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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

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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

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o The quality of an image depends on

o Magnification, the ratio of an objects image size
to its real size
o Resolution, the measure of the clarity of the
image, or the minimum distance of two
distinguishable points

o Contrast, visible differences in parts of the

sample
Brightfield

Phase Contrast

Hoffman modulation contrast

10 m
1m

Human height
Length of some
nerve and
muscle cells

0.1 m
Chicken egg

1 cm

Unaided eye

o LMs can magnify effectively to

about 1,000 times the size of
the actual specimen

Frog egg

(membrane-enclosed
compartments), are too small to

be resolved by an LM

Most plant and

animal cells

10 m
1 m
100 nm
10 nm

Nucleus
Most bacteria
Mitochondrion

Smallest bacteria
Viruses
Ribosomes
Proteins

Electron microscope

o Most subcellular structures,

including organelles

100 m

Light microscope

1 mm

o Various techniques enhance

contrast and enable cell
components to be stained or
labeled

Lipids

1 nm
Small molecules

0.1 nm

Atoms

50 m

Brightfield
(unstained specimen)

Brightfield
(stained specimen)

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50 m

Brightfield
(unstained specimen)

Phase-contrast

50 m

Brightfield
(unstained specimen)

Differential-interferencecontrast (Nomarski)

Super-resolution

Longitudinal section
of cilium

Deconvolution

Cross section
Confocal
of cilium

Cilia

Fluorescence
Transmission electron
microscopy (TEM)

Scanning electron
microscopy (SEM)

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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

Cilia

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

o Recent advances in light microscopy

o Confocal microscopy and deconvolution
microscopy provide sharper images of threedimensional tissues and cells
o New techniques for labeling cells improve
resolution
Confocal
Deconvolution

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

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Figure 6.4

TECHNIQUE

Homogenization
Tissue
cells
Homogenate
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

Centrifugation

Differential
centrifugation

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

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:
o No nucleus
o DNA in an unbound region called the nucleoid
o No membrane-bound organelles (none surrounded by
a phospholipid membrane)

o Cytoplasm bound by the plasma membrane

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Figure 6.5

Fimbriae
Nucleoid
Ribosomes
Plasma
membrane
Bacterial
chromosome

Cell wall
Capsule
0.5 m
Flagella

(a) A typical
rod-shaped
bacterium

(b) A thin section

through the
bacterium Bacillus
coagulans (TEM)

o Eukaryotic cells have internal membranes

that compartmentalize their functions
o Organelles

o Eukaryotic cells are characterized by

having
o DNA in a nucleus that is bounded by a
membranous nuclear envelope
o Membrane-bound organelles
o Cytoplasm in the region between the plasma
membrane and nucleus

o Eukaryotic cells are generally much larger

than prokaryotic cells

Eukaryotic Cell

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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

Carbohydrate side chains

Hydrophilic
region

Hydrophobic
region
Hydrophilic
region

Phospholipid

Proteins

(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

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Figure 6.7

Surface area increases while

total volume remains constant

5
1
1
Total surface area
[sum of the surface areas
(height width) of all box
sides number of boxes]

150

750

Total volume
[height width length
number of boxes]

125

125

Surface-to-volume
(S-to-V) ratio
[surface area volume]

1.2

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)

Flagellum

Rough
ER

Nuclear
envelope
Nucleolus
Chromatin

Smooth
ER

NUCLEUS

Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate filaments
Microtubules
Ribosomes
Microvilli
Golgi apparatus
Peroxisome
Mitochondrion

Lysosome

Animal Cell

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Figure 6.8c

Nuclear
envelope
NUCLEUS

Nucleolus
Chromatin

Rough
endoplasmic
reticulum

Smooth
endoplasmic
reticulum

Ribosomes
Central vacuole
Golgi
apparatus

Microfilaments
Intermediate
filaments
Microtubules

CYTOSKELETON

Mitochondrion
Peroxisome
Chloroplast

Plasma membrane
Cell wall

Plasmodesmata

Wall of adjacent cell

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

The Nucleus: Information Central

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

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Figure 6.9
1 m
Nucleus
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore

Rough ER

Surface of nuclear
envelope

Pore
complex
Ribosome

Chromatin

1 m

0.25 m

Close-up
of nuclear
envelope

Pore complexes (TEM)

Nuclear lamina (TEM)

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
o Network 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

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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)
o make proteins that stay within the cell

o On the outside of the endoplasmic reticulum or the

nuclear envelop (bound ribosomes)
o make 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

0.5 m
TEM showing ER and ribosomes

Small
subunit
Diagram of a ribosome

The endomembrane system regulates

protein traffic & performs metabolic
functions in the cell
o Components of the endomembrane system:
o Nuclear envelope
o Endoplasmic reticulum
o Golgi apparatus
o Lysosomes
o Vacuoles
o Plasma membrane
o These components are either continuous with
each other OR connected via transfer by vesicles

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The Endoplasmic Reticulum:

Biosynthetic Factory
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

Figure 6.11

Smooth ER

Nuclear
envelope

Rough ER

ER lumen
Cisternae

Transitional ER
Ribosomes
Transport vesicle

Smooth ER

Rough ER

200 nm

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

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The Golgi Apparatus:

Shipping and Receiving Center
o The Golgi apparatus consists of flattened
membranous sacs called cisternae

o Functions:
o Modifies products of the ER
o Manufactures certain macromolecules
o Sorts and packages materials into transport
vesicles

