Chapter 6:
A Tour of the Cell
Key Concepts
6.1 To study cells, biologists use microscopes and the tools of
biochemistry.
6.2 Eukaryotic cells have internal membranes that
compartmentalize their functions, and membrane bound
organelles.
6.3 The Eukaryotic cell’s genetic instructions are found in the
nucleus and carried out by the ribosomes.
6.4 The endomembrane system (ER) regulates protein traffic and
performs metabolic function of the cell.
6.5 Mitochondria and chloroplasts change energy from one form to
another.
6.6 The cytoskeleton is a network of fibers that organizes structures
and activities inside the cell.
6.7 Extracellular components (outside the cell) and connections
between cells (desmosomes, gap junctions, tight junctions, and
plasmodesmata) help coordinate cellular activities.
Microscopy
• The study of cells progressed with the
invention of the microscope in 1590, and their
improvement in the 17th century.
• Light Microscope- earliest form, uses beam of
light passed thru specimen and then thru
glass lenses.
• Electron Microscope- (1950’s) focuses a
beam of electrons thru a specimen, or onto its
surface. Highest magnification and resolution.
• Transmission EM- (TEM) used to study the
internal structures of a cell.
• Scanning EM- (SEM) used to study the
surface of a specimen.
Light Microscope
TEM
SEM
Fig. 6-4
TECHNIQUE
(a) Scanning electron
microscopy (SEM)
RESULTS
Cilia
1 µm
(b) Transmission electron Longitudinal Cross section
section of
of cilium
microscopy (TEM)
1 µm
cilium
Parameters in Microscopy
• Magnificationthe ratio of an
objects image
size to its real
size
• Resolution- a
measure of
the clarity of
an object
Staining Technique
• The addition of certain chemical
pigments allows for increased contrast
between cell structures.
• Makes structures easier to distinguish
and study.
• Examples- bromthymol blue, methylene
blue, crystal violet, safranin, malachite
green, eosin
Fig. 6-3ab
TECHNIQUE
RESULTS
(a) Brightfield (unstained
specimen)
50 µm
(b) Brightfield (stained
specimen)
Cell Fractionation
•The goal of cell fractionation is to take cells
apart and separate major organelles from
one another.
•The instrument used is a Centrifuge.
•The centrifuge spins test tubes holding
mixtures of disrupted cells at high speeds.
•Uses centrifugal force.
•Enable scientists to prepare specific
components of cells in bulk quantities to
study their composition and structure.
Fig. 6-5
TECHNIQUE
Homogenization
Tissue
cells
Homogenate
1,000 g
(1,000 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
150,000 g
3 hr
Pellet rich in
mitochondria
(and chloroplasts if cells
are from a plant)
Pellet rich in
“microsomes”
(pieces of plasma
membranes and
cells’ internal
membranes)
Pellet rich in
ribosomes
Fig. 6-5b
TECHNIQUE (cont.)
1,000 g
(1,000 times the
force of gravity)
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 chloroplasts if cells
are from a plant)
Pellet rich in
“microsomes”
(pieces of plasma
membranes and
cells’ internal
membranes)
Pellet rich in
ribosomes
Cells of Living Things
Prokaryotic
Usually single celled.
Can form colonies.
No nucleus or
membrane-bound
organelles.
Genetic material
localized (nucleoid)
Ex. Bacteria
Eukaryotic
Kingdoms: Protista,
Fungi, Plants,
Animals.
Nuclear membrane
encloses DNA.
Organelles that have
membrane.
Cell Size and Shape
• Surface to Volume Ratio limits size of cells. Large
cells require more raw materials.
• V = cm3 S.A. = cm2 Restrictions on
size and shape
• Cells compartmentalize to increase SA/Vol,
specialize rxn within, localize reactions where
needed.
