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BIOL 260 MICROBIOLOGY Study Questions

Ch.1 Humans and the Microbial World

1. Describe the contributions that Robert Hooke and Antony van Leeuwenhoek each made to microbiology.

2. Explain the theory of spontaneous generation and how Louis Pasteur disproved this theory.

3. Comment on these characteristics of bacteria: size, abundance, diversity, communities, metabolism, where
they live, genes, reproduction, genetic changes, how genetic diversity drives bacterial evolution, evolutionary
origins.

4. What is a microbiome? Describe the human microbiome, including a few essential functions of our body's
bacteria in human development and health.

5. Describe a few essential roles of bacteria and other microorganisms in the environment (e.g., soil, water).

6. Describe at least five practical applications of microbiology (uses of microorganisms) that benefit humans.

7. Define and list types of infectious agents.

8. Describe at least five factors that can cause an increase in the rate of an infectious disease in a population
(i.e., public health impact).

9. Explain what is meant by an emerging infectious disease vs a reemerging infectious disease.

10. Describe the organisms in each of the three Domains -- Bacteria, Archaea, and Eukaryotes -- and explain
their evolutionary origins.

11. Describe Bacteria, Archaea, Algae, Fungi, Protozoa, and Viruses. Include whether they are prokaryotes,
eukaryotes, or acellular, where and how they live, give examples, etc

Ch.2 The Molecules of Life -- Review these concepts on your own as necessary.

1. Understand the following concepts: types of chemical bonds (covalent bonds, ionic bonds, and hydrogen
bonds), pH scale (acidic to basic), inorganic compounds (salts), organic compounds, ATP, biomolecules.

2. Be familiar with the structures and functions of the major types of biomolecules: proteins, carbohydrates
(monosaccharides, disaccharides, polysaccharides), nucleic acids (DNA, RNA), lipids.

Ch.3 Bacterial Cell Biology

1. List and describe shapes and groupings of bacterial cells. Define and describe biofilms.

2. Explain several reasons why it is important to study bacterial cell structures and their functions. Comment on
forces that drive evolution of diverse bacterial surface structures.

3. Explain the main function of the cytoplasmic membrane for bacteria. Describe the organization and functions
of the phospholipid and protein components of the cytoplasmic membrane.

4. Describe osmosis. Explain the effects of the following surroundings on bacterial cells: a) low solute
concentration solution or no solutes (distilled water), b) a high solute (e.g., sugars, salts) concentration
solution.

5. Explain each of the following modes of transport across the cytoplasmic membrane: simple diffusion,
facilitated diffusion, active transport systems.
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6. What is the main function of the cell wall for bacteria? Describe the composition of peptidoglycan (PG),
including the chain of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), and tetrapeptide
crosslinks.

7. Describe the structure and composition of Gram-positive bacterial cell walls. List several functions of Gram-
positive cell wall proteins and polysaccharides for bacteria.

8. Describe the structure and composition and structure of Gram-negative cell walls. What are porins and
how do they function in the outer membrane of Gram-negative bacteria? Describe lipopolysaccharide (LPS),
including O polysaccharide and lipid A.

9. What is endotoxin? Explain how endotoxin can be released and cause the symptoms of disease in a human
host.

10. Describe the property of Gram-negative bacteria that enables them to survive exposure to lysozyme, bile salts,
and certain antibiotics (e.g., penicillin). Explain how Gram-positive vs Gram-negative bacteria would be affected
differently after being exposed to penicillin then placed in distilled water.

11. List the four steps of gram staining and explain the purpose of each step. What colors are Gram-positive
vs. Gram-negative bacteria after each step of the procedure?

12. Describe the exceptions to Gram-positive or Gram-negative cell walls: Mycobacteria, Mycoplasma, and Archaea.

13. Describe the structure and composition of bacterial capsules and slime layers. Describe how bacteria form
biofilms.

14. Explain the main functions of capsules and slime layers for bacteria. Explain how a capsule can help a bacteria
cause disease.

