Describe the types of movement seen in cells.

Chapter 4 A Tour of the Cell Chapter Objectives Opening Essay Introduction to the Cell Describe the types of movement seen in cells. 4.1 Compare the designs of and images produced by a light microscope, a scanning electron microscope, and a transmission electron microscope. Distinguish between magnification and resolving power. 4.1 Define cell theory and briefly describe the discoveries that led to its development. 4.2 Explain why there are upper and lower limits to cell size. 4.3 Distinguish between the structures of prokaryotic and eukaryotic cells. 4.4 Explain why compartmentalization is important in eukaryotic cells. 4.4 Compare the structures of plant and animal cells. Note the function of each cell part. 4.4 Describe the structures and functions of the four compartments of eukaryotic cells. 4.5 Describe the hydrophobic and hydrophilic components of a plasma membrane. Cell Structures Involved in Manufacturing and Breakdown 4.6 4.13 Describe the structure and functions of the nucleus, endomembrane system, smooth and rough endoplasmic reticulum, Golgi apparatus, lysosomes, and vacuoles. Energy-Converting Organelles 4.14 4.15 Compare the structures and functions of chloroplasts and mitochondria. 4.16 Describe the evidence that suggests that mitochondria and chloroplasts evolved by endosymbiosis. Internal and External Support: The Cytoskeleton and Cell Surfaces 4.17 Compare the structures and functions of microfilaments, intermediate filaments, and microtubules. 4.18 Relate the structure of cilia and flagella to their functions. 4.19 Describe examples of environmental and genetic causes of infertility in men. 4.20 Relate the structure of the extracellular matrix to its functions. 4.21 Compare the structures and functions of tight junctions, anchoring junctions, and gap junctions. 4.22 Relate the structure of plant cell walls to its functions. Functional Categories of Cell Structures 4.23 Describe the four functional categories of organelles in eukaryotic cells. 4.23 Describe the three fundamental features of all organisms. 21

22 Instructor s Guide to Text and Media Key Terms basal body cell theory cell wall cellular metabolism central vacuole centriole chloroplast chromatin chromosome cilia crista (plural, cristae) cytoplasm cytoskeleton electron microscope (EM) endomembrane system endoplasmic reticulum (ER) endosymbiosis eukaryotic cell extracellular matrix (ECM) flagellum (plural, flagella) glycoprotein Golgi apparatus granum (plural, grana) integrins intermediate filament intermembrane space light microscope (LM) lysosome microfilament micrograph microtubule mitochondrial matrix mitochondrion (plural, mitochondria) nuclear envelope nucleoid nucleolus nucleus (plural, nuclei) organelle peroxisome plasma membrane plasmodesma (plural, plasmodesmata) prokaryotic cell ribosome rough endoplasmic reticulum scanning electron microscope (SEM) smooth endoplasmic reticulum stroma thylakoid transmission electron microscope (TEM) transport vesicle vacuole vesicle Word Roots centro- center (centriole: an animal cell structure composed of cylinders of microtubule triplets; within the cell s centrosome, a pair of centrioles function in cell division) chloro- green; -plast molded (chloroplast: the site of photosynthesis in plants and algae) cili- hair (cilium: a short hair-like cellular appendage with a microtubule core, specialized for locomotion) cyto- cell; -plasm fluid (cytoplasm: everything inside a cell between the plasma membrane and the nucleus, consisting of a semifluid medium and organelles) -ell small (organelle: a membrane-enclosed structure with a specialized function within a cell) endo- inner (endomembrane system: the system of membranes within a cell that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane) endo- inner; sym- together; bios- living (endosymbiosis: when one organism lives inside another organism; the process by which the mitochondria and chloroplasts of eukaryotic cells probably evolved) eu- true; karyo- nucleus (eukaryotic cell: a cell with a membrane-enclosed nucleus and other membrane-enclosed organelles) extra- outside (extracellular matrix: the substance in which animal tissue cells are embedded) flagell- whip (flagellum: a long whiplike cellular appendage specialized for locomotion) glyco- sweet (glycoprotein: a macromolecule consisting of one or more polypeptides linked to short chains of sugars) lyso- loosen (lysosome: a digestive organelle containing hydrolytic enzymes used by eukaryotic cells to digest food and wastes) micro- small; -tubul a little pipe (microtubule: a straight, hollow tube of globular proteins in the cytoskeleton of eukaryotic cells that support the structure and movement of cilia and flagella)

