Introduction to Molecular and Cell Biology PDF

Introduction to Molecular and Cell Biology INTRODUCTION TO MOLECULAR AND CELL BIOLOGY For use in RWU BIO103 KATHERINE MATTAINI Introduction to Molecular and Cell Biology by Katherine R. Mattaini is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, excep...

Introduction to Molecular and Cell Biology INTRODUCTION TO MOLECULAR AND CELL BIOLOGY For use in RWU BIO103 KATHERINE MATTAINI Introduction to Molecular and Cell Biology by Katherine R. Mattaini is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted. CONTENTS Preface ix Part I. Part 1. What is life? Chapter 1. The Study of Life 3 Part II. Part 2. What molecules make up all living things? Chapter 2. The Chemical Context of Life 41 Chapter 3. Amino Acids & Proteins 95 Chapter 4. Carbohydrates 119 Chapter 5. Nucleotides & Nucleic Acids 145 Chapter 6. Lipids 162 Part III. Part 3. What are the main features and categories of cells? Chapter 7. Introduction to Cells 181 Chapter 8. Membrane Transport 245 Chapter 9. Cell Communication 302 Part IV. Part 4. How do living things acquire and use energy? Chapter 10: Introduction to Metabolism - 341 Enzymes and Energy Chapter 11. Cellular Respiration 385 Chapter 12. Photosynthesis 434 Part V. Part 5. How are heritable traits determined and passed on? Chapter 13. The Cell Cycle & Mitosis 477 Chapter 14. DNA Replication 523  Chapter 15. Meiosis & Sexual 561 Reproduction 1. Chapter 16. The Central Dogma: Genes to 608 Traits 2. Chapter 17. Regulation of Gene 656 Expression Chapter 18. Mendelian Genetics 684  PREFACE | IX PREFACE This book was modified from Biology at OpenStax.org. It was initially modified by instructors at Front Range Community College (FRCC, Colorado) in June 2019, and further modified by Katherine R. Mattaini in July 2020. Major changes made included reordering the chapters, replacing some images, and some rewording. The information page for Biology 2e, including the link to the first edition, can be found here: https://openstax.org/ details/books/biology-2e. The original book was licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/ by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. Senior Contributing Authors of the original book: Yael Avissar, Rhode Island College Jung Choi, Georgia Institute of Technology Jean DeSaix, University of North Carolina at Chapel Hill Vladimir Jurukovski, Suffolk County Community College Robert Wise, University of Wisconsin, Oshkosh X | PREFACE Connie Rye, East Mississippi Community College Contributing Authors of the Revised Book for Front Range Community College: Ann Riedl, Front Range Community College Christopher Wrobel, Front Range Community College Maria Carolina Pilonieta, Front Range Community College Richard Fulghum, Front Range Community College  PART 1. WHAT IS LIFE? | 1 PART I PART 1. WHAT IS LIFE? 2 | PART 1. WHAT IS LIFE?  CHAPTER 1. THE STUDY OF LIFE | 3 CHAPTER 1. THE STUDY OF LIFE Figure 1.1 Behold one of the more stunningly detailed images of the Earth yet created. This Blue Marble Earth montage, created from photographs taken by the VIIRS instrument on board the Suomi NPP satellite, shows many stunning details of our home planet. (Credit: NASA) 4 | CHAPTER 1. THE STUDY OF LIFE Chapter Outline 1.1 The Study of Biology 1.2 Themes and Concepts of Biology Introduction Viewed from space, Earth offers no 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 in the ocean 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.  CHAPTER 1. THE STUDY OF LIFE | 5 1.1 | The Study of Biology Learning Objectives By the end of this section, you will be able to: Describe the science of biology. Summarize the steps of the scientific method. What is biology? In simple terms, biology is the study of living organisms and their interactions with one another and their environment. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet (Figure 1.1). Listening to the daily news, you will quickly realize how many aspects of biology are discussed every day. For example, recent news topics include Escherichia coli (Figure 1.2) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding cures for diseases such as AIDS, Alzheimer disease, and cancer. On a global scale, many researchers are committed to finding ways to 6 | CHAPTER 1. THE STUDY OF LIFE protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology. Figure 1.2 Escherichia coli (E. coli) bacteria, seen in this scanning electron micrograph, are normal residents of our digestive tracts that aid in the absorption of vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease outbreaks. (Credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU) 1.1.1 The Process of Science Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines?  CHAPTER 1. THE STUDY OF LIFE | 7 Science (from the Latin scientia, meaning “knowledge”) can be defined as the process of acquiring knowledge about general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that the application of the scientific method plays a major role in science. 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 by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which can be tested. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology and geology, the scientific method becomes less applicable as it becomes more difficult to repeat experiments. These areas of study are still sciences, however. Consider archeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. Further hypotheses could be made about various characteristics of this culture, and these hypotheses may be found to be supported or false from other findings. Over time, as hypotheses continue to be supported, 8 | CHAPTER 1. THE STUDY OF LIFE they may contribute to the formulation of a theory. A theory is a tested and confirmed explanation that fits all of the observations or phenomena in a given field of study. Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals. 1.1.2 The Scientific Method Biologists study the living world by posing questions about it and seeking verifiable 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), who set up inductive methods for scientific inquiry. The scientific method can be applied to almost all fields of study as a logical, rational problem-solving method. The scientific process typically starts with an observation 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  CHAPTER 1. THE STUDY OF LIFE | 9 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?” Proposing a Hypothesis 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.” 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 formulated, the student can make a prediction. 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.” Testing a Hypothesis A valid hypothesis must be testable. It should also be falsifiable, meaning that it can be disproven by experimental results. Importantly, science does not claim to “prove” 10 | CHAPTER 1. THE STUDY OF LIFE anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. 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. Control variables are variables that are held constant in all parts of the experiment. The experimental variable is the one that is changed. Many experiments are designed to test whether one variable, the dependent variable, is influenced by another variable, the independent variable. The researcher manipulates, or investigates several cases of, the independent variable and observes changes in the dependent variable. For example, if a scientist hypothesizes that coat color in rabbits is influenced by temperature, she may observe rabbits at different temperatures (the independent variable) and observe the coat color (the dependent variable) in each case. To test the first hypothesis in the above example, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, this hypothesis should be rejected. To test the second hypothesis, the student could check if the lights in the classroom are functional. If  CHAPTER 1. THE STUDY OF LIFE | 11 so, there is no power failure and this hypothesis should be rejected. 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. Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected (Figure 1.3). The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. 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. Notice, too, that the scientific method can be applied to solving problems that are not necessarily scientific in nature. 12 | CHAPTER 1. THE STUDY OF LIFE Figure 1.3 The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by experimental data, a new hypothesis can be proposed.  CHAPTER 1. THE STUDY OF LIFE | 13 Figure 1.4 Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As is the case in this example, the conclusion from inductive reasoning can often become the premise for deductive reasoning. 14 | CHAPTER 1. THE STUDY OF LIFE Concept Check Decide if each of the following is an example of inductive or deductive reasoning. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase. Chromosomes, which are made of DNA, pass genetic information from parent to offspring during cell division. Therefore, DNA is the genetic material. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.  CHAPTER 1. THE STUDY OF LIFE | 15 Concept Check In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered items). Match these steps with the processes of solving the problem (lettered items). Based on the results of the experiment, is the hypotheses correct? If it is incorrect, propose some alternate hypotheses. 16 | CHAPTER 1. THE STUDY OF LIFE a. There is something wrong 1. Experiment with the electrical outlet. b. If something is wrong with the electrical outlet, my 2. Prediction coffeemaker also won’t work when plugged into it. c. My toaster doesn’t toast my 3. Question bread. d. I plug my coffeemaker into 4. Observation the outlet. 5. Result e. My coffeemaker works. f. Why doesn’t my toaster 6. Hypothesis work? 1.1.3 Reporting Scientific Work Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—are all important for scientific research. For this reason, important aspects of a scientist’s work are communicating with and disseminating results to peers. Scientists can share results by presenting them at a scientific  CHAPTER 1. THE STUDY OF LIFE | 17 meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed 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 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. A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. Scientific writing must be brief, concise, and accurate. Most scientific papers consist of the following: Abstract: a concise summary of the results of the study Introduction: background information about what is known in the field as well as the rationale of the work Materials and Methods: complete and accurate 18 | CHAPTER 1. THE STUDY OF LIFE description of the substances used, and the methods and techniques used by the researchers to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results. This section will also include information on how measurements were made and what types of calculations and statistical analyses were used. Results and/or Discussion: description of the findings, usually by means of tables or graphs. The researcher will interpret the results, describe how variables may be related, and attempt to explain the observations. Conclusion: summary of the importance of the experimental findings. References: It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, proper citations are included in this section. Review articles do not present original scientific findings, or primary literature; instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections. 1.2 | Themes and Concepts of  CHAPTER 1. THE STUDY OF LIFE | 19 Biology Learning Objectives 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. Summarize the three unifying theories of biology. Name and briefly characterize the three domains of life on Earth. Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always 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 all of the criteria that most biologists use to define life. 20 | CHAPTER 1. THE STUDY OF LIFE From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something “alive”? And once we know something is alive, how do we find meaningful levels of organization in its structure? And, finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions. 1.2.1. Properties of Life All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, growth and development, regulation, homeostasis, energy processing, adaptation, and evolution. When viewed together, these nine characteristics serve to define life. Order Organisms are highly organized, coordinated 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 organelles and other cellular inclusions. In multicellular organisms (Figure 1.5), similar cells form tissues. Tissues, in turn, collaborate  CHAPTER 1. THE STUDY OF LIFE | 21 to create organs (body structures with a distinct function). Organs work together to form organ systems. Figure 1.5 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (Credit: “Ivengo”/Wikimedia Commons) Sensitivity or Response to Stimuli Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond to touch (Figure 1.6). 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. 22 | CHAPTER 1. THE STUDY OF LIFE Figure 1.6 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to normal. (Credit: Alex Lomas) Reproduction Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive cells that will form new individuals. When reproduction occurs, genes containing DNA are passed along to an organism’s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics (Figure 1.7).  CHAPTER 1. THE STUDY OF LIFE | 23 Figure 1.7 Although no two are identical, these kittens have inherited genes from both parents and share many of the same characteristics. (Credit: Rocky Mountain Feline Rescue) Growth and Development Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young will grow up to exhibit many of the same characteristics as its parents (Figure 1.7). Regulation and Homeostasis Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues 24 | CHAPTER 1. THE STUDY OF LIFE working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body. In order to function properly, cells need to have appropriate conditions such as proper temperature, pH, and appropriate concentration 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 homeostasis (literally, “steady state”)—the ability of an organism to maintain constant internal conditions. For example, an organism needs to regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates have body structures, including fur, feathers, blubber, and fat, that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.  CHAPTER 1. THE STUDY OF LIFE | 25 Figure 1.8 Polar bears (Ursus maritimus) 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 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 in molecules they take in as food (Figure 1.9). 26 | CHAPTER 1. THE STUDY OF LIFE Figure 1.9 The California condor (Gymnogyps californianus) uses chemical energy derived from food to power flight. California condors are an endangered species; this bird has a wing tag that helps biologists identify the individual. (Credit: Pacific Southwest Region U.S. Fish and Wildlife Service) Adaptation and Evolution All organisms have DNA as the genetic material that allows parents to pass traits to their offspring. Due to the  CHAPTER 1. THE STUDY OF LIFE | 27 changeability of DNA, variability is introduced into populations as they reproduce. This causes species to change over time, or evolve. As variability increases, new species come into being (Figure 1.10). The mechanisms of this process will be discussed later. Figure 1.10 A single ancestral species of bird may be the progenitor for multiple species. This process is known as cladogenesis. 1.2.2 Levels of Organization of Living Things Living things are highly organized and structured, following a hierarchy that can be examined 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. 28 | CHAPTER 1. THE STUDY OF LIFE Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules that are biologically important are macromolecules, large molecules that are typically formed from repeating units. An example of a macromolecule is deoxyribonucleic acid (DNA) (Table 1.1), which contains the instructions for the structure and functioning of all living organisms. Table 1.1 The biological levels of organization of living things from small to large. From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. (Credit “macromolecules”: “Geoff Hutchison”/Flickr; credit “organelles”: “Przemyslawtarka95″/Wikimedia Commons; Credit “cells”: “Steve Begin”/Flickr; Credit “tissues”: “Circa24″/Wikimedia Commons; credit “organs”: anatomical drawing by Leonardo da Vinci; credit “organisms”: “dmitry.kaglik”/Flickr; credit “ecosystems”: “USFWS – Pacific Region”/Flickr; credit “biosphere”: GSFC/NASA Goddard.)  CHAPTER 1. THE STUDY OF LIFE | 29 Macromolecules – Ex: DNA double helix Organelles – Ex: chloroplasts in plant cells Cells – Ex: human red blood cells Tissues – Ex: hair follicles in mammalian skin Organs and organ systems – Ex: “The Principal Organs and Vascular and Urino-Genital Systems of a Woman” 30 | CHAPTER 1. THE STUDY OF LIFE Organisms, populations and communities – Ex: pine trees in a forest community Ecosystems – Ex: coral reef ecosystem Biosphere – The sum of all ecosystems on Earth Some cells contain small structures that exist within cells surrounded by membranes; these are called organelles. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. Some organisms consist of a single cell and others are multicellular. In larger organisms, cells combine to make tissues, which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing a common function. