Campbell Biology 2020-141-301 PDF

Unit 2 THE CELL Dr. Diana Bautista is an Associate Professor of to attend college and to pursue a career in science. Molecular and Cell Biology at the University of She and her laboratory members investigate the cell-...

Unit 2 THE CELL Dr. Diana Bautista is an Associate Professor of to attend college and to pursue a career in science. Molecular and Cell Biology at the University of She and her laboratory members investigate the cell- California, Berkeley, and a Howard Hughes Medical signaling pathways associated with pain and itch and Institute Faculty Scholar. Recipient of the Gill how their misregulation can result in chronic pain Transformative Investigator Award and the Society and chronic itch. Her research is interdisciplinary: for Neuroscience Young Investigator Award, she re- Dr. Bautista collaborates with computational biolo- ceived a B.S. in Biology from the University of Oregon gists, immunologists, and physiologists. She believes and a Ph.D. in Neuroscience from Stanford University. that science benefits most from a diverse group of Dr. Bautista grew up in Chicago, the first in her family colleagues, each bringing a different perspective. me, shining light on a fly eye and record- as the tissue heals, but in some patients, it AN INTERVIEW WITH ing an electrical signal from their nervous becomes a chronic debilitating disease. system in real time was just the coolest Diana M. Bautista thing I had ever seen. The lab was a really What does your lab work on now? inclusive, warm environment, and Peter We are interested in the sense of touch. What got you interested in biology, was an amazing mentor—if it weren’t for Touch-sensitive neurons innervate the and in neuroscience in particular? him, I wouldn’t be in science. I went to skin and mediate gentle touch sensa- I always liked science as a kid, but it was graduate school at Stanford in neurosci- tions and texture preferences: Do you like never a big focus in my life. I went to col- ence, where I worked with Dr. Richard wool sweaters, or do you find them itchy? lege interested in art, then took some Lewis on a newly discovered calcium chan- Touch-sensitive neurons also innervate time off because I was a terrible artist. I nel and how calcium signaling pathways our musculature, allowing us to detect ended up working with an environmental drive cellular behaviors. limb position and mediating coordinated group helping low-income communities movements, such as our ability to text or oppose a hazardous waste incinerator. Why did you focus your to walk in a straight line without staring That got me excited about science be- research on pain? at our feet. In someone suffering from cause it was at the interface of the envi- After my Ph.D., I wanted to continue work- chronic pain, a gentle touch feels incred- ronment and community empowerment, ing on cell signaling but from a more ibly painful, while a chronic itch sufferer so I decided to return to college and major organismal viewpoint, so I did my post- experiences light touch as itchy and pain in biology. Once I returned to school, at doctoral research with Dr. David Julius at as pleasure. When you scratch an itch, the University of Oregon, I found out the University of California, San Francisco. you’re scratching really hard—if you didn’t you could get a work-study job in a lab. His lab had recently identified the cel- have an itch it would hurt, but when you I ended up working in Peter O’Day’s lab lular protein (TRPV1) that is responsive to do have an itch it feels good. We have no studying vision in fruit flies by recording capsaicin—the molecule that gives chili idea how our body processes the same electrical signals in response to light. For peppers their “hotness”—and showed that type of stimulus under different injury or this protein is also activated by painful heat. disease conditions, and that’s what really. Dr. Bautista studies cell responses to That was really exciting to me because it excited me when I started my own lab. stimuli using equipment that measures involved thinking about proteins involved electrical signals. in cell signaling, but in the bigger context What is your advice to an of pain. Proteins like TRPV1 serve important protective functions—for example, by stop- undergraduate considering ping us from grabbing a hot frying pan that a career in biology? could cause a burn. One of my projects was I’m an advisor for undergraduates, so I talk to identify the wasabi receptor, a protein to a lot of students. I like to tell them about on the surface of nerve cells that plays a key my path and let them know that it doesn’t role in inflamma- matter what you did tory pain hyper- before or where you sensitivity. Once "It doesn’t matter what you come from—anybody you activate this receptor did before or where you can be a scientist. I think it’s sometimes protein—with come from—anybody can tough early on in biol- irritants such as ogy, because at first wasabi, mustard be a scientist." you’re taught facts, oil, or inflamma- but as you progress, tory mediators produced in the body by biology is about figuring out the unknown. tissue injury such as a burn—it activates and And if you can get into a lab early on, then makes pain cells more sensitive: Warmth you really see that side of science—that it’s triggers sensations of burning heat, and about learning what we know, and then light touch triggers pain. Normally, pain going beyond that, doing experiments to hypersensitivity dies down after a few days identify new mechanisms. 6 KEY CONCEPTS A Tour of the Cell 6.1 Biologists use microscopes and biochemistry to study cells p. 94 6.2 Eukaryotic cells have internal membranes that compartmentalize their functions p. 97 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes p. 102 6.4 The endomembrane system regulates protein traffic and performs metabolic functions p. 104 6.5 Mitochondria and chloroplasts change energy from one form to another p. 109 6.6 The cytoskeleton is a network of Figure 6.1 The cell is an organism’s basic unit of structure and function. Many forms of life exist as single-celled organisms, such as the Paramecium shown here. fibers that organizes structures and activities in the cell p. 112 Larger, more complex organisms, including plants and animals, are multicellular. In this chapter, we focus mainly on eukaryotic cells—cells with a nucleus. 