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Welcome to Biology 160!
General Biology w/ Lab
Dr. Colleen Sheridan
Mon/Wed 6-9:20p
Rm AS 1617
Section 08
Logistics
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
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Attendance/Wait List
Class Website: Please download and print Lab #2:Cell Diversity
TODAY:
 Media Reading Conference and
 Review Ch1,2,3 from last week
 20 min break
 Lecture Ch 4 & 5
Presentations
Media Reading
During your conference:
1) Each person read ONE summary
2) All discuss what evidence was
given for and against a reliable
resource
The Scope of Life
– Biology is the scientific study of
life.
Life is structured on a size
scale ranging from the
molecular to the global.
Biology’s scope stretches
across the enormous
diversity of life on Earth.
Biosphere
Ecosystem
African savanna
Community
All organisms in savanna
Organism
Zebra
Population
Herd of zebras
Organ system
Circulatory system
Organ
Heart
Cell
Tissue
Heart muscle
cell
Heart muscle tissue
Molecule
DNA
Atom
Oxygen atoms
Ecosystems
Each organism
interacts continuously
with its environment
and each is affected
by the other.
Inflow
of
light
energy
Loss
of
heat
energy
Chemical
energy
(food)
Ecosystem dynamics:
Producers
- Cycling of nutrients
- Flow of energy
Cycling
of
nutrients
Consumers
(plants and
other
photosynthetic
organisms)
(such as
animals)
Decomposers
Ecosystem
The
prokaryotic
cell is simple,
small, and
contains no
organelles.
The
eukaryotic
cell is larger
and more
complex
and
contains
organelles.
DNA!
– All cells use DNA as the chemical
material of genes.
• Genes are the units of inheritance that
transmit information from parents to
offspring.
– The language of DNA contains just
four letters:
• A, G, C, T
The Three Domains of Life
– The three domains of life are:
• Bacteria
• Archaea
• Eukarya
Prokaryotes
Eukaryotes
At least four kingdoms of Eukarya
-Plantae
-Fungi
-Animalia
-Protists (a group of multiple kingdoms)
The Darwinian View of Life
The
evolutionary
view of life
came into
focus in
1859 when
Charles
Darwin
published
The Origin
of Species.
Observing Natural Selection
– There are many examples of natural selection
in action.
• The development of antibiotic-resistant bacteria is
one.
Tuberculosis
- MDR-TB
- XDR-TB
Staphylcoccus aureus (staph)
- CA-MRSA
Observations
Question
Hypothesis
Prediction
Test does not
support hypothesis;
revise hypothesis or
pose new one
Test
Test supports
hypothesis
Chapter 2
Essential Chemistry for Biology
Matter: Elements and
Compounds
– Matter is anything that occupies space and has
mass.
– Matter is found on the Earth in three physical
states:
•Solid
•Liquid
•Gas
– Twenty-five elements are essential to life.
• Four of these make up about 96% of the weight
of the human body.
• Trace elements occur in smaller amounts.
Atoms
– Atoms are composed of subatomic
particles.
• A proton is positively charged.
• An electron is negatively charged.
• A neutron is electrically neutral.
Example:
a helium atom
Isotopes
– Isotopes are alternate mass forms of an
element.
• They have the same number of protons and
electrons.
• But they have a different number of neutrons.
– In radioactive isotopes,
• The nucleus decays, giving off particles and energy.
– Radioactive isotopes have many uses in
research and medicine.
• Example: PET scans
– Uncontrolled exposure to radioactive isotopes
can harm living organisms by damaging DNA.
• Example: the 1999 Chernobyl nuclear accident
Chemical Bonding and
Molecules
– Chemical reactions enable atoms to give up or
acquire electrons in order to complete their outer
shells.
• These interactions usually result in atoms staying
close together.
• The atoms are held together by chemical bonds.
Ionic Bonds
– When an atom loses or gains electrons, it
becomes electrically charged.
• Charged atoms are called ions.
• Ionic bonds are formed between oppositely
charged ions.
Covalent Bonds
– A covalent bond forms when two atoms
share one or more pairs of outer-shell
electrons.
Hydrogen Bonds
– Water is a compound in which the
electrons in its covalent bonds are shared
unequally.
