Advanced Microbiology
Midterm Exam
Course Introduction
Advanced Microbiology offers an in-depth exploration of the physiological, ecological, and genetic diversity of microorganisms. The course examines the molecular mechanisms underlying microbial processes, including metabolism, genetic regulation, pathogenesis, and the roles of microbes in natural and engineered environments. Students will analyze current research, advanced techniques in microbial genetics and genomics, and the application of microbiology in biotechnology, medicine, and environmental science. Emphasis is placed on critical thinking and the interpretation of primary scientific literature, preparing students for research and professional practice in the microbiological sciences.
Recommended Textbook
Microbiology An Evolving Science 2nd Edition by Joan Slonczewski
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Page 2
Chapter 1: Microbial Life: Origin and Discovery
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Q1) Describe the discoveries of Louis Pasteur while working with the French beer and wine manufacturers.
Answer: Previously, it was believed that the conversion of grapes and grain to wine and beer was a spontaneous chemical process. He discovered that this fermentation was caused by living yeast which did not require oxygen for growth. He also discovered that when the grapes or grain is contaminated with bacteria instead of yeast, acetic acid is produced instead of alcohol.
Q2) Suppose Pasteur's swan-necked flasks containing boiled broth became cloudy 24 hours after boiling. Which choice could best explain the turbidity or cloudiness in the broth without supporting spontaneous generation?
A) Endospores in the broth survived boiling and grew after the broth cooled.
B) Contaminating organisms in the broth killed by boiling became alive again after the broth cooled.
C) Chemicals in the broth came together to form living organisms.
D) The broth allowed light to pass through it with less interference after boiling.
E) Solid material in the broth dissolved during boiling.
Answer: A
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Page 3
Chapter 2: Observing the Microbial Cell
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Q1) As lens strength increases, the light cone __________ and the lens must be __________ the object.
A) narrows; nearer to B) narrows; farther from C) widens; nearer to D) widens; farther from E) widens; touch
Answer: C
Q2) In which one of the following types of microscopy is the specimen shadowed with heavy metal?
A) atomic force microscopy
B) SEM
C) TEM
D) X-ray diffraction
E) dark-field
Answer: B
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Chapter 3: Cell Structure and Function
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Q1) The 70S prokaryotic ribosome is composed of a 30S and a __________ subunit.
A) 30S
B) 40S
C) 50S
D) 60S
E) 70S
Answer: C
Q2) Which of the following is described as an attachment organelle that is a membrane-bound extension of the cytoplasm?
A) pili
B) fimbriae
C) sex pili
D) stalks
E) flagella
Answer: D
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Page 5
Chapter 4: Bacterial Culture, Growth, and Development
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Q1) The majority of nitrogen in soil and marine environments is fixed by:
A) free-living bacteria
B) symbionts
C) E. coli
D) biofilm organisms
E) UV light
Q2) Quorum sensing begins during which growth stage?
A) lag
B) early log
C) late log
D) stationary
E) death
Q3) Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?
Q4) Why can't most organisms use the nitrogen gas which is so prevalent in the atmosphere? How do these organisms acquire a usable form of nitrogen?
Q5) Compare and contrast complex media, synthetic media, and enriched media.
Q6) When studying the metabolism of an organism, why is it better to grow organisms in a defined synthetic medium instead of a complex medium?
Page 6
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) Describe the studies with Salmonella that showed that in vitro conditions do not always model what happens in vivo (in this case in the phagocytic vacuole).
Q2) A __________ medium is one of higher osmolarity than the cell.
A) hypertonic
B) hypotonic
C) isotonic
D) defined
E) complex
Q3) Organisms adapted to grow at overwhelmingly high pressures are called __________.
A) psychrophiles
B) thermophiles
C) barophiles
D) acidophiles
E) mesophiles
Q4) Briefly describe three techniques used to culture anaerobes in the laboratory.
Q5) What is a neutralophile? Neutralophiles were once referred to as neutrophiles. Why is this no longer the case?
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Q6) Why is oxygen so dangerous for cells and how do cells deal with these problems?
Chapter 6: Virus Structure and Function
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Q1) The destruction of cells as a result of viral lysis can be observed as a:
A) tissue culture
B) lawn
C) soft agar
D) plaque
E) host
Q2) To count the number of viruses in a solution, one can perform a plaque assay.
Describe how a plaque is generated in the case of a lytic virus and how a virus that does not lyse its host can be detected.
Q3) The genome of __________ ssRNA viruses can serve directly as mRNA.