6.7 Extracellular components and connections between cells help coordinate cellular activities p. 118 How does the internal organization of eukaryotic cells 6.8 A cell is greater than the sum of its allow them to perform the functions of life? parts p. 121 Internal membranes divide a cell, such as this plant cell, into Study Tip compartments where specific chemical reactions occur. Draw animal and plant cells: Draw an Energy and matter Genetic outline of an animal cell and add structures, transformations labels, and functions. Draw a plant cell information A system of internal storage and labeled with structures unique to plant cells. transmission membranes Plasma membrane: synthesizes and DNA in the nucleus a selective barrier modifies proteins, contains instructions lipids, and for making proteins. carbohydrates. Ribosomes are the Chloroplasts convert sites of protein light energy to synthesis. chemical energy. Ribosome Mitochondria break Go to Mastering Biology down molecules, generating ATP. For Students (in eText and Study Area) Protein Get Ready for Chapter 6 Figure 6.7 Walkthrough: Geometric Relationships between Surface Area and Interactions with Volume the environment BioFlix® Animations: Tour of an Animal Cell The plasma membrane and Tour of a Plant Cell controls what goes into For Instructors to Assign (in Item Library) and out of the cell. Tutorial: Tour of an Animal Cell: The Endomembrane System Plant cells have a Tutorial: Tour of a Plant Cell: Structures protective cell wall. and Functions 93. Figure 6.2 The size range of cells. Most cells are between 1 and CONCEPT 6.1 100 µm in diameter (yellow region of chart), and their components Biologists use microscopes and are even smaller (see Figure 6.32), as are viruses. Notice that the scale along the left side is logarithmic, to accommodate the range of sizes biochemistry to study cells shown. Starting at the top of the scale with 10 m and going down, each reference measurement marks a tenfold decrease in diameter or length. How can cell biologists investigate the inner workings of a cell, For a complete table of the metric system, see the back of the book. usually too small to be seen by the unaided eye? Before we tour the cell, it will be helpful to learn how cells are studied. 10 m Human height Microscopy 1m Length of some The development of instruments that extend the human nerve and Unaided eye senses allowed the discovery and early study of cells. muscle cells Microscopes were invented in 1590 and further refined dur- 0.1 m Chicken egg ing the 1600s. Cell walls were first seen on dead cells of oak bark by Robert Hooke in 1665 and living cells by Antoni van 1 cm Leeuwenhoek a few years later. The microscopes first used by Renaissance scientists, as Frog egg well as the microscopes you are likely to use in the laboratory, 1 mm are all light microscopes. In a light microscope (LM), vis- 100 om ible light is passed through the specimen and then through Light microscopy Human egg glass lenses. The lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected Most plant and 10 om into the eye or into a camera (see Appendix C). animal cells Three important parameters in microscopy are magnifica- Nucleus tion, resolution, and contrast. Magnification is the ratio of Most bacteria 1 om an object’s image size to its real size. Light microscopes can Mitochondrion Electron microscopy magnify effectively to about 1,000 times the actual size of the specimen; at greater magnifications, additional details cannot be seen clearly. Resolution is a measure of the clarity Smallest bacteria Super- 100 nm Viruses resolution of the image; it is the minimum distance two points can be microscopy separated and still be distinguished as separate points. For Ribosomes example, what appears to the unaided eye as one star in the 10 nm Proteins sky may be resolved as twin stars with a telescope, which has a higher resolving ability than the eye. Similarly, using stan- Lipids 1 nm dard techniques, the light microscope cannot resolve detail Small molecules finer than about 0.2 micrometer (µm), or 200 nanometers (nm), regardless of the magnification (Figure 6.2). The third 0.1 nm Atoms parameter, contrast, is the difference in brightness between 1 centimeter (cm) = 10 –2 meter (m) = 0.4 inch 1 micrometer (om) = 10 –3 mm = 10 –6 m the light and dark areas of an image. Methods for enhanc- 1 millimeter (mm) = 10 –3 m 1 nanometer (nm) = 10 –3 om = 10 –9 m ing contrast include staining or labeling cell components to stand out visually. Figure 6.3 shows some different types of microscopy; study this figure as you read this section. Mastering Biology Animation: Metric System Review Until recently, the resolution barrier prevented cell biolo- gists from using standard light microscopy when studying have much shorter wavelengths than visible light. Modern organelles, the membrane-enclosed structures within eukar- electron microscopes can theoretically achieve a resolution of yotic cells. To see these structures in any detail required the about 0.002 nm, though in practice they usually cannot resolve development of a new instrument. In the 1950s, the electron structures smaller than about 2 nm across. Still, this is a 100-fold microscope was introduced to biology. Rather than focusing improvement over the standard light microscope. light, the electron microscope (EM) focuses a beam of elec- The scanning electron microscope (SEM) is especially trons through the specimen or onto its surface (see Appendix C). useful for detailed study of the topography of a specimen (see Resolution is inversely related to the wavelength of the light (or Figure 6.3). The electron beam scans the surface of the sample, electrons) a microscope uses for imaging, and electron beams usually coated with a thin film of gold. The beam excites 94 UNIT TWO The Cell. Figure 6.3 Exploring Microscopy Light Microscopy (LM) Brightfield. Light passes directly Confocal. This image shows two types through the specimen. Unstained of fluorescence micrographs: confocal (left), the image has little contrast. (top) and standard (bottom). (Nerve cells Staining with dyes (right) enhances are green, support cells orange, areas of contrast. Most stains require cells to overlap yellow.) In confocal microscopy, 50 om be preserved, which kills them. a laser is used to create a single plane of Phase-contrast. Variations in fluorescence; out-of-focus light from density within the specimen are other planes is eliminated. By capturing amplified to enhance contrast in sharp images at many different planes, a 3-D reconstruction can unstained cells; this is especially be created. A standard fluorescence micrograph is blurry because useful for examining living, out-of-focus light is not excluded. Human unstained cells. cheek Deconvolution. The top of this image cells of a white blood cell was reconstructed from many blurry fluorescence images at different planes, each Differential interference processed using deconvolution contrast (Nomarski). As in software. This process digitally removes phase-contrast microscopy, optical out-of-focus light and reassigns it to its modifications are used to exagger- source, creating a much sharper 3-D ate differences in density; the 10 om image. The bottom is a compilation of 50 om image appears almost 3-D. standard fluorescent micrographs through the same cell. Super-resolution. To make this super- Fluorescence. Locations of specific molecules resolution image of a cow aorta cell (top), are revealed by labeling the molecules with individual fluorescent molecules were fluorescent dyes or antibodies, which absorb excited by UV light and their