1. Chapter 6 A Tour of the Cell
The Cell: A Living Unit Greater Than the Sum of Its Parts
Cells rely on the integration of structures and organelles in order to function
For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane
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2. Fig. 6-33
5 µm
Figure 6.33 The emergence of cellular functions

3. You should now be able to:
Distinguish between the following pairs of terms: 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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4. Describe the structure of a plant cell wall
Describe the structure and roles of the extracellular matrix in animal cells
Describe the intercellular junctions
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5. Overview: The Fundamental Units of Life
All organisms are made of cells- cell theory
The cell is the simplest collection of matter that can live
Cell structure is correlated to cellular function
All cells are related by their descent from earlier cells
For the Discovery Video Cells, go to Animation and Video Files.
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6. Microscopy 10 m 1 m 0.1 m 1 cm 1 mm 100 µm 10 µm 1 µm 100 nm 10 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
Microscopy
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

7. TEMs are used mainly to study the internal structure of cells
Two basic types of electron microscopes (EMs) are used to study subcellular structures
Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a specimen, providing images that look 3-D
Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen
TEMs are used mainly to study the internal structure of cells
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8. (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

9. Protists, fungi, animals, and plants all consist of eukaryotic cells
Concept 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions
The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic
Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells
Protists, fungi, animals, and plants all consist of eukaryotic cells
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10. Comparing Prokaryotic and Eukaryotic Cells
Basic features of all cells:
Plasma membrane
Semifluid substance called cytosol
Chromosomes (carry genes)
Ribosomes (make proteins)
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11. Prokaryotic cells are characterized by having
No nucleus
DNA in an unbound region called the nucleoid
No membrane-bound organelles
Cytoplasm bound by the plasma membrane
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12. A typical rod-shaped bacterium (b)
Fig. 6-6
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

13. Eukaryotic cells are characterized by having
DNA in a nucleus that is bounded by a membranous nuclear envelope
Membrane-bound organelles
Cytoplasm in the region between the plasma membrane and nucleus
Eukaryotic cells are generally much larger than prokaryotic cells
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14. 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

15. ENDOPLASMIC RETICULUM (ER) Nucleolus NUCLEUS Rough ER Smooth ER
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

16. Rough endoplasmic reticulum
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

17. The nucleus contains most of the DNA in a eukaryotic cell
Concept 6.3: The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes
The nucleus contains most of the DNA in a eukaryotic cell
Ribosomes use the information from the DNA to make proteins
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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. Chromatin condenses to form discrete chromosomes
In the nucleus, DNA and proteins form genetic material called chromatin
Chromatin condenses to form discrete chromosomes
The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis
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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. 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.
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22. 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)

23. Ribosomes: Protein Factories
Ribosomes are particles made of ribosomal RNA and protein
Ribosomes carry out protein synthesis in two locations:
In the cytosol (free ribosomes)
On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)
For the Cell Biology Video Staining of Endoplasmic Reticulum, go to Animation and Video Files.
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24. Endoplasmic reticulum (ER)
Fig. 6-11
Cytosol
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Large subunit
Figure 6.11 Ribosomes
Small subunit
0.5 µm
TEM showing ER and ribosomes
Diagram of a ribosome

25. Functions of Smooth ER The smooth ER Synthesizes lipids
Metabolizes carbohydrates
Detoxifies poison
Stores calcium
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26. 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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27. The Golgi Apparatus: Shipping and Receiving Center
The Golgi apparatus consists of flattened membranous sacs called cisternae
Functions of the Golgi apparatus:
Modifies products of the ER
Manufactures certain macromolecules
Sorts and packages materials into transport vesicles
For the Cell Biology Video ER to Golgi Traffic, go to Animation and Video Files.
For the Cell Biology Video Golgi Complex in 3D, go to Animation and Video Files.
For the Cell Biology Video Secretion From the Golgi, go to Animation and Video Files.
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28. (“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

29. Lysosomes: Digestive Compartments
A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules
Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids
Animation: Lysosome Formation
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30. A lysosome fuses with the food vacuole and digests the molecules
Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole
A lysosome fuses with the food vacuole and digests the molecules
Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy
For the Cell Biology Video Phagocytosis in Action, go to Animation and Video Files.
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31. Nucleus 1 µm Lysosome Digestive enzymes Lysosome Plasma membrane
Fig. 6-14a
Nucleus
1 µm
Lysosome
Digestive enzymes
Lysosome
Figure 6.14a Lysosome—phagocytosis
Plasma membrane
Digestion
Food vacuole
(a) Phagocytosis

