Sample Chapter

INSTANT DOWNLOAD COMPLETE TEST BANK

 

Microbiology An Evolving Science 4th Edition by John W. Foster – Test Bank

 

SAMPLE QUESTIONS

 

CHAPTER 4: Bacterial Culture, Growth, and Development

 

MULTIPLE CHOICE

 

  1. There is a constant struggle to survive in natural habitats because of a lack of
  2. food. d.            oxygen.
  3. sunlight. e.            minerals.
  4. water.

 

 

ANS:      A             DIF:        Easy       REF:       4.Intro

OBJ:       4.1a Explain how limiting nutrient supplies limits bacterial growth

MSC:     Remembering

 

  1. The most common form of chemical energy is contained in the high-energy phosphate bonds of
  2. water. d.            CO2.
  3. glucose. e.            NADH.
  4. ATP.

 

 

ANS:      C             DIF:        Easy       REF:       4.1

OBJ:       4.1d Recall the forms in which cells store energy               MSC:     Remembering

 

  1. Which of the following can consume glucose and, in the absence of oxygen, break it down into ethanol and carbon dioxide gas?
  2. E. coli d.            archaea
  3. phototrophs e.            nitrogen fixers
  4. yeast

 

 

ANS:      C             DIF:        Medium               REF:       4.Intro

OBJ:       4.1a Explain how limiting nutrient supplies limits bacterial growth

MSC:     Remembering

 

  1. The primary goal of biofilms is thought to be
  2. microbial communication. d.            to cause infection.
  3. cell differentiation. e.            environmental degradation.
  4. to stay where food is abundant.

 

 

ANS:      C             DIF:        Medium               REF:       4.5          OBJ:       4.5a Define biofilms

MSC:     Understanding

 

  1. Which of the following is a micronutrient?
  2. carbon d.            calcium
  3. nitrogen e.            zinc
  4. sulfur

 

 

ANS:      E              DIF:        Medium               REF:       4.1

OBJ:       4.1b Define essential nutrients, macronutrients, and micronutrients

MSC:     Remembering

 

  1. Which of the following occurs when a sessile biofilm (or a part of it) begins to starve or experiences oxygen depletion?
  2. attachment d.            dispersal
  3. quorum sensing e.            biofilm maturation
  4. EPS production

 

 

ANS:      D             DIF:        Easy       REF:       4.5

OBJ:       4.5c Describe the stages of biofilm development              MSC:     Understanding

 

  1. Which of the following are specific nutrients NOT required by other species?
  2. macronutrients d. trace elements
  3. micronutrients e.            essential nutrients
  4. growth factors

 

 

ANS:      C             DIF:        Medium               REF:       4.3

OBJ:       4.3c Explain why some microbes require growth factors for culture and why some cannot be grown in pure culture                                                MSC:     Understanding

 

  1. All known microorganisms have a set of genes coding for ________, whose RNA sequences are highly conserved across the phylogenetic tree.
  2. ribosomes d.            cell membranes
  3. chloroplasts e.            cell walls
  4. enzymes

 

 

ANS:      A             DIF:        Medium               REF:       4.3

OBJ:       4.3c Explain why some microbes require growth factors for culture and why some cannot be grown in pure culture                                                MSC:     Remembering

 

  1. All of Earth’s life-forms are based on
  2. hydrogen. d.            carbon.
  3. nitrogen. e.            phosphorus.
  4. oxygen.

 

 

ANS:      D             DIF:        Easy       REF:       4.1

OBJ:       4.1c Compare and contrast autotrophs, heterotrophs, chemotrophs, and phototrophs

MSC:     Remembering

 

  1. Left on their own, heterotrophs would deplete the world of ________ sources and starve to death.
  2. usable nitrogen d.            energy
  3. organic carbon e.            oxygen
  4. water

 

 

ANS:      B             DIF:        Easy       REF:       4.1

OBJ:       4.1c Compare and contrast autotrophs, heterotrophs, chemotrophs, and phototrophs

MSC:     Applying

 

  1. Which of the following are responsible for the CO2-fixation component of the carbon cycle?
  2. heterotrophs d.            chemotrophs
  3. symbionts e.            organotrophs
  4. autotrophs

 

 

ANS:      C             DIF:        Easy       REF:       4.1

OBJ:       4.1c Compare and contrast autotrophs, heterotrophs, chemotrophs, and phototrophs

MSC:     Understanding

 

  1. Quorum sensing is triggered in biofilms when
  2. they form microcolonies.
  3. they are dispersing.
  4. antibiotics are applied to them.
  5. the population reaches a certain number.
  6. cells attach to a surface.

 

 

ANS:      D             DIF:        Medium               REF:       4.5

OBJ:       4.5d Recall the role of quorum sensing in biofilm development

MSC:     Understanding

 

  1. A(n) ________ is an organism that lives in an intimate association with a second organism.
  2. commensal d.            endospore
  3. parasite e.            symbiont
  4. heterocyst

 

 

ANS:      E              DIF:        Easy       REF:       4.1

OBJ:       4.1e Describe the nitrogen cycle including the roles of microbial nitrogen fixers, nitrifiers, and denitrifiers                MSC:     Remembering

 

  1. The majority of nitrogen in soil and marine environments is fixed by
  2. free-living bacteria and archaea. d.            biofilm organisms.
  3. symbionts. e.            UV light.
  4. E. coli.

 

 

ANS:      A             DIF:        Medium               REF:       4.1

OBJ:       4.1e Describe the nitrogen cycle including the roles of microbial nitrogen fixers, nitrifiers, and denitrifiers                MSC:     Remembering

 

  1. Why do some members of a biofilm community live deep within the biofilm?
  2. They are not flagellated.
  3. They produce fewer exopolysaccharides.
  4. They were the first organisms to initiate attachment.
  5. Antibiotics do not penetrate deep into biofilms.
  6. Oxygen does not penetrate deep into biofilms.

 

 

ANS:      E              DIF:        Medium               REF:       4.5

OBJ:       4.5c Describe the stages of biofilm development              MSC:     Understanding

 

  1. Which of the following prokaryotic transport systems does NOT require the use of cellular energy to bring compounds into the cells?
  2. facilitated diffusion d.            group translocation
  3. ABC transport e.            endocytosis
  4. siderophores

 

 

ANS:      A             DIF:        Medium               REF:       4.2

OBJ:       4.2b Compare and contrast facilitated diffusion and active transport

MSC:     Understanding

 

  1. A(n) ________ cell loses membrane integrity and cannot carry out the simple transport functions needed to sustain growth.
  2. depolarized d.            heterocyst
  3. endospore e.            dormant
  4. planktonic

 

 

ANS:      A             DIF:        Medium               REF:       4.2

OBJ:       4.2b Compare and contrast facilitated diffusion and active transport

MSC:     Understanding

 

  1. Which of the following proteins represents a coupled transport system where two molecules travel in the same direction?
  2. aquaporin d.            porin
  3. symport e.            diffusion transporters
  4. antiport

 

 

ANS:      B             DIF:        Medium               REF:       4.2

OBJ:       4.2c Categorize different types of active transport           MSC:     Remembering

 

  1. Which of the following is NOT true about the substrate-binding protein (SBP) of the ABC transport system?
  2. It floats in the periplasm of Gram-negative cells.
  3. It is tethered to the cell surface in Gram-positive cells.
  4. It binds to the periplasmic face of the channel and releases the solute.
  5. It snags the appropriate solute.
  6. It is required for both the uptake and efflux systems.