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ systems, including the circulatory system and the digestive system. Organisms are individual living entities. For example, each tree in a forest is an organism. Some organisms are composed of a single cell. All the individuals of a species living within a specific area  CHAPTER 1. THE STUDY OF LIFE | 31 are collectively called a population. For example, a forest may include many pine trees. All of these pine trees represent the population of 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 sum 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, non-living parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization (Table 1.1), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and the atmosphere. Concept Check Which of the following statements is false? Tissues exist within organs which exist within organ systems. Communities exist within populations which 32 | CHAPTER 1. THE STUDY OF LIFE exist within ecosystems. Organelles exist within cells which exist within tissues. Communities exist within ecosystems which exist in the biosphere. 1.2.3 The Three Unifying Theories of Biology Scientists use the word theory differently than non-scientists do. In science, a theory is an explanation that encompasses all of the known information in a field of study. Although theories can continue to be modified, they are almost never replaced or dismissed entirely. Three of the most important theories in biology are cell theory, the chromosomal theory of inheritance, and the theory of evolution by natural selection. The details of these theories will be covered in later chapters, or in the case of evolution by natural selection, in other courses. The basic principles of these theories are described briefly below. Cell Theory Cell theory states that all living things are composed of cells,  CHAPTER 1. THE STUDY OF LIFE | 33 that cells are the basic unit of life, and that cells come from pre- existing cells. All cells have the same basic structure of a gel-like cytoplasm enclosed by a double layer of lipid molecules called the plasma membrane. In addition, all cells contain DNA as the genetic material. How did the first cells come into existence? Most scientists think that conditions on early Earth were ideal for the formation of living cells. The early seas were warm, contained a large number of carbon-based molecules, and had a lot of energy input from lightening and volcanos. Sometime around 3.5 billion years ago, carbon-based molecules became surrounded by lipid molecules and evolved the ability to reproduce. This was the first cell. Other scientists postulate that life may have arrived on earth from space on an asteroid or meteor. Since conditions on earth no longer support the formation of life, cells can only come from pre-existing cells at this time on Earth. The Chromosomal Theory of Inheritance The chromosomal theory of inheritance states that chromosomes carry the genetic material. Chromosomes are made of a single very long molecule of DNA wrapped around proteins that serve to pack it tightly into a cell (Figure 1.11). Segments of the chromosome called genes code for traits, or characteristics. Chromosomes are passed on from parents to offspring, which is the basis of inheritance. 34 | CHAPTER 1. THE STUDY OF LIFE Figure 1.11 Polytene chromosomes from the salivary glands of nonbiting midges larvae. (Credit: Doc. RNDr. Josef Reischig, CSc) The Theory of Evolution by Natural Selection Species change over time, or evolve. In 1869, Charles Darwin and Alfred Russel Wallace proposed a mechanism, called natural selection, for this observed evolution. They proposed that since not all of the members of a population can survive, the ones who are most fit will survive and reproduce at a higher rate and will therefore be more likely to pass on their traits. Therefore, over time, the characteristics that are present in a population will change. As populations change, new species come into existence. For natural selection to work, there must first be variation among individuals in a population. The variation arises through changes in the DNA, which leads to changes in the traits of individuals. Secondly, there must be a selective  CHAPTER 1. THE STUDY OF LIFE | 35 pressure, such as a shortage of food, a predator, a mating preference, etc. For example, if the selective pressure is a predator, individuals who are best able to avoid being eaten will survive and reproduce at a higher rate. Individuals may have different types of fitness: some may be able to move faster, others may be able to hide better, while still others may be able to convince the predator that they are poisonous. Regardless, some individuals get eaten and some survive. The final important part is that the survivors must be able to reproduce. Only the individuals who get to pass on their DNA to their offspring are truly fit. It is important to understand that evolution does not work on individuals, but on populations. Since the most fit individuals have more offspring, their traits become more prevalent in the population over time. Natural selection is very similar to breeding of domestic animals. Breeders choose animals or plants with favorable traits and allow them to breed. By continuing to choose the desired traits over many generations, breeders developed breeds or strains with strikingly different characteristics. Darwin called this process artificial selection. He reasoned that a similar process could take place with nature, rather than people, deciding who got to reproduce. 1.2.4 The Diversity of Life The fact that biology has such a broad scope has to do with 36 | CHAPTER 1. THE STUDY OF LIFE the tremendous diversity of life on Earth. The source of this diversity is evolution. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems. The evolution of various life forms on Earth can be summarized in a phylogenetic tree (Figure 1.12). Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled or colonial organisms that do not have membrane-bound nuclei; in contrast, the cells of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus. Eukaryotes can be either unicellular or multicellular. For most of the history of biology, scientists believed that the main division in the Tree of Life (the phylogenetic tree showing all organisms on Earth) was between prokaryotes and eukaryotes. However, in 1977, American microbiologist Carl Woese, refuted that hypothesis using data obtained from sequencing ribosomal RNA genes. He found that the most fundamental division in life on Earth is between three domains: Bacteria, Archaea, and Eukarya (eukaryotes). Although bacteria and archaea are both prokaryotes, archaea are more closely related to eukaryotes than they are to bacteria.  CHAPTER 1. THE STUDY OF LIFE | 37 Figure 1.12 Phylogenetic tree constructed by microbiologist Carl Woese. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (Credit: Eric Gaba; NASA Astrobiology Institute) 38 | CHAPTER 1. THE STUDY OF LIFE  PART 2. WHAT MOLECULES MAKE UP ALL LIVING THINGS? | 39 PART II PART 2. WHAT MOLECULES MAKE UP ALL LIVING THINGS? 40 | PART 2. WHAT MOLECULES MAKE UP ALL LIVING THINGS?  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 41 CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.1 Atoms are the building blocks of all the molecules found in the universe—air, soil, water, rocks... and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and sulfur (yellow) are shown in proportional atomic size. The silver rods indicate chemical bonds. (Credit: modification of work by Christian Guthier) 42 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Chapter Outline 2.1 Atoms 2.2 Chemical Bonding & Intermolecular Forces 2.3 Water, Acids & Bases 2.4 The Energy of Life 2.5 Carbon Introduction Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that make up molecules, allowing for the formation of cells, tissues, organ systems, and entire organisms. All biological processes follow the laws of physics and chemistry; so in order to understand how biological systems  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 43 work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of chemical reactions that follow chemical laws. The properties of water and the formation of hydrogen bonds are key to understanding living processes. Recognizing the properties of acids and bases is important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry are important for gaining insight into biological processes. 2.1 | Atoms Learning Objectives By the end of this section, you will be able to: Define matter and elements. Describe the interrelationship between 44 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE protons, neutrons, and electrons. Use atomic number to determine electron configuration. At its most fundamental level, life is made up of matter: any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable. Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already used for another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names; for example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium. The four most common elements in all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). These elements comprise 96% of living organisms. In the non-living world, elements are found in different proportions, and some elements common to living organisms  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 45 are relatively rare on the earth as a whole, as shown in Table 2.1. In spite of their differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or non-living world. Table 2.1. Percentage of elements in living organisms vs. the non-living world. Element Life (Humans) Atmosphere Earth’s Crust Oxygen (O) 65% 21% 46% Carbon (C) 18% trace trace Hydrogen (H) 10% trace 0.1% Nitrogen (N) 3% 78% trace 2.1.1 The Structure of the Atom An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold, such as that it is a solid metal at room temperature. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold. An atom is composed of two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outer region of the atom, which holds its 46 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE electrons in orbit around the nucleus (Figure 2.2). Atoms contain subatomic particles, the largest of which are protons, electrons, and neutrons. Figure 2.2 Elements, such as helium, depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus, with electrons in orbitals surrounding the nucleus. Protons are positively charged, electrons are negatively charged, and neutrons are uncharged (Table 2.2). Each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 47 Protons and neutrons have approximately the same mass, -24 about 1.67 × 10 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton (Da) (Table 2.2). Electrons are much smaller in mass -28 than protons, weighing only 9.11 × 10 grams, or about 1/ 1800 of an atomic mass unit. Hence, they do not contribute much to an element’s overall atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom’s mass based on the number of protons and neutrons alone. Accounting for the sizes of protons, neutrons, and electrons, most of the volume of an atom—greater than 99 percent—is, in fact, empty space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other. Table 2.2. Properties of subatomic particles. Charge Mass (amu) Location Proton +1 1 nucleus Neutron 0 1 nucleus Electron –1 0 orbitals 2.1.2 Atomic Number, Mass 48 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Number, Isotopes, and Atomic Weight Atoms of each element contain a characteristic number of protons. The number of protons determines an element’s atomic number and is used to distinguish one element from another. The number of neutrons in the atoms of a given element is variable. For example, the element carbon (C) has atomic number 6. Therefore, all neutral carbon atoms have 6 protons and 6 electrons. However, some carbon atoms have 6 neutrons, some have 7 neutrons, and some have 8 neutrons. Together, the number of protons plus the number of neutrons determines an atom’s mass number. Note that the small contribution of mass from electrons is disregarded when calculating the mass number. Isotopes are atoms that have the same number of protons but a different number of neutrons. Carbon atoms that have 6 neutrons have a mass number of 12 amu, and are referred to 12 as Carbon-12 or C. Carbon atoms with 7 neutrons have a mass number of 13 amu, and are referred to as Carbon-13 or 13 C. Carbon atoms that have 8 neutrons have a mass number 14 of 14 amu, and are referred to as Carbon-14 or C. These represent three naturally occurring isotopes of carbon (Figure 2.3).  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 49 Figure 2.3 Elements may have more than one isotope. For example, the three isotopes of carbon are shown here. They all have 6 protons and electrons, but the number of neutrons varies. Since an element’s isotopes have different mass numbers, scientists also determine the atomic weight, which is the calculated mean of the mass number for the naturally occurring isotopes of an element on earth. Often, the resulting number is not a whole number. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons). The atomic mass of carbon is 12.011 because the great majority of carbon on earth is Carbon-12. Some isotopes may emit neutrons, protons, and electrons in order to become more stable. These are radioactive 50 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE isotopes, or radioisotopes. Radioactive decay describes the loss of energy and/or mass that occurs when an unstable atom’s nucleus releases radiation. Carbon-14 is an example of a radioisotope (Figure 2.4). 14 Carbon DatingCarbon-14 ( C) is a naturally occurring radioisotope. In a living organism, the 14 relative amount of C is equal to the 14 concentration of C in the atmosphere. When an 14 12 organism dies, the ratio between C and C will 14 decrease as C decays.After approximately 5,730 14 years, half of the starting concentration of C decayed. 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. The number of half-lives since an object such as bones or wood was alive can be determined by comparing the 14 ratio of the C concentration in the object to the 14 amount of C detected in the atmosphere. The age of the material can be calculated with accuracy if it is not much older than about 50,000 years (Figure 2.4).  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 51 Figure 2.4 The age of carbon-containing remains less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (Credit: Bill Faulkner, NPS) 2.1.3 The Periodic Table The different elements are organized and displayed in the periodic table. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that share certain chemical properties. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements 52 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE also have specific chemical reactivity, the ability to chemically bond with each other. In the periodic table, shown in Figure 2.5, the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. Each square on the table gives the name, chemical symbol, atomic weight, and atomic mass for one element. For example, the first square contains hydrogen, its symbol (H), its atomic number of (1), and its atomic mass (1.01).  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 53 Figure 2.5 The periodic table shows the atomic mass and atomic number of each element. The atomic number appears above the symbol for the element and the approxim ate atomic mass appears below it. 2.1.4 Electron Shells and the Bohr Model An early model of the atom was developed in 1913 by Danish scientist Niels Bohr (1885–1962). The Bohr model shows 54 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE the atom with a central nucleus and the electrons in circular electron shells at specific distances from the nucleus. The closer an energy shell is the nucleus, the lower the energy of the electrons that occupy that shell. The first (1n) electron shell can hold two electrons, while the second (2n) and third (3n) shells can hold eight electrons each (Figure 2.6). Electron Orbitals Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model of the atom does not accurately reflect how electrons are spatially distributed surrounding the nucleus. They do not circle the Figure 2.6 In the Bohr model, nucleus like the earth orbits developed by Niels Bohrs in the sun, but are found in 1913, electrons exist in orbitals three-dimensional electron within electron shells. An electron normally exists in the orbitals. Mathematical electron shell with the lowest equations can predict available energy, which is the one closest to the nucleus. within a certain level of probability where an electron might be at any given time. The area where an electron is most likely to be found is called its orbital. Each electron orbital can hold only two electrons. Electrons fill orbitals in a consistent order: they first fill  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 55 the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, one electron will be added to each orbital before a second electron is added to any of the orbitals. For example, the second energy level in the nitrogen atom shown here has one electron in each of three orbitals and two electrons in the fourth orbital (Figure 2.6). The innermost shell has a single orbital, for a maximum of two electrons but the next two electron shells can each have four orbitals, for a maximum of eight electrons. The octet rule states that, with the exception of the innermost shell, atoms are most stable when they have eight electrons in their valence shell, the outermost electron shell. Examples of some neutral atoms and their electron configurations are shown in Figure 2.7. 