Introduction to the Cell

Introduction to the Cell
Figure Has our knowledge of cells grown? (photo: nuclei and cytoskeletons)

4.1 Microscopes reveal the world of the cell
Using microscopes, scientists studied microorganisms, animal and plant cells, and some structures within cells. In the 1800s, these studies led to cell theory, which states that all living things are composed of cells and all cells come from other cells. Light microscope Scanning Electron Microscope Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed.  Students often 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. The Active Lecture Tip that follows suggests another related exercise. Teaching Tips  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.  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 an 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 a 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! Active Lecture Tips  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). Transmission Electron Micrograph © 2015 Pearson Education, Inc. 2

Figure 4.1e-0 10 m Human height 1 m Length of some nerve and muscle cells 100 mm (10 cm) Chicken egg Unaided eye 10 mm (1 cm) Frog egg 1 mm Paramecium Human egg 100 μm Most plant and animal cells Light microscope 10 μm Nucleus Most bacteria Mitochondrion 1 μm Figure 4.1e-0 The size range of cells and related objects Electron microscope Smallest bacteria 100 nm Viruses Ribosome 10 nm Proteins Lipids 1 nm Small molecules 0.1 nm Atoms

4.2 The small size of cells relates to the need to exchange materials across the plasma membrane
Cell size must be large enough to house DNA, proteins, and structures needed to survive and reproduce, but remain small enough to allow for a surface-to- volume ratio that will allow adequate exchange with the environment. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed.  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.) Teaching Tips  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 to a micron: 1,000 to 1.  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.  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 self-healing. That the properties of phospholipids emerge from their organization is worth emphasizing to students.  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.) © 2015 Pearson Education, Inc. 4

The plasma membrane forms a flexible semi- permeable boundary between the living cell and its surroundings. Phospholipids form a two-layer sheet called a phospholipid bilayer. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed.  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.) Teaching Tips  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 to a micron: 1,000 to 1.  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.  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 self-healing. That the properties of phospholipids emerge from their organization is worth emphasizing to students.  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.) © 2015 Pearson Education, Inc. 5

Membrane proteins are embedded in the lipid bilayer. Some are channels that shield ions and other hydrophilic molecules Other proteins serve as pumps, moving molecules into or out of the cell. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed.  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.) Teaching Tips  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 to a micron: 1,000 to 1.  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.  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 self-healing. That the properties of phospholipids emerge from their organization is worth emphasizing to students.  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.) © 2015 Pearson Education, Inc. 6

4.3 Prokaryotic cells vs. eukaryotic cells
Prokaryotic cells are small and simpler in structure. Bacteria and archaea are prokaryotic cells. Eukaryotic cells have a membrane-enclosed nucleus and many membrane-enclosed organelles that perform specific functions. All other forms of life are composed of eukaryotic cells. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  A visual comparison of prokaryotic and eukaryotic cells, such as that found in Figures 1.3 and 4.1E, 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.  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 (the answer is about 1,000).  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 as 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).  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 © 2015 Pearson Education, Inc. 7

4.3 Prokaryotic cells vs. eukaryotic cells
Both prokaryotic and eukaryotic cells have: a plasma membrane, an interior filled with a thick, jellylike fluid called the cytosol, one or more chromosomes, which carry genes made of DNA, ribosomes, tiny structures that make proteins according to instructions from the genes. cytoplasm, the interior environment of a cell Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  A visual comparison of prokaryotic and eukaryotic cells, such as that found in Figures 1.3 and 4.1E, 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.  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 (the answer is about 1,000).  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 as 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).  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 © 2015 Pearson Education, Inc. 8

4.3 Prokaryotic cells In a prokaryotic cell,
the DNA is coiled into a nucleoid no membrane surrounds the DNA. outside the plasma membrane of most prokaryotes is a fairly rigid, chemically complex cell wall There may be surface projections Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  A visual comparison of prokaryotic and eukaryotic cells, such as that found in Figures 1.3 and 4.1E, 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.  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 (the answer is about 1,000).  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 as 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).  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 © 2015 Pearson Education, Inc. 9

