5/13/2013
1
A Tour of the Cell Chapter 6
You should be able to:
1. Distinguish between the following pairs of
terms: magnification and resolution;
prokaryotic and eukaryotic cell; free and bound
ribosomes; smooth and rough ER
2. Describe the structure and function of the
components of the endomembrane system
3. Briefly explain the role of mitochondria,
chloroplasts, and peroxisomes
4. Describe the functions of the cytoskeleton
5. Compare the structure and functions of
microtubules, microfilaments, and intermediate
filaments
6. Explain how the ultrastructure of cilia and
flagella relate to their functions
7. Describe the structure of a plant cell wall
8. Describe the structure and roles of the
extracellular matrix in animal cells
9. Describe four different intercellular junctions
5/13/2013
2
BioFlix Animal Cell Movie
Overview: The Fundamental Units
of Life
o All organisms are made of cells
o The cell is the simplest collection of matter
that can be alive
o Cell structure is correlated to cellular function
o Though usually too small to be seen by the
unaided eye, cells are complex
Microscopy
o Scientists use microscopes
to visualize cells too small
to see with the naked eye
o In a light microscope
(LM), visible light passes
through a specimen and
then through glass lenses,
which magnify the image
o Lenses refract (bend) the
light, so that the image is
magnified
5/13/2013
3
o The quality of an image depends on
oMagnification, the ratio of an objects image size to its real size
oResolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points
oContrast, visible differences in parts of the sample
Brightfield Phase Contrast Hoffman mod-
ulation contrast
o LMs can magnify effectively to about 1,000 times the size of the actual specimen
o Various techniques enhance contrast and enable cell components to be stained or labeled
o Most subcellular structures, including organelles (membrane-enclosed
compartments), are too small to be resolved by an LM
10 m
1 m
0.1 m
1 cm
1 mm
100 m
10 m
1 m
100 nm
10 nm
1 nm
0.1 nm Atoms
Small molecules
Lipids
Proteins
Ribosomes
Viruses
Smallest bacteria
Mitochondrion
Nucleus
Most bacteria
Most plant and animal cells
Frog egg
Chicken egg
Length of some nerve and muscle cells
Human height
Un
aid
ed
eye
Lig
ht
mic
ros
co
pe
Ele
ctr
on
mic
ros
co
pe
(unstained specimen)
50
m
Brightfield
Brightfield
(stained specimen)
5/13/2013
4
(unstained specimen)
50
m
Brightfield
Phase-contrast
(unstained specimen)
50
m
Brightfield
Differential-interference-
contrast (Nomarski)
Super-resolution
Fluorescence
Confocal
Deconvolution
Cilia
Scanning electron
microscopy (SEM)
Longitudinal section
of cilium
Cross section
of cilium
Transmission electron
microscopy (TEM)
5/13/2013
5
o Two basic types of electron
microscopes (EMs) are used to
study subcellular structures
o Scanning electron microscopes
(SEMs) focus a beam of electrons
onto the surface of a specimen,
providing images that look 3-D
o Transmission electron
microscopes (TEMs) focus a
beam of electrons through a
specimen
o TEMs are used mainly to study the
internal structure of cells
Cilia
o Recent advances in light microscopy o Confocal microscopy and deconvolution
microscopy provide sharper images of three-
dimensional tissues and cells
o New techniques for labeling cells improve
resolution
Deconvolution
Confocal
Cell Fractionation
o Cell fractionation takes cells apart and
separates the major organelles from one
another
o Centrifuges fractionate cells into their
component parts
o Cell fractionation enables scientists to determine
the functions of organelles
o Biochemistry and cytology help correlate cell
function with structure
5/13/2013
6
Figure 6.4 TECHNIQUE
Homogenization
Tissue
cells
Homogenate
Centrifugation
Differential
centrifugation
Centrifuged at
1,000 g
(1,000 times the
force of gravity)
for 10 min Supernatant
poured into
next tube
20,000 g
20 min
