Microbial Genetics Final Exam
Course Introduction
Microbial Genetics explores the genetic mechanisms and molecular principles that govern inheritance, variation, and function in microorganisms such as bacteria, archaea, and viruses. This course covers topics including the structure and function of microbial genomes, gene expression and regulation, mutation, genetic recombination, horizontal gene transfer, and modern genetic engineering techniques. Emphasis is placed on methods used in microbial genetics research, as well as applications in biotechnology, medicine, and evolutionary studies. Through lectures, laboratory exercises, and case studies, students gain a comprehensive understanding of how genetic information is manipulated and used to solve real-world problems involving microbes.
Recommended Textbook
Microbiology An Evolving Science 2nd Edition by Joan Slonczewski
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Chapter 1: Microbial Life: Origin and Discovery
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Q1) How are microbes classified today?
A) comparative genomics
B) microscopy
C) X-ray diffraction
D) DNA sequencing
E) rRNA sequencing
Answer: E
Q2) The word "vaccination" is derived from the Latin word vacca, which means:
A) inject
B) smallpox
C) immunize
D) cow
E) pustule
Answer: D
Q3) Robert Koch's postulates have not been used to prove HIV as the causative agent of AIDS. Why not?
Answer: Answers may vary, but a major reason is that humans cannot be injected with HIV to see if they develop AIDS!
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Chapter 2: Observing the Microbial Cell
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Q1) Explain phase-contrast microscopy and give one advantage and one disadvantage of phase-contrast microscopy.
Answer: Phase-contrast microscopy exploits differences in refractive index between cell components and transforms them into differences in intensity of transmitted light. Advantages are that live cells can be viewed and the organelles of eukaryotes are visible. A disadvantage is that it is less effective for organisms whose cytoplasm as a low refractive index.
Q2) How does laser scanning confocal microscopy produce images?
Answer: A laser beam is focused onto the specimen and scanned across it in two planes at right angles to each other. The laser beam excites a fluorophore and both the excitation and emitted light are focused together. This results in images with very high resolution.
Q3) List and describe three common shapes of bacteria.
Answer: Bacilli (singular, bacillus) are rod-shaped bacteria. Cocci (singular, coccus) are spherical-shaped bacteria. Spirochetes are tightly coiled spirals or corkscrew-shaped bacteria.
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Chapter 3: Cell Structure and Function
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Q1) Profiles of which component of the membrane may be used to identify certain kinds of pathogens?
A) phospholipids
B) proteins
C) fatty acids
D) polysaccharides
E) leaflets
Answer: C
Q2) How is supercoiling different in bacteria and archaea. Why is this important for archaea?
Answer: In bacteria, the extra turns oppose the natural twist of the DNA helix, which is called negative supercoiling. This unwinds the DNA slightly to expose base pairs for transcription. In archaea, the DNA is positively supercoiled, which winds the DNA more tightly and increases the stability. This is important for archaea because many archaea live in extreme environments so the macromolecules have to be stabilized to prevent denaturation.
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Chapter 4: Bacterial Culture, Growth, and Development
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Q1) Some bacteria form environmentally resistant forms called __________.
A) endospores
B) heterocysts
C) colonies
D) hyphae
E) actinomycetes
Q2) Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?
Q3) How do some cyanobacteria fix nitrogen while growing aerobically?
A) they don't because nitrogenase is destroyed by oxygen
B) by using special cells called heterocysts that protect the enzyme
C) by using cysts that protect the enzyme
D) they just do it, no special structures or mechanisms
E) they live symbiotically with other organisms that protect the enzyme
Q4) Which of the following is true of all biofilms?
A) They only contain a single species.
B) The EPS may be protein or polysaccharide.
C) Cells in the biofilm are dormant until the bacteria leave the biofilm.
D) The EPS is secreted by the bacteria.
E) It is a continuous monolayer surface deposit.
Page 6
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) What alkaliphile do pink flamingos eat and how is it involved in making the flamingo pink?
Q2) Many __________ have been isolated from the ocean floor environment.
A) psychrophiles
B) mesophiles
C) thermophiles
D) barophiles
E) acidophiles
Q3) The pressure (psi-pounds per square inch) at Earth's surface is:
A) 0 psi
B) 3 psi
C) 5 psi
D) 7 psi
E) 14 psi
Q4) __________ typically evolve to survive multiple extreme environments.
A) Psychrophiles
B) Extremophiles
C) Halophiles
D) Thermophiles
E) Acidophiles
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Chapter 6: Virus Structure and Function
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Q1) Some viral species may derive their __________ from intracellular membranes, such as the nuclear membrane or endoplasmic reticulum.
