Course Introduction
Pathogenic Microbiology Study Guide
Questions
Pathogenic Microbiology explores the biology of microorganisms that cause disease in humans. This course examines the mechanisms of microbial pathogenicity, including how bacteria, viruses, fungi, and parasites invade hosts, evade immune responses, and produce toxins. Students will learn about the epidemiology and diagnosis of infectious diseases, the role of host-microbe interactions, and modern approaches to treatment and prevention. Emphasis is placed on clinically significant pathogens, antimicrobial resistance, and public health strategies to control infectious outbreaks.
Recommended Textbook
Microbiology An Evolving Science 4th Edition by John W. Foster
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Page 2
Chapter 1: Microbial Life: Origin and Discovery
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Q1) Describe the effects of three microbial diseases that have significantly affected human populations throughout history.
Answer: Answers may vary. Some examples include bubonic plague, which killed one-third of Europe's population in the fourteenth century; tuberculosis, which was common in the nineteenth century; AIDS, which affects many people today; and smallpox, which killed a large number of native North Americans.
Q2) Carl Woese's discovery replaced the classification scheme of five kingdoms with a scheme of three
A) phyla.
B) domains.
C) classes.
D) orders.
E) genera.
Answer: B
Q3) What is the significance of the work of Ignaz Semmelweis and Joseph Lister?
Answer: They showed that use of antiseptics on doctors' hands and medical instruments drastically reduced the mortality rate of hospital patients. They made these observations before Robert Koch's germ theory of disease.
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3
Chapter 2: Observing the Microbial Cell
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Q1) List three different differential stains used in microbiology. What can be detected with each?
Answer: The most common differential stain is the Gram stain. This procedure allows one to distinguish between cells having one membrane (Gram-positive) and two membranes (Gram-negative). Another common differential stain is the acid-fast stain. Carbolfuchsin stains the mycolic acid-containing acid-fast cells of the genus Mycobacterium. The endospore stain is a differential stain that stains endospores with malachite green. Negative staining and antibody staining are also included in the text.
Q2) Which of the following techniques can visualize bacteria without focusing electromagnetic radiation?
A) cryo-electron microscopy
B) phase-contrast microscopy
C) dark-field microscopy
D) atomic force microscopy
E) X-ray diffraction
Answer: D
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Chapter 3: Cell Structure and Function
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Q1) Explain how bacteria can produce proteins more quickly than eukaryotes do.
Answer: Bacteria have no membrane around the nucleoid. This transcription and translation can be coupled with no need to transport the mRNA out of a nucleus.
Q2) Which of the following statements about the prokaryotic flagella is INCORRECT?
A) It is driven by the cell's transmembrane proton current.
B) It is embedded in the layers of the cell envelope.
C) It is observed by electron microscopy.
D) It moves with a whiplike motion.
E) It is used for chemotaxis.
Answer: D
Q3) Lipopolysaccharides are found in
A) all bacteria.
B) Gram-positive bacteria.
C) Gram-negative bacteria.
D) archaea.
E) eukaryotes.
Answer: C
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Chapter 4: Bacterial Culture, Growth, and Development
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Q1) Which of the following is the best technique for counting only viable cells?
A) direct microscopic count
B) spread plate
C) spectrophotometer
D) chemostat
E) dry weight measurements
Q2) Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?
Q3) Growth of most microorganisms occurs by
A) budding.
B) binary fission.
C) replication.
D) conjugation.
E) transformation.
Q4) Why can't most organisms use the nitrogen gas that is so prevalent in the atmosphere? How do these organisms acquire a usable form of nitrogen?
Q5) Why does a microbe's growth rate in its natural environment vary greatly from that in the laboratory? Give at least two reasons for this.
Q6) Discuss some disadvantages of viable counts of microorganisms.
6
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) Which best describes microaerophiles?
A) They require atmospheric oxygen levels to grow.
B) They cannot grow in the presence of oxygen.
C) They will use oxygen if it is present, but can grow even if oxygen is not present.
D) They require a small oxygen concentration to grow.
E) They can't use oxygen to grow, but oxygen won't kill them.
Q2) No one ever expected to find microbes thriving in our stomachs. What organism was found there, what problem does it cause, and how does it survive there?
