Applied Microbiology
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Course Introduction
Applied Microbiology explores the practical uses of microorganisms in industries such as food production, biotechnology, pharmaceuticals, agriculture, and environmental management. This course covers microbial physiology, genetics, and metabolism as they relate to real-world applications, including fermentation, bioremediation, antibiotic development, and the production of enzymes and biofuels. Students will examine case studies, learn laboratory techniques for the cultivation and identification of microbes, and analyze the role of microbiology in solving societal challenges such as disease control, waste management, and sustainable resource development.
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) Peter Mitchell and Jennifer Moyle discovered the ________ theory in the 1960s.
A) germplasm
B) evolution
C) chemiosmotic
D) DNA synthesis
E) polymerase chain reaction
Answer: C
Q2) How did European invaders to North America kill much of the native population?
A) tuberculosis
B) leprosy
C) smallpox
D) HIV
E) bubonic plague
Answer: C
Q3) Antonie van Leeuwenhoek worked as a cloth draper, inspecting the quality of cloth. How did this lead to his interest in microscopy?
Answer: His work introduced him to magnifying lenses. He began the hobby of grinding lenses, ultimately making a microscope that enabled him to observe single-celled microbes.
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Chapter 2: Observing the Microbial Cell
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Q1) If aqueous cytoplasm was submerged in a beaker of immersion oil, the slide would be
A) undetectable.
B) brighter than its surroundings.
C) darker than its surroundings.
D) fluorescent.
E) stained.
Answer: A
Q2) Which of the following would be MOST appropriate to visualize viral particles being assembled inside an infected bacterial cell?
A) dark-field microscopy
B) atomic force microscopy
C) fluorescence microscopy
D) scanning electron microscopy
E) transmission electron microscopy
Answer: E
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4
Chapter 3: Cell Structure and Function
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Q1) Which of these experiments would NOT be a reason to fractionate bacterial cells?
A) to obtain membrane fractions to study transport proteins
B) to purify ribosome subunits to study translation
C) to obtain periplasmic proteins to study chaperons from that space
D) to obtain cytoplasmic proteins such as FtsZ
E) to study the growth rate of E. coli in the presence of lactose
Answer: D
Q2) All of the following are true of supercoiling in chromosomal DNA EXCEPT that it A) doubles back and twists upon itself.
B) facilitates RNA transcription.
C) results in compaction.
D) is generated by gyrase.
E) is maintained by DNA-binding proteins.
Answer: B
Q3) Describe four ways cells can be broken open in order to isolate the cellular components.
Answer: Mild detergent lysis disrupts the cell membrane without denaturing cellular components. Sonication is the use of high-frequency sound waves to disrupt cell membranes. Enzymes are proteins that can be used to break open cells. Mechanical disruption uses methods such as a French press to lyse cells.
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Chapter 4: Bacterial Culture, Growth, and Development
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Q1) Bacteria divide at a constant time interval called the A) generation time.
B) growth time.
C) growth rate.
D) exponential rate.
E) log phase.
Q2) Siderophore-iron complexes enter cells with the help of A) porins.
B) diffusion.
C) aquaporins.
D) ABC transporters.
E) efflux pumps.
Q3) Why do some members of a biofilm community live deep within the biofilm?
A) They are not flagellated.
B) They produce fewer exopolysaccharides.
C) They were the first organisms to initiate attachment.
D) Antibiotics do not penetrate deep into biofilms.
E) Oxygen does not penetrate deep into biofilms.
Q4) Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) Microbes accumulate ________ in the cell to prevent cell water loss in a hypertonic environment.
A) water
B) proteins
C) sugars
D) protons
E) compatible solutes
Q2) The conditions used in an autoclave may be reproduced at home in
A) a rice cooker.
B) a double-boiler.
C) a microwave.
D) a pressure cooker.
E) boiling water.
Q3) Psychrophiles favor the cold, since their membranes are more fluid at low temperature as a result of the high proportion of ________ present.
A) saturated fatty acids
B) unsaturated fatty acids
C) lipopolysaccharides
D) transport proteins
E) water
Page 7
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Chapter 6: Viruses
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Q1) Why do many RNA viruses encode their own RNA-dependent RNA polymerase and package them in viral particles? How do we take advantage of these viral-specific polymerases?
Q2) What can be counted as representing individual infectious virions from a phage suspension?
A) plaques
B) viruses
C) genomes
D) proteomes
E) burst size
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.
