPTER 1 Charles Darwin's First Notebook on Transmutation of Species (1837) 1.5 The Tree of Life FIGURE 1.16 Darwin’s evolutionary tree. This entry from his notebook on the “transmutation of species” demonstrates that Charles Darwin first thought about the branching pattern of evolution in 1837, more than 20 years before he published On the Origin of Species. because they were so small. But everything changed when researchers started to apply the tools and techniques of molecular biology to the study of phylogenetics. For centuries, biologists had built phylogenetic trees based on how organisms looked: organisms that have similar structures and features (what we call morphology) were grouped more closely together than organisms that looked less similar. But, two organisms that look similar may in fact not share a similar evolutionary history, and by the 1970s, researchers realized that a more objective and powerful approach to building trees was to use differences in DNA sequence (the AGC and T nucleotides that make up DNA). The basis for this approach is quite simple: As one species splits into two and these two species diverge over time, their DNA sequences will accumulate DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 16 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com changes and become less and less similar to each other. If there aren’t very many differences in DNA sequence between two species, then they’re probably closely related and diverged from each other quite recently. If there are a lot of differences, they are likely to be more distantly related. If you want to use DNA to build a tree of life, this is the first question you need to consider: What is the sequence that you want to compare? You could determine the sequence of the entire genomes of species you want to include in your tree, but even today that can get expensive, and looking for similarities and differences between the millions of bases that make up whole genomes can take a long time. Instead, scientists have focused on looking at differences in the sequence of just one gene. But which one should they pick? There are two major criteria you need to consider: First, the specific gene you choose needs to be present in all organisms. It would make little sense to use a gene required for eye development to build a tree of life since 99% of species on Earth don’t have eyes. Second, the gene has to be relatively long (at least a thousand bases would be good). The longer the DNA sequence, the more information it contains to make comparisons among species. For example, having a gene made up of only six nucleotides (say, GAGCCT) isn’t very useful because many unrelated species would have that sequence simply by chance. One of the first researchers to use a DNA sequence to build phylogenetic trees was Carl Woese, a microbiologist at the University of Illinois. He focused his attention on a cell component that is common to all life: the ribosome, the organelle at the centre of protein synthesis that uses the information in messenger RNA (mRNA) molecules to synthesize its corresponding protein. The structure of a ribosome is built by a combination of protein and a specific kind of RNA called ribosomal RNA (rRNA), and these components are remarkably similar across all organisms (Figure 1.17). Woese settled on the specific gene that codes for the rRNA molecule that makes up the small subunit of the ribosome. The DNA sequence for this gene is about 1500 nucleotides in length, so it provides lots of information with which to compare species and build the tree. A small portion of this sequence is seen in Figure 1.17. In 1990, Woese and his colleagues published the first tree of life based on rRNA sequence data. It surprised many in the scientific community because, instead of showing 5 or 7 or maybe 10 distinct kingdoms of life, it clearly showed that all life could actually be grouped into 3 “superkingdoms” called domains: Bacteria, Archaea, and Eukarya (Figure 1.18a). The most surprising finding of what has become known as the three-domain tree of life is that it showed not one but two major groups of organisms that have prokaryotic cell structure: the Bacteria and Archaea. The Bacteria include many well-known microbes, including Escherichia coli (E. coli), and the domain Archaea includes microorganisms that are far less common and are often found in harsh environments, such as hot springs and salt marshes. The domain Eukarya includes the familiar animals, plants, and fungi and protists. The major distinguishing features of the Bacteria, Archaea, and Eukarya are shown in Table 1.1. We will discuss the organisms that comprise these domains in Unit 5 of this textbook. Bacteria Archaea Eukarya LUCA a. Three-domain tree Eukarya Protein Large subunit Bacteria Archaea Ribosomal RNA (rRNA) Small subunit Species 1 … ATCCGCTAGGCTGACGGCT TAGCCCATATCGA C… Species 2 … ATCCGGTAGGCTGACGGCT T TGCCCATATCGAC… Species 3 … ATCCGCTACGCAGATGGCT TAGCCGATA ACGAC… FIGURE 1.17 The ribosome is made of two subunits, each composed of protein and ribosomal RNA (rRNA). The sequence of the rRNA gene of the small subunit is widely used to infer evolutionary relationships among species. In the example shown here of a small portion of the sequence, Species 3 has more differences (shown in red) than Species 1 or 2. Based on these data, we can conclude that Species 3 is more distantly related to Species 1 than Species 2. LUCA b. Two-domain tree FIGURE 1.18 Trees of life with domains. (a) Three-domain tree of life. rRNA sequence comparisons suggest that Bacteria, Archaea, and Eukarya are three domains of living organisms, and that Eukarya are more closely related to Archaea than Bacteria. (b) Two-domain tree of life. The discovery of the Asgard group of archaeans that have key eukaryotic traits suggests that eukaryotes evolved from within the Archaea. LUCA stands for Last Universal Common Ancestor and is discussed in the text. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 17 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 17 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com TABLE 1.1 Some Differences among the Three Domains Character Bacteria Archaea Eukarya Chromosome structure Circular Circular Linear DNA location Nucleoid Nucleoid Nucleus Chromosome segregation Binary fission Binary fission Meiosis/ mitosis Introns in genes Rare Common Common Operons Present Present Absent Initiator tRNA Formylmethionine Methionine Methionine Ribosomes 70S 70S 80S Membraneenclosed organelles Absent Absent Present Membrane lipids Ester-linked Ether-linked Ester-linked Peptidoglycan in cell wall Present Absent Absent Methanogenesis Absent Present Absent Temperature tolerance Up to 90°C Up to 120°C Up to 70°C Before moving on, it’s worth mentioning the scientific impact of the three-domain tree of life. First, it illustrated the power of using molecular data to produce evolutionary trees; data that unlike morphology, could be more accurately interpreted. Second, the use of molecular data such as gene sequences allowed for the classification of microbes that are difficult to describe in other ways, not only because they are microscopic but also because some are very difficult to grow and study in the lab. Third, and perhaps most surprisingly, it showed that archaeans are more closely related to eukaryotes than they are to bacteria! Since it was first published, the three-domain tree of life has been well supported by additional gene sequencing projects, as well as detailed analyses showing how distinct the cell structure and physiology of archaeans are compared to bacteria. But microbiologists had long suspected that the bacteria and archaea that had been studied so far represented only a tiny fraction of the total microbial diversity on Earth. Many microbes live in extreme habitats, making them particularly difficult to study. Sediment cores taken in 2010 near a hydrothermal vent in the Arctic Ocean contained previously uncharacterized samples of archaeans that have since been assigned to a new group called Asgard. DNA sequencing of these samples showed something shocking. While the DNA of the Asgard samples contain key sequences that are found only in the Archaea, they also 18 CHAPTER 1 have genes that were previously thought to be present only in eukaryotes. These included genes for proteins involved in building the cytoskeleton, the process of phagocytosis, and certain core genes involved in fundamental cellular processes (e.g., transcription, translation). The analysis of the Asgard genes suggested that archaeans and eukaryotes are in fact more closely related than previously thought. That provided evidence that the three-domain tree of life is probably incorrect. What the most recent findings indicate is that there are only two primary domains of life: Bacteria and Archaea, and that Eukarya evolved from within the Archaea (Figure 1.18b). The current two-domain tree of life will be scrutinized and tested against a range of hypotheses, as it should. It is remarkable that, in comparing the Asgard samples with eukaryotic DNA, we are trying to reconstruct an ancient relationship by looking for DNA sequences that these two shared at the time they split into distinct lineages. This is estimated to have occurred more than 2 billion years ago. The Asgard samples used for the DNA sequencing project that showed they are closely related to eukaryotes came from sediment samples isolated from the environment, not from living cells. It was only in 2020 that a group of researchers in Japan was successfully able to isolate intact cells of Asgard and get them to grow successfully in a laboratory. This was a remarkable accomplishment and has already led to the start of a number of research projects aimed at not only better understanding the structure and physiology of the Asgard but also more direct testing of a range of hypotheses related to the evolution of eukaryotes. 1.5b All Present-Day Organisms Are Descended from a Common Ancestor, LUCA There are clear distinctions in structure and function between Bacteria, Archaea, and Eukarya that we will discuss in detail in Unit 5. Apart from all their differences, it is remarkable that all forms of life on Earth share a common set of features. This includes (1) cells defined by a membrane composed of a bilayer of lipid molecules; (2) a genetic system based on DNA; (3) a system of information transfer: DNA to RNA to protein; (4) ribosomes as the central feature of a protein assembly machinery that uses the information in messenger RNA (mRNA) and transfer RNA (tRNA) to produce peptide chains from a pool of amino acids; (5) reliance on proteins as the major structural and catalytic molecule; (6) use of ATP as the currency of chemical energy; and (7) common pathways of energy transformation (e.g., glycolysis, substrate-level phosphorylation, chemiosmosis). Given that all organisms share these seven characteristics, what is the likelihood that these traits arose independently in the three major groups of life? It is far more likely that the reason for these shared traits is that all organisms today are the descendants of one organism that possessed all these traits. This shared ancestor probably lived more than 3 billion years ago. DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 18 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Origin of life LUCA Eukarya Archaea FIGURE 1.19 Life before LUCA. It is likely that many forms of simple life predated the evolution of LUCA. As indicated by the light-green part of the figure, all of these are now extinct, as well as others that have become extinct more recently. Looking back at Figure 1.18, whether we consider a twodomain or a three-domain tree of life, both phylogenies show that all organisms today come from a common ancestor that has become known as LUCA, which stands for Last Universal Common Ancestor. In an amazing piece of research, scientists have pieced together a view of what LUCA was actually like. To reconstruct the structure, biochemistry, and ecology of LUCA, a research team looked at the common protein families found among 1800 sequenced bacterial genomes and 134 archaeal genomes. This research identified 355 proteins that were common to all the genomes. That these proteins were so highly conserved across many different species suggests that these proteins may have been present in LUCA. The analysis of these proteins and their possible function provides a remarkable glimpse into how LUCA lived (Figure 1.19). The research suggests that LUCA lived without O2 (was anaerobic), fixed CO2 into organic molecules, possessed a set of reactions similar to the reverse citric acid cycle, 1.6 Eukaryotes and the Rise of Multicellularity Compared to the prokaryotic cell structure of Archaea and Bacteria, present-day eukaryotic cells are much more complex in both structure and function. There are two major characteristics that distinguish eukaryotic cells from prokaryotic cells: (1) the separation of DNA and cytoplasm by a nuclear envelope and (2) the presence in the cytoplasm of membrane-bound organelles with specialized functions: mitochondria, chloroplasts, the endoplasmic reticulum (ER), and the Golgi complex, among others. In this section, we discuss how eukaryotes most probably evolved from associations of prokaryotic cells, and we end with a discussion of the rise of multicellular eukaryotes. STUDY BREAK QUESTIONS 1. What is the advantage of using DNA sequence over morphology as the data used to build an evolutionary tree? 2. We have moved recently from a three-domain tree of life to a two-domain tree of life. What caused the shift in thinking? 