Chapter 1 The Main Themes of Microbiology
Microbiology is introduced and the scope of this science is discussed. Microorganisms and their
impact on Earth, as well as on humans, are described. The origin and evolution of prokaryotes
and eukaryotes, as well as the ubiquitous nature of microorganisms are discussed. A history of
microbiology is given, highlighting the major scientific contributions to the development of the
field. The levels of classification are introduced and the basis of taxonomy is discussed. Two
different systems of presenting a universal tree of life are introduced.
Expected Learning Outcomes
1.01
1.02
1.03
1.04
1.05
1.06
1.07
1.08
1.09
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
Define microbiology and microorganisms and identify the major organisms included in the
science.
Name and define the primary areas of study within the science of microbiology.
Describe the basic characteristics of prokaryotic cells and eukaryotic cells and their
evolutionary origins.
State several ways that microbes are involved in the earth’s ecosystems.
Describe the cellular make up of microorganisms, their size range, and indicate how viruses differ
from cellular microbes.
Discuss the ways microorganisms may be applied to solve human problems.
Review the roles of microorganisms as pathogens that cause infection and disease.
Define what is meant by emerging and re-emerging diseases.
Outline the major events in the history of microbiology including the major contributors to the
early development of microscopy, medical advances, aseptic techniques, and the germ theory of
disease.
Explain the main features of the scientific method, and differentiate between inductive and
deductive reasoning and between hypothesis and theory.
Define taxonomy and its supporting terms classification, nomenclature, and identification.
Explain how the levels of a taxonomic scheme relate to each other. Give the names of the levels,
and place them in a hierarchy.
Describe the goals of nomenclature and how the binomial system is structured. Know how to
correctly write a scientific name.
Discuss the fundamentals of evolution, evidence used to verify evolutionary trends, and how it is
used in studying organisms.
Outline some of the primary evidence used to verify evolutionary trends.
Explain the basis for classification, taxonomy, and nomenclature. .
Recall the order of taxa and the system of notation used in creating scientific names.
Chapter Outline
1.1 The Scope of Microbiology
1.2 General Characteristics of Microorganisms and Their Roles in the Earth’s Environments
A. The Origins and Dominance of Microorganisms:
B. The Cellular Organization of Microorganisms:
C. Microbial Dimensions: How Small is Small?
D. Microbial Involvement in Energy and Nutrient Flow
1.3 Human Use of Microorganisms
1.4 Microbial Roles in Infectious Diseases
1.5 The Historical Foundations of Microbiology
A. The Development of the Microscope: "Seeing Is Believing"
1. Antonie van Leeuwenhoek
B. The Establishment of the Scientific Method
1. Hypothesis
2. Deductive Approach
3. Theory
4. Law
C. The Development of Medical Microbiology
D. The Discovery of Spores and Sterilization
1. The Development of Aseptic Techniques
2. The Discovery of Pathogens and the Germ Theory of Disease
1.6 Taxonomy: Organizing, Classifying, and Naming Microorganisms
A.
The Levels of Classification
1. Domain
2. Kingdom
3. Phylum or Division
4. Class
5. Order
6. Family
7. Genus
B. Assigning Specific Names
1. Binomial (Two-Name) System of Nomenclature
1.7 The Origin and Evolution of Microorganisms
A. Systems For Presenting a Universal Tree of Life
B. All Life Is Related and Connected Through Evolution
Key Terms and Phrases
emerging diseases
pathogens
bioremediation
genetic engineering
microbiology
microscopic
microorganisms
microbes
bacteria
viruses
fungi
protozoa
algae
helminths
macroscopic
adaptability
immunology
epidemiology
biotechnology
infectious
prokaryote
eukaryote
phylum
parasites
hosts
spontaneous generation
abiogenesis
biogenesis
scientific method
hypothesis
deduction
deductive
theory
law
sterilization
aseptic technique
germ theory of disease
nomenclature
taxonomy
taxa
classification
identification
domain
kingdom
division
class
order
family
genus
hierarchies
species
scientific names
evolutionary
morphology
physiology
genetics
bacteria
archaea
Kingdom Monera
Kingdom Protista
Kingdom Myceteae
Kingdom Animalia
Kingdom Plantae
Student Activities
1. Research if bioremediation is used for the treatment of municipal wastewater, solid
waste, or hazardous waste in your community. If so, have students visit the treatment
plants and landfills. Ask students to report on the kinds of microorganisms used in
bioremediation as well as the role of the microorganisms in bioremediation.