Page 8
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Chapter 7: Genomes and Chromosomes
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Q1) Hyperthermophilic archaea possess an unusual gyrase called ________, which introduces positive supercoils into the chromosome in order to protect the DNA from
A) reverse DNA gyrase; thermal denaturation
B) DNA helicase; thermal denaturation
C) topoisomerase I; gene overexpression
D) DNA ligase; thermal denaturation
E) reverse transcriptase; gene overexpression
Q2) Errors during replication are corrected by the DNA proofreading activity intrinsic to DNA Pol
A) I.
B) II.
C) III.
D) IV.
E) V.
Q3) Describe three practical applications of the polymerase chain reaction (PCR) and possible pitfalls.
Q4) Why is replication of the lagging DNA strand a problem, and how is this problem overcome?
Q5) Describe how the name of bacterial genes and their gene product are denoted.
Page 9
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) Molecules of sRNA do not encode proteins but are used to ________ the stability or translation of specific mRNAs into proteins.
A) start
B) regulate
C) stop
D) speed up
E) slow down
Q2) E. coli is being used in order to study various agents that inhibit protein synthesis. An agent will bind the 16S RNA of the 30S subunit and block aminoacyl tRNA from entering the ribosome. This agent is most likely related to A) chloramphenicol.
B) streptomycin.
C) puromycin.
D) tetracycline.
E) erythromycin.
Q3) What are the functions of the different types of RNA molecules?
Q4) Describe how Marshal Nirenberg and Heinrich Matthaei utilized an E. coli cell lysate to figure out the genetic code.
Q5) How does mRNA compare to the template and nontemplate DNA strand?
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) CRISPR is considered an example of adaptive immunity in bacteria and archaea because it
A) methylates host DNA and destroys invading DNA.
B) requires host "pac" sites in order to destroy invading DNA.
C) minimizes damage from foreign DNA by using guide RNA similar to the invader and cas proteins to cleave the foreign DNA.
D) prevents the production of cell surface receptors that allow phages to get into the cell.
E) prevents archaeal DNA from infecting bacteria.
Q2) During generalized recombination, ________ proteins catalyze branch migration at crossovers called ________.
A) RuvAB; Holliday junctions
B) RuvAB; duplexes
C) RecBCD; Holliday junctions
D) RecBCD; duplexes
E) RecA; duplexes
Q3) Compare and contrast general and site-specific recombination.
Q4) Why is SOS repair considered to be an error-prone repair mechanism? Why would an organism use an error-prone mechanism?
Page 11
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Chapter 10: Molecular Regulation
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Q1) How is sigma H degradation controlled by temperature, and why is this important to the cell?
Q2) Glucose transport into the cell brings about a phenomenon known as inducer exclusion.
Describe how this functions with respect to the lac operon.
Q3) 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?
Q4) Which of the following statements is true concerning the use of cyclic di-GMP as a second messenger?
A) It activates the expression of flagellin genes and thus enhances motility.
B) It is found in all microbes: bacteria, archaea, and eukaryotic microbes.
C) The action of diguanylate cyclase produces it.
D) It decreases in level as biofilm is produced.
E) Phosphodiesterase can convert GMP to cyclic di-GMP.
Q5) What happens when strand slippage occurs on the template or the newly synthesized DNA strand? How does Neisseria gonorrhoeae use slipped-strand mispairing to its advantage?
Q6) The stringent response downregulates rRNA synthesis. Does it similarly downregulate ribosomal protein synthesis?
Page 12
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Chapter 11: Viral Molecular Biology
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Q1) 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?
Q2) Which HIV protein is mismatched with its function?
A) nef-virion component
B) vpu-membrane protein
C) rev-reverse transcriptase
D) tat-transcription factor
E) env-envelope protein
Q3) Describe the several features of lentivectors. What are their molecular sources?
Q4) The segmentation of the influenza genome is conducive to ________, which can be defined as the process by which two different viruses swap genome segments to form a new genome.
A) recombination
B) hybridization
C) ligation
D) reassortment
E) shuffling
Page 13
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Chapter 12: Biotechniques and Synthetic Biology
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Q1) Annotation of sequences of transposon insertion sites in the chromosome of Escherichia coli O157:H7 cells that had lost their acid-resistance properties revealed four genes: two encoding isoforms of glutamate decarboxylase (GadA and GadB) and one encoding a glutamate/gamma-aminobutyric acid (GABA) antiporter. What does the fourth gene encode?