 

 

ANS:      E              DIF:        Difficult                REF:       4.2

OBJ:       4.2c Categorize different types of active transport           MSC:     Understanding

 

  1. When the intracellular iron concentration is low, iron-scavenging molecules called ________ are produced.
  2. siderophores d.            mycelia
  3. endospores e.            quorum sensors
  4. heterocysts

 

 

ANS:      A             DIF:        Easy       REF:       4.2

OBJ:       4.2d Describe how microbes obtain iron                                MSC:     Understanding

 

  1. Siderophore-iron complexes enter cells with the help of
  2. porins. d.            ABC transporters.
  3. diffusion. e.            efflux pumps.
  4. aquaporins.

 

 

ANS:      D             DIF:        Medium               REF:       4.2

OBJ:       4.2d Describe how microbes obtain iron                                MSC:     Remembering

 

  1. Which of the following statements is FALSE about the E. coli phosphotransferase system (PTS)?
  2. Enzyme II components are specific to the substrates being transported.
  3. The substrate is phosphorylated during transport by PTS, making it different from the external substrate; thus, the substrate always travels down its concentration gradient.
  4. The phosphate group transferred to the sugar comes from phosphoenolpyruvate (PEP).
  5. The PTS transport requires energy in the form of ATP.
  6. The system has a modular design that accommodates different substrates.

 

 

ANS:      D             DIF:        Difficult                REF:       4.2

OBJ:       4.2c Categorize different types of active transport           MSC:     Understanding

 

  1. You have isolated a bacterium from the rumen of a cow and wish to know how it transports glucose into the cell. You perform an experiment that shows uptake of radioactively labeled glucose is equal when the organism is grown in media in the presence and absence of inhibitors of energy production. What is the mechanism of glucose transport in this cell?
  2. group translocation d.            active transport
  3. diffusion e.            endocytosis
  4. facilitated diffusion

 

 

ANS:      C             DIF:        Difficult                REF:       4.2

OBJ:       4.2a Classify the ways that a cell achieves selective permeability across the cell membrane

MSC:     Applying

 

  1. The most widely used solidifying agent is ________, which is derived from seaweed.
  2. agar d.            cellulose
  3. gelatin e.            glycogen
  4. starch

 

 

ANS:      A             DIF:        Easy       REF:       4.3

OBJ:       4.3a Describe the different methods of obtaining single bacterial colonies

MSC:     Remembering

 

  1. Which term refers to the condition in which a culture growth covers the entire agar surface?
  2. dilution streaking d.            microcolony
  3. spread plate e.            colony
  4. confluent

 

 

ANS:      C             DIF:        Easy       REF:       4.3

OBJ:       4.3a Describe the different methods of obtaining single bacterial colonies

MSC:     Remembering

 

  1. The best method to isolate single colonies is the ________ plate, and the best method to count colonies is the ________ plate.
  2. streak; pour d.            complex; defined
  3. pour; streak e.            spread; streak
  4. defined; complex

 

 

ANS:      A             DIF:        Medium               REF:       4.3

OBJ:       4.3a Describe the different methods of obtaining single bacterial colonies | 4.3d Compare and contrast different types of direct and indirect microbial counts        MSC:     Understanding

 

  1. Metabolism of a microbe is best examined by growing the organism in a
  2. defined medium. d.            pour plate.
  3. complex medium. e.            cell culture.
  4. spread plate.

 

 

ANS:      A             DIF:        Medium               REF:       4.3

OBJ:       4.3b Differentiate among complex, synthetic, selective, and defined media

MSC:     Understanding

 

  1. Cyanobacterial heterocysts function to fix atmospheric
  2. hydrogen sulfide. d.            carbon dioxide.
  3. ammonia. e.            nitrogen.
  4. oxygen.

 

 

ANS:      E              DIF:        Easy       REF:       4.6

OBJ:       4.6d State the structure and function of cyanobacterial heterocysts

MSC:     Remembering

 

  1. Which of the following intercalates between DNA bases, causing dead cells to stain red under a fluorescence scope?
  2. propidium iodide d.            crystal violet
  3. syto-9 e.            safranin
  4. bile salt

 

 

ANS:      A             DIF:        Medium               REF:       4.3

OBJ:       4.3d Compare and contrast different types of direct and indirect microbial counts

MSC:     Remembering

 

  1. A problem with ________ of cell number is that dead cells also scatter light.
  2. direct microscopic counts d.            pour plate counts
  3. viable counts e.            optical density measurements
  4. spread plate counts

 

 

ANS:      E              DIF:        Medium               REF:       4.3

OBJ:       4.3d Compare and contrast different types of direct and indirect microbial counts

MSC:     Understanding

 

  1. Which of the following is the best technique for counting only viable cells?
  2. direct microscopic count d.            chemostat
  3. spread plate e.            dry weight measurements
  4. spectrophotometer

 

 

ANS:      B             DIF:        Medium               REF:       4.3

OBJ:       4.3d Compare and contrast different types of direct and indirect microbial counts

MSC:     Understanding

 

  1. Which forms are NOT made by Streptomyces?
  2. hyphae d. endospores
  3. germinating spores e.            mycelia
  4. filaments

 

 

ANS:      D             DIF:        Easy       REF:       4.6

OBJ:       4.6a List the various kinds of differentiated cells that bacteria can produce

MSC:     Understanding

 

  1. When the population doubles during each given unit of time, the growth is
  2. linear. d.            geometric.
  3. semilogarithmic. e.            arithmetic.
  4. exponential.

 

 

ANS:      C             DIF:        Easy       REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Understanding

 

  1. Growth of most microorganisms occurs by
  2. budding. d.            conjugation.
  3. binary fission. e.            transformation.
  4. replication.

 

 

ANS:      B             DIF:        Easy       REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Remembering

 

  1. Bacteria divide at a constant time interval called the
  2. generation time. d.            exponential rate.
  3. growth time. e.            log phase.
  4. growth rate.