3. LUCA wasn’t the first form of life to develop, so why is it so important to our understanding of the evolution of life? began increasing. Evidence for this comes from dating a type of sedimentary rock called banded iron (Figure 1.20). An obvious question to ask is, Where did the oxygen come from? Surprisingly, this oxygen did not have a geological origin; instead, its source was a group of photosynthetic bacteria called cyanobacteria. At the time, photosynthetic organisms used light © Commonwealth of Australia Bacteria was dependent upon H2 as a source of hydrogen atoms and electrons, was able to convert N2 into ammonia, and lived in a hot environment (thermophilic). Its biochemistry was dependent on FeS clusters and a range of other metals. This research further supports the notion that LUCA developed in a vent-like setting and took advantage of the abundance of molecules produced by a range of geochemical processes. You may think that LUCA was the first form of life to exist on early Earth, but that is not the case. Calling something the last common ancestor is like saying the last team to win the Super Bowl; what we mean is the most recent. LUCA is the most recent ancestor that gave rise to all the organisms we see on Earth today. Given that LUCA was quite complex in both structure and function, it was undoubtedly preceded by other simpler forms of life, as depicted in Figure 1.19. It is quite possible that life arose many times on early Earth, each form perhaps having only some of the seven attributes listed above. For example, perhaps some forms of early life did not use ATP as a common source of chemical energy or developed DNA as the repository of genetic information. The similarities across all domains of life present today indicate, however, that only one of these primitive life forms has descendants that survive today. 1.6a The Rise of Eukaryotes Is Linked to Increasing Oxygen Levels When life began, there was no oxygen (O2) in the atmosphere. But, starting about 2.5 billion years ago, oxygen levels in the atmosphere FIGURE 1.20 Banded iron. The rust layers in banded iron formations provide evidence for the rise of atmospheric oxygen. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 19 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 19 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com energy to extract hydrogen atoms and electrons from compounds such as hydrogen sulfide. In turn, these hydrogen atoms and electrons were used to fix carbon dioxide into carbohydrates. Instead of using hydrogen sulfide, cyanobacteria developed the remarkable ability to oxidize a molecule that was much more abundant: water (Figure 1.21). This gave cyanobacteria a huge ecological advantage over other photosynthetic organisms that relied on hydrogen sulfide because it meant they could thrive almost anywhere on the surface of Earth. After all, when was the last time you walked outside and stepped in a puddle of hydrogen sulfide? The ability to use water resulted in an explosion of cyanobacterial growth; the planet turned green. Although it evolved perhaps 2.5 billion years ago, the water-splitting form of photosynthesis developed by cyanobacteria is virtually identical to photosynthesis used today by plants and algae, as well as present-day cyanobacteria. The photosynthetic oxidation of water not only released valuable electrons, it also released as a by-product molecular oxygen (O2) (Figure 5.1). After the O2 began to accumulate in the atmosphere, it led to another amazing development in the evolution of early life: aerobic respiration. As we will discuss in Chapter 5, compared to anaerobic respiration (e.g., fermentation), aerobic respiration results in a huge increase in the amount of ATP that can be generated from the breakdown of food molecules (e.g., glucose). Those prokaryotic cells that developed the pathway of aerobic respiration (e.g., oxidative phosphorylation) had a huge advantage in terms of energy production. This in turn set the stage for the next huge step, the evolution of the eukaryotic cell. 1.6b The Theory of Endosymbiosis Suggests That Mitochondria and Chloroplasts Evolved from Ingested Prokaryotic Cells Bacteria and archaea outnumber eukaryotes on the planet by a massive margin. Compared to eukaryotes, archaea and bacteria show remarkable biochemical flexibility and thrive in harsh environments uninhabitable to eukaryotes. That said, prokaryotic cells are simple: they lack the complexity of eukaryotes, Biophoto Associates/Science Source a. b. 2H2O + light energy 4H+ + 4e– + O2 FIGURE 1.21 Cyanobacteria. (a) Micrograph of a filamentous cyanobacterium of the genus Nostoc. (b) Ancient cyanobacteria, like modern photosynthetic organisms, were able to use water as an electron donor for photosynthesis. A consequence was the formation of oxygen (O2), which accumulated in the atmosphere. 