Q3) The membrane needs to remain ________ so that it can expand as cells grow larger and so that proteins needed for solute transport can be inserted into the membrane.
A) rigid
B) warm
C) fluid
D) hypertonic
E) polarized
Q4) Describe three mechanisms organisms use to reduce osmotic stress.
Q5) What is biocontrol? Describe two examples.
Page 7
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Chapter 6: Viruses
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Q1) What happens when marine algae overgrows?
Q2) So far, the known mechanisms of replication and mRNA expression define how many fundamental groups of virus species?
A) five
B) six
C) seven
D) eight
E) nine
Q3) The integrated phage genome is called a(n)
A) temperate.
B) lysogen.
C) oncogene.
D) lytic.
E) prophage.
Q4) Some viruses require an RNA-dependent RNA polymerase. What does that mean? What would you call the host cell RNA polymerase (RNA pol)? What would you call reverse transcriptase (RTase)?
Q5) Discuss the role that marine viruses play in carbon balance.
Q6) Why are viruses not affected by antibiotics? Why are there so few antiviral drugs?
Page 8
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Chapter 7: Genomes and Chromosomes
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Q1) The ability of cohesive ends of DNA from different organisms to ________ constitutes the basis of recombinant DNA technology.
A) be methylated
B) be specifically cut
C) form complementary base pairs
D) repel each other E) be sequenced
Q2) The entire genetic complement of DNA in a cell of a particular organism is called A) genome.
B) transcriptome.
C) proteome.
D) metabolome.
E) lipidome.
Q3) Describe the role of the two RNA polymerases that are involved in the early stages of bacterial DNA replication.
Q4) Describe three practical applications of the polymerase chain reaction (PCR) and possible pitfalls.
Q5) How can plasmids ensure that they are passed on from one generation to the next?
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) Where is the Shine-Dalgarno sequence located and what is it responsible for?
Q2) E. coli is being used to study various agents that inhibit protein synthesis. One agent binds the 23S rRNA of the 50S subunit and prevents peptide bond formation. No new proteins are produced. To which antibiotic is this agent likely related?
A) chloramphenicol
B) streptomycin
C) puromycin
D) tetracycline
E) erythromycin
Q3) The typical bacterial ribosome is composed of
A) 16 RNAs and a variety of proteins.
B) an 80S (30S + 50S) component made of RNA and proteins.
C) 80S subunits along with several RNAs and at least 50 proteins.
D) two subunits made of three RNAs and at least 50 proteins.
E) three subunits containing both RNA and proteins.
Q4) A variety of online software tools are available to aid with analyzing DNA and protein sequences. Name any three and explain what they can be used for.
Q5) How are folded and unfolded proteins moved from the cytoplasm to the periplasm?
Q6) How does mRNA compare to the template and nontemplate DNA strand?
Page 10
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) What are the differences between replicative and nonreplicative transposition?
Q2) Describe four of the error-proof DNA repair mechanisms.
Q3) Numerous human genetic diseases are caused by mutations in homologs of bacterial
A) transposons.
B) ligases.
C) integrases.
D) polymerases.
E) repair genes.
Q4) Competence in Gram-positive organisms is induced by A) calcium and cold.
B) electrical currents.
C) competence factors made of peptides.
D) presence of biofilm.
E) Competence is not induced in Gram-positive bacteria.
Q5) Which of the following is NOT a feature of a transposon?
A) ability to move around a genome
B) presence of inverted repeats at each end
Page 11
C) the ability to transfer via a phage head
D) genes coding for a transposase activity
E) presence of antibiotic resistance genes
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Chapter 10: Molecular Regulation
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Q1) During the process of endospore formation, different sigma factors are active in the mother cell and forespore. How is this possible, and why is it important?
Q2) One benefit of operons in bacteria is that they
A) allow for alterations in DNA sequence by flipping promoters around.
B) allow for coordinated gene expression of related genes on one mRNA controlled by one promoter.
C) do not need ligands and regulatory proteins as single genes would.
D) do not need any modification of the proteins after they are expressed.
E) allow for the bacteria to utilize a wide variety of carbon sources.
Q3) A quorum-sensing gene system requires the accumulation of a secreted small molecule called a(n)
A) autoinducer.
B) activator.
C) repressor.
