1. Tour of the Eukaryotic Cell
Chapter 4:
Tour of the Eukaryotic Cell
© 2012 Pearson Education, Inc. 1

2. Table 4.22
Table 4.22 Eukaryotic Cell Structures and Functions 2

3. Eukaryotic cells have membrane-bound nucleus and organelles
Nucleus: membrane-bound compartment for DNA
Organelles: cell structures each wrapped with own membrane
Eukaryotes include: protists, plants, animals, fungi
Animal vs plants:
Lysosomes, centrioles, cilia and flagella are not found in plant cells.
Plant but not animal cells have
a rigid cell wall,
chloroplasts, and
a central vacuole
Plasmodesmata (cell to cell passageways)
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. 3

4. Each organelle has specific function
Why So Many Organelles?
Each organelle has specific function
Increases efficiency of cell function
Allows for opposing cellular functions to occur in different compartments
Allows eukaryotic cells to be larger!!
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
Teaching Tips
1. 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, some of the cells that produce gametes, and adult red blood cells in mammals.
2. If you wish to continue the text’s factory analogy, nuclear pores might be said to function most like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.
3. 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.
4. If you want to challenge your students further, ask them to consider the adaptive advantage of using mRNA to direct the production of proteins instead of using DNA directly. 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).
5. Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, yet DNA and RNA only specifically dictate the generation of proteins (and more copies of DNA and RNA). How is the production of specific types of carbohydrates and lipids in cells controlled? (Answer: primarily by the specific properties of enzymes.)
© 2012 Pearson Education, Inc. 4

5. Smooth endoplasmic reticulum Rough endoplasmic reticulum NUCLEUS:
In animal cells but not plant cells:
Lysosomes
Centrioles
Flagella (in some plant sperm)
Smooth endoplasmic reticulum
Rough endoplasmic reticulum
NUCLEUS:
Nuclear envelope
Chromatin
Nucleolus
NOT IN MOST PLANT CELLS:
Centriole
Lysosome
Peroxisome
Figure 4.4A An animal cell
Ribosomes
Golgi apparatus
CYTOSKELETON:
Microtubule
Mitochondrion
Intermediate filament
Microfilament
Plasma membrane 5

6. Rough endoplasmic reticulum NUCLEUS: Nuclear envelope Chromatin
Figure 4.4B
Rough endoplasmic reticulum
NUCLEUS:
Nuclear envelope
Chromatin
Ribosomes
Nucleolus
Smooth endoplasmic reticulum
Golgi apparatus
NOT IN ANIMAL CELLS:
CYTOSKELETON:
Microtubule
Central vacuole
Intermediate filament
Chloroplast
Cell wall
Microfilament
Plasmodesma
Figure 4.4B A plant cell
Mitochondrion
Peroxisome
Plasma membrane
In plant cells but not animal cells:
Chloroplasts
Central vacuole
Cell wall
Plasmodesmata
Cell wall of adjacent cell 6

7. Cell structures support cell functions
Cell reproduction, carry out genetic instructions, make new proteins
Nucleus, nucleolus, ribosomes, centrioles
Synthesize and distribute new molecules, degrade and remove wastes
Endomembrane system
Smooth and rough ER, golgi, lysosomes, vacuoles, transport vesicles
Energy processing
Mitochondria and chloroplasts
Cell shape/support, movement, communication to outside world
Plasma membrane, cytoskeleton, extracellular matrix (animals), cell wall (plants)
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
Teaching Tips
1. 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, some of the cells that produce gametes, and adult red blood cells in mammals.
2. If you wish to continue the text’s factory analogy, nuclear pores might be said to function most like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.
3. 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.
4. If you want to challenge your students further, ask them to consider the adaptive advantage of using mRNA to direct the production of proteins instead of using DNA directly. 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).
5. Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, yet DNA and RNA only specifically dictate the generation of proteins (and more copies of DNA and RNA). How is the production of specific types of carbohydrates and lipids in cells controlled? (Answer: primarily by the specific properties of enzymes.)
© 2012 Pearson Education, Inc. 7