A) a heat shock protein
B) a possible regulator
C) a glutamate/GABA symporter
D) a GABA uniporter
E) a glutamate carrier protein
Q2) The purpose of a DNA protection assay is to determine what nucleotide sequences directly interact with which macromolecules?
A) DNA-binding proteins
B) rRNA
C) endonucleases
D) exonucleases
E) tRNA
Q3) Describe the use of a primary and secondary antibody in a western blot.
Q4) What are translational fusions used for? How are they constructed?
Q5) How can a protein be detected on a western blot?
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Chapter 13: Energetics and Catabolism
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Q1) What technique can be used to determine entropy and enthalpy changes associated with biochemical reactions?
A) nuclear magnetic resonance
B) calorimetry
C) electron microscopy
D) mass spectroscopy
E) measurement of light levels
Q2) The process of prioritized consumption of substrates is known as catabolite
A) induction.
B) poisoning.
C) competition.
D) repression.
E) attenutation.
Q3) 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?
Q4) Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.
Q5) Define "organotroph" and "heterotroph." Are these terms equivalent?
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Chapter 14: Electron Flow in Organotrophy, Lithotrophy, and
Phototrophy
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Q1) In photosystem II of purple bacteria, electrons flow through cytochrome bc, coupled to pumping of protons and the proton potential drives synthesis of ATP. The cytochrome bc complex transfers the electrons back to bacteriochlorophyll P870. This type of ATP synthesis is called
A) reverse electron flow.
B) membrane potential.
C) noncyclic photophosphorylation.
D) cyclic photophosphorylation.
E) proton motive force.
Q2) In anaerobic soils, some yeasts and filamentous fungi can reduce nitrate to nitrite and nitrite to
A) ammonia (NH3).
B) nitric oxide (NO).
C) urea.
D) nitrogen gas (N ).
E) ammonium hydroxide (NH4OH).
Q3) Describe the role of the thylakoids in purple bacteria and cyanobacteria. Why is it that pumping protons into the lumen is essentially equivalent to pumping protons out of the cell?
Q4) What factors may affect p in metabolically active bacterial cells?
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Chapter 15: Biosynthesis
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Q1) Many of the antibiotics and other pharmaceutical agents isolated from Streptomyces species are
A) amides.
B) polyketides.
C) thioesters.
D) fatty acids.
E) lipids.
Q2) Which of the following molecules provides a way to simultaneously assimilate one carbon atom and one nitrogen atom during purine biosynthesis?
A) acetyl-CoA
B) acetyl-ACP
C) malonyl-ACP
D) carbamoyl phosphate
E) NADPH
Q3) The Calvin cycle is essentially
A) started by the oxygen capture by Rubisco.
B) a reductive pentose phosphate cycle.
C) the reductive, or reverse, tricarboxylic acid cycle.
D) a pathway to synthesize fatty acids but not sugars.
E) a pathway that is used only when light is present.
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Chapter 16: Food and Industrial Microbiology
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Q1) Another term for freeze-drying is
A) radiation.
B) dehydration.
C) filtration.
D) pasteurization.
E) lyophilization.
Q2) Describe some of the characteristics that industrial strains of microbes must possess.
Q3) In the process of ________, NO standard starter culture is available.
A) sourdough bread making
B) yogurt making
C) chocolate production
D) cheese making
E) beer making
Q4) The ________ of milk proteins results in the formation of curds.
A) filtration
B) lyophilization
C) pasteurization
D) coagulation
E) radiation
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Chapter 17: Origins and Evolution
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Q1) Which of the following is NOT correct about endolithic microorganisms?
A) They have been found in mines as deep as 3 kilometers.
B) Their discovery elicited interest in NASA scientists seeking life on Mars.
C) They can grow in Earth's core.
D) The term "endolithic" means living "within rocks."
E) They metabolize by oxidizing e- donors generated through decay of radioactive metals.
Q2) Discuss what horizontal gene transfer is. How does it occur and how might it obscure phylogenetic relationships among taxa?
Q3) All of the following are examples of "operational genes," EXCEPT ________ genes.
A) metabolic
B) ribosomal RNA
C) stress response
D) pathogenicity
E) resistance
Q4) What criteria must be met in order to prove that two bacterial strains belong in the same species?
Q5) Briefly discuss the types of geological evidence of early life and their advantages and limitations.
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Chapter 18: Bacterial Diversity
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Q1) How do Bacteroides fragilis and B. thetaiotaomicron contribute to 15% of human caloric intake? Are there other benefits provided by these microbes to human health? Are they potentially pathogenic?
