The Diversity and Commonality of Cells Cells come in an amazing variety of sizes and shapes (Figure 1-1). 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, others form colonies or live in close association with other types of organisms, such as the bacteria that help plants to ex- tract nitrogen from the air or the bacteria that live in our in- testines and help us digest food. Despite these and numerous 1.1 1 A single ~200 micrometer (�m) cell, the human egg, with sperm, which are also single cells. From the union of an egg and sperm will arise the 10 trillion cells of a human body. [Photo Researchers, Inc.] LIFE BEGINS WITH CELLS L ike ourselves, the individual cells that form our bodies can grow, reproduce, process information, respond to stimuli, and carry out an amazing array of chemical re- actions. These abilities define life. We and other multicellular organisms contain billions or trillions of cells organized into complex structures, but many organisms consist of a single cell. Even simple unicellular organisms exhibit all the hall- mark properties of life, indicating that the cell is the funda- mental unit of life. As the twenty-first century opens, we face an explosion of new data about the components of cells, what structures they contain, how they touch and influence each other. Still, an immense amount remains to be learned, particularly about how information flows through cells and how they decide on the most appropriate ways to respond. Molecular cell biology is a rich, integrative science that brings together biochemistry, biophysics, molecular biology, microscopy, genetics, physiology, computer science, and de- velopmental biology. Each of these fields has its own em- phasis and style of experimentation. In the following chapters, we will describe insights and experimental ap- proaches drawn from all of these fields, gradually weaving the multifaceted story of the birth, life, and death of cells. We start in this prologue chapter by introducing the diversity of cells, their basic constituents and critical functions, and what we can learn from the various ways of studying cells. 1 O U T L I N E 1.1 The Diversity and Commonality of Cells 1.2 The Molecules of a Cell 1.3 The Work of Cells 1.4 Investigating Cells and Their Parts 1.5 A Genome Perspective on Evolution other differences, all cells share certain structural features and carry out many complicated processes in basically the same way. As the story of cells unfolds throughout this book, we will focus on the molecular basis of both the differences and similarities in the structure and function of various cells. All Cells Are Prokaryotic or Eukaryotic The biological universe consists of two types of cells— prokaryotic and eukaryotic. Prokaryotic cells consist of a sin- gle closed compartment that is surrounded by the plasma membrane, lacks a defined nucleus, and has a relatively simple internal organization (Figure 1-2a). All prokaryotes have cells of this type. Bacteria, the most numerous prokaryotes, are single-celled organisms; the cyanobacteria, or blue-green algae, can be unicellular or filamentous chains of cells. Although bac- terial cells do not have membrane-bounded compartments, many proteins are precisely localized in their aqueous interior, or cytosol, indicating the presence of internal organization. A single Escherichia coli bacterium has a dry weight of about 2 CHAPTER 1 • Life Begins with Cells ▲ FIGURE 1-1 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; note dividing cells. These are Lactococcus lactis, which are used to produce cheese such as Roquefort, Brie, and Camembert. (b) A mass of archaebacteria (Methanosarcina) that produce their energy by converting carbon dioxide and hydrogen gas to methane. Some species that live in the rumen of cattle give rise to >150 liters of methane gas/day. (c) Blood cells, shown in false color. The red blood cells are oxygen-bearing erythrocytes, the white blood cells (leukocytes) are part of the immune system and fight infection, and the green cells are platelets that provide substances to make blood clot at a wound. (d) Large single cells: fossilized dinosaur eggs. (e) 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. (f) A single Purkinje neuron of the cerebellum, which can form more than a hundred thousand connections with other cells through the branched network of dendrites. The cell was made visible by introduction of a fluorescent protein; the cell body is the bulb at the bottom. (g) Cells can form an epithelial sheet, as in the slice through intestine shown here. Each finger-like tower of cells, a villus, contains many cells in a continuous sheet. Nutrients are transferred from digested food through the epithelial sheet to the blood for transport to other parts of the body. New cells form continuously near the bases of the villi, and old cells are shed from the top. (h) 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/ Photo Researchers, Inc. Part (b) Ralph Robinson/ Visuals Inlimited, Inc. Part (c) NIH/Photo Researchers, Inc. Part (d) John D. Cunningham/Visuals Unlimited, Inc. Part (e) Carolina Biological/Visuals Unlimited, Inc. Part (f) Helen M. Blau, Stanford University. Part (g) Jeff Gordon, Washington University School of Medicine. Part (h) Richard Kessel and C. Shih/Visuals Unlimited, Inc.] (e) (f) (g) (h) (a) (b) (c) (d) 25 � 10�14 g. Bacteria account for an estimated 1–1.5 kg of the average human’s weight. The estimated number of bacte- ria on earth is 5 � 1030, weighing a total of about 1012 kg. Prokaryotic cells have been found 7 miles deep in the ocean and 40 miles up in the atmosphere; they are quite adaptable! The carbon stored in bacteria is nearly as much as the carbon stored in plants. Eukaryotic cells, unlike prokaryotic cells, contain a de- fined membrane-bound nucleus and extensive internal mem- branes that enclose other compartments, the organelles (Fig- ure 1-2b). The region of the cell lying between the plasma membrane and the nucleus is the cytoplasm, comprising