 

 

ANS:      A             DIF:        Easy       REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Understanding

 

  1. The time between inoculation and the beginning of growth is usually called the ________ phase.
  2. lag d.            stationary
  3. early log e.            death
  4. late log

 

 

ANS:      A             DIF:        Easy       REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Remembering

 

  1. During which stage of bacterial growth is the culture growing exponentially?

 

  1. lag phase d.            stationary phase
  2. log phase e.            death phase
  3. growth phase

 

 

ANS:      B             DIF:        Easy       REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Remembering

 

  1. Quorum sensing begins during which growth stage?
  2. lag d.            stationary
  3. early log e.            death
  4. late log

 

 

ANS:      C             DIF:        Medium               REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Understanding

 

  1. The figure below represents what type of differentiation?

 

  1. heterocyst formation d.            fruiting body formation
  2. budding e.            filamentation
  3. sporulation

 

 

ANS:      C             DIF:        Medium               REF:       4.6

OBJ:       4.6c Describe spore formation   MSC:     Applying

 

  1. What type of growth pattern is represented here: 5  103; 1  104; 2  104; 4  104; 8  104?
  2. linear d.            generation
  3. exponential e.            semilogarithmic
  4. lag

 

 

ANS:      B             DIF:        Easy       REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Analyzing

 

  1. The shortest lag period would most likely be observed in the transfer
  2. from complex medium to fresh complex medium.
  3. from complex medium to minimal medium.
  4. to a lower temperature.
  5. to a different pH.
  6. to a different salt concentration.

 

 

ANS:      A             DIF:        Medium               REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Understanding

 

  1. In order to grow unculturable environmental microbes, Kim Lewis and colleagues derived the iChip. What is the purpose of this device?

 

  1. Antibiotics from the environment could pass into the chamber.
  2. Gram-positive organisms could not pass the semipermeable membrane.
  3. The semipermeable membranes let environmental organisms into the agar.
  4. Organisms from the environment grew in the chamber.
  5. Nutrients and growth factors made by organisms in the soil diffused into the chamber.

 

 

ANS:      E              DIF:        Medium               REF:       Special Topic 4.1

OBJ:       4.2a Classify the ways that a cell achieves selective permeability across the cell membrane

MSC:     Understanding

 

  1. You are measuring growth in a bacterial culture. The number of viable cells remains constant, and when you check the medium, you find that the carbon source has been used up. In which phase of growth is the culture?
  2. lag d.            stationary
  3. early log e.            death
  4. late log

 

 

ANS:      D             DIF:        Easy       REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Understanding

 

  1. A cafeteria worker who fails to wash his hands thoroughly and fails to wear gloves inoculates a quiche with 4 E. coli cells when he uses his finger to test whether it is done. By the time you purchase the quiche, there are 128 E. coli cells in it. How many generations did the cells go through?
  2. 4 d.            32
  3. 5 e.            64
  4. 8

 

 

ANS:      B             DIF:        Medium               REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Applying

 

  1. What is the classic approach for finding new antibiotics?
  2. screening animals for secreted antimicrobial compounds
  3. harvesting them from individuals with immunity
  4. screening bacteria and fungi for secreted antimicrobial compounds
  5. harvesting them from sick individuals
  6. synthesizing them in the laboratory

 

 

ANS:      C             DIF:        Medium               REF:       Special Topic 4.1

OBJ:       4.3b Differentiate among complex, synthetic, selective, and defined media

MSC:     Understanding

 

  1. Which of the following is true of all biofilms?
  2. They only contain a single species.
  3. The EPS are composed of proteins.
  4. Cells in the biofilm are dormant until the bacteria leave the biofilm.
  5. The EPS is secreted by the bacteria.
  6. It is a continuous monolayer surface deposit.

 

 

ANS:      D             DIF:        Medium               REF:       4.5          OBJ:       4.5a Define biofilms

MSC:     Understanding

 

  1. During biofilm formation, as more and more cells bind to the surface, they begin sending signals to each other in a process called
  2. quorum sensing. d.            polysaccharides uptake.
  3. homoserine lactone sensing. e.            density sensing.
  4. siderophore-iron acquisition.

 

 

ANS:      A             DIF:        Easy       REF:       4.5

OBJ:       4.5c Describe the stages of biofilm development              MSC:     Understanding

 

  1. Which of the following genera does NOT undergo differentiation?
  2. Anabaena d.            Escherichia
  3. Bacillus e. Streptomyces
  4. Clostridium

 

 

ANS:      D             DIF:        Easy       REF:       4.6

OBJ:       4.6a List the various kinds of differentiated cells that bacteria can produce

MSC:     Understanding

 

  1. Some bacteria form environmentally resistant dormant forms called
  2. endospores. d.            hyphae.
  3. heterocysts. e.            actinomycetes.
  4. colonies.

 

 

ANS:      A             DIF:        Easy       REF:       4.6

OBJ:       4.6b Recall the properties of spores                                        MSC:     Remembering

 

  1. How do some cyanobacteria fix nitrogen while growing aerobically?
  2. They do not, because nitrogenase is destroyed by oxygen.
  3. They use special cells called heterocysts that protect the enzyme.
  4. They use spores that protect the enzyme.
  5. They do it using no special structures or mechanisms.
  6. They live symbiotically with other organisms that protect the enzyme.

 

 

ANS:      B             DIF:        Medium               REF:       4.6

OBJ:       4.6d State the structure and function of cyanobacterial heterocysts

MSC:     Understanding

 

SHORT ANSWER

 

  1. How do scientists know of the existence of “unculturable” organisms?

 

ANS:

They know by using molecular biology tools such as PCR and gene sequencing. PCR is used to screen environmental samples for the presence of specific DNA sequences. Comparing DNA sequences of the PCR products with sequences of known organisms reveals insights into the physiology of undiscovered organisms and relationships with known organisms.

 

DIF:        Medium               REF:       4.3

OBJ:       4.3c Explain why some microbes require growth factors for culture and why some cannot be grown in pure culture                                                MSC:     Understanding

 

  1. Why can’t most organisms use the nitrogen gas that is so prevalent in the atmosphere? How do these organisms acquire a usable form of nitrogen?

 

ANS:

Nitrogen gas has triple bonds holding the two atoms together. These triple bonds are very stable and require a large amount of energy to break, and most organisms are unable to break the bonds. Organisms that cannot use atmospheric nitrogen as a nitrogen source must rely on other organisms to fix the nitrogen into a usable form. Fixing nitrogen means converting it into ammonium ions that can be used by many types of organisms.

 

DIF:        Medium               REF:       4.1

OBJ:       4.1e Describe the nitrogen cycle including the roles of microbial nitrogen fixers, nitrifiers, and denitrifiers                MSC:     Understanding

 

  1. What type of medium and conditions would you need to have in order to select for photoautotrophs?

 

ANS:

Phototrophs can generate energy from absorption of light and autotrophs can use CO2 as their sole carbon source, so the medium would not need to contain an energy source or an organic carbon source. The lack of these substances would inhibit the growth of other types of organisms, resulting in a selection for photoautotrophs. The sample would need to be incubated near a light source.

 

DIF:        Difficult                REF:       4.1

OBJ:       4.1c Compare and contrast autotrophs, heterotrophs, chemotrophs, and phototrophs

MSC:     Evaluating

 

  1. Compare and contrast the difference between electrogenic and electroneutral coupled transport and give an example of each.