position ultraviolet radiation and emit visible light. In this recorded. (DNA is blue, mitochondria fluorescently labeled uterine cell, DNA is blue, red, and part of the cytoskeleton green.) organelles called mitochondria are orange, and Combining information from many part of the cell’s “skeleton” (called the molecules in different places ”breaks” 10 om 10 om cytoskeleton) is green. the resolution limit, resulting in the sharp image on top. The size of each dot is well below the 200-nm resolution of a standard light microscope, as seen in the confocal image (bottom) of the same cell. Electron Microscopy (EM) Scanning electron microscopy Cryo-electron microscopy (cryo-EM). (SEM). Micrographs taken with a Cilia Specimens of tissue or aqueous scanning electron microscope Longitudinal solutions of proteins are frozen rapidly show a 3-D image of the surface section of cilium at temperatures less than –160°C, of a specimen. This SEM shows locking the molecules into a rigid state. Cross section the surface of a cell from a trachea A beam of electrons is passed through of cilium (windpipe) covered with cell the sample to visualize the molecules projections called cilia. Electron by electron microscopy, and software is micrographs are black and used to merge a series of such micro- white but are often artificially graphs, creating a 3-D image like the colorized to highlight particular one below. structures, as has been done with all three electron micrographs 2 om shown here. SEM Transmission electron microscopy (TEM). A transmission electron microscope profiles a thin section of a specimen. This TEM shows a section 2 om through a tracheal cell, revealing its internal structure. In preparing the specimen, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections. TEM bacterial enzyme d-galactosidase, which Abbreviations used in figure legends in this text: Computer-generated image of the LM 5 Light Micrograph VISUAL SKILLS When the tissue was sliced, what was SEM 5 Scanning Electron Micrograph the orientation of the cilia in the lower portion of the breaks down lactose. This image was TEM 5 Transmission Electron Micrograph TEM? The upper portion? Explain how the orientation of compiled from more than 90,000 the cilia determined the type of sections we see. cryo-EM images. CHAPTER 6 A Tour of the Cell 95 electrons on the surface, and these secondary electrons are. Figure 6.4 Research Method detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen. The result is an image Cell Fractionation of the specimen’s surface that appears three-dimensional. Application Cell fractionation is used to separate (fraction- The transmission electron microscope (TEM) is used ate) cell components based on size and density. to study the internal structure of cells (see Figure 6.3). The Technique Cells are homogenized in a blender to break TEM aims an electron beam through a very thin section of the them up. The resulting mixture (homogenate) is centrifuged. specimen, much as a light microscope aims light through a The liquid above the pellet (supernatant) is poured into sample on a slide. For the TEM, the specimen has been stained another tube and centrifuged at a higher speed for a longer with atoms of heavy metals, which attach to certain cellular period. This process is repeated several times. This process, called differential centrifugation, results in a series of pellets, structures, thus enhancing the electron density of some parts each containing different cell components. of the cell more than others. The electrons passing through the specimen are scattered more in the denser regions, so fewer are transmitted. The image displays the pattern of transmitted electrons. Instead of using glass lenses, both the SEM and TEM use electromagnets as lenses to bend the paths of the electrons, ultimately focusing the image onto a monitor for viewing. Electron microscopes have revealed many subcellular Homogenization structures that were impossible to resolve with the light micro- Tissue scope. But the light microscope offers advantages, especially cells in studying living cells. A disadvantage of electron microscopy Homogenate is that the methods customarily used to prepare the specimen Centrifuged at 1,000 g kill the cells and can introduce artifacts, structural features (1,000 times the Centrifugation seen in micrographs that do not exist in the living cell. force of gravity) In the past several decades, light microscopy has been revital- for 10 min Supernatant ized by major technical advances (see Figure 6.3). Labeling indi- poured into next vidual cellular molecules or structures with fluorescent markers tube has made it possible to see such structures with increasing detail. Differential 20,000 g centrifugation In addition, both confocal and deconvolution microscopy 20 min have produced sharper images of three-dimensional tissues and cells. Finally, a group of new techniques and labeling molecules developed in recent years, called super-resolution microscopy, has allowed researchers to “break” the resolution barrier and distin- 80,000 g guish subcellular structures as small as 10–20 nm across. 60 min Pellet rich in A recently developed new type of TEM called cryo-electron nuclei and microscopy (cryo-EM) (see Figure 6.3) allows specimens to be cellular debris preserved at extremely low temperatures. This avoids the use 150,000 g of preservatives, allowing visualization of structures in their 3 hr cellular environment. This method is increasingly used to Pellet rich in complement X-ray crystallography in revealing protein com- mitochondria (and chloro- plexes and subcellular structures like ribosomes, described plasts if cells later. Cryo-EM has even been used to resolve some individual are from a plant) proteins. The Nobel Prize for Chemistry was awarded in 2017 Pellet rich in to the developers of this valuable technique. Results In early experiments, “microsomes” Microscopes are the most important tools of cytology, the researchers used microscopy to (pieces of plasma identify the organelles in each membranes and study of cell structure. Understanding the function of each pellet and biochemical methods cells’ internal structure, however, required the integration of cytology and to determine their metabolic membranes) Pellet rich in biochemistry, the study of the chemical processes (metabo- functions. These identifications ribosomes established a baseline for this method, enabling lism) of cells. today’s researchers to know which cell fraction they should collect in order to isolate and study particular organelles. Cell Fractionation MAKE CONNECTIONS If you wanted to study the process of translation of proteins from mRNA, which part of which fraction A useful technique for studying cell structure and function would you use? (See Figure 5.22.) is cell fractionation (Figure 6.4), which takes cells apart 96 UNIT TWO The Cell and separates major organelles and other subcellular struc- CONCEPT 6.2 tures from one another. The piece of equipment that is used for