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

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Figure 6.13

Vesicle containing
two damaged
organelles

1 m

Nucleus

1 m

Mitochondrion
fragment
Peroxisome
fragment

Lysosome

Digestive
enzymes

Lysosome

Lysosome
Plasma membrane

Peroxisome
Digestion

Food vacuole
Vesicle

Mitochondrion

Digestion

(b) Autophagy

(a) Phagocytosis

Vacuoles:
Diverse Maintenance Compartments
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

Figure 6.14

Central vacuole
Cytosol

Nucleus

Central
vacuole

Cell wall
Chloroplast
5 m

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The Endomembrane System: A

Review
o The endomembrane system is a complex and
dynamic player in the cells compartmental
organization

Figure 6.15-1

Nucleus

Rough ER
Smooth ER

Plasma
membrane

Figure 6.15-2

Nucleus

Rough ER
Smooth ER
cis Golgi

trans Golgi

Plasma
membrane

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Figure 6.15-3

Nucleus

Rough ER
Smooth ER
cis Golgi

trans Golgi

Plasma
membrane

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

The Evolutionary Origins of

Mitochondria and Chloroplasts
o Mitochondria and chloroplasts have
similarities with bacteria:
o (Are not part of the endomembrane system)
o Have a double membrane (2 membranes with a
space between)
o Contain free ribosomes and circular DNA
molecules
o Grow and reproduce somewhat independently
in cells

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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

Figure 6.16

Endoplasmic
reticulum

Engulfing of oxygenusing nonphotosynthetic

prokaryote, which
becomes a mitochondrion

Nucleus

Nuclear
envelope

Ancestor of
eukaryotic cells
(host cell)

Mitochondrion

Nonphotosynthetic
eukaryote

At least
one cell

Engulfing of
photosynthetic
prokaryote
Chloroplast

Mitochondrion
Photosynthetic eukaryote

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

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Figure 6.17

10 m
Intermembrane space
Mitochondria

Outer
membrane

DNA
Inner
membrane

Free
ribosomes
in the
mitochondrial
matrix

Mitochondrial
DNA

Cristae
Matrix

Nuclear DNA
0.1 m
(b) Network of mitochondria in a protist
cell (LM)

(a) Diagram and TEM of mitochondrion

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

50 m

Ribosomes
Stroma
Inner and outer
membranes
Granum

DNA
Intermembrane space
Thylakoid
(a) Diagram and TEM of chloroplast

Chloroplasts
(red)
1 m
(b) Chloroplasts in an algal cell

oChloroplast structure includes:

oThylakoids, membranous sacs, stacked
to form a granum

oStroma, the internal fluid

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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:

Microtubule

o Microtubules
o Microfilaments
o Intermediate filaments
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

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Components of the
Cytoskeleton
o Three main types of fibers make up the
cytoskeleton:
o Microtubules are the thickest of the three
components of the cytoskeleton
o Microfilaments, also called actin filaments, are
the thinnest components
o Intermediate filaments are fibers with diameters
in a middle range

Table 6.1

10 m

10 m

5 m

Column of tubulin dimers

Keratin proteins
Fibrous subunit (keratins
coiled together)

Actin subunit
25 nm
7 nm

812 nm

Tubulin dimer

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
o Guiding movement of organelles
o Separating chromosomes during cell division

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Table 6.1a

10 m

Column of tubulin dimers

25 nm

Tubulin dimer

Centrosomes and Centrioles

o In many cells, microtubules grow out from a
centrosome near the nucleus
o The centrosome is a microtubuleorganizing 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)

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Fig. 6-23

Direction of swimming

(a) Motion of flagella

5 m

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

Outer microtubule
doublet

0.1 m

Plasma
membrane

Dynein proteins
Central
microtubule
Radial
spoke
Protein crosslinking outer
doublets

Microtubules

Plasma
membrane

(b) Cross section of

cilium

Basal body

0.5 m

(a) Longitudinal
section of cilium

0.1 m
Triplet

(c) Cross section of basal body

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Microtubule
doublets

ATP

o How dynein walking moves

flagella and cilia:
o Dynein 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

Dynein
protein
(a) Effect of unrestrained dynein movement
ATP

Cross-linking proteins
inside outer doublets

Anchorage
in cell

(b) Effect of cross-linking proteins

1

3
2

Animation: Cilia and Flagella

(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

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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

Table 6.1b

10 m

Actin subunit

7 nm

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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

Table 6.1c

5 m

Keratin proteins
Fibrous subunit (keratins
coiled together)
812 nm

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:
o Cell walls of plants
o The extracellular matrix (ECM) of animal cells
o Intercellular junctions

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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
o maintains 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
o Middle 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
o
o
o

Support
Adhesion
Movement
Regulation

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Fig. 6-30

Collagen

Proteoglycan
complex

EXTRACELLULAR FLUID

Polysaccharide
molecule
Carbohydrates

Fibronectin

Core
protein
Integrins

Proteoglycan
molecule

Plasma
membrane

Proteoglycan complex

Microfilaments

CYTOPLASM

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
o Desmosomes
o Gap junctions

Plasmodesmata in Plant Cells

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
Cell walls
Interior
of cell

Interior
of cell
0.5 m

Plasmodesmata Plasma membranes

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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
Tight junctions prevent
fluid from moving
across a layer of cells

0.5 m

Tight junction
Intermediate
filaments

Desmosome

Gap
junctions

Space
between
cells
Plasma membranes
of adjacent cells

Desmosome

1 m

Extracellular
matrix
Gap junction

0.1 m

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

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Figure 6.UN01
Nucleus

(ER)

(Nuclear
envelope)

Figure 6.UN01a

Nucleus

(ER)

Figure 6.UN01b

(Nuclear
envelope)

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Figure 6.UN01c

31