 

ANS:

Electrogenic coupled transport results in an unequal distribution of charge across the cell membrane. A good example is the lactose symporter, which brings the neutral lactose molecule in along with a proton.

Electroneutral coupled transport results in no net charge. An example of this is the sodium ion/proton antiporter.

 

DIF:        Difficult                REF:       4.2          OBJ:       4.2c Categorize different types of active transport

MSC:     Analyzing

 

  1. Compare and contrast the ABC transporters and group translocation in terms of energy requirements and concentration gradients.

 

ANS:

Both forms of transport require energy. The ABC transporters utilize ATP, and group translocation actually begins the process with the expenditure of phosphoenolpyruvate (PEP).

ABC transporters bring a solute against the concentration gradient. The same cannot be said about the phosphotransferase system (PTS) because the solute is phosphorylated during the transfer.

 

DIF:        Difficult                REF:       4.2          OBJ:       4.2c Categorize different types of active transport

MSC:     Analyzing

 

  1. Why is iron so often a limiting nutrient, when it seems to be so abundant in the environment, and how can organisms overcome this problem?

 

ANS:

Iron is usually not free in nature but locked up as Fe(OH)3, which is insoluble and unavailable to cells. Siderophores are molecules produced by some cells that have a very high affinity for soluble ferric iron. These molecules scavenge any small amount of soluble iron and transport it into the cell.

 

DIF:        Medium               REF:       4.2          OBJ:       4.2d Describe how microbes obtain iron

MSC:     Understanding

 

  1. Compare and contrast complex media, synthetic media, and enriched media.

 

ANS:

Complex media contain things such as yeast extract or beef extract, making the exact composition of each chemical unknown. Their composition is thought to mimic the rich environments that some organisms may encounter in their natural environment.

Synthetic media are fully defined. They contain precise amounts of various salts, carbon, nitrogen, and energy sources. Some organisms need special additives to survive in these media.

Enriched media contain additional components such as blood that are required for the growth of fastidious organisms.

 

DIF:        Difficult                REF:       4.3

OBJ:       4.3b Differentiate among complex, synthetic, selective, and defined media

MSC:     Analyzing

 

  1. When studying the metabolism of an organism, why is it better to grow organisms in a defined synthetic medium instead of a complex medium?

 

ANS:

It is difficult to characterize an organism’s metabolism when it is growing in a complex medium because the organism is supplied with all of its needs, so it is impossible to determine which metabolic pathways the organism possesses. In a synthetic medium, various substances can be added to determine which ones the organism needs and which ones it can make.

 

DIF:        Medium               REF:       4.3

OBJ:       4.3b Differentiate among complex, synthetic, selective, and defined media

MSC:     Applying

 

  1. MacConkey medium contains bile salts, crystal violet, lactose, and the pH indicator neutral red. Some organisms can ferment lactose, producing acids as a by-product. Is this medium likely to be selective and/or differential? Explain.

 

ANS:

Since MacConkey contains bile salts and crystal violet, it is selective for Gram-negative bacteria. MacConkey is also differential for lactose fermentation. Some organisms ferment lactose to produce acids, which causes lactose-fermenting colonies to be red and nonfermenting colonies to be white.

 

DIF:        Difficult                REF:       4.3

OBJ:       4.3b Differentiate among complex, synthetic, selective, and defined media

MSC:     Applying

 

  1. Define the terms “viable” and “viable but unculturable.” Why are so many environmental organisms believed to be viable but unculturable?

 

ANS:

Viable means that the organism can replicate and form colonies on a plate, making it possible to grow the organism in a laboratory setting.

Viable but unculturable means that the cells appear to metabolize, but we cannot get them to replicate. It is possible that we just have not figured out how to culture them yet.

 

DIF:        Difficult                REF:       4.3 | Special Topic 4.1

OBJ:       4.3c Explain why some microbes require growth factors for culture and why some cannot be grown in pure culture                                                MSC:     Understanding

 

  1. Using the figure below, explain the function of stages 2 and 3 in biofilm development and how they affect biofilm growth, function, and treatment.

 

 

ANS:

The establishment of microcolonies triggers quorum sensing, which triggers the increased resistance of biofilms to antibiotics and to phagocytosis by white blood cells. The cells in a microcolony form a thick extracellular matrix of polysaccharide polymers and entrapped organic (DNA and proteins) and inorganic materials that tether cells and strengthen the biofilm, making them more resistant to antibiotics and physical removal.

 

DIF:        Medium               REF:       4.5

OBJ:       4.5b List some function of biofilms | 4.5c Describe the stages of biofilm development

MSC:     Understanding

 

  1. If you determined the number of cells in a sample using viable plate counts and optical density measurements, why would the results from the two methods be so different?

 

ANS:

Cell numbers from optical density measurements will be much higher than those from viable plate counts. Viable plate counts only count cells that are able to replicate to form colonies on the plates. Some cells will not form colonies due to cell damage or inability to grow on the artificial culture media. Also, organisms that grow in chains or clusters will form a colony from several cells instead of just one. Finally, optical density measurements count both living and dead cells.

 

DIF:        Difficult                REF:       4.3

OBJ:       4.3d Compare and contrast different types of direct and indirect microbial counts

MSC:     Analyzing

 

  1. Discuss some disadvantages of viable counts of microorganisms.

 

ANS:

Colony counting will not reflect the size or growth stage of the cells. The results might also underestimate the number of living cells because some may be damaged and unable to divide, but are still alive. Also, some organisms grow in chains and clusters. If these are not dissociated prior to plating, you will get a false low count.

 

DIF:        Medium               REF:       4.3

OBJ:       4.3d Compare and contrast different types of direct and indirect microbial counts

MSC:     Evaluating

 

  1. Why does binary fission result in an exponential and not a linear growth rate?

 

ANS:

Bacteria replicate by binary fission. In this process, one cell grows and divides, producing two daughter cells. Those two will each do the same, and so forth. That means that 1 becomes 2, 2 become 4, and 4 become 8. The relationship then becomes 2n, where n corresponds to the number of generations. It is 2n, since two daughters are formed from each cell. (A linear relationship would be 1 to 2, 2 to 3, 3 to 4, and so forth.)

 

DIF:        Medium               REF:       4.4

OBJ:       4.4a Compute the generation time, growth rate constant, or number of cells present given the appropriate starting information        MSC:     Understanding

 

  1. Why does a microbe’s growth rate in its natural environment vary greatly from that in the laboratory? Give at least two reasons for this.

 

ANS:

Answers will vary. A laboratory setting usually affords a very rich medium, and the organism is usually in pure culture and is not competing for nutrients.

In the natural environment, nutrient levels are most likely less. Other organisms may be competing more effectively for the nutrients. Also, some organisms may form waste products that are toxic to other organisms.

 

DIF:        Difficult                REF:       4.3 | 4.4

OBJ:       4.3c Explain why some microbes require growth factors for culture and why some cannot be grown in pure culture | 4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Analyzing

 

  1. Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?