4.4 Eukaryotic cells are partitioned into functional compartments
A eukaryotic cell contains a membrane-enclosed nucleus and various other organelles (“little organs”), which perform specific functions in the cell. Eukaryotic organelles can be grouped on the basis of four functions: genetic control, manufacturing, distribution, and breakdown of materials, energy processing, and structural support, movement, and intercellular communication. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  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 cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. © 2015 Pearson Education, Inc. 10

Almost all of the organelles and other structures of animals cells are present in plant cells. A few exceptions exist. Lysosomes and centrosomes containing centrioles are not found in plant cells. Only the sperm cells of a few plant species have flagella. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  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 cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. © 2015 Pearson Education, Inc. 11

Plant but not animal cells have a rigid cell wall that contains cellulose, plasmodesmata, cytoplasmic channels through cell walls that connect adjacent cells, chloroplasts, where photosynthesis occurs, and a central vacuole, a compartment that stores water and a variety of chemicals. Student Misconceptions and Concerns  Students can easily feel overwhelmed by the large numbers of structures and related functions in this chapter. For such students, Module 4.22 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 4.22 and referring to it regularly as the chapter is studied and/or discussed. Teaching Tips  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 cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. © 2015 Pearson Education, Inc. 12

Rough endoplasmic reticulum Chromatin CYTOSKELETON Microtubule
Figure 4.4a NUCLEUS Nuclear envelope Nucleolus Rough endoplasmic reticulum Chromatin CYTOSKELETON Microtubule Microfilament Intermediate filament Ribosomes Peroxisome Smooth endoplasmic reticulum Plasma membrane Figure 4.4a An animal cell Golgi apparatus Centrosome with pair of centrioles Lysosome Mitochondrion

Rough endoplasmic reticulum Nuclear envelope
Figure 4.4b NUCLEUS Rough endoplasmic reticulum Nuclear envelope Smooth endoplasmic reticulum Nucleolus Chromatin Mitochondrion CYTOSKELETON Microfilament Microtubule Central vacuole Ribosomes Chloroplast Cell wall Figure 4.4b A plant cell Plasmodesma Cell wall of adjacent cell Golgi apparatus Peroxisome Plasma membrane

THE NUCLEUS AND RIBOSOMES
© 2015 Pearson Education, Inc. 16

4.5 The nucleus contains the cell’s genetic instructions
contains the cell’s DNA and controls the cell’s activities by directing protein synthesis by making messenger RNA (mRNA). DNA is associated with many proteins and is organized into structures called chromosomes. When a cell is not dividing, this complex of proteins and DNA, called chromatin, appears as a scattered mass within the nucleus. Student Misconceptions and Concerns  Students often enter college with misunderstandings about the interrelationship between DNA, a chromosome, and a replicated chromosome often photographed just prior to mitosis or meiosis. Consider specifically distinguishing between these important cellular components early in your discussions of the nucleus.  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. Teaching Tips  Not all human cells have 46 chromosomes per human cell. Some of your more knowledgeable students may like to guess the exceptions. These include gametes and adult red blood cells in mammals.  If you wish to continue the text’s factory analogy, nuclear pores might be said to function like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.  Noting the main flow of genetic information on the board as DNA to RNA to 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.  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. One advantage is 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 (perhaps like the U.S. Constitution).  Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, and 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.) Active Lecture Tips  See the Activity, Students Perform a Protein Synthesis Play on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 17