A) capsid
B) genome
C) envelope
D) neck
E) tail fibers
Q2) The number of virus particles released at lysis is referred to as:
A) lytic number
B) burst size
C) lysogenic number
D) temperate number
E) release number
Q3) Tegument proteins may be found:
A) in the capsid
B) between the capsid and envelope
C) in the envelope
D) in the nucleus
E) in the spikes
Q4) What is the advantage of symmetry in viral particles?
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Chapter 7: Genomes and Chromosomes
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Q1) Bacteria are able to conduct __________ transmission-the transfer of genetic information from one cell to another.
A) vertical
B) horizontal
C) linear
D) transformation
E) pseudogene
Q2) Which statement is NOT true about bacteriophage T4 and its replication?
A) It has a linear genome.
B) It circularizes within the host cell.
C) It uses rolling-circle replication.
D) It forms long, linear concatemers.
E) It precisely packages one full-length genome.
Q3) It takes approximately how many minutes to move the entire E. coli chromosome from one cell to another?
A) 10
B) 20
C) 50
D) 100
E) 200
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) What is the importance of the stop codon UAG?
A) It tells the DNA polymerase to stop replicating the chromosome.
B) It tells the RNA polymerase to stop transcribing the chromosome.
C) It tells the tRNA to stop transcribing the DNA.
D) It tells the ribosome to stop translating the mRNA.
E) It signals the end of the operon.
Q2) __________ serves as a molecular clock that measures the approximate time since two species diverged.
A) tRNA
B) mRNA
C) rRNA
D) sRNA
E) tmRNA
Q3) __________ RNA polymerase plus sigma factor together are called
A) Transcription; translation
B) Translation; transcription
C) Ribosome; rRNA
D) Holoenzyme; core
E) Core; holoenzyme
Q4) Name two antibiotics that affect transcription and explain their mode of action.
Page 10
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) Newly replicated, and consequently __________, DNA sequences are invisible to a restriction enzyme.
A) mutated
B) restricted
C) modified
D) hemimethylated
E) single-stranded
Q2) A special sigma factor, __________, is used to transcribe genes encoding the translocasome necessary for cell competency.
A) SigH
B) Sig70
C) SigT
D) SigC
E) Sig20
Q3) Which of the following mutagens may cause frameshift mutations?
A) caffeine
B) 5-bromouracil
C) nitrosoguanidine
D) nitrites
E) acridine dyes
Page 11
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Chapter 10: Molecular Regulation
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Q1) Which form of control is the most rapid?
A) alterations of DNA sequence
B) control of transcription
C) mRNA stability
D) translational control
E) posttranslational control
Q2) The AraC-like regulators share homology with each other at which locations?
A) both their C-terminal end and their N-terminal end
B) neither their C-terminal end nor their N-terminal end
C) their C-terminal end only
D) their N-terminal end only
E) the center
Q3) Finding an inverted repeated sequence within 100-200 bases of a promoter suggests the presence of a __________ binding site.
A) DNA
B) regulatory
C) RNA
D) ribosome
E) corepressor
Q4) Explain a way that organisms sense and respond to their environment.
Page 12
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Chapter 11: Viral Molecular Biology
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Q1) Cyclophilin A is a host protein that:
A) acts as a coreceptor for HIV
B) facilitates HIV entry into the nucleus
C) is incorporated in the HIV envelope
D) inhibits HIV replication
E) cuts the polyprotein into subunits
Q2) The RNA dimer packed in the HIV virion includes two host tRNA molecules hybridized so as to present a 3' OH for __________ synthesis of DNA.
A) increasing
B) preventing
C) priming
D) decreasing
E) terminating
Q3) Flu pandemics are associated with reassortment of which virus genes?
A) hemagglutinin
B) neuraminidase
C) matrix
D) A and B
E) all of the above
Q4) 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) Both Southern and Northern blots involve the use of agarose gels. How do the types of agarose gels differ and why?
Q2) The colorless molecule o-nitrophenyl galactoside (ONPG) can be used as an artificial substrate in assays of \(\beta\)-gal in E. coli extracts. Which of the following statements is NOT true with respect to the use of ONPG?
A) Hydrolysis of ONPG by \(\beta\)-gal produces yellow o-nitrophenol.
B) o-nitrophenol can be measured with a spectrophotometer.
C) Hydrolysis of ONPG by \(\beta\)-gal also releases colorless galactose.
D) The o-nitrophenol moiety is blue and more suitable for use in solid media.