20 CHAPTER 1 which evolved into a tremendous diversity of forms, including plants, fungi, and animals. Within each of these groups are cells with remarkable specialization in form and function (think of the flowers of a plant or the brain cells of animals). Contrast this to archaea and bacteria, which have remained remarkably simple even though they evolved as early as 4 billion years ago. A compelling hypothesis for why bacteria and archaea have remained simple is that increased complexity requires increased energy production, and eukaryotic cells can generate huge amounts of it and prokaryotic cells cannot. How can eukaryotes generate so much more energy? Because they contain energytransducing organelles: mitochondria and chloroplasts. But how did these organelles develop? Where did they come from? A wealth of evidence indicates that mitochondria and chloroplasts are actually descended from free-living prokaryotic cells (Figure 1.22): mitochondria are descended from aerobic bacteria, and chloroplasts are descended from cyanobacteria. The established model of endosymbiosis states that the prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells, forming a mutually advantageous relationship called a symbiosis. Slowly, over time, the host cell and the endosymbionts became inseparable parts of the same single-celled organism. If the theory of endosymbiosis is correct, and both mitochondria and chloroplasts are indeed descendants of bacteria, then these organelles should share some clear structural and biochemical features with the forms of life that they evolved from. Six lines of evidence suggest that both chloroplasts and mitochondria have distinctly prokaryotic characteristics that are not found in other eukaryotic organelles: Morphology. The shape and size of both mitochondria and chloroplasts are similar to those of prokaryotic cells. Reproduction. A cell cannot synthesize a mitochondrion or a chloroplast. Just like free-living prokaryotic cells, where daughter cells arise by cell division, new mitochondria and chloroplasts are derived from the division of preexisting organelles. Both chloroplasts and mitochondria divide by binary fission, which is how prokaryotic cells divide (see Chapter 20). Genetic information. If the ancestors of mitochondria and chloroplasts were free-living cells, then these organelles should contain their own DNA. Both mitochondria and chloroplasts contain their own DNA, which contains both protein-coding and non-coding genes (see Chapter 12) that are essential for organelle function. As with prokaryotic cells, the DNA molecule in most mitochondria and chloroplasts is circular; the DNA molecules in the nucleus are linear. Transcription and translation. Both chloroplasts and mitochondria contain a complete transcription and translational machinery. They contain ribosomes and tRNAs that are necessary to translate organelle mRNAs into proteins. DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 20 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com ∼1.5 billion years ago 0 Original prokaryotic host cell Billions of years ago 1 2 DNA Unicellular eukaryotes Aerobic bacteria Multiple invaginations of the plasma membrane 3 4 5 The bacteria become mitochondria. Endoplasmic reticulum and nuclear envelope form from the plasma membrane invaginations (not part of endosymbiotic theory). Photosynthetic bacteria… …become chloroplasts. Eukaryotic cells: plants, some protists Eukaryotic cells: animals, fungi, some protists FIGURE 1.22 The theory of endosymbiosis. The mitochondrion is thought to have originated from an aerobic prokaryote that lived as an endosymbiont within an anaerobic prokaryote. The chloroplast is thought to have originated from a photosynthetic prokaryote that became an endosymbiont within an aerobic cell that had mitochondria. Electron transport. Similar to free-living prokaryotic cells, both mitochondria and chloroplasts have electron transport chains and the enzyme ATP synthase, which together are used to generate chemical energy. The electron transport chains of bacteria and archaea are found associated with the plasma membrane. Sequence analysis. Sequencing of the genes that encode the RNA component of the ribosome (ribosomal RNA or rRNA) firmly establishes that these organelles belong on the bacterial branch of the tree of life (we will discuss this later in the chapter). The sequence of chloroplast rRNA most closely matches that of cyanobacteria, and the sequence of mitochondrial rRNA is most similar to that of heterotrophic bacteria. Whereas virtually all eukaryotic cells contain mitochondria, only plants and algae contain both mitochondria and chloroplasts. This fact suggests that endosymbiosis occurred in stages (see Figure 1.22), with the event leading to the evolution of mitochondria occurring first. Once eukaryotic cells with the ability for aerobic respiration developed, some became photosynthetic after taking up cyanobacteria, evolving into the plants and algae of today. Endosymbiosis resulted in eukaryotic cells gaining the ability to generate large amounts of energy. And this in turn led to remarkable changes. More energy meant that cells could become larger, as now there was enough energy to support more proteins, carbohydrates, and lipids that make up the greater cell volume. And cells could become more complex. This complexity comes about by having the energy to support a larger genome that codes for a greater number of proteins. By overcoming an energy production barrier, eukaryotes could support a wider variety of genes, which led to what we know today to be eukaryotic-specific traits such as the cell cycle, sexual reproduction, phagocytosis, endomembrane trafficking, the nucleus, and multicellularity. 1.6c The Endomembrane System May Be Derived from the Plasma Membrane As detailed in the next chapter, in addition to energy-transforming organelles (mitochondria and chloroplasts), eukaryotic cells are characterized by an endomembrane system: a collection of internal membranes that divide the cell into structural and functional regions. These include the nuclear envelope, the ER, and the Golgi complex. As we have just seen, there is very strong evidence in support of the endosymbiotic origin of chloroplasts and mitochondria; however, the origin of the endomembrane system remains less clear. The most widely held hypothesis is that it is derived from the infolding of the plasma membrane (Figure 1.23). Researchers hypothesize that, in cell lines leading from prokaryotic cells to eukaryotes, pockets of the plasma membrane may have extended inward and surrounded the nuclear region. Some of these membranes fused around the DNA, forming the nuclear envelope, which defines the nucleus. The remaining membranes formed vesicles in the cytoplasm that gave rise to the ER and the Golgi complex. CHAPTER 1 D e f i n i n g L i f e a n d It s O r i g i n s Get Complete eBook Download By email at student.support@hotmail.com 21 Get Complete eBook Download By email at student.support@hotmail.com Cytoplasm Endoplasmic reticulum Nuclear region Nuclear envelope FIGURE 1.23 A hypothetical route for the formation of the nuclear envelope and ER through segments of the plasma membrane that were brought into the cytoplasm by endocytosis 1.6d Horizontal Gene Transfer Two major processes led to the integration of function between the proto-mitochondrion, proto-chloroplast, and the parent cell. First, some of the genes that were