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Microbial Physiology explores the functional processes of microorganisms at the molecular, cellular, and systems levels. This course examines the mechanisms by which bacteria, archaea, and microbial eukaryotes obtain nutrients, generate energy, and regulate growth and metabolism. Topics include cell structure, transport systems, metabolic pathways, environmental adaptation, stress response, and the integration of physiological processes. Emphasis is placed on experimental methods and their application to understanding how microbes thrive in diverse habitats and respond to environmental changes. This foundational understanding is critical for advancements in fields such as biotechnology, medicine, and environmental microbiology.
Recommended Textbook
Brock Biology of Microorganisms Global 14th Edition by Michael T. Madigan
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Q1) Which of the following statements is FALSE?
A) Microbial cells exist as single cells.
B) Microbial cells carry out their life processes of growth independently.
C) Microbial cells include both bacteria and viruses.
D) Microbial cells exclude the cells of plants and animals.
Answer: C
Q2) Explain why microbial cells are excellent models for understanding cell function in higher organisms.
Answer: Answers will vary but should include commonality of function,biochemical and genetic similarities,and ease and speed with which they can be grown in large quantities.
Q3) Provide evidence supporting the statement that an ecosystem is controlled by microbial activities.
Answer: Answers will vary,but one example could be oxygen depletion,where a loss of oxygen would then favor anaerobic microorganisms.
Q4) Sergei Winogradsky worked with bacteria involved in cycling nitrogen and sulfur.
A)True
B)False
Answer: True
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Q1) Compared to Eukaryotes,Bacteria and Archaea have ________ surface-to-volume ratios,causing ________ nutrient exchange and growth rates.
A) lower / lower
B) lower / higher
C) higher / lower
D) higher / higher
Answer: D
Q2) All eukaryotes contain
A) a membrane-enclosed nucleus.
B) mitochondria.
C) hydrogenosomes.
D) a nucleus, mitochondria, and hydrogenosomes.
Answer: A
Q3) The energy source derived from the charge separation across the cytoplasmic membrane is referred to as
A) the proton motive force.
B) carbohydrate charging.
C) adenosine triphosphate.
D) the voltage source.
Answer: A
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Q1) A catalyst
A) requires more reactants but makes the reaction rate faster.
B) increases the amount of reactants produced but does not change the rate.
C) changes the rate of the reaction but does not change the end amount of products.
D) changes both the rate of a reaction and the amount of the product that will be obtained as the reaction is completed.
Answer: C
Q2) Each amino acid made during protein biosynthesis first requires a separate biosynthetic pathway to be invoked by a cell.
A)True
B)False
Answer: False
Q3) One example of an electron acceptor that can be used in anaerobic respiration is A) NADH.
B) water.
C) nitrate.
D) FMN.
Answer: C
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Q1) Transfer RNA molecules
A) function to transfer ribonucleotides to RNA polymerase during transcription.
B) function to transfer the correct amino acids to the ribosome during translation.
C) contain codons that bind to ribosomes during translation.
D) are only present in the nucleus or eukaryotes.
Q2) Genes that encoded for polymerases,gyrases,ribosomal proteins,and other proteins essential to replication,transcription,and translation are present on A) chromosomes.
B) plasmids.
C) chromosomes and plasmids.
D) neither chromosomes nor plasmids.
Q3) rRNA has an enzymatic role in all stages of protein synthesis.
A)True
B)False
Q4) Aminoacyl-tRNA synthetase catalyzes the reaction between the appropriate amino acid and ATP to form an activated amino acid: amino acid + ATP aminoacyl-AMP + P-P.
A)True
B)False
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Q1) In a chemostat,growth rate and growth yield can be controlled independently.
A)True
B)False
Q2) A microbe growing in a refrigerator is likely
A) psychrophilic.
B) mesophilic.
C) psychrotolerant or psychrophilic.
D) hyperthermophilic.
Q3) Bacteria that are able to grow in humans and cause disease have likely evolved to be
A) psychrophiles.
B) mesophiles.
C) thermophiles.
D) hyperthermophiles.
Q4) Identifying bactoprenol inside the rare bacteria that lack peptidoglycan would be unexpected considering its role in membrane biosynthesis.
