How does a heterozygous organisms differ from a homozygous organism
How does a heterozygous organisms differ from a homozygous organism.
- In Chapter 8, we learn about Mendel and his experiments that led to the Laws of Inheritance. After reading this chapter, summarize the following in your own words:
- Difference between phenotype and genotype and how they are related.
- How does a heterozygous organisms differ from a homozygous organism in terms of the alleles they contribute to the population?
- Provide your best explanation for the law of segregation in 1-2 sentences.
- Understanding evolutionary relationships is an important element to understanding why organisms are placed in similar groups. In this step, you will be searching for a phylogenetic tree online, and making some observations related to the characteristics that group those organisms. You should use Chapter 12.1 as a guide. Here are the steps to follow for this section:
- Pick a group of organisms that you would like to find a phylogenetic tree for from the following list: Plants, animals, vertebrates or invertebrates
- In the google search bar, search for the following “plants (or whichever you pick), phylogenetic tree).
- Click on “Images” below the Google search bar. You should see several trees that pop up. Find one that contains some characters (physical descriptions) so you can make some conclusions regarding the organisms.
- Provide the following in your response:
- A copy of the phylogenetic tree you found.
- Write a summary of the characters or traits that are responsible for grouping organisms. Include an assessment of which organisms in the group are more closely related, as well as anything interesting or odd you found about the evolutionary relationships of the organisms.
Concepts of Biology
SENIOR CONTRIBUTING AUTHORS SAMANTHA FOWLER, CLAYTON STATE UNIVERSITY REBECCA ROUSH, SANDHILLS COMMUNITY COLLEGE JAMES WISE, HAMPTON UNIVERSITY
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Table of Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Unit 1. The Cellular Foundation of Life
Chapter 1: Introduction to Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.1 Themes and Concepts of Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2 The Process of Science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 2: Chemistry of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 2.1 The Building Blocks of Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 2.2 Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 2.3 Biological Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Chapter 3: Cell Structure and Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.1 How Cells Are Studied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.2 Comparing Prokaryotic and Eukaryotic Cells . . . . . . . . . . . . . . . . . . . . . . . 59 3.3 Eukaryotic Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 3.4 The Cell Membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 3.5 Passive Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 3.6 Active Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Chapter 4: How Cells Obtain Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 4.1 Energy and Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 4.2 Glycolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 4.3 Citric Acid Cycle and Oxidative Phosphorylation . . . . . . . . . . . . . . . . . . . . . 104 4.4 Fermentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 4.5 Connections to Other Metabolic Pathways . . . . . . . . . . . . . . . . . . . . . . . . 111
Chapter 5: Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 5.1 Overview of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 5.2 The Light-Dependent Reactions of Photosynthesis . . . . . . . . . . . . . . . . . . . . 122 5.3 The Calvin Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Unit 2. Cell Division and Genetics Chapter 6: Reproduction at the Cellular Level . . . . . . . . . . . . . . . . . . . . . . . . . . 135
6.1 The Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 6.2 The Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 6.3 Cancer and the Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 6.4 Prokaryotic Cell Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Chapter 7: The Cellular Basis of Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 7.1 Sexual Reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 7.2 Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 7.3 Errors in Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Chapter 8: Patterns of Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 8.1 Mendel’s Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174 8.2 Laws of Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 8.3 Extensions of the Laws of Inheritance . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Unit 3. Molecular Biology and Biotechnology Chapter 9: Molecular Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
9.1 The Structure of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200 9.2 DNA Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 9.3 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210 9.4 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 9.5 How Genes Are Regulated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Chapter 10: Biotechnology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225 10.1 Cloning and Genetic Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225 10.2 Biotechnology in Medicine and Agriculture . . . . . . . . . . . . . . . . . . . . . . . 232 10.3 Genomics and Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Unit 4. Evolution and the Diversity of Life Chapter 11: Evolution and Its Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
11.1 Discovering How Populations Change . . . . . . . . . . . . . . . . . . . . . . . . . . 250 11.2 Mechanisms of Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255 11.3 Evidence of Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258 11.4 Speciation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
11.5 Common Misconceptions about Evolution . . . . . . . . . . . . . . . . . . . . . . . . 266 Chapter 12: Diversity of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
12.1 Organizing Life on Earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 12.2 Determining Evolutionary Relationships . . . . . . . . . . . . . . . . . . . . . . . . . 280
Chapter 13: Diversity of Microbes, Fungi, and Protists . . . . . . . . . . . . . . . . . . . . . 291 13.1 Prokaryotic Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292 13.2 Eukaryotic Origins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302 13.3 Protists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304 13.4 Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
Chapter 14: Diversity of Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325 14.1 The Plant Kingdom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326 14.2 Seedless Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332 14.3 Seed Plants: Gymnosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338 14.4 Seed Plants: Angiosperms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
Chapter 15: Diversity of Animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355 15.1 Features of the Animal Kingdom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356 15.2 Sponges and Cnidarians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 15.3 Flatworms, Nematodes, and Arthropods . . . . . . . . . . . . . . . . . . . . . . . . . 367 15.4 Mollusks and Annelids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374 15.5 Echinoderms and Chordates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380 15.6 Vertebrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
Unit 5. Animal Structure and Function Chapter 16: The Body’s Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
16.1 Homeostasis and Osmoregulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404 16.2 Digestive System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408 16.3 Circulatory and Respiratory Systems . . . . . . . . . . . . . . . . . . . . . . . . . . 414 16.4 Endocrine System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420 16.5 Musculoskeletal System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426 16.6 Nervous System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
Chapter 17: The Immune System and Disease . . . . . . . . . . . . . . . . . . . . . . . . . 449 17.1 Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450 17.2 Innate Immunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456 17.3 Adaptive Immunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459 17.4 Disruptions in the Immune System . . . . . . . . . . . . . . . . . . . . . . . . . . . 468
Chapter 18: Animal Reproduction and Development . . . . . . . . . . . . . . . . . . . . . . 477 18.1 How Animals Reproduce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478 18.2 Development and Organogenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482 18.3 Human Reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Unit 6. Ecology Chapter 19: Population and Community Ecology . . . . . . . . . . . . . . . . . . . . . . . . 499
19.1 Population Demographics and Dynamics . . . . . . . . . . . . . . . . . . . . . . . . 500 19.2 Population Growth and Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . 504 19.3 The Human Population . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510 19.4 Community Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Chapter 20: Ecosystems and the Biosphere . . . . . . . . . . . . . . . . . . . . . . . . . . . 529 20.1 Energy Flow through Ecosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530 20.2 Biogeochemical Cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537 20.3 Terrestrial Biomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547 20.4 Aquatic and Marine Biomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Chapter 21: Conservation and Biodiversity . . . . . . . . . . . . . . . . . . . . . . . . . . . 567 21.1 Importance of Biodiversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568 21.2 Threats to Biodiversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575 21.3 Preserving Biodiversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 582
Appendix A: The Periodic Table of Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 593 Appendix B: Geological Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595 Appendix C: Measurements and the Metric System . . . . . . . . . . . . . . . . . . . . . . . . . 597 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605
This OpenStax book is available for free at http://cnx.org/content/col11487/1.9
PREFACE Welcome to Concepts of Biology, an OpenStax resource. This textbook has been created with several goals in mind: accessibility, customization, and student engagement—all while encouraging students toward high levels of academic scholarship. Instructors and students alike will find that this textbook offers a strong introduction to biology in an accessible format.
About OpenStax OpenStax is a non-profit organization committed to improving student access to quality learning materials. Our free textbooks are developed and peer-reviewed by educators to ensure they are readable, accurate, and meet the scope and sequence requirements of today’s college courses. Unlike traditional textbooks, OpenStax resources live online and are owned by the community of educators using them. Through our partnerships with companies and foundations committed to reducing costs for students, OpenStax is working to improve access to higher education for all. OpenStax is an initiative of Rice University and is made possible through the generous support of several philanthropic foundations.
About OpenStax’s Resources OpenStax resources provide quality academic instruction. Three key features set our materials apart from others: they can be customized by instructors for each class, they are a “living” resource that grows online through contributions from science educators, and they are available free or for minimal cost.
Customization OpenStax learning resources are designed to be customized for each course. Our textbooks provide a solid foundation on which instructors can build, and our resources are conceived and written with flexibility in mind. Instructors can select the sections most relevant to their curricula and create a textbook that speaks directly to the needs of their classes and student body. Teachers are encouraged to expand on existing examples by adding unique context via geographically localized applications and topical connections.
Concepts of Biology can be easily customized using our online platform. Simply select the content most relevant to your syllabus and create a textbook that speaks directly to the needs of your class. Concepts of Biology is organized as a collection of sections that can be rearranged, modified, and enhanced through localized examples or to incorporate a specific theme of your course. This customization feature will help bring biology to life for your students and will ensure that your textbook truly reflects the goals of your course.
Curation To broaden access and encourage community curation, Concepts of Biology is “open source” licensed under a Creative Commons Attribution (CC-BY) license. The scientific community is invited to submit examples, emerging research, and other feedback to enhance and strengthen the material and keep it current and relevant for today’s students. You can submit your suggestions to [email protected].
Cost Our textbooks are available for free online, and in low-cost print and e-book editions.
About Concepts of Biology Concepts of Biology is designed for the single-semester introduction to biology course for non-science majors, which for many students is their only college-level science course. As such, this course represents an important opportunity for students to develop the necessary knowledge, tools, and skills to make informed decisions as they continue with their lives. Rather than being mired down with facts and vocabulary, the typical non-science major student needs information presented in a way that is easy to read and understand. Even more importantly, the content should be meaningful. Students do much better when they understand why biology is relevant to their everyday lives. For these reasons, Concepts of Biology is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. We also strive to show the interconnectedness of topics within this extremely broad discipline. In order to meet the needs of today’s instructors and students, we maintain the overall organization and coverage found in most syllabi for this course. A strength of Concepts of Biology is that instructors can customize the book,
Preface 1
adapting it to the approach that works best in their classroom. Concepts of Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.