Chapter 4 A Tour of the Cell 23 micro- small; -graphy a picture (micrograph: a photograph taken through a microscope) nucle- nucleus; -oid like (nucleoid: a dense region of DNA in a prokaryotic cell) a band or bond (plasmodesmata: an open channel in a plant cell wall) pro- before; (prokaryotic cell: a cell that has no nucleus) -soma a body (chromosome: the structure carrying the genetic material found in the nucleus of a eukaryotic cell; also, the main gene-carrying structure of a prokaryotic cell; ribosome: a cell structure consisting of RNA and protein organized into two subunits and functioning as the site of protein synthesis in the cytoplasm; peroxisome: an organelle containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide) thylaco- sac or pouch (thylakoid: a flattened membranous sac inside the chloroplast that serves as the site of the light reactions of photosynthesis) trans- across; -port a harbor; vesic- sac or bladder (transport vesicle: a membranous compartment used to enclose and transport materials from one part of a cell to another) vacu- empty (vacuole: a membrane-enclosed sac that is part of the endomembrane system of a eukaryotic cell) Student Media Introduction to the Cell BioFlix: Tour of an Animal Cell (4.4) BioFlix: Tour of a Plant Cell (4.4) MP3 Tutor: Cell Organelles (4.4) Activity: Metric System Review (4.1) Activity: Prokaryotic Cell Structure and Function (4.3) Process of Science: Connection: What is the Size and Scale of Our World? (4.1) Discovery Channel Video Clip: Cells (4.1) Video: Cytoplasmic Streaming (4.4) BLAST Animation: Eukaryotic Cell Shape and Surface Area (4.2) BLAST Animation: Surface Area to Volume Calculator (4.2) BLAST Animation: Prokaryotic Cell Size (4.3) BLAST Animation: Animal Cell Overview (4.4) BLAST Animation: Plant Cell Overview (4.4) Cell Structures Involved in Manufacturing and Breakdown Activity: Overview of Protein Synthesis (4.9) Activity: The Endomembrane System (4.13) Activity: Build a Chloroplast and a Mitochondrion (4.13) Video: Paramecium Vacuole (4.12) BLAST Animation: Vesicle Transport (4.8) BLAST Animation: Vacuole (4.12)

24 Instructor s Guide to Text and Media Energy-Converting Organelles Video: Chlamydomonas (4.15) BLAST Animation: Mitochondrion (4.14) Internal and External Support: The Cytoskeleton and Cell Surfaces Activity: Cilia and Flagella (4.18) Activity: Cell Junctions (4.21) Video: Vorticella Habitat (4.17) Video: Paramecium Cilia (4.18) Video: Prokaryotic Flagella (4.18) Video: Euglena (4.18) Video: Euglena Motion (4.18) Video: Stentor (4.18) Video: Stentor Ciliate Movement (4.18) Video: Vorticella Cilia (4.18) Video: Vorticella Detail (4.18) Video: Dinoflagellate (4.18) BLAST Animation: Signaling: Direct (4.21) BLAST Animation: Plant Cell Wall (4.22) Functional Categories of Cell Structures Activity: Review: Animal Cell Structure and Function (4.23) Activity: Review: Plant Cell Structure and Function (4.23) Chapter Guide to Teaching Resources Introduction to the Cell (4.1 4.5) Student Misconceptions and Concerns 1. Students typically cannot distinguish between the concepts of resolution and magnification. However, pixels and resolution of digital images can help clarify the distinction. Consider printing the same image at high and low resolution and enlarging the same image at two different levels of resolution. Teaching Tip 2 below suggests another related exercise. (4.1) 2. Students often think of the function of cell membranes as mainly containment, like that of a plastic bag. Consider relating the functions of membranes to our human skin. (For example, both membranes and our skin detect stimuli, engage in gas exchange, and serve as sites of excretion and absorption.) (4.3) Teaching Tips 1. Challenge students to identify other examples of technology that have extended our senses. Chemical probes can identify what we cannot taste, listening devices detect what we do not normally hear, night vision and ultraviolet (UV) cameras see or magnify wavelengths beyond our vision, etc. Students can be assigned the task of preparing a short report on one of these technologies. (4.1)

