1. Chapter 6
A Tour of the Cell

2. Fig. 6-1
Figure 6.1 How do cellular components cooperate to help the cell function?

3. Microscopy
Scientists use microscopes to visualize cells too small to see with the naked eye
In a light microscope (LM), this is the type of scope you use, which magnifies about up to 1,000x the actual size
The quality of an image depends on 3 things:
Magnification
Resolution (clarity)
Contrast (visible differences), can be enhanced with stains
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4. 10 m 1 m 0.1 m 1 cm 1 mm 100 µm 10 µm 1 µm 100 nm 10 nm 1 nm 0.1 nm
Fig. 6-2
10 m
Human height
1 m
Length of some nerve and muscle cells
0.1 m
Unaided eye
Chicken egg
1 cm
Frog egg
1 mm
100 µm
Most plant and animal cells
Light microscope
10 µm
Nucleus
Most bacteria
1 µm
Mitochondrion
Figure 6.2 The size range of cells
Smallest bacteria
Electron microscope
100 nm
Viruses
Ribosomes
10 nm
Proteins
Lipids
1 nm
Small molecules
0.1 nm
Atoms

5. Cheek epithelial cells
Fig. 6-3
TECHNIQUE
RESULTS
(a) Brightfield (unstained
specimen)
Cheek epithelial cells
50 µm
(b) Brightfield (stained
specimen)
(c) Phase-contrast
(d) Differential-interference-
contrast (Nomarski)
(e) Fluorescence
Figure 6.3a-d Light microscopy
50 µm
(f) Confocal
50 µm

6. Electron microscopes (EMs) are used to study subcellular structures
Scanning electron microscopes (SEMs) focus e- onto the surface of a specimen, providing images that look 3-D
Transmission electron microscopes (TEMs) focus e- through a specimen, used to study internal cellular structures
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7. (b) Transmission electron microscopy (TEM) Longitudinal section of
Fig. 6-4
TECHNIQUE
RESULTS
1 µm
(a) Scanning electron
microscopy (SEM)
Cilia
(b) Transmission electron
microscopy (TEM)
Longitudinal
section of
cilium
Cross section
of cilium
1 µm
Figure 6.4 Electron microscopy

8. What do you remember about Prokaryotic and Eukaryotic Cells?????
Eukaryote
Prokaryote
Both

9. Prokaryotic = bacteria and Archaea Eukaryotic = everything else
Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions
Prokaryotic = bacteria and Archaea
Eukaryotic = everything else
Basic features of all cells:
Plasma membrane
Semifluid substance called cytosol (aka cytoplasm)
Chromosomes (carry genes)
Ribosomes (make proteins)
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10. Prokaryotic cells are characterized by having No nucleus
DNA in an unbound region called the nucleoid
No membrane-bound organelles
Cytoplasm
Circular chromosome called a plasmid
Eukaryotic cells are characterized by having
DNA in a nucleus that is bounded by a membranous nuclear envelope
Membrane-bound organelles
Cytoplasm Eukaryotic cells are generally much larger than prokaryotic cells
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11. Which class of cell is this?
Fig. 6-6
Which class of cell is this?
Fimbriae
Nucleoid
Ribosomes
Plasma membrane
Bacterial
chromosome
Cell wall
Capsule
0.5 µm
Flagella
(a)
A typical rod-shaped bacterium
(b)
A thin section through the bacterium Bacillus coagulans (TEM)
Figure 6.6 A prokaryotic cell

12. Generally made up of a bilayer of phospholipids
The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell
Generally made up of a bilayer of phospholipids
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13. Carbohydrate side chain
Fig. 6-7
(a)
TEM of a plasma
membrane
Outside of cell
Inside of
cell
0.1 µm
Carbohydrate side chain
Hydrophilic
region
Figure 6.7 The plasma membrane
Hydrophobic
region
Hydrophilic
region
Phospholipid
Proteins
(b) Structure of the plasma membrane

14. The surface area to volume ratio of a cell is critical
The logistics of carrying out cellular metabolism sets limits on the size of cells (what does this mean????)
The surface area to volume ratio of a cell is critical
As the surface area increases by a factor of n2, the volume increases by a factor of n3
Small cells have a greater surface area relative to volume
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15. BioFlix: Tour Of An Animal Cell
Fig. 6-9a
Nuclear
envelope
ENDOPLASMIC RETICULUM (ER)
Nucleolus
NUCLEUS
Rough ER
Smooth ER
Flagellum
Chromatin
Centrosome
Plasma membrane
CYTOSKELETON:
Microfilaments
Intermediate
filaments
Microtubules
Ribosomes
Figure 6.9 Animal and plant cells—animal cell
Microvilli
Golgi
apparatus
Peroxisome
Mitochondrion
Lysosome
BioFlix: Tour Of An Animal Cell

