© 2015 Pearson Education, Inc.

Introduction to the Cell
© 2015 Pearson Education, Inc. 2

4.3 Prokaryotic cells are structurally simpler than eukaryotic cells
Bacteria and archaea are prokaryotic cells. All other forms of life are composed of eukaryotic cells. Eukaryotic cells are distinguished by having a membrane-enclosed nucleus and many membrane-enclosed organelles that perform specific functions. Prokaryotic cells are smaller and simpler in structure. 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. 3

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, and ribosomes, tiny structures that make proteins according to instructions from the genes. 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. 4

The inside of both types of cells is called the cytoplasm. However, in eukaryotic cells, this term refers only to the region between the nucleus and the plasma membrane. 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. 5

In a prokaryotic cell, the DNA is coiled into a region called the nucleoid (nucleus-like) and no membrane surrounds the DNA. 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. 6

Outside the plasma membrane of most prokaryotes is a fairly rigid, chemically complex cell wall, which protects the cell and helps maintain its shape. Some prokaryotes have surface projections. Short projections help attach prokaryotes to each other or their substrate. Longer projections called flagella (singular, flagellum) propel a prokaryotic cell through its liquid 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. 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

A colorized TEM of the bacterium Escherichia coli
Figure 4.3-0 Fimbriae Ribosomes Nucleoid Plasma membrane Cell wall Bacterial chromosome Capsule A colorized TEM of the bacterium Escherichia coli A typical rod-shaped bacterium Figure A diagram (left) and electron micrograph (right) of a typical prokaryotic cell Flagella

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. 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. 9

The structures and organelles of eukaryotic cells perform four basic functions. The nucleus and ribosomes are involved in the genetic control of the cell. The endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and peroxisomes are involved in the manufacture, distribution, and breakdown of molecules. 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

Mitochondria in all cells and chloroplasts in plant cells are involved in energy processing. Structural support, movement, and communication between cells are functions of the cytoskeleton, plasma membrane, and cell wall. 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

The internal membranes of eukaryotic cells partition it into compartments. Cellular metabolism, the many chemical activities of cells, occurs within organelles. 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

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. 13

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. 14

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

4.5 The nucleus contains the cell’s genetic instructions
contains most of 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 diffuse 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. 18

The double membrane nuclearenvelope has pores that regulate the entry and exit of large molecules and connect 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. 19

The nucleolus is a prominent structure in the nucleus and 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. 20

Endoplasmic reticulum Chromatin Pore
Figure 4.5 Nucleolus Nuclear envelope Endoplasmic reticulum Chromatin Pore Figure 4.5 A diagram with a superimposed TEM of the nucleus Ribosome

4.6 Ribosomes make proteins for use in the cell and 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. Cells that make a lot of proteins have a large number of ribosomes. 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. 22

4.6 Ribosomes make proteins for use in the cell and 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. 23

Endoplasmic reticulum
Figure 4.6 Rough ER Bound ribosome Endoplasmic reticulum Protein Figure 4.6 The locations and structure of ribosomes Ribosome Free ribosome mRNA

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. 26

Many of these organelles interact in the synthesis, distribution, storage, and export of molecules. 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. 27

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. 28

The largest component of the endomembrane system is the endoplasmic reticulum (ER), an extensive network of flattened sacs and tubules. 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. 29

4.8 The endoplasmic reticulum is a biosynthetic workshop
There are two kinds of endoplasmic reticulum, which differ in structure and function. SmoothER lacks attached ribosomes. RoughERhas 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  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. 30

Rough ER Smooth ER Ribosomes Rough ER Smooth ER Figure 4.8a
Figure 4.8a A diagram and TEM of smooth and rough endoplasmic reticulum Rough ER Smooth ER

Transport vesicle buds off
Figure 4.8b Transport vesicle buds off 4 Secretory protein inside transport vesicle mRNA Bound ribosome 3 1 Sugar chain Figure 4.8b Synthesis and packaging of a secretory protein by the rough ER Glycoprotein 2 Growing polypeptide Rough ER

Smooth ER is involved in a variety of metabolic processes, including 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. 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. 33

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. 34

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 serves as a receiving dock for transport vesicles produced by the ER. 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. 35

4.9 The Golgi apparatus modifies, sorts, and ships cell products
Products of the ER are modified as a Golgi sac progresses through the stack. 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. © 2012 Pearson Education, Inc. 36

“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 made by rough ER and processed in the Golgi apparatus 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. 38

4.10 Lysosomes are digestive compartments within a cell
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. 39

Vesicle containing damaged mitochondrion Digestion
Figure 4.10b-3 Lysosome Vesicle containing damaged mitochondrion Digestion Figure 4.10b-3 Lysosome fusing with a vesicle containing a damaged organelle and digesting and recycling its contents (step 3)

