Chapter Introduction
Molecules, Cells, and Model Organisms
Two cells in mortal combat: a malaria parasite invading a human red blood cell.
[Courtesy Dr. Stuart Ralph, University of Melbourne.]
OUTLINE
1.1 The Molecules of Life
1.2 Prokaryotic Cell Structure and Function
1.3 Eukaryotic Cell Structure and Function
1.4 Unicellular Eukaryotic Model Organisms
1.5 Metazoan Structure, Differentiation, and Model Organisms
Nothing in biology makes sense except in the light of evolution.
—Theodosius Dobzhansky, 1973, essay in American Biology Teacher 35:125–129
Biology is a science fundamentally different from physics or chemistry, which deal with unchanging properties of matter that can be described by mathematical equations. Biological systems, of course, follow the rules of chemistry and physics, but biology is a historical science, as the forms and structures of the living world today are the results of billions of years of evolution. Through evolution, all organisms are related in a family tree extending from primitive single-celled organisms that lived in the distant past to the diverse plants, animals, and microorganisms of the present era (Figure 1-1, Table 1-1). The great insight of Charles Darwin (Figure 1-2) was the principle of natural selection: organisms vary randomly and compete within their environment for resources. Only those that survive and reproduce are able to pass down their genetic traits.
FIGURE 1-1 All living organisms descended from a common ancestral cell. All organisms, from simple bacteria to complex mammals, probably evolved from a common single-celled ancestor. This family tree depicts the evolutionary relationships among the three major lineages of organisms. The structure of the tree was initially ascertained from morphological criteria: creatures that look alike were put close together. More recently, the sequences of DNA and proteins found in organisms have provided more information-rich criteria for assigning relationships. The greater the similarities in these macromolecular sequences, the more closely related organisms are thought to be. The trees based on morphological comparisons and the fossil record generally agree well with those based on molecular data.
[Data from J. R. Brown, 2005, “Universal tree of life,” in Encyclopedia of Life Sciences, Wiley InterScience (online).]
FIGURE 1-2 Charles Darwin (1809–1882). Four years after his epic voyage on HMS Beagle, Darwin had already begun formulating in private notebooks his concept of natural selection, which would be published in his Origin of Species (1859).
[Charles Darwin on the Galapagos Islands by Howat, Andrew (20th century)/Private Collection/© Look and Learn/Bridgeman Images.]
At first glance, the biological universe does appear amazingly diverse—from tiny ferns to tall fir trees, from single-celled bacteria and protozoans visible only under a microscope to multicellular animals of all kinds. Indeed, cells come in an astonishing variety of sizes and shapes (Figure 1-3). Some move rapidly and have fast-changing structures, as we can see in movies of amoebae and rotifers. Others are largely stationary and structurally stable. Oxygen kills some cells but is an absolute requirement for others. Most cells in multicellular organisms are intimately involved with other cells. Although some unicellular organisms live in isolation (Figure 1-3a), others form colonies or live in close association with other types of organisms (Figure 1-3b, d), such as the bacteria that help plants to extract nitrogen from the air or the bacteria that live in our intestines and help us digest food.
FIGURE 1-3 Cells come in an astounding assortment of shapes and sizes. Some of the morphological variety of cells is illustrated in these photographs. In addition to morphology, cells differ in their ability to move, internal organization (prokaryotic versus eukaryotic cells), and metabolic activities. (a) Eubacteria: Lactococcus lactis, which are used to produce cheese such as Roquefort, Brie, and Camembert. Note the dividing cells. (b) A mass of archaeans (Methanosarcina) that produce their energy by converting carbon dioxide and hydrogen gas to methane. Some species that live in the rumens of cattle give rise to >150 liters of methane gas each day. (c) Human blood cells, shown in false color. The red cells are oxygen-bearing erythrocytes, the white cells (leukocytes) are part of the immune system and fight infection, and the green cells are platelets that plug wounds and contain substances to initiate blood clotting. (d) A colonial single-celled green alga, Volvox aureus. The large spheres are made up of many individual cells, visible as blue or green dots. The yellow masses inside are daughter colonies, each made up of many cells. (e) A single Purkinje neuron of the cerebellum, which can form more than a hundred thousand connections with other cells through its branched network of dendrites. The cell was made visible by introduction of a green fluorescent protein; the cell body is the bulb at the upper right. (f) Plant cells are fixed firmly in place in vascular plants, supported by a rigid cellulose skeleton. Spaces between the cells are joined into tubes for transport of water and food.
[Part (a) Gary Gaugler/Science Source. Part (b) Power and Syred/Science Source. Part (c) Science Source. Part (d) micro_photo/iStockphoto/Getty Images. Part (e) Courtesy of Dr. Helen M. Blau (Stanford University School of Medicine) and Dr. Clas B. Johansson (Karolinska Institutet). Part (f) Biophoto Associates/Science Source.]