Basic Aspects of Cell Structure
and Function
• Plasma membrane
• Lipid bilayer
• Proteins
– Channels, transport, pumps, receptors
• DNA-containing region
• Cytoplasm
Prokaryotic Cells
•Highly disorganized
•No membrane bound organelles
•Have a nucleoid (like a nucleus)
•Nucleoid contains genetic material (DNA)
•Have a plasma membrane
•Have cytosol inside the cell in which the
organelles are found
•Have ribosomes
•Smaller than Eukaryotic cells
•Examples- Bacteria, Archae
Typical Prokaryote (Bacterial) Cell
Fig. 6-6
Fimbriae
Nucleoid
Ribosomes
Plasma membrane
Bacterial
chromosome
Cell wall
Capsule
0.5 µm
(a) A typical
rod-shaped
bacterium
Flagella
(b) A thin section
through the
bacterium
Bacillus
coagulans (TEM)
Eukaryotic Cells
•
•
•
•
Have membrane bound organelles
Are very organized
Have a nucleus (DNA)
Surrounded by either a cell wall or a
plasma membrane
• Examples- plants, animals, fungi,
protists (amoeba, paramecium,euglena)
Defining Structures of Eukaryotic
Cells
A Plant Cell
An Animal Cell
Plant vs. Animal Cell
Fig. 6-9a
Nuclear
envelope
ENDOPLASMIC RETICULUM (ER)
Flagellum
Rough ER
NUCLEUS
Nucleolus
Smooth ER
Chromatin
Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate
filaments
Microtubules
Ribosomes
Microvilli
Golgi
apparatus
Peroxisome
Mitochondrion
Lysosome
Fig. 6-9b
NUCLEUS
Nuclear envelope
Nucleolus
Chromatin
Rough endoplasmic
reticulum
Smooth endoplasmic
reticulum
Ribosomes
Central vacuole
Golgi
apparatus
Microfilaments
Intermediate
filaments
Microtubules
Mitochondrion
Peroxisome
Chloroplast
Plasma
membrane
Cell wall
Plasmodesmata
Wall of adjacent cell
CYTOSKELETON
Structures in the Cell
• The tiny organs found inside the cell are
called organelles.
• Each of these structures performs a
specific function that allows the cell to
survive.
Major Cellular Components
• Nucleus
• Ribosomes
• Endoplasmic reticulum
– Smooth and Rough
• Golgi body
• Various vesicles
• Mitochondria
• Cytoskeleton
Structures found in both Plant
and Animal Cells
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Plasma membrane
Nucleus
Chromatin
Nucleolus
Ribosomes
Endoplasmic Reticulum
Golgi Apparatus
Mitochondria
Peroxisomes
Cytoskeleton
Centrosomes
Structures Associated with
Animal Cells
1.
2.
3.
4.
5.
6.
7.
Lysosomes
Centrioles
Flagella
Extracellular matrix
Tight Junctions
Desmosomes
Gap Junctions
Structures Associated with
Plant Cells
1.
2.
3.
4.
Central Vacuoles
Chloroplasts
Cell Wall
Plasmodesmata
Components of the Nucleus
• Nuclear envelope - Surrounds nucleus
• Chromosome - One DNA molecule and associated
proteins. Organized DNA.
• Chromatin - DNA molecules and histone proteins.
Condenses to form DNA.
• Nucleolus - RNA and proteins that will be assembled
into ribosomal subunits. Cells may have more than
one.
The Nuclear Envelope
• Double - membrane system
– Two lipid bilayers. 20-40 nm thick.
– Surrounds chromatin/nucleoplasm
• Pores allow exchange. Composed of about 100
proteins.
Ribosomes
• Smallest, most numerous
organelle.
• Composed of rRNA and proteins.
Synthesized by nucleolus.
• Large and small subunits.
• Found free and bound to E.R.
Differ only in what they are
making.
• Catalyzes formation of peptide
bonds.
The Endomembrane System
• Organelles in which lipids are assembled and
proteins are produced and modified
• Are in direct contact or send vesicles (membranebound sacs).
• Occupy ½ of cell volume.