Chapter 4 A Tour of the Cell 25 2. Here is a chance to demonstrate resolving power in the classroom. Use a marker and your classroom marker board to make several pairs of dots separated by shorter and shorter distances. Start out with two dots clearly separated apart perhaps by 4 5 cm and end with a pair of dots that touch. Label them a, b, c, etc. Ask your students to indicate the letters of the pairs of points that they can distinguish as separate; this is the definition of resolution for their eyes (they need not state their answers publicly, to avoid embarrassment). (4.1) 3. Most biology laboratories have two types of microscopes for student use: a dissection (or stereo-) microscope, and a compound light microscope using microscope slides. The way these scopes function parallels the workings of electron microscopes. Dissection microscopes are like a SEM both rely upon a beam reflected off a surface. As you explain this to your class, hold up an object, identify a light source in the room, and explain that our eyes see most images when our eyes detect light that has reflected off the surface of an object. Compound light microscopes are like TEMs, in which a beam is transmitted through a thin sheet of material. If you have an overhead or other strong light source, hold up a piece of paper between your eye and the light source. You will see the internal detail of the paper as light is transmitted through the paper to your eye... the same way a compound light microscope or TEM works! (4.1) 4. Even in college, students still struggle with the metric system. When discussing the scale of life, consider bringing a meter stick to class. The ratio of a meter to a millimeter is the same as the ratio of a millimeter is to a micron: 1,000 to 1. (4.2) 5. Here is another way to explain surface-to-volume ratios. Have your class consider this situation. You purchase a set of eight coffee mugs, each in its own cubic box, for a wedding present. You can wrap the eight boxes together as one large cube, or wrap each of the eight boxes separately. Either way, you will be wrapping the same volume. However, wrapping the mugs separately requires much more paper. This is because the surface-to-volume ratio is greater for smaller objects. (4.2) 6. A visual comparison of prokaryotic and eukaryotic cells, such as that found in Figure 1.4, can be very helpful when discussing the key differences between these cell types. These cells are strikingly different in size and composition. Providing students with a visual reference point rather than simply listing these traits will help them better retain this information. (4.3) 7. Students might wrongly conclude that prokaryotes are typically one-tenth the volume of eukaryotic cells. A difference in diameter of a factor of ten translates into a much greater difference in volume. If students recall enough geometry, you may want to challenge them to calculate the difference in the volume of two cells with diameters that differ by a factor of ten. (4.3) 8. Germs here is a term that we learn early in our lives but that is rarely well-defined. Students may appreciate a biological explanation. The general use of germs is a reference to anything that causes disease. This may be a good time to sort the major disease-causing agents into three categories: (1) bacteria (prokaryotes), (2) viruses (not yet addressed), and (3) single-celled and multicellular eukaryotes (athlete s foot is a fungal infection; malaria is caused by a unicellular eukaryote). (4.3) 9. Module 4.3 mentions how antibiotics can specifically target prokaryotic but not eukaryotic cells, providing a good segue into discussion of the evolution of antibiotic resistance. Teaching tips and ideas for related lessons can be found at http://www.pbs.org/wgbh/evolution/educators/lessons/lesson6/act1.html. (4.3) 10. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a