D) inducer.
E) corepressor.
Q4) What does the gene inversion in Salmonella enterica accomplish with respect to its course of infection? Briefly describe how this mechanism works.
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Chapter 11: Viral Molecular Biology
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Q1) Pigs function as "mixing bowls" for avian, human, and swine influenza strains. What is the biochemical mechanism for this phenomenon?
Q2) Compare and contrast the advantages and disadvantages of lentiviral vectors with respect to adenoviral vectors.
Q3) Which of the following is a mismatched pair?
A) herpes simplex virus 2-genital lesions
B) varicella-zoster virus-chickenpox, shingles
C) papillomavirus-genital warts
D) variola major virus-smallpox
E) None of the examples are mismatched.
Q4) What is the Escherichia coli protein used by bacteriophage lambda as a receptor? Why has this protein not been lost in the process of evolution?
Q5) Sequences of endogenous retroviruses (HERVs) are remnants of retroviral infections. HERVs have accumulated over millions of years and comprise about 8% of the human genome. Briefly describe the evidence for the expression of HERV-K proteins and virus-like particles in the human embryo. What are the implications of HERV-K products interacting with embryonic factors?
Q6) Describe the several features of lentivectors. What are their molecular sources?
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Chapter 12: Biotechniques and Synthetic Biology
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Q1) Potential vaccine antigens made by transgenic plants include
A) foot-and-mouth surface antigen.
B) Norwalk virus glycoprotein.
C) rabies virus glycoprotein.
D) Entertoxin A subunit.
E) Hepatitis A virus.
Q2) The role of kill switches in genetically engineered microorganisms is to A) serve as a fail-safe mechanism to timely kill the organisms after they have fulfilled their purpose.
B) induce proliferation of reproduction to kill a host cell.
C) destroy organisms that have a risk of biological contamination or invasion.
D) block the translation of CcdB.
E) elimiate toxins within the cell.
Q3) What are translational fusions used for? How are they constructed?
Q4) What is synthetic biology? Provide an example of its potential applications.
Q5) How were GadE and GadX demonstrated to be transcription factors for the gadA gene?
Q6) Both southern and northern blots involve the use of agarose gels. How do the types of agarose gels differ and why?
Q7) How do operon fusions reveal transcriptional control of a target gene?
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Chapter 13: Energetics and Catabolism
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Q1) How does the efficiency of energy capture by ATP formation in bacterial tricarboxylic acid cycle compare with that of mitochondria?
Q2) Hans Krebs's strategy to determine the biochemical intermediates involved in aerobic respiration was to use substrate molecules of varying lengths. What led Krebs to take this approach?
Q3) Ethanolic fermentation is used in making beverages such as beer, wine, and pulque. It is carried out by yeast and A) lactobacillus.
B) leuconostoc.
C) propionibacterium.
D) zymomonas.
E) clostridium.
Q4) What is the phosphotransferase system (PTS) and why is the advantage for a microbial cell to have a PTS?
Q5) How can a technique such as calorimetry be used to measure DG?
Q6) What metabolic pathway does Mycobacterium tuberculosis use that allows it to grow slowly inside macrophages? What led to this discovery, and what practical application can further analysis of this pathway have?
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Chapter 14: Electron Flow in Organotrophy, Lithotrophy, and
Phototrophy
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Q1) Some respiratory bacteria, such as the nitrate oxidizer, nitospira, pack their ETS within intracytoplasmic pockets called
A) insoluable particles.
B) mitochondrial inner membrane.
C) inner membrane space.
D) cristae.
E) lamellae.
Q2) Why and how is it that mitochondria have only a single electron transport system (ETS), unlike many bacteria?
Q3) Enzymes transferring electrons at the start of the ETS are referred to as __________, whereas enzymes transferring electrons to the terminal electron acceptor are designated as __________.
A) dehydrogenases; oxidases
B) oxidases; dehydrogenases
C) sulfatases; nitrogenases
D) permeases; proton pumps
E) lyases; hydrolases
Q4) What are methanotrophs? What is their role in the global carbon cycle?
Q5) What is photoheterotrophy? Give examples of photoheterotrophic organisms.