this task is the centrifuge, which spins test tubes holding Eukaryotic cells have internal mixtures of disrupted cells at a series of increasing speeds, a process called differential centrifugation. At each speed, the membranes that compartmentalize resulting force causes a subset of the cell components to their functions settle to the bottom of the tube, forming a pellet. At lower Cells—the basic structural and functional units of every speeds, the pellet consists of larger components, and higher organism—are of two distinct types: prokaryotic and eukary- speeds result in a pellet with smaller components. otic. Organisms of the domains Bacteria and Archaea consist Cell fractionation enables researchers to prepare spe- of prokaryotic cells. Organisms of the domain Eukarya— cific cell components in bulk and identify their functions, protists, fungi, animals, and plants—all consist of eukary- a task not usually possible with intact cells. For example, otic cells. (“Protist” is an informal term referring to a diverse on one of the cell fractions, biochemical tests showed group of mostly unicellular eukaryotes.) the presence of enzymes involved in cellular respiration, while electron microscopy revealed large numbers of Comparing Prokaryotic and Eukaryotic Cells the organelles called mitochondria. Together, these data All cells share certain basic features: They are all bounded by a helped biologists determine that mitochondria are the selective barrier, called the plasma membrane (or the cell mem- sites of cellular respiration. Biochemistry and cytology brane). Inside all cells is a semifluid, jellylike substance called thus complement each other in correlating cell function cytosol, in which subcellular components are suspended. All with structure. cells contain chromosomes, which carry genes in the form of DNA. And all cells have ribosomes, tiny complexes that make proteins according to instructions from the genes. CONCEPT CHECK 6.1 A major difference between prokaryotic and eukaryotic 1. How do stains used for light microscopy compare with those cells is the location of their DNA. In a eukaryotic cell, used for electron microscopy? most of the DNA is in an organelle called the nucleus, which 2. WHAT IF? Which type of microscope would you use to study (a) the changes in shape of a living white blood cell? (b) the is bounded by a double membrane (see Figure 6.8). In a details of surface texture of a hair? prokaryotic cell, the DNA is concentrated in a region that For suggested answers, see Appendix A. is not membrane-enclosed, called the nucleoid (Figure 6.5).. Figure 6.5 A prokaryotic cell. Lacking a true nucleus and the other membrane-enclosed organelles of the eukaryotic cell, the prokaryotic cell appears much simpler in internal structure. Prokaryotes include bacteria and archaea; the general cell structure of these two domains is quite similar. Fimbriae: attachment structures on the surface of some prokaryotes (not visible on TEM) Nucleoid: region where the cell’s DNA is located (not enclosed by a membrane) Ribosomes: complexes that synthesize proteins Plasma membrane: membrane enclosing the cytoplasm Bacterial Cell wall: rigid structure outside chromosome the plasma membrane Glycocalyx: outer coating 0.5 om of many prokaryotes, consisting of a capsule or a slime layer (b) A thin section through the (a) A typical bacterium Corynebacterium rod-shaped bacterium Flagella: locomotion diphtheriae (colorized TEM) organelles of Mastering Biology Animation: some prokaryotes Prokaryotic Cell Structure and Function CHAPTER 6 A Tour of the Cell 97 Eukaryotic means “true nucleus” (from the Greek eu, true,. Figure 6.6 The plasma membrane. The plasma membrane and karyon, kernel, referring to the nucleus), and prokaryotic and the membranes of organelles consist of a double layer (bilayer) of phospholipids with various proteins attached to or embedded means “before nucleus” (from the Greek pro, before), reflect- in it. The hydrophobic parts of phospholipids and membrane ing the earlier evolution of prokaryotic cells. proteins are found in the interior of the membrane, while the The interior of either type of cell is called the cytoplasm; hydrophilic parts are in contact with aqueous solutions on either in eukaryotic cells, this term refers only to the region between side. Carbohydrate side chains may be attached to proteins or lipids on the outer surface of the plasma membrane. the nucleus and the plasma membrane. Within the cyto- plasm of a eukaryotic cell, suspended in cytosol, are a vari- (a) Colorized TEM of a plasma membrane. The plasma membrane ety of organelles of specialized form and function. These appears as a pair of dark bands separated by a gold band. membrane-bounded structures are absent in almost all pro- Outside of cell karyotic cells, another distinction between prokaryotic and Plasma membrane eukaryotic cells. In spite of the absence of organelles, though, 0.04 om the prokaryotic cytoplasm is not a formless soup. For exam- Inside of cell ple, some prokaryotes contain regions surrounded by proteins (cytoplasm) (not membranes), within which specific reactions take place. Eukaryotic cells are generally much larger than prokaryotic Carbohydrate side chains cells (see Figure 6.2). Size is a general feature of cell structure that relates to function. The logistics of carrying out cellular Phospholipid metabolism sets limits on cell size. At the lower limit, the smallest cells known are bacteria called mycoplasmas, which Hydrophilic have diameters between 0.1 and 1.0 µm. These are perhaps region the smallest packages with enough DNA to program metabo- lism and enough enzymes and other cellular equipment to Hydrophobic carry out the activities necessary for a cell to sustain itself and region reproduce. Typical bacteria are 1–5 µm in diameter, about ten Hydrophilic times the size of mycoplasmas. Eukaryotic cells are typically region Proteins 10–100 µm in diameter. (b) Structure of the plasma membrane Metabolic requirements also impose theoretical upper lim- VISUAL SKILLS What parts of the membrane diagram in its on the size that is practical for a single cell. At the boundary (b) correspond to the dark bands in the TEM in (a)? What parts of every cell, the plasma membrane functions as a selective correspond to the gold band? (Review Figure 5.11.) barrier that allows passage of enough oxygen, nutrients, and Mastering Biology BioFlix® Animation: Membranes wastes to service the entire cell (Figure 6.6). For each square micrometer of membrane, only a limited amount of a particu- lar substance can cross per second, so the ratio of surface area. Figure 6.7 Geometric relationships between surface area to volume is critical. As a cell (or any other object) increases and volume. In this diagram, cells are represented as cubes. Using in size, its surface area grows proportionately less than its arbitrary units of length, we can calculate the cell’s surface area (in square units, or units2), volume. (Area is proportional to a linear dimension squared, Surface area increases while volume (in cubic units, or total volume remains constant whereas volume is proportional to the linear dimension 3 units ), and ratio of surface cubed.) Thus, a smaller cell has a greater ratio of surface area to area to volume. A high volume: Compare the calculations for the first two “cells” in surface area-to-volume ratio facilitates the exchange of Figure 6.7. The Scientific Skills Exercise gives you a chance to 5 materials between a cell calculate the volumes and surface areas of two actual cells—a and its environment. 