32. two damaged organelles 1 µm
Fig. 6-14b
Vesicle containing
two damaged organelles
1 µm
Mitochondrion fragment
Peroxisome fragment
Lysosome
Figure 6.14b Lysosomes—autophagy
Peroxisome
Mitochondrion
Digestion
Vesicle
(b) Autophagy

33. Video: Paramecium Vacuole
Vacuoles- 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
Video: Paramecium Vacuole
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34. Central vacuole Cytosol Nucleus Central vacuole Cell wall Chloroplast
Fig. 6-15
Central vacuole
Cytosol
Nucleus
Central vacuole
Figure 6.15 The plant cell vacuole
Cell wall
Chloroplast
5 µm

35. The Endomembrane System: A Review
The endomembrane system is a complex and dynamic player in the cell’s compartmental organization
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36. Nucleus Rough ER Smooth ER cis Golgi Plasma membrane trans Golgi
Fig
Nucleus
Rough ER
Smooth ER
cis Golgi
Figure 6.16 Review: relationships among organelles of the endomembrane system
Plasma membrane
trans Golgi

37. Peroxisomes are oxidative organelles
Concept 6.5: Mitochondria and chloroplasts change energy from one form to another
Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP
Chloroplasts, found in plants and algae, are the sites of photosynthesis
Peroxisomes are oxidative organelles
For the Cell Biology Video ER and Mitochondria in Leaf Cells, go to Animation and Video Files.
For the Cell Biology Video Mitochondria in 3D, go to Animation and Video Files.
For the Cell Biology Video Chloroplast Movement, go to Animation and Video Files.
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38. Mitochondria and chloroplasts
Are not part of the endomembrane system
Have a double membrane
Have proteins made by free ribosomes
Contain their own DNA
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39. Mitochondria: Chemical Energy Conversion
Fig. 6-17
Mitochondria: Chemical Energy Conversion
Intermembrane space
Outer membrane
Free ribosomes
in the mitochondrial matrix
Inner membrane
Cristae
Figure 6.17 The mitochondrion, site of cellular respiration
Matrix
0.1 µm

40. Chloroplasts: Capture of Light Energy
The chloroplast is a member of a family of organelles called plastids
Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis
Chloroplasts are found in leaves and other green organs of plants and in algae
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41. Chloroplast structure includes:
Fig. 6-18
Chloroplast structure includes:
Thylakoids, membranous sacs, stacked to form a granum
Stroma, the internal fluid
Ribosomes
Stroma
Inner and outer membranes
Granum
1 µm
Thylakoid
Figure 6.18 The chloroplast, site of photosynthesis

42. Cytoskeleton is composed of three types of molecular structures:
Fig. 6-20
Cytoskeleton is composed of three types of molecular structures:
Microtubules
Microfilaments
Intermediate filaments
Microtubule
Figure 6.20 The cytoskeleton
Microfilaments
0.25 µm

43. Roles of the Cytoskeleton: Support, Motility, and Regulation
The cytoskeleton helps to support the cell and maintain its shape
It interacts with motor proteins to produce motility
Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton
Recent evidence suggests that the cytoskeleton may help regulate biochemical activities
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44. Receptor for motor protein
Fig. 6-21
Vesicle
ATP
Receptor for motor protein
Motor protein (ATP powered)
Microtubule
of cytoskeleton
(a)
Microtubule
Vesicles
0.25 µm
Figure 6.21 Motor proteins and the cytoskeleton
(b)

45. Components of the Cytoskeleton
Three main types of fibers make up the cytoskeleton:
Microtubules are the thickest of the three components of the cytoskeleton
Microfilaments, also called actin filaments, are the thinnest components
Intermediate filaments are fibers with diameters in a middle range
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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46. 10 µm Column of tubulin dimers Tubulin dimer   25 nm Table 6-1a

47. Table 6-1b
10 µm
Table 6-1b
Actin subunit
7 nm

48. Microtubules Centrosomes and Centrioles
In many cells, microtubules grow out from a centrosome near the nucleus
The centrosome is a “microtubule-organizing center”
In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring
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49. Longitudinal section of one centriole Microtubules Cross section
Fig. 6-22
Centrosome
Microtubule
Centrioles
0.25 µm
Figure 6.22 Centrosome containing a pair of centrioles
Longitudinal section of one centriole
Microtubules
Cross section
of the other centriole

50. Direction of organism’s movement
Fig. 6-23
Direction of swimming
(a) Motion of flagella
Microtubules- Cilia and 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

51. Cross section of cilium
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
Figure 6.24 Ultrastructure of a eukaryotic flagellum or motile cilium
Triplet
(c) Cross section of basal body