80,000 g
60 min Pellet rich in
nuclei and
cellular debris
150,000 g
3 hr
Pellet rich in
mitochondria
(and chloro-
plasts if cells
are from a plant)
Pellet rich in
microsomes
(pieces of plasma
membranes and
cells internal
membranes) Pellet rich in
ribosomes
Prokaryotic and Eukaryotic Cells
o Basic features of ALL cells (EUK and PROK)
1. Plasma membrane (the outer border, a phospholipid bilayer)
2. Semifluid substance called cytosol inside
3. DNA/Chromosomes (carry genes)
4. Ribosomes (make proteins)
o The basic cell(s) of every organism is either
prokaryotic or eukaryotic
o Only organisms of the domains Bacteria and Archaea
consist of prokaryotic cells
o Protists, fungi, animals, and plants all consist of
eukaryotic cells
o Prokaryotic cells are characterized by
having:
oNo nucleus
oDNA in an unbound region called the nucleoid
oNo membrane-bound organelles (none surrounded by a phospholipid membrane)
oCytoplasm bound by the plasma membrane
5/13/2013
7
Fimbriae
Bacterial
chromosome
A typical rod-shaped bacterium
(a)
Nucleoid
Ribosomes
Plasma
membrane
Cell wall
Capsule
Flagella A thin section through the bacterium Bacillus coagulans (TEM)
(b)
0.5 m
Figure 6.5
o Eukaryotic cells have internal membranes that compartmentalize their functions
oOrganelles
o Eukaryotic cells are characterized by having
oDNA in a nucleus that is bounded by a membranous nuclear envelope
oMembrane-bound organelles
oCytoplasm in the region between the plasma membrane and nucleus
o Eukaryotic cells are generally much larger than prokaryotic cells
Eukaryotic Cell
5/13/2013
8
o The plasma membrane is a selective
barrier that allows sufficient passage of
oxygen, nutrients, and waste to service the
volume of every cell
o The general structure of a biological
membrane is a double layer of
phospholipids
Figure 6.6
Outside of cell
Inside of cell 0.1 m
(a) TEM of a plasma membrane
Hydrophilic region
Hydrophobic region
Hydrophilic region
Carbohydrate side chains
Proteins Phospholipid
(b) Structure of the plasma membrane
o Metabolic requirements set upper limits on
the size of cells
o The surface area to volume ratio of a cell is
critical
o As the surface area increases by a factor of
n2, the volume increases by a factor of n3
o Small cells have a greater surface area
relative to volume
5/13/2013
9
Surface area increases while
total volume remains constant
Total surface area [sum of the surface areas (height width) of all box sides number of boxes]
Total volume [height width length number of boxes]
Surface-to-volume (S-to-V) ratio [surface area volume]
1
5
6 150 750
1
125 125 1
1.2 6 6
Figure 6.7
A Panoramic View of the
Eukaryotic Cell
o A eukaryotic cell has internal membranes that
partition the cell into organelles
o Plant and animal cells have most of the same
organelles
BioFlix: Tour of an Animal Cell
BioFlix: Tour of a Plant Cell
Figure 6.8a
ENDOPLASMIC RETICULUM (ER)
Rough ER
Smooth ER
Nuclear envelope
Nucleolus
Chromatin
Plasma membrane
Ribosomes
Golgi apparatus
Lysosome Mitochondrion
Peroxisome
Microvilli
Microtubules
Intermediate filaments
Microfilaments
Centrosome
CYTOSKELETON:
Flagellum NUCLEUS
Animal Cell
5/13/2013
10
NUCLEUS
Nuclear envelope
Nucleolus
Chromatin
Golgi apparatus
Mitochondrion
Peroxisome
Plasma membrane
Cell wall
Wall of adjacent cell
Plasmodesmata
Chloroplast
Microtubules
Intermediate filaments
Microfilaments
CYTOSKELETON
Central vacuole
Ribosomes
Smooth endoplasmic reticulum
Rough endoplasmic
reticulum
Figure 6.8c
Plant Cell
The eukaryotic cells genetic instructions are housed in the nucleus
and carried out by the ribosomes
o The nucleus contains most of the DNA in a
eukaryotic cell
o Ribosomes use the information from the
DNA to make proteins
o The nucleus contains most of the cells genes and is usually the most conspicuous organelle
o The nuclear envelope encloses the nucleus,
separating it from the cytoplasm