Coverage and Scope Our Concepts of Biology textbook adheres to the scope and sequence of most one-semester non-majors courses nationwide. We also strive to make biology, as a discipline, interesting and accessible to students. In addition to a comprehensive coverage of core concepts and foundational research, we have incorporated features that draw learners into the discipline in meaningful ways. Our scope of content was developed after surveying over a hundred biology professors and listening to their coverage needs. We provide a thorough treatment of biology’s fundamental concepts with a scope that is manageable for instructors and students alike.
Unit 1: The Cellular Foundation of Life. Our opening unit introduces students to the sciences, including the process of science and the underlying concepts from the physical sciences that provide a framework within which learners comprehend biological processes. Additionally, students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.
Unit 2: Cell Division and Genetics. Our genetics unit takes learners from the foundations of cellular reproduction to the experiments that revealed the basis of genetics and laws of inheritance.
Unit 3: Molecular Biology and Biotechnology. Students will learn the intricacies of DNA, protein synthesis, and gene regulation and current applications of biotechnology and genomics.
Unit 4: Evolution and the Diversity of Life. The core concepts of evolution are discussed in this unit with examples illustrating evolutionary processes. Additionally, the evolutionary basis of biology reappears throughout the textbook in general discussion and is reinforced through special call-out features highlighting specific evolution-based topics. The diversity of life is explored with detailed study of various organisms and discussion of emerging phylogenetic relationships between and among bacteria, protist kingdoms, fungi, plants, and animals.
Unit 5: Animal Structure and Function. An introduction to the form and function of the animal body is followed by chapters on the immune system and animal development. This unit touches on the biology of all organisms while maintaining an engaging focus on human anatomy and physiology that helps students connect to the topics.
Unit 6: Ecology. Ecological concepts are broadly covered in this unit, with features highlighting localized, real-world issues of conservation and biodiversity.
Pedagogical Foundation and Features Because of the impact science has on students and society, an important goal of science education is to achieve a scientifically literate population that consistently makes informed decisions. Scientific literacy transcends a basic understanding of scientific principles and processes to include the ability to make sense of the myriad instances where people encounter science in day-to-day life. Thus, a scientifically literate person is one who uses science content knowledge to make informed decisions, either personally or socially, about topics or issues that have a connection with science. Concepts of Biology is grounded on a solid scientific base and designed to promote scientific literacy. Throughout the text, you will find features that engage the students in scientific inquiry by taking selected topics a step further.
Evolution in Action features uphold the importance of evolution to all biological study through discussions like “Global Decline of Coral Reefs” and “The Red Queen Hypothesis.”
Career in Action features present information on a variety of careers in the biological sciences, introducing students to the educational requirements and day-to-day work life of a variety of professions, such as forensic scientists, registered dietitians, and biogeographers.
Biology in Action features tie biological concepts to emerging issues and discuss science in terms of everyday life. Topics include “Invasive Species” and “Photosynthesis at the Grocery Store.”
Art and Animations that Engage Our art program takes a straightforward approach designed to help students learn the concepts of biology through simple, effective illustrations, photos, and micrographs. Concepts of Biology also incorporates links to relevant animations and interactive exercises that help bring biology to life for students.
Art Connection features call out core figures in each chapter for student attention. Questions about key figures, including clicker questions that can be used in the classroom, engage students’ critical thinking and analytical abilities to ensure their genuine understanding of the concept at hand.
2 Preface
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Concepts in Action features direct students to online interactive exercises and animations to add a fuller context and examples to core content.
About Our Team Concepts of Biology would not be possible if not for the tremendous contributions of the authors and community reviewing team
Senior Contributing Authors
Samantha Fowler Clayton State University
Rebecca Roush Sandhills Community College
James Wise Hampton University
Contributing Authors and Reviewers
Mark Belk Brigham Young University
Lisa Boggs Southwestern Oklahoma State University
Sherryl Broverman Duke University
David Byres Florida State College at Jacksonville
Aaron Cassill The University of Texas at San Antonio
Karen Champ College of Central Florida
Sue Chaplin University of St. Thomas
Diane Day Clayton State University
Jean DeSaix University of North Carolina at Chapel Hill
David Hunnicutt St. Norbert College
Barbara Kuehner Hawaii Community College
Brenda Leady University of Toledo
Bernie Marcus Genesee Community College
Flora Mhlanga Lipscomb University
Madeline Mignone Dominican College
Elizabeth Nash Long Beach City College
Mark Newton San Jose City College
Diana Oliveras University of Colorado Boulder
Ann Paterson Williams Baptist College
Joel Piperberg Millersville University
Nick Reeves Mt. San Jacinto College
Ann Reisenauer San Jose State University
Lynn Rumfelt Gordon College
Michael Rutledge Middle Tennessee State University
Edward Saiff Ramapo College of New Jersey
Brian Shmaefsky Kingwood College
Gary Shultz Marshall University
Donald Slish SUNY Plattsburgh
Preface 3
Anh-Hue Tu Georgia Southwestern State University
Elena Zoubina Bridgewater State University
Learning Resources Wiley Plus for Biology-Fall 2013 Pilot
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1 | INTRODUCTION TO BIOLOGY
Figure 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: modification of work by NASA)
Chapter Outline 1.1: Themes and Concepts of Biology
1.2: The Process of Science
Introduction Viewed from space, Earth (Figure 1.1) offers few clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.
1.1 | Themes and Concepts of Biology
By the end of this section, you will be able to:
• Identify and describe the properties of life
• Describe the levels of organization among living things
• List examples of different sub disciplines in biology
Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life.
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From its earliest beginnings, biology has wrestled with four questions: What are the shared properties that make something “alive”? How do those various living things function? When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? And, finally—what biologists ultimately seek to understand—how did this diversity arise and how is it continuing? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.
Properties of Life All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. When viewed together, these eight characteristics serve to define life.
Order
Organisms are highly organized structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole. How these specialized cells come together to form organs such as the heart, lung, or skin in organisms like the toad shown in Figure 1.2 will be discussed later.
Figure 1.2 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit: “Ivengo(RUS)”/Wikimedia Commons)
Sensitivity or Response to Stimuli
Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or respond to touch (Figure 1.3). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.
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Figure 1.3 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to its normal state. (credit: Alex Lomas)
Watch this video (http://openstaxcollege.org/l/thigmonasty) to see how the sensitive plant responds to a touch stimulus.
Reproduction
Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells. Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism’s offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type.
Adaptation
All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. All adaptations enhance the reproductive potential of the individual exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes.
Growth and Development
Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure 1.4) will grow up to exhibit many of the same characteristics as its parents.
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Figure 1.4 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Pieter & Renée Lanser)
Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses. For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.
Homeostasis
To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through a process called homeostasis or “steady state”—the ability of an organism to maintain constant internal conditions. For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure 1.5), have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.
Figure 1.5 Polar bears and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: “longhorndave”/Flickr)
Energy Processing
All organisms (such as the California condor shown in Figure 1.6) use a source of energy for their metabolic activities. Some organisms capture energy from the Sun and convert it into chemical energy in food; others use chemical energy from molecules they take in.
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Figure 1.6 A lot of energy is required for a California condor to fly. Chemical energy derived from food is used to power flight. California condors are an endangered species; scientists have strived to place a wing tag on each bird to help them identify and locate each individual bird. (credit: Pacific Southwest Region U.S. Fish and Wildlife)
Levels of Organization of Living Things Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure 1.7), which contains the instructions for the functioning of the organism that contains it.
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Figure 1.7 A molecule, like this large DNA molecule, is composed of atoms. (credit: “Brian0918″/Wikimedia Commons)
To see an animation of this DNA molecule, click here (http://openstaxcollege.org/l/rotating_DNA2) .
Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of eukaryotes do have membrane-bound organelles and nuclei.
In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.
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Figure 1.8 From an atom to the entire Earth, biology examines all aspects of life. (credit “molecule”: modification of work by Jane Whitney; credit “organelles”: modification of work by Louisa Howard; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer, National Cancer Institute; credit “tissue”: modification of work by “Kilbad”/Wikimedia Commons; credit “organs”: modification of work by Mariana Ruiz Villareal, Joaquim Alves Gaspar; credit “organisms”: modification of work by Peter Dutton; credit “ecosystem”: modification of work by “gigi4791″/Flickr; credit “biosphere”: modification of work by NASA)
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Which of the following statements is false?
a. Tissues exist within organs which exist within organ systems.
b. Communities exist within populations which exist within ecosystems.
c. Organelles exist within cells which exist within tissues.
d. Communities exist within ecosystems which exist in the biosphere.
All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater. At the highest level of organization (Figure 1.8), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere.
The Diversity of Life The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.
In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on (Figure 1.9).
Figure 1.9 This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species.
The highest level, domain, is a relatively new addition to the system since the 1990s. Scientists now recognize three domains of life, the Eukarya, the Archaea, and the Bacteria. The domain Eukarya contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists. The Archaea, are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs. The Bacteria are another quite different group of single-celled organisms without nuclei (Figure 1.10). Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the 1990s that certain “bacteria,” now known as the Archaea, were as different genetically and biochemically from other bacterial cells as they were from eukaryotes, motivated the recommendation to divide life into three domains. This dramatic change in our knowledge of the tree of life demonstrates that classifications are not permanent and will change when new information becomes available.
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In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system. Before Linnaeus, the use of common names to refer to organisms caused confusion because there were regional differences in these common names. Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to. For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens.
Figure 1.10 These images represent different domains. The scanning electron micrograph shows (a) bacterial cells belong to the domain Bacteria, while the (b) extremophiles, seen all together as colored mats in this hot spring, belong to domain Archaea. Both the (c) sunflower and (d) lion are part of domain Eukarya. (credit a: modification of work by Rocky Mountain Laboratories, NIAID, NIH; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Frank Vassen)
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Carl Woese and the Phylogenetic Tree The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time.
In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree (Figure 1.11). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.
Figure 1.11 This phylogenetic tree was constructed by microbiologist Carl Woese using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba)
Branches of Biological Study The scope of biology is broad and therefore contains many branches and sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.
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Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub discipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.
Figure 1.12 Researchers work on excavating dinosaur fossils at a site in CastellĂłn, Spain. (credit: Mario Modesto)
Paleontology, another branch of biology, uses fossils to study life’s history (Figure 1.12). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study the interactions of organisms in their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives.