 

ANS:

Batch culture represents growth in a closed system. At some point, one or more essential nutrients will be depleted, or waste products will become insurmountable, both of which, of course, would lead to cessation of growth of the organism and eventually to cell death.

Chemostat growth regulates the flow of nutrients in and the collection of wastes out, so that growth may be maintained at the exponential stage. For industrial purposes, a chemostat is a plus when one is collecting a cellular product that is produced during exponential growth. It would be desirable to maintain the organism in conditions where it would produce the most product.

 

DIF:        Difficult                REF:       4.4

OBJ:       4.4c Compare and contrast batch culture and continuous culture

MSC:     Applying

 

  1. During the stationary phase, E. coli reprograms itself. What does it do to protect itself?

 

ANS:

It decreases its size so that less nutrient is required for maintenance. When it is under stress, it synthesizes various enzymes to protect itself. Some of these handle oxygen radicals, protect DNA and proteins, and increase the amount of cross-linking in peptidoglycan. All of these adaptations result in a stronger, more resistant cell.

 

DIF:        Difficult                REF:       4.4

OBJ:       4.4b List and describe the four stages of bacterial growth in batch culture

MSC:     Understanding

 

  1. What are some specific problems that biofilms can cause in the medical field, and why are they so difficult to prevent and destroy?

 

ANS:

Biofilms can grow in medical devices such as catheters and cause infections in patients. They cause damage to equipment such as ventilators. They can grow in lungs of cystic fibrosis patients or on medical transplants. As they grow, they form a thick polysaccharide matrix that increases antibiotic resistance within the biofilms and is difficult to remove with cleaning agents.

 

DIF:        Medium               REF:       4.5          OBJ:       4.5a Define biofilms

MSC:     Analyzing

 

  1. Why would an organism go through the process of sporulation? How might endospores cause problems in the food industry?

 

ANS:

When nutrients are not as readily available, the starvation response of some organisms results in the formation of a dormant endospore. Because endospores are resistant to heat and desiccation, if foods are not properly sterilized, endospores could survive in the food, then germinate and cause food spoilage or food-borne illness.

 

DIF:        Difficult                REF:       4.6

OBJ:       4.6b Recall the properties of spores | 4.6c Describe spore formation

MSC:     Evaluating

 

  1. How does Anabaena overcome the challenge of performing both photosynthesis and nitrogen fixation?

 

ANS:

The autotrophic cyanobacteria Anabaena can generate oxygen by photosynthesis and fix nitrogen to make ammonia. This seems as if it would prevent nitrogen fixation since the nitrogenase required for nitrogen fixation is extremely sensitive to oxygen. The organism overcomes this by having every tenth cell differentiate from a photosynthetic cell to a heterocyst, which no longer fixes carbon dioxide or produces oxygen but rather develops a specialized envelope that limits oxygen access, allowing nitrogen fixation.

 

DIF:        Medium               REF:       4.6

OBJ:       4.6d State the structure and function of cyanobacterial heterocysts

MSC:     Understanding                  CHAPTER 6: Viruses

 

MULTIPLE CHOICE

 

  1. All of the following are true about the measles virus EXCEPT that it
  2. is encased by an envelope of membrane.
  3. fuses with the host cell membrane during infection.
  4. has progeny that bud out of the host cell.
  5. generates a rash of red spots on the skin of infected patients.
  6. is never fatal.

 

 

ANS:      E              DIF:        Easy       REF:       6.1          OBJ:       6.1a Define virus

MSC:     Applying

 

  1. Which of the following is a term for the observable destruction of cells as a result of viral lysis?
  2. tissue culture d.            plaque
  3. lawn e.            host
  4. soft agar

 

 

ANS:      D             DIF:        Easy       REF:       6.1          OBJ:       6.1a Define virus

MSC:     Understanding

 

  1. What can be counted as representing individual infectious virions from a phage suspension?
  2. plaques d.            proteomes
  3. viruses e.            burst size
  4. genomes

 

 

ANS:      A             DIF:        Easy       REF:       6.4

OBJ:       6.4b Recall examples of prophages or endogenous viruses contributing to host cell physiology

MSC:     Analyzing

 

  1. Which of the following is INCORRECT about a virus?
  2. It may cause human pneumonia.
  3. It may be as large as some bacteria.
  4. It conducts DNA repair.
  5. It conducts protein folding by chaperones.
  6. It is a cellular particle.

 

 

ANS:      E              DIF:        Medium               REF:       6.1          OBJ:       6.1a Define virus

MSC:     Applying

 

  1. What role do acute viruses play in their ecosystem?
  2. transfer genes across species
  3. act as predator or parasite
  4. evolve symbiotically with host
  5. act as a bioweapon
  6. act as a viral shunt

 

 

ANS:      B             DIF:        Easy       REF:       6.1

OBJ:       6.1c List the roles viruses play in ecosystems       MSC:     Applying

 

  1. Which of the following is NOT one of the three forms a virus can assume?
  2. prion
  3. viral genome integrated within host DNA
  4. intracellular replication complex
  5. virion
  6. virus particle

 

 

ANS:      A             DIF:        Easy       REF:       6.1

OBJ:       6.1b Describe the three forms a virus can assume             MSC:     Applying

 

  1. An icosahedral capsid is classified as having how many sides?
  2. 4 d.            10
  3. 6 e.            20
  4. 8

 

 

ANS:      E              DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Analyzing

 

  1. A polyhedron with 20 sides has identical ________ faces.
  2. helical d.            triangular
  3. filamentous e.            asymmetrical
  4. rectangular

 

 

ANS:      D             DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Understanding

 

  1. Which infectious agent is identified by the nucleic acid genome being the entire infectious particle?
  2. viruses d.            virions
  3. prions e.            bacteria
  4. viroids

 

 

ANS:      C             DIF:        Medium               REF:       6.2

OBJ:       6.2c Contrast virions, viroids, and prions                                MSC:     Analyzing

 

  1. Some viral species may derive their ________ from intracellular membranes, such as the nuclear membrane or endoplasmic reticulum.
  2. capsid d.            neck
  3. genome e.            tail fibers
  4. envelope

 

 

ANS:      C             DIF:        Medium               REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Remembering

 

  1. Which structure of a virion protects it from degradation and enables it to be transmitted outside the host?
  2. capsule d. nucleus
  3. capsid e.            spikes
  4. envelope

 

 

ANS:      B             DIF:        Easy       REF:       6.2

OBJ:       6.2a State the functions of the structures that are present in all virions

MSC:     Understanding

 

  1. What phages have been used to nucleate the growth of crystalline “nanowires” for electronic devices?
  2. icosahedral d.            filamentous
  3. complex e.            viroid
  4. asymmetrical

 

 

ANS:      D             DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Applying

 

  1. Filamentous viruses are classified in part by the pattern of capsid monomers, which form a ________ tube around the genome.
  2. icosahedral d.            complex
  3. filamentous e.            helical
  4. asymmetrical

 

 

ANS:      E              DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Analyzing

 

  1. In bacteriophage T4, the DNA genome is contained in the head, and binding to the host is facilitated by attachment of the
  2. capsid. d.            envelope.
  3. neck. e.            tegument.
  4. tail fibers.