• This causes it to be a polar molecule, one with
opposite charges on opposite ends.
+
-
– The polarity of water results in weak
electrical attractions between neighboring
water molecules.
• These interactions are called hydrogen bonds.
Chemical Reactions
– Cells constantly rearrange molecules by
breaking and forming chemical bonds.
• These processes are called chemical reactions.
– Chemical reactions cannot create or destroy
matter,
• They only rearrange it.
Water’s Life-Supporting
Properties
– The polarity of water molecules and the
hydrogen bonding that results explain most of
water’s life-supporting properties:
•
•
•
•
Water’s cohesive nature
Water’s ability to moderate temperature
Floating ice
Versatility of water as a solvent
To describe the acidity
of a solution,
we use the pH scale
Chapter 3
The Molecules of Life
Carbon Chemistry
– Carbon is a versatile atom.
• It has four electrons in an outer shell
that holds eight.
• Carbon can share its electrons with other
atoms to form up to four covalent bonds.
– The simplest organic compounds are
hydrocarbons.
• These are organic molecules containing only
carbon and hydrogen atoms.
• The simplest hydrocarbon is methane.
– The unique properties of an organic
compound depend not only on its carbon
skeleton but also on the atoms attached to
the skeleton.
• These atoms are called functional groups.
– Most macromolecules are polymers.
• Polymers are made by stringing together many
smaller molecules called monomers.
• Cells link monomers by dehydration reactions.
– Organisms also have to break down
macromolecules.
• Cells do this by a process called hydrolysis.
Biological Molecules
– There are four categories of large molecules in
cells:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
Monosaccharides
small
sugar
molecules
– Monosaccharides are simple sugars.
• Glucose is found in sports drinks.
• Fructose is found in fruit.
Monomer - means “one” unit
Dimer - means “two” units
Polymer - means “many” units
Isomers
– The monosaccharides glucose and fructose
are isomers.
• They have the same formula, but their atoms are
arranged differently.
– In aqueous solutions, monosaccharides
form rings.
Monosaccharides are the main fuel that
cells use to do work.
Disaccharides
– A disaccharide is a double sugar.
• It is constructed from two monosaccharides.
– Disaccharides are joined through a
dehydration reaction.
Polysaccharides
– Complex carbohydrates are called
polysaccharides.
• They are long chains of sugar units.
• They are polymers of monosaccharides.
Fats
– Dietary fat consists largely of the molecule
triglyceride.
• Triglyceride is a combination of glycerol and
three fatty acids.
– Unsaturated fatty acids
• Have less than the maximum number of hydrogens
bonded to the carbons. (double and triple bonds)
– Saturated fatty acids
• Have the maximum number of hydrogens bonded to
the carbons. (all single bonds)
Saturated Fatty Acids:
Too much of a good thing can be bad
– Most animal fats have a high proportion of
saturated fatty acids, which can be unhealthy.
• Example: butter
– Most plant oils tend to be low in saturated fatty
acids.
• Example: corn oil
WHY are too many saturated fats unhealthy?
– Synthetic anabolic steroids are
controversial.
• They are variants of testosterone.
Proteins
– A protein is a polymer constructed from
amino acid monomers.
– Proteins perform most of the tasks the
body needs to function.
Structural Proteins
Receptor Proteins
Storage Proteins
Enzymes
Contractile Proteins
Hormonal Proteins
Transport Proteins
Sensory Proteins
Defensive Proteins
Gene Regulatory
Proteins
Structure of an
Amino Acid
Proteins as Polymers
– Cells link amino acids together by
dehydration reactions.
• The resulting bond between them is called a
peptide bond.
Protein
Shape
– Proteins
have four
levels of
structure.
Nucleic Acids
– Nucleic acids are information storage
molecules.
• They provide the directions for building
proteins.
Transcription
Translation
– Nucleic acids are polymers of nucleotides.
– Each DNA nucleotide has one of the following
bases:
– Nucleotide
monomers are
linked into long
chains.
• These chains are
called
polynucleotides, or
DNA strands.
• A sugar-phosphate
backbone joins them
together.
– Two strands of DNA
join together to form a
double helix.
– RNA, ribonucleic acid, is different from
DNA.