the cytosol (aqueous phase) and the organelles. Eukaryotes com- prise all members of the plant and animal kingdoms, includ- ing the fungi, which exist in both multicellular forms (molds) and unicellular forms (yeasts), and the protozoans (proto, primitive; zoan, animal), which are exclusively unicellular. Eukaryotic cells are commonly about 10–100 �m across, 1.1 • The Diversity and Commonality of Cells 3 Inner (plasma) membrane (a) Prokaryotic cell (b) Eukaryotic cell Cell wall Periplasmic space Outer membrane Nucleus Nuclear membrane Plasma membrane Golgi vesicles Lysosome Secretory vesicle Peroxisome Mitochondrion Rough endoplasmic reticulum Periplasmic space and cell wall Outer membrane Inner (plasma) membrane Nucleoid 0.5 �m 1 �m Nucleus Golgi vesicles Lysosome Mitochondrion Endoplasmic reticulum Nucleoid ▲ FIGURE 1-2 Prokaryotic cells have a simpler internal organization than eukaryotic cells. (a) Electron micrograph of a thin section of Escherichia coli, a common intestinal bacterium. The nucleoid, consisting of the bacterial DNA, is not enclosed within a membrane. E. coli and some other bacteria are surrounded by two membranes separated by the periplasmic space. The thin cell wall is adjacent to the inner membrane. (b) Electron micrograph of a plasma cell, a type of white blood cell that secretes antibodies. Only a single membrane (the plasma membrane) surrounds the cell, but the interior contains many membrane-limited compartments, or organelles. The defining characteristic of eukaryotic cells is segregation of the cellular DNA within a defined nucleus, which is bounded by a double membrane. The outer nuclear membrane is continuous with the rough endoplasmic reticulum, a factory for assembling proteins. Golgi vesicles process and modify proteins, mitochondria generate energy, lysosomes digest cell materials to recycle them, peroxisomes process molecules using oxygen, and secretory vesicles carry cell materials to the surface to release them. [Part (a) courtesy of I. D. J. Burdett and R. G. E. Murray. Part (b) from P. C. Cross and K. L. Mercer, 1993, Cell and Tissue Ultrastructure: A Functional Perspective, W. H. Freeman and Company.] generally much larger than bacteria. A typical human fi- broblast, a connective tissue cell, might be about 15 �m across with a volume and dry weight some thousands of times those of an E. coli bacterial cell. An amoeba, a single- celled protozoan, can be more than 0.5 mm long. An ostrich egg begins as a single cell that is even larger and easily visi- ble to the naked eye. All cells are thought to have evolved from a common pro- genitor because the structures and molecules in all cells have so many similarities. In recent years, detailed analysis of the DNA sequences from a variety of prokaryotic organisms has revealed two distinct types: the so-called “true” bacteria, or eu- bacteria, and archaea (also called archaebacteria or archaeans). Working on the assumption that organisms with more similar genes evolved from a common progenitor more recently than those with more dissimilar genes, researchers have developed the evolutionary lineage tree shown in Figure 1-3. According to this tree, the archaea and the eukaryotes diverged from the true bacteria before they diverged from each other. Many archaeans grow in unusual, often extreme, envi- ronments that may resemble ancient conditions when life first appeared on earth. For instance, halophiles (“salt lov- ing”) require high concentrations of salt to survive, and thermoacidophiles (“heat and acid loving”) grow in hot (80� C) sulfur springs, where a pH of less than 2 is common. Still other archaeans live in oxygen-free milieus and generate methane (CH4) by combining water with carbon dioxide. Unicellular Organisms Help and Hurt Us Bacteria and archaebacteria, the most abundant single-celled organisms, are commonly 1–2 �m in size. Despite their small size and simple architecture, they are remarkable biochemi- cal factories, converting simple chemicals into complex bio- logical molecules. Bacteria are critical to the earth’s ecology, but some cause major diseases: bubonic plague (Black Death) from Yersinia pestis, strep throat from Streptomyces, tuber- culosis from Mycobacterium tuberculosis, anthrax from Bacillus anthracis, cholera from Vibrio cholerae, food poi- soning from certain types of E. coli and Salmonella. Humans are walking repositories of bacteria, as are all plants and animals. We provide food and shelter for a stag- gering number of “bugs,” with the greatest concentration in our intestines. Bacteria help us digest our food and in turn are able to reproduce. A common gut bacterium, E. coli is also a favorite experimental organism. In response to signals from bacteria such as E. coli, the intestinal cells form appro- priate shapes to provide a niche where bacteria can live, thus facilitating proper digestion by the combined efforts of the bacterial and the intestinal cells. Conversely, exposure to in- testinal cells changes the properties of the bacteria so that they participate more effectively in digestion. Such commu- nication and response is a common feature of cells. The normal, peaceful mutualism of humans and bacteria is sometimes violated by one or both parties. When bacteria begin to grow where they are dangerous to us (e.g., in the blood- stream or in a wound), the cells of our immune system fight back, neutralizing or devouring the intruders. Powerful antibi- otic medicines, which selectively poison prokaryotic cells, provide rapid assistance to our relatively slow-developing immune response. Understanding the molecular biology of bac- terial cells leads to an understanding of how bacteria are nor- mally poisoned by antibiotics, how they become resistant to antibiotics, and what processes or structures present in bacter- ial but not human cells might be usefully targeted by new drugs. 