A) positive (+) sense
B) negative (-) sense
C) all
D) double-stranded
E) prion
Q4) What is the advantage of symmetry in viral particles?
Q5) Why was the 2009 influenza virus called the swine flu? How was it transmitted and why were people so concerned?
Q6) How does genome uncoating occur with animal viruses?
Q7) What are prions and how do they cause disease?
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Chapter 7: Genomes and Chromosomes
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Q1) Describe the similarities and differences between DNA and RNA.
Q2) Which of the following terms refers to gene duplications that have decayed into nonfunctional entities?
A) introns
B) contigs
C) orthologs
D) pseudogenes
E) Okazaki fragments
Q3) The lagging strand is synthesized __________ , while the leading strand can be synthesized __________.
A) continuously; discontinuously
B) discontinuously; continuously
C) 5'-to-3'; 3'-to-5'
D) 3'-to-5'; 5'-to-3'
E) quickly; slowly
Q4) How has the study of metagenomics allowed discovery of so many new species? How is it possible to know about these organisms without being able to grow them in a laboratory?
Q5) DNA contains structural genes and control sequences. Describe each.
Q6) Describe three functions of DNA polymerase III.
Page 9
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) Post-translational modification may involve:
A) adenylylation
B) phosphorylation
C) acetylation
D) all of the above
E) none of the above
Q2) Which of the following is an example of a heat shock protein?
A) Clp protease
B) tolC
C) SecB
D) Gro EL
E) Rho
Q3) In eukaryotes, protein degradation occurs through organelles called __________.
A) proteases
B) lysosomes
C) RNases
D) proteasomes
E) vacuoles
Q4) Explain the process of transcription initiation.
Q5) How do sigma factors regulate major physiological responses?
10
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) Because the F plasmid can exist in extrachromosomal and integrated forms, it is sometimes called a/an __________.
A) episome
B) F'
C) Hfr
D) lysogen
E) tranducing phage
Q2) A __________ colony is the result of a high mutation rate.
A) colored
B) wrinkled
C) large
D) sectored
E) convex
Q3) Which of the following forms of DNA repair is error-prone?
A) SOS repair
B) methyl mismatch
C) base excision
D) nucleotide excision
E) photoreactivation
Q4) Is an Hfr cell also considered to be F<sup>+</sup>? Why or why not?
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Chapter 10: Molecular Regulation
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Q1) What occurs when an inducer is added to a medium containing an organism with a metabolic pathway controlled by a repressor?
A) The inducer combines with the repressor and activates the repressor
B) The inducer combines with the repressor and inactivates the repressor
C) The inducer combines with the substrate and blocks induction
D) The inducer combines with the substrate and activates induction
E) The inducer does not combine with but functions as a chaperone molecule for the enzyme-substrate complex
Q2) If the newly synthesized DNA strand slips back relative to the template strand, one copy of the repeated unit is __________ the growing strand.
A) inserted in
B) deleted from C) folded over D) folded under E) bound to
Q3) Explain the process of attenuation in regulating transcription of the tryptophan operon.
Q4) What is diauxic growth and why does this occur?
Q5) Explain a way that organisms sense and respond to their environment.
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Chapter 11: Viral Molecular Biology
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Q1) The __________ separation of early genes and late genes is common to the replicative cycles of many phages as well as viruses of eukaryotes.
A) spatial
B) physical
C) temporal
D) genetic
E) lytic
Q2) Which was the first virus demonstrated to cause cancer?
A) human immunodeficiency virus
B) Rous sarcoma virus
C) herpes simplex virus
D) coxsackievirus
E) rhinovirus
Q3) What types of infections are caused by herpes viruses? Describe the two possible types of replication cycles that occur with the herpes viruses.
Q4) Why are capsids of icosahedral symmetry so common among viruses?
Q5) How can viruses be used to treat cancer? What are some features the viruses must have to be used in cancer therapy?
Q6) Why isn't there a cure or vaccine for AIDS yet?
Page 13
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Chapter 12: Molecular Techniques and Biotechnology
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Q1) When designing the primer sets for multiplex PCR, what are some concerns?
Q2) Traditionally, vaccines used to prevent microbial diseases have consisted of:
A) incapacitated microorganisms
B) inactivated proteins
C) attenuated viruses
D) all of the above
E) none of the above
Q3) The electromobility shift assay (EMSA) is utilized to monitor molecular interactions between:
A) two proteins
B) RNA and protein
C) DNA and protein
D) DNA and RNA
E) none of the above
Q4) Which kind of phage vectors is most frequently used in phage display technology?
A) T-odd
B) T-even
C) filamentous single-stranded DNA phages
D) lambda-based vectors
E) none of the above
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Chapter 13: Energetics and Catabolism
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Q1) A bacterium capable of producing methane and water from carbon dioxide and hydrogen performs a type of metabolism called __________ and, given its sources of electrons, it is a __________.
A) methanogenesis; lithotroph
B) respiration; heterotroph
C) fermentation; organotroph
D) carbon fixation; phototroph
E) none of the above
Q2) The laws of thermodynamics indicate that systems tend to become less ordered and that the __________, a measure of disorder or randomness of the universe, always increases.
A) entropy
B) enthalpy
C) Gibbs free energy
D) all of the above
E) none of the above
Q3) What is isothermal titration and how does it work?
Q4) The genome of Treponema pallidum, the causative agent of syphilis, was surveyed and annotated. What did this survey reveal about its obligate association with the host cells?
Page 15
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Chapter 14: Respiration, Lithotrophy, and Photolysis
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Q1) The chlorophyll chromophore consists of a heteroaromatic ring complexed to a
A) calcium ion
B) chloride ion
C) magnesium ion
D) manganese ion
E) potassium ion
Q2) In Gram-negative bacteria, the ETS is embedded in the:
A) inner membrane
B) cell wall
C) periplasm
D) outer membrane
E) none of the above
Q3) Cyanobacteria have __________-based photosynthesis and are the only __________-producing bacteria.
A) H<sub>2</sub>S; S<sup>0</sup>
B) Mg<sup>2+</sup>; NO
C) H<sub>2</sub>O; O<sub>2</sub>
D) succinate; O<sub>2</sub>
E) none of the above
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Chapter 15: Biosynthesis
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Q1) What technique was used to demonstrate that gene expression of the CO<sub>2</sub>-concentrating mechanism (CCM) transporters is induced by low levels of CO<sub>2</sub>? Briefly explain the basis of the technique.
Q2) The most ancient CO<sub>2</sub> fixation pathway in methanogens is
A) the reverse TCA cycle
B) the 3-hydroxypropionate cycle
C) the Calvin cycle
D) the reductive acetyl-CoA pathway
E) none of the above
Q3) The following is NOT correct regarding nitrogen assimilation into biomass:
A) Different oxidation states of nitrogen require different amounts of reducing energy.
B) It is easy for living organisms to assimilate nitrogen due to its great stability (N\(\equiv\)N).
C) Nitrogen forms must be fully reduced to NH<sub>3</sub>/ NH.
D) All of the above.
E) None of the above.
Q4) Discuss nutritional and environmental influences on the synthesis of tetrapyrroles in bacteria
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Chapter 16: Food and Industrial Microbiology
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Q1) Mold ripening refers to the secondary __________ stage of cheese production.
A) respiration
B) curd
C) contamination
D) bacterial
E) fermentation
Q2) Which of the following mushrooms is NOT grown on logs or wooden blocks?
A) portobello
B) black forest
C) shiitake
D) oyster
E) enoki
Q3) The filtered mash in beer making is referred to as __________.
A) hops
B) barley
C) yeast
D) malt
E) wort
Q4) Why is it better nutritionally to ferment soybeans than to consume them without fermenting?
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Chapter 17: Origins and Evolution
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Q1) Using traditional taxonomic rank, which of the following is a smaller rank than family?
A) order
B) domain
C) genus
D) phylum
E) subclass
Q2) In the domains of life, Archaea and Bacteria differ from each other in that:
A) Archaea contain membrane bound organelles, Bacteria do not
B) Bacteria can be extreme thermophiles, Archaea cannot
C) Archaea contain ester-linked membrane fatty acids, Bacteria do not
D) Bacteria start protein production with formylmethionine, Archaea do not
E) Bacteria have introns, Archaea do not
Q3) Why are bacterial antibiotics having a greater effect on diminishing the nematode infection caused by Brugia malayi (the etiologic agent of filariasis) than are current antinematode agents?
Q4) Why was the discovery of endolithic bacteria of interest to NASA scientists studying Mars?
Q5) Explain how banded iron formations could arise in the geologic record due to photoferrotrophy?
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Chapter 18: Bacterial Diversity
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Q1) The epsilonproteobacterium Helicobacter pylori is the cause of gastritis and stomach ulcers. What mechanism allows it to survive the acidic conditions of the mammalian stomach?
Q2) A new bacterial group is discovered, and its physiology is partially characterized. Its genome had been previously sequenced in a metagenomics project. What is its taxonomical status?
A) species status automatically conferred
B) provisional, with Candidatus preceding a provisional species binomial name
C) assignation to a family or order with a note about its physiological traits
D) remains as "Unknown" until more of its morphology is described
E) none of the above
Q3) Bacteria in the genera __________ produce durable endospores that remain viable for millennia.
A) Carboxydothermus and Listeri
B) Lactobacillus and Streptococcus
C) Bacillus and Clostridium
D) all of the above
E) none of the above
Q4) What is photoheterotrophy? Provide two examples.
Q5) Describe the metabolic characteristics of Chlorobium species.
Page 20
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Chapter 19: Archaeal Diversity
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Q1) 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?
Q2) The energy-yielding process of __________ occurs only in the archaea.
A) fermentation
B) sulfur oxidation
C) hydrogen oxidation
D) methanogenesis
E) anaerobic respiration
Q3) Where are methanogens found in nature? What are some of the problems they can cause in these habitats?
Q4) Which of the following is responsible for movement away from DNA-damaging light?
A) bacteriorhodopsin
B) halorhodopsin
C) sensory rhodopsin I
D) sensory rhodopsin II
E) sensory rhodopsin III
Q5) Explain why, when growing Halobacterium on agar plates, some colonies may be pink, some red, and some sectored.
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Chapter 20: Eukaryotic Diversity
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Q1) Giardia lamblia is an infectious problem in day care centers because it is a/an:
A) intestinal pathogen passed via fecal-oral transmission
B) aerosol pathogen passed via sneezing and coughing
C) mucosal pathogen passed via mucus contamination
D) skin pathogen passed via direct skin contact
E) bloodborne pathogen passed via contact with open wound
Q2) Which of the following could be classified in the clade Viridiplantae?
A) primary endosymbiont algae
B) animals
C) true fungi
D) microsporidia
E) amebas
Q3) A major group of marine phytoplankton that is essential to the marine food chain includes:
A) microsporidia
B) dinoflagellates
C) apicomplexan
D) excavates
E) yeasts
Q4) Why are PAD1 and PAD2 important in Trypanosoma brucei infection.
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Chapter 21: Microbial Ecology
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Q1) Describe haustorial parasitism.
Q2) The salt concentration of marine water is about 3.5%. Which of the following is NOT a major ion in seawater?
A) Na+
B) Cl<sup>-</sup>
C) Br<sup>-</sup>
D) Cu<sup>2+</sup>
E) I<sup>-</sup>
Q3) Feeding cattle grain generates high rumen acidity, selecting for acid-resistant pathogens such as:
A) Sulfolobus sp.
B) E. coli O157:H7
C) Halobacterium NRC-1
D) fuselloviruses
E) Helicobacter pylori
Q4) Explain how the benthic interface between the ocean floor and water can act as a charged battery to generate electricity.
Q5) How would a high cereal or grain diet for cattle affect the growth of pathogens like E. coli?
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Chapter 22: Microbes and the Global Environment
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Q1) In the marine photic zone, the rate of photosynthesis:
A) is equal to the amount of CO<sub>2</sub> released from the niche
B) exceeds the rate of respiration
C) is less than the respiration rate
D) does not affect carbon cycling
E) is inversely related to rate of respiration
Q2) The conversion of nitrate to dinitrogen gas is called:
A) nitrogen fixation
B) nitrification
C) nitrate assimilation
D) ammonification
E) denitrification
Q3) Which of the following would be more problematic in Kansas than Florida?
A) mercury-contaminated fish
B) nitrite-induced blue baby syndrome
C) uranium-contaminated soil
D) iron-corroded pipes
E) sulfur-contaminated coal
Q4) What is the role of predators in wastewater treatment plants?
Q5) What types of evidence suggest the past existence of water on Mars?
Page 24
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Chapter 23: Human Microbiota and Nonspecific Host Defenses
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Q1) How does IFN-gamma protect the host?
A) It induces dsRNA endonucleases.
B) It interferes directly with viral replication.
C) It has an immunomodulatory role.
D) It induces fever at the hypothalamus.
E) It blocks adhesion of pathogens.
Q2) Lysozyme and the antibiotic penicillin have similar mechanisms of action in that they both cause damage to the bacterial:
A) cell membrane
B) capsule
C) cell wall
D) DNA
E) ribosomes
Q3) Are the Langerhans cells of the skin-associated lymphoid tissue (SALT) related to the islets of Langerhans of the pancreas that secrete insulin? What is their function?