The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter.
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Forensic Scientist Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace material associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have updated the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure 1.13) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect parts or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses.
Figure 1.13 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory. (credit: U.S. Army CID Command Public Affairs)
1.2 | The Process of Science
By the end of this section, you will be able to:
• Identify the shared characteristics of the natural sciences
• Understand the process of scientific inquiry
• Compare inductive reasoning with deductive reasoning
• Describe the goals of basic science and applied science
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Figure 1.14 Formerly called blue-green algae, the (a) cyanobacteria seen through a light microscope are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; scale- bar data from Matt Russell; credit b: modification of work by Ruth Ellison)
Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on methods. In this sense, biology, like all sciences is a social enterprise like politics or the arts. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed experiment is commonly described as elegant, or beautiful. Like politics, science has considerable practical implications and some science is dedicated to practical applications, such as the prevention of disease (see Figure 1.15). Other science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so.
Figure 1.15 Biologists may choose to study Escherichia coli (E. coli), a bacterium that is a normal resident of our digestive tracts but which is also sometimes responsible for disease outbreaks. In this micrograph, the bacterium is visualized using a scanning electron microscope and digital colorization. (credit: Eric Erbe; digital colorization by Christopher Pooley, USDA-ARS)
The Nature of Science Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge about the natural world.
Science is a very specific way of learning, or knowing, about the world. The history of the past 500 years demonstrates that science is a very powerful way of knowing about the world; it is largely responsible for the technological revolutions
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that have taken place during this time. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science has cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured.
The scientific method is a method of research with defined steps that include experiments and careful observation. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses. A hypothesis is a suggested explanation for an event, which can be tested. Hypotheses, or tentative explanations, are generally produced within the context of a scientific theory. A scientific theory is a generally accepted, thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge. In addition, in many scientific disciplines (less so in biology) there are scientific laws, often expressed in mathematical formulas, which describe how elements of nature will behave under certain specific conditions. There is not an evolution of hypotheses through theories to laws as if they represented some increase in certainty about the world. Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description.
Natural Sciences
What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure 1.16). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.
Figure 1.16 Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics. (credit: “Image Editor”/Flickr)
There is no complete agreement when it comes to defining what the natural sciences include. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on two sciences and are interdisciplinary.
Scientific Inquiry
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them.
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These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.
Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis- based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.
Hypothesis Testing Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) (Figure 1.17), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.
Figure 1.17 Sir Francis Bacon is credited with being the first to document the scientific method.
The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”
Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.”
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But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”
Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”
A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis.
Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure 1.18). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.
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Figure 1.18 The scientific method is a series of defined steps that include experiments and careful observation. If a hypothesis is not supported by data, a new hypothesis can be proposed.
In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.
1. My toaster doesn’t toast my bread.
2. Why doesn’t my toaster work?
3. There is something wrong with the electrical outlet.
4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
5. I plug my coffeemaker into the outlet.
6. My coffeemaker works.
In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.
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Basic and Applied Science The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.
Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that in the end it may not result in an application.
In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher.
Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science.
One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project (Figure 1.19) relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases.
Figure 1.19 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project was completed in 2003. (credit: the U.S. Department of Energy Genome Programs)
While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in
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the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.
Reporting Scientific Work Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists.
There are many journals and the popular press that do not use a peer-review system. A large number of online open- access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.
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applied science
atom
basic science
biology
biosphere
cell
community
control
deductive reasoning
descriptive science
ecosystem
eukaryote
evolution
falsifiable
homeostasis
hypothesis
hypothesis-based science
inductive reasoning
life science
macromolecule
molecule
natural science
organ
organ system
organelle
organism
peer-reviewed article
phylogenetic tree
physical science
population
prokaryote
KEY TERMS a form of science that solves real-world problems
a basic unit of matter that cannot be broken down by normal chemical reactions
science that seeks to expand knowledge regardless of the short-term application of that knowledge
the study of living organisms and their interactions with one another and their environments
a collection of all ecosystems on Earth
the smallest fundamental unit of structure and function in living things
a set of populations inhabiting a particular area
a part of an experiment that does not change during the experiment
a form of logical thinking that uses a general statement to forecast specific results
a form of science that aims to observe, explore, and find things out
all living things in a particular area together with the abiotic, nonliving parts of that environment
an organism with cells that have nuclei and membrane-bound organelles
the process of gradual change in a population that can also lead to new species arising from older species
able to be disproven by experimental results
the ability of an organism to maintain constant internal conditions
a suggested explanation for an event, which can be tested
a form of science that begins with a specific explanation that is then tested
a form of logical thinking that uses related observations to arrive at a general conclusion
a field of science, such as biology, that studies living things
a large molecule typically formed by the joining of smaller molecules
a chemical structure consisting of at least two atoms held together by a chemical bond
a field of science that studies the physical world, its phenomena, and processes
a structure formed of tissues operating together to perform a common function
the higher level of organization that consists of functionally related organs
a membrane-bound compartment or sac within a cell
an individual living entity
a scientific report that is reviewed by a scientist’s colleagues before publication
a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both
a field of science, such as astronomy, physics, and chemistry, that studies nonliving matter
all individuals within a species living within a specific area
a unicellular organism that lacks a nucleus or any other membrane-bound organelle
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science
scientific law
scientific method
scientific theory
tissue
variable
knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
a description, often in the form of a mathematical formula, for the behavior of some aspect of nature under certain specific conditions
a method of research with defined steps that include experiments and careful observation
a thoroughly tested and confirmed explanation for observations or phenomena
a group of similar cells carrying out the same function
a part of an experiment that can vary or change
CHAPTER SUMMARY 1.1 Themes and Concepts of Biology
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. Evolution is the source of the tremendous biological diversity on Earth today. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is very broad and includes many branches and sub disciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.
1.2 The Process of Science
Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences.
A hypothesis is a tentative explanation for an observation. A scientific theory is a well-tested and consistently verified explanation for a set of observations or phenomena. A scientific law is a description, often in the form of a mathematical formula, of the behavior of an aspect of nature under certain circumstances. Two types of logical reasoning are used in science. Inductive reasoning uses results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method. Scientists present their results in peer-reviewed scientific papers published in scientific journals.
Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short- term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.
ART CONNECTION QUESTIONS 1. Figure 1.8 Which of the following statements is false?
A. Tissues exist within organs which exist within organ systems.
B. Communities exist within populations which exist within ecosystems.
C. Organelles exist within cells which exist within tissues.
D. Communities exist within ecosystems which exist in the biosphere.
2. Figure 1.18 In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction?
Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.
1. My toaster doesn’t toast my bread. 2. Why doesn’t my toaster work? 3. There is something wrong with the electrical
outlet. 4. If something is wrong with the outlet, my
coffeemaker also won’t work when plugged into it.
5. I plug my coffeemaker into the outlet. 6. My coffeemaker works.
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REVIEW QUESTIONS 3. The smallest unit of biological structure that meets the functional requirements of “living” is the ________.
a. organ b. organelle c. cell d. macromolecule
4. Which of the following sequences represents the hierarchy of biological organization from the most complex to the least complex level?
a. organelle, tissue, biosphere, ecosystem, population
b. organ, organism, tissue, organelle, molecule c. organism, community, biosphere, molecule,
tissue, organ
d. biosphere, ecosystem, community, population, organism
5. A suggested and testable explanation for an event is called a ________.
a. hypothesis b. variable c. theory d. control
6. The type of logical thinking that uses related observations to arrive at a general conclusion is called ________.
a. deductive reasoning b. the scientific method c. hypothesis-based science d. inductive reasoning
CRITICAL THINKING QUESTIONS 7. Using examples, explain how biology can be studied from a microscopic approach to a global approach.
8. Give an example of how applied science has had a direct effect on your daily life.
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2 | CHEMISTRY OF LIFE
Figure 2.1 Foods such as bread, fruit, and cheese are rich sources of biological macromolecules. (credit: modification of work by Bengt Nyman)
Chapter Outline 2.1: The Building Blocks of Molecules
2.2: Water
2.3: Biological Molecules
Introduction The elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form the carbohydrates, nucleic acids, proteins, and lipids (all of which will be defined later in this chapter) that are the fundamental molecular components of all organisms. In this chapter, we will discuss these important building blocks and learn how the unique properties of the atoms of different elements affect their interactions with other atoms to form the molecules of life.
Food provides an organism with nutrients—the matter it needs to survive. Many of these critical nutrients come in the form of biological macromolecules, or large molecules necessary for life. These macromolecules are built from different combinations of smaller organic molecules. What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, we will explore these questions.
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2.1 | The Building Blocks of Molecules
By the end of this section, you will be able to:
• Describe matter and elements
• Describe the interrelationship between protons, neutrons, and electrons, and the ways in which electrons can be donated or shared between atoms
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected.
Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.
Atoms An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.
At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.
All atoms contain protons, electrons, and neutrons (Figure 2.2). The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.
Figure 2.2 Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.
Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.
Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small.
As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.
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These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements (Figure 2.2)—often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.
Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.
Figure 2.3 Arranged in columns and rows based on the characteristics of the elements, the periodic table provides key information about the elements and how they might interact with each other to form molecules. Most periodic tables provide a key or legend to the information they contain.
How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
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Carbon Dating Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process.
After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years (Figure 2.4). Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.
Figure 2.4 The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner/NPS)
To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site (http://openstaxcollege.org/l/isotopes) and run the simulation.
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Chemical Bonds How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.
The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.
Looking at the periodic table again (Figure 2.3), you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.
Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.
When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions.
For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.
The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As Figure 2.5 illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.
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Figure 2.5 Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons from other elements.
Ionic Bonds
There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl– ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.
Covalent Bonds
Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when an electron is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.
The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.
There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds (Figure 2.6).
In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared
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electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge.
Figure 2.6 The water molecule (left) depicts a polar bond with a slightly positive charge on the hydrogen atoms and a slightly negative charge on the oxygen. Examples of nonpolar bonds include methane (middle) and oxygen (right).
Hydrogen Bonds
Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.
When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules (Figure 2.7). Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.