15. Describe the structure, composition, arrangements, and movement of bacterial flagella. Describe the main
function of flagella for bacteria, including a definition of chemotaxis.

16. Describe the structure, composition, and main function of bacterial pili (common pili) or fimbriae), including
how pili contribute to disease. Describe another function of some common pili.

17. Explain the function of sex pili, including definitions of F plus and F minus bacteria and a brief description of
conjugation.

18. Describe typical bacterial genomes, including composition and organization of the chromosome.

19. Describe plasmids, give examples of functions of genes on plasmids, and explain how plasmids contribute to
bacterial diversity.

20. Describe the structure and composition of bacterial ribosomes and their function.

21. Describe the bacterial cytoskeleton and its function.

22. List some substances stored in bacterial inclusions (storage granules).

23. Describe the types of bacteria that can form endospores, and name 2 of the most common endospore-forming
genera. Explain the conditions under which these bacteria form endospores, and describe the process of
sporulation.

24. Describe the structure and composition of endospores. Explain how endospores can help bacteria to survive,
and the clinical importance of endospore forming bacteria. Describe the process of germination.
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25. Describe the structure and function of the plasma membrane of eukaryotic cells. List some functions
of eukaryotic plasma membrane proteins (e.g., glycoproteins).

26. Explain how phagocytes (e.g., macrophages) destroy bacteria by phagocytosis. Include how a
phagocyte “recognizes” bacteria, and define phagosome, lysosomes and phagolysosomes,

27. Describe the following eukaryotic cell structures and functions: ribosomes, cytoskeleton, flagella and
cilia, nucleus, chromosomes, mitochondria, and chloroplasts.

28. Compare and contrast the structures and functions in eukaryotic vs prokaryotic cells.

29. Explain the endosymbiotic theory of the evolutionary origin of eukaryotes. Summarize the evidence that
supports this theory.

Ch.4 Prokaryotic Growth

1. What are vegetative cells? Define bacterial growth and explain the process of binary fission. What is meant
by exponential growth of bacteria?

2. What is meant by the generation time, or doubling time, of a bacterial population?

3. Be able to answer growth rate problems such as the following: If the generation time of a bacteria is 20
minutes, how long does it take for 6 x 103 cells to produce 4.8 x 104 cells?

4. Describe the formation and properties of biofilms, give examples of where biofilms form and how biofilms
contribute to disease.

5. Identify and explain what is occurring during each of the stages of the growth curve: lag phase, log or
exponential phase, stationary phase, death phase, and prolonged decline phase.

6. What are the temperature conditions for growth of each of the following microorganisms?: psychrophiles,
psychrotrophs, mesophiles, thermophiles, hyperthermophiles.

7. For each of the following classes of microbes, what are a) the O2 conditions for growth and b) the metabolic
process(es) for obtaining energy to make ATP:

i. obligate aerobes ii. obligate anaerobes iii. facultative anaerobes

iv. microaerophiles v. aerotolerant anaerobes

8. What are the two main toxic derivatives of oxygen produced in cells? Name and explain the activities of the
two enzymes that destroy them.

9. For each of the microbe classes in question 7, describe a) where the microorganisms grows in a shake tube
and b) which enzymes the microorganism produces to neutralize the toxic derivatives of oxygen.

10. What are the pH conditions for growth of most bacteria? What are acidophiles and alkaliphiles?

11. What is meant by water availability? Describe the growth conditions of halotolerant microbes, halophiles, and
extreme halophiles.

12. What do heterotrophs use as their source of carbon for biosynthesis? What do autotrophs use?

13. What do chemotrophs use as their source of energy (to make ATP)? What do phototrophs use?

14. Explain the energy and carbon sources of the following groups of prokaryotes: photoautotrophs,
photoheterotrophs, chemolithoautotrophs, and chemoorganoheterotrophs.
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15. Define each type of media, and give reasons for its use: complex, chemically defined, selective, and
differential. Give at least one example of each type of media.