26 Instructor s Guide to Text and Media cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. (4.4) 11. The hydrophobic and hydrophilic ends of a phospholipid molecule create a lipid bilayer. The hydrophobic edges of the layer will naturally seal to other such edges, eventually wrapping a sheet into a sphere that can enclose water (a simple cell). Furthermore, because of these hydrophobic properties, lipid bilayers are also selfhealing. That the properties of phospholipids emerge from their organization is worth emphasizing to students. (4.5) 12. You might wish to share a very simple analogy that works very well for some students. A cell membrane is a little like a peanut butter and jelly sandwich with jellybeans poked into it. The bread represents the hydrophilic portions of the bilayer (and bread does indeed quickly absorb water). The peanut butter and jelly represent the hydrophobic regions (and peanut butter, containing plenty of oil, is generally hydrophobic). The jellybeans stuck into the sandwich represent proteins variously embedded partially into or completely through the membrane. Transport proteins would be like the jellybeans that poke completely through the sandwich. Analogies are rarely perfect. Challenge your students to critique this analogy by finding exceptions. (For example, this analogy does not include a model of the carbohydrates on the cell surface.) (4.5) Cell Structures Involved in Manufacturing and Breakdown (4.6 4.13) Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6 4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. (4.6 4.13) 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. (4.6 4.13) Teaching Tips 1. Noting the main flow of genetic information on the board as DNA RNA protein will provide a useful reference for students when explaining these processes. As a review, have students note where new molecules of DNA, rrna, mrna, ribosomes, and proteins are produced in a cell. (4.6) 2. If you wish to continue the text s factory analogy, nuclear pores might be said to function most like the door to the boss s office. (4.6) 3. Some of your more knowledgeable students may like to guess the exceptions to the rule of 46 chromosomes per human cell. These exceptions include gametes, some of the cells that produce them, and adult red blood cells in mammals. (4.6) 4. If you want to challenge your students further, ask them to consider the adaptive advantage of using mrna to direct the production of proteins instead of using DNA directly. Some biologists suggest that DNA is better protected in the nucleus and that mrna, exposed to more damaging cross-reactions in the cytosol, is the temporary working copy of the genetic material. In some ways, this is like making a working photocopy of an important document, keeping the original copy safely stored away. (4.6)

Chapter 4 A Tour of the Cell 27 5. Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, yet DNA and RNA only specifically dictate the generation of proteins (and more copies of DNA and RNA). How is the production of specific types of carbohydrates and lipids in cells controlled? (Answer: primarily by the specific properties of enzymes.) (4.7) 6. Point out to your students that the endoplasmic reticulum is continuous with the outer nuclear membrane. This explains why the ER is usually found close to the nucleus. (4.8) 7. Students often learn that a human body can build up a tolerance to a drug. Here, in Module 4.9, they learn about one of the specific mechanisms of this response. Liver cells exposed to certain toxins or drugs increase the amount of smooth ER, which functions in the processing of these chemicals. Thus, there is a structural and functional explanation to a developing drug tolerance. (4.9) 8. Some people think the Golgi apparatus looks like a stack of pita bread. (4.10) 9. If you continue the factory analogy, the addition of a molecular tag by the Golgi apparatus is like adding address labels in the shipping department of a factory. (4.10) 10. As noted in Module 4.11, lysosomes help to recycle damaged cell components. Challenge your students to explain why this is adaptive. Recycling, whether in human society or in our cells, can be an efficient way to reuse materials. The recycled components, which enter the lysosomes in a highly organized form, would require a much greater investment to produce from scratch. (4.11) 11. Challenge your students to identify animal cell organelles other than mitochondria that are not involved in the synthesis of proteins. (Vacuoles and peroxisomes are not involved in protein synthesis). (4.12) 12. Challenge students to identify two regions in a cell where detoxification occurs. These were discussed in separate modules. (Answer: SER and peroxisomes). (4.13) Energy-Converting Organelles (4.14 4.16) Student Misconceptions and Concerns 1. Students often mistakenly think that chloroplasts are a substitute for mitochondria in plant cells. They might think that cells either have mitochondria or they have chloroplasts. You might challenge this thinking by asking how plant cells generate ATP at night. (4.14 4.15) 2. The evidence that mitochondria and chloroplasts evolved from free-living prokaryotes is further supported by the small size of these organelles, similar to the size of a prokaryote. Mitochondria and chloroplasts are therefore helpful in comparing the general size of eukaryotic and prokaryotic cells. You might think of these organelles as built-in comparisons. (4.16) Teaching Tips 1. ATP functions in cells much like money functions in modern societies. Each holds value that can be generated in one place and spent in another. This analogy has been very helpful for many students. (4.14) 2. Mitochondria and chloroplasts are each wrapped by multiple membranes. In both organelles, the innermost membranes are the sites of greatest molecular activity and the outer membranes have fewer significant functions. These outer membranes best correspond to the plasma membrane of the eukaryotic cells that originally wrapped the free-living prokaryotes during endocytosis. (4.14 4.16)