o The nuclear membrane is a double membrane;
each membrane consists of a lipid bilayer
The Nucleus: Information Central
5/13/2013
11
Nucleus
Rough ER
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Ribosome
Pore complex
Close-up of nuclear envelope
Surface of nuclear envelope
Pore complexes (TEM)
0.2
5
m
1
m
Nuclear lamina (TEM)
Chromatin
1 m
Figure 6.9
o Pores regulate the entry and exit of
molecules from the nucleus
o The shape of the nucleus is maintained by
the nuclear lamina, which is composed of
protein
oNetwork of strong fibers (intermediate fibers)
o In the nucleus, DNA is organized into discrete units
called chromosomes
o Each chromosome is composed of a single DNA
molecule associated with proteins
o The DNA and proteins of chromosomes are together
called chromatin
o Chromatin condenses to form discrete chromosomes
as a cell prepares to divide
o The nucleolus is located within the nucleus and is the
site of ribosomal RNA (rRNA) synthesis
Chromosomes
5/13/2013
12
Ribosomes: Protein Factories
o Ribosomes are particles made of ribosomal
RNA and protein
o Ribosomes carry out protein synthesis in two
locations:
o In the cytosol (free ribosomes)
omake proteins that stay within the cell
oOn the outside of the endoplasmic reticulum or the
nuclear envelop (bound ribosomes)
omake proteins that will incorporate into the plasma
membrane or proteins that are secreted from the cell
Fig. 6-11
Cytosol
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Large subunit
Small subunit
Diagram of a ribosome TEM showing ER and ribosomes
0.5 m
The endomembrane system regulates
protein traffic & performs metabolic
functions in the cell
o Components of the endomembrane system:
oNuclear envelope
o Endoplasmic reticulum
oGolgi apparatus
o Lysosomes
o Vacuoles
o Plasma membrane
o These components are either continuous with
each other OR connected via transfer by vesicles
5/13/2013
13
o The endoplasmic reticulum (ER) accounts for
more than half of the total membrane in many
eukaryotic cells
o The ER membrane is continuous with the nuclear
envelope
o There are 2 distinct regions: of ER:
o Smooth ER, which lacks ribosomes
o Rough ER, surface is studded with
ribsosomes
The Endoplasmic Reticulum: Biosynthetic Factory
Figure 6.11 Smooth ER
Rough ER
ER lumen
Cisternae Ribosomes
Smooth ER
Transport vesicle
Transitional ER
Rough ER 200 nm
Nuclear
envelope
Functions of ER o The smooth ER
o Synthesizes lipids
o Metabolizes carbohydrates
o Detoxifies poison
o Stores calcium
o The rough ER
o Has bound ribosomes, which secrete glycoproteins
(proteins covalently bonded to carbohydrates)
o Distributes transport vesicles, proteins surrounded
by membranes
o Is a membrane factory for the cell
5/13/2013
14
o The Golgi apparatus consists of flattened
membranous sacs called cisternae
o Functions:
oModifies products of the ER
oManufactures certain macromolecules
o Sorts and packages materials into transport vesicles
The Golgi Apparatus: Shipping and Receiving Center
Lysosomes:
Digestive Compartments
o A lysosome is a membranous sac of
hydrolytic enzymes that can digest
macromolecules
o Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids
o Lysosomal enzymes work best in the acidic environment inside the lysosome
o Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole
o A lysosome fuses with the food vacuole and digests the molecules
o Lysosomes also use enzymes to recycle the cells own organelles and macromolecules, a process called autophagy
5/13/2013
15
Figure 6.13
Nucleus
Lysosome
1 m
Digestive
enzymes
Digestion
Food vacuole
Lysosome
Plasma membrane
(a) Phagocytosis
Vesicle containing
two damaged
organelles 1 m
Mitochondrion
fragment
Peroxisome
fragment
(b) Autophagy
Peroxisome
Vesicle Mitochondrion
Lysosome
Digestion
o A plant cell or fungal cell may have one or several vacuoles, derived from the ER or Golgi apparatus
o Food vacuoles are formed by phagocytosis
