Chapter 13 Biology - Cell Organization PDF

# Organization of the Cell The cell is the smallest unit that can carry out all activities we associate with life. When provided with essential nutrients and an appropriate environment, some cells can be kept alive and growing in the laboratory for many years. By contrast, no isolated part of a cel...

# Organization of the Cell The cell is the smallest unit that can carry out all activities we associate with life. When provided with essential nutrients and an appropriate environment, some cells can be kept alive and growing in the laboratory for many years. By contrast, no isolated part of a cell is capable of sustained survival. As you read this chapter, recall the discussion of systems biology in Chapter 1. Even as we describe individual components of cells, each of which is a system, we discuss how these structures work together to generate ever more complex interacting biological systems within the cell. The cell itself is a highly intricate biological system, and groups of cells make up tissues, organs, and organisms that are biological systems of ever increasing complexity. Most prokaryotes and many protists and fungi consist of a single cell. In contrast, most plants and animals are composed of millions of cells. Cells are the building blocks of complex multicellular organisms. Although they are basically similar, cells are also extraordinarily diverse and versatile. They are modified in a variety of ways to carry out specialized functions. Cell biology is an interdisciplinary science. It draws on increasingly sophisticated tools from a wide array of scientific fields in the quest to better understand cellular structure and function. For example, investigation of the cytoskeleton (cell skeleton), currently an active and exciting area of research, has been greatly enhanced by advances in microscopy, biochemistry, molecular biology, genetics, and computational biology. The photomicrograph illustrates the extensive distribution of cytoskeletal fibers known as microfilaments (composed of the protein actin) and tubulin in cells. Biochemical studies of these cytoskeletal structures, combined with computer-generated 3-D images of their protein subunits, have led to deep insights into how cells rapidly assemble and disassemble these dynamic and complex structures. Further understanding of their functions comes from molecular genetic studies of cells that contain mutations in genes that regulate their assembly and disassembly. Through this combination of approaches, scientists are developing a comprehensive picture of how the cytoskeletal system maintains cell shape and functions in cell movement. ## Key Concepts * **4.1 The cell is the basic unit of life**: Its organization is critical to its ability to carry out all life activities, and its size and shape are adapted for its functions. * **4.2 Biologists connect cellular structures to their functions** with an interdisciplinary approach that includes microscopy, biochemistry, genetics, and computational methods. * **4.3 Unlike prokaryotic cells, eukaryotic cells have internal membranes** that divide the cell into compartments, allowing them to conduct specialized activities within separate, small spaces. * **4.4 In eukaryotic cells, genetic information coded in DNA is located in the nucleus**, which is typically the most prominent organelle in the cell. * **4.5 Among the many organelles in the cytoplasm are ribosomes**, which synthesize proteins; endoplasmic reticulum and Golgi complexes, which process proteins; and mitochondria and chloroplasts, which convert energy from one form to another. * **4.6 The cytoskeleton is a dynamic internal framework** that functions in various types of cell movement. * **4.7 Most eukaryotic cells are surrounded by a cell coat**: In addition, many animal cells are surrounded by an extracellular matrix; cells of most bacteria, archaea, fungi, and plants are surrounded by a cell wall. ## The Cell: Basic Unit of Life **Learning Objectives** 1. Connect the cell theory to the evolution of life. 2. Relate the organizational similarities of all cells to the need to conduct essential life functions. 3. Explain the functional significance of cell size and cell shape. Cells, the building blocks of organisms, are dramatic examples of the underlying unity of all living things. ### The cell theory is a unifying concept of biology From their own microscopic observations and those of other scientists, botanist Matthias Schleiden in 1838 and zoologist Theodor Schwann in 1839, reasoned that all plants and animals consist of cells. Later, Rudolf Virchow, another German scientist, observed cells dividing and giving rise to daughter cells. In 1855, Virchow proposed that new cells form only by the division of previously existing cells. The work of Schleiden, Schwann, and Virchow contributed greatly to the development of the cell theory, the unifying concept that (1) cells are the basic living units of organization and function in all organisms and (2) all cells come from other cells. Around 1880, another German biologist, August Weismann, added an important