2. Ask students to list ways in which microbes contribute to the biosphere. After students
have completed their lists, spend time discussing how the contributions of microbes have
affected the evolution of microbes.
3. After reading the Making Connections 1.2, have students come up with simple
experiments, similar to the work of Francesco Redi, that could have been done in the
mid-1600s to support the idea of biogenesis. This is a good way to have students put the
scientific method to work. Also, this will introduce the concept that experiments do not
have to be complex.
4. After discussing Table 1.1 in class, have students come up with examples of work being
done in the areas of basic and applied microbiology listed. Good places for students to
look for these examples include the “Science in the News” section of their local
newspaper as well as online searches.
Classroom Discussion
1. Have students read the original article written by Dr. Oliver Wendell Holmes discussing
the transmission of puerperal fever in a hospital setting. The essay was originally
published in the New England Quarterly Journal of Medicine and Surgery, April 1843
(1):503–529. After students have read the article, discuss the dangers of infection in
giving birth and how a simple act (such as hand washing) can drastically reduce the
transmission of microorganisms. This article also can serve to highlight the tremendous
advances that have occurred in the field of microbiology over the last 163 years.
2. Walk students through the systems presenting the universal tree of life. Explain how the
grouping/phylogeny of organisms is based on their evolutionary development.
3. The Making Connections Box 1.1 contains a statement by Surgeon General David
Satcher “Organisms changed and people changed.” As this section is covered in class,
spend time discussing how the average human life span is increasing, how individuals
with cancer and AIDS in developed countries have longer life expectancies, how the
density of a population can affect transmission of microorganisms, and how
microorganisms have adapted to become resistant to antibiotics.
4. Scientists must be willing and able to change a theory in response to new data. A recent
example of a theory that was changed in response to new data occurred in the treatment
of stomach ulcers. For decades, ulcers were believed to be the result of stress and were
often treated by surgery. Dr. Bruce Marshall believed that stomach ulcers were the result
of bacterial infections. Physicians did not believe his hypothesis because they did not
think bacteria could survive in the acidic conditions of the stomach. In order to test his
hypothesis, Dr. Marshall drank a culture of Helicobacter pylori. A week later he
exhibited signs of an ulcer, which he then treated with antibiotics. This work was
published in the scientific journal Lancet 1983, June 4;1(8336):1273–5, and today ulcers
are treated with antibiotics and research is underway on a vaccine for Helicobacter
pylori. Ask the students to identify other researchers who have voluntarily infected
themselves to prove their hypotheses. How many of these researchers have died due to
this experimentation?
5. The general public often focuses on the devastating effects microorganisms can have on
the human population. While microorganisms can cause human mortality through
infection, it is also important to remember that the absence of all microorganisms would
result in a biosphere in which humans would not survive. Discuss the importance of the
massive communities of microorganisms seen by satellite photo in the photo at the start
of the chapter.
Chapter 2 The Chemistry of Biology
Chemistry is introduced in this chapter. Matter, atoms, elements, and molecules are defined. Chemical
bonds are discussed in terms of their strength and formation, and the concept of polar versus nonpolar
compounds is highlighted. Chemical reactions, such as oxidation-reduction and ionization, are examined
in terms of their importance in cellular metabolism. The structures of proteins, fats, carbohydrates, and
lipids are elucidated. Finally, the idea that the structure of macromolecules determines their properties is
discussed.
Expected Learning Outcomes
2.01
2.02
2.03
2.04
2.05
2.06
2.07
2.08
2.09
2.10
2.11
2.12
2.13
2.14
2.15
2.16
2.17
2.18
2.19
2.20
2.21
2.22
2.23
2.24
Describe the properties of atoms and identify the relationships of the particles that they contain.
Characterize elements and their isotopes.