Figure 2.7 Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of polar covalent molecules, such as water.
Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible for some of the three-dimensional structure of proteins.
van der Waals Interactions
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.
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Radiography Technician Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radiowaves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.
MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.
Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.
Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.
2.2 | Water
By the end of this section, you will be able to:
• Describe the properties of water that are critical to maintaining life
Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.
Water Is Polar The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape seen in Figure 2.7. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats (Figure 2.8). These nonpolar compounds are hydrophobic (“water- fearing”) and will not dissolve in water.
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Figure 2.8 As this macroscopic image of oil and water show, oil is a nonpolar compound and, hence, will not dissolve in water. Oil and water do not mix. (credit: Gautam Dogra)
Water Stabilizes Temperature The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.
Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure 2.9a). When frozen, ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water (Figure 2.9b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a block of ice and could not move freely, making life in cold temperatures difficult or impossible.
Figure 2.9 (a) The lattice structure of ice makes it less dense than the freely flowing molecules of liquid water. Ice’s lower density enables it to (b) float on water. (credit a: modification of work by Jane Whitney; credit b: modification of work by Carlos Ponte)
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Click here (http://openstaxcollege.org/l/ice_lattice) to see a 3-D animation of the structure of an ice lattice. (credit: image created by Jane Whitney using Visual Molecular Dynamics (VMD) software
[1] )
Water Is an Excellent Solvent Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water (Figure 2.10), the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.
Figure 2.10 When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.
Water Is Cohesive Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop
1. Humphrey, W., Dalke, A. and Schulten, K., “VMD—Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38. http://www.ks.uiuc.edu/Research/vmd/
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a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension (Figure 2.11).
Figure 2.11 The weight of a needle on top of water pulls the surface tension downward; at the same time, the surface tension of the water is pulling it up, suspending the needle on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)
These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.
Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.
To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website. (http://openstaxcollege.org/l/about_water)
Buffers, pH, Acids, and Bases The pH of a solution is a measure of its acidity or alkalinity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (alkalinity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale (Figure 2.12). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.
The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).
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Figure 2.12 The pH scale measures the amount of hydrogen ions (H+) in a substance. (credit: modification of work by Edward Stevens)
Acids are substances that provide hydrogen ions (H+) and lower pH, whereas bases provide hydroxide ions (OH–) and raise pH. The stronger the acid, the more readily it donates H+. For example, hydrochloric acid and lemon juice are very acidic and readily give up H+ when added to water. Conversely, bases are those substances that readily donate OH–. The OH– ions combine with H+ to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up OH– rapidly when placed in water, thereby raising the pH.
Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.
So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffers readily absorb excess H+ or OH–, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H2CO3) and bicarbonate (HCO3–) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH– is introduced into the system, carbonic acid will rapidly dissociate into bicarbonate and H+ ions. The H+ ions can combine with the OH– ions, limiting the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.
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2.3 | Biological Molecules
By the end of this section, you will be able to:
• Describe the ways in which carbon is critical to life
• Explain the impact of slight changes in amino acids on organisms
• Describe the four major types of biological molecules
• Understand the functions of the four major types of molecules
The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.
Carbon It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.
Carbon Bonding Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom (Figure 2.13).
Figure 2.13 Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH4), depicted here.
However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 2.14a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2.14b). The molecules may also form rings, which themselves can link with other rings (Figure 2.14c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms.
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Figure 2.14 These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.
Carbohydrates Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.
Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms).
Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring form.
The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed on plants.
Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers) because of differing arrangements of atoms in the carbon chain (Figure 2.15).
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Figure 2.15 Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula but slightly different structures.
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a water molecule occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar molecules.
Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.
A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are examples of polysaccharides.
Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.
Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose.
Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the glucose molecule.
Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called dietary fiber. While the glucose-glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix also contains bacteria that break down cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal.
Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the biological macromolecule chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen.
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Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and glycogen) and structural support and protection (cellulose and chitin) (Figure 2.16).
Figure 2.16 Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have the chemical formula (CH2O)n.
Registered Dietitian Obesity is a worldwide health concern, and many diseases, such as diabetes and heart disease, are becoming more prevalent because of obesity. This is one of the reasons why registered dietitians are increasingly sought after for advice. Registered dietitians help plan food and nutrition programs for individuals in various settings. They often work with patients in health-care facilities, designing nutrition plans to prevent and treat diseases. For example, dietitians may teach a patient with diabetes how to manage blood-sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices.
To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and functions of food (proteins, carbohydrates, and fats).
Lipids Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water- fearing”), or insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals (Figure 2.17). For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.
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Figure 2.17 Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit: Ken Bosma)
A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond (Figure 2.18).
Figure 2.18 Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.
During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or dissimilar. These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common
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names that specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the carbon skeleton is maximized.
When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid.
Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).
Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid contained in meat, and the fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.
Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases the risk of a heart attack.
In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation. This forms a trans-fat from a cis-fat. The orientation of the double bonds affects the chemical properties of the fat (Figure 2.19).
Figure 2.19 During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a cis-fat. This changes the chemical properties of the molecule.
Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans- fat content.
Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega-6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third carbon from the end of the fatty acid participates in a double bond.
Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and development. They may also prevent heart disease and reduce the risk of cancer.
Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also
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provide insulation for the body. Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis.
Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the glycerol backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.
A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from water, whereas the phosphate is hydrophilic and interacts with water.
Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.
Steroids and Waxes
Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Although they do not resemble other lipids, they are grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like cholesterol, have a short tail.
Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells.
Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out.
For an additional perspective on lipids, explore “Biomolecules: The Lipids” through this interactive animation (http://openstaxcollege.org/l/lipids) .
Proteins Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.
The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch.
Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels.
Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape
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of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise, the amino acids are identical (Figure 2.20).
Figure 2.20 Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.
The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar).
The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.
The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.
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The Evolutionary Significance of Cytochrome c Cytochrome c is an important component of the molecular machinery that harvests energy from glucose. Because this protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of sequence similarity among cytochrome c molecules of different species; evolutionary relationships can be assessed by measuring the similarities or differences among various species’ protein sequences.
For example, scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule that has been sequenced to date from different organisms, 37 of these amino acids appear in the same position in each cytochrome c. This indicates that all of these organisms are descended from a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, a single difference was found in one amino acid. In contrast, human-to-yeast comparisons show a difference in 44 amino acids, suggesting that humans and chimpanzees have a more recent common ancestor than humans and the rhesus monkey, or humans and yeast.
Protein Structure
As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary (Figure 2.21).
The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a single amino acid of the 600.
Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease.
Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.
In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.
The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.
In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits.
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Figure 2.21 The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute)
Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.
For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation (http://openstaxcollege.org/l/proteins) .
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Nucleic Acids Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure 2.22). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.
Figure 2.22 A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.
DNA Double-Helical Structure DNA has a double-helical structure (Figure 2.23). It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral.
Figure 2.23 The double-helix model shows DNA as two parallel strands of intertwining molecules. (credit: Jerome Walker, Dennis Myts)
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The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.
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acid
adhesion
amino acid
anion
atomic number
base
buffer
carbohydrate
cation
cellulose
chemical bond
chitin
cohesion
covalent bond
denaturation
deoxyribonucleic acid (DNA)
disaccharide
electron
electron transfer
element
enzyme
evaporation
fat
glycogen
hormone
hydrogen bond
KEY TERMS a substance that donates hydrogen ions and therefore lowers pH
the attraction between water molecules and molecules of a different substance
a monomer of a protein
a negative ion formed by gaining electrons
the number of protons in an atom
a substance that absorbs hydrogen ions and therefore raises pH
a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions
a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells
a positive ion formed by losing electrons
a polysaccharide that makes up the cell walls of plants and provides structural support to the cell
an interaction between two or more of the same or different elements that results in the formation of molecules
a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and crustaceans, and the cell walls of fungi
the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension
a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements
the loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals
a double-stranded polymer of nucleotides that carries the hereditary information of the cell
two sugar monomers that are linked together by a peptide bond
a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of –1
the movement of electrons from one element to another
one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties
a catalyst in a biochemical reaction that is usually a complex or conjugated protein
the release of water molecules from liquid water to form water vapor
a lipid molecule composed of three fatty acids and a glycerol (triglyceride) that typically exists in a solid form at room temperature
a storage carbohydrate in animals
a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine gland or group of endocrine cells; acts to control or regulate specific physiological processes
a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules
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hydrophilic
hydrophobic
ion
ionic bond
isotope
lipids
litmus paper
macromolecule
mass number
matter
monosaccharide
neutron
nonpolar covalent bond
nucleic acid
nucleotide
nucleus
octet rule
oil
periodic table of elements
pH scale
phospholipid
polar covalent bond
polypeptide
polysaccharide
protein
proton
radioactive isotope
ribonucleic acid (RNA)
saturated fatty acid
describes a substance that dissolves in water; water-loving
describes a substance that does not dissolve in water; water-fearing
an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge
a chemical bond that forms between ions of opposite charges
one or more forms of an element that have different numbers of neutrons
a class of macromolecules that are nonpolar and insoluble in water
filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator
a large molecule, often formed by polymerization of smaller monomers
the number of protons plus neutrons in an atom
anything that has mass and occupies space
a single unit or monomer of carbohydrates
a particle with no charge that resides in the nucleus of an atom; has a mass of 1
a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds
a biological macromolecule that carries the genetic information of a cell and carries instructions for the functioning of the cell
a monomer of nucleic acids; contains a pentose sugar, a phosphate group, and a nitrogenous base
(chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons
states that the outermost shell of an element with a low atomic number can hold eight electrons
an unsaturated fat that is a liquid at room temperature
an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key information about the properties of elements
a scale ranging from 0 to 14 that measures the approximate concentration of hydrogen ions of a substance
a major constituent of the membranes of cells; composed of two fatty acids and a phosphate group attached to the glycerol backbone
a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule
a long chain of amino acids linked by peptide bonds
a long chain of monosaccharides; may be branched or unbranched
a biological macromolecule composed of one or more chains of amino acids
a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1
an isotope that spontaneously emits particles or energy to form a more stable element
a single-stranded polymer of nucleotides that is involved in protein synthesis
a long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
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solvent
starch
steroid
surface tension
temperature
trans-fat
triglyceride
unsaturated fatty acid
van der Waals interaction
a substance capable of dissolving another substance
a storage carbohydrate in plants
a type of lipid composed of four fused hydrocarbon rings
the cohesive force at the surface of a body of liquid that prevents the molecules from separating
a measure of molecular motion
a form of unsaturated fat with the hydrogen atoms neighboring the double bond across from each other rather than on the same side of the double bond
a fat molecule; consists of three fatty acids linked to a glycerol molecule
a long-chain hydrocarbon that has one or more than one double bonds in the hydrocarbon chain
a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms
CHAPTER SUMMARY 2.1 The Building Blocks of Molecules
Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
2.2 Water
Water has many properties that are critical to maintaining life. It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is added to the system. Water’s cohesive forces allow for the property of surface tension. All of these unique properties of water are important in the chemistry of living organisms.