56 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.7 Bohr diagrams indicate how many electrons fill each shell. Group 18 elements (e.g., helium, neon, and argon) have a full valence shell. A full valence shell is the most stable electron configuration. Elements in other groups, with partially filled valence shells, gain or lose electrons to achieve a stable configuration. Concept Check Draw Bohr’s diagrams for oxygen and magnesium atoms.  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 57 How many electrons do oxygen atoms need to gain in order to achieve a stable electron configuration? How many electrons do magnesium atoms need to lose to achieve a stable configuration? The periodic table is arranged in columns and rows based on the number of electrons and where these electrons are located. Note that elements in the far right column of the periodic table (Figure 2.5) all have filled valence shells. These atoms are highly stable, making it unnecessary for them to share electrons with other atoms. They are therefore non- reactive and are called inert gases (or noble gases). In general, atoms with 4-7 electrons in their valence shell will either gain electrons to become negatively charged ions, or will share electrons with other atoms to form covalently bonded molecules. Atoms with 1-3 electrons in their valence shell will tend to donate their electrons to other atoms until they have a full outer shell. As a result of losing negatively charged electrons, they become positively charged ions. 58 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE 2.2 | Chemical Bonding & Intermolecular Forces Learning Objectives By the end of this section, you will be able to: Compare the ways in which electrons can be donated or shared between atoms. Explain the ways in which naturally occurring elements combine to create molecules. Identify intermolecular forces that hold molecules together. 2.2.1 Chemical Reactions and Molecules The octet rule drives the chemical behavior of atoms. Atoms will chemically react and bond to each other form molecules, which are simply two or more atoms chemically bonded together. A compound is a type of molecule that contains  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 59 two or more different types of atoms. In short, atoms form chemical bonds with other atoms, thereby obtaining the electrons they need to attain a stable electron configuration. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom bonded together (Figure 2.8). Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells. Figure 2.8 Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via covalent bonds, a water molecule is formed. Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants and the substances found at the end of the reaction are known as the products. An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction. 60 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Most chemical reactions can go in either direction. For the creation of the water molecule shown above, the chemical equation would be: 2 H2 + O2 → 2 H2O This is an example of a balanced chemical equation, wherein the number of atoms of each element is the same on each side of the equation. 2.2.2. Ions and Ionic Bonds Some atoms are more stable when they gain or lose an electrons and form ions. This fills their outermost electron shell and makes them more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Anions are negative ions that are formed by gaining electrons. Certain ions, such as sodium, potassium, and calcium, are referred to in physiology as electrolytes. These ions are necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise. Movement of electrons from one atom or molecule to another is referred to as electron transfer or as a redox  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 61 reaction. As Figure 2.9 illustrates, sodium (Na) only has one electron in its outer electron shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, making it a sodium cation with an overall charge of +1. Chlorine (Cl) has seven electrons in its outer shell. If it gains an electron, it now has 17 protons and 18 electrons, making it a chloride anion with an overall charge of -1. Both ions now satisfy the octet rule and have complete outermost shells. Figure 2.9 In the formation of an ionic compound, an electron is transferred from one atom to another, forming two oppositely charged ions, which are then attracted to each other. An ionic bond is the electrical attraction that forms between ions with opposite charges. For example, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge. 2.2.3 Covalent Bonds Another way the octet rule can be satisfied is by the sharing 62 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE of electrons between atoms to form covalent bonds. One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The formation of water molecules provides an example of covalent bonding (Figure 2.8). To completely fill the outer shell of oxygen, which has six electrons in its outer shell, two electrons (one from each hydrogen atom) are needed. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable. Polar Covalent Bonds Although atoms share electrons in covalent bonds, they do not always share the electrons equally. Atoms have different electronegativities, or Figure 2.10 Electronegativity attraction for electrons values for selected elements. (Figure 2.10). When a covalent bond is formed between two atoms with different electronegativities, the shared electrons will spend more time around the nucleus of the atom with the higher electronegativity and less time around the nucleus with lower electronegativity. Since electrons are negatively charged, the atom that gets more time with the electron acquires a slightly negative charge (δ–). The atom with  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 63 lower electronegativity gets less time with the electron and acquires a slightly positive charge (δ+). The type of covalent bond that forms between two atoms with different electronegativities is called a polar covalent bond. Molecules with polar covalent bonds are called polar molecules, due to the separation of charges across the molecule. For example, water is a polar molecule, since oxygen has an electronegativity of 3.5 and hydrogen has an electronegativity of 2.1. The oxygen atom in a water molecule attracts the shared electrons more and acquires a partial negative charge, while the hydrogen atoms attract the shared electrons less and acquire a partial positive charge (Figure 2.11). Many of the important properties of water result from its polarity. Nonpolar Covalent Bonds Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms. Another example of a nonpolar covalent bond is methane (CH4), also shown in Figure 2.11. Carbon and hydrogen have similar electronegativity values. Therefore, these elements share electrons equally, creating a nonpolar covalent molecule. Some molecules are nonpolar due to 64 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE symmetry, as seen in the carbon dioxide molecule in Figure 2.11. Figure 2.11 Whether a molecule is polar or nonpolar depends both on electronegativity values and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out. 2.2.4 Hydrogen Bonds and Van Der Waals Interactions As described above, covalent and ionic bonds occur  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 65 between atoms to form molecules. Other types of interactions occur between molecules and are therefore called intermolecular forces. Two examples of weak attractions that occur frequently between molecules are hydrogen bonds and van der Waals interactions. Without these two types of attractions, life as we know it would not exist. Hydrogen bonds are weak interactions between two polar molecules or between partially charged parts of molecules. The δ+ of the hydrogen from one molecule is attracted to the δ– charge on the more electronegative atoms (usually oxygen or nitrogen) of another molecule. Hydrogen bonds can also occur between different parts of the same molecule. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, forming very strong cumulative interactions. Hydrogen bonds between water molecules provide many of the critical, life- sustaining properties of water and also stabilize the structures of proteins and DNA. Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, around an atom. For these attractions to happen, the molecules need to be very close to one another. Although weaker than hydrogen bonds, van der Waals 66 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE interactions are also additive and can be quite strong in great numbers. Pharmaceutical Chemist Pharmaceutical chemists are responsible for developing new drugs and for trying to determine the mode of action of drugs. Drugs can be found in nature or can be synthesized in the laboratory. In many cases, potential drugs found in nature are changed chemically in the laboratory to make them safer and more effective. After the initial discovery or synthesis of a drug, the chemist develops the drug, perhaps by chemically altering it, testing to see if it is toxic, and designing methods for large-scale production. Next, the process of getting the drug approved for human use by the Food and Drug Administration  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 67 (FDA) begins. This involves a series of large-scale experiments using human subjects to make sure the drug is safe and effective. Approval often takes several years and requires the participation of physicians and chemists. An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, which was originally isolated from willow tree bark. Both of these drugs are now produced synthetically. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if any biologically active compounds are found within them. Sometimes, traditional medicine can give modern medicine clues to where an active compound can be found. For example, the use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s, 68 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE however, that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use. Occasionally, drugs developed for one use are found to have unforeseen effects that allow these drugs to be used in other, unrelated ways. For example, the drug minoxidil (Rogaine) was originally developed to treat high blood pressure. When tested on humans, it was noticed that individuals taking the drug would grow new hair. Eventually the drug was marketed to men and women with baldness to restore lost hair. The career of the pharmaceutical chemist may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 69 2.3 | Water, Acids & Bases Learning Objectives By the end of this section, you will be able to: Describe the properties of water that are critical to maintaining life. Explain why water is an excellent solvent. Provide examples of water’s cohesive and adhesive properties. Discuss the role of acids, bases, and buffers in homeostasis. Why do scientists spend time looking for water on other planets? It is because water is essential to life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Approximately 60–70 percent of the human body is made up of water. Without it, life as we know it simply would not exist. The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with 70 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Special properties of water include its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to the generation of pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life. 2.3.1 The Properties of Water The Polarity of Water One of water’s important properties is that it is composed of polar molecules. While there is no net charge to a water molecule, the slight positive charges on the hydrogen atoms and the slight Figure 2.12 Oil and water do negative charges on the not mix. Since oil is nonpolar, oxygen atoms contribute to it does not dissolve in water water’s properties of but forms droplets instead. (Credit: Gautam Dogra). attraction.  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 71 As a result of their polarity, water molecules form hydrogen bonds with each other. Water also attracts, or is attracted to, other polar molecules and ions. A polar substance that interacts readily with or dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, non-polar molecules, such as oils and fats, do not interact well with water, and separate from it rather than dissolving in it (Figure 2.12). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic = “fearing”). Water’s States: Gas, Liquid, and Solid Its many hydrogen bonds cause water to have some unique chemical characteristics compared to other liquids. Since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. The bonds break due to the motion (kinetic energy) of the water molecules due to the heat contained in the system. As water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). On the other hand, when water freezes, the water molecules form a crystalline structure that makes ice less dense than liquid water. Water is less dense as a solid because as water freezes the water molecules are pushed farther apart 72 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE by the hydrogen bonds. In most other substances, molecules pack more tightly as they freeze, making the solid more dense than the liquid. The lower density of ice causes it to float on liquid water (Figure 2.13). In lakes and ponds, ice will form on the surface of the water creating an insulating barrier that protects the living organisms in the pond from freezing. Without this layer of insulating ice, organisms living in the pond would freeze in the solid block of ice and could not survive. Figure 2.13 The (a) lattice structure of ice due to hydrogen bonding makes it less dense than liquid water, enabling it to (b) float on water. (Credit a: modification of work by Jane Whitney, image created using Visual Molecular Dynamics (VMD) software; b: modification of work by Carlos Ponte) Water’s High Heat Capacity Water has the highest specific heat capacity of any liquid. Specific heat is defined as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. Because of all of the hydrogen bonds  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 73 between water molecules, it takes water a long time to heat and long time to cool. In fact, the specific heat capacity of water is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, water is used by warm blooded animals to help maintain an even temperature. Water’s Heat of Vaporization Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy is required to accomplish this change in water. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, in order for it to enter its gaseous phase (steam). As a result, water requires much more heat to boil than most other liquids. Eventually, as water reaches its boiling point, the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, individual water molecules acquire enough energy from other water molecules that some can escape, in a process known as evaporation. Since the evaporation of water requires heat energy, it cools the environment where the evaporation is taking place. In many living organisms, including humans, the evaporation of 74 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE sweat allows the organism to cool so that homeostasis of body temperature can be maintained. Water’s Solvent Properties Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent, a substance capable of dissolving other molecules. The substance that is dissolved in a liquid is called a solute. The mixture of a solute dissolved in a solvent is called a solution. If the solvent is water, the solution is called an aqueous solution. Due to their charge, polar molecules and ions form hydrogen bonds with water and become surrounded by water molecules. The resulting sphere of hydration, or hydration shell, serves to keep the particles separated in the water. When ionic compounds are added to water, the individual ions react with the water molecules and their ionic bonds are disrupted in the process of dissociation. For example, when crystals of table salt (NaCl, or sodium chloride) are added to water, the molecules of NaCl dissociate into Na+ and Cl– ions, and spheres of hydration form around the ions. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule’s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule (Figure 2.14).  