Q4) Explain how differences in gut microbiota can account for obesity and leanness in humans.
Q5) Describe distinguishing characteristics of innate and adaptive immunity.
Q6) Why is acne treated with antibiotics? Describe the process of acne formation.
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Chapter 24: The Adaptive Immune Response
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Q1) 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
Q2) RAG1 and RAG2 are enzymes that control gene splicing on B-cell antibody genes, which order are segments worked on in the creation of the heavy-chain gene segment?
A) VD spliced together, then J, then C
B) DJ spliced together, then V
C) VJ spliced together, then D
D) VC spliced together, then D, then J
E) VDJ segments are all spliced together simultaneously
Q3) A surgical patient infected with a bloodborne Staphylococcus would initially produce an anti-staphylococcal antibody of the IgM class. Why is that?
Q4) 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) What do the anthrax, E. coli, cholera, and Bordetella toxins have in common?
A) inhibit of protein synthesis
B) possess ADP ribisytransferase activity
C) cause diarrhea
D) disrupt cell membrane
E) trigger apoptosis
Q2) Urease is a virulence factor produced by:
A) uropathogenic E. coli
B) Vibrio cholerae
C) Bordetella pertussis
D) Helicobacter pylori
E) Pseudomonas aeruginosa
Q3) Which of the following HIV proteins down-regulates cell surface CD4 and MHC class I?
A) Tat
B) Vpr
C) Nef
D) Vif
E) Vpu
Q4) Describe the mode of action of diphtheria toxin.
Page 27
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Chapter 26: Microbial Diseases
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Q1) A commonly implicated causative agent of subacute endocarditis (SBE) is:
A) Pseudomonas aeruginosa
B) Staphylococcus epidermidis
C) viridans streptococci
D) Streptococcus pyogenes
E) Borrelia burgdorferi
Q2) How would a chest X-ray and blood counts look different for a fungal versus bacterial lung infection?
Q3) __________ diseases are often called spongiform encephalopathies.
A) Meningitis
B) Cytotoxin
C) Neurotoxin
D) Prion
E) Virus
Q4) Many infectious diseases display similar __________, making diagnosis difficult.
A) syndromes
B) symptoms
C) vectors
D) disease mechanisms
E) modes of transmission
Page 28
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Chapter 27: Antimicrobial Chemotherapy
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Q1) Which of the following statements about the Kirby-Bauer assay is true?
A) used to test multiple bacteria simulataneously on a single plate.
B) uses serial dilutions of specific antibiotics to detremine MIC.
C) zones of inhibition that are smaller are better antibiotics than antibiotics that from larger zones.
D) can test up to 12 different antibiotic disks at one time.
E) cannot be corrected with in vivo tissue concentrations.
Q2) Describe the mechanism by which the influenza virus enters OR exits a host cell and one potential drug target that is being used to prevent infection.
Q3) Quorum sensing is a new approach to antibiotic therapy that works by:
A) preventing horizontal transfer of genes
B) stopping bacterial motility
C) binding virulence transcription factors
D) halting bacterial cell-cell communications
E) regulating nutrient uptake to decrease metabolism
Q4) How have modern agricultural practices contributed to the increase of antibiotic resistance seen today?
Q5) What is the definition of "antibiotic"? Where are antibiotics isolated from and why are these compounds made in nature?
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Chapter 28: Clinical Microbiology and Epidemiology
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Q1) Chocolate agar is considered __________ in comparison to blood agar.
A) more nutrient rich (capable of growing greater variety of bacteria)
B) less nutrient rich (capable of growing less variety of bacteria)
C) equally nutrient rich (since they both contain red blood cells)
D) a chemically-defined media (whereas blood agar is not)
E) better for determining hemolytic bacterial reactions
Q2) How could the molecular method of restriction fragment length polymorphisms (RFLP) be used to determine if a patient is infected with a new unknown strain of infectious Escherichia coli or an existing strain of infectious Escherichia coli?
Q3) Which of the following genera of bacteria would NOT change the color of N,N,N',N'-tetramethyl-p-phenylenediamine to purple/black upon exposure?
A) Salmonella
B) Brucella
C) Pseudomonas
D) Bordetella
E) Campylobacter
Q4) Compare and contrast the utility of traditional culture-based methods for detection of Borrelia burgdorferi (the etiologic agent of Lyme disease) with the PCR-based methods?
To view all questions and flashcards with answers, click on the resource link above. Page 30