8. Cells Must Make New Cells and Proteins
© 2012 Pearson Education, Inc. 8

9. Reproduction, control center, protein synthesis
Nucleus - houses DNA
DNA + packing proteins = chromatin
nuclear envelope surrounds nucleus
Double membrane
Ribosomes built from rRNA and protein
Reads mRNA copy of gene and directs synthesis of protein
Free ribosomes - in cytoplasm - produce proteins that work in cytoplasm
Bound ribosomes - associated with rough ER - produce proteins that work within endomembrane system or outside cell
Nucleolus (nucleoli) - site of rRNA and ribosome production
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
Teaching Tips
1. 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, some of the cells that produce gametes, and adult red blood cells in mammals.
2. If you wish to continue the text’s factory analogy, nuclear pores might be said to function most like the door to the boss’s office. Through these doors, directions to the rest of the factory, including ribosomal components, are transmitted.
3. 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.
4. If you want to challenge your students further, ask them to consider the adaptive advantage of using mRNA to direct the production of proteins instead of using DNA directly. 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).
5. Consider challenging your students to explain how we can have four main types of organic molecules functioning in specific roles in our cells, yet DNA and RNA only specifically dictate the generation of proteins (and more copies of DNA and RNA). How is the production of specific types of carbohydrates and lipids in cells controlled? (Answer: primarily by the specific properties of enzymes.)
© 2012 Pearson Education, Inc. 9

10. Two membranes of nuclear envelope
Nucleus - houses DNA
DNA + packing proteins = chromatin
nuclear envelope surrounds nucleus
Double membrane
Nucleolus (nucleoli) - site of ribosome production
Nucleus
Two membranes of nuclear envelope
Chromatin
Nucleolus
Pore
Figure 4.5 Transmission electron micrograph (left) and diagram (right) of the nucleus
Endoplasmic reticulum
Ribosomes 10

11. Colorized TEM showing ER and ribosomes
Cytoplasm
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Ribosomes built from rRNA and protein
Reads mRNA copy of gene and directs synthesis of protein
Free ribosomes - in cytoplasm - produce proteins that work in cytoplasm
Bound ribosomes - associated with rough ER - produce proteins that work within endomembrane system or outside cell
Colorized TEM showing ER and ribosomes
Figure 4.6 The locations and structure of ribosomes
mRNA
Diagram of a ribosome
Protein 11

12. Cells Must Distribute Materials and Dispose of Wastes
© 2012 Pearson Education, Inc. 12

13. Endomembrane system
Synthesis, storage, export and destruction of molecules and wastes
Rough ER
‘studded’ with ribosomes
Proteins made here enter into ER to be transported or exported
Site of phospholipid production
Smooth ER
Synthesis of lipids, cholesterol
Detoxify drugs and wastes
Storage of calcium
Golgi apparatus
Shipping and receiving center for cell
Receives products from ER and routes them to appropriate location
Lysosomes
Hydrolytic enzymes; degrades macromolecules or old organelles
Vacuoles
Site of waste/nutrient storage
Plants - central vacuole
Protists - contractile vacuoles and food vacuoles
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
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.
© 2012 Pearson Education, Inc. 13

14. Rough ER Smooth ER ‘studded’ with ribosomes
Proteins made here enter into ER to be transported around or exported out of cell
Site of phospholipid production
Nuclear envelope
Smooth ER
Synthesis of lipids, cholesterol
Detoxify drugs and wastes
Storage of calcium
Ribosomes
Smooth ER
Rough ER
Figure 4.8A Smooth and rough endoplasmic reticulum 14

15. Transport vesicle buds off
Figure 4.8B
Transport vesicle buds off 4
Secretory protein inside trans- port vesicle
mRNA
Ribosome 3 1
Sugar chain
Figure 4.8B Synthesis and packaging of a secretory protein by the rough ER
Glycoprotein 2
Polypeptide
Rough ER 15

16. Golgi apparatus Shipping and receiving center for cell
Receives products from ER and routes them to appropriate location
“Receiving” side of Golgi apparatus
Golgi apparatus
Golgi apparatus 1
Transport vesicle from ER
Transport vesicle from the Golgi 2
Figure 4.9 The Golgi apparatus 3 4
“Shipping” side of Golgi apparatus 4 16