E) None of the above.
Q3) What is the principle of the electrophoretic mobility shift assay (EMSA)? What is its main application? Mention a possible limitation.
Q4) What variation of PCR methods can be used in directed evolution?
A) quantitative PCR
B) error-prone PCR
C) real-time PCR
D) multiplex PCR
E) none of the above
Q5) Describe the difference between autoradiography and phosphorimaging.
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Chapter 13: Energetics and Catabolism
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Q1) Why do the TCA cycle and the ETS have a larger ATP yield in mitochondria than in bacteria?
Q2) Describe the Entner-Doudoroff (ED) pathway. What are the advantages to microorganisms that display the ED pathway?
Q3) E. coli degrades human waste in the colon using mixed-acid fermentation. Why is this a factor of concern in some medical procedures such as colonoscopy?
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?
Q5) The Gibbs-Helmholtz equation describes the relationship between the components of free energy change and can be generally expressed as:
A) \(\Delta\)G = \(\Delta\)G° + RT ln
B) \(\Delta\)G = \(\Delta\)H - T\(\Delta\)S
C) ADP + PiATP + H<sub>2</sub>O
D) K = T°C + 273
E) none of the above
Q6) What is mixed-acid fermentation? Provide examples of industrial uses of its products.
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Chapter 14: Respiration, Lithotrophy, and Photolysis
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Q1) In seawater, sulfate is the most common anion after chloride. The following is correct with respect to the use of oxidized sulfate by some bacterial groups:
A) Oxidized sulfur molecules have potentials lower than those of the nitrogen series.
B) Oxidized sulfur molecules such as sulfate and sulfite serve as electron acceptors.
C) Sulfate and sulfite can receive electrons from hydrocarbons.
D) Sulfate-reducing archaea and bacteria are widespread in the ocean.
E) All of the above.
Q2) How has the Geobacter metallireducens redox energy been harnessed in the production of electricity?
Q3) Alkaliphiles maintain an inverted pH gradient in which:
A) the pH in their immediate environment is lower than the cytoplasmic pH
B) their immediate environment has a pH several units above that of the cytoplasm
C) pH in the immediate environment is equal to that of the cytoplasm
D) all of the above
E) none of the above
Q4) What is photoheterotrophy? Give examples of photoheterotrophic organisms.
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Page 16
Chapter 15: Biosynthesis
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Q1) What kind of reaction is the formation of oxaloacetate from phosphoenolpyruvate?
A) anabolic
B) anaplerotic
C) carboxylation
D) all of the above
E) none of the above
Q2) What are the molecules used in the extension reactions during polyketide biosynthesis?
A) acetyl-CoA units
B) malonyl-ACP units
C) coenzyme A
D) acyl-carrier protein
E) none of the above
Q3) What is denitrification?
A) conversion of nitrate or nitrite to N<sub>2</sub> by anaerobic respirers
B) oxidation of NHto nitrate or nitrite by lithotrophs
C) conversion of N<sub>2 </sub>to NH
D) all of the above
E) none of the above
Q4) How does the reductive or reverse TCA cycle differ from the regular TCA cycle?
Page 17
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Chapter 16: Food and Industrial Microbiology
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Q1) Acetic acid results from the reduction of:
A) maltose
B) glucose
C) carbon dioxide
D) ethanol
E) fructose
Q2) __________ is another term for freeze-drying.
A) Radiation
B) Dehydration
C) Filtration
D) Pasteurization
E) Lyophilization
Q3) Products of __________ fermentation include a stimulant and an antidepressant.
A) cocoa
B) coffee
C) barley
D) ethanolic
E) lactic acid
Q4) List four different types of fermentations and the end products of each and an example of a product that is made from each type.
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Chapter 17: Origins and Evolution
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Q1) Many phylogenic trees can be calibrated in time based on:
A) fossil and/or geological record
B) frequency of mutations
C) number of nodes and branches
D) whether the tree is rooted or unrooted
E) "housekeeping" genes
Q2) Which branch of taxonomy deals with the recognition of all the different classes of life?
A) identification
B) classification
C) nomenclature
D) genus
E) species
Q3) Which of the following is an example of an endosymbiotic relationship?
A) parasitic fungus on leaf cutter ants
B) Staphylococcus sp. on the skin
C) Enterobacter sp. in intestinal flora
D) human ringworm infection
E) lichen formations
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Page 19
Chapter 18: Bacterial Diversity
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Q1) The phylum Deinococcus-Thermus contains organisms that thrive in very different environments. Compare and contrast Deinococcus species and Thermus species. Why are these organisms assigned to the same phylum?