16. Describe how obligate anaerobes can be grown in the lab.

17. Explain the purpose and procedure of an enrichment culture.

18. Describe how direct cell counts and spectrophotometry can be used to determine bacterial concentration
(e.g. number of cells per ml). Describe how serial dilutions and viable plate counts are performed, and an
important difference between this and the above methods of bacterial quantification.

Ch.5 Control of Microbial Growth

1. Describe Joseph Lister’s important contribution in the history of microbiology.

2. Define each of the following terms: sterilization, disinfection, disinfectants and antiseptics, degerming,
pasteurization, sanitization, and preservation.

3. Give examples of how the purpose of reducing numbers of microorganisms differs in different settings:
hospitals and other healthcare facilities, food production and distribution, water treatment, home and
workplace.

4. Explain each of these factors and why it is important to consider when choosing methods of microbial growth
control: types of microorganisms, numbers of microorganisms, risk of infection (host-microbe contact).

5. Which microorganisms are the most difficult to destroy, and explain why. List a couple of other types of
microorganisms that are more difficult to destroy than most viruses and vegetative bacteria.

6. Explain how heat kills microorganisms. Which works faster to kill microorganisms, moist or dry heat?

7. For each of these physical methods, say whether it is a sterilization method and give an example of use:
boiling pressurized steam
high temp-short time (HTST) pasteurization dry heat
ultra-high temp (UHT) or ultra-pasteurization

8. Explain the purpose of filtration, whether it can sterilize and give two examples of uses.

9. Describe properties of ionizing radiation and ultraviolet radiation, and examples of uses. What is high pressure
processing used for?

10. For each of these chemical methods, say whether it is a sterilization method, give examples of specific
chemicals and an example of use:
alcohols aldehydes biguanides ethylene oxide halogens
metals ozone peroxygens phenolics quaternary ammonium compounds
chemical preservatives

11. Explain how each of the following affects microorganisms and give at least one example of use:
low temperature reducing available water

12. Explain several of the most important risk factors for food borne illness. Describe several things that can be
done (or avoided) in order to reduce the risk of food borne illness. Give the names of at least five microorganisms
that commonly cause food-borne illness.
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Ch.6 Metabolism: Fueling Cell Growth

1. Distinguish between the energy sources used by chemoorganotrophic vs chemolithotrophic bacteria.

Which is our focus, and why?

2. Explain the role of the following types of metabolic processes in bacterial growth: a) biosynthesis,
b) reactions that break down organic compounds.

3. Give several important applications of knowledge about bacterial metabolism.

4. Define and distinguish between catabolic vs anabolic pathways of metabolism. Which includes pathways that
require an input of ATP? Which includes pathways that release energy, and use that energy to make ATP?

5. Explain how molecules undergo reactions and explain the meaning of the activation energy (Eact) of a reaction.

6. Explain the role of enzymes in each chemical reaction in a living cell. Explain how enzyme activity affects the
Eact of a reaction, and consequently the rate of the reaction? Define substrate(s) for a reaction.

7. Describe enzyme structure and specificity. Explain the events that occur in an enzyme-catalyzed reaction
(include active site, reactant(s) and products).

8. What occurs when enzymes are denatured, and how is the cell affected? As temperature increases, why do
reaction rates initially increase, and then rapidly decline? How do changes in pH affect enzymes?

9. Define cofactors and explain their role in enzyme activity. Differentiated between organic cofactors (i.e.,
coenzymes) and inorganic cofactors, and give examples.

10. Explain how a competitive enzyme inhibitor prevents a reaction.

11. Explain the mechanism by which sulfa drugs (sulfonamide) inhibit bacterial growth. Explain why these drugs
are less effective if taken at less than the prescribed dose.

12. What is ATP, and why does it need to be made continually in order for bacteria to grow? Write the reactions
of ATP hydrolysis and ATP synthesis (phosphorylation). Which requires an input of energy, and which releases
energy for anabolism and other types of cell work?