corollary to Virchow's concept by pointing out that the ancestry of all the cells alive today can be traced back to ancient times. Evidence that all living cells have a common origin is provided by the basic similarities in their structures and in the molecules of which they are made. When we examine a variety of diverse organisms, ranging from simple bacteria to the most complex plants and animals, we find striking similarities at the cellular level. Careful studies of shared cell characteristics help us trace the evolutionary history of various organisms and furnish powerful evidence that all organisms alive today had a common origin. ### The organization and basic functions of all cells are similar The organization of cells and their small size are critical properties that allow them to maintain an appropriate internal environment necessary for their biochemical systems to function. For the cell to maintain its interior composition, its contents must be separated from the external environment. The **plasma membrane** is a structurally distinctive surface membrane that surrounds all cells. By making the interior of the cell an enclosed compartment, the **plasma membrane** allows the chemical composition of the cell to be different from that outside the cell. The **plasma membrane** has unique properties that enable it to serve as a selective barrier between the cell contents and the exterior, permitting the cell to exchange materials with the environment and accumulate substances needed to drive its biochemical reactions. Cells have internal structures, called **organelles**, that are specialized to carry out cell activities. Most of the organelles of eukaryotic cells (cells that possess a nucleus) consist of one or more **membrane-enclosed compartments** capable of regulating their own internal environments for specialized functions such as converting energy to usable forms, processing nutrients, and recycling damaged or unneeded structures. Genetic information stored in DNA molecules of all cells, for example, is contained, duplicated, and transcribed in the **nuclear compartment** of eukaryotic cells (see Chapter 15). Cell membranes also serve as organizing surfaces for interacting proteins that function in certain types of biochemical reactions. These stepwise reactions are more efficient and more rapid when their components are arranged to minimize the distance reactants must travel. As you will see in this chapter and in Chapter 8, the inner membrane of the eukaryotic **mitochondrial compartment** (as well as the plasma membrane of prokaryotes) contains tightly packed protein complexes that rapidly exchange electrons and protons, converting energy from food stores into ATP, which supplies energy to hundreds of different biochemical reactions that occur every moment in a living cell. These chemical reactions that convert energy from one form to another are essentially the same in all cells, from the reactions in bacteria to those of large, multicellular plants and animals. Such fundamental similarities are strong evidence of their evolutionary relationships. ### Cell size is limited Although their sizes vary over a wide range (FIG. 4-1), most cells are microscopic and must be measured by very small units. The basic unit of linear measurement in the metric system (see inside back cover) is the **meter (m)**, which is just a little longer than 1 yard. One **millimeter (mm)** is 1/1000 of 1 meter and is about as long as the bar enclosed in parentheses (-). The **micrometer (μm)** is the most convenient unit for measuring cells. A bar 1 µm long is 1/1,000,000 (1 millionth) of a meter, or 1/1000 of a millimeter, which is far too short to be seen with the unaided eye. Most of us have difficulty thinking about units that are too small to see, but it is helpful to remember that a micrometer has the same relationship to a millimeter that a millimeter has to a meter (1/1000). As small as it is, the micrometer is actually too large to measure most cell components. For this purpose biologists use the **nanometer (nm)**, which is 1/1,000,000,000 (1 billionth) of a meter, or 1/1000 of a micrometer. To mentally move down to the world of the nanometer, recall that a millimeter is 1/1000 of a meter, a micrometer is 1/1000 of a millimeter, and a nanometer is 1/1000 of a micrometer. A few specialized algae and animal cells are large enough to be seen with the naked eye. A human egg cell, for example, is about 130 µm in diameter, or approximately the size of the period at the end of this sentence. The largest cells are birds' eggs, but they are not typical cells because they include large amounts of food reserves: the yolk and the egg white. The functioning part of the cell is a small mass on the surface of the yolk. Why are most cells so small? If you consider what a cell must do to maintain its functions and to grow, it may be easier to understand the reasons for its small size. A cell must take in food and other materials and must rid itself of waste products generated by metabolic reactions. Everything that enters or leaves a cell must pass through its **plasma membrane**. The **plasma membrane** contains specialized "pumps" and channels with "gates" that selectively regulate the passage of materials into and out of the cell. The **plasma membrane** must be large enough relative to the cell volume to keep up with the demands of regulating the passage of materials. Thus, a critical factor in determining cell size is the ratio of its **surface area** (the plasma membrane) to its **volume** (FIG. 4-2). As a cell becomes larger, its volume increases at a greater rate than its surface area (its plasma membrane), which effectively places an upper limit on cell size. Above some critical size, the number of molecules required by the cell could not be transported into the cell fast enough to sustain its needs. In addition, the cell would not be able to regulate its concentration of various ions or efficiently export its wastes. Of course, not all cells are spherical or cuboid. Because of their shapes, some very large cells have relatively favorable ratios of surface area to volume. In fact, some variations in cell shape represent a strategy for increasing the ratio of surface area to volume. For example, many large plant cells are long and thin, which increases their **surface area-to-volume ratio**. Some cells, such as epithelial cells lining the small intestine, have fingerlike projections of the **plasma membrane**, called **microvilli**, that significantly increase the surface area for absorbing nutrients and other materials (see Fig. 47-10). Another reason for the small size of cells is that, once inside, molecules must be transported to the locations where they are converted into other forms. Because cells are small, the distances molecules travel within them are relatively short. Thus, molecules are rapidly available for cell activities. ### Cell size and shape are adapted to function The sizes and shapes of cells are adapted to the particular functions they perform. Some cells, such as amoebas and white blood cells, change their shape as they move about. Sperm cells have long, whiplike tails, called **flagella**, for locomotion. Nerve cells have long, thin extensions that enable them to transmit messages over great distances. The extensions of some nerve cells in the human body may be as long as 1 meter! Certain epithelial cells are almost rectangular and are stacked much like building blocks to form sheetlike tissues. (Epithelial tissue covers the body and lines body cavities.) ## Methods for Studying Cells **Learning Objectives** 4. Compare methods that biologists use to study cells and point out the ways in which many of these approaches are complementary. One of the most important tools biologists use for studying cell structures is the microscope. Using a microscope he had made, Robert Hooke, an English scientist, first described cells in 1665 in his book *Micrographia*. Hooke examined a piece of cork and then drew and described what he saw. Hooke chose the term *cell* because the tissue reminded him of the small rooms monks lived in. Interestingly, what Hooke saw were not actually living cells but the walls of dead cork cells (FIG. 4-3a). Much later, scientists recognized that the interior enclosed by the walls is the important part of living cells. A few years after Hooke's discovery and inspired by Hooke's work, Dutch naturalist Antonie van Leeuwenhoek viewed living cells with small lenses that he made. Leeuwenhoek was highly skilled at fabricating lenses and was able to magnify images more than 200 times. Among his important discoveries were bacteria, protists, blood cells, and sperm cells. Leeuwenhoek was among the first scientists to report cells in animals. He was a merchant and was not formally trained as a scientist, but his skill, curiosity, and diligence in sharing his discoveries with scientists at the Royal Society of London brought an awareness of microscopic life to the scientific world. Unfortunately, Leeuwenhoek did not share his techniques. Not until more than 170 years later, in the late 19th century, were microscopes sufficiently developed for biologists to seriously focus their attention on the study of cells. ### Light microscopes are used to study stained or living cells The **light microscope (LM)**, the type used by most students, consists of a tube with glass lenses at each end. Because it contains several lenses, the modern light microscope is referred to as a **compound microscope**. Visible light passes through the specimen being observed and through the lenses. Light is refracted (bent) by the lenses, magnifying the image. Images obtained with light microscopes are referred to as **light micrographs**, or LMs. Two features of a microscope determine how clearly a small object can be viewed: **magnification** and **resolving power**. **Magnification** is the ratio of the size of the image seen with the microscope to the actual size of the object. The best light microscopes usually magnify an object no more than 2000 times. **Resolution**, or resolving power, is the capacity to distinguish fine detail in an image; it is defined as the minimum distance between two points at which they can both be seen separately