The double membrane surrounding the nucleus is called the nuclear envelope has pores that regulate the entry and exit of large molecules connects with the cell’s network of membranes called the endoplasmic reticulum. Student Misconceptions and Concerns  Students often enter college with misunderstandings about the interrelationship between DNA, a chromosome, and a replicated chromosome often photographed just prior to mitosis or meiosis. Consider specifically distinguishing between these important cellular components early in your discussions of the nucleus.  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. Teaching Tips  Not all human cells have 46 chromosomes per human cell. Some of your more knowledgeable students may like to guess the exceptions. These include gametes and adult red blood cells in mammals.  If you wish to continue the text’s factory analogy, nuclear pores might be said to function like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.  Noting the main flow of genetic information on the board as DNA to RNA to 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.  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. One advantage is 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 (perhaps like the U.S. Constitution).  Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, and 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.) Active Lecture Tips  See the Activity Students Perform a Protein Synthesis Play on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 18

The nucleolus is the site of ribosomal RNA (rRNA) synthesis. Student Misconceptions and Concerns  Students often enter college with misunderstandings about the interrelationship between DNA, a chromosome, and a replicated chromosome often photographed just prior to mitosis or meiosis. Consider specifically distinguishing between these important cellular components early in your discussions of the nucleus.  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. Teaching Tips  Not all human cells have 46 chromosomes per human cell. Some of your more knowledgeable students may like to guess the exceptions. These include gametes and adult red blood cells in mammals.  If you wish to continue the text’s factory analogy, nuclear pores might be said to function like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.  Noting the main flow of genetic information on the board as DNA to RNA to 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.  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. One advantage is 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 (perhaps like the U.S. Constitution).  Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, and 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.) Active Lecture Tips  See the Activity Students Perform a Protein Synthesis Play on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 19

4.6 Ribosomes make proteins for use in the cell and for export
Ribosomes are involved in the cell’s protein synthesis. Ribosomes are the cellular components that use instructions from the nucleus, written in mRNA, to build proteins. Student Misconceptions and Concerns  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. Teaching Tips  If you wish to continue the text’s factory analogy, nuclear pores might be said to function like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.  Noting the main flow of genetic information on the board as DNA to RNA to 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.  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. One advantage is 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 (perhaps like the U.S. Constitution).  Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, and 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.) Active Lecture Tips  See the Activity Students Perform a Protein Synthesis Play on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 20

4.6 Ribosomes make proteins for use in the cell and for export
Some ribosomes are free ribosomes; others are bound. Free ribosomes are suspended in the cytosol. Bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope. Student Misconceptions and Concerns  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. Teaching Tips  If you wish to continue the text’s factory analogy, nuclear pores might be said to function like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.  Noting the main flow of genetic information on the board as DNA to RNA to 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.  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. One advantage is 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 (perhaps like the U.S. Constitution).  Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, and 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.) Active Lecture Tips  See the Activity Students Perform a Protein Synthesis Play on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 21

THE ENDOMEMBRANE SYSTEM

4.7 Many organelles are connected in the endomembrane system
Many of the membranes within a eukaryotic cell are part of the endomembrane system. Some of these membranes are physically connected, and others are linked when tiny vesicles (sacs made of membrane) transfer membrane segments between them. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  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. © 2015 Pearson Education, Inc. 23

Many of these organelles interact in the synthesis, distribution, storage, and export of molecules. The endomembrane system includes the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and plasma membrane. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  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. © 2015 Pearson Education, Inc. 24

The largest component of the endomembrane system is the endoplasmic reticulum (ER), an extensive network of flattened sacs and tubules. There are two kinds of endoplasmic reticulum, which differ in structure and function. Smooth ER lacks attached ribosomes. Rough ER has bound ribosomes that stud the outer surface of the membrane. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  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. © 2015 Pearson Education, Inc. 25

4.8 The endoplasmic reticulum is a biosynthetic workshop
Smooth ER is involved in a variety of metabolic processes the production of enzymes important in the synthesis of lipids, oils, phospholipids, and steroids, the production of enzymes that help process drugs, alcohol, and other potentially harmful substances, and the storage of calcium ions. Rough ER makes additional membrane for itself and secretory proteins. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  Students often learn that a human body can build up a tolerance to a drug. Here, in Module 4.8, students 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 the development of drug tolerance. © 2015 Pearson Education, Inc. 27