1 mature yeast cell and a cell budding from it. To explore differ- 1 ent ways that the surface area of cells is maximized in various Total surface area organisms, see Make Connections Figure 33.8. [(height 3 width of 1 side) 6 150 750 The need for a surface area large enough to accommodate 3 6 sides 3 number of cells] units2 units2 units2 the volume helps explain the microscopic size of most cells Total volume and the narrow, elongated shapes of some cells, such as nerve [(height 3 width 3 length 1 125 125 cells. Larger organisms do not generally have larger cells than of 1 cell) 3 number of cells] unit3 units3 units3 smaller organisms—they simply have more cells (see the far Surface area-to- right of Figure 6.7). A sufficiently high ratio of surface area volume ratio 6 1.2 6 to volume is especially important in cells that exchange a lot [surface area 4 volume] of material with their surroundings, such as intestinal cells. Such cells may have many long, thin projections from their Mastering Biology Figure Walkthrough 98 UNIT TWO The Cell Scientific Skills Exercise Using a Scale Bar to Calculate Volume and Surface Area of a Cell INTERPRET THE DATA 1. Examine the micrograph of the yeast cells. The scale bar under How Much New Cytoplasm and Plasma Membrane the photo is labeled 1 µm. The scale bar works in the same way Are Made by a Growing Yeast Cell? The unicellular yeast as a scale on a map, where, for example, 1 inch equals 1 mile. Saccharomyces cerevisiae divides by budding off a small new cell In this case the bar represents one thousandth of a millimeter. that then grows to full size (see the yeast cells at the bottom of Using the scale bar as a basic unit, determine the diameter of Figure 6.8). During its growth, the new cell synthesizes new cyto- the mature parent cell and the new cell. Start by measuring the plasm, which increases its volume, and new plasma membrane, scale bar and the diameter of each cell. The units you use are ir- which increases its surface area. In this exercise, you will use a relevant, but working in millimeters is convenient. Divide each scale bar to determine the sizes of a mature parent yeast cell and diameter by the length of the scale bar and then multiply by the a cell budding from it. You will then calculate the volume and scale bar’s length value to give you the diameter in micrometers. surface area of each cell. You will use your calculations to deter- 2. The shape of a yeast cell can be approximated by a sphere. mine how much cytoplasm and plasma membrane the new cell (a) Calculate the volume of each cell using the formula for the needs to synthesize to grow to full size. volume of a sphere: 4 How the Experiment Was Done Yeast cells were grown V = pr 3 3 r d under conditions that promoted division by budding. The cells were then viewed with a differential interference contrast light microscope and photographed. Data from the Experiment This light micrograph shows a bud- ding yeast cell about to be released from the mature parent cell: Note that π (the Greek letter pi) is a constant with an approxi- mate value of 3.14, d stands for diameter, and r stands for radius, which is half the diameter. (b) What volume of new cytoplasm will the new cell have to synthesize as it matures? To determine Mature parent this, calculate the difference between the volume of the full-sized cell cell and the volume of the new cell. Budding 3. As the new cell grows, its plasma membrane needs to expand to cell contain the increased volume of the cell. (a) Calculate the sur- face area of each cell using the formula for the surface area of a sphere: A = 4pr 2. (b) How much area of new plasma membrane 1 om will the new cell have to synthesize as it matures? 4. When the new cell matures, it will be approximately how many times greater in volume and how many times greater in Micrograph from K. Tatchell, using yeast cells grown for experiments described surface area than its current size? in L. Kozubowski et al., Role of the septin ring in the asymmetric localization of proteins at the mother-bud neck in Saccharomyces cerevisiae, Molecular Biology Instructors: A version of this Scientific Skills Exercise can be of the Cell 16:3455–3466 (2005). assigned in Mastering Biology. surface called microvilli, which increase surface area without membranes also participate directly in the cell’s metabolism an appreciable increase in volume. because many enzymes are built right into the membranes. The evolutionary relationships between prokaryotic and The basic fabric of most biological membranes is a double eukaryotic cells will be discussed later in this chapter, and layer of phospholipids and other lipids. Embedded in this lipid prokaryotic cells will be described in detail elsewhere (see bilayer or attached to its surfaces are diverse proteins (see Figure Chapter 27). Most of the discussion of cell structure that 6.6). However, each type of membrane has a unique composi- follows in this chapter applies to eukaryotic cells. tion of lipids and proteins suited to that membrane’s specific functions. For example, enzymes embedded in the membranes of the organelles called mitochondria function in cellular respi- A Panoramic View of the Eukaryotic Cell ration. Because membranes are so fundamental to the organi- In addition to the plasma membrane at its outer surface, a zation of the cell, Chapter 7 will discuss them in detail. eukaryotic cell has extensive, elaborately arranged internal Before continuing with this chapter, examine the eukary- membranes that divide the cell into compartments—the otic cells in Figure 6.8. The generalized diagrams of an animal organelles mentioned earlier. The cell’s compartments pro- cell and a plant cell introduce the various organelles and vide different local environments that support specific meta- show the key differences between animal and plant cells. The bolic functions, so incompatible processes can occur simulta- micrographs at the bottom of the figure give you a glimpse of neously in a single cell. The plasma membrane and organelle cells from different types of eukaryotic organisms. CHAPTER 6 A Tour of the Cell 99. Figure 6.8 Exploring Eukaryotic Cells Animal Cell (cutaway view of generalized cell) Nuclear envelope: double ENDOPLASMIC RETICULUM (ER): network membrane enclosing the of membranous sacs and tubes; active in nucleus; perforated by membrane synthesis and other synthetic pores; continuous with ER Flagellum: motility and