The pH of a solution is a measure of the concentration of hydrogen ions in the solution. A solution with a high number of hydrogen ions is acidic and has a low pH value. A solution with a high number of hydroxide ions is basic and has a high pH value. The pH scale ranges from 0 to 14, with a pH of 7 being neutral. Buffers are solutions that moderate pH changes when an acid or base is added to the buffer system. Buffers are important in biological systems because of their ability to maintain constant pH conditions.
2.3 Biological Molecules
Living things are carbon-based because carbon plays such a prominent role in the chemistry of living things. The four covalent bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions, accounting for the importance of carbon in living things. Carbohydrates are a group of macromolecules that are a vital energy source for the cell, provide structural support to many organisms, and can be found on the surface of the cell as receptors or for cell recognition. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides, depending on the number of monomers in the molecule.
Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats and oils are a stored form of energy and can include triglycerides. Fats and oils are usually made up of fatty acids and glycerol.
Proteins are a class of macromolecules that can perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers or as hormones. The building blocks of proteins are amino acids. Proteins are organized at four levels: primary, secondary, tertiary, and quaternary. Protein shape and function are intricately linked; any change in shape caused by changes in temperature, pH, or chemical exposure may lead to protein denaturation and a loss of function.
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Nucleic acids are molecules made up of repeating units of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA.
ART CONNECTION QUESTIONS 1. Figure 2.3 How many neutrons do (K) potassium-39 and potassium-40 have, respectively?
REVIEW QUESTIONS 2. Magnesium has an atomic number of 12. Which of the following statements is true of a neutral magnesium atom?
a. It has 12 protons, 12 electrons, and 12 neutrons. b. It has 12 protons, 12 electrons, and six neutrons. c. It has six protons, six electrons, and no neutrons. d. It has six protons, six electrons, and six
neutrons.
3. Which type of bond represents a weak chemical bond?
a. hydrogen bond b. ionic bond c. covalent bond d. polar covalent bond
4. An isotope of sodium (Na) has a mass number of 22. How many neutrons does it have?
a. 11 b. 12 c. 22 d. 44
5. Which of the following statements is not true?
a. Water is polar. b. Water stabilizes temperature. c. Water is essential for life. d. Water is the most abundant atom in Earth’s
atmosphere.
6. Using a pH meter, you find the pH of an unknown solution to be 8.0. How would you describe this solution?
a. weakly acidic b. strongly acidic c. weakly basic d. strongly basic
7. The pH of lemon juice is about 2.0, whereas tomato juice’s pH is about 4.0. Approximately how much of an increase in hydrogen ion concentration is there between tomato juice and lemon juice?
a. 2 times b. 10 times c. 100 times d. 1000 times
8. An example of a monosaccharide is ________.
a. fructose b. glucose c. galactose d. all of the above
9. Cellulose and starch are examples of ________.
a. monosaccharides b. disaccharides c. lipids d. polysaccharides
10. Phospholipids are important components of __________.
a. the plasma membrane of cells b. the ring structure of steroids c. the waxy covering on leaves d. the double bond in hydrocarbon chains
11. The monomers that make up proteins are called _________.
a. nucleotides b. disaccharides c. amino acids d. chaperones
CRITICAL THINKING QUESTIONS 12. Why are hydrogen bonds and van der Waals interactions necessary for cells?
13. Why can some insects walk on water?
14. Explain why water is an excellent solvent.
15. Explain at least three functions that lipids serve in plants and/or animals.
16. Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.
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3 | CELL STRUCTURE AND FUNCTION
Figure 3.1 (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (viewed using a scanning electron microscope) are from very different organisms, yet all share certain characteristics of basic cell structure. (credit a: modification of work by Ed Uthman, MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D’Onofrio; scale-bar data from Matt Russell)
Chapter Outline 3.1: How Cells Are Studied
3.2: Comparing Prokaryotic and Eukaryotic Cells
3.3: Eukaryotic Cells
3.4: The Cell Membrane
3.5: Passive Transport
3.6: Active Transport
Introduction Close your eyes and picture a brick wall. What is the basic building block of that wall? It is a single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells.
Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, red blood cells carry oxygen throughout the body. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, all cells share certain fundamental characteristics.
3.1 | How Cells Are Studied
By the end of this section, you will be able to:
• Describe the roles of cells in organisms
• Compare and contrast light microscopy and electron microscopy
• Summarize the cell theory
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A cell is the smallest unit of a living thing. A living thing, like you, is called an organism. Thus, cells are the basic building blocks of all organisms.
In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example, stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems functioning together form an organism (such as an elephant, for example).
There are many types of cells, and all are grouped into one of two broad categories: prokaryotic and eukaryotic. Animal cells, plant cells, fungal cells, and protist cells are classified as eukaryotic, whereas bacteria and archaea cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let us first examine how biologists study cells.
Microscopy Cells vary in size. With few exceptions, individual cells are too small to be seen with the naked eye, so scientists use microscopes to study them. A microscope is an instrument that magnifies an object. Most images of cells are taken with a microscope and are called micrographs.
Light Microscopes
To give you a sense of the size of a cell, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as µm) in diameter; the head of a pin is about two thousandths of a meter (millimeters, or mm) in diameter. That means that approximately 250 red blood cells could fit on the head of a pin.
The optics of the lenses of a light microscope changes the orientation of the image. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Due to the manner in which light travels through the lenses, this system of lenses produces an inverted image (binoculars and a dissecting microscope work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).
Most student microscopes are classified as light microscopes (Figure 3.2a). Visible light both passes through and is bent by the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.
Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the degree of enlargement of an object. Resolving power is the ability of a microscope to allow the eye to distinguish two adjacent structures as separate; the higher the resolution, the closer those two objects can be, and the better the clarity and detail of the image. When oil immersion lenses are used, magnification is usually increased to 1,000 times for the study of smaller cells, like most prokaryotic cells. Because light entering a specimen from below is focused onto the eye of an observer, the specimen can be viewed using light microscopy. For this reason, for light to pass through a specimen, the sample must be thin or translucent.
For another perspective on cell size, try the HowBig (http://openstaxcollege.org/l/cell_sizes2) interactive.
A second type of microscope used in laboratories is the dissecting microscope (Figure 3.2b). These microscopes have a lower magnification (20 to 80 times the object size) than light microscopes and can provide a three-dimensional view of the specimen. Thick objects can be examined with many components in focus at the same time. These microscopes are designed to give a magnified and clear view of tissue structure as well as the anatomy of the whole organism. Like light
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microscopes, most modern dissecting microscopes are also binocular, meaning that they have two separate lens systems, one for each eye. The lens systems are separated by a certain distance, and therefore provide a sense of depth in the view of their subject to make manipulations by hand easier. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample, but may also be directed from below.
Figure 3.2 (a) Most light microscopes used in a college biology lab can magnify cells up to approximately 400 times. (b) Dissecting microscopes have a lower magnification than light microscopes and are used to examine larger objects, such as tissues.
Electron Microscopes
In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 3.3), it also provides higher resolving power. Preparation of a specimen for viewing under an electron microscope will kill it; therefore, live cells cannot be viewed using this type of microscopy. In addition, the electron beam moves best in a vacuum, making it impossible to view living materials.
In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, rendering the details of cell surface characteristics by reflection. Cells and other structures are usually coated with a metal like gold. In a transmission electron microscope, the electron beam is transmitted through the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than are light microscopes.
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(a) (b) Figure 3.3 (a) Salmonella bacteria are viewed with a light microscope. (b) This scanning electron micrograph shows Salmonella bacteria (in red) invading human cells. (credit a: modification of work by CDC, Armed Forces Institute of Pathology, Charles N. Farmer; credit b: modification of work by Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt Russell)
Cytotechnologist Have you ever heard of a medical test called a Pap smear (Figure 3.4)? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.
Cytotechnologists (cyto- = cell) are professionals who study cells through microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits or are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis.
Cytotechnologists play vital roles in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of successful treatment.
Figure 3.4 These uterine cervix cells, viewed through a light microscope, were obtained from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)
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Cell Theory The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”
In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” (from the Latin cella, meaning “small room”) for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see different components inside cells.
By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, that the cell is the basic unit of life, and that all new cells arise from existing cells. These principles still stand today.
3.2 | Comparing Prokaryotic and Eukaryotic Cells
By the end of this section, you will be able to:
• Name examples of prokaryotic and eukaryotic organisms
• Compare and contrast prokaryotic cells and eukaryotic cells
• Describe the relative sizes of different kinds of cells
Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus). Animal cells, plant cells, fungi, and protists are eukaryotes (eu- = true).
Components of Prokaryotic Cells All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.
A prokaryotic cell is a simple, single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the cell: a darkened region called the nucleoid (Figure 3.5).
Figure 3.5 This figure shows the generalized structure of a prokaryotic cell.
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Unlike Archaea and eukaryotes, bacteria have a cell wall made of peptidoglycan, comprised of sugars and amino acids, and many have a polysaccharide capsule (Figure 3.5). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion, while most pili are used to exchange genetic material during a type of reproduction called conjugation.