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, 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. 41

Contractile vacuoles Nucleus Figure 4.11a
Figure 4.11a Contractile vacuoles in Paramecium, a single-celled organism

Central vacuole Chloroplast Nucleus Figure 4.11b
Figure 4.11b Central vacuole in a plant cell

4.12 A review of the structures involved in manufacturing and breakdown
The following figure summarizes the relationships among the major organelles of the endomembrane system. 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 students to suggest two changes in cell structure associated with high exposure to drugs or harmful compounds. These were discussed in separate modules. (Answer: increased amounts of SER and abundant peroxisomes.) © 2015 Pearson Education, Inc. 44

Nucleus Nuclear envelope Smooth ER Rough ER Golgi apparatus
Figure 4.12 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. 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 students to suggest two changes in cell structure associated with high exposure to drugs or harmful compounds. These were discussed in separate modules. (Answer: increased amounts of SER and abundant peroxisomes.) © 2015 Pearson Education, Inc. 46

Energy-Converting Organelles

4.13 Mitochondria harvest chemical energy from food
Mitochondria are organelles that carry out cellular respiration in nearly all eukaryotic cells. Cellular respiration converts the chemical energy in foods to chemical energy in ATP (adenosine triphosphate). 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. 48

Mitochondria have two internal compartments. The intermembrane space is the narrow region between the inner and outer membranes. The mitochondrialmatrix contains the mitochondrial DNA, ribosomes, and many enzymes that catalyze some of the reactions of cellular respiration. 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. 49

Folds of the inner mitochondrial membrane, called cristae, increase the membrane’s surface area, enhancing the mitochondrion’s ability to produce 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. 50

Mitochondrion Intermembrane space Outer membrane Inner membrane Crista
Figure 4.13 Mitochondrion Intermembrane space Outer membrane Inner membrane Figure 4.13 The mitochondrion Crista Matrix

4.14 Chloroplasts convert solar energy to chemical energy
Photosynthesis is the conversion of light energy from the sun to the chemical energy of sugar molecules. Chloroplasts are the photosynthesizing organelles of plants and algae. 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. © 2015 Pearson Education, Inc. 52

4.14 Chloroplasts convert solar energy to chemical energy
Chloroplasts are partitioned into compartments. Between the outer and inner membrane is a thin intermembrane space. Inside the inner membrane is a thick fluid called stroma, which contains the chloroplast DNA, ribosomes, many enzymes, and a network of interconnected sacs called thylakoids, where green chlorophyll molecules trap solar energy. In some regions, thylakoids are stacked like poker chips. Each stack is called a granum. 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. © 2015 Pearson Education, Inc. 53

Inner and outer membranes
Figure 4.14 Chloroplast Granum Figure 4.14 The chloroplast Stroma Thylakoid Inner and outer membranes

4.15 EVOLUTION CONNECTION: Mitochondria and chloroplasts evolved by endosymbiosis
Mitochondria and chloroplasts contain DNA and ribosomes. The structure of this DNA and these ribosomes is very similar to that found in prokaryotic cells. 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. © 2015 Pearson Education, Inc. 55

4.15 EVOLUTION CONNECTION: Mitochondria and chloroplasts evolved by endosymbiosis
The endosymbionttheory states that mitochondria and chloroplasts were formerly small prokaryotes and they began living within larger cells. 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. © 2015 Pearson Education, Inc. 56

Endoplasmic reticulum Nucleus
Figure 4.15 Endoplasmic reticulum Nucleus Engulfing of oxygen- using prokaryote Ancestor of eukaryotic cells (host cell) Mitochondrion Engulfing of photosynthetic prokaryote At least one cell Nonphotosynthetic eukaryote Figure Endosymbiotic origin of mitochondria and chloroplasts (step 3) Mitochondrion Chloroplast Photosynthetic eukaryote

The Cytoskeleton and Cell Surfaces

4.16 The cell’s internal skeleton helps organize its structure and activities
Cells contain a network of protein fibers, called the cytoskeleton, which organize the structures and activities of the cell. 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. © 2015 Pearson Education, Inc. 59

Microtubules (made of tubulin) shape and support the cell and act as tracks along which organelles equipped with motor proteins move. In animal cells, microtubules grow out from a region near the nucleus called the centrosome, which contains a pair of centrioles, each composed of a ring of microtubules. 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. © 2015 Pearson Education, Inc. 60

Intermediatefilaments are found in the cells of most animals, reinforce cell shape and anchor some organelles, and are often more permanent fixtures in the cell. 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. © 2015 Pearson Education, Inc. 61

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. © 2015 Pearson Education, Inc. 62

Intermediate filament Microfilament
Figure Nucleus Nucleus Figure Three types of fibers of the cytoskeleton 10 nm 7 nm 25 nm Intermediate filament Microfilament Microtubule