rather than as a single, blurred point. Resolving power depends on the quality of the lenses and the wavelength of the illuminating light. As the wavelength decreases, the resolution increases. The visible light used by ordinary light microscopes has wavelengths ranging from about 400 nm (violet) to 700 nm (red); this limits the resolution of the light microscope to details no smaller than the diameter of a small bacterial cell (about 0.2 µm or 200 nm). By the early 20th century, refined versions of the light microscope became available. The interior of many cells is transparent, and it is difficult to discern specific structures. Organic chemists contributed greatly to light microscopy by developing biological stains that enhance contrast in the microscopic image. Staining has enabled biologists to discover the many different internal cell structures, the **organelles**. Unfortunately, most methods used to prepare and stain cells for observation also kill them in the process. Light microscopes with special optical systems now permit biologists to study living cells. In **bright-field microscopy**, an image is formed by transmitting light through a cell (or other specimen) (FIG. 4-3b). Because there is little contrast, the details of cell structure are not visible. In **dark-field microscopy**, rays of light are directed from the side, and only light scattered by the specimen enters the lenses. The cell is seen as a bright image against a dark background (FIG. 4-3c). The specimen does not need to be stained. ### Phase contrast microscopy and Nomarski differential-interference-contrast microscopy take advantage of variations in density within the cell (FIG. 4-3d and e). These differences in density affect how various regions of the cytoplasm refract (bend) light. Using these microscopes, scientists can observe living cells in action and can view numerous internal structures that are constantly changing shape and location. ### Biologists also use genetic engineering methods (see Chapter 15) to link the gene coding for a protein under study to part of another gene that encodes a green fluorescent protein (GFP) derived from a species of jellyfish When the protein encoded by the modified gene is synthesized by the cell, it contains the GFP amino acid sequence as a "tag." The GFP tag functions as a fluorophore, allowing the intracellular movement of these "tagged" proteins to be tracked and measured in live cells by sensitive photodetectors. ### Fluorescence microscopy identifies the intracellular locations of specific molecules Cell biologists today widely use different types of **fluorescence microscopes** to detect the locations of specific molecules in cells. In the **fluorescence microscope**, filters transmit light that is emitted by fluorescent molecules, or **fluorophores**. **Fluorophores** are molecules that absorb light energy of one wavelength and then release some of that energy as light of a longer wavelength (like paints that glow under black light, see Fig. 9-3). Look closely at the chapter-opening photograph, which shows three different types of fluorophores. The nucleus is stained with an organic compound that becomes a fluorophore when it binds within the grooves of double-stranded DNA molecules. When ultraviolet light is passed through the specimen, each fluorophore molecule absorbs the energy from an ultraviolet light photon and then releases part of that energy in the form of another photon that has the longer wavelength of visible blue light. The red color is derived from a fluorophore that is chemically bonded to phalloidin, a molecule isolated from a mushroom that specifically binds to actin microfilaments. The green color comes from a fluorophore that is chemically bonded to an antibody that binds to the microtubule protein ẞ-tubulin. **Antibodies** are proteins derived from the immune system (discussed in Chapter 45). Each type of antibody molecule can bind to only one specific region of another molecule (such as a small patch of amino acids on the surface of a protein). In the chapter-opening photograph, the green fluorescing antibody binds only to a small region of a microtubule subunit protein, and the red fluorescing antibody binds only to a specific region of a microfilament protein. Note that there are also yellow colors in the photograph. They are caused by the mixing of the green and red light from the microfilament and microtubule proteins that are very close to one another. This method (using highly sensitive microscopy) is commonly used to study the corresponding localizations (and possible interactions) of different proteins in cells. **Fluorescence microscopy** using antibody labels must be done with nonliving cells that have been "fixed" by chemicals that form cross links between cellular proteins and other macromolecules to preserve them in their normal locations. Biologists today also employ other types of fluorescent molecules to study the internal dynamics of living cells (in vivo). Certain types of fluorophores have been developed that will naturally diffuse into cells without killing them. Available today are wide arrays of