Ch1 PDF - Biochemistry and the Unity of Life
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Idaho State University
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Summary
This document provides an introduction to biochemistry, exploring its principles and applications, particularly in the context of the study of living organisms at the molecular level.
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SECTION 1 Biochemistry Helps Us to Understand Our World CHAPTER 1 Biochemistry and the Unity of Life CHAPTER 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 121 The ultimate goal of all scientific endeavors is to develop a deeper, richer understanding of...
SECTION 1 Biochemistry Helps Us to Understand Our World CHAPTER 1 Biochemistry and the Unity of Life CHAPTER 2 Water, Weak Bonds, and the Generation of Order Out of Chaos 121 The ultimate goal of all scientific endeavors is to develop a deeper, richer understanding of ourselves and the world in which we live. Biochemistry has had and will continue to have an extensive role in helping us to develop this understanding. Biochemistry—the study of living organisms at the molecular level—has shown us many of the details of the most fundamental processes of life. For instance, biochemistry has shown us how information flows from genes to molecules that have functional capabilities. In recent years, biochemistry has also unraveled some of the mysteries of the molecular generators that provide the energy that powers living organisms. The realization that we can understand such essential life processes has significant philosophical implications. What does it mean, biochemically, to be human? What are the biochemical differences between a human being, a chimpanzee, a mouse, and a fruit fly? Are we more similar than we are different? The understanding achieved through biochemistry is greatly influencing medicine and other fields. Although we may not be 122 accustomed to thinking of illness in relation to molecules, illness is ultimately some sort of malfunction at the molecular level. The molecular lesions causing sickle-cell anemia, cystic fibrosis, hemophilia, and many other genetic diseases have been elucidated at the biochemical level. Biochemistry is also contributing richly to clinical diagnostics. For example, elevated levels of heart enzymes in the blood reveal whether a patient has recently had a myocardial infarction (heart attack). Agriculture, too, is employing biochemistry to develop more effective, environmentally safer herbicides and pesticides and to create genetically engineered plants that are, for example, more resistant to insects. In this section, we will learn some of the key concepts that structure the study of biochemistry. We begin with an introduction to the molecules of biochemistry, followed by an overview of the fundamental unit of biochemistry and life itself —the cell. Finally, we examine the weak reversible bonds that enable the formation of biological structures and permit the interplay between molecules that makes life possible. By the end of this section, you should be able to: 1 Describe the key classes of biomolecules and differentiate between them. 2 List the steps of the central dogma. 3 Identify the key features that differentiate eukaryotic cells from prokaryotic cells. 4 Describe the chemical properties of water and explain how water 123 affects biochemical interactions. 5 Describe the types of noncovalent, reversible interactions and explain why reversible interactions are important in biochemistry. 6 Define pH and explain why changes in pH may affect biochemical systems. 124 CHAPTER 1 Biochemistry and the Unity of Life Despite their vast differences in mass—the African elephant has a mass times as great as that of the bacterium E. coli—and complexity, the biochemical workings of these two organisms are remarkably similar. 1.1 Living Systems Require a Limited Variety of Atoms and Molecules 1.2 There Are Four Major Classes of Biomolecules 1.3 The Central Dogma Describes the Basic Principles of Biological Information Transfer 1.4 Membranes Define the Cell and Carry Out Cellular 125 Functions A key goal of biochemistry, one that has been met with striking success, is to understand what it means to be alive at the molecular level. Another goal is to extend this understanding to the organismic level—that is, to understand the effects of molecular manipulations on the life that an organism leads. For instance, understanding how the hormone insulin works at the molecular level illuminates how the organism controls the levels of common fuels—glucose and fats—in its blood. Often, such understanding facilitates an understanding of disease states, such as diabetes, which results when insulin signaling goes awry. In turn, this knowledge can be a source of insight into how the disease can be treated. Biochemistry has been an active area of research for more than a century. Much knowledge has been gained about how a variety of organisms manipulate energy and information. However, one of the most exciting outcomes of biochemical research has been the realization that all organisms have much in common biochemically. Organisms are remarkably uniform at the molecular level. This observation is frequently referred to as the unity of biochemistry, but in reality, it illustrates the unity of life. French biochemist Jacques Monod encapsulated this idea in 1954 with the phrase “Anything found to be true of [the bacterium] E. coli must also be true of elephants.” This uniformity reveals that all organisms on Earth have arisen from a common ancestor. A core of essential biochemical processes, 126 common to all organisms, appeared early in the evolution of life. The diversity of life in the modern world has been generated by evolutionary processes acting on these core processes through millions and even billions of years. We begin our study of biochemistry by looking at commonalities. We will examine the molecules and molecular constituents that are used by all life forms and will then consider the rules that govern how biochemical information is accessed and how it is passed from one generation to the next. Finally, we will take an overview of the fundamental unit of life —the cell. This is just the beginning. All of the molecules and structures that we see in this chapter we will meet again and again as we explore the chemical basis of life. 127 1.1 Living Systems Require a Limited Variety of Atoms and Molecules Ninety naturally occurring elements have been identified, yet only three—oxygen, hydrogen, and carbon—make up 98% of the atoms in an organism. Moreover, the abundance of these three elements in life is vastly different from their abundance in the Earth’s crust (TABLE 1.1). What can account for the disparity between what is available and what organisms are made of? TABLE 1.1 Chemical compositions as percentage of total number of atoms Composition in Element Human beings (%) Seawater (%) Earth’s crust (%) Hydrogen 63 66 0.22 Oxygen 25.5 33 47 Carbon 9.5 0.0014 0.19 Nitrogen 1.4