Explain the differences between atomic number, mass number, and atomic weight.
List the major elements that are associated with life.
Describe the electron orbitals and energy shells, and how they are filled.
Explain how elements make chemical bonds to form molecules and compounds.
State the relationship among an atom, molecule, and compound.
Identify the differences between covalent, ionic, and hydrogen bonds.
Summarize the concepts of valence, polarity, and diatomic elements.
Describe ionization and distinguish between anions and cations.
Compare oxidation and reduction and their effects.
Classify different forms of chemical shorthand and types of reactions.
Explain solutes, solvents, and hydration.
Differentiate between hydrophilic and hydrophobic.
Describe the pH scale and how it was derived; define acid, base, and neutral levels.
Describe the chemistry of carbon and the difference between inorganic and organic compounds.
Identify functional groups and know some examples.
Relate what macromolecules, polymers, and monomers are.
Define a carbohydrate and know the functional groups that characterize carbohydrates.
Distinguish among mono-, di-, and polysaccharides, and describe how their bonds are made.
Discuss the functions of carbohydrates in cells.
Define lipid, triglyceride, phospholipid, fatty acid, and cholesterol.
Describe how an ester bond is formed.
Discuss major functions of lipids in cells.
2.25
2.26
2.27
2.28
2.29
2.30
Describe the structures of peptides and polypeptides and how their bonds form.
Characterize the four levels of protein structure and describe the pattern of folding.
Summarize some of the essential functions of proteins.
Identify a nucleic acid and differentiate between DNA and RNA.
Describe the structures of nucleotides and list the nitrogen bases.
Explain how the DNA code may be copied, and describe the basic functions of RNA.
CHAPTER
Chapter Outline
2.1. Atoms: Fundamental Building Blocks of All Matter in the Universe
A. Different Types of Atoms: Elements and Their Properties
B. The Major Elements of Life and Their Primary Characteristics
Electron Orbitals and Shells
2.2. Bonds and Molecules
A. Covalent Bonds: Molecules with Shared Electrons
1. Polarity in Molecules
B. Ionic Bonds: Electron Transfer among Atoms
1. Ionization: Formation of Charged Particles
2. Hydrogen Bonding
C. Electron Transfer and Oxidation–Reduction Reactions
2.3. Chemical Reactions, Solutions, and PH
A. Formulas, Models, and Equations
B. Solutions: Homogeneous Mixtures of Molecules
C. Acidity, Alkalinity, and pH Scale
2.4. The Chemistry of Carbon and Organic Compounds
A. Functional Groups of Organic Compounds
B. Organic Macromolecules: Superstructures of Life
2.5. Molecules of Life: Carbohydrates
A. The Nature of Carbohydrate Bonds
B. The Functions of Carbohydrates in Cells
2.6. Molecules of Life: Lipids
A. Membrane Lipids
B. Miscellaneous Lipids
2.7. Molecules of Life: Proteins
A. Protein Structure and Diversity
2.8. The Nucleic Acids: A Cell Computer and Its Programs
A. The Double Helix of DNA
B. Making New DNA: Passing on the Genetic Message
C. RNA: Organizers of Protein Synthesis
D. ATP: The Energy Molecule of Cells
Key Terms and Phrases
matter
atom
protons
neutrons
electrons
nucleus
elements
atomic number (AN)
mass number (MN)
isotopes
atomic mass/weight
orbitals
molecule
compounds
formula mass
molecular weight
chemical bonds
valence
covalent bonds
polar
nonpolar
ionic bonds
ionization
ions
cations
anions
electrolytes
hydrogen bond
Van der Waals forces
oxidation reaction
reduction reaction
redox reaction
reducing agent
oxidizing agent
products
reactants
synthesis reaction
catalyst
solution
solute
solvent
hydrated
hydrophilic
hydrophobic
amphipathic
concentration
hydrogen ion
hydroxide ion
acidic
basic
pH
neutralization
metabolism
inorganic chemicals
organic chemicals
functional groups
biochemistry
macromolecules
monomers
polymers
carbohydrate
aldehydes
ketones
monosaccharide
disaccharide
polysaccharide
hexose
pentose
fructose
lactose
maltose
sucrose
glycosidic bonds
dehydration synthesis
cellulose
agar
chitin
peptidoglycan
lipopolysaccharide
glycocalyx
starch
glycogen
hydrolysis
lipid
triglycerides
fatty acids
glycerol
ester bond
membrane lipids
phospholipids
cholesterol
proteins
amino acids
peptide bond
peptide
polypeptide
primary structure
secondary structure
tertiary structure
cysteine
quaternary structure
enzymes
antibodies
deoxyribonucleic acid (DNA)
ribonucleic acid (RNA)
nucleotides
nitrogen base
adenine (A)
guanine (G)
thymine (T)
cytosine (C)
uracil (U)
replication
adenine triphosphate (ATP)
electronegativity
Student Activities
1. After covering the section on Protein Structure and Diversity, and discussing the primary,
secondary, tertiary, and quaternary structures of proteins, have students research diseases which
have been attributed to improperly folded proteins. The list will vary but should include
Alzheimer’s disease, cystic fibrosis, cancer, Creutzfeldt-Jakob disease (CJD), and diabetes.