within the proto-mitochondrion or proto-chloroplast were lost. Most of these lost genes would have been redundant as the nucleus would already have genes that encode proteins with the same function. Second, many of the genes within the protomitochondrion and proto-chloroplast were relocated to the nucleus through horizontal gene transfer. It is understood that gene transfer to the nucleus was evolutionarily advantageous, as it would have centralized genetic information and its control in one place, the nucleus. It’s important to realize that the outcome of this horizontal gene transfer was not a change in gene function, only a change in its location. In a typical eukaryotic cell today, over 90% of the thousands of proteins required for mitochondrial or chloroplast function are encoded by genes that are found in the nucleus. To go along with this change of location, a large protein-trafficking and sorting machinery had to evolve (Figure 1.24). Following transcription in the nucleus and translation on cytosolic ribosomes, proteins destined for the chloroplast or mitochondrion need to be correctly sorted and imported into these energy-transducing organelles, where they are trafficked to the correct location. Our ideas about the movement of genes between the various domains of life are supported by a wealth of genome sequence analysis. This has led to the conclusion that an even more accurate tree of life is shown in Figure 1.25. The next unit Inheritance from one generation to the next can be referred to as vertical gene transfer, and it explains why the next generation of a particular species is similar to the current generation in any given population. It is what has given rise to the distinct species we see today. What you may not realize is it’s possible for genetic information (DNA) to move between unrelated organisms in what is referred to as horizontal gene transfer. Only recently has horizontal gene transfer been recognized as making an important contribution to evolution. Horizontal gene Chloroplast transfer is known to be quite common in bacteria where genes from one species become integrated into the genome of another. As a consequence of Gene transfer Integration of gene Chloroplastendosymbiosis, horizontal gene transfer has also into nuclear genome encoded proteins shaped the evolution of eukaryotic cells with bacterial genes ending up in the nucleus. Following the initial endosymbiosis event, the Chloroplast genome early eukaryotic cell would have contained two disNuclear genome tinct compartments, each with its own genome: the nucleus and the early mitochondrion (protomitochondrion). The ancestor to modern plants and Protein synthesis Nuclear-encoded algae would have also had a proto-chloroplast. These and import proteins Nucleus compartments (and their genomes) would have continued to function as the independent organisms they were before the endosymbiotic event. Each contained DNA instructions for molecules (RNAs and proteins) required for their own structure and function. But that FIGURE 1.24 Horizontal gene transfer. Over evolutionary time, some proteinis a very different situation compared to a modern coding genes that were once part of the chloroplast or mitochondrial genome have eukaryotic cell, where the metabolism of the been relocated to the nuclear genome. Following transcription of these genes, mitochondria and chloroplast is well integrated into translation occurs in the cytosol before protein import into the organelle (mitochondrion or chloroplast). the overall function of the cell. 22 CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 22 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com all cells are structurally and functionally autonomous (independent). This gave way to a key trait of more advanced multicellular organisms: division of labour. Over time, cells became structurally and functionally distinct. For example, some cells may have specialized in harvesting energy, whereas others developed a role related to the motility of the organism. In a multicellular system, the cells cooperate with one another for the benefit of the entire organism. Over evolutionary time, this specialization of cell function led to the development of the specialized tissues and organs that are so clearly evident in larger eukaryotes. Like the earliest forms of life, there is little, if any, evidence in the fossil record of the earliest multicellular organisms. How they arose and developed is still an area of intense research. It is thought, however, that multicellularity arose more than once, most probably independently along each of the lineages leading to fungi, plants, and animals. A very useful model for the study of multicellularity is found in a group of green algae called the volvocine. All the members of this group are evolutionarily closely related and span the full range of size and complexity, from the unicellular Chlamydomonas through various colonial genera to the multicellular Volvox (Figure 1.26). Unlike a true multicellular organism, a cell colony is a group of cells that are all of one type; there is no specialization in cell structure or function. Volvox consists of a sphere of 2000 to 3000 small, flagellated Chlamydomonas-like cells that provide the individual Volvox with the ability to move. In addition, within the sphere lie about 16 large nonmotile cells that serve a specialized role in reproduction. Eukarya Bacteria Archaea n LUCA FIGURE 1.25 A tree of life incorporating the endosymbiotic events from Bacteria to Eukarya. While the host eukaryotic cell and the nuclear genome are directly descended from the Archaea, the energy-transducing organelles, the mitochondria and chloroplast, are descended from freeliving bacteria. of this book is devoted to detailed analyses of the biology and evolutionary relationships between and within the three domains: Bacteria, Archaea, and Eukarya. 