16. BioFlix: Tour Of A Plant Cell
Fig. 6-9b
Nuclear envelope
Rough endoplasmic reticulum
NUCLEUS
Nucleolus
Chromatin
Smooth endoplasmic reticulum
Ribosomes
Central vacuole
Golgi
apparatus
Microfilaments
Intermediate filaments
CYTO-
SKELETON
Microtubules
Figure 6.9 Animal and plant cells—plant cell
Mitochondrion
Peroxisome
Chloroplast
Plasma membrane
Cell wall
Plasmodesmata
Wall of adjacent cell
BioFlix: Tour Of A Plant Cell

17. Is there any organelle you are unclear about from your pre-reading?
You should know the major components of the cell and their fxns, do you?
Is there any organelle you are unclear about from your pre-reading?
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18. Close-up of nuclear envelope
Fig. 6-10
Nucleus
1 µm
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Pore complex
Rough ER
Surface of
nuclear envelope
Ribosome
1 µm
Figure 6.10 The nucleus and its envelope
0.25 µm
Close-up of nuclear envelope
Pore complexes (TEM)
Nuclear lamina (TEM)

19. Pores regulate the entry and exit of molecules from the nucleus
The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein
A net-like array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope
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20. Components of the endomembrane system:
Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell
Components of the endomembrane system:
Nuclear envelope
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane
These components are either continuous or connected via transfer by vesicles
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21. How are they related?
We mentioned that all of these are part of the endomembrane system, so what does that mean? Can you determine any similarities that there may be between them? What would they be made of?

22. The Endoplasmic Reticulum: Biosynthetic Factory
The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells
The ER membrane is continuous with the nuclear envelope
There are two distinct regions of ER:
Smooth ER, which lacks ribosomes
Rough ER, with ribosomes studding its surface
For the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

23. Smooth ER Nuclear envelope Rough ER ER lumen Cisternae Transitional ER
Fig. 6-12
Smooth ER
Nuclear envelope
Rough ER
ER lumen
Cisternae
Transitional ER
Ribosomes
Transport vesicle
200 nm
Smooth ER
Rough ER
Figure 6.12 Endoplasmic reticulum (ER)

24. Functions of Rough ER The rough ER
Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates)
Distributes transport vesicles, proteins surrounded by membranes
Is a membrane factory for the cell
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25. Functions of Smooth ER and Golgi Apparatus
The smooth ER
Synthesizes lipids
Metabolizes carbohydrates
Detoxifies poison
Stores calcium
Functions of the Golgi apparatus:
Modifies products of the ER
Manufactures certain macromolecules
Sorts and packages materials into transport vesicles
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26. (“receiving” side of Golgi apparatus) 0.1 µm
Fig. 6-13
cis face
(“receiving” side of Golgi apparatus)
0.1 µm
Cisternae
Figure 6.13 The Golgi apparatus
trans face
(“shipping” side of Golgi apparatus)
TEM of Golgi apparatus

27. Fig. 6-14a
Nucleus
1 µm
Phagocytosis – “ingestion” of food/solid materials into the cell thru vesicles
Lysosome
Digestive enzymes
Lysosome
Figure 6.14a Lysosome—phagocytosis
Plasma membrane
Digestion
Food vacuole
(a) Phagocytosis

28. Vacuoles: Diverse Maintenance Compartments
A plant cell or fungal cell may have one or several vacuoles
Food vacuoles are formed by phagocytosis
Contractile vacuoles, found in many freshwater protists, pump excess water out of cells
Central vacuoles, found in many mature plant cells, hold organic compounds and water
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29. Endomembrane system Nucleus Rough ER Smooth ER cis Golgi
Fig
Nucleus
Rough ER
Smooth ER
cis Golgi
Figure 6.16 Review: relationships among organelles of the endomembrane system
Endomembrane system
Plasma membrane
trans Golgi

30. Other Organelles Peroxisomes are oxidative organelles
Mitochondria and chloroplasts
Are not part of the endomembrane system
Have a double membrane
Have proteins made by free ribosomes
Contain their own DNA
Question: anyone know why mitochondria and chloroplasts contain their own DNA?
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31. Peroxisomes: Oxidation
Peroxisomes are specialized metabolic compartments bounded by a single membrane
Peroxisomes produce hydrogen peroxide and convert it to water
Oxygen is used to break down different types of molecules
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32. Chloroplast Peroxisome Mitochondrion 1 µm Fig. 6-19
Figure 6.19 A peroxisome
1 µm

33. It is composed of three types of molecular structures:
Concept 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell
The cytoskeleton is a network of fibers extending throughout the cytoplasm
It organizes the cell’s structures and activities, anchoring many organelles
It is composed of three types of molecular structures:
Microtubules
Microfilaments
Intermediate filaments
Use motor proteins (dynein) to move
For the Cell Biology Video The Cytoskeleton in a Neuron Growth Cone, go to Animation and Video Files
For the Cell Biology Video Cytoskeletal Protein Dynamics, go to Animation and Video Files.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