Q2) How do "purple sulfur bacteria" and "purple nonsulfur bacteria" differ in their metabolism? Are they really purple?
Q3) All of the following are mechanisms that provide an anoxic environment for nitrogenase activity in cyanobacteria EXCEPT:
A) formation of heterocysts
B) formation of chlorosomes
C) temporal separation of photosynthesis and nitrogen fixation
D) formation of large aggregates of cells
E) symbiotic associations with plants
Q4) Which gammaproteobacterial genera include species that oxidize H<sub>2</sub>S to S<sup>0</sup>?
A) Escherichia and Enterobacter
B) Chromatium and Beggiatoa
C) Klebsiella and Shigella
D) Proteus and Erwinia
E) none of the above
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Chapter 19: Archaeal Diversity
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Q1) The energy-yielding process of __________ occurs only in the archaea.
A) fermentation
B) sulfur oxidation
C) hydrogen oxidation
D) methanogenesis
E) anaerobic respiration
Q2) What are some of the unique features of archaeal gene regulation?
Q3) __________ is sensitive to penicillin.
A) Peptidoglycan
B) Pseudopeptidoglycan
C) S-layer
D) Protein cell wall
E) all of the above
Q4) What are "vent polymerases," why are they better than previously used polymerases, and from where are they acquired?
Q5) Why are extremophiles important to industry?
Q6) 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?
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Q7) Why are hot springs and geysers important habitats for many crenarchaeotes?
Chapter 20: Eukaryotic Diversity
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Q1) The taxa in which the food-grade mushrooms of morels and truffles can be found in:
A) Lichens
B) Zygomycota
C) Chytridiomycota
D) Basidiomycota
E) Ascomycota
Q2) Amoeba proteus is a large fresh-water ameba that moves using lobed-shaped pseudopodia. Describe the mechanism by which this pseudopodia structure moves this ameba using cytoplasmic streaming.
Q3) Why are sponges, jellyfish, worms, reptiles, humans, yeast, and microsporidia placed in the same eukaryotic clade?
Q4) What are nanoeukaryotes and how has their discovery changed our biological understanding?
Q5) Why would an organism benefit from undergoing more than one endosymbiont event throughout evolution? Give an example to support your argument.
Q6) What is the life cycle of Plasmodium and how does that life cycle cause Plasmodium to be categorized as an apicomplexan?
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Page 22
Chapter 21: Microbial Ecology
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Q1) Define cryptogamic crust and explain its vital role in desert ecosystems.
Q2) Which of the following is responsible for the characteristic odor of soil?
A) Vibrio sp.
B) Bacillus sp.
C) Streptomyces sp.
D) Staphylococcus sp.
E) Pseudomonas sp.
Q3) Define BOD, which can be used to measure the pollution level of lakes. Describe how effluents carrying high levels of nutrients can cause eutrophication.
Q4) Describe the interaction of Vibrio cholerae with copepods. How can saris help decrease the incidence of cholera in Bangladesh?
Q5) Which class of extremophile would you expect to find within rock crystals down to a depth of 3 km?
A) acidophile
B) barophile
C) endolith
D) halophile
E) oligotroph
Q6) Explain how endoliths derive energy inside bedrock where there is no sunlight.
Page 23
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Chapter 22: Microbes and the Global Environment
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Q1) Which of the following is a major concern regarding biogeochemical and industrial sources of atmospheric sulfur?
A) greenhouse effect
B) acid rain
C) ozone depletion
D) inhibition of photosynthesis
E) all of the above
Q2) What is the role of predators in wastewater treatment plants?
Q3) Explain how isotope ratios can be used to indicate the type of organism present in an ecosystem.
Q4) Desulfovibrio desulfuricans plays a role in the corrosion of sewer pipes but is also used in a beneficial way for uranium decontamination. Describe its role in the latter.
Q5) 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
Q6) How do certain marine organisms adapt to the paucity of phosphorous supply?
Page 24
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Chapter 23: Human Microbiota and Nonspecific Host Defenses
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Q1) How is it that Gram-positive cells are more resistant to complement than Gram-negative cells?
Q2) Which of the following is a process normally used by the host to kill unwanted host cells?
A) invagination
B) secretion
C) osmotic lysis
D) apoptosis
E) efflux
Q3) Why is it important for people with mitral valve prolapse (MVP) to take antibiotics prior to a dental exam or procedure?
Q4) Which of the following, produced by natural killer cells, punctures the membrane of target cells, causing them to burst?