4.17 SCIENTIFIC THINKING: Scientists discovered the cytoskeleton using the tools of biochemistry and microscopy In the 1940s, biochemists first isolated and identified the proteins actin and myosin from muscle cells. In 1954, scientists, using newly developed techniques of microscopy, established how filaments of actin and myosin interact in muscle contraction. In the next decade, researchers identified actin filaments in all types of cells. Teaching Tips  Challenge students to speculate on how increasing computer technologies have helped us better understand the structure and functions of the cytoskeleton. © 2015 Pearson Education, Inc. 64

4.17 SCIENTIFIC THINKING: Scientists discovered the cytoskeleton using the tools of biochemistry and microscopy In the 1970s, scientists were able to visualize actin filaments using fluorescent tags and in living cells. In the 1980s, biologists were able to record the changing architecture of the cytoskeleton. Teaching Tips  Challenge students to speculate on how increasing computer technologies have helped us better understand the structure and functions of the cytoskeleton. © 2015 Pearson Education, Inc. 65

Figure 4.17 Figure 4.17 A fluorescence micrograph of the cytoskeleton (microtubules are green, microfilaments are red)

4.18 Cilia and flagella move when microtubules bend
The short, numerous appendages that propel protists such as Paramecium are called cilia (singular, cilium). Other protists may move using flagella, which are longer than cilia and usually limited to one or a few per cell. Some cells of multicellular organisms also have cilia or flagella. 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.) © 2015 Pearson Education, Inc. 67

Figure 4.18b Figure 4.18b Undulating flagellum on a human sperm cell Flagellum

A flagellum, longer than cilia, propels a cell by an undulating, whiplike motion. Cilia work more like the oars of a boat. Although differences exist, flagella and cilia have a common structure and mechanism of movement. 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.) © 2015 Pearson Education, Inc. 69

Both flagella and cilia are composed of microtubules wrapped in an extension of the plasma membrane. In nearly all eukaryotic cilia and flagella, a ring of nine microtubule doublets surrounds a central pair of microtubules. This arrangement is called the 9  2 pattern. The microtubule assembly is anchored in a basal body with nine microtubule triplets arranged in a ring. 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.) © 2015 Pearson Education, Inc. 70

Outer microtubule doublet
Figure 4.18c-0 Outer microtubule doublet Central microtubules Cross-linking proteins Motor proteins (dyneins) Figure 4.18c-0 Internal structure of a eukaryotic flagellum or cilium Plasma membrane

Cilia and flagella move by bending motor proteins called dynein feet. These feet attach to and exert a sliding force on an adjacent doublet. This “walking” causes the microtubules to bend. 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.) © 2015 Pearson Education, Inc. 72

4.19 The extracellular matrix of animal cells functions in support and regulation
Animal cells synthesize and secrete an elaborate extracellularmatrix (ECM), which helps hold cells together in tissues and 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! © 2015 Pearson Education, Inc. 73

4.19 The extracellular matrix of animal cells functions in support and regulation
The ECM may attach to the cell through other glycoproteins that then bind to membrane proteins called integrins. Integrins span the membrane and attach on the other side to proteins connected to microfilaments of the cytoskeleton. 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! © 2015 Pearson Education, Inc. 74

Glycoprotein complex with long polysaccharide EXTRACELLULAR FLUID
Figure 4.19 Glycoprotein complex with long polysaccharide EXTRACELLULAR FLUID Collagen fiber Connecting glycoprotein Integrin Plasma membrane Figure 4.19 The extracellular matrix (ECM) of an animal cell CYTOPLASM Microfilaments of cytoskeleton

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. © 2015 Pearson Education, Inc. 76

Tight junctions prevent fluid from moving across a layer of cells
Figure 4.20 Tight junctions prevent fluid from moving across a layer of cells Tight junction Anchoring junction Gap junction Figure 4.20 Three types of cell junctions in animal tissues Plasma membranes of adjacent cells Ions or small molecules Extracellular matrix

4.21 Cell walls enclose and support plant cells
A plant cell, but not an animal cell, has a rigid cellwall 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! © 2015 Pearson Education, Inc. 78

Plant cell walls Vacuole Plasmodesmata Primary cell wall
Figure 4.21 Plant cell walls Vacuole Plasmodesmata Primary cell wall Secondary cell wall Figure 4.21 Plant cell walls and plasmodesmata Plasma membrane Cytosol

4.22 Review: Eukaryotic cell structures can be grouped on the basis of four main functions
Eukaryotic cell structures 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. Teaching Tips  Some students might benefit by creating a concept map integrating the information in Table 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. © 2015 Pearson Education, Inc. 80

Table Table Eukaryotic cell structures and functions

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