Eukaryotic Cells In nature, the relationship between form and function is apparent at all levels, including the level of the cell, and this will become clear as we explore eukaryotic cells. The principle “form follows function” is found in many contexts. For example, birds and fish have streamlined bodies that allow them to move quickly through the medium in which they live, be it air or water. It means that, in general, one can deduce the function of a structure by looking at its form, because the two are matched.
A eukaryotic cell is a cell that has a membrane-bound nucleus and other membrane-bound compartments or sacs, called organelles, which have specialized functions. The word eukaryotic means “true kernel” or “true nucleus,” alluding to the presence of the membrane-bound nucleus in these cells. The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions.
Cell Size At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10–100 µm (Figure 3.6). The small size of prokaryotes allows ions and organic molecules that enter them to quickly spread to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly move out. However, larger eukaryotic cells have evolved different structural adaptations to enhance cellular transport. Indeed, the large size of these cells would not be possible without these adaptations. In general, cell size is limited because volume increases much more quickly than does cell surface area. As a cell becomes larger, it becomes more and more difficult for the cell to acquire sufficient materials to support the processes inside the cell, because the relative size of the surface area across which materials must be transported declines.
Figure 3.6 This figure shows the relative sizes of different kinds of cells and cellular components. An adult human is shown for comparison.
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3.3 | Eukaryotic Cells
By the end of this section, you will be able to:
• Describe the structure of eukaryotic plant and animal cells
• State the role of the plasma membrane
• Summarize the functions of the major cell organelles
• Describe the cytoskeleton and extracellular matrix
At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us first examine two important components of the cell: the plasma membrane and the cytoplasm.
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(a)
(b) Figure 3.7 This figure shows (a) a typical animal cell and (b) a typical plant cell.
What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?
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The Plasma Membrane Like prokaryotes, eukaryotic cells have a plasma membrane (Figure 3.8) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.
Figure 3.8 The plasma membrane is a phospholipid bilayer with embedded proteins. There are other components, such as cholesterol and carbohydrates, which can be found in the membrane in addition to phospholipids and protein.
The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a structure.
People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.
The Cytoplasm The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure 3.7). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.
The Cytoskeleton If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules (Figure 3.9).
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Figure 3.9 Microfilaments, intermediate filaments, and microtubules compose a cell’s cytoskeleton.
Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and two microtubules in the center.
The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.
The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.
Flagella and Cilia
Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that move particulate matter toward the throat that mucus has trapped).
The Endomembrane System The endomembrane system (endo = within) is a group of membranes and organelles (Figure 3.13) in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.
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The Nucleus
Typically, the nucleus is the most prominent organelle in a cell (Figure 3.7). The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure 3.10).
Figure 3.10 The outermost boundary of the nucleus is the nuclear envelope. Notice that the nuclear envelope consists of two phospholipid bilayers (membranes)—an outer membrane and an inner membrane—in contrast to the plasma membrane (Figure 3.8), which consists of only one phospholipid bilayer. (credit: modification of work by NIGMS, NIH)
The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure 3.10). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers.
The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and the cytoplasm.
To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and proteins. This combination of DNA and proteins is called chromatin. In eukaryotes, chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number is eight.
Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, the chromosomes resemble an unwound, jumbled bunch of threads.
We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus, called the nucleolus (plural = nucleoli), aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores into the cytoplasm.
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) (Figure 3.13) is a series of interconnected membranous tubules that collectively modify proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.
The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope.
The ribosomes synthesize proteins while attached to the ER, resulting in transfer of their newly synthesized proteins into the lumen of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell membranes.
If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported from the RER by budding from the membrane (Figure 3.13). Since the RER is engaged in modifying proteins that will be secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.
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The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (see Figure 3.7). The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones; detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.
The Golgi Apparatus
We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs (Figure 3.11).
Figure 3.11 The Golgi apparatus in this transmission electron micrograph of a white blood cell is visible as a stack of semicircular flattened rings in the lower portion of this image. Several vesicles can be seen near the Golgi apparatus. (credit: modification of work by Louisa Howard; scale-bar data from Matt Russell)
The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then tagged with small molecular groups to enable them to be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory vesicles, fuse with the plasma membrane and release their contents outside the cell.
The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundant number of Golgi.
In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.
Lysosomes
In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure 3.12).
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Figure 3.12 A macrophage has phagocytized a potentially pathogenic bacterium into a vesicle, which then fuses with a lysosome within the cell so that the pathogen can be destroyed. Other organelles are present in the cell, but for simplicity, are not shown.
Vesicles and Vacuoles
Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.
Figure 3.13 The endomembrane system works to modify, package, and transport lipids and proteins. (credit: modification of work by Magnus Manske)
Why does the cis face of the Golgi not face the plasma membrane?
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Ribosomes Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum (Figure 3.7). Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.
Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in the transport of oxygen throughout the body.
Mitochondria Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure 3.14) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.
In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.
Figure 3.14 This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the inner and outer membranes, the cristae, and the mitochondrial matrix. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell)
Peroxisomes Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.
Animal Cells versus Plant Cells Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table 3.1). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.
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The Cell Wall
In Figure 3.7b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also have cell walls.
While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is referring to the cellulose content of food.
Chloroplasts
Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.
Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure 3.15). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.
Figure 3.15 This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and stroma.
The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.
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Endosymbiosis We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.
Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.
Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.
The Central Vacuole
Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure 3.7, you will see that plant cells each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in developing seed cells.
Extracellular Matrix of Animal Cells Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called the extracellular matrix (Figure 3.16). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.
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Figure 3.16 The extracellular matrix consists of a network of substances secreted by cells.
Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.
Intercellular Junctions Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.
In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure 3.17a).
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Figure 3.17 There are four kinds of connections between cells. (a) A plasmodesma is a channel between the cell walls of two adjacent plant cells. (b) Tight junctions join adjacent animal cells. (c) Desmosomes join two animal cells together. (d) Gap junctions act as channels between animal cells. (credit b, c, d: modification of work by Mariana Ruiz Villareal)
A tight junction is a watertight seal between two adjacent animal cells (Figure 3.17b). Proteins hold the cells tightly against each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.
Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure 3.17c). They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.
Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure 3.17d). Structurally, however, gap junctions and plasmodesmata differ.
Components of Prokaryotic and Eukaryotic Cells and Their Functions
Cell Component Function
Present in Prokaryotes?
Present in
Animal Cells?
Present in Plant Cells?
Plasma membrane
Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cell
Yes Yes Yes
Table 3.1
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Components of Prokaryotic and Eukaryotic Cells and Their Functions
Cell Component Function
Present in Prokaryotes?
Present in
Animal Cells?
Present in Plant Cells?
Cytoplasm Provides structure to cell; site of many metabolic reactions; medium in which organelles are found
Yes Yes Yes
Nucleoid Location of DNA Yes No No
Nucleus Cell organelle that houses DNA and directssynthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidizes and breaks down fatty acids andamino acids, and detoxifies poisons No Yes Yes
Vesicles and vacuoles
Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; organizing center of microtubules in animal cells
No Yes No
Lysosomes Digestion of macromolecules; recycling ofworn-out organelles No Yes No
Cell wall Protection, structural support andmaintenance of cell shape
Yes, primarily peptidoglycan in bacteria but not Archaea
No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, anddistributes lipids and proteins No Yes Yes
Cytoskeleton
Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently
Yes Yes Yes
Flagella Cellular locomotion Some Some
No, except for some plant sperm.
Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration
No Some No
Table 3.1
This table provides the components of prokaryotic and eukaryotic cells and their respective functions.
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3.4 | The Cell Membrane
By the end of this section, you will be able to:
• Understand the fluid mosaic model of membranes
• Describe the functions of phospholipids, proteins, and carbohydrates in membranes
A cell’s plasma membrane defines the boundary of the cell and determines the nature of its contact with the environment. Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux. The plasma membrane must be sufficiently flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital as tissues and organs form during early development, and which later plays a role in the “self” versus “non-self” distinction of the immune response.
The plasma membrane also carries receptors, which are attachment sites for specific substances that interact with the cell. Each receptor is structured to bind with a specific substance. For example, surface receptors of the membrane create changes in the interior, such as changes in enzymes of metabolic pathways. These metabolic pathways might be vital for providing the cell with energy, making specific substances for the cell, or breaking down cellular waste or toxins for disposal. Receptors on the plasma membrane’s exterior surface interact with hormones or neurotransmitters, and allow their messages to be transmitted into the cell. Some recognition sites are used by viruses as attachment points. Although they are highly specific, pathogens like viruses may evolve to exploit receptors to gain entry to a cell by mimicking the specific substance that the receptor is meant to bind. This specificity helps to explain why human immunodeficiency virus (HIV) or any of the five types of hepatitis viruses invade only specific cells.
Fluid Mosaic Model In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the plasma membrane that, compared to earlier understanding, better explained both microscopic observations and the function of the plasma membrane. This was called the fluid mosaic model. The model has evolved somewhat over time, but still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—in which the components are able to flow and change position, while maintaining the basic integrity of the membrane. Both phospholipid molecules and embedded proteins are able to diffuse rapidly and laterally in the membrane. The fluidity of the plasma membrane is necessary for the activities of certain enzymes and transport molecules within the membrane. Plasma membranes range from 5–10 nm thick. As a comparison, human red blood cells, visible via light microscopy, are approximately 8 µm thick, or approximately 1,000 times thicker than a plasma membrane. (Figure 3.18)
Figure 3.18 The fluid mosaic model of the plasma membrane structure describes the plasma membrane as a fluid combination of phospholipids, cholesterol, proteins, and carbohydrates.
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The plasma membrane is made up primarily of a bilayer of phospholipids with embedded proteins, carbohydrates, glycolipids, and glycoproteins, and, in animal cells, cholesterol. The amount of cholesterol in animal plasma membranes regulates the fluidity of the membrane and changes based on the temperature of the cell’s environment. In other words, cholesterol acts as antifreeze in the cell membrane and is more abundant in animals that live in cold climates.
The main fabric of the membrane is composed of two layers of phospholipid molecules, and the polar ends of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure 3.18) are in contact with aqueous fluid both inside and outside the cell. Thus, both surfaces of the plasma membrane are hydrophilic. In contrast, the interior of the membrane, between its two surfaces, is a hydrophobic or nonpolar region because of the fatty acid tails. This region has no attraction for water or other polar molecules.