1.6e The Evolution of Multicellular Eukaryotes Led to Increased Specialization STUDY BREAK QUESTIONS 1. The Earth’s atmosphere contains 21% O2. Where did that oxygen come from? 2. What are the major lines of evidence in support of the theory that mitochondria and chloroplasts are descendants of prokaryotic cells? Cristian A. Solari, University of Arizona Cristian A. Solari, University of Arizona One of the most profound transitions in the history of life was the evolution of multicellular eukaryotes. Clear evidence of multicellularity, in the form of species of algae, appears in the fossil record starting about 1.2 billion years ago. The actual events that led to the development of multicellularity are a mystery, but it is easy to envision how it may have occurred. Perhaps a group of individual cells of a particular species came together to form a colony, or a single cell divided and the resulting two cells did not separate. In the simplest of multicellular organisms, Chlamydomonas reinhardtii, a unicellular alga Gonium pectorale, a group of eight undifferentiated cells Eudorina elegans, a spherical colony of undifferentiated cells Cristian A. Solari, University of Arizona ho toc Mi a dri Cristian A. Solari, University of Arizona ts las rop lo Ch Volvox aureu, smaller somatic cells and a few reproductive cells FIGURE 1.26 Differences in degree of multicellularity among volvocine algae CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 23 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 23 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com In all our previous discussions on the origins of life and LUCA, we need to remind ourselves that there is no direct evidence for the earliest forms of life. This section provides an overview of what we actually do know about the history of life on Earth as reflected by the remains of organisms that have been preserved in the fossil record. 1.7a The Fossil Record Is Invaluable but Incomplete The fossil record provides the only direct evidence about what life was like millions of years ago. Fossilized skeletons, shells, stems, leaves, and flowers tell us about the size and appearance of ancient animals and plants. The fossil record has also allowed scientists to see how species have changed over time as it chronicles the proliferation and extinction of evolutionary lineages, and it provides data on the geographical distribution of extinct species. As discussed in Chapter 16, Darwin’s ability to compare fossil specimens with living relatives was very influential in his development of the notion of natural selection. Obviously, the fossil record is an invaluable resource to understand the past, but it is important to note that it represents only a small fraction of the organisms that once lived on Earth, and thus it vastly underrepresents the diversity of life. The fossil record only really represents a record of the most successful of organisms; those that were very abundant, had wide distributions, and possessed hard parts that could be fossilized. Soft-bodied organisms with small geographic distributions that lived in environments where erosion was a dominant process are underrepresented in the fossil record—if they are in it at all. a. Sedimentation 1.7b Fossils Form When Organisms Are Buried by Sediments or Preserved in Oxygen-Poor Environments Most fossils form in sedimentary rocks. Rain and runoff constantly erode the land, carrying fine particles of rock and soil downstream to a swamp, a lake, or the sea. Particles settle to the bottom as sediments, forming successive layers, called strata, over millions of years (Figure 1.27). The weight of newer sediments compresses the older layers beneath them into a solid matrix: sand into sandstone and silt, or mud into shale. Fossils form within the layers when the remains of organisms are buried in the accumulating sediments. Because sedimentation superimposes new layers over old ones, the lowest strata in a sedimentary rock formation are usually the oldest, and the highest layers are the newest. The process of fossilization is a race against time because the soft remains of organisms are quickly consumed by scavengers or decomposed by microorganisms. Thus, fossils usually preserve the details of hard structures, such as the bones, teeth, and shells of animals and the wood, leaves, and pollen of plants. During fossilization, dissolved minerals replace some parts molecule by molecule, leaving a fossil made of stone (Figure 1.28a); other fossils form as moulds, casts, or impressions in material that is later transformed into solid rock (Figure 1.28b). In some environments, the near absence of oxygen prevents decomposition, and even soft-bodied organisms are preserved. Some plants, insects, and tiny lizards and frogs are embedded in amber, the fossilized resin of coniferous trees (Figure 1.28c). Other organisms are preserved in glacial ice, deeply frozen soil, coal, tar pits, or the highly acidic water of peat bogs (Figure 1.28d). Sometimes organisms are so well preserved that researchers can examine their internal anatomy, cell structure, food in their digestive tracts, and even their DNA sequences. Highest strata contain the most recent fossils. b. Geological strata in the Painted Desert, Arizona Lowest strata contain the oldest fossils. iStock.com/Habesen 1.7 The Fossil Record FIGURE 1.27 Sedimentation and geological strata. (a) Sedimentation deposits successive layers at the bottom of a lake or sea. (b) Over millions of years, the upper layers compress those below them into rock. When the rocks are later exposed by uplifting or erosion, the different layers are evident as geological strata. 24 CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 24 20/03/22 12:27 PM Get Complete eBook Download By email at student.support@hotmail.com Newman Mark/Age Fotostock a. Petrified wood (Araucariaceae) b. Sphenopteris a. Stromatolites date to ∼3.4 billion years ago Tobkatrina/Shutterstock.com David Lyons/AGE Fotostock c. Flying insects in amber cussion of isotopes). Researchers have discovered sedimentary rocks originating from the ocean floor that contain deposits that have lower levels of the 13C isotope than expected. The most likely explanation is that the deposits are actually the remains of carbon molecules of ancient microbes. These sediments have been dated to approximately 3.9 billion years ago. If correct, this would push the origins of life to perhaps as early as 4 billion years ago, approximately 600 million years after Earth was formed. The earliest conclusive evidence of life is found in the fossilized remains of structures called stromatolites, the oldest being formed about 3.5 billion years ago. A stromatolite is a type of layered rock formed when microorganisms bind particles of sediment together, forming thin sheets (Figure 1.29). b. Cyanobacteria Dr. Tony Brain/Science Source Monica Johansen/Shutterstock.com South China Morning Post/Getty Images d. Mammoth (Mammonteus) c. Possible microfossils date to ∼3.4 billion years ago 1.7c The Earliest Fossils The earliest indirect evidence of life, which