Q2) Clades of microbes that are recently defined or characterized are referred to as A) hyperthermophiles.
B) archaea.
C) phyla.
D) deep branching.
E) emerging.
Q3) What bacterial groups use actin as a means to leave their host cells? What advantage does this type of cellular invasion provide to intracellular pathogens?
Q4) Which gammaproteobacteria genera include species that oxidize H S to S ?
A) Escherichia and Enterobacter
B) Chromatium and Beggiatoa
C) Klebsiella and Shigella
D) Proteus and Erwinia
E) Rhodobacter and Nitrosomonas
Q5) Describe the photosynthetic machinery of cyanobacteria.
Q6) Describe the metabolic characteristics of Chlorobium species.
Page 20
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Chapter 19: Archaeal Diversity
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Q1) What are methane gas hydrates and where are they found? Discuss the idea of benthic mining.
Q2) What are some of the unique features of archaeal gene regulation?
Q3) Nanoarchaeum equitans is a hyperthermophilic symbiont of
A) Ignicoccus.
B) Sulfolobus.
C) Halobacterium.
D) Methanococcus.
E) Thermoplasma.
Q4) The Sulfolobus species maintains an internal pH ________ that of its habitat. A) equivalent to B) higher than C) lower than
D) variable enough that it cannot be measured against E) not determined to be different to
Q5) Discuss the role of the four different types of rhodopsins found in the Halobacterium species (bacteriorhodopsin, halorhodopsin, and sensory rhodopsins I and II).
Q6) Why are the archaea so difficult to classify?
Q7) What is the Ancient Archaeal Group and what is known about these organisms?
Page 21
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Chapter 20: Eukaryotic Diversity
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Q1) Physarum polycephalum is a type of plasmodial slime mold that can be seen as a yellow mass growing on decaying wood. This organism produces
A) a fruiting body in which individual cells remain unicellular.
B) no fruiting bodies and no spore formations.
C) a giant multinucleated cell that produces fruiting bodies.
D) fruiting bodies within a calcified shell structure.
E) no fruiting bodies and spores that move using pseudopodia.
Q2) The term "protist" describes single-cell and colonial eukaryotic organisms other than A) paramecia.
B) diatoms.
C) dinoflagellates.
D) fungi.
E) amebas.
Q3) The Zygomycota taxon comprises saprophytes, mycorrhiza, and insect parasites. They are characterized by having nonmotile gametes that must grow toward each other to fuse and form a zygote (zygospore). Explain why this taxon is classified under the larger taxa of Opisthokonta, which includes organisms with flagellated reproductive cells.
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22
Chapter 21: Microbial Ecology
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Q1) Compare and contrast the photic zones of freshwater lake and pelagic ecosystems.
Q2) Rhizosphere bacteria benefit their host plant by
A) degrading plant lignin.
B) attracting symbiotic nematodes.
C) improving water uptake.
D) producing large amounts of photosynthate.
E) discouraging growth of plant pathogens.
Q3) Which of the following plays an important role in keeping the water column clear enough for the penetration of light?
A) algae
B) bacteria
C) fish
D) invertebrates
E) viruses
Q4) Lignin decomposition forms
A) arbuscules.
B) detritus.
C) fruiting bodies.
D) humus.
E) rhizopus.
Page 23
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Chapter 22: Microbes in Global Elemental Cycles
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Q1) Describe the difference between a source, sink, and reservoir of an element.
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) Which contaminant in water is especially prevalent in agricultural regions of the United States?
A) carbon
B) sulfur
C) phosphate
D) nitrate
E) magnesium
Q4) What would happen if household wastewater was emptied into local receiving rivers without prior treatment?
Q5) Some bacteria are responsible for degrading concrete. How do they accomplish this?
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Chapter 23: Human Microbiota and Innate Immunity
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Q1) Which of the following is NOT a lymphoid organ?
A) tonsils and adenoids
B) spleen
C) appendix
D) stomach
E) bone marrow
Q2) Which part of the genitourinary tract is considered sterile?
A) kidney
B) bladder
C) distal urethra
D) genital tract
E) vagina
Q3) Microbes in and on humans sharpen immunity and protect from infection. Explain why these benefits also come with considerable risk.
Q4) Which of the following creates a channel in target cell membranes?