13. Explain substrate-level phosphorylation vs. oxidative phosphorylation.

14. Define what happens to a molecule when it undergoes oxidation vs reduction. Describe how you can tell
whether an organic compound becomes oxidized or reduced in a biochemical reaction or pathway.

15. In a pathway of glucose catabolism, does glucose get oxidized or reduced? Explain the role of a glucose
catabolism pathway in bacterial growth.

16. What is the role of the electron donor in an energy-releasing catabolic pathway. What type of compound does a
chemoorganotroph vs. a chemolithotroph use as an electron donor?

17. Define NAD+/NADH (and FADH/FADH2) and explain the roles of these compounds in energy-releasing catabolic
pathways. Which is the oxidized and which is the reduced form of these compounds? Which
provides reducing power in metabolism, and what does this mean?

18. Summarize what happens during each of the following: Glycolysis; the Transition step; the
Tricarboxylic Acid (TCA) cycle. For each pathway, list the reactants (inputs) and products (outputs),
what is accomplished, including net ATP yield, and how ATP is synthesized.

19. Explain the process of respiration, including the reactions of the electron transport chain (ETC), proton (H+)
pumps, location in the cell. Explain the role of NAD+/NADH (and FADH/FADH2) in the ETC.
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20. What is the final electron acceptor in aerobic respiration, and what product is formed by reduction of this
molecule? Write the overall reaction for aerobic respiration. What is the total yield of ATP per glucose?
Under what conditions can cells do aerobic respiration?

21. How does the ETC generate a proton (H+) concentration gradient? Explain the proton motive force and
synthesis of ATP.

22. What type of molecule is the final electron acceptor in anaerobic respiration? Give a couple of examples,
including the products formed by reduction of these molecules. Compare the ATP yields in anaerobic vs.
aerobic respiration.

23. Which pathway or pathways is/are used by each of the following?: facultative anaerobes in the absence of
oxygen or a suitable final inorganic electron acceptor; aerotolerant anaerobes; obligate anaerobes.

24. Describe the role of glycolysis in fermentation. List reactants and products, list and explain the role of the
coenzymes, give the yield of reducing power and/or ATP. ATP is synthesized by what type of phosphorylation?

25. Explain the role of NAD+/NADH in the production of fermentation products.

26. Give the reaction(s) after glycolysis that occurs in a) lactic acid fermentation b) ethanol fermentation.

27. List three general types of chemicals produced by microbial fermentation. List some of these compounds
and some foods made by fermentation processes.

Ch.7 The Blueprint of Life: From DNA to Protein

1. What is DNA? Explain what each of these statements mean: a) DNA is the heritable material in cells
b) DNA is the information-coding material in cells.

2. Define the following terms: genome, gene, gene expression (transcription & translation), genotype, phenotype.

3. Define and describe a) a typical bacterial chromosome (average size, organization, etc); b) plasmids.

4. Give several important applications of knowledge about bacterial genetics.

5. Define and describe the structure of DNA. Define nucleotides, and describe the three parts of a DNA
nucleotide: the sugar, phosphate and nitrogenous base.

6. Describe how nucleotides are connected to each other in a DNA strand (chain). What chemical group is at the 5’
end and what chemical group is at the 3’ end of a DNA strand? What is meant by a "DNA sequence"?

7. What is complementary base pairing? What holds together the two complementary strands of a DNA molecule?
Be able to write the DNA sequence complementary to a given DNA strand. Do complementary DNA strands pair
in the same or in opposite 5’ to 3’ directions?

8. Describe the properties of RNA that are different from DNA.

9. What is accomplished by DNA replication? Explain what is meant by semi-conservative DNA replication.

10. Name the enzyme that synthesizes DNA by adding nucleotides to the 3' end of a new DNA strand. In what
direction is a DNA strand elongated? Describe leading and lagging strand DNA synthesis at a replication fork.

11. What is accomplished by transcription? Name the enzyme that synthesizes RNA by adding nucleotides to
the 3' end of a new RNA strand. What is the promoter sequence? In what direction is RNA synthesized?
What is the DNA template strand?