A)True
B)False
Q5) Explain why a hyperthermophile is unlikely to be a human pathogen.
Q6) Explain the difference between the division rate and the generation time.
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Q1) Genome assembly relies on
A) accurate gene annotation.
B) overlap of a large numbers of short sequences.
C) codon bias.
D) systems biology.
Q2) The advantage(s)of second-generation DNA sequencing compared to the Sanger method are the result of
A) miniaturization of reaction size.
B) increased computing power.
C) increased length of DNA sequences obtained.
D) miniaturization of reaction size and increased computer power.
Q3) Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally.What "-omic" approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs?
A) metabolomics
B) metagenomics
C) transcriptomics
D) proteomics
Q4) How does the FoodExpert-ID identify macroorganisms and why is this significant?
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Q1) Which organism would likely harbor the MOST two-component regulatory systems?
A) an archaeon living in an extreme environment
B) a bacterium occupying a heterogeneous niche will high nutrient mixing
C) an organism capable of quorum sensing
D) a parasitic bacterium living inside another organism
Q2) Cyclic AMP (cAMP)is involved in the global regulation of catabolic pathways in Escherichia coli,including the lac operon,and a low activity of adenylate cyclase that makes cAMP is suggestive of catabolite repression.
A)True
B)False
Q3) Which of the following mechanisms leads to INCREASED transcriptional activity?
A) An sRNA binds to the ribosome binding site.
B) Ribonuclease activity is blocked by sRNA complementary binding to the end of a transcript.
C) The ribosome binding site is made available from sRNA binding to part of it.
D) Recruitment of RNA polymerase is enhanced when sRNA binds to and removes a repressor.
Q4) Defend why is it unsurprising that two-component regulatory systems are all but absent in bacteria that live at the expense of a host?
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Q1) Which statement is TRUE?
A) All viruses contain their own nucleic acid polymerases.
B) Many viruses contain their own nucleic acid polymerases.
C) Viruses do not contain their own nucleic acid polymerases.
D) The origins of the nucleic acid polymerases used by viruses are eukaryotic.
Q2) The concentration of infectious plaque forming units (pfu)per volume of fluid is known as the
A) infectivity.
B) virulence.
C) titer.
D) fluid infectivity.
Q3) Retroviruses are medically important viruses because
A) they include the viruses the cause hepatitis.
B) some retroviruses cause cancer.
C) they include the virus that causes AIDS.
D) they include viruses that cause cancer and AIDS.
Q4) There is at least one known virus whose genome is actually larger than a cellular genome.
A)True
B)False
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Q1) Knowing the genome of Mu bacteriophage now enables researchers to locate where it incorporates into bacterial genomes.
A)True
B)False
Q2) Varied transcription mechanisms distinguish the different DNA virus Baltimore classes,whereas varied translational mechanisms distinguish RNA viruses.
A)True B)False
Q3) What is the purpose of synthesizing a negative strand RNA in positive stranded ssRNA viruses?
A) enable rolling circle amplification of the genome, which requires both strands of RNA B) enable transcription of genes occurring on both the negative and positive strands of the genome, such as overlapping genes
C) proofreading of the genome to minimize mutations generated by the polymerase being passed onto virion progeny
D) to serve as the complementary template sequence in genome amplification of the positive strand
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Q1) Transposition is a(n)
A) homologous recombination event.
B) analogous recombination event.
C) site-specific recombination event.
D) general recombination event.
Q2) Compare and contrast generalized transduction with specialized transduction.
Q3) When UV radiation damage occurs,DNA repair occurs only in the absence of template instruction.
A)True
B)False
Q4) Consider the map shown below of a portion of a prokaryotic genome.How might the elements indicated affect the stability and structure of the genome? Assume that IS2 encodes for a transposase that catalyzes conservative transposition.Re-draw the genome map to illustrate your prediction if necessary. | IS2 |__gene1
Q5) UV radiation is a useful tool in producing mutants of microbial cultures.
A)True
B)False
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Q1) The lacZ gene is commonly used as a reporter gene,because its substrate lactose is well known and easily measured.
A)True
B)False
Q2) Compare and contrast operon and protein fusions.