A) complement
B) defensins
C) natural killer cells
D) complement and defensins
E) complement, defensins, and natural killer cells
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Chapter 24: The Adaptive Immune Response
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Q1) The chickenpox vaccine is created with an attenuated virus, and the rabies vaccine with an inactivated virus. This means that the chickenpox virus is a ________, and the rabies virus is ________.
A) subunit vaccine; a genetic vaccine
B) genetic vaccine; a subunit vaccine
C) nonfunctional form; living but weakened
D) subunit vaccine; nonfunctional
E) living weakened form; nonfunctional
Q2) The gut is able to distinguish between indigenous microbiota and pathogens by using which part of epithelial cells?
A) TLRs and NLRs
B) SIgA
C) cytokines
D) IL-22
E) ILCs
Q3) Some patients suffering from bare lymphocyte syndrome (BLS), a rare immunodeficiency, have a genetic mutation in their TAP1/TAP2 genes causing the production of a defective TAP transporter. Describe what effect this has on antigen processing and in what cells.
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Chapter 25: Microbial Pathogenesis
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Q1) Yellow fever and West Nile virus are both
A) cancer causing.
B) hemorrhagic viruses.
C) close relatives of herpes virus.
D) diarrheagenic viruses.
E) flaviviruses.
Q2) Which of the following is a nonproteinaceous, yet toxic, compound found in all Gram-negative bacteria?
A) endotoxin
B) exotoxin
C) type I pili
D) type III pili
E) type IV pili
Q3) Which of the following species causes whooping cough?
A) Streptococcus mutans
B) Staphylococcus aureus
C) Bordetella pertussis
D) Neisseria gonorrhoeae
E) Mycoplasma
Q4) Diphtheria toxin is a classic AB exotoxin. How does it cause host cell damage?
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Chapter 26: Microbial Diseases
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Q1) Describe epigenetic silencing and the role it plays in malaria.
Q2) Which of the following STDs is caused by a protozoan infection?
A) Treponema pallidum
B) Trichomonas vaginalis
C) Chlamydophila pneumoniae
D) HIV
E) Neisseria gonorrhoeae
Q3) In urinary tract infections (UTIs), what is the implication of the ability of bacteria to actually hide urinary tract epithelial cells and form biofilms?
A) UTIs can never be cured.
B) A reservoir for reinfection is created.
C) The kidney will invariably be infected.
D) Intracellular pathogens are the etiologies for UTI.
E) The ureter is the usual route for bladder infection.
Q4) Giardia causes more diarrhea than any other protozoan globally. Interpret the reasons for its success in causing disease.
Q5) Name and describe the role of the three domains found in tetanus and botulism neurotoxins.
Q6) Compare and contrast the characteristic symptoms of the common cold and the flu.
Page 28
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Chapter 27: Antimicrobial Therapy
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Q1) The antiviral nucleoside inhibitor zidovudine, used in treating HIV infection, works by A) fooling reverse transcriptase to incorporate it, causing a chain termination reaction.
B) disabling protease and preventing HIV protein folding.
C) blocking gag and pol genes from transcription.
D) binding directly to reverse transcriptase and allosterically inactivating the enzyme.
E) sterically hindering integrase from cutting into the host nuclear DNA.
Q2) An example of an antibiotic that binds to the 30S ribosomal subunit would be A) streptogramins.
B) macrolides.
C) beta-lactams.
D) fluoroquinolones.
E) aminoglycosides.
Q3) Outline and discuss the steps that a research laboratory would go through to discover a new antibiotic to treat a systemic infection with methicillin-resistant Staphylococcus aureus (MRSA).
Q4) How have modern agricultural practices contributed to the increase of antibiotic resistance seen today?
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Chapter 28: Clinical Microbiology and Epidemiology
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Sample Questions
Q1) Shigella sonnei is the cause of an infection commonly seen in infant day-care facilities due to
A) a high prevalence of the microbe in young children.
B) its ability to contaminate and grow on plastic toys.
C) its inherent antimicrobial nature (it is bleach and cleaning-product resistant).
D) diaper changes and hands not being properly washed.
E) Gram-positive cell wall structure making the bacteria environmentally resistant.
Q2) How have changes within our human culture caused new diseases to emerge? Explain your answer using a specific example that supports your statements.
Q3) The use of a laminar flow hood when studying the organism Francisella tularensis is an example of level ________ biological safety.
A) 0
B) I
C) II
D) III
E) IV
Q4) How would a serum antibody ELISA work in the detection of Lyme disease?
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