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 75 Figure 2.14 When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. Water’s Cohesive and Adhesive Properties Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water 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, keeping the molecules together at the water-air interface. Cohesion allows for the development of surface tension, the capacity of a substance to withstand being ruptured when placed under tension or stress. This is also why water forms droplets when placed on a dry surface rather than being flattened out by gravity. It is even possible to “float” a 76 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE needle on top of a glass of water or for a water strider to stay afloat on the surface layer of water (Figure 2.15). Figure 2.15 a. The weight of the needle pulls the surface of the water down while surface tension is pulling it up, suspending it on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle. b. Water’s cohesive property allows this water strider to stay afloat. (credit: a. Cory Zanker; b. Tim Vickers)  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 77 Hydrogen bonding also leads to water’s property of adhesion, or the attraction of water molecules to other molecules. Adhesion is observed when water “climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the water molecules are attracted to the charged glass walls of the capillary and therefore adhere to it. This type of adhesion is called capillary action (Figure 2.16). Cohesion and adhesion are important for the transport of water from the roots to the leaves in plants. As water molecules are evaporated from the surface of leaves, they tend to stay connected to water molecules below them, creating a “pull” up the water column. Ultimately, water is pulled into the roots, allowing the plant to receive the dissolved minerals they require from the soil. 78 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.16 Capillary action in a glass tube is caused by the adhesion of water molecules to the charges on the glass. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia Foundation) 2.3.2 Acids and Bases pH is a measure of the concentration of hydrogen ions + [H ]in a solution. Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of + – hydrogen ions (H ) and hydroxide ions (OH ) ions. While the hydroxide ions are kept in solution by hydrogen bonding  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 79 with other water molecules, the hydrogen ions are immediately attracted to water molecules, forming + hydronium ions (H30 ). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water. + – H2O ↔ H +OH + H +H2O ↔H3O+ The concentration of hydrogen ions dissociating from -7 + pure water is 1 × 10 moles H ions per liter of water. One 23 mole of a substance is equal to 6.02 x 10 particles of the substance. pH is calculated as the negative of the base 10 + -7 logarithm of the H concentration. The log10 of 1 × 10 is -7.0, and the negative of this number yields a pH of 7.0, which is also known as neutral pH. The pH inside cells (6.8) and the pH of human blood (7.4) are both very close to neutral. Extremes in pH in either direction are usually considered inhospitable to life. + An acid is a substance that increases the H concentration in a solution, usually by having one of its hydrogen atoms – dissociate. A base provides either OH or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules. + The stronger the acid, the more readily it donates H. For example, hydrochloric acid (HCl) completely dissociates into 80 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE hydrogen and chloride ions and is highly acidic, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids. Conversely, strong bases are – those substances that readily donate OH or take up hydrogen ions. Sodium hydroxide (NaOH) and many – household cleaners are highly alkaline and give up OH rapidly when placed in water, the reby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it. The pH scale ranges from 0 to 14 (Figure 2.17). Anything below 7.0 is Figure 2.17 The pH scale acidic, and anything above measures the concentration of hydrogen ions (H+) in a 7.0 is basic, or alkaline. Since solution. (credit: modification the pH scale is a negative of work by Edward Stevens) logarithmic scale, a ten-fold + change in [H ] results in a change of one in pH in the + opposite direction. For example, increasing the [H ] from 1 x -4 -3 10 to 1 x 10 decreases the pH from pH 4 to pH 3. So how can organisms that require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice,  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 81 for example) and survive? Buffers are the key. Buffers readily + – absorb excess H or OH , keeping the pH of the body in homeostasis. For example, the buffer maintaining the pH of human blood is a mixture of carbonic acid (H2CO3), – bicarbonate ion (HCO ), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH increases. Excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Conversely, if too much OH– is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy (Figure 2.18). Figure 2.18 This diagram shows the body’s buffering of blood pH levels. The blue arrows show the raising of pH as more CO2 is made. The purple arrows indicate the lowering of pH as more bicarbonate is created. Other examples of buffers are antacids used to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least 82 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” after eating. 2.4 | Energy and Life Learning Objectives By the end of this section, you will be able to: Explain the concept of metabolism. Explain the difference between potential and kinetic energy. Explain how the first two laws of thermodynamics relate to living organisms. 2.4.1 Metabolism Virtually every task performed by living organisms requires energy. In fact, the living cells of every organism constantly use energy. Just as energy is required to both build and demolish a building, energy is required for both the synthesis  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 83 and breakdown of molecules. Other cellular process that require energy include transport of signaling molecules, such as hormones and neurotransmitters; ingesting and breaking down pathogens, such as bacteria and viruses; importing nutrients and exporting waste; and many others. The cellular processes listed above require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This section will discuss different forms of energy and the physical laws that govern energy transfer. Cellular processes such as building and breaking down complex molecules occur through series of chemical reactions. All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are the cell’s metabolism. Chemical reactions that require energy to synthesize complex molecules from simpler ones are called anabolic reactions, and chemical reactions that release energy as complex molecules are broken down are called catabolic reactions. 2.4.2. Potential vs. Kinetic Energy Energy is defined as the capacity to do work. When an object is in motion, there is energy associated with that object because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. 84 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE However, a wrecking ball that is not in motion is incapable of performing work. Energy associated with objects in motion is called kinetic energy. A speeding bullet, a walking person, the rapid movement of molecules in the air, and electromagnetic radiation all have kinetic energy. Now what if that same motionless wrecking ball is lifted two stories above a car with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The suspended wrecking ball has energy that results from the fact that there is the potential for the wrecking ball to do work. This type of energy is called potential energy. Another example of potential energy is the energy of water held behind a dam (Figure 2.19). Figure 2.19 Water behind a dam has potential energy. Moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy. (Credit “dam”: modification of work by “Pascal”/Flickr; credit “waterfall”: modification of work by Frank Gualtieri) Potential energy is not only associated with the location of  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 85 matter (such as a wrecking ball being held up), but also with the structure of matter. A spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. Living cells rely heavily on structural potential energy. On a chemical level, the bonds that hold the atoms of molecules together have potential energy. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, because these bonds can release energy when broken. This type of potential energy is called chemical energy (Figure 2.20). Chemical energy provides cells with energy by breaking the molecular bonds within fuel molecules. 86 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.20 The molecules in gasoline (octane, the chemical formula shown) contain chemical energy within the chemical bonds. This energy is transformed into kinetic energy that allows a car to race on a racetrack. (credit “car”: modification of work by Russell Trow)  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 87 2.4.3 The Laws of Thermodynamics Thermodynamics refers to the study of energy and energy transfer. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe. The first and second laws of thermodynamics are relevant to biological systems and how they convert and exchange energy with their surroundings. The First Law of Thermodynamics The first law of thermodynamics states that the total amount of energy in the universe is constant. In other words, energy cannot be created or destroyed. However, energy may be transferred from one form to another. Transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants convert energy of sunlight into chemical energy stored within organic molecules. Some examples of energy transformations are shown in Figure 2.21. 88 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.21 Shown are two examples of energy being transferred from one system to another and transformed from one form to another. Humans can convert the chemical energy in food, like this ice cream cone, into kinetic energy (the energy of movement to ride a bicycle). Plants can convert electromagnetic radiation (light energy) from the sun into chemical energy. (Credit “ice cream”: modification of  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 89 work by D. Sharon Pruitt; credit “kids on bikes”: modification of work by Michelle Riggen-Ransom; credit “leaf”: modification of work by Cory Zanker) 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 very well. Chemical energy stored within organic molecules such as sugars and fats is transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. The Second Law of Thermodynamics The second law of thermodynamics states that the disorder, or entropy, in the universe is always increasing. None of the energy transfers and transformations in the universe is completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. In most cases, the energy is lost in the form of heat energy. Thermodynamically, heat energy is the energy transferred from one system to another that is not doing work. For example, when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction actually heats the air 90 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE by temporarily increasing the speed of air molecules. Likewise, during cellular metabolic reactions, some energy is lost as heat energy. (This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature.) In another example, as molecules at a high concentration in one place diffuse and spread out, entropy increases (Figure 2.22). Figure 2.22 Entropy is a measure of randomness or disorder in a system. Gases have higher entropy than liquids, and liquids have higher entropy than solids.  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 91 Since living things are highly ordered, they require a constant input of energy. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy. 2.5 | Carbon Learning Objectives By the end of this section, you will be able to: Explain why carbon is important for life. Describe the role of functional groups in biological molecules. Cells are made of many complex organic (carbon- containing) molecules, such as proteins and carbohydrates, which are especially important for life. The fundamental component of all of these macromolecules is carbon. Carbon atoms can form covalent bonds with up to four different atoms, making them ideal to form the “backbone” of macromolecules. 92 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE 2.5.1 Hydrocarbons Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen. We often use hydrocarbons as fuels—like the propane in Figure 2.23 Methane, CH4, is the simplest hydrocarbon. a gas grill or the butane in a lighter. The covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule (Figure 2.23). Hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to- carbon bonds may be single, double, or triple covalent bonds. 2.5.2 Functional Groups Functional groups are groups of atoms that occur commonly within molecules and confer specific chemical properties to those molecules. They are found attached to the carbon “backbone” of macromolecules. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of  CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE | 93 functional groups that contributes greatly to its differing chemical properties and its function in living organisms. Some of the important functional groups in biological molecules are shown in Figure 2.24. Functional groups are often classified as polar or non-polar, since that determines whether they are hydrophobic or hydrophilic. For example, non-polar methyl groups are hydrophobic and polar hydroxyl groups are hydrophilic. Functional groups can also be classified as acidic or basic, depending on whether they release + + or accept H in solution. Releasing H results in a negatively charged functional group, such as phosphate groups or + carboxyl groups. Accepting H results in a positively charged functional group, such as amino groups. 94 | CHAPTER 2. THE CHEMICAL CONTEXT OF LIFE Figure 2.24 The functional groups shown here are found in many different biological molecules. Properties of the functional groups affect the properties of the macromolecules that they are part of. For example, since DNA contains phosphate groups, it is both acidic and negatively charged.  CHAPTER 3. AMINO ACIDS & PROTEINS | 95 CHAPTER 3. AMINO ACIDS & PROTEINS Figure 4.1 Atomic structure of the large subunit of a ribosome from Haloarcula marismortui. Ribosomes are large composites of nucleic acid (RNA) and proteins. In this figure, proteins are colored in blue and RNA in ochre. (Credit: by Yikrazuul. Data were taken from PDB 3CC2, rendered with PyMOL.) 96 | CHAPTER 3. AMINO ACIDS & PROTEINS Chapter Outline 3.1 Biological Macromolecules 3.2 Types and Functions of Proteins 3.3 Amino Acids 3.4 Protein Structure Introduction We will now begin our tour of the four major types of macromolecules found in living organisms. The first type of molecule, proteins, are molecular machines that do the work of cells. They have a huge variety of structure and function. But before we delve into how protein structure relates to protein function, we first have to discuss macromolecules.  CHAPTER 3. AMINO ACIDS & PROTEINS | 97 3.1 | Biological Macromolecules Learning Objectives By the end of this section, you will be able to: Name the four major classes of biological macromolecules. Understand the synthesis of macromolecules. Describe dehydration synthesis and hydrolysis reactions. Biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass). Biological macromolecules are organic, 98 | CHAPTER 3. AMINO ACIDS & PROTEINS meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements. 3.1.1 Dehydration Synthesis Reactions Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is known as dehydration synthesis (also known as condensation), which means “to make while losing water.” Figure 3.2 In the dehydration synthesis reaction shown above, two molecules of glucose are linked together to form the disaccharide maltose. In the process, a water molecule is formed. In a dehydration synthesis reaction, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water (Figure 3.2). At the same time, the monomers share electrons and form covalent  CHAPTER 3. AMINO ACIDS & PROTEINS | 99 bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers: for example, glucose monomers are the constituents of starch, glycogen, and cellulose. 3.1.2 Hydrolysis Reactions Polymers are broken down into monomers in a process known as hydrolysis, which means “to split water.” (Figure 3.3). During these reactions, the polymer is broken into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule. Figure 3.3 In the hydrolysis reaction shown here, the disaccharide maltose is broken down to form two glucose monomers with the addition of a water molecule. Note that this reaction is the reverse of the synthesis reaction shown in Figure 3.2. 100 | CHAPTER 3. AMINO ACIDS & PROTEINS Dehydration and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, in our bodies, food is hydrolyzed, or broken down, into smaller molecules by catalytic enzymes in the digestive system. This allows for easy absorption of nutrients by cells in the intestine. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken down by lipases. Breakdown of these macromolecules provides energy for cellular activities. 3.2 | Types and Functions of Proteins Learning Objectives  CHAPTER 3. AMINO ACIDS & PROTEINS | 101 By the end of this section, you will be able to: Describe the functions proteins perform in the cell and in tissues. Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. They are all, however, polymers of amino acids, arranged in a linear sequence. 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 proteins, each with a unique function. Their structures, like their functions, vary greatly. Structural proteins make up the cytoskeleton inside cells and the scaffold outside of cells. They include the keratin of our skin and the collagen of our connective tissue. Contractile proteins include actin and myosin, which allow muscles to contract. Antibodies that help mount an immune response are proteins, as is hemoglobin, which transports oxygen in our blood. Cell membranes contain many proteins, including receptors, channels, and pumps, and many of the signaling molecules that bind to