• Its sugar has an extra OH group.
• It has the base uracil (U) instead of thymine (T).
Evolution Connection:
DNA and Proteins as Evolutionary Tape Measures
You can use
DNA and protein
sequences to
test how closely
related two
species are in
evolution.
Copyright © 2007 Pearson Education, Inc. publishing as Pearson Benjamin Cummings
Figure 4.6a
The Microscopic World of
Cells
– Organisms are either:
• Single-celled, such as most bacteria and protists
• Multicelled, such as plants, animals, and most fungi
Microscopes as a Window on
the World of Cells
– The light microscope is used by many
scientists.
• Light passes through the specimen.
• Lenses enlarge, or magnify, the image.
Euglena in a light microscope
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Characteristics of Microscopes
– Magnification
• Is an increase in the specimen’s apparent size.
– Resolving power
• Is the ability of an optical instrument to show
two objects as being separate.
The Discovery of Cells
and the
Cell Theory
– Cells were first discovered
in 1665 by Robert Hooke.
– The accumulation of scientific evidence led to
the cell theory.
• All living things are composed of cells.
• All cells are formed from previously existing cells.
– The electron microscope (EM) uses a beam of
electrons.
• It has a higher resolving power than the light
microscope.
– The electron microscope can magnify up to
100,000X.
• Such power reveals the diverse parts within a cell.
– The scanning electron microscope (SEM)
is used to study the detailed architecture of
the surface of a cell.
– The transmission electron microscope
(TEM) is useful for exploring the internal
structure of a cell.
The Two Major Categories of
Cells
– The countless cells on earth fall into two
categories:
• Prokaryotic cells
• Eukaryotic cells
– Prokaryotic and eukaryotic cells differ in several
respects.
The Two Major Categories of
Cells
– The countless cells on earth fall into two
categories:
• Prokaryotic cells
• Eukaryotic cells
– Prokaryotic and eukaryotic cells differ in several
respects.
Figure 4.4
– Prokaryotic cells
• Are smaller than eukaryotic cells.
• Lack internal structures surrounded by
membranes.
• Lack a nucleus.
A Panoramic View of Eukaryotic Cells
– An idealized animal cell
– An idealized plant cell
Cytoplasmic Streaming
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and
Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Membrane Structure
– The plasma membrane separates the living
cell from its nonliving surroundings.
The Plasma Membrane:
A Fluid Mosaic of Lipids and
Proteins
– The membranes of cells are composed
mostly of:
• Lipids
• Proteins
Copyright © 2007 Pearson Education, Inc. publishing as Pearson Benjamin Cummings
– The lipids belong to a special category
called phospholipids.
– Phospholipids form a two-layered
membrane, the phospholipid bilayer.
– Most membranes have specific proteins
embedded in the phospholipid bilayer.
– Membrane phospholipids and proteins can drift
about in the plane of the membrane.
– This behavior leads to the description of a
membrane as a fluid mosaic:
• Molecules can move freely within the membrane.
• A diversity of proteins exists within the membrane.
Cell Surfaces
– Most cells secrete materials for coats of one
kind or another
• That are external to the plasma membrane.
– These extracellular coats help protect and
support cells
• And facilitate interactions between cellular neighbors
in tissues.
– Plant cells have cell walls,
• Which help protect the cells, maintain their shape,
and keep the cells from absorbing too much water.
– Animal cells have an extracellular matrix,
• Which helps hold cells together in tissues and
protects and supports them.
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
The Nucleus and Ribosomes:
Genetic Control of the Cell
– The nucleus is the manager of the cell.
• Genes in the nucleus store information necessary to
produce proteins.
Structure and Function of the Nucleus
– The nucleus is bordered by a double membrane
called the nuclear envelope.
• It contains chromatin and a nucleolus.
Chromatin: long strands of DNA and associated proteins
Nucleolus: makes the component parts of ribosomes
Ribosomes:
Protein Synthesis
– Ribosomes are responsible for protein
synthesis.
How DNA Controls the Cell
– DNA controls the cell by transferring its coded
information into RNA.
• The information in the RNA is used to make proteins.
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
The Endomembrane System: Manufacturing
and Distributing Cellular Products
– Many of the membranous organelles in the cell
belong to the endomembrane system.