metabolic processes; has rough structure present in (ribosome-studded) and smooth regions Nucleolus: nonmembranous some animal cells, structure involved in production composed of a cluster of of ribosomes; a nucleus has NUCLEUS Rough ER Smooth ER microtubules within an one or more nucleoli extension of the plasma membrane Chromatin: material consisting of DNA and proteins; visible in a dividing cell as individual Centrosome: region condensed chromosomes where the cell’s microtubules are initiated; contains a pair of centrioles Plasma membrane: membrane enclosing the cell CYTOSKELETON: reinforces cell’s shape; functions in cell movement; components are made of protein. Includes: Microfilaments Intermediate filaments Ribosomes (small brown Microtubules dots): complexes that make proteins; free in cytosol or bound to Microvilli: rough ER or nuclear membrane envelope projections that increase the cell’s surface area Golgi apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products Peroxisome: organelle with various specialized metabolic Lysosome: digestive functions; produces hydrogen organelle where peroxide as a by-product and macromolecules are then converts it to water hydrolyzed Mitochondrion: organelle where cellular respiration occurs and most ATP is generated Mastering Biology BioFlix® Animation: Tour of an Animal Cell Parent 1 om 10 om cell Unicellular Fungi Cell wall Animal Cells Buds Vacuole Cell 5 om Nucleus Nucleolus Nucleus Yeast cells: reproducing by budding (above, colorized SEM) and a single cell Human cells from lining of uterus (colorized TEM) (right, colorized TEM) Mitochondrion 100 UNIT TWO The Cell  Plant Cell (cutaway view of generalized cell) Nuclear envelope Rough NUCLEUS endoplasmic Nucleolus reticulum Chromatin Smooth endoplasmic reticulum Ribosomes (small brown dots) Central vacuole: prominent organelle in older plant cells; functions include storage, breakdown of waste products, and hydrolysis Golgi apparatus of macromolecules; enlargement of the vacuole is a major mechanism of plant growth Microfilaments CYTOSKELETON Microtubules Mitochondrion Peroxisome Chloroplast: photosynthetic Plasma membrane organelle; converts energy of sunlight to chemical energy stored in sugar molecules Cell wall: outer layer that maintains cell’s shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein Plasmodesmata: cytoplasmic Mastering Biology channels through cell walls BioFlix® Animation: Tour of a Plant Cell Wall of adjacent cell that connect the cytoplasms Video: Turgid Elodea of adjacent cells Video: Chlamydomonas Cell Flagella 1 om 5 om 8 om Cell wall Unicellular Algae Chloroplast Nucleus Plant Cells Mitochondrion Nucleolus Nucleus Vacuole Nucleolus Unicellular green alga Chlamydomonas Chloroplast Cells from duckweed (Spirodela oligorrhiza), (above, colorized SEM; right, colorized a floating plant (colorized TEM) TEM) Cell wall CHAPTER 6 A Tour of the Cell 101  CONCEPT CHECK 6.2 Within the nucleus, the DNA is organized into discrete units called chromosomes, structures that carry the genetic 1. Briefly describe the structure and function of the nucleus, the mitochondrion, the chloroplast, and the endoplasmic information. Each chromosome contains one long DNA reticulum. molecule associated with many proteins, including small 2. DRAW IT Draw a simplified elongated cell that measures basic proteins called histones. Some of the proteins help coil 125 * 1 * 1 arbitrary units. A nerve cell would be roughly this the DNA molecule of each chromosome, reducing its length shape. Predict how its surface-to-volume ratio would com- pare with those in Figure 6.7. Then calculate the ratio and and allowing it to fit into the nucleus. The complex of DNA check your prediction. and proteins making up chromosomes is called chromatin. For suggested answers, see Appendix A. When a cell is not dividing, stained chromatin appears as a diffuse mass in micrographs, and the chromosomes cannot be distinguished from one another, even though discrete chro- CONCEPT 6.3 mosomes are present. As a cell prepares to divide, however, the The eukaryotic cell’s genetic chromosomes form loops and coil, condensing and becoming thick enough to be distinguished under a microscope as sepa- instructions are housed in the rate structures (see Figure 16.23). Each eukaryotic species has a nucleus and carried out by the characteristic number of chromosomes. For example, a typical human cell has 46 chromosomes in its nucleus; the excep- ribosomes tions are human sex cells (eggs and sperm), which have only On the first stop of our detailed tour of the eukaryotic cell, 23 chromosomes. A fruit fly cell has 8 chromosomes in most let’s look at two cellular components involved in the genetic cells and 4 in the sex cells. control of the cell: the nucleus, which houses most of the A prominent structure within the nondividing nucleus is cell’s DNA, and the ribosomes, which use information from the nucleolus (plural, nucleoli), which appears through the the DNA to make proteins. electron microscope as a mass of densely stained granules and fibers adjoining part of the chromatin. Here a type of RNA called ribosomal RNA (rRNA) is synthesized The Nucleus: Information Central from genes in the DNA. Also in the nucleo- The nucleus contains most of the genes in the lus, proteins imported from the cytoplasm Nucleus eukaryotic cell. (Some genes are located in are assembled with rRNA into large and mitochondria and chloroplasts.) It is usu- small subunits of ribosomes. These sub- ally the most conspicuous organelle (see units then exit the nucleus through the the purple structure in the fluorescence nuclear pores to the cytoplasm, where a micrograph), averaging about 5 µm in large and a small subunit can assemble diameter. The nuclear envelope encloses into a ribosome. Sometimes there are the nucleus (Figure 6.9), separating its con- two or more nucleoli; the number tents from the cytoplasm. depends on the species and the stage in The nuclear envelope is a double mem- the cell’s reproductive cycle. The nucleoli brane. The two membranes, each a lipid may also play a role in controlling cell divi- 5 om bilayer with associated proteins, are separated sion and the life span of a cell. by a space of 20–40 nm. The envelope is perforated As we saw in Figure 5.22, the nucleus directs by pore structures that are about 100 nm in diameter. At protein synthesis by synthesizing messenger RNA (mRNA) the lip of each pore, the inner and outer membranes of that carries information from the DNA. The mRNA is then the nuclear envelope are continuous. An intricate protein transported to the cytoplasm via nuclear pores. Once an structure called a pore complex lines each pore and plays mRNA molecule reaches the cytoplasm, ribosomes translate an important role in the cell by regulating the entry and the mRNA’s genetic message into the primary structure of a exit of proteins and RNAs, as well as large complexes of specific polypeptide. (This process of transcribing and translat- macromolecules. Except at the pores, the nuclear side of the ing genetic information is described in detail in Chapter 17.) envelope is lined by the nuclear lamina, a netlike array of protein filaments (in animal cells, called intermediate fila- Mastering Biology BioFlix® Animation: Nucleus and Ribosomes ments) that maintains the shape of the nucleus by mechani- cally supporting the nuclear envelope. There is also much Ribosomes: Protein Factories evidence for a nuclear matrix, a framework of protein fibers Ribosomes, which are complexes made of ribosomal RNAs extending throughout the nuclear interior. The nuclear and proteins, are the cellular components that carry out lamina and matrix may help organize the genetic material protein synthesis (Figure 6.10). (Note that ribosomes are not so it functions efficiently. membrane bounded and thus are not considered organelles.) 