12. Be able to write the RNA sequence transcribed from a given DNA template strand.
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13. What is accomplished by translation? Describe each of the following, including the role in translation:
mRNA, the genetic code, codons, amino acids, tRNAs, anticodons, ribosomes, rRNA, polypeptide.
Can an mRNA be translated by only one, or by more than one ribosome at a time?

14. What is meant by gene regulation, and why is gene regulation important in bacteria? What is meant when
transcription and translation are described as occurring simultaneously? How do eukaryotes differ?

15. Define and describe the organization of an operon. Are there operons in eukaryotes as well as in prokaryotes?
Explain the activities and functions of repressor and activator proteins in gene regulation.

16. What is the function of the lac operon, and why is it important for this operon to be regulated? Describe the
organization of the lac operon, including regulatory DNA sequences and structural genes.

17. Explain how lac operon expression is regulated by lactose: Explain the molecular events that occur when
lactose is present vs. absent, including the roles of the repressor protein and the inducer allolactose.

18. Which carbohydrate, glucose or lactose, provides a better energy source for E. coli growth? Explain how the
availability of glucose and/or lactose affects growth rate.

19. Explain how lac operon expression is regulated by glucose: Explain the molecular events that occur when
glucose is present vs. absent (lactose present).

Ch.8 Bacterial Genetics

1. Describe the two general ways that genetic change occurs in bacteria. Explain the importance of genetic
variations in bacterial populations.

2. Explain one way that a mutation (e.g., base substitution) can cause bacteria to become resistant to an antibiotic.

3. Explain one way that acquiring a new gene(s) can cause bacteria to become resistant to an antibiotic.

4. Explain how natural selection acts as a force for evolution of bacterial populations. As an example,
explain how antibiotic-resistant bacterial strains can develop.

5. Distinguish between a wild type vs. mutant bacterial strain. How do most spontaneous mutations occur?

6. Define each of the following and describe how they can alter the resulting protein: base substitution;
insertion or deletion (frameshift). Explain how a mutation can have no effect on the resulting protein.

7. Explain how mutations are induced by each of the following: chemicals that modify or replace bases;
ultraviolet light; ionizing radiation.

8. Describe each mechanism of horizontal (lateral) gene transfer mechanism: a) bacterial transformation;
b) transduction; c) conjugation

9. Define F plus and F minus bacteria and explain the process and outcome of conjugation between an F plus
and an F minus bacteria. Also describe how conjugation with an Hfr bacteria can enable an F minus bacteria
to acquire new chromosomal DNA.

10. Explain how horizontal gene transfer contributes to the development of new strains of antibiotic resistant
bacteria.

11. Define the core genome vs the mobile gene pool in a bacterial species. Give examples of gene functions on
plasmids. Define and describe transposons and describe transposon induced genetic changes.

12. Describe how CRISPR systems defend bacteria against invading DNA.
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Ch.9 Biotechnology

1. Describe DNA cloning in bacteria, including definitions and functions of the following: restriction
enzyme, plasmid, ligase, recombinant DNA, transformation. Define and describe gene editing using the
CRISPR/Cas9 system. Describe several examples of uses for genetically modified microorganisms.

2. Describe a few important uses of high-throughput DNA sequencing ("next-gen" sequencing) in microbiology.

3. Explain the purpose of Polymerase Chain Reaction (PCR). Summary how PCR amplifies a specific DNA
region, including the roles of the primers, polymerase and nucleotide components of PCR. Explain a few
applications of PCR related to microbiology.

4. What is a DNA probe? Describe a probe array, and explain how a probe array can be used to identify and
characterize a microorganism.

5. Give three examples of questions related to microbiology that can be investigated by RNA sequencing.

Ch.10 Identification and Classification of Prokaryotic Organisms

1. What is meant by the classification of two bacteria as the same species? the same strain?

2. Describe the three Domains of Life. Which organisms evolved from a common ancestor that existed
~3.5 billion years ago, much earlier than the last common ancestor of any other group of organisms?