28 Instructor s Guide to Text and Media 3. Mitochondria and chloroplasts are not cellular structures that are synthesized in a cell like ribosomes and lysosomes. Instead, mitochondria only come from other mitochondria and chloroplasts only come from other chloroplasts. This is further evidence of the independent evolution of these organelles from free-living ancestral forms. (4.16) Internal and External Support: The Cytoskeleton and Cell Surfaces (4.17 4.22) Student Misconceptions and Concerns 1. Students often regard the cytosol as little more than a watery fluid that suspends the organelles. The diverse functions of thin, thick, and intermediate filaments are rarely appreciated before college. Module 4.17 describes the dynamic and diverse functions of the cytoskeleton. (4.17) 2. Students often think that the cilia on the cells lining our trachea function like a comb, removing debris from the air. Except in cases of disease or damage, these respiratory cilia are covered by mucus. Cilia do not reach the air to comb it free of debris. Instead, these cilia sweep dirty mucus up our respiratory tracts to be expelled or swallowed. (4.18) 3. The structure and functions of the extracellular matrix (ECM) are closely associated with the cells that it contacts. Students might suspect that like roots from a tree, cells are anchored to the matrix indefinitely. However, some cells can detach from the ECM and migrate great distances, often following molecular trails (such as fibronectin and laminin) that direct them along the journey. (4.20) Teaching Tips 1. Analogies between the infrastructure of human buildings and the cytoskeleton are limited by the dynamic nature of the cytoskeleton. Few human structures have a structural framework that is routinely constructed, deconstructed, and then reconstructed in a new configuration on a regular basis. (Tents are often constructed, deconstructed, and then reconstructed repeatedly, but typically rely upon the same basic design.) Thus, caution is especially warranted when using such analogies. (4.17) 2. Students might enjoy this brief class activity. Have everyone in the class clear their throats at the same time. Wait a few seconds. Have them notice that after clearing, they swallowed. The mucus that trapped debris is swept up the trachea by cilia. When we clear our throats, this dirty mucus is disposed of down our esophagus and among the strong acids of our stomach! (4.18) 3. Primary ciliary dyskinesia results in nonmotile cilia. Module 4.19 describes infertility in males due to immotile sperm. Challenge your students to suggest reasons why this same disease might reduce fertility in an affected woman. (In the oviduct, cilia convey the egg along the oviduct toward the uterus.) (4.19) 4. The extracellular matrix forms a significant structural component of many connective tissues, including cartilage and bone. Many of the properties of cartilage and bone are directly related to the large quantities of material sandwiched between the bone (osteocyte) and cartilage (chondrocyte) cells. (4.20) 5. Tight junctions form a seal that prevents the movement of fluids past the region of the junction. Functionally, this is similar to the lengthy zipper-like seal at the top of plastic food storage bags. (4.21) 6. Consider challenging your students to suggest analogies to the structure and function of plasmodesmata. Critically examining the similarities and differences of their suggestions requires a careful understanding of structure and function. (4.22)

Chapter 4 A Tour of the Cell 29 7. The text in Module 4.22 compares the fibers-in-a-matrix construction of a plant cell wall to fiberglass. Students familiar with highway construction or the pouring of concrete might also be familiar with the frequent use of reinforcing bar (rebar) to similarly reinforce concrete. (4.22) Functional Categories of Cell Structures (4.23) Student Misconceptions and Concerns 1. Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.23 might be the best place to start when approaching this chapter. Students might best comprehend the content in Chapter 4 by reviewing the categories of organelles and related functions in Table 4.23 and referring to it regularly as the chapter is studied and/or discussed. (4.23) Teaching Tips 1. The chapter ends noting the three fundamental features of all organisms. Challenge students to explain if viruses are organisms according to this definition. (4.23) 2. Some students might benefit by creating a concept map integrating the information in Table 4.23. Such a map would note the components of a cell interconnected by lines and relationships between these cellular components. Such techniques may also be beneficial in later chapters, depending upon the learning style of particular students. (4.23)