Yet the bewildering array of outward biological forms overlies a powerful uniformity: thanks to our common ancestry, all biological systems are composed of cells containing the same types of chemical molecules and employing similar principles of organization at the cellular level. Although the basic kinds of biological molecules have been conserved during the billions of years of evolution, the patterns in which they are assembled to form functioning cells and organisms have undergone considerable change.
We now know that genes, which chemically are composed of deoxyribonucleic acid (DNA), ultimately define biological structure and maintain the integration of cellular function. Many genes encode proteins, the primary molecules that make up cell structures and carry out cellular activities. Alterations in the structure and organization of genes, or mutations, provide the random variation that can alter biological structure and function. While the vast majority of random mutations have no observable effect on a gene’s or protein’s function, many are deleterious, and only a few confer an evolutionary advantage on the organism. In all organisms, mutations in DNA are constantly occurring, allowing over time the small alterations in cellular structures and functions that may prove to be advantageous. Entirely new cellular structures are rarely created; more often, existing cellular structures undergo changes that better adapt the organism to new circumstances. Slight changes in a protein can cause important changes in its function or abolish its function entirely.
For instance, in a particular organism, one gene may randomly become duplicated, after which one copy of the gene and its encoded protein retain their original function while, over time, the second copy of the gene mutates such that its protein takes on a slightly different or even a totally new function. During the evolution of some organisms, the entire genome became duplicated, allowing the second copies of many genes to undergo mutations and acquire new functions. The cellular organization of organisms plays a fundamental role in this process because it allows these changes to come about by small alterations in previously evolved cells, giving them new abilities. The result is that closely related organisms have very similar genes and proteins as well as similar cellular and tissue organizations.
Multicellular organisms, including the human body, consist of such closely interrelated elements that no single element can be fully appreciated in isolation from the others. Organisms contain organs, organs are composed of tissues, tissues consist of cells, and cells are formed from molecules (Figure 1-4). The unity of living systems is coordinated by many levels of interrelationship: molecules carry messages from organ to organ and cell to cell, and tissues are delineated and integrated with other tissues by molecules secreted by cells. Generally all the levels into which we fragment biological systems interconnect.
FIGURE 1-4 Living systems such as the human body consist of closely interrelated elements. (a) The surface of the hand is covered by a living organ, skin, that is composed of several layers of tissue. (b) An outer covering of hard, dead skin cells protects the body from injury, infection, and dehydration. This layer is constantly renewed by living epidermal cells, which also give rise to hair and fur in animals. Deeper layers of muscle and connective tissue give skin its tone and firmness. (c) Tissues are formed through subcellular adhesion structures (desmosomes and hemidesmosomes) that join cells to one another and to an underlying layer of supporting fibers. (d) At the heart of cell-cell adhesion are its structural components: phospholipid molecules that make up the cell-surface membrane, and large protein molecules. Protein molecules that traverse the cell membrane often form strong bonds with internal and external fibers made of multiple proteins.
To learn about biological systems, however, we must examine one small portion of a living system at a time. The biology of cells is a logical starting point because an organism can be viewed as consisting of interacting cells, which are the closest thing to autonomous biological units that exist. The last common ancestor of all life on Earth was a single cell (see Figure 1-1), and at the cellular level all life is remarkably similar. All cells use the same molecular building blocks, similar methods for the storage, maintenance, and expression of genetic information, and similar processes of energy metabolism, molecular transport, signaling, development, and structure.
In this chapter, we introduce the common features of cells. We begin with a brief discussion of the principal small molecules and macromolecules found in biological systems. Next we discuss the fundamental aspects of cell structure and function that are conserved in present-day organisms, focusing first on prokaryotic organisms—single-celled organisms without a nucleus—and their uses in studying the basic molecules of life. Then we discuss the structure and function of eukaryotic cells—cells with a defined nucleus—focusing on their many organelles. This discussion is followed by a section describing the use of unicellular eukaryotic organisms in investigations of molecular cell biology, focusing on yeasts and the parasite that causes malaria.
We now have the complete sequences of the genomes of several thousand metazoans (multicellular animals), and these sequences have provided considerable insight into the evolution of genes and organisms. The final section in this chapter shows us how this information can be used to refine the evolutionary relationships among organisms as well as our understanding of human development. Indeed, biologists use evolution as a research tool: if a gene and its protein have been conserved in all metazoans but are not found in unicellular organisms, the protein probably has an important function in all metazoans and thus can be studied in whatever metazoan organism is most suitable for the investigation. Because the structure and function of many types of metazoan cells is also conserved, we now understand the structure and function of many cell types in considerable detail, including muscle and liver cells and the sheets of epithelial cells that line the intestine and form our skin. But other cells—especially the multiple types that form our nervous and immune systems—still remain mysterious; much important cell biological experimentation is needed on these and other cell systems and organs that form our bodies.