 

 

ANS:      C             DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Remembering

 

  1. The RNA genome of the potato spindle tuber viroid requires which type of modified host polymerase for replication?
  2. DNA-dependent DNA polymerase
  3. DNA-dependent RNA polymerase
  4. RNA-dependent DNA polymerase
  5. RNA-dependent RNA polymerase
  6. reverse transcriptase

 

 

ANS:      D             DIF:        Medium               REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Applying

 

  1. Which filamentous virus causes a fatal disease in humans and is also related to primates?
  2. HIV d.            cowpox
  3. Ebola e.            herpes virus
  4. smallpox

 

 

ANS:      B             DIF:        Easy       REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Applying

 

  1. What type of diseases are unique in that they can be transmitted by an infective protein that propagates conformational change of existing molecules without synthesizing entirely new infective molecules?
  2. viral d.            virion
  3. viroid e.            prion
  4. bacterial

 

 

ANS:      E              DIF:        Easy       REF:       6.2

OBJ:       6.2c Contrast virions, viroids, and prions                                MSC:     Understanding

 

  1. Large asymmetrical viruses are distinguished in that they
  2. have no envelope. d.            have nucleic acids.
  3. are protein fragments. e.            have many enzymes.
  4. have few enzymes.

 

 

ANS:      E              DIF:        Medium               REF:       6.3

OBJ:       6.3a Describe the diversity of viral genomes                        MSC:     Analyzing

 

  1. All of the following criteria are used to classify viruses according to the International Committee on Taxonomy of Viruses EXCEPT
  2. genome composition. d.            capsid symmetry.
  3. size of the virus particle. e.            mutation rate.
  4. envelope.

 

 

ANS:      E              DIF:        Medium               REF:       6.3

OBJ:       6.3b List the criteria by which the International Committee on Taxonomy of Viruses (ICTV) classifies viruses                MSC:     Understanding

 

  1. If something descended from a common ancestor, it is
  2. monomeric. d.            monosyllabic.
  3. monophyletic. e.            monolithic.
  4. monogrammed.

 

 

ANS:      B             DIF:        Medium               REF:       6.3

OBJ:       6.3d Compare and contrast genome and proteome analysis for viral phylogeny construction

MSC:     Understanding

 

  1. Which of the following is an example of double-stranded RNA viruses?
  2. herpes viruses d.            orthomixoviruses
  3. corona viruses e.            hepadnaviruses
  4. retrovirus

 

 

ANS:      C             DIF:        Easy       REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Understanding

 

  1. What viruses are classified by using the suffix viridae?
  2. genera d.            orders
  3. families e.            classes
  4. species

 

 

ANS:      B             DIF:        Medium               REF:       6.3

OBJ:       6.3b List the criteria by which the International Committee on Taxonomy of Viruses (ICTV) classifies viruses                MSC:     Analyzing

 

  1. Viruses may be classified by the ________ method.
  2. Annapolis d.            Augusta
  3. Baltimore e.            Portland
  4. Orono

 

 

ANS:      B             DIF:        Easy       REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Remembering

 

  1. So far, the known mechanisms of replication and mRNA expression define how many fundamental groups of virus species?
  2. five d.            eight
  3. six e.            nine
  4. seven

 

 

ANS:      C             DIF:        Medium               REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Remembering

 

  1. David Baltimore proposed that the primary distinction among classes of viruses was the ________ composition and the route used to express messenger RNA.
  2. genome d.            tegument
  3. envelope e.            neck
  4. capsid

 

 

ANS:      A             DIF:        Easy       REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Remembering

 

  1. The genome of ________ ssRNA viruses can serve directly as mRNA.
  2. positive-sense () d.            double-stranded
  3. negative-sense () e.            prion
  4. all

 

 

ANS:      A             DIF:        Easy       REF:       6.3

OBJ:       6.3a Describe the diversity of viral genomes                        MSC:     Remembering

 

  1. A key factor in the evolution of killer strains of influenza is that they
  2. only have eight genes. d.            have a segmented genome.
  3. have an RNA genome. e.            have a circular chromosome.
  4. contain reverse transcriptase.

 

 

ANS:      D             DIF:        Medium               REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Remembering

 

  1. Which of the following is NOT true of the pararetroviruses?
  2. They have an RNA genome.
  3. They do not make a DNA intermediate.
  4. Some have a viral reverse transcriptase.
  5. Some use a host reverse transcriptase.
  6. They consist of human and plant pathogens.

 

 

ANS:      A             DIF:        Medium               REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Remembering

 

  1. Which of the following are genes of common ancestry in two genomes that share the same function?
  2. homologs d.            orthologs
  3. open reading frames e.            lysogenic
  4. proteomes

 

 

ANS:      D             DIF:        Difficult                REF:       6.3

OBJ:       6.3d Compare and contrast genome and proteome analysis for viral phylogeny construction

MSC:     Remembering

 

  1. The proteomic tree of bacteriophages is based on comprehensive analysis of viral
  2. DNAs. d.            capsids.
  3. RNAs. e.            host ranges.
  4. proteins.

 

 

ANS:      C             DIF:        Easy       REF:       6.3

OBJ:       6.3d Compare and contrast genome and proteome analysis for viral phylogeny construction

MSC:     Remembering

 

  1. Proteomic analysis predicts seven major evolutionary categories of phage species with subgroups based on
  2. type of genetic material. d.            transcriptional strategy.
  3. virion structure. e.            replicase gene sequence.
  4. shared hosts.

 

 

ANS:      C             DIF:        Medium               REF:       6.3

OBJ:       6.3d Compare and contrast genome and proteome analysis for viral phylogeny construction

MSC:     Understanding

 

  1. Which structure remains outside, attached to the cell surface, after the genome is inserted?
  2. an envelope d.            a ghost
  3. a neck e.            temperate
  4. tail fibers

 

 

ANS:      D             DIF:        Easy       REF:       6.4

OBJ:       6.4a Distinguish the lytic, lysogenic, and slow-release viral cycles

MSC:     Understanding

 

  1. Which of the following steps is NOT part of the life cycle of a lytic phage?
  2. Phage DNA is injected into the bacterial cell.
  3. The phage DNA integrates into the bacterial chromosome.
  4. Many copies of phage DNA are made.
  5. The phage DNA is transcribed, and the resulting mRNA is translated to make capsid proteins.
  6. All of the steps listed are part of the life cycle of a lytic phage.

 

 

ANS:      B             DIF:        Difficult                REF:       6.4

OBJ:       6.4a Distinguish the lytic, lysogenic, and slow-release viral cycles

MSC:     Applying

 

  1. The number of virus particles released at lysis is referred to as
  2. the lytic number. d.            the temperate number.
  3. burst size. e.            the release number.
  4. the lysogenic number.

 

 

ANS:      B             DIF:        Easy       REF:       6.4

OBJ:       6.4b Recall examples of prophages or endogenous viruses contributing to host cell physiology

MSC:     Remembering

 

  1. A(n) ________ phage may integrate its genome into that of the host cell.
  2. lytic d.            asymmetrical
  3. temperate e.            oncogenic
  4. viroid

 

 

ANS:      B             DIF:        Easy       REF:       6.4

OBJ:       6.4a Distinguish the lytic, lysogenic, and slow-release viral cycles

MSC:     Remembering

 

  1. The integrated phage genome is called a(n)
  2. temperate. d.            lytic.
  3. lysogen. e.            prophage.
  4. oncogene.

 

 

ANS:      E              DIF:        Easy       REF:       6.4

OBJ:       6.4b Recall examples of prophages or endogenous viruses contributing to host cell physiology

MSC:     Remembering

 

  1. CRISPR is a(n)
  2. bacterial gene. d.            inactive viral RNA.
  3. bacterial enzyme. e.            cascade protein.
  4. bacterial immune system.

 

 

ANS:      C             DIF:        Easy       REF:       6.4

OBJ:       6.4c Explain how bacteria defend themselves against viruses

MSC:     Remembering

 

  1. When a bacterial cell is infected, the virus protection coat
  2. enters the host cell with the viral genome.
  3. remains on the outside of the host cell.
  4. enters the host cell separately from the viral genome.
  5. is released to attach to and inject another host cell.
  6. becomes part of the host cell membrane.

 

 

ANS:      B             DIF:        Easy       REF:       6.4

OBJ:       6.4b Recall examples of prophages or endogenous viruses contributing to host cell physiology

MSC:     Understanding

 

  1. Hershey & Chase (1952) showed that the transmission of DNA by a bacteriophage to a host cell led to the production of progeny bacteriophages. What did this confirm?
  2. DNA is the hereditary material.
  3. Viruses can infect bacteria.
  4. Phage genomes can integrate into a bacterial genome.
  5. Phages inject their genome through the cell envelope.
  6. Various host molecules can serve as a phage receptor.

 

 

ANS:      A             DIF:        Difficult                REF:       6.4

OBJ:       6.4b Recall examples of prophages or endogenous viruses contributing to host cell physiology

MSC:     Understanding

 

  1. Dysbiosis is the result of
  2. deterioration of health due to loss of bacteria.
  3. increase in health due to loss of bacteria.
  4. host bacterium undergoing a lytic cycle.
  5. host bacterium undergoing a lysogenic cycle.
  6. slow release.

 

 

ANS:      A             DIF:        Difficult                REF:       6.4

OBJ:       6.4d Describe the impact of bacteriophages in the human intestinal tract

MSC:     Understanding

 

  1. Within a host, receptor molecules can also determine the ________, or tendency to infect a particular tissue type.
  2. tropism d.            burst size
  3. host range e.            plaque
  4. virulence

 

 

ANS:      A             DIF:        Easy       REF:       6.5

OBJ:       6.5a Explain how animal viruses exhibit host and tissue tropism

MSC:     Remembering

 

  1. The primary factor determining the life cycle of an animal virus is the physical form of the
  2. envelope. d.            receptor.
  3. capsid. e.            burst.
  4. genome.

 

 

ANS:      C             DIF:        Difficult                REF:       6.5

OBJ:       6.5c Compare and contrast animal virus replication cycles

MSC:     Analyzing

 

  1. The proteins found in animals and plants that can recognize general signs of viral infections are
  2. RNA interference. d.            surface receptors.
  3. interferons. e.            antibodies.
  4. T-lymphocytes.

 

 

ANS:      B             DIF:        Easy       REF:       6.5

OBJ:       6.5e Describe animal and plant viral defenses     MSC:     Remembering

 

  1. Which virus is differentiated by being taken up by endocytosis?
  2. hepatitis C
  3. human immunodeficiency virus (HIV)
  4. gonorrhea
  5. syphilis
  6. chlamydia

 

 

ANS:      A             DIF:        Medium               REF:       6.5

OBJ:       6.5b Categorize animal virus uncoating strategies              MSC:     Analyzing

 

  1. In contrast to animal viruses and bacteriophages, plant viruses infect cells by mechanisms that do NOT involve specific
  2. receptors. d.            vectors.
  3. membranes. e.            hosts.
  4. envelopes.

 

 

ANS:      A             DIF:        Medium               REF:       6.5

OBJ:       6.5d Recall how plant viruses enter a host cell and transmit to uninfected cells

MSC:     Analyzing

 

  1. Which of the following is FALSE concerning HIV?
  2. It is the causative agent of AIDS.
  3. It makes a DNA copy of its RNA genome.
  4. Reverse transcriptase is translated from an early gene.
  5. The virion contains two copies of the HIV genome.
  6. The viral RNA is copied into double-stranded DNA.

 

 

ANS:      C             DIF:        Medium               REF:       6.5

OBJ:       6.5f State the conditions that favor the emergence of viral pathogens

MSC:     Applying

 

  1. Which is the period of time that is categorized by virtually undetectable virions inside the infected cell?
  2. eclipse d.            burst
  3. latent e.            lag
  4. rise

 

 

ANS:      A             DIF:        Easy       REF:       6.6

OBJ:       6.6b Express what is happening during the different stages of a one-step growth curve of viral batch culture                MSC:     Analyzing

 

  1. What is NOT a difficulty of culturing viruses?
  2. tropism for particular tissue
  3. tissue culture may not show organ property
  4. loss of virulence
  5. able to observe a large population
  6. need a double culture of host cell and viruses

 

 

ANS:      D             DIF:        Difficult                REF:       6.6

OBJ:       6.6a Outline some of the difficulties involved in culturing viruses

MSC:     Applying

 

  1. Tissue cultures are more feasible than whole animals for viral growth because they
  2. can develop vaccines.
  3. can test a multitude of chemical and antibiotic agents.
  4. are more time-consuming.
  5. are less expensive.
  6. are more expensive.

 

 

ANS:      D             DIF:        Difficult                REF:       6.6

OBJ:       6.6c Summarize the advantages and disadvantages of culturing animal viruses in tissue culture versus whole animals                                 MSC:     Applying

 

  1. Who was distinguished for modifying tissue culture procedure for plaque assays?
  2. David Baltimore d.            Paulo Verardi
  3. Renato Dulbecco e.            Howard Temin
  4. Xinzheng Zhang

 

 

ANS:      B             DIF:        Difficult                REF:       6.6

OBJ:       6.6d Recall what plaques are and explain how they are useful to microbiologists

MSC:     Analyzing

 

SHORT ANSWER

 

  1. What happens when marine algae overgrows?

 

ANS:

They can generate a bloom that covers thousands of square kilometers. The pale clouds in the water are the reflected light from billions of calcite plates, or “coccoliths,” that coat each algal cell. Yet within a few days, this gigantic bloom is dissipated by viruses.