3. Give several examples of cell morphology, staining, growth, and biochemical characteristics that are used
for bacterial identification.

4. Explain how a microbe can be identified by its antigens (i.e., serotype) using an ELISA test.

5. Explain the use of a) probe-based technologies and b) DNA sequence analysis for bacterial identification.
Explain why PCR is critical for detecting and identifying microbes.

6. Explain why classification of prokaryotes is mainly based on genotypic characteristics (as opposed to
morphology, biochemistry, etc).

7. Explain how a phylogenetic tree reveals the evolutionary relatedness of two organisms.

Ch.13 Viruses

1. Describe, in general, how viruses multiply. Describe the different shapes of animal viruses and
bacteriophages.

2. Define each of the following terms: virion, capsid, capsomeres, nucleocapsid. Describe the structure and
function of spikes, and give a couple of examples.

3. Describe the structures of naked and enveloped viruses.

4. Describe the size and types of viral genomes. What is special about influenza A virus' genome?

5. Describe the transmittance (spread) of enteric, respiratory, zoonotic, and sexually-transmitted viruses.

6. Explain what happens during the attachment step of viral infection. Explain why a particular virus only
infects certain host species and cell-types.

7. Describe the main cell types that HIV can infect, and explain why (include HIVs gp120, & host CD4 & CCR5)
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8. Describe how naked vs enveloped viruses can enter host cells.

9. Which type of virus, DNA or RNA, generally replicates its genome and transcribes its genes in the host
cell's nucleus? Which type of virus, DNA or RNA, generally replicates its genome and transcribes its
genes in the host cell's cytoplasm? Which type of virus requires viral enzymes for genome replication?

10. Explain what happens during viral assembly.

11. Explain how naked viruses vs enveloped viruses are released from host cells. For each viral release
mechanism, comment on the effect on the host cell.

12. Explain what it means to say that the outcome of exposure to a virus depends in large part on host defenses.

13. Is it possible for a viral infection to exist in a host without disease symptoms? If yes, can virus be transmitted?

14. Explain what is meant by acute vs persistent viral infections.

15. How can viruses remain in host cells for long periods of time? Can viruses that persist in host cells produce
new viral particles, and if so, how?

16. Explain what is meant by a latent or chronic viral infection. Give an example of each.

17. Describe the general characteristics of retroviruses (e.g., HIV). Explain how retroviruses reproduce in host
cells. What is reverse transcriptase? What is a provirus?

18. Describe cancer. Describe how viruses can cause cancer and give examples.

19. Explain how viruses undergo mutations. Which types of viruses mutate more frequently, DNA or RNA viruses?

20. Explain how viral mutations can enable a virus to infect more hosts and/or cause more severe disease
symptoms. Explain how viral mutations can enable a virus to become resistant to an antiviral drug (and what
is done to avoid this problem).

21. Explain how viral mutations can result in antigenic drift, and what this means. Explain how antigenic drift can
enable a virus to cause more infections in a population.

22. Explain what vaccines are and how they work to prevent viral infection. Explain how antigenic drift in some
viruses makes it difficult to design broadly effective vaccines (e.g., flu).

23. Explain the process of genetic reassortment in influenza viruses (type A), which have segmented RNA
genomes. Explain how genetic reassortment can result in antigenic shift, and what this means. Explain
how antigenic shift can enable flu viruses to infect new hosts. Explain why antigenic shift can lead to a flu
epidemic.

24. Describe prions, including composition, how prions reproduce and how they can cause infectious disease.

Ch.14-15 The Innate and Adaptive Immune Response

1. The host defenses include the a) first line defenses, b) innate immune system, and c) adaptive immune
system. Which host defenses are responses to foreign molecules? Which is always present (i.e., not a
response)? Which is a response to pathogen-associated molecular patterns (PAMPs) (or microbe-associated
molecular patterns, MAMPs)? Which is a response to specific antigens? Which has a faster and higher
magnitude response after subsequent exposure to a pathogen?