4 CHAPTER 1 • Life Begins with Cells Plants Fungi EUKARYOTA EUBACTERIA ARCHAEA Animals Microsporidia Euglena Sulfolobus Thermococcus Methanobacterium Halococcus Halobacterium Methanococcus jannaschii Borrelia burgdorferi E. coli B. subtilus Diplomonads (Giardia lamblia) Ciliates Slime molds Thermotoga Flavobacteria Green sulfur bacteria Presumed common progenitor of all extant organisms Presumed common progenitor of archaebacteria and eukaryotes ▲ FIGURE 1-3 All organisms from simple bacteria to complex mammals probably evolved from a common, single- celled progenitor. This family tree depicts the evolutionary relations 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 have been examined as a more information-rich criterion 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 those based on molecular data. Although all organisms in the eubacterial and archaean lineages are prokaryotes, archaea are more similar to eukaryotes than to eubacteria (“true” bacteria) in some respects. For instance, archaean and eukaryotic genomes encode homologous histone proteins, which associate with DNA; in contrast, bacteria lack histones. Likewise, the RNA and protein components of archaean ribosomes are more like those in eukaryotes than those in bacteria. Like bacteria, protozoa are usually beneficial members of the food chain. They play key roles in the fertility of soil, con- trolling bacterial populations and excreting nitrogenous and phosphate compounds, and are key players in waste treat- ment systems—both natural and man-made. These unicellu- lar eukaryotes are also critical parts of marine ecosystems, consuming large quantities of phytoplankton and harboring photosynthetic algae, which use sunlight to produce biologi- cally useful energy forms and small fuel molecules. However, some protozoa do give us grief: Entamoeba histolytica causes dysentery; Trichomonas vaginalis, vagini- tis; and Trypanosoma brucei, sleeping sickness. Each year the worst of the protozoa, Plasmodium falciparum and related species, is the cause of more than 300 million new cases of malaria, a disease that kills 1.5 to 3 million people annually. These protozoans inhabit mammals and mosquitoes alter- nately, changing their morphology and behavior in response to signals in each of these environments. They also recog- nize receptors on the surfaces of the cells they infect. The complex life cycle of Plasmodium dramatically illustrates how a single cell can adapt to each new challenge it encoun- ters (Figure 1-4). All of the transformations in cell type that 1.1 • The Diversity and Commonality of Cells 5 (a) Red blood cell Merozoites Liver Sporozoites Oocyst Mosquito Human Gametocytes Sporulation Merozoites Sperm Egg Zygote 2 1 8 7 6 5 4 3 ▲ FIGURE 1-4 Plasmodium organisms, the parasites that cause malaria, are single-celled protozoans with a remarkable life cycle. Many Plasmodium species are known, and they can infect a variety of animals, cycling between insect and vertebrate hosts. The four species that cause malaria in humans undergo several dramatic transformations within their human and mosquito hosts. (a) Diagram of the life cycle. Sporozoites enter a human host when an infected Anopheles mosquito bites a person . They migrate to the liver where they develop into merozoites, which are released into the blood . Merozoites differ substantially from sporozoites, so this transformation is a metamorphosis (Greek, “to transform” or “many shapes”). Circulating merozoites invade red blood cells (RBCs) and reproduce within them . Proteins produced by some Plasmodium species move to the surface of infected RBCs, causing the cells to adhere to the walls of blood vessels. This prevents infected RBCs cells from circulating to the spleen where cells of the immune system would destroy the RBCs and the Plasmodium organisms they harbor. After growing and reproducing in RBCs for a period of time characteristic of each Plasmodium species, the merozoites suddenly burst forth in synchrony from large numbers of infected cells . It is this 4 3 2 1 event that brings on the fevers and shaking chills that are the well-known symptoms of malaria. Some of the released merozoites infect additional RBCs, creating a cycle of production and infection. Eventually, some merozoites develop into male and female gametocytes , another metamorphosis. These cells, which contain half the usual number of chromosomes, cannot survive for long unless they are transferred in blood to an Anopheles mosquito. In the mosquito’s stomach, the gametocytes are transformed into sperm or eggs (gametes), yet another metamorphosis marked by development of long hairlike flagella on the sperm . Fusion of sperm and eggs generates zygotes , which implant into the cells of the stomach wall and grow into oocysts, essentially factories for producing sporozoites. Rupture of an oocyst releases thousands of sporozoites ; these migrate to the salivary glands, setting the stage for infection of another human host. (b) Scanning electron micrograph of mature oocysts and emerging sporozoites. Oocysts abut the external surface of stomach wall cells and are encased within a membrane that protects them from the host immune system. [Part (b) courtesy of R. E. Sinden.] 8 7 6 5 (b) M E D I A C O N N E C T I O N S Video: Plasmodium Sporozoite Entering and Exiting a Liver Cell occur during the Plasmodium life cycle are governed by in- structions encoded in the genetic material of this parasite and triggered by environmental inputs. The other group of single-celled eukaryotes, the yeasts, also have their good and bad points, as do their multicellular cousins, the molds. Yeasts and molds, which collectively con- stitute the fungi, have an important ecological role in break- ing down plant and animal remains for reuse. They also make numerous antibiotics and are used in the manufacture of bread, beer, wine, and cheese. Not so pleasant are fungal diseases, which range from relatively innocuous skin infec- tions, such as jock itch and athlete’s foot, to life-threatening Pneumocystis carinii pneumonia, a common cause of death among AIDS patients. Even Single Cells Can Have Sex The common