102 UNIT TWO The Cell. Figure 6.9 The nucleus and its envelope. Within the nucleus are the chromosomes, which appear as a mass of chromatin (DNA and associated proteins) and one or more nucleoli (singular, Nuclear envelope: nucleolus), which function in ribosome synthesis. The nuclear envelope, which consists of two Outer membrane membranes separated by a narrow space, is perforated with pores and lined by the nuclear lamina. Inner membrane 1 om Nucleus Nucleolus Chromatin Nuclear envelope: Outer membrane Inner membrane Nuclear pores Rough ER m Surface of nuclear envelope Pore (TEM). This specimen complex was prepared by a technique Ribosome known as freeze-fracture, which DNA cuts from the outer membrane to the inner membrane, revealing both. Histone b Close-up protein m Chromatin. This 0.25 om of nuclear segment of a chromosome envelope shows two states of chromatin (DNA—blue—wrapped around histone proteins--purple) in a nondividing cell. In preparation for 0.5 om cell division, the chromatin will become more condensed. m Pore complexes (TEM). Each pore is ringed by protein particles. MAKE CONNECTIONS Chromosomes c Nuclear lamina (TEM). The netlike lamina contain the genetic material and reside in the lines the inner surface of the nuclear envelope. nucleus. How does the rest of the cell get access (The light circular spots are nuclear pores.) to the information they carry? (See Figure 5.22.). Figure 6.10 Ribosomes. This electron micrograph of a pancreas Mastering Biology cell shows both free and bound ribosomes. The simplified diagram and Interview with Venki Ramakrishnan: computer model show the two subunits of a ribosome. 0.25 om Studying ribosome structure Ribosomes ER Free ribosomes in cytosol Endoplasmic reticulum (ER) Ribosomes bound to ER Large subunit Small subunit TEM showing ER and ribosomes Diagram of a ribosome Computer model of a ribosome DRAW IT After you have read the section on ribosomes, circle a ribosome in the micrograph that might be making a protein that will be secreted. CHAPTER 6 A Tour of the Cell 103 Cells with high rates of protein synthesis have particularly Having already looked at the nuclear envelope, we will now large numbers of ribosomes as well as prominent nucleoli, focus on the endoplasmic reticulum and the other endomem- which makes sense, given the role of nucleoli in ribosome branes to which the endoplasmic reticulum gives rise. assembly. For example, a human pancreas cell, which makes many digestive enzymes, has a few million ribosomes. Ribosomes build proteins in two cytoplasmic regions: The Endoplasmic Reticulum: At any given time, free ribosomes are suspended in the cyto- Biosynthetic Factory sol, while bound ribosomes are attached to the outside of the The endoplasmic reticulum (ER) is such an extensive endoplasmic reticulum or nuclear envelope (see Figure 6.10). network of membranes that it accounts for more than half Bound and free ribosomes are structurally identical, and the total membrane in many eukaryotic cells. (The word ribosomes can play either role at different times. Most of the endoplasmic means “within the cytoplasm,” and reticulum is proteins made on free ribosomes function within the cytosol; Latin for “little net.”) The ER consists of a network of mem- examples are enzymes that catalyze the first steps of sugar branous tubules and sacs called cisternae (from the Latin breakdown. Bound ribosomes generally make proteins that cisterna, a reservoir for a liquid). The ER membrane separates are destined for insertion into membranes, for packaging the internal compartment of the ER, called the ER lumen within certain organelles such as lysosomes (see Figure 6.8), (cavity) or cisternal space, from the cytosol. And because the or for export from the cell (secretion). Cells that specialize in ER membrane is continuous with the nuclear envelope, the protein secretion—for instance, the cells of the pancreas that space between the two membranes of the envelope is con- secrete digestive enzymes—frequently have a high propor- tinuous with the lumen of the ER (Figure 6.11). tion of bound ribosomes. (You will learn more about ribo- There are two distinct, though connected, regions of the some structure and function in Concept 17.4.) ER that differ in structure and function: smooth ER and rough ER. Smooth ER is so named because its outer surface lacks CONCEPT CHECK 6.3 ribosomes. Rough ER is studded with ribosomes on the outer 1. What role do ribosomes play in carrying out genetic instructions? surface of the membrane and thus appears rough through the 2. Describe the molecular composition of nucleoli and explain electron microscope. As already mentioned, ribosomes are their function. also attached to the cytoplasmic side of the nuclear envelope’s 3. WHAT IF? As a cell begins the process of dividing, its outer membrane, which is continuous with rough ER. chromosomes become shorter, thicker, and individually visible in an LM (light micrograph). Explain what is happening at the molecular level. Functions of Smooth ER For suggested answers, see Appendix A. The smooth ER functions in diverse metabolic processes, which vary with cell type. These processes include synthesis CONCEPT 6.4 of lipids, metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions. The endomembrane system Enzymes of the smooth ER are important in the synthesis regulates protein traffic and of lipids, including oils, steroids, and new membrane phos- pholipids. Among the steroids produced by the smooth ER performs metabolic functions in animal cells are the sex hormones of vertebrates and the Many of the different membrane-bounded organelles of the various steroid hormones secreted by the adrenal glands. The eukaryotic cell are part of the endomembrane system, cells that synthesize and secrete these hormones—in the tes- which includes the nuclear envelope, the endoplasmic reticu- tes and ovaries, for example—are rich in smooth ER, a struc- lum, the Golgi apparatus, lysosomes, various kinds of vesicles tural feature that fits the function of these cells. and vacuoles, and the plasma membrane. This system carries Other enzymes of the smooth ER help detoxify drugs out a