2. Explain the role of the body's first line defenses against microbial invaders. List the main types of first line
defenses, and give examples.
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3. Define cytokines, give examples, and roles of cytokines in the innate and adaptive immune systems.

4. Describe pattern recognition receptors (PRRs), and give examples. List several microbial molecules
that bind to PRRs (i.e., PAMPs), and describe the cell's response.

5. Describe the complement system and give two examples. Describe three general ways that complement
activation protects the host from invading bacteria.

6. Describe opsonization.

7. What are the two types of phagocytes? Explain the process of phagocytosis, including the following events:
chemotaxis; recognition and attachment; engulfment; fusion of phagosome with lysosome; destruction and
digestion; exocytosis.

8. Describe the process of inflammation, including the role of cytokines, and local vs systemic inflammation
symptoms.

9. Contrast innate vs adaptive immune responses with respect to how long it takes to develop after exposure to
a foreign invader.

10. Distinguish the response of the adaptive immune response to first exposure vs later exposures to a pathogen.

11. What types of invaders can the humoral immune system defend against? What types of lymphocytes are
responsible for the humoral immune response?

12. What types of invaders can the cellular immune system defend against? What types of lymphocytes are
responsible for the cellular immune response?

13. Define the terms antigen, antigenic determinant or epitope, and antibody. Describe the composition and
structure of antibodies. Differentiate between IgM, IgG, and IgA antibody classes.

14. Describe several protective outcomes of antibody-antigen binding.

15. Summarize the primary humoral response. Include the following: B cells, free antigen, B cell receptors,
helper T (TH) cells, cytokines, plasma cells, antibodies, and memory B cells.

16. Summarize the secondary humoral response. What is IgG? Explain the relationship between the
secondary humoral response and immunity (e.g., conferred by vaccination) against a pathogen.

17. Summarize the primary cellular immune response. Include the following: T cells, intracellular invaders,
antigens, T cell receptors, macrophages as antigen presenting (APC) cells, cytokines, and memory T cells.

18. Explain functions of cytotoxic T (Tc, CD8+) and helper T (TH, CD4+) cells in the adaptive immune response.

Ch.16 Host-Microbe Interactions

1. Define each type of host-microbe relationships: mutualism, commensalism, and parasitism. Give examples.

2. Describe the areas of the human body locations that have the most normal microbiota. Which location has the
highest concentration of bacteria? Give examples of host factors that influence numbers and types of bacteria.

3. Describe and explain at least four essential functions of the human microbiome.

4. Define the terms infection, subclinical infection, infectious disease, primary pathogen, opportunistic
pathogen, and virulence factors. Give examples

5. Describe at least four examples of host factors that increase the risk of opportunistic infections.
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6. Define the infectious dose of pathogen, and how a pathogen's virulence affects infectious dose.

7. Define each of the following types of infections: acute, chronic, latent. Give an example of each type.
What is a carrier of an infectious disease?

8. Distinguish between local vs. systemic pathogen distribution. Describe examples of symptoms of each type
of infection.

9. Define and describe sepsis. Explain risk factors and causes of sepsis, signs and symptoms of sepsis and
severe sepsis, i.e., systemic inflammatory response syndrome (SIRS).

10. Explain the purpose and list the steps of Koch's postulates.

11. Describe examples how bacterial virulence factors contribute to pathogenesis.

12. Describe how bacteria colonize a host, including the two main requirements for establishment of infection.
Describe a couple of ways that microbes can invade host tissues.

13. Explain several ways that bacteria can avoid being eliminated by complement, phagocytosis, or antibodies.

14. Define and describe bacterial exotoxins, and give several examples of mechanisms, types, and effects of
exotoxins. Define and describe endotoxin, and describe how it can cause symptoms.

Ch.18 (18.1-18.2) Immunization and Vaccines

1. Explain what it means for an individual to have immunity (e.g, to a virus), as opposed to lacking immunity.

2. Describe the first vaccine, discovered by Edward Jenner in 1798. Define the terms active vs. passive
immunity. Explain why active immunity can provide long term protection but passive immunity can’t.