• Nuclear envelope, endoplasmic reticulum, golgi
apparatus, lysosomes, vacuole
The Endoplasmic Reticulum
• Network of tubes and sacs that are continuous with
nuclear membrane. Most extensive mem. Sys.
• Rough (ribosome studded) and Smooth.
– Rough: production of secretory proteins. Signal sequence
on polypeptide instructs ribosome to attach to ER.
– Smooth: Lipids production, CH2O metabolism, storage of
ions, detoxification of drugs/alcohol
Fig. 6-11
Cytosol
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Large
subunit
0.5 µm
TEM showing ER and ribosomes
Small
subunit
Diagram of a ribosome
Fig. 6-10
Nucleus
1 µm
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Pore
complex
Surface of
nuclear envelope
Rough ER
Ribosome
1 µm
0.25 µm
Close-up of nuclear
envelope
Pore complexes (TEM)
Nuclear lamina (TEM)
Fig. 6-12
Smooth ER
Rough ER
ER lumen
Cisternae
Ribosomes
Transport vesicle
Smooth ER
Nuclear
envelope
Transitional ER
Rough ER
200 nm
Fig. 6-16-1
Nucleus
Rough ER
Smooth ER
Plasma
membrane
Fig. 6-16-2
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
Fig. 6-16-3
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
Golgi Bodies
• Enzymatic finishes on proteins
and lipids, and packaging in
vesicles.
Trans (exit) face
• Polarity of cisternae.
• Forms glycolipids,
glycoproteins,
• Products of Golgi leave as
vessicles. From one cisternae
to another or out of cell.
Cis (forming) face
Lysosomes
• Membrane-bound organelle that
contains hydrolytic enzymes
responsible for the digestion of
macromolecules, autolysis,
intracellular digestion.
• Dead cells no longer able to
maintain H+ gradient (use H+
pump) so organelle breaks down
releasing contents.
• Made by ER and Golgi.
Lysosome
Function and
Production
From Production to Export
Vacuoles
• Storage of water or ions,
pigments, hold food, pump
out water.
• Are larger than vesicles
formed from golgi/E.R.
• In plants is enclosed by
Tonoplast (membrane) and
provides cell with hydrostatic
pressure
Peroxisomes
• Contain enzymes
(catalase) that
break down H2O2
formed during
metabolism of
alcohols, F.A.’s.
• Specialized forms
[glyoxysome] found
in seeds and
function during
germination.
Mitochondria
•
Production of ATP
•
Double-membrane system
–
Two distinct compartments
•
Have their own DNA. Maternal in
origin.
•
Divide on their own, independent
of cell.
•
Have ribosomes, produce
enzymes necessary for ATP
production.
Chloroplast
• Found in photosynthetic eukaryotes
• Two outer membranes
• Semifluid stroma; site of carbon fixation.
• Inner thylakoid membrane system; converts l.e. into c.e.
• Photosynthetic pigments found in other plastids.
Cytoskeleton
• Protein fibers that support and give shape to a cell,
involved in organelle movement throughout cell,
chromosome movement during cell division and large
cell movements (cell motility and cytokinesis)
• 3 Groups of Fibers classified according to size:
– Mircrotubules (thickest)
– Intermediated filaments (middle sized)
– Microfilaments (thinnest)
Components of the Cytoskeleton
• Microtubules
–  and Tubulin subunits; form hollow tube.
– Provide framework for cell, organized by
centrosome from which they usu. originate.
– “Rail” system for organelle transport.
•
Component of Centriole.
– Replicated prior to mitosis.
•
Form Cilia and Flagella.
– 9 + 2 arrangement (eukaryotic characteristic)
Fig. 6-UN3
Cilia and Flagella and the
Structural Basis of Cell Motility
• Surrounded by
plasma membrane.
• Motor proteins
(dynein) on
microtubules use ATP
to change shape and
“ratchet” past one
another.
• Movement causes
bending of
cilia/flagella.