4.9 The Golgi apparatus modifies, sorts, and ships cell products
The Golgi apparatus serves as a molecular warehouse and processing station for products manufactured by the ER. Products travel in transport vesicles from the ER to the Golgi apparatus. One side of the Golgi stack acts as a receiving dock. Products of the ER are modified in the Golgi stacks. The “shipping” side of the Golgi functions as a depot, where products in vesicles bud off and travel to other sites. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  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.  Some people think that the Golgi apparatus looks like a stack of pita bread. Active Lecture Tips  See the Activity Customize Your Auto Like Proteins Are Customized in the Cell on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 28

“Receiving” side of Golgi apparatus
Figure 4.9 “Receiving” side of Golgi apparatus Transport vesicle from the ER 1 2 3 Golgi apparatus 4 Transport vesicle from the Golgi Figure 4.9 The Golgi apparatus receiving, processing, and shipping products “Shipping” side of Golgi apparatus

4.10 Lysosomes are digestive compartments within a cell
A lysosome is a membrane-enclosed sac of digestive enzymes fuse with food vacuoles and digest food, destroy bacteria engulfed by white blood cells, or fuse with other vesicles containing damaged organelles or other materials to be recycled within a cell. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  As noted in Module 4.10, 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.” © 2015 Pearson Education, Inc. 30

4.11 Vacuoles function in the general maintenance of the cell
Vacuoles are large vesicles that have a variety of functions. Some protists have contractile vacuoles, which help to eliminate water from the protist. In plants, vacuoles may have digestive functions, store water, nutrients contain pigments, or contain poisons that protect the plant. Student Misconceptions and Concerns  Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.7–4.12 introduce the primary organelles in the general 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 can help students to remember the function of individual organelles as they recall the steps of the sequence.  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. Teaching Tips  Challenge your students to identify animal cell organelles other than mitochondria and chloroplasts that are not involved in the synthesis of proteins. (Lysosomes, vacuoles, and peroxisomes are also not involved in protein synthesis.) © 2015 Pearson Education, Inc. 32

Nucleus Nuclear envelope Smooth ER Rough ER Golgi apparatus
The following figure summarizes the relationships among the major organelles of the endomembrane system. Nucleus Nuclear envelope Smooth ER Rough ER Golgi apparatus Transport vesicle Plasma membrane Figure 4.12 Connections among the organelles of the endomembrane system Lysosome Transport vesicle

4.12 A review of the structures involved in manufacturing and breakdown
Peroxisomes are metabolic compartments that do not originate from the endomembrane system. How they are related to other organelles is still unknown. Some peroxisomes break down fatty acids to be used as cellular fuel.

ENERGY-CONVERTING ORGANELLES

4.13 Mitochondria harvest chemical energy from food
Mitochondria are organelles that carry out cellular respiration eukaryotic cells. converts the chemical energy in foods to chemical energy in ATP. Student Misconceptions and Concerns  Students often mistakenly think that chloroplasts are a substitute for mitochondria in plant cells. They might think that cells either have mitochondria or have chloroplasts. You might challenge this thinking by asking how plant cells generate ATP at night. Teaching Tips  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.  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. This makes sense when we consider that the outer membranes correspond to the plasma membrane of the eukaryotic cells that originally wrapped the free-living prokaryotes during endocytosis. Biology makes sense in light of evolution. Active Lecture Tips  See the Activity Energy Conversion and iPods on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.  See the Activity Phone Batteries and Cellular Energy on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. © 2015 Pearson Education, Inc. 36