52. How dynein “walking” moves flagella and cilia:
Dynein arms alternately grab, move, and release the outer microtubules
Protein cross-links limit sliding
Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum
For the Cell Biology Video Motion of Isolated Flagellum, go to Animation and Video Files.
For the Cell Biology Video Flagellum Movement in Swimming Sperm, go to Animation and Video Files.
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53. Cross-linking proteins inside outer doublets
Fig. 6-25b
ATP
Cross-linking proteins inside outer doublets
Anchorage in cell
(b) Effect of cross-linking proteins 1 3
Figure 6.25b, c How dynein “walking” moves flagella and cilia 2
(c) Wavelike motion

54. Microfilaments (actin filaments)
Fig. 6-26
Microvillus
Plasma membrane
Microfilaments (actin filaments)
Figure 6.26 A structural role of microfilaments
Intermediate filaments
0.25 µm

55. These extracellular structures include:
Concept 6.7: Extracellular components and connections between cells help coordinate cellular activities
Most cells synthesize and secrete materials that are external to the plasma membrane
These extracellular structures include:
Cell walls of plants
The extracellular matrix (ECM) of animal cells
Intercellular junctions
For the Cell Biology Video Ciliary Motion, go to Animation and Video Files.
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56. Prokaryotes, fungi, and some protists also have cell walls
Cell Walls of Plants
The cell wall is an extracellular structure that distinguishes plant cells from animal cells
Prokaryotes, fungi, and some protists also have cell walls
The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water
Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein
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57. 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

58. Proteoglycan complex Collagen EXTRACELLULAR FLUID Fibronectin
Fig. 6-30a
Collagen
Proteoglycan complex
EXTRACELLULAR FLUID
Fibronectin
Integrins
Plasma membrane
Figure 6.30 Extracellular matrix (ECM) of an animal cell, part 1
Micro-filaments
CYTOPLASM

59. 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
Tight junctions
Desmosomes
Gap junctions
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60. Figure 6.32 Intercellular junctions in animal tissues
Tight junction
Tight junctions prevent
fluid from moving
across a layer of cells
0.5 µm
Tight junction
Intermediate
filaments
Desmosome
Desmosome
Gap
junctions
1 µm
Figure 6.32 Intercellular junctions in animal tissues
Extracellular
matrix
Space
between
cells
Gap junction
Plasma membranes
of adjacent cells
0.1 µm

61. Fig. 6-UN1a Cell Component Structure Function Concept 6.3 Nucleus
Surrounded by nuclear
envelope (double membrane)
perforated by nuclear pores.
The nuclear envelope is
continuous with the
endoplasmic reticulum (ER).
Houses chromosomes, made of
chromatin (DNA, the genetic
material, and proteins); contains
nucleoli, where ribosomal
subunits are made. Pores
regulate entry and exit os
materials.
The eukaryotic cell’s genetic
instructions are housed in
the nucleus and carried out
by the ribosomes
(ER)
Ribosome
Two subunits made of ribo-
somal RNA and proteins; can be
free in cytosol or bound to ER
Protein synthesis

62. Fig. 6-UN1b Cell Component Structure Function Concept 6.4
Endoplasmic reticulum
Extensive network of
membrane-bound tubules and
sacs; membrane separates
lumen from cytosol;
continuous with
the nuclear envelope.
Smooth ER: synthesis of
lipids, metabolism of carbohy-
drates, Ca2+ storage, detoxifica-
tion of drugs and poisons
The endomembrane system
regulates protein traffic and
performs metabolic functions
in the cell
(Nuclear
envelope)
Rough ER: Aids in sythesis of
secretory and other proteins
from bound ribosomes; adds
carbohydrates to glycoproteins;
produces new membrane
Golgi apparatus
Stacks of flattened
membranous
sacs; has polarity
(cis and trans
faces)
Modification of proteins, carbo-
hydrates on proteins, and phos-
pholipids; synthesis of many
polysaccharides; sorting of
Golgi products, which are then
released in vesicles.
Breakdown of ingested sub-
stances cell macromolecules, and damaged organelles for recycling
Lysosome
Membranous sac of hydrolytic
enzymes (in animal cells)
Vacuole
Large membrane-bounded
vesicle in plants
Digestion, storage, waste
disposal, water balance, cell
growth, and protection

63. Fig. 6-UN1c Cell Component Structure Function Concept 6.5
Mitochondrion
Bounded by double
membrane;
inner membrane has
infoldings (cristae)
Cellular respiration
Mitochondria and chloro-
plasts change energy from
one form to another
Chloroplast
Typically two membranes
around fluid stroma, which
contains membranous thylakoids
stacked into grana (in plants)
Photosynthesis
Peroxisome
Specialized metabolic
compartment bounded by a
single membrane
Contains enzymes that transfer
hydrogen to water, producing
hydrogen peroxide (H2O2) as a
by-product, which is converted
to water by other enzymes
in the peroxisome