Components of the Cytoskeleton
• Microfilaments (aka actin
filaments)
– Solid “rope”of two actin
proteins
– Thinner and more flexible
than microtubules
– Principle component of
muscle fibers.
– Provide mechanism to
support cell shape. Found
just inside the c. mem.
– Enable cell movement,
phagocytosis and
cytokinesis.
Components of the Cytoskeleton
•
Intermediate Filaments
– Tough and durable; made of
keratin.
– Mechanically
strengthen/reinforce cells or
cell parts that are under
stresses.
• Provide structure to long
cells.
• Found in desmosomes.
• Give nucleus shape
(nuclear lamina)
Cell-to Cell Junctions
• Plants
– Plasmodesmata
• Perforations in cell wall that allow passage for water/solutes to adjacent
cells.
• Animals
– Tight Junctions. Prevent leakage between cells (ie. Stomach)
– Desmosomes. Mechanically attach cells to each other. Serve as
anchoring sites for inter. filaments in cell.
– Gap Junctions. Analogous to plasmodesma. Fxn as comm.
Pathway between cells. Cardiac muscle, nerves.
Intracellular Junctions
Fig. 6-32
Tight junction
Tight junctions prevent
fluid from moving
across a layer of cells
0.5 µm
Tight junction
Intermediate
filaments
Desmosome
Gap
junctions
Space
between
cells
Plasma membranes
of adjacent cells
Desmosome
1 µm
Extracellular
matrix
Gap junction
0.1 µm
Fig. 6-32a
Tight junctions prevent
fluid from moving
across a layer of cells
Tight junction
Intermediate
filaments
Desmosome
Gap
junctions
Space
between
cells
Plasma membranes
of adjacent cells
Extracellular
matrix
Fig. 6-32b
Tight junction
0.5 µm
Fig. 6-32c
Desmosome
1 µm
Fig. 6-32d
Gap junction
0.1 µm
Plant Cell Walls
• Protect plants, allow for
shape and prevent excess
H2O uptake.
• Composed of cellulose
• Plasmodesmata connect
neighboring cells.
• Secondary cell wall inside of
primary wall. Forms wood
Plant Cell Wall
• Cell secretions form
pectin (polysaccharide
glue) which acts as
adhesive. Laid down in
middle lamella to hold
cells together.
Fig. 6-31
Cell walls
Interior
of cell
Interior
of cell
0.5 µm
Plasmodesmata Plasma membranes
Plasma Membrane
•
•
•
•
•
Forms the boundary for a cell
Selectively permeable
Made up of phospholipids
Fluid mosaic of lipids and proteins
Integral proteins are embedded in
the membrane
• Peripheral proteins are loosely bound to the
membrane’s surface
• Carbohydrates on the membrane’s surface
are crucial in cell to cell recognition
• Found in both plant and animal cells
Fig. 6-7
Outside of cell
Inside of
cell
0.1 µm
(a) TEM of a plasma
membrane
Carbohydrate side chain
Hydrophilic
region
Hydrophobic
region
Hydrophilic
region
Phospholipid
Proteins
(b) Structure of the plasma membrane
Fig. 6-30
Collagen
Proteoglycan
complex
EXTRACELLULAR FLUID
Polysaccharide
molecule
Carbohydrates
Fibronectin
Core
protein
Integrins
Proteoglycan
molecule
Plasma
membrane
Proteoglycan complex
Microfilaments
CYTOPLASM
Fig. 6-30a
Collagen
Proteoglycan
complex
EXTRACELLULAR FLUID
Fibronectin
Integrins
Plasma
membrane
Microfilaments
CYTOPLASM
Extracellular matrix (ECM)
• Intricate network of proteins and polysaccharides that
are organized into a meshwork on the outside of cells.
• Large polysaccharides and proteoglygans form a “gellike” material that resist compression.
• Proteins like collagen (most abundant protein in animals as part of
bone and skin) and elastin (stretch and recoil) provide structure
and strength.
• Adhesive-like proteins (fibronectins and laminin) help
cells attach to the appropriate part of the ECM.