The Endoplasmic Reticulum
– The endoplasmic reticulum (ER)
• Produces an enormous variety of molecules.
• Is composed of smooth and rough ER.
Rough ER
– The “roughness” of the rough ER is due to
ribosomes that stud the outside of the ER
membrane.
– The functions of the rough ER include:
• Producing two types of membrane proteins
– Membrane proteins
– Secretory proteins
• Producing new membrane
Rough ER
– The “roughness” of the rough ER is due to
ribosomes that stud the outside of the ER
membrane.
– The functions of the rough ER include:
• Producing two types of membrane proteins
– Membrane proteins
– Secretory proteins
• Producing new membrane
– After the rough ER synthesizes a molecule,
it packages the molecule into transport
vesicles.
Smooth ER
– The smooth ER lacks the surface
ribosomes of ER and produces lipids,
including steroids.
The Golgi Apparatus
– The Golgi apparatus
• Works in partnership with the ER.
• Refines, stores, and distributes the chemical
products of cells.
Lysosomes
– A lysosome is a membrane-enclosed sac.
• It contains digestive enzymes.
• The enzymes break down macromolecules.
– Lysosomes have several types of digestive
functions.
• They fuse with food vacuoles to digest the food.
– They break down damaged organelles.
Vacuoles
– Vacuoles are membranous sacs.
• Two types are the contractile vacuoles of
protists and the central vacuoles of plants.
– A review of the endomembrane system
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Energy Conversion:
Chloroplasts & Mitochondria
– Cells require a constant energy supply to do all
the work of life.
Chloroplasts
– Chloroplasts are the sites of
photosynthesis, the conversion of light
energy to chemical energy.
Mitochondria
– Mitochondria are the sites of cellular
respiration, which involves the production
of ATP from food molecules.
– Mitochondria and chloroplasts share another
feature unique among eukaryotic organelles.
• They contain their own DNA.
– The existence of separate “mini-genomes” is
believed to be evidence that
• Mitochondria and chloroplasts evolved from
free-living prokaryotes in the distant past.
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
The Cytoskeleton:
Cell Shape and Movement
– The cytoskeleton is an infrastructure of the
cell consisting of a network of fibers.
Maintaining Cell Shape
– One function of the cytoskeleton
• Is to provide mechanical support to the cell and
maintain its shape.
– The cytoskeleton can change the shape of
a cell.
• This allows cells like amoebae to move.
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Structure Meets Function
in a
Eukaryotic Cell
• Plasma Membrane and Cell Surface
• Nucleus and Ribosomes
• Endomembrane System
–
–
–
–
Endoplasmic Reticulum (ER)
Golgi Body
Lysosomes
Vacuoles
• Energy Conversion: Chloroplasts and Mitochondria
• Cytoskeleton
• Cilia and Flagella
Cilia and Flagella
– Cilia and flagella are motile appendages.
– Flagella propel the cell in a whiplike
motion.
– Cilia move in a coordinated back-and-forth
motion.
Paramecium Cilia
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
– Some cilia or flagella extend from
nonmoving cells.
• The human windpipe is lined with cilia.
Using scientific data some
computer scientists put
together a movie of the inside
of a living cell:
http://www.studiodaily.com/main/technique/tprojects/6850.html
Some Basic Energy Concepts
– Energy makes the world go around.
• What is energy?
Conservation of Energy
– Energy is defined as the capacity to
perform work.
– Kinetic energy is the energy of motion.
– Potential energy is stored energy.
– Energy can be changed from one form to
another.
• However, it cannot be created or destroyed.
• This is the conservation of energy principle.
Heat
• Is a type of kinetic energy.
• Is a product of all energy conversions.
Entropy
– Scientists use the term entropy as a
measure of disorder, or randomness.
• All energy conversions increase the entropy of
the universe.
Chemical Energy
• Is a form of potential energy.
• Is found in food, gasoline, and other fuels.
– Living cells and automobile engines use
the same basic process to make chemical
energy do work.
Combustion
Cellular Respiration
– Cellular respiration
• Is the energy-releasing chemical breakdown of
fuel molecules.
• Provides energy for the cell to do work.