o Contractile vacuoles, found in many
freshwater protists, pump excess water out of
cells
o Central vacuoles, found in many mature plant
cells, hold organic compounds and water
Vacuoles: Diverse Maintenance Compartments
Figure 6.14
Central vacuole
Cytosol
Nucleus
Cell wall
Chloroplast
Central
vacuole
5 m
5/13/2013
16
The Endomembrane System: A
Review o The endomembrane system is a complex and
dynamic player in the cells compartmental organization
Figure 6.15-1
Smooth ER
Nucleus
Rough ER
Plasma
membrane
Figure 6.15-2
Smooth ER
Nucleus
Rough ER
Plasma
membrane
cis Golgi
trans Golgi
5/13/2013
17
Figure 6.15-3
Smooth ER
Nucleus
Rough ER
Plasma
membrane
cis Golgi
trans Golgi
Mitochondria and Chloroplasts change
energy from one form to another
o Mitochondria are the sites of cellular
respiration, a metabolic process that
generates ATP
o Chloroplasts, found in plants and algae,
are the sites of photosynthesis
o Peroxisomes are oxidative organelles
o Mitochondria and chloroplasts have
similarities with bacteria:
o (Are not part of the endomembrane system)
oHave a double membrane (2 membranes with a
space between)
oContain free ribosomes and circular DNA
molecules
oGrow and reproduce somewhat independently
in cells
The Evolutionary Origins of
Mitochondria and Chloroplasts
5/13/2013
18
o The Endosymbiont theory
o An early ancestor of eukaryotic cells engulfed
a nonphotosynthetic prokaryotic cell, which
formed an endosymbiont relationship with its
host
o The host cell and endosymbiont merged into
a single organism, a eukaryotic cell with a
mitochondrion
o At least one of these cells may have taken up
a photosynthetic prokaryote, becoming the
ancestor of cells that contain chloroplasts
Nucleus Endoplasmic
reticulum
Nuclear
envelope
Ancestor of
eukaryotic cells
(host cell)
Engulfing of oxygen-
using nonphotosynthetic
prokaryote, which
becomes a mitochondrion
Mitochondrion
Nonphotosynthetic
eukaryote
Mitochondrion
At least
one cell
Photosynthetic eukaryote
Engulfing of
photosynthetic
prokaryote
Chloroplast
Figure 6.16
Mitochondria: Chemical Energy Conversion
o Mitochondria are in nearly all eukaryotic cells
o They have a smooth outer membrane and an
inner membrane folded into cristae
o The inner membrane creates two compartments:
intermembrane space and mitochondrial matrix
o Some metabolic steps of cellular respiration are
catalyzed in the mitochondrial matrix
o Cristae present a large surface area for enzymes
that synthesize ATP
5/13/2013
19
Figure 6.17
Intermembrane space
Outer
membrane
DNA
Inner
membrane
Cristae
Matrix
Free
ribosomes
in the
mitochondrial
matrix
(a) Diagram and TEM of mitochondrion (b) Network of mitochondria in a protist
cell (LM)
0.1 m
Mitochondrial
DNA
Nuclear DNA
Mitochondria
10 m
Chloroplasts: Capture of Light Energy
o Chloroplasts are found in leaves and other green organs of plants and in algae
o The chloroplast is a member of a family of organelles called plastids
o Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis
o Produce Sugars
o Typically used by Mitochondria
oChloroplast structure includes:
oThylakoids, membranous sacs, stacked to form a granum
oStroma, the internal fluid
Ribosomes
Stroma
Inner and outer
membranes
Granum
1 m Intermembrane space Thylakoid
(a) Diagram and TEM of chloroplast (b) Chloroplasts in an algal cell
Chloroplasts
(red)
50 m
DNA
5/13/2013
20
Peroxisomes: Oxidation
o Peroxisomes are specialized metabolic compartments bounded by a single membrane
o Peroxisomes a) produce hydrogen peroxide (H2O2) and b) convert it to water (H2O)
o Used to metabolize other foods (like fatty acids) & toxins
o How peroxisomes are related to other organelles is still unknown
The Cytoskeleton is a network of fibers that
organizes structures and activities in the cell
o The cytoskeleton is a network of fibers
extending throughout the cytoplasm
o It organizes the cells structures and activities, anchoring many organelles