yeast used to make bread and beer, Saccha- romyces cerevisiae, appears fairly frequently in this book be- cause it has proven to be a great experimental organism. Like many other unicellular organisms, yeasts have two mating types that are conceptually like the male and female gametes (eggs and sperm) of higher organisms. Two yeast cells of op- posite mating type can fuse, or mate, to produce a third cell type containing the genetic material from each cell (Figure 1-5). Such sexual life cycles allow more rapid changes in ge- netic inheritance than would be possible without sex, result- ing in valuable adaptations while quickly eliminating detrimental mutations. That, and not just Hollywood, is probably why sex is so ubiquitous. Viruses Are the Ultimate Parasites Virus-caused diseases are numerous and all too familiar: chicken pox, influenza, some types of pneumonia, polio, measles, rabies, hepatitis, the common cold, and many oth- ers. Smallpox, once a worldwide scourge, was eradicated by a decade-long global immunization effort beginning in the mid-1960s. Viral infections in plants (e.g., dwarf mosaic virus in corn) have a major economic impact on crop pro- duction. Planting of virus-resistant varieties, developed by traditional breeding methods and more recently by genetic engineering techniques, can reduce crop losses significantly. Most viruses have a rather limited host range, infecting cer- tain bacteria, plants, or animals (Figure 1-6). Because viruses cannot grow or reproduce on their own, they are not considered to be alive. To survive, a virus must infect a host cell and take over its internal machinery to syn- thesize viral proteins and in some cases to replicate the viral genetic material. When newly made viruses are released, the cycle starts anew. Viruses are much smaller than cells, on the order of 100 nanometer (nm) in diameter; in comparison, bacterial cells are usually �1000 nm (1 nm�10�9 meters). A virus is typically composed of a protein coat that encloses a core containing the genetic material, which carries the infor- mation for producing more viruses (Chapter 4). The coat protects a virus from the environment and allows it to stick to, or enter, specific host cells. In some viruses, the protein coat is surrounded by an outer membrane-like envelope. The ability of viruses to transport genetic material into cells and tissues represents a medical menace and a medical opportunity. Viral infections can be devastatingly destructive, causing cells to break open and tissues to fall apart. However, many methods for manipulating cells depend upon using 6 CHAPTER 1 • Life Begins with Cells ▲ FIGURE 1-5 The yeast Saccharomyces cerevisiae reproduces sexually and asexually. (a) Two cells that differ in mating type, called a and �, can mate to form an a/� cell . The a and � cells are haploid, meaning they contain a single copy of each yeast chromosome, half the usual number. Mating yields a diploid a/� cell containing two copies of each chromosome. During vegetative growth, diploid cells multiply by mitotic budding, an asexual process . Under starvation conditions, diploid cells undergo meiosis, a special type of cell division, to form haploid ascospores . Rupture of an ascus releases four haploid spores, which can germinate into haploid cells . These also can multiply asexually . (b) Scanning electron micrograph of budding yeast cells. After each bud breaks free, a scar is left at the budding site so the number of previous buds can be counted. The orange cells are bacteria. [Part (b) M. Abbey/Visuals Unlimited, Inc.] 5 4 3 2 1 Vegetative growth of diploid cells Bud Starvation causes ascus formation, meiosis Four haploid ascospores within ascus Vegetative growth of haploid cells Ascus ruptures, spores germinate a Mating between haploid cells of opposite mating type Diploid cells (a/ ) α α (b) 1 2 3 4 5 (a) Budding (S. cerevisiae) viruses to convey genetic material into cells. To do this, the portion of the viral genetic material that is potentially harm- ful is replaced with other genetic material, including human genes. The altered viruses, or vectors, still can enter cells tot- ing the introduced genes with them (Chapter 9). One day, dis- eases caused by defective genes may be treated by using viral vectors to introduce a normal copy of a defective gene into patients. Current research is dedicated to overcoming the con- siderable obstacles to this approach, such as getting the in- troduced genes to work at the right places and times. We Develop from a Single Cell In 1827, German physician Karl von Baer discovered that mammals grow from eggs that come from the mother’s ovary. Fertilization of an egg by a sperm cell yields a zygote, a visually unimpressive cell 200 �m in diameter. Every human being begins as a zygote, which houses all the neces- sary instructions for building the human body containing about 100 trillion (1014) cells, an amazing feat. Development begins with the fertilized egg cell dividing into two, four, then eight cells, forming the very early embryo (Figure 1-7). Con- tinued cell proliferation and then differentiation into distinct cell types gives rise to every tissue in the body. One initial cell, the fertilized egg (zygote), generates hundreds of differ- ent kinds of cells that differ in contents, shape, size, color, mobility, and surface composition. We will see how genes and signals control cell diversification in Chapters 15 and 22. Making different kinds of cells—muscle, skin, bone, neu- ron, blood cells—is not enough to produce the human body. The cells must be properly arranged and organized into tis- sues, organs, and appendages. Our two hands have the same kinds of cells, yet their different arrangements—in a mirror image—are critical for function. In addition, many cells ex- hibit distinct functional and/or structural asymmetries, a property often called polarity. From such polarized cells arise 1.1 • The Diversity and Commonality of Cells 7 (a) T4 bacteriophage (b) Tobacco mosaic virus (c) Adenovirus 