Food Calories
– A calorie is the amount of energy that raises
the temperature of one gram of water by one
degree Celsius.
– The kilocalorie is
• 1,000 calories.
• The unit used to measure the energy in food.
Potential (Chemical) Energy
In Foods
Kinetic Energy Used
by Activities
ATP and Cellular Work
– The chemical energy of organic molecules
is released in cellular respiration to make
ATP in the mitochondria. ATP is the
currency of the cell.
The Structure of ATP
– ATP (adenosine triphosphate)
• Consists of adenosine plus a tail of three
phosphate groups.
• Is broken down to ADP, accompanied by the
release of energy.
Phosphate Transfer
– ATP can energize other molecules by
transferring phosphate groups.
• This energy can be used to drive cellular work.
The ATP Cycle
– Cellular work spends ATP.
– ATP is recycled from ADP and phosphate
through cellular respiration.
Enzymes
– Metabolism is the sum total of all chemical
reactions that occur in organisms.
– Few metabolic reactions occur without the
assistance of enzymes.
Biology and Society:
Stonewashing Without the
Stones
– The sturdy cotton fabric denim has been worn
because of its toughness and appeal.
– Stonewashing jeans with pumice stone can
damage the fabric.
– Recently the enzyme cellulase has been used to
achieve better results.
Copyright © 2007 Pearson Education, Inc. publishing as Pearson Benjamin Cummings
Activation Energy
– Activation energy
• Is the energy that activates the reactants in a
chemical reaction.
• Triggers a chemical reaction to proceed.
– Enzymes
• Lower the activation energy for chemical reactions.
Figure 5.8
Induced Fit
– Each enzyme is very selective.
• It catalyzes specific reactions.
– Each enzyme recognizes a specific substrate.
• The active site fits to the substrate, and the enzyme
changes shape slightly.
• This interaction is called induced fit.
– Enzymes can function over and over again.
How Enzymes Work
Enzyme Inhibitors
– Enzyme inhibitors
• Can inhibit a metabolic reaction.
• Bind to the active site, as substrate imposters.
– Other inhibitors
• Bind at a remote site, changing the enzyme’s
shape.
• In some cases, this is called feedback
regulation.
Membrane Function
– Working cells control the transport of materials to
and from the environment with membranes.
Transport
of materials
Passive Transport:
Diffusion Across Membranes
– Molecules contain heat energy.
• They vibrate and wander randomly.
– Diffusion is one result of the movement of
molecules.
• Molecules tend to spread into the available space.
• Diffusion is passive transport; no energy is needed.
– Another type of passive transport is
facilitated diffusion, the transport of some
substances by specific transport proteins
that act as selective corridors.
Osmosis and Water Balance
in Cells
– Osmosis is the passive transport of water
across a selectively permeable membrane.
[solute]
= [solute]
[solute]
Plasmolysis
Water Balance in Cells
– Osmoregulation is the control of water
balance in animals.
Contractile vacuoles in Protists
Kidneys and gills in freshwater fish
– Water balance in plant cells is different.
• They have rigid cell walls.
• They are at the mercy of the environment.
Membrane Function
– Working cells control the transport of materials to
and from the environment with membranes.
– They do this with the aid of membrane proteins.
Active Transport: The Pumping of
Molecules Across Membranes
– Active transport requires energy to move
molecules across a membrane.
Exocytosis and Endocytosis:
Traffic of Large Molecules
– Exocytosis
• Secretes substances outside of the cell.
– Endocytosis
• Takes material into the cell.
– In phagocytosis (“cellular eating”), a cell
engulfs a particle and packages it within a
food vacuole.
– In pinocytosis (“cellular drinking”), a cell
“gulps” droplets of fluid by forming tiny
vesicles.
– Phagocytosis at work…
A macrophage
(big eater)
Plasma membrane
= green
QuickTime™ and a
decompressor
are needed to see this picture.
Infectious agent
= red
– Receptor-mediated endocytosis
• Is triggered by the binding of external
molecules to membrane proteins.
The Role of Membranes in
Cell Signaling
– Cellular communication
• Begins with the reception of an extracellular signal.
– The signal transduction pathway
• Consists of proteins and other molecules that relay
the signal.
Figure 5.20