Extracellular matrix (ECM)
Table 6-1
10 µm
10 µm
10 µm
Column of tubulin dimers
Keratin proteins
Actin subunit
Fibrous subunit (keratins
coiled together)
25 nm
7 nm


Tubulin dimer
8–12 nm
Table 6-1a
10 µm
Column of tubulin dimers
25 nm


Tubulin dimer
Table 6-1b
10 µm
Actin subunit
7 nm
Table 6-1c
5 µm
Keratin proteins
Fibrous subunit (keratins
coiled together)
8–12 nm
Fig. 6-UN1
Cell Component
Concept 6.3
The eukaryotic cell’s genetic
instructions are housed in
the nucleus and carried out
by the ribosomes
Structure
Surrounded by nuclear
envelope (double membrane)
perforated by nuclear pores.
The nuclear envelope is
continuous with the
endoplasmic reticulum (ER).
Nucleus
Function
Houses chromosomes, made of
chromatin (DNA, the genetic
material, and proteins); contains
nucleoli, where ribosomal
subunits are made. Pores
regulate entry and exit of
materials.
(ER)
Two subunits made of riboProtein synthesis
somal RNA and proteins; can be
free in cytosol or bound to ER
Ribosome
Concept 6.4
The endomembrane system
regulates protein traffic and
performs metabolic functions
in the cell
Concept 6.5
Mitochondria and chloroplasts change energy from
one form to another
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 carbohydrates, Ca2+ storage, detoxification of drugs and poisons
Golgi apparatus
Stacks of flattened
membranous
sacs; has polarity
(cis and trans
faces)
Modification of proteins, carbohydrates on proteins, and phospholipids; synthesis of many
polysaccharides; sorting of Golgi
products, which are then
released in vesicles.
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
Mitochondrion
Bounded by double
membrane;
inner membrane has
infoldings (cristae)
Cellular respiration
Endoplasmic reticulum
(Nuclear
envelope)
Chloroplast
Peroxisome
Rough ER: Aids in synthesis of
secretory and other proteins from
bound ribosomes; adds
carbohydrates to glycoproteins;
produces new membrane
Breakdown of ingested substances,
cell macromolecules, and damaged
organelles for recycling
Typically two membranes
Photosynthesis
around fluid stroma, which
contains membranous thylakoids
stacked into grana (in plants)
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
Fig. 6-UN1a
Structure
Cell Component
Concept 6.3
The eukaryotic cell’s genetic
instructions are housed in
the nucleus and carried out
by the ribosomes
Nucleus
Function
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.
Two subunits made of ribosomal RNA and proteins; can be
free in cytosol or bound to ER
Protein synthesis
(ER)
Ribosome
Fig. 6-UN1b
Cell Component
Concept 6.4
Endoplasmic reticulum
The endomembrane system
(Nuclear
regulates protein traffic and
envelope)
performs metabolic functions
in the cell
Golgi apparatus
Lysosome
Vacuole
Structure
Function
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 carbohydrates, Ca2+ storage, detoxification of drugs and poisons
Stacks of flattened
membranous
sacs; has polarity
(cis and trans
faces)
Rough ER: Aids in sythesis of
secretory and other proteins
from bound ribosomes; adds
carbohydrates to glycoproteins;
produces new membrane
Modification of proteins, carbohydrates on proteins, and phospholipids; synthesis of many
polysaccharides; sorting of
Golgi products, which are then
released in vesicles.
Breakdown of ingested subMembranous sac of hydrolytic stances cell macromolecules,
enzymes (in animal cells)
and damaged organelles for
recycling
Large membrane-bounded
vesicle in plants
Digestion, storage, waste
disposal, water balance, cell
growth, and protection
Fig. 6-UN1c
Cell Component
Concept 6.5
Mitochondrion
Mitochondria and chloroplasts change energy from
one form to another
Structure
Bounded by double
membrane;
inner membrane has
infoldings (cristae)
Function
Cellular respiration
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