o It is composed of three types of molecular
structures: oMicrotubules
oMicrofilaments
o Intermediate filaments
Microtubule
Microfilaments
Roles of the Cytoskeleton:
Support, Motility, and Regulation
o The cytoskeleton helps to support the cell
and maintain its shape
o It interacts with motor proteins to produce
motility
o Inside the cell, vesicles can travel along
monorails provided by the cytoskeleton
o Recent evidence suggests that the
cytoskeleton may help regulate biochemical
activities
5/13/2013
21
Components of the
Cytoskeleton
o Three main types of fibers make up the
cytoskeleton:
oMicrotubules are the thickest of the three
components of the cytoskeleton
oMicrofilaments, also called actin filaments, are
the thinnest components
o Intermediate filaments are fibers with diameters
in a middle range
Column of tubulin dimers
Tubulin dimer
25 nm
Actin subunit
7 nm
Keratin proteins
812 nm
Fibrous subunit (keratins
coiled together)
10 m 10 m 5 m
Table 6.1
Microtubules
o Microtubules are hollow rods about 25
nm in diameter and about 200 nm to 25
microns long
o Functions of microtubules:
o Shaping the cell
oGuiding movement of organelles
o Separating chromosomes during cell division
5/13/2013
22
Tubulin dimer
25 nm
Column of tubulin dimers
10 m
Table 6.1a
Centrosomes and Centrioles
o In many cells, microtubules grow out from a
centrosome near the nucleus
o The centrosome is a microtubule-organizing center
o In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring
Cilia and Flagella
o Microtubules control the beating of cilia and flagella, locomotor appendages of some cells
o Cilia and flagella differ in their beating patterns (& length)
5/13/2013
23
Fig. 6-23
5 m
Direction of swimming
(a) Motion of flagella
Direction of organisms movement
Power stroke Recovery stroke
(b) Motion of cilia 15 m
Cilia and flagella share common
ultrastructure:
o A core of microtubules sheathed by the plasma
membrane
o A basal body that anchors the cilium or
flagellum
o A motor protein called dynein, which drives the
bending movements of a cilium or flagellum
Fig. 6-24
0.1 m
Triplet
(c) Cross section of basal body
(a) Longitudinal section of cilium
0.5 m
Plasma membrane
Basal body
Microtubules
(b) Cross section of cilium
Plasma membrane
Outer microtubule doublet
Dynein proteins
Central microtubule
Radial spoke
Protein cross-linking outer doublets
0.1 m
5/13/2013
24
o How dynein walking moves flagella and cilia:
oDynein arms alternately grab, move, and release the outer microtubules
o Protein cross-links limit sliding
o Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum
Animation: Cilia and Flagella
Microtubule doublets
Dynein protein
ATP
ATP
(a) Effect of unrestrained dynein movement
Cross-linking proteins inside outer doublets
Anchorage in cell
(b) Effect of cross-linking proteins
1 3
2
(c) Wavelike motion
Microfilaments (Actin Filaments)
o Microfilaments are solid rods about 7 nm in
diameter, built as a twisted double chain of
actin subunits
o The structural role of microfilaments is to bear tension, resisting pulling forces within the cell
o They form a 3-D network called the cortex just inside the plasma membrane to help support the cells shape
o Bundles of microfilaments make up the core of microvilli of intestinal cells
o Microfilaments that function in cellular
motility contain the protein myosin in
addition to actin
o In muscle cells, thousands of actin filaments
are arranged parallel to one another
o Thicker filaments composed of myosin
interdigitate with the thinner actin fibers
5/13/2013
25
o Localized contraction brought about by actin and
myosin also drives amoeboid movement
o Pseudopodia (cellular extensions) extend and
contract through the reversible assembly and
contraction of actin subunits into microfilaments
o Cytoplasmic streaming is a circular flow of
cytoplasm within cells