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Chapter 15: Biosynthesis
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Q1) What technique was used to demonstrate that gene expression of the CO -concentrating mechanism (CCM) transporters is induced by low levels of CO ? Briefly explain the basis of the technique.
Q2) How do cyanobacteria benefit from their heterocysts attracting heterotrophic bacteria?
Q3) What is the health risk of having nitrates in drinking water? What conditions favor the accumulation of nitrates and nitrites in bodies of water?
Q4) Rubisco catalyzes which of the following reactions?
A) \( \mathrm{CO}_{2}+ \) ribulose 1,5 -bisphosphate \( \rightarrow 2,3 \)-phosphoglycerate
B) \( \mathrm{HCO}_{3}{ }^{-}+ \)acetyl-CoA \( \rightarrow \) malonyl-CoA + NADPH \( \triangle 3 \)-hydroxypropionate
C) \( \mathrm{H}_{2} \mathrm{~S}+ \) light \( \rightarrow \mathrm{S}^{0}+2 \mathrm{H}^{+}+2 \mathrm{e}^{-} \)
D) Ribulose-1,5-bisphosphate \( +\mathrm{CO}_{2}{ }^{-} \rightarrow \) Fructose- 1,6 -bisphosphate
E) 2-carboxy-3-ketoarabinitol-1,5-bisphosphate \( \rightarrow \) G3P
Q5) Briefly describe the biosynthetic pathway for arginine.
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Chapter 16: Food and Industrial Microbiology
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Q1) What type of processing refers to steps in product recovery and purification?
A) pasteurization
B) finishing
C) upstream
D) downstream
E) lyophilization
Q2) Leavening of commercial bread dough is brought about by CO from ________ fermentation by ________.
A) mixed; Propionibacterium species
B) ethanolic; Oenococcus
C) alkaline; Bacillus species
D) ethanolic; Saccharomyces cerevisiae
E) acid; lactic acid bacteria
Q3) Within a mound of cocoa beans, ________ generates heat so that the mound temperature increases up to 50°C.
A) indigenous fungi
B) aerobic acetic acid bacteria
C) Candida and Kloeckera yeasts
D) Saccharomyces and other yeasts
E) Lactobacillus species
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Chapter 17: Origins and Evolution
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Q1) The word "symbiosis" is usually understood to mean ________, a relationship in which both partners benefit and may absolutely require each other.
A) comensalism
B) parasitism
C) mutualism
D) predation
E) competition
Q2) Briefly discuss the types of geological evidence of early life and their advantages and limitations.
Q3) Explain how banded iron formations could arise in the geologic record due to photoferrotrophy.
Q4) What criteria must be met in order to prove that two bacterial strains belong in the same species?
Q5) All of the following are examples of "operational genes," EXCEPT ________ genes.
A) metabolic
B) ribosomal RNA
C) stress response
D) pathogenicity
E) resistance
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Chapter 18: Bacterial Diversity
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Q1) How could nitrifiers be utilized in treatment of wastewater?
Q2) What is unique about the genome of Borrelia species?
Q3) Which is NOT a typical characteristic of Verrucomicrobia?
A) They contain a cytoskeleton made from tubulin.
B) They are oligotrophic.
C) They are rarely cultured.
D) They appear to have acquired genes through horizontal transfer from eukaryotes.
E) They are obligate intracellular parasites.
Q4) What distinguishes bacterial cell walls from those in archaea and eukarya?
Q5) Cyanobacteria are the only prokaryotes that use ________ to photolyze water to produce oxygen.
A) photosystem I alone
B) bacteriochlorophyll
C) both photosystems I and II
D) plastocyanin
E) carboxyzomes
Q6) Compare and contrast the double membrane found in Planctomycetes versus that found in the eukaryotic nucleus.
Q7) Describe the lifestyle and development of Streptomyces mycelia.
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Chapter 19: Archaeal Diversity
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Q1) Nitrosopumilus maritimus is able to oxidize
A) nitrate.
B) ammonia.
C) sulfide.
D) sulfate.
E) methane.
Q2) Which archaea uses light energy to drive a retinal-based ion pup to establish a proton potential?
A) all archaea
B) hyperthermophilic Crenarchaeota
C) Methanobacteriales
D) Haloarchaea
E) Sulfolobales
Q3) What are some of the unique features of archaeal gene regulation?