2. Visualizing molecules, compounds, and macromolecules is often difficult for students,
particularly when they always see the structures on a flat sheet of paper. Use molecular model
kits (most likely available in your chemistry department) to build methane, a polysaccharide, and
lipids. These kits can also be used to demonstrate the formation of covalent bonds. To do this,
first construct two separate monosaccharides (monomers), then remove an OH group from one
monomer and an H group from the other monomer, join them together—thus performing
dehydration synthesis (see Figure 2.16).
3. Bring two see-through bottles with lids, water, salt, and cooking oil to class. Fill both the bottles
¾ full with water, then add some oil to one bottle and some salt to the other. Have students shake
the bottles, then discuss the concept of hydrophilic versus hydrophobic as the salt dissolves in the
water and the oil coalesces into droplets.
4. Bring some pH paper, small paper cups, and ammonia (any household cleaner with a basic pH
will work) to class. As students enter the classroom have them pour small amounts of their
beverages (cola, flavored water, coffee) into the cups. Determine the pH of the beverages and
ammonia using the pH paper. Then place their beverages and the cleaner onto the pH scale in
Figure 2.13. Have them determine the concentration of hydrogen ions in the beverages and the
concentration of hydrogen ions in the cleaner.
5. After discussing Figure 2.26 on DNA replication, have students visit the site
http://www.pbs.org/wgbh/aso/tryit/dna/# and click on the link “DNA workshop activity.” After
selecting replication, students will be led through the steps in DNA replication (unzipping and
matching the base pairs).
Classroom Discussion
1. Ask students the following question: changing the number of which subatomic particle (proton,
neutron, or electron) changes the element? Through answering this question students will define
isotopes and ions.
2. Students may have a pre-formed opinion of the definition of organic. Spend time discussing the
definition of organic as it relates to chemistry as opposed to the definition of organic in terms of
agriculture.
3. As you cover the periodic table (Figure 2.2), explain that the table is arranged vertically
according to the number of electrons present in the outer shell (except for helium). With this
knowledge it is easy for students to determine the reactivity of the different atoms (without
having to draw out all the shells). Also, it is a good way for students to check their models to
make sure they have the proper number of electrons present in the outer shell.
4. When lecturing on the various types of chemical bonds, have students discuss which bonds they
think would be the strongest. List the order of strength of the bonds (covalent, ionic, hydrogen,
and Van der Waals) and discuss how the strength of the bond correlates with the structure of the
bond. This discussion will allow you to focus on the difference between sharing electrons and
donating or accepting electrons as opposed to electrostatic forces.
5. Show Figure 2.15 and discuss the fact that glucose, fructose, and galactose all have the
same chemical formula (C6H12O6). Then look at the structures of maltose, sucrose, and
lactose that also have the same chemical formulas, but have different structures. The
difference in their structures becomes readily apparent in lactose intolerant individuals,
who can digest sucrose but not lactose. This discussion can also highlight the specificity
of enzymes and proteins, and how the structure of compounds influences their function.