Proteins make up the second major chemical component of plasma membranes. Integral proteins are embedded in the plasma membrane and may span all or part of the membrane. Integral proteins may serve as channels or pumps to move materials into or out of the cell. Peripheral proteins are found on the exterior or interior surfaces of membranes, attached either to integral proteins or to phospholipid molecules. Both integral and peripheral proteins may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites.
Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2–60 monosaccharide units and may be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other.
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How Viruses Infect Specific Organs Specific glycoprotein molecules exposed on the surface of the cell membranes of host cells are exploited by many viruses to infect specific organs. For example, HIV is able to penetrate the plasma membranes of specific kinds of white blood cells called T-helper cells and monocytes, as well as some cells of the central nervous system. The hepatitis virus attacks only liver cells.
These viruses are able to invade these cells, because the cells have binding sites on their surfaces that the viruses have exploited with equally specific glycoproteins in their coats. (Figure 3.19). The cell is tricked by the mimicry of the virus coat molecules, and the virus is able to enter the cell. Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens (or proteins associated with invasive pathogens). These same sites serve as places for antibodies to attach, and either destroy or inhibit the activity of the virus. Unfortunately, these sites on HIV are encoded by genes that change quickly, making the production of an effective vaccine against the virus very difficult. The virus population within an infected individual quickly evolves through mutation into different populations, or variants, distinguished by differences in these recognition sites. This rapid change of viral surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns.
Figure 3.19 HIV docks at and binds to the CD4 receptor, a glycoprotein on the surface of T cells, before entering, or infecting, the cell. (credit: modification of work by US National Institutes of Health/National Institute of Allergy and Infectious Diseases)
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3.5 | Passive Transport
By the end of this section, you will be able to:
• Explain why and how passive transport occurs
• Understand the processes of osmosis and diffusion
• Define tonicity and describe its relevance to passive transport
Plasma membranes must allow certain substances to enter and leave a cell, while preventing harmful material from entering and essential material from leaving. In other words, plasma membranes are selectively permeable—they allow some substances through but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from the extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that ensure transport. Most cells expend most of their energy, in the form of adenosine triphosphate (ATP), to create and maintain an uneven distribution of ions on the opposite sides of their membranes. The structure of the plasma membrane contributes to these functions, but it also presents some problems.
The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different concentration of a single substance is said to have a concentration gradient.
Selective Permeability Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes.
Recall that plasma membranes have hydrophilic and hydrophobic regions. This characteristic helps the movement of certain materials through the membrane and hinders the movement of others. Lipid-soluble material can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs also gain easy entry into cells and are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and pass through by simple diffusion.
Polar substances, with the exception of water, present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, whereas small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have a special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes.
Diffusion Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the perfume as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure 3.20). Diffusion expends no energy. Rather the different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that potential energy as materials move down their concentration gradients, from high to low.
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Figure 3.20 Diffusion through a permeable membrane follows the concentration gradient of a substance, moving the substance from an area of high concentration to one of low concentration. (credit: modification of work by Mariana Ruiz Villarreal)
Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. Additionally, each substance will diffuse according to that gradient.
Several factors affect the rate of diffusion.
• Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
• Mass of the molecules diffusing: More massive molecules move more slowly, because it is more difficult for them to move between the molecules of the substance they are moving through; therefore, they diffuse more slowly.
• Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion.
• Solvent density: As the density of the solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium.
For an animation of the diffusion process in action, view this short video (http://openstaxcollege.org/l/passive_trnsprt) on cell membrane transport.
Facilitated transport In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers.
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Osmosis Osmosis is the diffusion of water through a semipermeable membrane according to the concentration gradient of water across the membrane. Whereas diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other substances, moves from an area of higher concentration to one of lower concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves (Figure 3.21). On both sides of the membrane, the water level is the same, but there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent, on either side of the membrane.
Figure 3.21 In osmosis, water always moves from an area of higher concentration (of water) to one of lower concentration (of water). In this system, the solute cannot pass through the selectively permeable membrane.
A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living systems.
Watch this video (http://openstaxcollege.org/l/passive_trnsprt) that illustrates diffusion in hot versus cold solutions.
Tonicity Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may cause an animal cell to burst, or lyse.
In a hypertonic solution (the prefix hyper- refers to the extracellular fluid having a higher concentration of solutes than the cell’s cytoplasm), the fluid contains less water than the cell does, such as seawater. Because the cell has a lower
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concentration of solutes, the water will leave the cell. In effect, the solute is drawing the water out of the cell. This may cause an animal cell to shrivel, or crenate.
In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the concentration of solutes of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell. Blood cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure 3.22).
Figure 3.22 Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions. (credit: modification of work by Mariana Ruiz Villarreal)
A doctor injects a patient with what the doctor thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic compared to the cellular environment, and water will always enter a cell if water is available. This influx of water produces turgor pressure, which stiffens the cell walls of the plant (Figure 3.23). In nonwoody plants, turgor pressure supports the plant. If the plant cells become hypertonic, as occurs in drought or if a plant is not watered adequately, water will leave the cell. Plants lose turgor pressure in this condition and wilt.
Figure 3.23 The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit: modification of work by Mariana Ruiz Villarreal)
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3.6 | Active Transport
By the end of this section, you will be able to:
• Understand how electrochemical gradients affect ions
• Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
• Understand the process of exocytosis
Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight material, such as ions, through the membrane.
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.
Electrochemical Gradient We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because ions move into and out of cells, there is an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed; at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion into the cell, but the concentration gradient of K+ promotes diffusion out of the cell (Figure 3.24). The combined gradient that affects an ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.
Figure 3.24 Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. (credit: modification of work by “Synaptitude”/Wikimedia Commons)
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Moving Against a Gradient
To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins, work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.
Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different number of sodium ions out of the cell (Figure 3.25). The action of this pump results in a concentration and charge difference across the membrane.
Figure 3.25 The sodium-potassium pump move potassium and sodium ions across the plasma membrane. (credit: modification of work by Mariana Ruiz Villarreal)
Secondary active transport describes the movement of material using the energy of the electrochemical gradient established by primary active transport. Using the energy of the electrochemical gradient created by the primary active transport system, other substances such as amino acids and glucose can be brought into the cell through membrane channels. ATP itself is formed through secondary active transport using a hydrogen ion gradient in the mitochondrion.
Endocytosis Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created vacuole that is formed from the plasma membrane.
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Figure 3.26 Three variations of endocytosis are shown. (a) In one form of endocytosis, phagocytosis, the cell membrane surrounds the particle and pinches off to form an intracellular vacuole. (b) In another type of endocytosis, pinocytosis, the cell membrane surrounds a small volume of fluid and pinches off, forming a vesicle. (c) In receptor- mediated endocytosis, uptake of substances by the cell is targeted to a single type of substance that binds at the receptor on the external cell membrane. (credit: modification of work by Mariana Ruiz Villarreal)
Phagocytosis is the process by which large particles, such as cells, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil removes the invader through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure 3.26).
A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this process takes in solutes that the cell needs from the extracellular fluid (Figure 3.26).
A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain substances (Figure 3.26). The particles bind to the proteins and the plasma membrane invaginates, bringing the substance and the proteins into the cell. If passage across the membrane of the target of receptor-mediated endocytosis is ineffective, it will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by a failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor- mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear the chemical from their blood.
See receptor-mediated endocytosis in action and click on different parts for a focused animation (http://openstaxcollege.org/l/endocytosis2) to learn more.
Exocytosis In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the particle is expelled into the extracellular space (Figure 3.27).
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Figure 3.27 In exocytosis, a vesicle migrates to the plasma membrane, binds, and releases its contents to the outside of the cell. (credit: modification of work by Mariana Ruiz Villarreal)
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active transport
cell wall
central vacuole
chloroplast
cilium
concentration gradient
cytoplasm
cytoskeleton
cytosol
desmosome
diffusion
electrochemical gradient
endocytosis
endomembrane system
endoplasmic reticulum (ER)
eukaryotic cell
exocytosis
extracellular matrix
facilitated transport
flagellum
fluid mosaic model
gap junction
KEY TERMS the method of transporting material that requires energy
a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides structural support, and gives shape to the cell
a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation
a plant cell organelle that carries out photosynthesis
(plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
an area of high concentration across from an area of low concentration
the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move
the gel-like material of the cytoplasm in which cell structures are suspended
a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments
a passive process of transport of low-molecular weight material down its concentration gradient
a gradient produced by the combined forces of the electrical gradient and the chemical gradient
a type of active transport that moves substances, including fluids and particles, into a cell
the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and proteins
a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
a cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs
a process of passing material out of a cell
the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue
a process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
(plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell
a model of the structure of the plasma membrane as a mosaic of components, including phospholipids, cholesterol, proteins, and glycolipids, resulting in a fluid rather than static character
a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass between the cells, enabling the cells to communicate
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Golgi apparatus
hypertonic
hypotonic
isotonic
lysosome
microscope
mitochondria
nuclear envelope
nucleolus
nucleus
organelle
osmolarity
osmosis
passive transport
peroxisome
phagocytosis
pinocytosis
plasma membrane
plasmodesma
prokaryotic cell
receptor-mediated endocytosis
ribosome
rough endoplasmic reticulum (RER)
selectively permeable
smooth endoplasmic reticulum (SER)
solute
a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
describes a solution in which extracellular fluid has higher osmolarity than the fluid inside the cell
describes a solution in which extracellular fluid has lower osmolarity than the fluid inside the cell
describes a solution in which the extracellular fluid has the same osmolarity as the fluid inside the cell
an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles
the instrument that magnifies an object
(singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule
the double-membrane structure that constitutes the outermost portion of the nucleus
the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits
the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins
a membrane-bound compartment or sac within a cell
the total amount of substances dissolved in a specific amount of solution
the transport of water through a semipermeable membrane from an area of high water concentration to an area of low water concentration across a membrane
a method of transporting material that does not require energy
a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
a process that takes macromolecules that the cell needs from the extracellular fluid; a variation of endocytosis
a process that takes solutes that the cell needs from the extracellular fluid; a variation of endocytosis
a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment
(plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell
a unicellular organism that lacks a nucleus or any other membrane-bound organelle
a variant of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles
a cellular structure that carries out protein synthesis
the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification
the characteristic of a membrane that allows some substances through but not others
the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and stores calcium ions
a substance dissolved in another to form a solution
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tight junction
tonicity
unified cell theory
vacuole
vesicle
a firm seal between two adjacent animal cells created by protein adherence
the amount of solute in a solution.
the biological concept that states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells
a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport
a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus
CHAPTER SUMMARY 3.1 How Cells Are Studied
A cell is the smallest unit of life. Most cells are so small that they cannot be viewed with the naked eye. Therefore, scientists must use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.