Q4) Compare and contrast the supercoiling in hyperthermophilic archaeal species with bacteria and eukaryotes. What is responsible for this feature, and what does it accomplish for these archaea?
Q5) What are "vent polymerases," why are they better than previously used polymerases, and from where are they acquired?
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Chapter 20: Eukaryotic Diversity
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Q1) Which of the following is mismatched?
A) Ascomycota-Penicillium, yeasts, fungal component of lichens
B) Basidiomycota-Amanita, Licoperdon, Cryptococcus neoformans
C) Chytridiomycota-Batrachochytrium dendrobatidis, Neocallomastix
D) Zygomycota-saprophytes, insect parasites
E) Microsporidia-arbuscular mycorrhizae
Q2) Phytoplankton refers to
A) heterotrophic bacteria present in aquatic and marine environments.
B) mixotrophic algae and amebas present in aquatic environments.
C) photosynthetic algae and bacteria present in aquatic and marine environments.
D) heterotrophic algae, bacteria, and protists present in aquatic, marine, and terrestrial environments.
E) photosynthetic algae and plants present in aquatic, marine, and terrestrial environments.
Q3) New and emerging drug therapy targets for Plasmodium falciparum include
A) spore-release inhibitors.
B) uncoupling agents.
C) conjugation inhibitors.
D) hemoglobin protease inhibitors.
E) cilia inhibitors.
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Chapter 21: Microbial Ecology
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Q1) Which of the following is NOT true regarding food webs in ecosystems?
A) Primary producers assimilate minerals into biomass.
B) Primary producers absorb energy from outside the ecosystem.
C) Grazers convert 10% of carbon back to carbon dioxide.
D) Consumers convert 90% of biomass carbon to atmospheric CO .
E) All energy gained by an ecosystem is eventually lost as heat.
Q2) The Dutch microbiologist van Niel first demonstrated anoxygenic photosynthesis in soil and water bacteria. He generalized his work by hypothesizing that
A) every molecule in nature can be used as a source of nitrogen by some microorganism.
B) photosynthesis results in oxygen production.
C) microbes are found in every environment on Earth.
D) microbes cannot live deep within Earth.
E) photosynthesis occurs deep within Earth.
Q3) How do microbes live if their metabolic process to generate energy has a positive DG?
Q4) Explain how endoliths derive energy inside bedrock, where there is no sunlight.
Q5) Describe the process of haustorial parasitism.
Q6) Explain the difference between assimilation and dissimilation.
Page 24
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Chapter 22: Microbes in Global Elemental Cycles
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Q1) Which of the following is NOT an example of a reduced form of carbon in the carbon cycle?
A) methane
B) biomass
C) hydrocarbons
D) carbon dioxide
E) methanol
Q2) On which of the following does humankind expect to find life because of the similarity of its geology to that of Earth?
A) Jupiter
B) Venus
C) Mars
D) Jupiter's moon Europa
E) Pluto
Q3) Compare and contrast assimilatory and dissimilatory nitrate reduction.
Q4) Compare and contrast carbon cycling in aerobic versus anaerobic terrestrial systems.
Q5) Explain how the Mississippi River drainage into the Gulf of Mexico off the coast of Louisiana leads to a large dead zone.
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Chapter 23: Human Microbiota and Innate Immunity
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Q1) Which of the following is/are Type I interferon?
A) NOD-receptors
B) TLR4
C) IFN-beta
D) IFN-gamma
E) cytokines
Q2) A man has been taking excessive amounts of antacids for heartburn. These tablets are very alkaline. Which innate defense mechanism might be altered by his actions?
A) mucociliary elevator
B) lysozyme
C) pH of stomach
D) flushing action of urine
E) skin pH
Q3) C-reactive protein is an acute-phase reactant that will bind to components of A) IL-1.
B) TNF-alpha.
C) bacterial cell surfaces.
D) host cell membranes.
E) cytokines.
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Chapter 24: The Adaptive Immune Response
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Q1) If a person is infected with the cold virus one year, why can he or she still catch a cold again the next year, even if his or her immune system is working properly?
Q2) Immunization with the childhood DPT (diphtheria, pertussis, and tetanus) vaccine protects against subsequent exposure to tetanus by A) stopping isotype switching of B cells from IgM to IgA. B) preloading antigen-presenting cells.