predates any actual fossil evidence, comes from research looking at the carbon composition of ancient rocks. Early photosynthetic organisms would have had the ability to take CO2 from the atmosphere and use it to synthesize various organic molecules (see Chapter 6 for details). During this process, organisms would have preferentially incorporated the carbon-12 isotope (12C) over other isotopes such as carbon-13 (13C) (see The Purple Pages for a dis- © J. William Schopf FIGURE 1.28 Fossils. (a) Petrified wood in Arizona formed when minerals replaced the wood of dead trees, molecule by molecule. These forests lived during the late Triassic period, about 225 million years ago. (b) The remains of a fern (Sphenopteris) from the Carboniferous period, 300 million years ago, were preserved in coal. (c) These 10-million-year-old mosquitoes were trapped in the oozing resin of a coniferous tree and are now encased in amber. (d) A frozen baby mammoth that lived about 40 000 years ago was discovered embedded in Siberian permafrost in 1977. FIGURE 1.29 Early fossil evidence of life. (a) Stromatolites exposed at low tide in Western Australia’s Shark Bay. These mounds, which consist of mineral deposits made by cyanobacteria, are about 2000 years old; they are highly similar in structure to fossil stromatolites that formed more than 3 billion years ago. (b) Modern cyanobacteria filaments. These photosynthetic bacteria use water as an electron donor for photosynthesis and, as a by-product, release oxygen. (c) Microfossils. The left panel shows a cross-section through rock from Western Australia that has been dated to 3.4 billion years ago. On the right are further magnifications of three microfossils that have been interpreted as filamentous, possibly cyanobacteria. CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns 25 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 25 20/03/22 12:28 PM Get Complete eBook Download By email at student.support@hotmail.com The sediments found in any one place form recognizable strata (layers) that differ in colour, mineral composition, particle size, and thickness (see Figure 1.27b). If they have not been disturbed, the strata are arranged in the order in which they formed, with the youngest layers on top. Geologists of the early 19th century deduced that the fossils discovered in a particular sedimentary stratum, no matter where on Earth it is found, represent organisms that lived and died at roughly the same time in the past. Because each stratum formed at a specific time, the sequence of fossils in the lowest (oldest) to the highest (newest) strata reveals their relative ages. Geologists originally used the sequence of strata and their distinctive fossil assemblages to establish the geological time scale (Table 1.2). Although the geological time scale provides a relative dating system for sedimentary strata, it does not tell us how old the rocks and fossils actually are. But many rocks contain unstable radioisotopes, which, from the moment they form, begin to break down into other, more stable elements. The breakdown proceeds at a steady rate that is unaffected by chemical reactions or environmental conditions such as temperature or pressure. Using a technique called radiometric dating, scientists can estimate the age of a rock by noting how much of an unstable “parent” isotope has decayed to another form. By measuring the relative amounts of the parent radioisotope and its breakdown products, and comparing this ratio with the isotope’s half-life (the time it takes for half a given amount of radioisotope to decay), researchers can estimate the absolute age of the rock. Table 1.2 presents these age estimates along with the major geological and evolutionary events of each period. Phanerozoic Eon Era Period Epoch Cenozoic Quaternary Holocene Pleistocene Pliocene Mesozoic Neogene Miocene Paleozoic Oligocene Paleogene Eocene Paleocene Proterozoic 1.7d Scientists Assign Relative and Absolute Dates to Geological Strata and the Fossils They Contain TABLE 1.2 The Geological Time Scale and Major Evolutionary Events Cretaceous Jurassic Triassic Permian Carboniferous Devonian Archean Modern stromatolites are found in habitats characterized by warm shallow water and are most common in Australia. Modern-day stromatolites are formed by the action of a specific group of photosynthetic bacteria called cyanobacteria. Because they were able to undertake oxygenic photosynthesis, cyanobacteria (see Figure 1.21) were not the earliest forms of life but, rather, must have been preceded by much simpler organisms. STUDY BREAK QUESTIONS Silurian Ordovician Cambrian Hadean 1. What biological materials are the most likely to fossilize? 2. Why does the fossil record provide an incomplete portrait of life in the past? 3. What sorts of information can paleobiologists discern from the fossil record? 26 CHAPTER 1 DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 26 20/03/22 12:28 PM Get Complete eBook Download By email at student.support@hotmail.com Millions of Years Ago Major Evolutionary Events 0.01 2.6 5.3 Mass Extinctions RIP Origin of modern humans; major glaciations Origin of bipedal human ancestors Angiosperms and mammals further diversify and dominate terrestrial habitats 23.0 Primates diversify; origin of apes 33.9 Angiosperms and insects diversify; modern orders of mammals differentiate 55.8 65.5 Grasslands and deciduous woodlands spread; modern birds, mammals, snakes, pollinating insects diversify; continents approach current positions First angiosperms; insects, marine invertebrates, fishes, dinosaurs diversify; asteroid impact causes mass extinction at end of period, eliminating most dinosaurs and many other groups 145.5 201.6 251.0 299.0 Gymnosperms abundant in terrestrial habitats; modern fishes diversify; dinosaurs diversify and dominate terrestrial habitats; frogs, salamanders, lizards, birds, and placental mammals appear; continents continue to separate Predatory fishes and reptiles dominate oceans; gymnosperms dominate terrestrial habitats; diversification of dinosaurs; early mammals; Pangaea starts to break up; mass extinction at end of period Insects and amniotes abundant and diverse in swamp forests; some amniotes colonize oceans; fishes colonize freshwater habitats; continents coalesce into Pangaea, causing glaciation and decline in sea level; huge volcanic eruptions cause mass extinction at end of period, eliminating 85% of species worldwide RIP Cretaceous RIP Triassic RIP Permian Vascular