34. Video? Microtubule Microfilaments 0.25 µm Fig. 6-20
Figure 6.20 The cytoskeleton
Microfilaments
0.25 µm

35. Components of the Cytoskeleton
Three main types of fibers make up the cytoskeleton:
Microtubules – thickest, shape cell, guide organelle mvmt, separate chroms during cell division
Microfilaments, also called actin filaments, are the thinnest components (make up micro-villi in your intestines)
Intermediate filaments are fibers with diameters in a middle range, more permanent, fix organelles in place and help with cell shape
For the Cell Biology Video Actin Network in Crawling Cells, go to Animation and Video Files.
For the Cell Biology Video Actin Visualization in Dendrites, go to Animation and Video Files.
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36. Video: Paramecium Cilia
Cilia and Flagella
Microtubules control the beating of cilia and flagella, locomotor appendages of some cells
Cilia and flagella differ in their beating patterns
Video: Chlamydomonas
Video: Paramecium Cilia
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37. Direction of organism’s movement
Fig. 6-23
Direction of swimming
(a) Motion of flagella
5 µm
Direction of organism’s movement
Figure 6.23a A comparison of the beating of flagella and cilia—motion of flagella
Power stroke
Recovery stroke
(b) Motion of cilia
15 µm

38. Animation: Cilia and Flagella
Cilia and flagella share a common ultrastructure: (what would this suggest?)
A core of microtubules sheathed by the plasma membrane
A basal body that anchors the cilium or flagellum
Animation: Cilia and Flagella
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39. Notice the arrangement of the microtubules
Fig. 6-24
Outer microtubule doublet
Plasma membrane
0.1 µm
Dynein proteins
Central microtubule
Radial spoke
Protein cross-linking outer doublets
Microtubules
(b)
Cross section of cilium
Plasma membrane
Basal body
0.5 µm
(a)
Longitudinal section of cilium
0.1 µm
Notice the arrangement of the microtubules
Figure 6.24 Ultrastructure of a eukaryotic flagellum or motile cilium
Triplet
(c) Cross section of basal body

40. Cell Wall Plant cell walls may have multiple layers:
Primary cell wall: relatively thin and flexible
Middle lamella: thin layer between primary walls of adjacent cells
Secondary cell wall (in some cells): added between the plasma membrane and the primary cell wall
Plasmodesmata are channels between adjacent plant cells
For the Cell Biology Video E-cadherin Expression, go to Animation and Video Files.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

41. Secondary cell wall Primary cell wall Middle lamella Central vacuole
Fig. 6-28
Secondary cell wall
Primary cell wall
Middle lamella
1 µm
Central vacuole
Cytosol
Plasma membrane
Figure 6.28 Plant cell walls
Plant cell walls
Plasmodesmata

42. The Extracellular Matrix (ECM) of Animal Cells
Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM)
The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin
ECM proteins bind to receptor proteins in the plasma membrane called integrins
For the Cell Biology Video Cartoon Model of a Collagen Triple Helix, go to Animation and Video Files.
For the Cell Biology Video Staining of the Extracellular Matrix, go to Animation and Video Files.
For the Cell Biology Video Fibronectin Fibrils, go to Animation and Video Files.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

43. Figure 6.30 Extracellular matrix (ECM) of an animal cell, part 1
Collagen
Proteoglycan
complex
Polysaccharide
molecule
EXTRACELLULAR FLUID
Carbo-
hydrates
Fibronectin
Core
protein
Integrins
Proteoglycan
molecule
Plasma
membrane
Proteoglycan complex
Figure 6.30 Extracellular matrix (ECM) of an animal cell, part 1
Micro-
filaments
CYTOPLASM

44. Functions of the ECM: Support Adhesion Movement Regulation
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45. Intercellular Junctions
Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact
Intercellular junctions facilitate this contact
There are several types of intercellular junctions
Plasmodesmata (cell with cell walls) – perforate cell walls
Tight junctions -membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
Desmosomes – anchoring junctions
Gap junctions – communicating junctions
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46. Cell walls Interior of cell Interior of cell 0.5 µm Plasmodesmata
Fig. 6-31
Cell walls
Interior of cell
Interior of cell
Figure 6.31 Plasmodesmata between plant cells
0.5 µm
Plasmodesmata
Plasma membranes

47. Tight junctions prevent fluid from moving across a layer of cells
Fig. 6-32a
Tight junctions prevent fluid from moving across a layer of cells
Tight junction
Intermediate filaments
Desmosome
Gap junctions
Figure 6.32 Intercellular junctions in animal tissues—tight junctions
Extracellular matrix
Space between cells
Plasma membranes of adjacent cells

48. You should now be able to:
Distinguish between the following pairs of terms: magnification and resolution; prokaryotic and eukaryotic cell; free and bound ribosomes; smooth and rough ER
Describe the structure and function of the components of the endomembrane system
Briefly explain the role of mitochondria, chloroplasts, and peroxisomes
Describe the functions of the cytoskeleton
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49. Describe the structure of a plant cell wall
Compare the structure and functions of microtubules, microfilaments, and intermediate filaments
Explain how the ultrastructure of cilia and flagella relate to their functions
Describe the structure of a plant cell wall
Describe the structure and roles of the extracellular matrix in animal cells
Describe four different intercellular junctions
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings