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Chapter 6: A Tour of the Cell
• All organisms are
made of cells
• The cell is the simplest
collection of matter
that can live
• Cell structure is
correlated to cellular
function
10 µm
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Microscopy
• Light microscopes (LMs)
– Pass visible light through a specimen and
magnify cellular structures with lenses
• Cells were discovered by ________in 1665 but their
ultrastructure was largely unknown until the development
of the ____________ in the 1950s.
• Electron microscopes (EMs)
– Focus a beam of electrons through a specimen
(TEM) or onto its surface (SEM)
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• Three scanning electron
microscopes (SEM) and one
transmission electron
microscope (TEM) provide
ultra high-resolution
microscopy (magnification to
1,000,000x) to identify
extremely small particles. All
are equipped with energy
dispersive x-ray spectroscopy
(EDS) to provide elemental
analysis.
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10 m
Human height
Length of some
nerve and
muscle cells
0.1 m
Chicken egg
1 cm
Light microscope
Frog egg
100 µm
10 µ m
1µm
100 nm
Most plant
and Animal
cells
Nucleus
Most bacteria
Mitochondrion
Smallest bacteria
Viruses
10 nm
Ribosomes
Electron microscope
1 mm
Electron microscope
Unaided eye
• Different types of
microscopes can be
used to visualize
different sized cellular
structures
1m
Proteins
1 nm
Lipids
Small molecules
Figure 6.2
0.1 nm
Atoms
Measurements
1 centimeter (cm) = 102 meter (m) = 0.4 inch
1 millimeter (mm) = 10–3 m
1 micrometer (µm) = 10–3 mm = 10–6 m
1 nanometer (nm) = 10–3 mm = 10–9 m
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– Use different methods for enhancing
visualization of cellular structures
TECHNIQUE
RESULT
(a) Brightfield (unstained specimen).
Passes light directly through specimen.
Unless cell is naturally pigmented or
artificially stained, image has little
contrast. [Parts (a)–(d) show a
human cheek epithelial cell.]
50 µm
(b) Brightfield (stained specimen).
Staining with various dyes enhances
contrast, but most staining procedures
require that cells be fixed (preserved).
(c) Phase-contrast. Enhances contrast
in unstained cells by amplifying
variations in density within specimen;
especially useful for examining living,
unpigmented cells.
Figure 6.3
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(d) Differential-interference-contrast (Nomarski).
Like phase-contrast microscopy, it uses optical
modifications to exaggerate differences in
density, making the image appear almost 3D.
(e) Fluorescence. Shows the locations of specific
molecules in the cell by tagging the molecules
with fluorescent dyes or antibodies. These
fluorescent substances absorb ultraviolet
radiation and emit visible light, as shown
here in a cell from an artery.
50 µm
(f) Confocal. Uses lasers and special optics for
“optical sectioning” of fluorescently-stained
specimens. Only a single plane of focus is
illuminated; out-of-focus fluorescence above
and below the plane is subtracted by a computer.
A sharp image results, as seen in stained nervous
tissue (top), where nerve cells are green, support
cells are red, and regions of overlap are yellow. A
standard fluorescence micrograph (bottom) of this
relatively thick tissue is blurry.
50 µm
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• The scanning electron microscope (SEM)
– Provides for detailed study of the surface of a
specimen
TECHNIQUE
RESULTS
1 µm
Cilia
(a) Scanning electron microscopy (SEM). Micrographs taken
with a scanning electron microscope show a 3D image of the
surface of a specimen. This SEM
shows the surface of a cell from a
rabbit trachea (windpipe) covered
with motile organelles called cilia.
Beating of the cilia helps move
inhaled debris upward toward
the throat.
Figure 6.4 (a)
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• The transmission electron microscope (TEM)
– Provides for detailed study of the internal
ultrastructure of cells
Longitudinal
section of
cilium
(b) Transmission electron microscopy (TEM). A transmission electron
microscope profiles a thin section of a
specimen. Here we see a section through
a tracheal cell, revealing its ultrastructure.
In preparing the TEM, some cilia were cut
along their lengths, creating longitudinal
sections, while other cilia were cut straight
across, creating cross sections.
Figure 6.4 (b)
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Cross section
of cilium
1 µm
Interactive Question
a.
Define cytology
b.
What do cell biologists use a TEM to study?
c.
What does and SEM show best?
d.
What advantages does light microscopy have over TEM
and SEM?
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Isolating Organelles by Cell Fractionation
• Cell fractionation
– Takes cells apart and separates the major
organelles from one another
• The centrifuge
– Is used to fractionate cells
into their component parts
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• The process of cell
fractionation
APPLICATION
Cell fractionation is used to
isolate (fractionate) cell components, based on size
and density.
TECHNIQUE First, cells are homogenized in a
blender to break them up. The resulting mixture (cell
homogenate) is then centrifuged at various speeds and
durations to fractionate the cell components, forming a
series of pellets.
RESULTS In the original experiments, the
Homogenization
Tissue
cells
1000 g
Homogenate
(1000 times the
force of gravity)
Differential centrifugation
10 min
Supernatant poured
into next tube
20,000 g
20 min
Pellet rich in
nuclei and
cellular debris
80,000 g
60 min
Pellet rich in
researchers used microscopy to identify the organelles
mitochondria
in each pellet, establishing a baseline for further experiments.
(and chloroplasts if cells
In the next series of experiments, researchers used
are from a Pellet rich in
biochemical methods to determine the metabolic functions
plant)
“microsomes”
(pieces of
associated with each type of organelle. Researchers currently
plasma membranes and
use cell fractionation to isolate particular organelles in order to
cells’ internal
study further details of their function.
Figure 6.5
membranes)
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150,000 g
3 hr
Pellet rich in
ribosomes
What do all cells have in common?
1. _____, 2. _____, 3. _____, 4. _____
• Prokaryotic cells do not contain a _______ and
have their DNA located in a region called
the _________
• Eukaryotic cells
– Contain a true nucleus, bounded by a
membranous nuclear envelope
– Are generally quite a bit ______(in size) when
compared to prokaryotic cells
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Pili: attachment structures on
the surface of some prokaryotes
Nucleoid: region where the
cell’s DNA is located (not
enclosed by a membrane)
Ribosomes: organelles that
synthesize proteins
Bacterial
chromosome
(a) A typical
rod-shaped bacterium
Plasma membrane: membrane
enclosing the cytoplasm
Cell wall: rigid structure outside
the plasma membrane
Capsule: jelly-like outer coating
of many prokaryotes
0.5 µm
Flagella: locomotion
organelles of
some bacteria
Figure 6.6 A, B
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(b) A thin section through the
bacterium Bacillus coagulans
(TEM)
The logistics of carrying out cellular metabolism sets
limits on the size of cells
• A smaller cell
– Has a higher surface to volume ratio, which
facilitates the exchange of materials into and
out of the cell
Surface area increases while
total volume remains constant
5
1
1
Total surface area
(height  width 
number of sides 
number of boxes)
6
150
750
Total volume
(height  width  length
 number of boxes)
1
125
125
Surface-to-volume
ratio
(surface area  volume)
6
12
6
Figure 6.7
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• The plasma membrane
– Functions as a selective barrier
– Allows sufficient passage of nutrients
and waste
Outside of cell
Carbohydrate side chain
Hydrophilic
region
Inside of cell
0.1 µm
Hydrophobic
region
Figure 6.8 A, B
(a) TEM of a plasma
membrane. The
plasma membrane,
here in a red blood
cell, appears as a
pair of dark bands
separated by a
light band.
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Hydrophilic
region
Phospholipid
Proteins
(b) Structure of the plasma membrane
A panoramic view: a eukaryotic cell
• A animal cell
ENDOPLASMIC RETICULUM (ER)
Rough ER
Smooth ER
Nuclear envelope
Nucleolus
NUCLEUS
Chromatin
Flagelium
Plasma membrane
Centrosome
CYTOSKELETON
Microfilaments
Intermediate filaments
Ribosomes
Microtubules
Microvilli
Golgi apparatus
Peroxisome
Figure 6.9
Mitochondrion
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Lysosome
In animal cells but not plant cells:
Lysosomes
Centrioles
Flagella (in some plant sperm)
A panoramic view: a eukaryotic cell II
• A plant cell
Nuclear envelope
Nucleolus
Chromatin
NUCLEUS
Centrosome
Rough
endoplasmic
reticulum Smooth
endoplasmic
reticulum
Ribosomes (small brwon dots)
Central vacuole
Tonoplast
Golgi apparatus
Microfilaments
Intermediate
filaments
CYTOSKELETON
Microtubules
Mitochondrion
Peroxisome
Plasma membrane
Chloroplast
Cell wall
Plasmodesmata
Wall of adjacent cell
Figure 6.9
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In plant cells but not animal cells:
Chloroplasts
Central vacuole and tonoplast
Cell wall
Plasmodesmata
The Nucleus: Genetic Library of the Cell
• The nucleus
contains most of
the genes in the
eukaryotic cell
Nucleus
1 µm
Nucleolus
Chromatin
Nucleus
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
• The nuclear
envelope
encloses the
nucleus,
separating its
contents from the
cytoplasm
Pore
complex
Rough ER
Surface of nuclear
envelope.
1 µm
Ribosome
0.25 µm
Close-up of
nuclear
envelope
Nuclear lamina (TEM).
Pore complexes (TEM).
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Figure 6.10
Ribosomes: Protein Factories in the Cell
• Ribosomes are particles made of ribosomal RNA
and protein, and they carry out protein synthesis
Ribosomes
Cytosol
Free ribosomes
Bound ribosomes
Large
subunit
0.5 µm
TEM showing ER and ribosomes
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Small
subunit
Diagram of a ribosome
Interactive Question
• How does the nucleus control protein synthesis
in cytoplasm?
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The ER membrane
• Accounts for more than
half the total membrane in
many eukaryotic cells
• Is continuous with the
nuclear envelope
• 2 kinds of ER
• Smooth: lacks ribosomes
• Rough: contains ribosomes
Figure 6.12
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Smooth ER
Rough ER
Nuclear
envelope
ER lumen
Cisternae
Ribosomes
Transitional ER
Transport vesicle
Smooth ER
Rough ER 200 µm
Functions of Smooth ER
• The smooth ER
– Synthesizes lipids
– Metabolizes carbohydrates
– Stores calcium
– Detoxifies poison
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Functions of Rough ER
• The rough ER
– Has bound ribosomes
– Produces proteins and membranes, which are
distributed by transport vesicles
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The Golgi Apparatus: Shipping and
Receiving Center
• The Golgi apparatus
– Receives many of the transport vesicles
produced in the rough ER
– Consists of flattened membranous sacs called
cisternae
• Functions of the Golgi apparatus include
– Modification of the products of the rough ER
– Manufacture of certain macromolecules
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• Functions of the Golgi apparatus
Golgi
apparatus
cis face
(“receiving” side of
Golgi apparatus)
1 Vesicles move
2 Vesicles coalesce to
6 Vesicles also
form new cis Golgi cisternae
from ER to Golgi
transport certain
Cisternae
proteins back to ER
3 Cisternal
maturation:
Golgi cisternae
move in a cisto-trans
direction
Figure 6.13
5 Vesicles transport specific
proteins backward to newer
Golgi cisternae
4 Vesicles form and
leave Golgi, carrying
specific proteins to
other locations or to
the plasma membrane for secretion
trans face
(“shipping” side of
Golgi apparatus)
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0.1 0 µm
TEM of Golgi apparatus
Lysosomes: Digestive Compartments
• A lysosome
– Is a membranous sac of hydrolytic enzymes
– Can digest all kinds of macromolecules
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• Lysosomes carry out intracellular digestion by
– Phagocytosis
Nucleus
1 µm
Lysosome
Lysosome contains
active hydrolytic
enzymes
Food vacuole
fuses with
lysosome
Hydrolytic
enzymes digest
food particles
Digestive
enzymes
Lysosome
Plasma membrane
Digestion
Food vacuole
Figure 6.14 A
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(a) Phagocytosis: lysosome digesting food
• Autophagy
Lysosome containing
two damaged organelles
1µm
Mitochondrion
fragment
Peroxisome
fragment
Lysosome fuses with
vesicle containing
damaged organelle
Hydrolytic enzymes
digest organelle
components
Lysosome
Vesicle containing
damaged mitochondrion
Digestion
(b) Autophagy: lysosome breaking down damaged organelle
Figure 6.14 B
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Vacuoles: Diverse Maintenance Compartments
• A plant or fungal cell
– May have one or several vacuoles
• Food vacuoles
– Are formed by phagocytosis
• Contractile vacuoles
– Pump excess water out of protist cells
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• Central vacuoles
Central vacuole
– Are found in plant
cells
Cytosol
Tonoplast
– Hold reserves of
important organic
compounds and
water
Figure 6.15
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Nucleus
Central
vacuole
Cell wall
Chloroplast
5 µm
• Relationships among organelles of the
endomembrane system
1 Nuclear envelope is
connected to rough ER,
which is also continuous
with smooth ER
Nucleus
Rough ER
2
Membranes and proteins
produced by the ER flow in
the form of transport vesicles
to the Golgi
Smooth ER
cis Golgi
Nuclear envelop
3
Golgi pinches off transport
Vesicles and other vesicles
that give rise to lysosomes and
Vacuoles
Plasma
membrane
trans Golgi
4
Lysosome available
for fusion with another
vesicle for digestion
Figure 6.16
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5 Transport vesicle carries 6
proteins to plasma
membrane for secretion
Plasma membrane expands
by fusion of vesicles; proteins
are secreted from cell
• Concept 6.5: Mitochondria and chloroplasts
change energy from one form to another
• Mitochondria
– Are the sites of cellular respiration
• Chloroplasts
– Found only in plants, are the sites of
photosynthesis
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• Mitochondria are enclosed by two membranes
– Are found in nearly all eukaryotic cells and
have smooth outer membrane
– An inner membrane folded into cristae
Mitochondrion
Intermembrane space
Outer
membrane
Free
ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix
Figure 6.17
Mitochondrial
DNA
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100 µm
Chloroplasts: Capture of Light Energy
• The chloroplast contains chlorophyll
• Is a specialized member of a family of closely related plant
organelles called plastids; this is where photosythesis takes
place
• Are found in leaves and other green organs of plants and in
algae
Chloroplast
Ribosomes
Stroma
Inner and outer
membranes
Granum
Chloroplast
DNA
1 µm
Thylakoid
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• Chloroplast structure includes
– Thylakoids, membranous sacs
– Stroma, the internal fluid
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Peroxisomes: Oxidation
• Peroxisomes
– Convert hydrogen peroxide to water (because
H2O2 is a toxic by-product
Chloroplast
Peroxisome
Mitochondrion
Figure 6.19
1 µm
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• The cytoskeleton
– Is a network of fibers extending throughout the
cytoplasm and gives mechanical support to the cell
Microtubule
Figure 6.20
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0.25 µm
Microfilaments
– Is involved in cell motility, which utilizes motor
proteins
ATP
Vesicle
Receptor for
motor protein
Motor protein
Microtubule
(ATP powered)
of cytoskeleton
(a) Motor proteins that attach to receptors on organelles can “walk”
the organelles along microtubules or, in some cases, microfilaments.
Vesicles
Microtubule
0.25 µm
Figure 6.21 A, B
(b) Vesicles containing neurotransmitters migrate to the tips of nerve cell
axons via the mechanism in (a). In this SEM of a squid giant axon, two
vesicles can be seen moving along a microtubule. (A separate part of the
experiment provided the evidence that they were in fact moving.)
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• There are three main types of fibers that make
up the cytoskeleton
Table 6.1
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Microtubules
• Microtubules
– Shape the cell
– Guide movement of organelles
– Help separate the chromosome copies in
dividing cells
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• The centrosome
– Is considered to be a “microtubule-organizing
center” and contains a pair of centrioles
Centrosome
Microtubule
Centrioles
0.25 µm
Figure 6.22
Longitudinal section
of one centriole
Microtubules
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Cross section
of the other centriole
Cilia and Flagella
• Cilia and flagella
– Contain specialized arrangements of
microtubules
– Are locomotor appendages of some cells
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• Flagella beating pattern
(a) Motion of flagella. A flagellum
usually undulates, its snakelike
motion driving a cell in the same
direction as the axis of the
flagellum. Propulsion of a human
sperm cell is an example of
flagellatelocomotion (LM).
Direction of swimming
Figure 6.23 A
1 µm
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• Ciliary motion
(b) Motion of cilia. Cilia have a backand-forth motion that moves the
cell in a direction perpendicular
to the axis of the cilium. A dense
nap of cilia, beating at a rate of
about 40 to 60 strokes a second,
covers this Colpidium, a
freshwater protozoan (SEM).
Figure 6.23 B
15 µm
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• Cilia and flagella share a common
ultrastructure
Outer microtubule
doublet
Dynein arms
0.1 µm
Central
microtubule
Outer doublets
cross-linking
proteins inside
Microtubules
Radial
spoke
Plasma
membrane
Basal body
(b)
0.5 µm
(a)
0.1 µm
Triplet
(c)
Figure 6.24 A-C
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Cross section of basal body
Plasma
membrane
• The protein dynein
– Is responsible for the bending movement of
cilia and flagella
Microtubule
doublets
ATP
Dynein arm
(a) Powered by ATP, the dynein arms of one microtubule doublet
grip the adjacent doublet, push it up, release, and then grip again.
If the two microtubule doublets were not attached, they would slide
relative to each other.
Figure 6.25 A
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ATP
Outer doublets
cross-linking
proteins
Anchorage
in cell
(b) In a cilium or flagellum, two adjacent doublets cannot slide far because
they are physically restrained by proteins, so they bend. (Only two of
the nine outer doublets in Figure 6.24b are shown here.)