100 nm 50 nm 50 nm ▲ FIGURE 1-6 Viruses must infect a host cell to grow and reproduce. These electron micrographs illustrate some of the structural variety exhibited by viruses. (a) T4 bacteriophage (bracket) attaches to a bacterial cell via a tail structure. Viruses that infect bacteria are called bacteriophages, or simply phages. (b) Tobacco mosaic virus causes a mottling of the leaves of infected tobacco plants and stunts their growth. (c) Adenovirus causes eye and respiratory tract infections in humans. This virus has an outer membranous envelope from which long glycoprotein spikes protrude. [Part (a) from A. Levine, 1991, Viruses, Scientific American Library, p. 20. Part (b) courtesy of R. C. Valentine. Part (c) courtesy of Robley C. Williams, University of California.] (a) (b) (c) � FIGURE 1-7 The first few cell divisions of a fertilized egg set the stage for all subsequent development. A developing mouse embryo is shown at (a) the two-cell, (b) four-cell, and (c) eight-cell stages. The embryo is surrounded by supporting membranes. The corresponding steps in human development occur during the first few days after fertilization. [Claude Edelmann/Photo Researchers, Inc.] M E D I A C O N N E C T I O N S Video: Early Embryonic Development asymmetric, polarized tissues such as the lining of the intes- tines and structures like hands and hearts. The features that make some cells polarized, and how they arise, also are cov- ered in later chapters. Stem Cells, Cloning, and Related Techniques Offer Exciting Possibilities but Raise Some Concerns Identical twins occur naturally when the mass of cells com- posing an early embryo divides into two parts, each of which develops and grows into an individual animal. Each cell in an eight-cell-stage mouse embryo has the potential to give rise to any part of the entire animal. Cells with this capabil- ity are referred to as embryonic stem (ES) cells. As we learn in Chapter 22, ES cells can be grown in the laboratory (cul- tured) and will develop into various types of differentiated cells under appropriate conditions. The ability to make and manipulate mammalian embryos in the laboratory has led to new medical opportunities as well as various social and ethical concerns. In vitro fertiliza- tion, for instance, has allowed many otherwise infertile cou- ples to have children. A new technique involves extraction of nuclei from defective sperm incapable of normally fertiliz- ing an egg, injection of the nuclei into eggs, and implantation of the resulting fertilized eggs into the mother. In recent years, nuclei taken from cells of adult animals have been used to produce new animals. In this procedure, the nucleus is removed from a body cell (e.g., skin or blood cell) of a donor animal and introduced into an unfertilized mammalian egg that has been deprived of its own nucleus. This manipulated egg, which is equivalent to a fertilized egg, is then implanted into a foster mother. The ability of such a donor nucleus to direct the development of an entire animal suggests that all the information required for life is retained in the nuclei of some adult cells. Since all the cells in an ani- mal produced in this way have the genes of the single origi- nal donor cell, the new animal is a clone of the donor (Figure 1-8). Repeating the process can give rise to many clones. So far, however, the majority of embryos produced by this tech- nique of nuclear-transfer cloning do not survive due to birth defects. Even those animals that are born live have shown abnormalities, including accelerated aging. The “rooting” of plants, in contrast, is a type of cloning that is readily ac- complished by gardeners, farmers, and laboratory technicians. The technical difficulties and possible hazards of nuclear- transfer cloning have not deterred some individuals from pur- suing the goal of human cloning. However, cloning of humans per se has very limited scientific interest and is op- posed by most scientists because of its high risk. Of greater scientific and medical interest is the ability to generate specific cell types starting from embryonic or adult stem cells. The sci- entific interest comes from learning the signals that can un- leash the potential of the genes to form a certain cell type. The medical interest comes from the possibility of treating the nu- merous diseases in which particular cell types are damaged or missing, and of repairing wounds more completely. The Molecules of a Cell Molecular cell biologists explore how all the remarkable properties of the cell arise from underlying molecular events: the assembly of large molecules, binding of large molecules to each other, catalytic effects that promote particular chem- ical reactions, and the deployment of information carried by giant molecules. Here we review the most important kinds of molecules that form the chemical foundations of cell struc- ture and function. Small Molecules Carry Energy, Transmit Signals, and Are Linked into Macromolecules Much of the cell’s contents is a watery soup flavored with small molecules (e.g., simple sugars, amino acids, vitamins) and ions (e.g., sodium, chloride, calcium ions). The locations and concentrations of small molecules and ions within the cell are controlled by numerous proteins inserted in cellular membranes. These pumps, transporters, and ion channels move nearly all small molecules and ions into or out of the cell and its organelles (Chapter 7). 