Q3) Which of those listed below is LEAST similar in what is measured and concluded?
A) fluorescence in situ hybridization
B) GFP fusion protein
C) Northern blot
D) RT-PCR
Q4) Describe the methodology employed when antibodies are used to detect proteins.
Q5) The genes encoding luciferase,green fluorescent protein (GFP),and -galactosidase are typically used in cloning as
A) transcription regulators.
B) global control genes.
C) promoter sequences.
D) reporter genes.
Q6) Describe the three main steps to clone a gene into an organism.
Q7) Describe the procedure used for colony hybridization and why it is useful.
Q8) Explain how a DNA library is created and how a particular vector is selected.
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Q1) Which is NOT a characteristic of a "primitive" state of microbial evolution?
A) hyperthermophilic
B) aerobic metabolism
C) small genome
D) branching near the root of the evolutionary tree of life
Q2) What characteristics make a gene a good candidate for determining the evolutionary relationships between organisms?
A) highly conserved
B) universally distributed
C) transferred horizontally between species
D) highly conserved and universally distributed
Q3) When exposed to UV light,oxygen gas produces ozone gas.
A)True
B)False
Q4) Construct a chart to demonstrate the molecular features of the primary domains of life.Why are there overlapping or shared molecular features between all three domains? Relate the shared and unique molecular features of each domain to early evolution,the last universal common ancestor (LUCA),and the evolution of the three domains
Q5) How did cyanobacteria,oxygen,and ozone impact the evolution of eukaryotic cells?
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Q1) Some sulfur-oxidizing bacteria can simultaneously reduce nitrate,which enables them to grow anaerobically.
A)True
B)False
Q2) What will happen to a cyanobacterium that has its photosystem II (PSII)blocked?
A) Additional electron acceptors, such as NADP , will be required to oxidize oxygen and overcome the lost PSII process.
B) Anoxygenic photosynthesis only using photosystem I (PSI) could occur by using cyclic photophosphorylation and an alternative electron donor such as H S.
C) It will die from being unable to obtain energy for photosynthesis.
D) Photons will generate excessive reactive oxygen species and the cyanobacterium will die as a consequence.
Q3) In what types of organisms are carboxysomes found and what advantage do they provide for a cell?
Q4) Compare and contrast the prokaryotic and eukaryotic light-gathering machinery function and spatial organization.Why do various chlorophylls show different absorption spectra?
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Q1) Which of the following conditions would you use to enrich purple nonsulfur bacteria from lake sediments?
A) anoxic media with a good light source
B) mineral media with ammonia and oxygen in the dark
C) anoxic mineral media with an organic acid and a good light source
D) mineral media with nitrate and acetate in the dark
Q2) All phototrophic bacteria use a monophyletic photosystem in photosynthesis,thus there is intense competition for light between different phototrophic bacteria.
A)True
B)False
Q3) Anoxygenic phototrophs may or may not be autotrophs.
A)True
B)False
Q4) Nitrogenase is an oxygen-sensitive enzyme even though many diazotrophs are aerobic microorganisms.
A)True
B)False
Q5) How do Cyanobacteria impact the ecology of both aquatic and terrestrial environments on Earth?
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Q1) Which group of bacteria is most famous for their diversity of antibiotics produced? Hypothesize an ecological role production of these antibiotics might have in such environments where they are not produced at high enough levels to kill bacteria.
Q2) The hypothesis that H was a key electron donor for energy metabolism in primitive organisms is supported by it being such a common trophic strategy in Aquificae.
A)True
B)False
Q3) Considering the evolution of Bacteria,the criteria used for taxonomy,and the genetic requirements for individual metabolic pathways,explain how it is unlikely to observe three genera of the same family where one genus has strict anaerobes that degrade only small aromatics,another genus degrades large molecular weight sugars aerobically,and a third is a photoautotroph.
Q4) Agrobacterium tumefaciens can form root nodules in plants and can mate with bacteria,which makes it an excellent host organism for genetic transformations among different domains of life.
A)True
B)False
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Q1) Extremely halophilic Archaea often form ________ in order to access ________.