compounds used to detect changes in intracellular pH, ion concentrations within intracellular compartments, and electrical charge differences across membranes. This is done by measuring shifts in the wavelength or the intensity of the emitted fluorescence. ### Confocal microscopy has led to significant advances in our understanding of intracellular structural dynamics These microscopes produce a sharper image than standard fluorescence microscopy (FIG. 4-3f). A **confocal microscope** uses a laser to excite fluorophores in just a thin "slice" through a cell, enabling an investigator to visualize objects in a single plane of sharp focus. In the chapter-opening photograph, a computer has assembled a series of stacked images of a series of confocal optical sections taken from the bottom to the top of the cell to construct a 3-D image. ### Recently, the use of powerful computer-imaging methods and ultrasensitive photodetectors has greatly improved the resolution of structures labeled by fluorescent dyes New developments in **fluorescence imaging** have led to breakthroughs in the "resolution barrier" of 200 nm by using the shortest wavelengths of visible light. These **super-resolution technologies** can now resolve images of less than 70 nm derived from single molecules of fluorophores in living cells. For example, these advanced technologies have enabled researchers to monitor the intracellular movement within cells of brain tissue (FIG. 4-4). ## Electron microscopes provide a high-resolution image that can be greatly magnified Even with improved microscopes and techniques for staining cells, ordinary light microscopes can distinguish only the gross details of many cell parts (FIG. 4-5a). With the development of the **electron microscope (EM)**, which came into wide use in the 1950s, researchers could begin to study the fine details, or **ultrastructure**, of cells at the dimensions that could define the structure of cellular compartments and structures associated with cell membranes. Because electrons have very short wavelengths on the order of about 0.1-0.2 nm, **electron microscopes** have resolving powers of just less than 1 nm. This high degree of resolution permits magnifications of more than 1 million times, compared with typical magnifications of no more than 1500 to 2000 times in light microscopy. The image formed by the **electron microscope** is not directly visible. The electron beam itself consists of energized electrons, which, because of their negative charge, can be focused by electromagnets just as images are focused by glass lenses in a light microscope (FIG. 4-5b). Two main types of **electron microscopes** are the **transmission electron microscope (TEM)** and the **scanning electron microscope (SEM)**. The acronyms TEM and SEM also identify that a micrograph was prepared using a transmission or scanning EM. Electron micrographs are black and white. They are often artificially colorized to highlight various structures. In **transmission electron microscopy**, the specimen is embedded in plastic and then cut into extraordinarily thin sections (50 to 100 nm thick) with a glass or diamond knife. A section is then placed on a small metal grid. The electron beam passes through the specimen and then falls onto a photographic plate or a fluorescent screen. When you look at TEMs in this chapter (and elsewhere), keep in mind that each represents only a thin cross section of a cell. Researchers can also detect certain specific molecules in electron microscope images by using antibody molecules to which very tiny gold particles are bound. The dense gold particles block the electron beam and identify the location of the proteins recognized by the antibodies as precise black spots on the electron micrograph. In the **scanning electron microscope**, the electron beam does not pass through the specimen. Instead, the specimen is coated with a thin film of gold or some other metal. When the electron beam strikes various points on the surface of the specimen, secondary electrons are emitted whose intensity varies with the contour of the surface. The recorded emission patterns of the secondary electrons give a 3-D picture of the surface (FIG. 4-5c). The SEM provides information about the shape and external features of the specimen that cannot be obtained with the TEM. Note that the LM, TEM, and SEM are focused by similar principles. A beam of light or an electron beam is directed by the condenser lens onto the specimen, and it is magnified by the objective lens and the eyepiece in the light microscope or by the objective lens and the projector lens in the TEM. The TEM image is focused onto a fluorescent screen, and the SEM image is viewed on a type of television screen. Lenses in electron microscopes are actually electromagnets that bend the beam of electrons. ## Biologists use biochemical and genetic methods to connect cell structures with their functions The EM and light microscopes are powerful tools for studying cell structure, but they have limitations. The methods used to prepare cells for electron microscopy kill them and may alter their structure. Furthermore, electron