4.14 Chloroplasts convert solar energy to chemical energy
Chloroplasts are the photosynthesizing organelles of plants and algae. conversion of light energy from the sun to the chemical energy of sugar molecules. Student Misconceptions and Concerns  Students often mistakenly think that chloroplasts are a substitute for mitochondria in plant cells. They might think that cells either have mitochondria or have chloroplasts. You might challenge this thinking by asking how plant cells generate ATP at night. Teaching Tips  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. This makes sense when we consider that the outer membranes correspond to the plasma membrane of the eukaryotic cells that originally wrapped the free-living prokaryotes during endocytosis. Biology makes sense in light of evolution. 37

4.15 EVOLUTION CONNECTION: Mitochondria and chloroplasts evolved by endosymbiosis
The endosymbiosis theory states that mitochondria and chloroplasts were formerly small prokaryotes they began living within larger cells. they both contain DNA and ribosomes Student Misconceptions and Concerns  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. Teaching Tips  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. This makes sense when we consider that the outer membranes correspond to the plasma membrane of the eukaryotic cells that originally wrapped the free-living prokaryotes during endocytosis. Biology makes sense in light of evolution.  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. Active Lecture Tips  See the Activity A Chance Discovery of Endosymbiosis? A Case Study on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. 38

The Cytoskeleton and Cell Surfaces

4.16 The cell’s internal skeleton
Cells contain a network of protein fibers, called the cytoskeleton. Microtubules: straight, hallow tubes made of tubulin, shape and support the cell, act as tracks which help organelles move Intermediate filaments: found in most animal cells, reinforce cell shape and anchor some organelles Microfilaments (actin filaments): support the cell’s shape and are involved in motility Student Misconceptions and Concerns  Students often regard the fluid of the cytoplasm as little more than cell broth, a watery fluid that suspends the organelles. The diverse functions of thin, thick, and intermediate filaments are rarely appreciated before college. Module 4.16 describes the dynamic and diverse functions of the cytoskeleton. Teaching Tips  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. Active Lecture Tips  See the Activity Using Ropes to Demonstrate the Pulling Forces of Actin and Myosin on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. 40

4.18 Cilia and flagella move when microtubules bend
A flagellum propels a cell by an undulating, whiplike motion. Cilia work more like the oars of a boat. Both have a common structure and mechanism of movement. Both are composed of microtubules wrapped in an extension of the plasma membrane. Student Misconceptions and Concerns  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. Teaching Tips  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!  Primary ciliary dyskinesia results in nonmotile cilia. Module 4.18 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.) 41

4.19 The extracellular matrix of animal cells functions in support and regulation
Animal cells synthesize and secrete an elaborate extracellular matrix (ECM) helps hold cells together in tissues protects and supports the plasma membrane. Student Misconceptions and Concerns  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 their journey. Teaching Tips  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. For example, elastin fibers in the matrix of elastic cartilage allow our ears to spring back to shape after being bent! 42

4.20 Three types of cell junctions are found in animal tissues
Adjacent cells adhere, interact, and communicate through specialized junctions between them. Tight junctions prevent leakage of fluid across a layer of epithelial cells. Anchoring junctions fasten cells together into sheets. Gap junctions are channels that allow small molecules to flow through protein-lined pores between cells. Teaching Tips  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 commonly found along the top of plastic storage bags. 43

4.21 Cell walls enclose and support plant cells
A plant cell has a rigid cell wall that protects and provides skeletal support that helps keep the plant upright and is primarily composed of cellulose. Plant cells have cell junctions called plasmodesmata that allow plants tissues to share water, nourishment, and chemical messages. Teaching Tips  Consider challenging your students to suggest analogies to the structure and function of plasmodesmata (perhaps air ducts between offices in a building). Consider discussing the advantages of interconnected cytoplasm.  The text in Module 4.21 compares the fibers-in-a-matrix construction of a plant cell wall to steel-reinforced concrete. Students familiar with highway construction or the pouring of concrete might have noticed this frequent use of reinforcing bar (rebar) to reinforce concrete. This fibers-in-a-matrix technique is also found in fiberglass and was the basis for adding animal hair to plaster long ago! 44

Introduction to the Cell

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