plants form large swamp forests; first flying insects; amphibians diversify; first amniotes appear 359.0 RIP Terrestrial vascular plants diversify; fungi, invertebrates, tetrapod vertebrates colonize land; first insects and seed plants; major glaciation at end of period; mass extinction, mostly of marine life Devonian 416.0 Jawless fishes diversify; first jawed fishes, first terrestrial arthropods and vascular plants RIP 444.0 Major radiations of marine invertebrates and jawless fishes; first terrestrial plants, fungi, and animals; major glaciation at end of period causes mass extinction of marine life Ordovician Appearance of modern animal phyla, including vertebrates (Cambrian explosion); simple marine communities; mass extinctions eliminate many groups at end of period Cambrian 488.0 RIP 542.0 High concentration of oxygen in atmosphere; origin of eukaryotic cells; evolution and diversification of protists, fungi, soft-bodied animals 2500 Origin of life; evolution of prokaryotes, including anaerobic and photosynthetic bacteria; oxygen starts to accumulate in atmosphere; origin of aerobic respiration 3850 Formation of Earth, including crust, atmosphere, and oceans 4600 Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 27 20/03/22 12:28 PM Get Complete eBook Download By email at student.support@hotmail.com self - test questions Recall/Understand 1. Why are viruses NOT considered a form of life? a. They do not have a nucleus. b. They are not made of protein. c. They lack ribosomes. d. They lack nucleic acid. 2. According to the Oparin–Haldane hypothesis, what was the composition of the primordial atmosphere? a. water, molecular nitrogen (N2), and carbon dioxide b. molecular hydrogen (H2), water, ammonia, and methane c. water, molecular oxygen (O2), and ammonia d. molecular hydrogen (H2), water, argon, and neon 3. Clay may have played an important role in what aspect of the development of life? a. formation of monomers, such as amino acids, and membrane-bound compartments, such as liposomes b. formation of polymers such as short proteins or nucleic acids c. formation of multicellular organisms with membranebound compartments, such as liposomes d. formation of multicellular organisms using polymers such as short proteins or nucleic acids 4. Which of these statements best describes ribozymes? a. They are composed of only RNA. b. They are able to catalyze reactions faster than enzymes. c. They are found only in ancient cells. d. They are polymers of amino acids. 5. Which of these statements is the reason why DNA is thought to have replaced RNA as the means to store genetic information? a. The sugar ribose, which is present in DNA but not RNA, is less prone to breakdown. b. DNA contains uracil, which is more stable than the thymine present in RNA. c. Unlike RNA, DNA can exist in very complex threedimensional shapes, which are very stable. d. The presence of complementary strands in DNA means that single-base mutations can be easily repaired. 6. As part of the evolution of eukaryotic cells, infolding of the plasma membrane is thought to have led to the formation of which of these structures? a. ribosomes b. microtubules c. mitochondria d. endoplasmic reticulum Apply/Analyze 7. Which of these statements supports the theory of endosymbiosis? a. The plasma membrane is a made of phospholipid bilayer. b. Both mitochondria and chloroplasts possess their own genomes. c. Both mitochondria and chloroplasts are surrounded by a membrane. d. The nuclear envelope is derived from infolding of the plasma membrane. 28 CHAPTER 1 8. Which of these lists of events is in the correct order by first appearance? a. O2 in the atmosphere, anoxygenic photosynthesis, aerobic respiration, oxygenic photosynthesis b. O2 in the atmosphere, aerobic respiration, oxygenic photosynthesis, anoxygenic photosynthesis c. anoxygenic photosynthesis, oxygenic photosynthesis, O2 in the atmosphere, aerobic respiration d. anoxygenic photosynthesis, aerobic respiration, O2 in the atmosphere, oxygenic photosynthesis 9. The Asgard is a group of archaeans that evidence suggests is closely related to eukaryotes. What is the evidence to support this claim? a. Like eukaryotes, Asgard cells have been shown to contain structures similar to nuclei. b. Asgard cells have been shown to contain mitochondria. c. Asgard DNA contains genes that are similar to ones found only in eukaryotes. d. Similar to eukaryotes, Asgard DNA contains genes that code from ribozymes. 10. Suppose that the Miller–Urey experiment contained oxygen in its chamber. How would the results of the experiment change? a. The presence of oxygen would not affect the synthesis of organic compounds, but it would prevent the accumulation of their precursors. b. The presence of oxygen would prevent the accumulation of organic compounds by quickly oxidizing them or their precursors. c. The presence of oxygen would speed up the accumulation of organic compounds. d. The presence of oxygen would speed up the accumulation of inorganic precursors. Create/Evaluate 11. Thinking about the origin of life on Earth was transformed by the discovery that RNA molecules act as catalysts in living cells. Why is this discovery revolutionary? a. RNA may have been able to carry genes on it. b. RNA may have been capable of self-replication and catalysis of simple reactions, before DNA and enzymes arose. c. RNA may have been a precursor in the evolution of DNA. d. RNA viruses might have been involved in the evolution of life. 12. The Miller–Urey experiment was a huge breakthrough in our understanding of the origins of life. What was its major conclusion? a. Abiotic synthesis of molecules requires oxygen (O2). b. Biological molecules could be formed without energy. c. Proteins could be synthesized without ribosomes. d. Abiotic synthesis of amino acids was possible. 13. Explain how scientists determine relative and absolutes dates of geological strata and the fossils they contain. 14. We have no physical evidence that LUCA existed, but we are quite certain that it did. Why are we so certain that LUCA existed? 15. Compare the three domains regarding their chromosome structure, DNA location, chromosome segregation, and the presence of introns in their genes. DEFInInG LIFE AnD ITs ORIGIns Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 28 20/03/22 12:28 PM Get Complete eBook Download By email at student.support@hotmail.com Get Complete eBook Download By email at student.support@hotmail.com 11140_ch01_ptg01.indd 29 20/03/22 12:28 PM