17. Lysosomes are digestive compartments
A lysosome contains digestive enzymes (produced by ER and transferred to lysosomes via Golgi and transport vesicles)
Lysosomes help digest food particles engulfed by a cell.
Lysosomes also help remove or recycle damaged parts of a cell.
Digestive enzymes
Lysosome
Digestion
Food vacuole
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
Teaching Tips
1. 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.
2. Some people think that the Golgi apparatus looks like a stack of pita bread.
Plasma membrane
Animation: Lysosome Formation
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18. Video: Paramecium Vacuole
Vacuoles
Contractile vacuoles
Nucleus
Vacuoles are large vesicles that have a variety of functions.
Some protists have contractile vacuoles that help to eliminate water from the protist.
In plants, vacuoles may
have digestive functions,
contain pigments, or
contain poisons that protect the plant.
Central vacuole
Chloroplast
Nucleus
Student Misconceptions and Concerns
1. 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.
2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking.
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).
Video: Paramecium Vacuole
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19. ENERGY-CONVERTING ORGANELLES
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20. Cells require energy!! Mitochondria - site of cellular respiration
Cellular respiration converts the chemical energy in foods to chemical energy in ATP (adenosine triphosphate).
Chloroplasts - site of photosynthesis
Mitochondria and chloroplasts have
DNA and
ribosomes.
The structure of this DNA and these ribosomes is very similar to that found in prokaryotic cells.
Endosymbiosis theory
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 they have chloroplasts. You might challenge this thinking by asking how plant cells generate ATP at night.
Teaching Tips
1. ATP functions in cells much like money functions in modern societies. Each holds value that can be generated in one place and spent in another. This analogy has been very helpful for many students.
2. Mitochondria and chloroplasts are each wrapped by multiple membranes. In both organelles, the innermost membranes are the sites of greatest molecular activity and the outer membranes have fewer significant functions. 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.
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21. Mitochondrion Outer membrane Intermembrane space Inner membrane
Figure 4.13
Mitochondrion
Outer membrane
Intermembrane space
Figure 4.13 The mitochondrion
Inner membrane
Cristae
Matrix 21

22. Inner and outer membranes Granum Stroma
Figure 4.14
Chloroplast
Inner and outer membranes
Granum
Stroma
Figure 4.14 The chloropast
Thylakoid 22

23. The Great ENERGY Circle of Life
sun
Photosynthesis
ATP
plants
glucose sugar
CO2 +
H2O + O2
Respiration
animals & plants
ATP

24. THE CYTOSKELETON AND CELL SURFACES
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25. Cytoskeleton gives cell shape and allows for movement
Cytoskeleton = network of protein fibers,
Functions: Structural support and motility.
The cytoskeleton is composed of three kinds of proteins:
Microfilaments (actin filaments)
support the cell’s shape and are
involved in function of muscle cells
Intermediate filaments
Microtubules (made of tubulin)
composes flagella and cilia; allows for movement by pseudopodia
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.
Video: Cytoplasmic Streaming
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26. Intermediate filament Microtubule
Figure 4.16
Nucleus
Nucleus
Actin subunit
Fibrous subunits
Tubulin subunits
Figure 4.16 Three types of fibers of the cytoskeleton
7 nm
10 nm
25 nm
Microfilament
Intermediate filament
Microtubule 26

27. Video: Paramecium Cilia
Cilia and flagella
Cilia
Functions of cilia and flagella:
Movement
Animal sperm cells
protists
Trap food particles/debris
Cells that sweep mucus out of our lungs have cilia
Oviducts of females
Sensory
Lining of nostrils; hair cells in ears
Composed of microtubules
Flagellum
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!
Video: Paramecium Cilia
Video: Chlamydomonas
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28. Outer microtubule doublet
Figure 4.17C
Outer microtubule doublet
Central microtubules
Radial spoke
Dynein proteins
Figure 4.17C Structure of a eukaryotic flagellum or cilium
Plasma membrane 28

29. Extracellular Matrix in Animals
Animal cells synthesize and secrete an elaborate ECM
Composed of sugar-protein polymers
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 the 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.
© 2012 Pearson Education, Inc. 29

30. ECM is glue that holds animal cells together!!
EXTRACELLULAR FLUID
CYTOPLASM
Microfilaments of cytoskelton
Plasma membrane
Integrin
Connecting glycoprotein
Glycoprotein complex with long polysaccharide
Collagen fiber
Figure 4.19 The extracellular matrix (ECM) of an animal cell 30