1.2 8 CHAPTER 1 • Life Begins with Cells ▲ FIGURE 1-8 Five genetically identical cloned sheep. An early sheep embryo was divided into five groups of cells and each was separately implanted into a surrogate mother, much like the natural process of twinning. At an early stage the cells are able to adjust and form an entire animal; later in development the cells become progressively restricted and can no longer do so. An alternative way to clone animals is to replace the nuclei of multiple single-celled embryos with donor nuclei from cells of an adult sheep. Each embryo will be genetically identical to the adult from which the nucleus was obtained. Low percentages of embryos survive these procedures to give healthy animals, and the full impact of the techniques on the animals is not yet known. [Geoff Tompkinson/Science Photo Library/Photo Researchers, Inc.] One of the best-known small molecules is adenosine triphosphate (ATP), which stores readily available chemical energy in two of its chemical bonds (see Figure 2-24). When cells split apart these energy-rich bonds in ATP, the released energy can be harnessed to power an energy-requiring process like muscle contraction or protein biosynthesis. To obtain energy for making ATP, cells break down food mole- cules. For instance, when sugar is degraded to carbon diox- ide and water, the energy stored in the original chemical bonds is released and much of it can be “captured” in ATP (Chapter 8). Bacterial, plant, and animal cells can all make ATP by this process. In addition, plants and a few other or- ganisms can harvest energy from sunlight to form ATP in photosynthesis. Other small molecules act as signals both within and be- tween cells; such signals direct numerous cellular activities (Chapters 13–15). The powerful effect on our bodies of a frightening event comes from the instantaneous flooding of the body with epinephrine, a small-molecule hormone that mobilizes the “fight or flight” response. The movements needed to fight or flee are triggered by nerve impulses that flow from the brain to our muscles with the aid of neuro- transmitters, another type of small-molecule signal that we discuss in Chapter 7. Certain small molecules (monomers) in the cellular soup can be joined to form polymers through repetition of a single type of chemical-linkage reaction (see Figure 2-11). Cells produce three types of large polymers, commonly called macromolecules: polysaccharides, proteins, and nucleic acids. Sugars, for example, are the monomers used to form polysaccharides. These macromolecules are critical structural components of plant cell walls and insect skeletons. A typical polysaccharide is a linear or branched chain of repeating identical sugar units. Such a chain carries information: the number of units. However if the units are not identical, then the order and type of units carry additional information. As we see in Chapter 6, some polysaccharides exhibit the greater informational complexity associated with a linear code made up of different units assembled in a particular order. This property, however, is most typical of the two other types of biological macromolecules—proteins and nucleic acids. Proteins Give Cells Structure and Perform Most Cellular Tasks The varied, intricate structures of proteins enable them to carry out numerous functions. Cells string together 20 dif- ferent amino acids in a linear chain to form a protein (see Figure 2-13). Proteins commonly range in length from 100 to 1000 amino acids, but some are much shorter and others longer. We obtain amino acids either by synthesizing them from other molecules or by breaking down proteins that we eat. The “essential” amino acids, from a dietary standpoint, are the eight that we cannot synthesize and must obtain from food. Beans and corn together have all eight, making their combination particularly nutritious. Once a chain of amino acids is formed, it folds into a complex shape, conferring a distinctive three-dimensional structure and function on each protein (Figure 1-9). 1.2 • The Molecules of a Cell 9 Glutamine synthetase Insulin Hemoglobin Immunoglobulin Adenylate kinase DNA molecule Lipid bilayer ▲ FIGURE 1-9 Proteins vary greatly in size, shape, and function. These models of the water-accessible surface of some representative proteins are drawn to a common scale and reveal the numerous projections and crevices on the surface. Each protein has a defined three-dimensional shape (conformation) that is stabilized by numerous chemical interactions discussed in Chapters 2 and 3. The illustrated proteins include enzymes (glutamine synthetase and adenylate kinase), an antibody (immunoglobulin), a hormone (insulin), and the blood’s oxygen carrier (hemoglobin). Models of a segment of the nucleic acid DNA and a small region of the lipid bilayer that forms cellular membranes (see Section 1.3) demonstrate the relative width of these structures compared with typical proteins. [Courtesy of Gareth White.] Some proteins are similar to one another and therefore can be considered members of a protein family. A few hun- dred such families have been identified. Most proteins are de- signed to work in particular places within a cell or to be released into the extracellular (extra, “outside”) space. Elab- orate cellular pathways ensure that proteins are transported to their proper intracellular (intra, within) locations or se- creted (Chapters 16 and 17). Proteins can serve as structural components of a cell, for example, by forming an internal skeleton (Chapters 5, 19, and 20). They can be sensors that change shape as temperature, ion concentrations, or other properties of the cell change. They can import and export substances across the plasma mem- brane (Chapter 7). They can be enzymes, causing chemical re- actions to occur much more rapidly than they would without the aid of these protein catalysts (Chapter 3). They can bind to a specific gene, turning it on or off (Chapter 11). They can be extracellular signals, released from one cell to communicate with other cells, or intracellular signals, carrying information within the cell (Chapters 13–15). They can be motors that move other molecules around, burning chemical energy (ATP) to do so (Chapters 19 and 20). How can 20 amino acids form all the different proteins needed to perform these varied tasks? Seems impossible at first glance. But if a “typical” protein is about 400 amino acids long, there are 20400 possible different protein se- quences. Even assuming that many of these would be func- tionally equivalent, unstable, or otherwise discountable, the