A) perforins
B) trypsins
C) magainins
D) lysins
E) defensins
Page 25
Q5) Why would complement NOT be considered a part of adaptive immunity?
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Chapter 24: The Adaptive Immune Response
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Q1) Of the following cells, which could be considered a "professional" antigen-presenting cell?
A) neutrophil
B) T lymphocyte
C) natural killer cell
D) dendritic cell
E) fibroblast
Q2) The immune response elicited from each individual antigenic determinant found within an antigen is best described as:
A) monoclonal
B) mutliclonal
C) biclonal
D) polyclonal
E) triclonal
Q3) How can a person who has taken penicillin for a childhood ear infection later develop an allergy to penicillin when prescribed that drug again?
Q4) If a person was unable to undergo negative selection during T-cell education, what is T-cell education and why would this be a severe immune problem?
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Chapter 25: Microbial Pathogenesis
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Q1) Some bacterial pathogens develop a latent stage in the host, where they are undetectable as a distinct entity but are still able to emerge and cause disease at certain times. Why doesn't the host eliminate such pathogens by apoptosis?
Q2) E. coli O157:H7 has a very low infectious dose because:
A) it is encapsulated
B) disease results from a synergistic action with Shigella
C) it is resistant to the gastric acid kill
D) the intestine has many receptors for the toxin
E) it secretes a superantigen
Q3) Which of the following protein secretory systems injects effector molecules directly from the bacterial cytoplasm into the host cytoplasm?
A) type I
B) type II
C) type III
D) type IV
E) all of the above
Q4) How does a pathogenicity island increase the "fitness" of a microorganism (pathogen) to interact with a host and cause disease?
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Page 27
Chapter 26: Microbial Diseases
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Q1) Define herd immunity and explain why it is only effective against infections spread by person-to-person contact.
Q2) Toxic shock syndrome is associated with which of the following:
A) E. coli O157:H7
B) enterotoxin of Staphylococcus aureus
C) superantigens of some Gram-positive cocci
D) meningococcal capsular antigen
E) pertactin of whooping cough
Q3) Herd immunity requires that at least what percentage of the population be vaccinated?
A) 50%
B) 60%
C) 80%
D) 90%
E) 99%
Q4) Explain how Clostridium botulinum, an obligate anaerobe, secretes its potent toxins in food.
Q5) Why is antibiotic treatment NOT recommended for E. coli O157:H7 (EHEC)?
Q6) How would a chest X-ray and blood counts look different for a fungal versus bacterial lung infection?
Page 28
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Chapter 27: Antimicrobial Chemotherapy
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Q1) Compare and contrast the utility of the antibiotic polymyxin vs. cephalosporins in clearing up an Escherichia coli skin infection that has become systemic?
Q2) A molecular microbiologist identified a unique sequence of DNA causing an amino acid shift mutation within the gene encoding for peptidoglycan transpeptidase in a clinical strain of Streptococcus pneumoniae. What does this molecule do and of what benefit could this mutation be to the organism?
Q3) How does saving the rainforest (and other endangered habitats) correlate with the fight to prevent human morbidity and morality caused by bacterial disease? Give an example to support your argument.
Q4) Which of the following would be best to target a new antibiotic to?
A) phospholipids in plasma membrane
B) glycolysis pathway
C) pyrimidine bases
D) nuclear envelope
E) ribosomes
Q5) Why are bacteria that create biofilms so hard to destroy/clear by antibiotics or the immune system? What discoveries are being made to combat biofilm infections?
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Chapter 28: Clinical Microbiology and Epidemiology
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Sample Questions
Q1) As a disease detective investigating an outbreak in the cafeteria of your college, what would be some of the first steps you would need to take to to begin your investigation (other than laboratory testing)?
Q2) Penicillinase-producing Neisseria gonorrhoeae (PPNG) experienced a significant increase during the 1970s because of the:
A) start of the HIV epidemic
B) women's liberation movement
C) U.S. soldiers fighting in Vietnam
D) doctors overprescribing fluoroquinolones
E) concurrent swine flu epidemic in the mid-1970s
Q3) How would a serum antibody ELISA test work in the detection of someone with Lyme disease?
Q4) A serum antibody ELISA assay would be looking for which of the following in a person who is presumed to have a necrotizing fasciitis infection?
A) anti-group A streptococcal antibodies
B) antimeningococcal antibodies
C) group A streptococcal-specific antigens
D) enzyme-linked antibody
E) anti-group B streptococcal antibodies
To view all questions and flashcards with answers, click on the resource link above. Page 30