variety of tasks in the cell, including synthesis of pro- and poisons, especially in liver cells. Detoxification usually teins, transport of proteins into membranes and organelles involves adding hydroxyl groups to drug molecules, mak- or out of the cell, metabolism and movement of lipids, and ing them more water-soluble and easier to flush from the detoxification of poisons. The membranes of this system are body. The sedative phenobarbital and other barbiturates are related either through direct physical continuity or by the examples of drugs metabolized in this manner by smooth ER transfer of membrane segments as tiny vesicles (sacs made in liver cells. In fact, barbiturates, alcohol, and many other of membrane). Despite these relationships, the various mem- drugs induce the proliferation of smooth ER and its associated branes are not identical in structure and function. Moreover, detoxification enzymes, thus increasing the rate of detoxifica- the thickness, molecular composition, and types of chemical tion. This, in turn, increases tolerance to the drugs, meaning reactions carried out in a given membrane are not fixed, but that higher doses are required to achieve a particular effect, may be modified several times during the membrane’s life. such as sedation. Also, because some of the detoxification 104 UNIT TWO The Cell enzymes have relatively broad action, the proliferation of The smooth ER also stores calcium ions. In muscle cells, for smooth ER in response to one drug can increase the need for example, the smooth ER membrane pumps calcium ions from higher dosages of other drugs as well. Barbiturate abuse, for the cytosol into the ER lumen. When a muscle cell is stimu- instance, can decrease the effectiveness of certain antibiotics lated by a nerve impulse, calcium ions rush back across the and other useful drugs. ER membrane into the cytosol and trigger contraction of the muscle cell. In other cell types, release of calcium ions from. Figure 6.11 Endoplasmic reticulum (ER). A membranous the smooth ER triggers different responses, such as secretion system of interconnected tubules and flattened sacs called of vesicles carrying newly synthesized proteins. cisternae, the ER is also continuous with the nuclear envelope, as shown in the cutaway diagram at the top. The membrane of the ER encloses a continuous compartment called the ER lumen Functions of Rough ER (or cisternal space). Rough ER, which is studded on its outer Many cells secrete proteins that are produced by ribosomes surface with ribosomes, can be distinguished from smooth ER in attached to rough ER. For instance, certain pancreatic cells the electron micrograph (TEM). Transport vesicles bud off from a region of the rough ER called transitional ER and travel to the Golgi synthesize the protein insulin in the ER and secrete this apparatus and other destinations. hormone into the bloodstream. As a polypeptide chain grows from a bound ribosome, the chain is threaded into the ER lumen through a pore formed by a protein complex in the ER membrane. The new polypeptide folds into its functional shape as it enters the ER lumen. Most secretory proteins are glycoproteins, proteins with carbohydrates covalently bonded to them. The carbohydrates are attached to the proteins in the ER lumen by enzymes built into the ER membrane. After secretory proteins are formed, the ER membrane Smooth ER keeps them separate from proteins in the cytosol, which are produced by free ribosomes. Secretory proteins depart from Rough ER Nuclear the ER wrapped in the membranes of vesicles that bud like envelope bubbles from a specialized region called transitional ER (see Figure 6.11). Vesicles in transit from one part of the cell to another are called transport vesicles; we will examine their fate shortly. In addition to making secretory proteins, rough ER is a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane. As polypeptides destined to be membrane proteins grow ER lumen from the ribosomes, they are inserted into the ER membrane itself and anchored there by their hydrophobic portions. Cisternae Transitional ER Ribosomes Like the smooth ER, the rough ER also makes membrane Transport vesicle phospholipids; enzymes built into the ER membrane assem- ble phospholipids from precursors in the cytosol. The ER 0.2 om membrane expands, and portions of it are transferred in the Smooth ER Ribosomes Rough ER form of transport vesicles to other components of the endo- membrane system. The Golgi Apparatus: Shipping and Receiving Center After leaving the ER, many transport vesicles travel to the Golgi apparatus. We can think of the Golgi as a warehouse for receiving, sorting, shipping, and even some manufactur- ing. Here, products of the ER, such as proteins, are modified and stored and then sent to other destinations. Not surpris- ingly, the Golgi apparatus is especially extensive in cells specialized for secretion. CHAPTER 6 A Tour of the Cell 105  The Golgi apparatus consists of a group of associated, flat- producing a large variety of carbohydrates. Membrane phos- tened membranous sacs—cisternae—looking like a stack of pita pholipids may also be altered in the Golgi. bread (Figure 6.12). A cell may have many, even hundreds, of In addition to its finishing work, the Golgi apparatus also these stacks. The membrane of each cisterna in a stack separates manufactures some macromolecules. Many polysaccharides its internal space from the cytosol. Vesicles concentrated in the secreted by cells are Golgi products. For example, pectins and vicinity of the Golgi apparatus are engaged in the transfer of certain other noncellulose polysaccharides are made in the material between parts of the Golgi and other structures. Golgi of plant cells and then incorporated along with cellu- A Golgi stack has a distinct structural directionality, with lose into their cell walls. Like secretory proteins, nonprotein the membranes of cisternae on opposite sides of the stack dif- Golgi products that will be secreted depart from the trans face fering in thickness and molecular composition. The two sides of the Golgi inside transport vesicles that eventually fuse with of a Golgi stack are referred to as the cis face and the trans face; the plasma membrane. The contents are released and the ves- these act, respectively, as the receiving and shipping depart- icle membrane is incorporated into the plasma membrane, ments of the Golgi apparatus. The term cis means “on the same adding to the surface area. side,” and the cis face is usually located near the ER. Transport The Golgi manufactures and refines its products in stages, vesicles move material from the ER to the Golgi apparatus. A with different cisternae containing unique teams of enzymes. vesicle that buds from the ER can add its membrane and the Until recently, biologists viewed the Golgi as a static struc- contents of its lumen to the cis face by fusing with a Golgi ture, with products in various stages of processing trans- membrane on that side. The trans face (“on the opposi