number of possible proteins is well along toward infinity. Next we might ask how many protein molecules a cell needs to operate and maintain itself. To estimate this num- ber, let’s take a typical eukaryotic cell, such as a hepatocyte (liver cell). This cell, roughly a cube 15 �m (0.0015 cm) on a side, has a volume of 3.4 � 10�9 cm3 (or milliliters). As- suming a cell density of 1.03 g/ml, the cell would weigh 3.5 � 10�9 g. Since protein accounts for approximately 20 percent of a cell’s weight, the total weight of cellular pro- tein is 7 � 10�10 g. The average yeast protein has a mo- lecular weight of 52,700 (g/mol). Assuming this value is typical of eukaryotic proteins, we can calculate the total number of protein molecules per liver cell as about 7.9 � 109 from the total protein weight and Avogadro’s number, the number of molecules per mole of any chemical com- pound (6.02 � 1023). To carry this calculation one step further, consider that a liver cell contains about 10,000 different proteins; thus, a cell contains close to a million molecules of each type of protein on average. In actuality the abundance of different proteins varies widely, from the quite rare insulin-binding receptor protein (20,000 mole- cules) to the abundant structural protein actin (5 � 108 molecules). Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place The information about how, when, and where to produce each kind of protein is carried in the genetic material, a polymer called deoxyribonucleic acid (DNA). The three-dimensional structure of DNA consists of two long helical strands that are coiled around a common axis, forming a double helix. DNA strands are composed of monomers called nucleotides; these often are referred to as bases because their structures contain cyclic organic bases (Chapter 4). Four different nucleotides, abbreviated A, T, C, and G, are joined end to end in a DNA strand, with the base parts projecting out from the helical backbone of the strand. Each DNA double helix has a simple construction: wherever there is an A in one strand there is a T in the other, and each C is matched with a G (Figure 1-10). This complementary match- ing of the two strands is so strong that if complementary strands are separated, they will spontaneously zip back to- gether in the right salt and temperature conditions. Such hybridization is extremely useful for detecting one strand using the other. For example, if one strand is purified and attached to a piece of paper, soaking the paper in a solution contain- ing the other complementary strand will lead to zippering, 10 CHAPTER 1 • Life Begins with Cells Parental strands A G T C Daughter strands ▲ FIGURE 1-10 DNA consists of two complementary strands wound around each other to form a double helix. (Left) The double helix is stabilized by weak hydrogen bonds between the A and T bases and between the C and G bases. (Right) During replication, the two strands are unwound and used as templates to produce complementary strands. The outcome is two copies of the original double helix, each containing one of the original strands and one new daughter (complementary) strand. even if the solution also contains many other DNA strands that do not match. The genetic information carried by DNA resides in its se- quence, the linear order of nucleotides along a strand. The information-bearing portion of DNA is divided into discrete functional units, the genes, which typically are 5000 to 100,000 nucleotides long. Most bacteria have a few thou- sand genes; humans, about 40,000. The genes that carry in- structions for making proteins commonly contain two parts: a coding region that specifies the amino acid sequence of a protein and a regulatory region that controls when and in which cells the protein is made. Cells use two processes in series to convert the coded in- formation in DNA into proteins (Figure 1-11). In the first, called transcription, the coding region of a gene is copied into a single-stranded ribonucleic acid (RNA) version of the double-stranded DNA. A large enzyme, RNA polymerase, catalyzes the linkage of nucleotides into a RNA chain using DNA as a template. In eukaryotic cells, the initial RNA product is processed into a smaller messenger RNA (mRNA) molecule, which moves to the cytoplasm. Here the ribosome, an enormously complex molecular machine composed of both RNA and protein, carries out the second process, called translation. During translation, the ribosome assembles and links together amino acids in the precise order dictated by the mRNA sequence according to the nearly universal genetic code. We examine the cell components that carry out tran- scription and translation in detail in Chapter 4. All organisms have ways to control when and where their genes can be transcribed. For instance, nearly all the cells in our bodies contain the full set of human genes, but in each cell type only some of these genes are active, or turned on, and used to make proteins. That’s why liver cells produce some proteins that are not produced by kidney cells, and vice versa. Moreover, many cells can respond to external signals or changes in external conditions by turning specific genes on or off, thereby adapting their repertoire of proteins to meet current needs. Such control of gene activity depends on DNA-binding proteins called transcription factors, which bind to DNA and act as switches, either activating or re- pressing transcription of particular genes (Chapter 11). Transcription factors are shaped so precisely that they are able to bind preferentially to the regulatory regions of just a few genes out of the thousands present in a cell’s DNA. Typ- ically a DNA-binding protein will recognize short DNA se- quences about 6–12 base pairs long. A segment of DNA containing 10 base pairs can have 410 possible sequences (1,048,576) since each position can be any of four nu- cleotides. Only a few copies of each such sequence will occur in the DNA of a cell, assuring the specificity of gene activation and repression. Multiple