Figure 6.25 B
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1
3
2
(c) Localized, synchronized activation of many dynein arms
probably causes a bend to begin at the base of the Cilium or
flagellum and move outward toward the tip. Many successive
bends, such as the ones shown here to the left and right,
result in a wavelike motion. In this diagram, the two central
microtubules and the cross-linking proteins are not shown.
Figure 6.25 C
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Microfilaments (Actin Filaments)
• Microfilaments
– Are built from
Microvillus
molecules of the
protein actin and
Plasma membrane
are found in
microvilli
Microfilaments (actin
filaments)
Intermediate filaments
Figure 6.26
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0.25 µm
• Microfilaments that function in cellular motility
– Contain the protein myosin in addition to actin
Muscle cell
Actin filament
Myosin filament
Myosin arm
Figure 6.27 A
(a) Myosin motors in muscle cell contraction.
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• Amoeboid movement
– Involves the contraction of actin and myosin
filaments
Cortex (outer cytoplasm):
gel with actin network
Inner cytoplasm: sol
with actin subunits
Extending
pseudopodium
Figure 6.27 B
(b) Amoeboid movement
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• Cytoplasmic streaming
– Is another form of locomotion created by
microfilaments
Nonmoving
cytoplasm (gel)
Chloroplast
Streaming
cytoplasm
(sol)
Parallel actin
filaments
Figure 6.27 C
(b) Cytoplasmic streaming in plant cells
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Cell wall
Intermediate Filaments
• Intermediate filaments
– Support cell shape
– Fix organelles in place
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Cell Walls of Plants
– The cell wall is an extracellular structure of plant cells
that distinguishes them from animal cells
– Are made of cellulose fibers embedded in other
polysaccharides and protein
– May have multiple layers
Central
vacuole
of cell
Plasma
membrane
Secondary
cell wall
Primary
cell wall
Central
vacuole
of cell
Middle
lamella
1 µm
Central vacuole
Cytosol
Plasma membrane
Plant cell walls
Figure 6.28
Plasmodesmata
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Interactive Question
• If you sketched two adjacent plant cells, could
you show the location of the primary and
secondary cell walls and the middle lamella?
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The Extracellular Matrix (ECM) of Animal Cells
• Animal cells lack cell walls and are covered by an
elaborate matrix, the ECM, which is made up of
glycoproteins and other macromolecules
EXTRACELLULAR FLUID
Collagen
A proteoglycan
complex
Polysaccharide
molecule
Carbohydrates
Core
protein
Fibronectin
Plasma
membrane
Integrin
Integrins
Microfilaments
Figure 6.29
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CYTOPLASM
Proteoglycan
molecule
• Functions of the ECM include
– Support
– Adhesion
– Movement
– Regulation
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Plants: Plasmodesmata
• Plasmodesmata
– Are channels that perforate plant cell walls
Cell walls
Interior
of cell
Interior
of cell
Figure 6.30
0.5 µm
Plasmodesmata
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Plasma membranes
Animals: Tight Junctions, Desmosomes, and Gap Junctions
• In animals, there are three types of intercellular
junctions
– Tight junctions
– Desmosomes
– Gap junctions
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• Types of intercellular junctions in animals
TIGHT JUNCTIONS
Tight junction
Tight junctions prevent
fluid from moving
across a layer of cells
0.5 µm
At tight junctions, the membranes of
neighboring cells are very tightly pressed
against each other, bound together by
specific proteins (purple). Forming continuous seals around the cells, tight junctions
prevent leakage of extracellular fluid across
A layer of epithelial cells.
DESMOSOMES
Desmosomes (also called anchoring
junctions) function like rivets, fastening cells
Together into strong sheets. Intermediate
Filaments made of sturdy keratin proteins
Anchor desmosomes in the cytoplasm.
Tight junctions
Intermediate
filaments
Desmosome
Gap
junctions
Space
between Plasma membranes
cells
of adjacent cells
1 µm
Extracellular
matrix
Gap junction
Figure 6.31
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0.1 µm
GAP JUNCTIONS
Gap junctions (also called communicating
junctions) provide cytoplasmic channels from
one cell to an adjacent cell. Gap junctions
consist of special membrane proteins that
surround a pore through which ions, sugars,
amino acids, and other small molecules may
pass. Gap junctions are necessary for communication between cells in many types of tissues,
including heart muscle and animal embryos.
The Cell: A Living Unit Greater Than the Sum of Its Parts
5 µm
• Cells rely on the integration of structures and
organelles in order to function
Figure 6.32
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