C) stimulating quick inflammation upon future exposure. D) producing life-spanning antitetanus IgE antibodies.
E) generating tetanus-specific memory B cells.
Q3) The antigen-binding receptor expressing hepatitis antigen in an infected liver cell would be
A) TCR.
B) MHC II.
C) MHC I.
D) CD4.
E) CD8.
Q4) Would taking probiotic health supplements be good for the average person's immunity?
Q5) Why are antihistamines good for allergic rhinitis but not for atopic asthma?
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Chapter 25: Microbial Pathogenesis
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Q1) Pathogenicity islands include all of the following EXCEPT that A) genes are not expressed as operons.
B) GC/AT ratio differs from the rest of the genome.
C) residual phage genomes flank the island.
D) they are often linked to tRNA.
E) they encode the type III protein secretion (T3SS) export systems.
Q2) The disease filariasis, commonly known as elephantiasis, is caused by a(n) A) ectoparasite.
B) endoparasite.
C) insect.
D) bacterium.
E) fungus.
Q3) The likely mode of transmission of a bacterial disease in which incidence increases with a prolonged warm summer is A) direct transmission.
B) airborne transmission.
C) insect vector transmission.
D) common source fomite.
E) sexual transmission.
Q4) Diphtheria toxin is a classic AB exotoxin. How does it cause host cell damage?
Page 28
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Chapter 26: Microbial Diseases
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Q1) How can prescribing an antibiotic for a sick patient actually lead to triggering gastrointestinal illness? Explain and give an example.
Q2) All of the following are true for a positive tuberculin skin test EXCEPT that
A) latent tuberculosis is indicated.
B) it signifies active disease in all patients.
C) a delayed-type hypersensitivity reaction occurred.
D) the purified protein derivative is the antigen.
E) redness and some swelling was observed.
Q3) Which of the following respiratory infections is caused by a viral pathogen?
A) diphtheria
B) whooping cough
C) tuberculosis
D) Legionnaires' disease
E) severe acute respiratory syndrome
Q4) Giardia lamblia enters a human or other host in what form?
A) spore
B) endospore
C) cyst
D) worm
E) trophozoite
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Chapter 27: Antimicrobial Therapy
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Q1) Which of the following would NOT be considered a way to fight bacterial resistance?
A) creating molecules without antibiotic activity that can compete and bind antibiotic-resistance enzymes
B) increase the amount of antibiotics in our foods to prevent food-borne infection
C) alter the structure of antibiotics to sterically hinder the binding of antibiotic-resistance enzymes
D) link different antibiotics together, forming hybrid antibiotics with dual action and targets
E) administer antibiotics more prudently when possible
Q2) Compare and contrast the utility of the antibiotic polymyxin versus cephalosporin in clearing up an Escherichia coli skin infection that has become systemic.
Q3) An MIC test can determine all of the following EXCEPT
A) the lowest level of an antibiotic that kills a particular bacteria.
B) the highest level of an antibiotic that kills a particular bacteria.
C) levels of an antibiotic that do not kill a particular bacteria.
D) drug susceptibility and resistance.
E) whether the drug is bacteriostatic or bactericidal.
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Chapter 28: Clinical Microbiology and Epidemiology
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Sample Questions
Q1) Molecular screening is now being used to detect individuals with early stages of TB because
A) skin testing is unreliable and needs refrigeration that many countries may not have.
B) vaccination with Bacille Calmette-Guérin does not protect against multidrug resistance.
C) many countries do not have disposable needles for skin testing.
D) it can detect infection earlier than chest X-rays and sputum sampling.
E) it can be used more safely on children with the disease.
Q2) Tuberculosis has become a reemerging pathogen today in large part due to A) increased incidence of HIV infection.
B) airline travel reducing geographical distances.
C) surge in reservoir animal populations carrying the disease to humans.
D) strict compliance with drug regimens.
E) concurrent increases in hepatitis C infection.
Q3) Compare and contrast the use of the serum antibody ELISA with the antigen-capture ELISA in the detection of Ebola.
Q4) Compare and contrast the dichotomous key approach to bacterial determination with the seven-digit-number approach when using the API strip system.
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