o This streaming speeds distribution of
materials within the cell
o In plant cells, actin-myosin interactions and
sol-gel transformations drive cytoplasmic
streaming
Video: Cytoplasmic Streaming
10 m
Actin subunit
7 nm
Table 6.1b
5/13/2013
26
Intermediate Filaments
o Intermediate filaments range in diameter
from 812 nanometers, larger than microfilaments but smaller than
microtubules
o They support cell shape and fix organelles
in place
o Intermediate filaments are more permanent
cytoskeleton fixtures than the other two
classes
5 m
Keratin proteins
Fibrous subunit (keratins
coiled together)
812 nm
Table 6.1c
Extracellular components and
connections between cells help
coordinate cellular activities
o Most cells synthesize and secrete materials
that are external to the plasma membrane
o These extracellular structures include:
oCell walls of plants
o The extracellular matrix (ECM) of animal cells
o Intercellular junctions
5/13/2013
27
Cell Walls of Plants
o The cell wall is an extracellular structure that distinguishes plant cells from animal cells
o Prokaryotes, fungi, and some protists also have cell walls
o The cell wall:
o protects the plant cell
omaintains its shape
o prevents excessive uptake of water
o Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein
o Plant cell walls may have multiple layers:
o Primary cell wall: relatively thin and flexible
oMiddle lamella: thin layer between primary
walls of adjacent cells
o Secondary cell wall (in some cells): added
between the plasma membrane and the primary
cell wall
o Plasmodesmata are channels between adjacent
plant cells
The Extracellular Matrix (ECM) of
Animal Cells
o Animal cells lack cell walls, but are covered by an
elaborate extracellular matrix (ECM)
o The ECM is made up of glycoproteins such as
collagen, proteoglycans, and fibronectin
o ECM proteins bind to receptor proteins in the
plasma membrane called integrins
o Functions of the ECM: o Support o Adhesion o Movement o Regulation
5/13/2013
28
Fig. 6-30
EXTRACELLULAR FLUID Collagen
Fibronectin
Plasma membrane
Micro- filaments
CYTOPLASM
Integrins
Proteoglycan complex
Polysaccharide
molecule
Carbo- hydrates
Core protein
Proteoglycan molecule
Proteoglycan complex
Intercellular Junctions
o Neighboring cells in tissues, organs, or organ
systems often adhere, interact, and
communicate through direct physical contact
o Intercellular junctions facilitate this contact
o There are several types of intercellular
junctions
o Plasmodesmata
o Tight junctions
oDesmosomes
oGap junctions
Plasmodesmata in Plant Cells
Interior of cell
Interior of cell
0.5 m Plasmodesmata Plasma membranes
Cell walls
o Plasmodesmata are channels that
perforate plant cell walls
o Through plasmodesmata, water and small
solutes (and sometimes proteins and RNA)
can pass from cell to cell
5/13/2013
29
Tight Junctions, Desmosomes, and
Gap Junctions in Animal Cells
o At tight junctions, membranes of neighboring
cells are pressed together, preventing leakage
of extracellular fluid
o Desmosomes (anchoring junctions) fasten
cells together into strong sheets
o Gap junctions (communicating junctions)
provide cytoplasmic channels between
adjacent cells
o Ions can flow
Fig. 6-32
Tight junction
0.5 m
1 m Desmosome
Gap junction
Extracellular matrix
0.1 m
Plasma membranes of adjacent cells
Space between cells
Gap
junctions
Desmosome
Intermediate filaments
Tight junction
Tight junctions prevent fluid from moving across a layer of cells
The Cell: A Living Unit Greater
Than the Sum of Its Parts
o Cells rely on the integration of structures
and organelles in order to function
o For example, a macrophages ability to destroy bacteria involves the whole cell,
coordinating components such as the
cytoskeleton, lysosomes, and plasma
membrane
5/13/2013
30
Figure 6.UN01
Nucleus
(ER)
(Nuclear
envelope)
Figure 6.UN01a
Nucleus
(ER)
Figure 6.UN01b
(Nuclear
envelope)
5/13/2013
31
Figure 6.UN01c