copies of one type of transcription factor can coordinately regulate a set of genes if binding sites for that factor exist near each gene in the set. Transcription factors often work as multiprotein complexes, with more than one protein contributing its own DNA-binding speci- ficity to selecting the regulated genes. In complex organisms, hundreds of different transcription factors are employed to form an exquisite control system that activates the right genes in the right cells at the right times. The Genome Is Packaged into Chromosomes and Replicated During Cell Division Most of the DNA in eukaryotic cells is located in the nucleus, extensively folded into the familiar structures we know as chromosomes (Chapter 10). Each chromosome contains a sin- gle linear DNA molecule associated with certain proteins. In prokaryotic cells, most or all of the genetic information resides 1.2 • The Molecules of a Cell 11 Nucleus Cytosol Transcription factor DNA pre-mRNA mRNA Ribosome RNA polymerase Transcribed region of DNA Nontranscribed region of DNA Protein-coding region of RNA Noncoding region of RNA Protein Start Activation Transcription Processing Translation 1 2 3 4 Amino acid chain ▲ FIGURE 1-11 The coded information in DNA is converted into the amino acid sequences of proteins by a multistep process. Step : Transcription factors bind to the regulatory regions of the specific genes they control and activate them. Step : Following assembly of a multiprotein initiation complex bound to the DNA, RNA polymerase begins transcription of an activated gene at a specific location, the start site. The polymerase moves along the DNA linking nucleotides into a single-stranded pre-mRNA transcript using one of the DNA strands as a template. Step : The transcript is processed to remove noncoding sequences. Step : In a eukaryotic cell, the mature messenger RNA (mRNA) moves to the cytoplasm, where it is bound by ribosomes that read its sequence and assemble a protein by chemically linking amino acids into a linear chain. 4 3 2 1 in a single circular DNA molecule about a millimeter in length; this molecule lies, folded back on itself many times, in the cen- tral region of the cell (see Figure 1-2a). The genome of an or- ganism comprises its entire complement of DNA. With the exception of eggs and sperm, every normal human cell has 46 chromosomes (Figure 1-12). Half of these, and thus half of the genes, can be traced back to Mom; the other half, to Dad. Every time a cell divides, a large multiprotein replication machine, the replisome, separates the two strands of double- helical DNA in the chromosomes and uses each strand as a template to assemble nucleotides into a new complementary strand (see Figure 1-10). The outcome is a pair of double he- lices, each identical to the original. DNA polymerase, which is responsible for linking nucleotides into a DNA strand, and the many other components of the replisome are described in Chapter 4. The molecular design of DNA and the remarkable properties of the replisome assure rapid, highly accurate copy- ing. Many DNA polymerase molecules work in concert, each one copying part of a chromosome. The entire genome of fruit flies, about 1.2 � 108 nucleotides long, can be copied in three minutes! Because of the accuracy of DNA replication, nearly all the cells in our bodies carry the same genetic instructions, and we can inherit Mom’s brown hair and Dad’s blue eyes. A rather dramatic example of gene control involves in- activation of an entire chromosome in human females. Women have two X chromosomes, whereas men have one X chromosome and one Y chromosome, which has differ- ent genes than the X chromosome. Yet the genes on the X chromosome must, for the most part, be equally active in fe- male cells (XX) and male cells (XY). To achieve this balance, one of the X chromosomes in female cells is chemically mod- ified and condensed into a very small mass called a Barr body, which is inactive and never transcribed. Surprisingly, we inherit a small amount of genetic mate- rial entirely and uniquely from our mothers. This is the cir- cular DNA present in mitochondria, the organelles in eukaryotic cells that synthesize ATP using the energy released by the breakdown of nutrients. Mitochondria contain mul- tiple copies of their own DNA genomes, which code for some of the mitochondrial proteins (Chapter 10). Because each human inherits mitochondrial DNA only from his or her mother (it comes with the egg but not the sperm), the dis- tinctive features of a particular mitochondrial DNA can be used to trace maternal history. Chloroplasts, the organelles that carry out photosynthesis in plants, also have their own circular genomes. Mutations May Be Good, Bad, or Indifferent Mistakes occasionally do occur spontaneously during DNA replication, causing changes in the sequence of nucleotides. Such changes, or mutations, also can arise from radiation 12 CHAPTER 1 • Life Begins with Cells ▲ FIGURE 1-12 Chromosomes can be “painted” for easy identification. A normal human has 23 pairs of morphologically distinct chromosomes; one member of each pair is inherited from the mother and the other member from the father. (Left) A chromosome spread from a human body cell midway through mitosis, when the chromosomes are fully condensed. This preparation was treated with fluorescent-labeled staining reagents that allow each of the 22 pairs and the X and Y chromosomes to appear in a different color when viewed in a fluorescence microscope. This technique of multiplex fluorescence in situ hybridization (M-FISH) sometimes is called chromosome painting (Chapter 10). (Right) Chromosomes from the preparation on the left arranged in pairs in descending order of size, an array called a karyotype. The presence of X and Y chromosomes identifies the sex of the individual as male. [Courtesy of M. R. Speicher.] that causes damage to the nucleotide chain or from chemi- cal poisons, such as those in cigarette smoke, that lead to er- rors during the DNA-copying proces...