A) stalks / nutrients
B) intracellular inclusions / elemental sulfur
C) gas vesicles / oxygen
D) intracellular membranes / sunlight
Q2) The Archaea are
A) primarily ancient organisms that have not evolved very much in the last billion years.
B) phylogenetically diverse, but functionally restricted to extremophiles and chemolithotrophs.
C) diverse microorganisms that inhabit almost every environment on Earth, including the colon of humans and other mammals.
D) functionally diverse, but restricted to thermophilic or hyperthermophilic environments.
Q3) Laboratory isolation of Nanoarchaeum equitans requires the presence of A) fatty acids.
B) oxygen.
C) Ignicoccus.
D) sunlight.
Q4) Detail the mechanism by which halophilic Archaea obtain energy from light.
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Q1) Among protists,only the ciliates have a micronucleus and macronucleus where genes are located in two discrete areas within each cell for redundancy.
A)True
B)False
Q2) Sporozoites observed in an insect's body likely indicate infection by an apicomplexan.
A)True
B)False
Q3) A thin,crescent-shaped organism with a single flagellum originating from a basal body and which folds back laterally across the cell would most likely be a member of the genus
A) Trypanosoma.
B) Glossina.
C) Entamoeba.
D) Gambiense.
Q4) What is an endolithic algal community? Where are these found,and how do they survive?
Q5) Describe the differences between the algae and the cyanobacteria.
Q6) Compare and contrast the ectomycorrhizae and the endomycorrhizae.
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Q1) Which fluorescent molecule enables visualization of living microorganisms?
A) acridine orange
B) DAPI
C) GFP
D) SYBR Green
Q2) A study of the human gut performed in 1982 used various types of plates under different growth conditions to describe and enumerate the microbes in the human gut.They concluded that the majority of the microbes in the human gut are Gammaproteobacteria.A study conducted in 2010 using next-generation sequencing to characterize 16S rRNA sequences concluded that the majority of the microbes in the human gut are Firmicutes and Bacteriodetes.Why did these studies have different conclusions? Which study do you think is most accurate?
Q3) The goal of environmental genomics is to detect as many genes as possible and then,if possible,to determine to the phylogeny of the organisms to which the genes belong.
A)True
B)False
Q4) Using specific examples,when is it appropriate to use CARD-FISH rather than the traditional FISH method and vice-versa?
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Q1) Gammaproteobacteria can be used for biodegradation of hydrocarbons.
A)True
B)False
Q2) Which are the MOST dominant chemolithotrophs in pelagic waters?
A) ammonia-oxidizing Archaea
B) ammonia-oxidizing Bacteria
C) sulfate-reducing Bacteria
D) Prochlorococcus
Q3) The photosynthetic pigments bacteriorhodopsin and proteorhodopsin are present in ________ and ________,respectively.
A) Archaea / Bacteria
B) Bacteria / Archaea
C) Bacteria / Bacteria
D) Bacteria / Eukarya
Q4) Which bacterial genus is responsible for producing ferrous iron (Fe² )in groundwater?
A) Alteromonas
B) Aquifex
C) Geobacter
D) Loktanella
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Q1) The oxidation of ________ occurs both biotically and abiotically; however,at ________ pH values biotic oxidation is more common.
A) Si / low
B) ammonia / high
C) Fe² / low
D) Hg / low
Q2) Bacterial oxidation of Fe² occurs BEST under which environmental condition?
A) cold temperature
B) high sunlight
C) low (acidic) pH
D) nutrient-replete
Q3) In a global sense,ALL nutrient cycles are coupled together.
A)True
B)False
Q4) Coal contains substantial amounts of mercury.When coal is burned to generate heat or electricity,the mercury is released into the atmosphere.Most of this mercury is eventually deposited in the ocean or other aquatic environments.What happens to the mercury once it is deposited in the ocean?
Q5) What are the similarities and differences between the Fe cycle and Ca cycle?
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Q1) Microbes are involved in which step(s)of wastewater treatment?
A) primary only
B) secondary and tertiary
C) secondary only
D) primary and secondary
Q2) During secondary aerobic wastewater treatment,some of the activated sludge goes ________ while the rest goes ________.
A) back to the aerator / to the anoxic sludge digestor
B) back to the primary system / to the aerator
C) to the anoxic digestor / back to the primary system
D) back to the primary system / to the tertiary digestor
Q3) The goal of tertiary wastewater treatment is to sharply reduce the levels of ________ from the final effluent.
A) organic compounds
B) heavy metals
C) methane
D) inorganic nutrients
Q4) In water,MOST taste- and odor-producing compounds are inorganic in nature.
A)True
B)False
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Q1) How are symbiotic relationships important in agriculture and food production? Use at least two different examples to support your answer and explain how understanding these symbioses could help produce more food.
Q2) Plant diversity is generally lower in environments where mycorrhizae are associated with plants due to strong coevolution,which leads to competitive exclusion.
A)True
B)False
Q3) Due to the close interactions with other organisms,obligate symbionts generally have larger genome sizes compared to other non-symbiotic bacteria.
A)True
B)False
Q4) How are root nodule and arbuscular mycorrhizal symbioses similar?
A) They both use lipochitin oligosaccharide signaling factors to initiate root colonization.
B) They both supply nitrogen to the host plant through nitrogen fixation.
C) They both increase absorption of nutrients from soil.
D) They are both required for the growth and reproduction of their host plants.
Q5) Explain how leeches are used today in medical replants and transplants.
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Q1) Which of the following are NOT found in the gastrointestinal tract of healthy humans?
A) Bacteroides
B) Clostridium
C) Escherichia coli
D) protists
Q2) Streptocoocus pyogens utilizes M protein and ________ to form microfibrils that facilitate attachment to host cells.
A) lipoteichoic acid
B) mucus
C) plaque
D) None of the answers are correct.
Q3) ________ are microbial infections acquired by hospital patients with noninfectious diseases because they are compromised hosts.
A) Healthcare-associated infections
B) Immunocompromised infections
C) Pathogenic infections
D) Virulent infections
Q4) How do dental lactic acid bacteria cause dental caries?
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Q1) Symptoms of delayed-type hypersensitivity may appear several hours to days after secondary exposure to the eliciting antigen.
A)True
B)False
Q2) Which of the following is TRUE about cytokines?
A) They are proteins.
B) They play an important role in immunity.
C) They play a role in the growth of stem cells.
D) They are proteins that play an important role in immunity and the growth of stem cells.
Q3) A child is stung by a bee at the beginning of the summer and has mild swelling and itching at the site of the sting.In late summer,the child is stung again,but this time rapidly develops anaphylaxis and is diagnosed with type I hypersensitivity to bee venom.If the child is allergic to bee venom,why was there no reaction after the first bee sting? What specifically happened after the first sting that led to the allergic reaction?
Q4) Superantigens activate more T cells than a normal immune response.
A)True
B)False
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Q1) ________ are cytotoxins produced by Tc cells that cause apoptosis.
A) Perforins
B) Granzymes
C) Phagocytes
D) Macrophages
Q2) The first cell type active in the innate response is usually a(n)
A) phagocyte.
B) erythrocyte.
C) fibroblast.
D) antibody.
Q3) Phagocytes have a pathogen-recognition system known as ________ that leads to the recognition,containment,and destruction of a pathogen.
A) collagen
B) fibrin
C) pattern recognition receptors (PRR)
D) pathogen associated molecular pattern (PAMP)
Q4) Nonencapsulated strains of Streptococcus pneumoniae are highly virulent.
A)True
B)False
Q5) Briefly describe classical complement activation and cell damage.
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Q1) Chemokines produced by activated macrophages include
A) CXL8.
B) CCL2.
C) MCP-1.
D) CXL8, CCL2, and MCP-1.
Q2) Which of the following roles do B cells play?
A) antigen presentation
B) antigen processing
C) antigen uptake
D) antigen presentation, processing, and uptake
Q3) In clonal selection,cells that have not interacted with antigen do not proliferate.
A)True
B)False
Q4) The ________ is a highly conserved amino acid sequence found in immunoglobulin,TCR,and MHC proteins.
A) heavy chain
B) V domain
C) C domain
D) light chain
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Q1) Common contaminants in blood drawn from a vein include all EXCEPT which of the following?
A) Staphylococcus epidermidis
B) Coryneform bacteria
C) Propionibacteria
D) Escherichia coli
Q2) What is the basis for inferring infection of a pathogen when a serological EIA is performed? In this context,what does a positive result indicate?
Q3) ALL positive HIV-EIA tests must be confirmed by another independent test,usually the HIV Western blot.
A)True
B)False
Q4) To detect antibodies in human serum,the direct EIA is most commonly employed.
A)True
B)False
Q5) Nucleic acid probes are NOT suitable for the detection of viruses.
A)True
B)False
Q6) Describe mechanisms of transfer of healthcare-associated infections (HAIs).
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Q1) Which of the following is NOT a public health measure used to control the transmission of disease?
A) sanitary water and waste disposal methods
B) immunization
C) forced quarantine
D) genetic engineering
Q2) Which of the following are NOT vectors important in disease transmission?
A) fomites
B) insects
C) ticks
D) rodents
Q3) Potential candidates for biological warfare
A) are generally gram-negative rather than gram-positive.
B) can be virtually any pathogenic bacterium or virus.
C) are eukaryotic rather than prokaryotic.
D) must be genetically engineered to be effective.
Q4) Reservoirs of infectious disease agents may be either animate or inanimate.
A)True
B)False
Q5) Explain the concept of coevolution in terms of host-pathogen interactions.
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Q1) The most common infectious disease(s)is/are A) gonorrhea.
B) influenza.
C) hepatitis.
D) colds.
Q2) In an HIV infection the TH cells and macrophages are NOT commonly infected.
A)True B)False
Q3) More than one type of influenza virus can infect a given cell at a given time.
A)True B)False
Q4) Pus formation in skin lesions caused by Staphylococcus aureus infections is in part due to production of A) coagulase.
B) hemolysins.
C) leukocidin.
D) catalase.
Q5) Salt in mannitol salt agar inhibits the growth of Staphylococcus aureus.
A)True B)False

31
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Sample Questions
Q1) Wild animals are a natural reservoir for Clostridium tetani.
A)True
B)False
Q2) Rabies infection in humans leads to symptoms a few days after exposure.
A)True
B)False
Q3) A person is MOST likely to contract diseases such as Rocky Mountain spotted fever and ehrlichiosis if he or she visits/participates in
A) camping and hiking in the backcountry.
B) metropolitan cities.
C) snow skiing.
D) European countries.
Q4) Anthrax is an emerging disease for which there is no treatment or vaccine available.
A)True
B)False
Q5) Epizootic diseases often occur in wild animals on a periodic or cyclic basis.
A)True
B)False
Q6) Using a specific example,explain the term "accidental host."
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Q1) The MOST common source of individual foodborne botulism outbreaks are due to consumption of
A) honey.
B) dairy products.
C) nonacid, home-canned vegetables.
D) egg and meat salads.
Q2) BOTH physical and chemical methods are used to treat and purify water.
A)True
B)False
Q3) The U.S.Environmental Protection Agency (EPA)regulates the concentration of Escherichia coli in public recreational waters as well as private swimming pools,spas,and hot tubs to minimize waterborne disease outbreaks.
A)True
B)False
Q4) Verotoxin can cause
A) hemorrhagic diarrhea.
B) liver failure.
C) brain damage.
D) hemorrhagic diarrhea, liver failure, and brain damage.
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Q5) Why is Staphylococcus aureus often described as an international picnic pest?
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Q1) Roughly half of all adults in the United States are infected with ________ but are asymptomatic.
A) Toxoplasma gondii
B) Trichomoniasis vaginalis
C) Cryptosporidium parvum
D) Cyclospora cayetanensis
Q2) Plasmodium vivax causes a more serious form of malaria than does P.falciparum.
A)True
B)False
Q3) Based on the life cycle of Schistosoma species,which of the following would be MOST effective in controlling schistosomiasis?
A) elimination of stagnate water
B) bed nets
C) proper sewage and water treatment
D) frequent sanitization of shared toilets, showers, and saunas
Q4) Eukaryotic human parasites are ALL respiratory aerobes.
A)True
B)False

Page 34
Q5) With respect to their life cycles,how are fungal pathogens different than bacterial pathogens?
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