3. Which type of immunity, active or passive, is provided by each of the following?: vaccination; inoculation
with antiserum (immune serum or gamma globulin); natural exposure to infectious agents; antibodies
transferred from mother to fetus during pregnancy. Answer whether each of these is naturally or artificially
acquired.

4. Explain the concept of population-level or herd immunity. Give two examples of how herd immunity of is
achieved. Describe the transmittance and spread of a virus in a population that has herd immunity versus one
that does not. Explain why a virus is unable to persist in a population that has herd immunity.

5. Define attenuated vaccine, and describe advantages of attenuated vaccines. Define and give examples of
types of inactive vaccines, and explain advantages of inactive vaccines.

Ch.19 Epidemiology

1. Describe Ignatz Semmelweis' 1840's contribution to microbiology.

2. Explain the meaning of communicable (contagious) disease. Explain the causes of infectious diseases that are
non-communicable.

3. Define epidemiology, and list questions investigated by infectious disease epidemiologists.

4. Define each of the following measurements of infectious disease in a population: rate of disease;
morbidity rate; mortality rate; incidence; prevalence.
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5. Define each of the following frequencies of occurrence of infectious disease: endemic; epidemic,
outbreak; pandemic. Give examples of each.

6. List the main reservoirs of infection and give examples of each.

7. Define and list the main portals of exit from the body. Define and give examples of each of the following
modes of transmission: direct contact; droplet; airborne; vehicle; vector. Define and list the main portals
of entry into the body.

8. List host factors and pathogen factors that affect the spread of infectious disease, and explain how.

9. List the factors that contribute to healthcare-associated (nosocomial) infections, the most common types
of infections, and most common pathogens that cause them. List prevention strategies.

10. Explain several factors that contribute to emerging and reemerging disease.

Ch.20 Antimicrobial Medications

1. Describe Paul Ehrlich's contribution to microbiology. Explain how Alexander Fleming discovered penicillin.
Which types of organisms produce natural antibiotics? What are semi-synthetic and synthetic antibiotics?

2. What is meant by the selective toxicity of an antibiotic? Explain the selective toxicity of ß-lactam antibiotics.

3. Define the therapeutic index of an antimicrobial drug. Define and distinguish between bacteriostatic and
bacteriocidal effect of an antibiotic.

4. Define and distinguish between broad vs. narrow spectrum drug activity. Explain a few advantages and
disadvantages of each.

5. Give a couple of reasons why antimicrobial drugs are often prescribed in combination.

6. Define innate resistance vs. acquired resistance. Why do Gram-negative bacteria often have innate
resistance to certain antibiotics (e.g., penicillin)? Give a few other examples of innate resistance.

7. Describe the actions of each of the following types of antibiotics: cell wall synthesis inhibitors; protein
synthesis inhibitors; nucleic acid synthesis inhibitors; antimetabolites (folate synthesis inhibitors).

8. Explain the selective toxicity of each of the above antibiotic actions.

9. Explain how Kirby-Bauer disc diffusion test works, including how comparing the diameter of the zone of
inhibition to a standard value is used to determine antibiotic susceptibility (sensitivity).

10. Explain how a dilution series works, including how it used to determine the minimum inhibitory concentration
(MIC) of an antibiotic. Distinguish between minimum inhibitory concentration (MIC) and minimum
bacteriocidal concentration (MBC).

11. Explain how each type of genetic change (mutation and gene transfer) can cause bacteria to survive
exposure to antibiotics, and how natural selection drives the development of new antibiotic-resistant strains.

12. Explain antibiotic resistance by each of the following mechanisms: inactivation of the antibiotic, changes
in the target, and decreased access of the antibiotic to the target.

13. Explain several ways that we can reduce infectious disease rates and antibiotic-resistance, including medical
practices, individual and societal behaviors, and basic and applied research.