microscopy provides few clues about the functions of organelles and other cell components. To determine what organelles actually do, researchers use a variety of biochemical techniques. ### Cell fractionation is a technique for separating (fractionating) different parts of cells so that they can be studied by physical and chemical methods Generally, cells are broken apart in a blender. The resulting mixture, called the cell homogenate, is subjected to centrifugal force by spinning in a centrifuge (FIG. 4-6a). **Differential centrifugation** involves the separation of cell components through a series of centrifugation stages run at increasingly higher speeds. This allows various cell components to be separated on the basis of their different sizes and densities (FIG. 4-6b). At each step centrifugal force separates the extract into two fractions: a pellet and a supernatant. The pellet that forms at the bottom of the tube contains heavier materials packed together. (In the first low-speed step, this pellet is typically composed of nuclei.) The supernatant, the liquid above the pellet, contains lighter organelles, dissolved molecules, and ions. After the pellet is removed, the supernatant is centrifuged again at a higher speed to obtain a pellet that contains the next-heaviest cell components, for example, mitochondria and chloroplasts. To separate smaller, less dense components, the supernatant is then centrifuged in the powerful **ultracentrifuge**, which can spin at speeds exceeding 100,000 revolutions per minute (rpm), generating a centrifugal force of 500,000 × G (1 G is equal to the force of gravity). Pellets can be resuspended and their components further purified by **density gradient centrifugation**. In this procedure, the ultracentrifuge tube is filled with a series of solutions of decreasing density. For example, sucrose solutions can be used. The concentration of sucrose is highest at the bottom of the tube and decreases gradually so that it is lowest at the top. The resuspended pellet is placed in a layer on top of the density gradient. Because the densities of organelles differ, each migrates during centrifugation to a position in the sucrose gradient that corresponds to its own density (FIG. 4-6c). These purified organelles can then be studied to determine what kinds of proteins and other molecules they might contain, or what types of biochemical reactions take place within them. Antibodies are also widely used in laboratories to detect specific proteins in subcellular fractions, measure their intracellular levels, and study how they interact with other proteins. FIGURE 4-7 shows how an antibody molecule that is linked to small polymer beads can be used to rapidly purify a specific protein from a cell extract that contains thousands of different proteins. Another application might use a bead-linked antibody to identify a protein that binds to, and functions with, another protein inside the cell. For example, an antibody that specifically binds to a microtubule subunit protein might be used to find other proteins that bind to microtubules and regulate their activity. The microtubule-specific, antibody-coated beads would be added to a cell extract (or a purified cell fraction). The beads would then be washed extensively to remove all substances in the extract that did not bind to the antibody-bound microtubule subunit protein. Proteins that remain attached to the antibody-bound microtubule subunit can then be released from the complex and analyzed to determine their identities. Cell biologists also use genetic methods together with microscopy or biochemical methods to connect cellular proteins with their functions. When a protein has been identified as a critical component in a cell structure, researchers can use genetic engineering methods to alter or delete the gene that encodes that protein, effectively "turning off" its activity. By observing the differences between cells that contain the genetically altered protein with normal cells, researchers can gain insights into its function and how it interacts with other cellular proteins. ## Prokaryotic and Eukaryotic Cells **Learning Objectives** 5. Compare and contrast the general characteristics of prokaryotic and eukaryotic cells, and contrast plant and animal cells. 6. Describe three functions of cell membranes. Recall from Chapter 1 that two basic types of cells are known: **prokaryotic cells** and **eukaryotic cells**. Bacteria and archaea are **prokaryotic cells**. All other known organisms consist of one or more **eukaryotic cells**. ### Organelles of prokaryotic cells are not surrounded by membranes **Prokaryotic cells** are typically smaller than **eukaryotic cells**. In fact, the average **prokaryotic cell** is only about 1/10 the diameter of the average **eukaryotic cell**. In **prokaryotic cells**, the DNA is typically located in a limited region of the cell called a **nuclear area**, or **nucleoid**. Unlike the **nucleus** of **eukaryotic cells**, the **nuclear area** is not enclosed by a membrane (FIG. 4-8). The term prokaryotic, meaning "before the nucleus," refers to this major difference