3.2 Comparing Prokaryotic and Eukaryotic Cells
Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Many also have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1–5.0 µm.
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. Eukaryotic cells tend to be 10 to 100 times the size of prokaryotic cells.
3.3 Eukaryotic Cells
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.
Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.
Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.
The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.
The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.
Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.
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3.4 The Cell Membrane
The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane. These form complexes that function to identify the cell to other cells. The fluid nature of the membrane owes itself to the configuration of the fatty acid tails, the presence of cholesterol embedded in the membrane (in animal cells), and the mosaic nature of the proteins and protein-carbohydrate complexes, which are not firmly fixed in place. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.
3.5 Passive Transport
The passive forms of transport, diffusion and osmosis, move material of small molecular weight. Substances diffuse from areas of high concentration to areas of low concentration, and this process continues until the substance is evenly distributed in a system. In solutions of more than one substance, each type of molecule diffuses according to its own concentration gradient. Many factors can affect the rate of diffusion, including concentration gradient, the sizes of the particles that are diffusing, and the temperature of the system.
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is only made possible by protein channels and carriers. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins.
3.6 Active Transport
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. Living cells need certain substances in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel the transport. Active transport of small molecular-size material uses integral proteins in the cell membrane to move the material—these proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In secondary transport, energy from primary transport can be used to move another substance into the cell and up its concentration gradient.
Endocytosis methods require the direct use of ATP to fuel the transport of large particles such as macromolecules; parts of cells or whole cells can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle wholly enclosed by an envelope of plasma membrane. Vacuoles are broken down by the cell, with the particles used as food or dispatched in some other way. Pinocytosis is a similar process on a smaller scale. The cell expels waste and other particles through the reverse process, exocytosis. Wastes are moved outside the cell, pushing a membranous vesicle to the plasma membrane, allowing the vesicle to fuse with the membrane and incorporating itself into the membrane structure, releasing its contents to the exterior of the cell.
ART CONNECTION QUESTIONS 1. Figure 3.7 What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?
2. Figure 3.13 Why does the cis face of the Golgi not face the plasma membrane?
3. Figure 3.22 A doctor injects a patient with what he thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?
REVIEW QUESTIONS 4. When viewing a specimen through a light microscope, scientists use _________ to distinguish the individual components of cells.
a. a beam of electrons b. radioactive isotopes
c. special stains d. high temperatures
5. The ___________ is the basic unit of life. a. organism
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b. cell c. tissue d. organ
6. Which of these do all prokaryotes and eukaryotes share?
a. nuclear envelope b. cell walls c. organelles d. plasma membrane
7. A typical prokaryotic cell __________________ compared to a eukaryotic cell.
a. is smaller in size by a factor of 100 b. is similar in size c. is smaller in size by a factor of one million d. is larger in size by a factor of 10
8. Which of the following is found both in eukaryotic and prokaryotic cells?
a. nucleus b. mitochondrion c. vacuole d. ribosome
9. Which of the following is not a component of the endomembrane system?
a. mitochondrion b. Golgi apparatus c. endoplasmic reticulum d. lysosome
10. Which plasma membrane component can be either found on its surface or embedded in the membrane structure?
a. protein
b. cholesterol c. carbohydrate d. phospholipid
11. The tails of the phospholipids of the plasma membrane are composed of _____ and are _______?
a. phosphate groups; hydrophobic b. fatty acid groups; hydrophilic c. phosphate groups; hydrophilic d. fatty acid groups; hydrophobic
12. Water moves via osmosis _________. a. throughout the cytoplasm b. from an area with a high concentration of other
solutes to a lower one c. from an area with a low concentration of solutes
to an area with a higher one d. from an area with a low concentration of water
to one of higher concentration
13. The principal force driving movement in diffusion is __________.
a. temperature b. particle size c. concentration gradient d. membrane surface area
14. Active transport must function continuously because __________.
a. plasma membranes wear out b. cells must be in constant motion c. facilitated transport opposes active transport d. diffusion is constantly moving the solutes in the
other direction
CRITICAL THINKING QUESTIONS 15. What are the advantages and disadvantages of light, transmission, and scanning electron microscopes?
16. Describe the structures that are characteristic of a prokaryote cell.
17. In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?
18. Why is it advantageous for the cell membrane to be fluid in nature?
19. Why does osmosis occur?
20. Where does the cell get energy for active transport processes?
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4 | HOW CELLS OBTAIN ENERGY
Figure 4.1 A hummingbird needs energy to maintain prolonged flight. The bird obtains its energy from taking in food and transforming the energy contained in food molecules into forms of energy to power its flight through a series of biochemical reactions. (credit: modification of work by Cory Zanker)
Chapter Outline 4.1: Energy and Metabolism
4.2: Glycolysis
4.3: Citric Acid Cycle and Oxidative Phosphorylation
4.4: Fermentation
4.5: Connections to Other Metabolic Pathways
Introduction Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use energy while thinking, and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported into the cell, metabolized (broken down) and possibly synthesized into new molecules, modified if needed, transported around the cell, and possibly distributed to the entire organism. For example, the large proteins that make up muscles are built from smaller molecules imported from dietary amino acids. Complex carbohydrates are broken down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required for the synthesis and breakdown of molecules as well as the transport of molecules into and out of cells. In addition, processes such as ingesting and breaking down pathogenic bacteria and viruses, exporting wastes and toxins, and movement of the cell require energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.
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4.1 | Energy and Metabolism
By the end of this section, you will be able to:
• Explain what metabolic pathways are
• State the first and second laws of thermodynamics
• Explain the difference between kinetic and potential energy
• Describe endergonic and exergonic reactions
• Discuss how enzymes function as molecular catalysts
Scientists use the term bioenergetics to describe the concept of energy flow (Figure 4.2) through living systems, such as cells. Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish their energy supplies, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place. Together, all of the chemical reactions that take place inside cells, including those that consume or generate energy, are referred to as the cell’s metabolism.
Figure 4.2 Ultimately, most life forms get their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat the plants to obtain energy. Carnivores eat the herbivores, and eventual decomposition of plant and animal material contributes to the nutrient pool.
Metabolic Pathways Consider the metabolism of sugar. This is a classic example of one of the many cellular processes that use and produce energy. Living things consume sugars as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. For the most part, photosynthesizing organisms like plants produce these sugars. During photosynthesis, plants use energy (originally from sunlight) to convert carbon dioxide gas (CO2) into sugar molecules (like glucose: C6H12O6). They consume carbon dioxide and produce oxygen as a waste product. This reaction is summarized as:
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6CO2 + 6H2 O–>C6 H12 O6 + 6O2
Because this process involves synthesizing an energy-storing molecule, it requires energy input to proceed. During the light reactions of photosynthesis, energy is provided by a molecule called adenosine triphosphate (ATP), which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. In contrast, energy-storage molecules such as glucose are consumed only to be broken down to use their energy. The reaction that harvests the energy of a sugar molecule in cells requiring oxygen to survive can be summarized by the reverse reaction to photosynthesis. In this reaction, oxygen is consumed and carbon dioxide is released as a waste product. The reaction is summarized as:
C6 H12 O6 + 6O2–>6H2 O + 6CO2
Both of these reactions involve many steps.
The processes of making and breaking down sugar molecules illustrate two examples of metabolic pathways. A metabolic pathway is a series of chemical reactions that takes a starting molecule and modifies it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product. In the example of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic pathways (building polymers) and catabolic pathways (breaking down polymers into their monomers), respectively. Consequently, metabolism is composed of synthesis (anabolism) and degradation (catabolism) (Figure 4.3).
It is important to know that the chemical reactions of metabolic pathways do not take place on their own. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.
Figure 4.3 Catabolic pathways are those that generate energy by breaking down larger molecules. Anabolic pathways are those that require energy to synthesize larger molecules. Both types of pathways are required for maintaining the cell’s energy balance.
Energy Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter relevant to a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. In an open system, energy can be exchanged with its surroundings. The stovetop system is open because heat can be lost to the air. A closed system cannot exchange energy with its surroundings.
Biological organisms are open systems. Energy is exchanged between them and their surroundings as they use energy from the sun to perform photosynthesis or consume energy-storing molecules and release energy to the environment by doing work and releasing heat. Like all things in the physical world, energy is subject to physical laws. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.
In general, energy is defined as the ability to do work, or to create some kind of change. Energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. To appreciate the way energy flows into and out of biological systems, it is important to understand two of the physical laws that govern energy.
Thermodynamics The first law of thermodynamics states that the total amount of energy in the universe is constant and conserved. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many
Chapter 4 | How Cells Obtain Energy 93
different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light and heat energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight to chemical energy stored within organic molecules (Figure 4.2). Some examples of energy transformations are shown in Figure 4.4.
The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge. Chemical energy stored within organic molecules such as sugars and fats is transferred and transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the motion of cilia or flagella, and contracting muscle fibers to create movement.
Figure 4.4 Shown are some examples of energy transferred and transformed from one system to another and from one form to another. The food we consume provides our cells with the energy required to carry out bodily functions, just as light energy provides plants with the means to create the chemical energy they need. (credit “ice cream”: modification of work by D. Sharon Pruitt; credit “kids”: modification of work by Max from Providence; credit “leaf”: modification of work by Cory Zanker)
How does a heterozygous organisms differ from a homozygous organism
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