between **prokaryotic** and **eukaryotic cells**. Other types of internal **membrane-enclosed organelles** are also absent in **prokaryotic cells**. Like **eukaryotic cells**, **prokaryotic cells** have a **plasma membrane** that surrounds the cell. The **plasma membrane** confines the contents of the cell to an internal compartment. In some **prokaryotic cells**, the **plasma membrane** may be folded inward to form a complex of membranes along which many of the cell's metabolic reactions take place. Most **prokaryotic cells** have cell walls, which are **extracellular structures** that enclose the entire cell, including the **plasma membrane**. Many **prokaryotes** have **flagella** (sing., flagellum), long fibers that project from the surface of the cell. **Prokaryotic flagella**, which operate like propellers, are important in locomotion. Their structure is different from that of **flagella** found in **eukaryotic cells**. Some **prokaryotes** also have hairlike projections called **fimbriae**, which are used to adhere to one another or to attach to cell surfaces of other organisms. The dense internal material of the bacterial cell contains **ribosomes**, small complexes of ribonucleic acid (RNA) and protein that synthesize polypeptides. The **ribosomes** of **prokaryotic cells** are smaller than those found in **eukaryotic cells**. **Prokaryotic cells** also contain **storage granules** that hold glycogen, lipid, or phosphate compounds. This chapter focuses primarily on **eukaryotic cells**. **Prokaryotes** are discussed in more detail in Chapter 25. ### Membranes divide the eukaryotic cell into compartments **Eukaryotic cells** are characterized by highly organized **membrane-enclosed organelles**, including a prominent **nucleus**, which contains DNA, the hereditary material. The term **eukaryotic** means "true nucleus." Early biologists thought that cells consisted of a homogeneous jelly, which they called **protoplasm**. With the electron microscope and other modern research tools, perception of the environment within the cell has been greatly expanded. We now know that the cell is highly organized and complex (FIGS. 4-9 and 4-10). The **eukaryotic cell** has its own control center, internal transportation system, power plants, factories for making needed materials, packaging plants, and even a "self-destruct" system. Biologists refer to the part of the cell outside the **nucleus** as **cytoplasm** and the part of the cell within the **nucleus** as **nucleoplasm**. Various **organelles** are suspended within the fluid component of the **cytoplasm**, which is called the **cytosol**. **Eukaryotic proteins** are synthesized in the **cytoplasmic compartment** by **ribosomes**. These large macromolecular complexes can function as components of the **cytosol** when they produce **soluble proteins**. Alternatively, they can be firmly bound to the **cytosolic surfaces** of **membranes**, where they form **proteins** that are either attached to **membranes** or enclosed in **compartments** bounded by **membranes**. The term **cytoplasm** includes both the **cytosol** and all the **organelles** other than the **nucleus**. The many specialized **organelles** of **eukaryotic cells** solve some of the problems associated with large size, so **eukaryotic cells** can be larger than **prokaryotic cells**. **Eukaryotic cells** also differ from **prokaryotic cells** in having a supporting framework, or **cytoskeleton**, important in maintaining shape and transporting materials within the cell. Some **organelles** are present only in specific cells. For example, **chloroplasts**, structures that trap sunlight for energy conversion, are only in cells that carry on photosynthesis, such as certain plant or algal cells. Cells of fungi and plants are surrounded by a cell wall external to the **plasma membrane**. Plant cells also contain a large, **membrane-enclosed vacuole**. We discuss these and other differences among major types of cells throughout this chapter. ## The unique properties of biological membranes allow eukaryotic cells to carry on many diverse functions **Cell membranes** have unique properties that enable membranous organelles to carry out a wide variety of functions. For example, **cell membranes** never have free ends. As a result, a membranous organelle always contains at least one enclosed internal space or compartment. These **membrane-enclosed compartments** allow certain cell activities to be localized within specific regions of the cell. Reactants confined to only a small part of the total cell volume are far more likely to come in contact, dramatically increasing the rate of the reaction. **Membrane-enclosed compartments** also keep certain reactive compounds away from other parts of the cell that they might adversely affect, allowing many different activities to go on simultaneously. **Membranes** serve as important work surfaces. For example, many chemical reactions in cells are carried out by **enzymes** that are bound to **membranes**. Because the **enzymes that carry out successive steps of a series of reactions** are organized close together on a **membrane surface**, certain series of chemical reactions occur more rapidly. **Membranes** allow cells to store energy. The **membrane** serves as a barrier that is somewhat analogous to a dam on a river. As we will discuss in Chapter 5, there is both an electric charge difference and a concentration difference of ions on the two sides of certain cell membranes. These differences constitute an electrochemical gradient. Such gradients store energy and so have potential energy (discussed in Chapter 7). As particles of a substance move across the membrane from the side of higher concentration to the side of lower concentration, the cell can convert some of this potential energy to the chemical energy of ATP molecules. This process of energy conversion (discussed in Chapters 7, 8, and 9) is a basic mechanism that cells use to capture and convert the energy necessary to sustain life. ## The Cell Nucleus **Learning Objective** 7. Relate the structure of the nucleus to its function as the control center of the eukaryotic cell. The **nucleus** is typically the most prominent organelle in the cell. It is usually spherical or oval in shape and averages 5 µm in diameter. Most of the cell's DNA is located inside the **nucleus**. Unlike **prokaryotic cells**, whose DNA is in the form of circular molecules, **eukaryotic DNA molecules** are very long, linear molecules (much longer than the diameter of the cell), and they have distinctive ends (see Chapter 10). The **nuclear envelope** consists of two concentric membranes that separate the **nuclear contents** from the surrounding **cytoplasm** (FIG. 4-11). These membranes are separated by about 20 to 40 nm. At intervals the membranes come together to form **nuclear pores**, which are the largest and most complex assembly of proteins in most eukaryotic cells. Each **nuclear pore** consists of 500-1000 molecules made up of many copies of about 30 different proteins. A typical vertebrate cell that is not growing or dividing will usually have several thousand **pores** distributed across its **nuclear surface**. These complexes regulate the passage of large materials (including large proteins as well as macromolecular complexes such as ribosomes) across the **nuclear membranes**; however, ions and biological molecules (including small proteins) can pass freely through the **nuclear pores**. Each protein from the cytoplasm that must be actively transported through the pore contains a **nuclear localization signal (NLS)** as part of its amino acid sequence. Special proteins called **importins** bind with the NLS sequence, forming a "cargo complex" that can then be captured by the **nuclear pore machinery** and transported through the pore into the **nucleus**. These sequences are not only found on soluble proteins synthesized by ribosomes, but also on proteins that are embedded in **cytoplasmic membranes** and must then be moved to the inner **nuclear membrane** (FIG. 4-12). The transport mechanism through **nuclear pores** can be very fast. Fluorescent-labeled proteins containing an NLS sequence have been observed moving through the **nuclear pores** at rates approaching 2000 molecules/second, whereas deletion of the NLS sequence from the same protein has been shown to effectively block its entry into the **nucleus**. A fibrous network of protein filaments, called the **nuclear lamins**, forms the **nuclear lamina**, an inner lining for the **nuclear envelope**. The **nuclear lamina** supports the inner **nuclear membrane** and helps organize the **nuclear contents**. It also plays a role in DNA duplication and in regulating the cycle of growth and division (the cell cycle; see Chapter 10). Mutations in genes encoding proteins that make up the **nuclear lamina** are associated with several human genetic diseases, including some muscular dystrophies and premature aging (progeria). When a cell divides, the information stored in DNA must be duplicated exactly through a process called replication (discussed in Chapter 12). Each copy is then passed intact to one of the two daughter cells. DNA molecules include sequences of nucleotides called genes, which contain the chemically coded instructions for producing the proteins and specialized RNA molecules needed by the cell. The nucleus controls protein synthesis by transcribing its information from DNA into **messenger RNA (mRNA)** molecules, which are then moved into the cytoplasm, where proteins are manufactured by **ribosomes**. DNA in the **nucleus** is associated with RNA and certain proteins, forming a complex known as **chromatin** (see Chapter 10). In the light microscope this complex appears as a network of granules and strands in nondividing cells. Although **chromatin** appears disorganized, it is not. Because DNA molecules are extremely long and thin, each molecule is packed inside the **nucleus** in a regular fashion as part of a structure called a **chromosome**. In dividing cells, the chromosomes become visible as distinct threadlike structures. If the DNA molecules in the 46 chromosomes of one human cell could be stretched end to end, they would extend for 2 meters! Most **nuclei