 

DIF:        Difficult                REF:       6.1          OBJ:       6.1c List the roles viruses play in ecosystems

MSC:     Understanding

 

  1. Discuss the role that marine viruses play in carbon balance.

 

ANS:

The carbon cycle in a marine environment is usually described as grazers consuming phytoplankton and then being consumed by carnivores. One must realize that viral infection of each of these leads to lysis and the formation of detritus. This organic material is consumed by bacteria that respire, returning carbon dioxide to the atmosphere.

 

DIF:        Medium               REF:       6.1          OBJ:       6.1c List the roles viruses play in ecosystems

MSC:     Understanding

 

  1. Why are viruses not affected by antibiotics? Why are there so few antiviral drugs?

 

ANS:

Viruses are not cellular entities. Common antibiotics disrupt cell wall synthesis or interact with ribosomes and disrupt the translation process. Viruses do not have either cell walls or ribosomes, so these antibiotics would be ineffective.

Viruses that infect humans commandeer the host cell to make more viruses. One cannot target the host machinery because then the host would be harmed. There are few viral targets that can be attacked without harming the host cell.

 

DIF:        Difficult                REF:       6.1          OBJ:       6.1a Define virus

MSC:     Understanding

 

  1. What are prions and how do they cause disease?

 

ANS:

Prions are aberrant forms of naturally occurring proteins that assume an abnormal conformation. They cause disease by binding to normally folded proteins of the same type and altering their conformation. Harmful aggregates of these proteins cause cell death.

 

DIF:        Medium               REF:       6.2          OBJ:       6.2c Contrast virions, viroids, and prions

MSC:     Understanding

 

  1. What is the advantage of symmetry in viral particles?

 

ANS:

Symmetry provides a way to form a package out of repeating protein units. This requires a small number of genes, since the same protein unit is repeated. Viral genomes are generally very small, so they have few genes. They can also devote more resources to copying their genome for viral replication if it takes few resources to make the capsid proteins.

 

DIF:        Medium               REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Applying

 

  1. Identify the outer structure shown in the figure below. What is it composed of and how does it differ from the bacterial version?

 

 

ANS:

The viral envelope is composed of the phospholipid portion of the membrane from the host cell from which it came and proteins encoded by the virus genome. The bacterial cell envelope refers to the layers outside of the cell membrane.

 

DIF:        Medium               REF:       6.2

OBJ:       6.2b Identify ways virions can differ from each other      MSC:     Understanding

 

  1. Compare and contrast the Baltimore classification of viruses to the proteomic analysis of bacteriophages. Which more accurately reflects the significant impact of phage evolution?

 

ANS:

The Baltimore classification divides the viruses into seven groups based on the genome of the virus and the route used to get to mRNA. Proteomic analysis is a comparison of the proteins encoded by the genomes. The proteomic tree also yields seven categories of phages. These categories, however, group the phages by host bacteria. Phages with different types of genomes may be grouped together. The proteomic tree analogy more truly reflects the evolutionary process. Viruses that share a host have the ability to exchange genetic information.

 

DIF:        Difficult                REF:       6.3

OBJ:       6.3d Compare and contrast genome and proteome analysis for viral phylogeny construction

MSC:     Applying

 

  1. Name the different types of receptors shown in the figure below.

 

 

ANS:

Different types of receptors shown include the following: LPS, which is a lipid polysaccharide molecule; ompF molecules, which are transport channels; and TOLC, which is a bacteria membrane protein.

 

DIF:        Difficult                REF:       6.4

OBJ:       6.4c Explain how bacteria defend themselves against viruses

MSC:     Understanding

 

  1. 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)?

 

ANS:

An RNA-dependent RNA polymerase means that the polymerase requires an RNA template (RNA-dep) to synthesize RNA (RNA pol). The host cell RNA pol would be called a DNA-dependent RNA polymerase, since it requires a DNA template to synthesize RNA. RTase would be referred to as an RNA-dependent DNA polymerase since it utilizes an RNA template to synthesize DNA.

 

DIF:        Difficult                REF:       6.3

OBJ:       6.3c Categorize the genome composition and the route used to express messenger RNA (mRNA) in the Baltimore virus classification scheme           MSC:     Applying

 

  1. 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?

 

ANS:

Animal or bacterial cells lack RNA-dependent RNA polymerase and thus cannot replicate RNA regardless of whether they are single- or double-stranded RNA. The initial replication of viral RNA genomes must be accomplished by existing RNA-dependent RNA polymerase. Subsequent replication and/or transcription of viral RNA genome and mRNA could be accomplished by viral RNA-dependent RNA polymerase produced in the hosts.

These viral-specific polymerases could be the targets for antiviral therapies with lowered side effects. They could also be utilized for in vitro replication/amplification of RNA molecules.

 

DIF:        Difficult                REF:       6.3

OBJ:       6.3b List the criteria by which the International Committee on Taxonomy of Viruses (ICTV) classifies viruses                MSC:     Applying

 

  1. Evaluate what determines which cycle a temperate phage will go through as shown in the figure below.

 

 

ANS:

Proteins bind DNA to repress viral replication genes during lysogeny. The switch to the lytic cycle can occur randomly or can be triggered by environmental stresses that damage the cell’s DNA. Events that threaten a cell’s survival can trigger the lytic cycle. If the host cells are growing well, the virus can continue to survive and be propagated as a prophage.

 

DIF:        Difficult                REF:       6.4

OBJ:       6.4a Distinguish the lytic, lysogenic, and slow-release viral cycles

MSC:     Evaluating

 

  1. How can a virus be used to transfer genes from one bacterial cell to another?

 

ANS:

In the process of transduction, a lysogenic phage is triggered to begin the lytic cycle. When this occurs, the viral DNA is excised from the host chromosome, and sometimes some of the host chromosome is excised with the viral DNA. A combination of viral DNA and host DNA can be packaged into a viral capsid, which then infects a new host and brings both viral and host DNA to the new host. In other cases, a viral infection causes host DNA to be cut into small pieces, and some of those pieces are accidentally packaged into viral capsids. This host DNA in the viral capsid can be transferred to a new host when the virus infects the new host.

 

DIF:        Difficult                REF:       6.4

OBJ:       6.4c Explain how bacteria defend themselves against viruses

MSC:     Applying

 

  1. What determines the host range and tropism of a virus?

 

ANS:

Viruses must attach to specific host cell receptors to cause infection. Only host cells with the specific receptors that a particular virus recognizes can be infected with that viral species. Receptors may also only be found on specific tissues, meaning that the receptors also determine tropism, or which tissues can be infected.

 

DIF:        Medium               REF:       6.5

OBJ:       6.5a Explain how animal viruses exhibit host and tissue tropism

MSC:     Understanding

 

  1. Explain the process shown in the figure below.

 

 

ANS:

This is an adenovirus infecting a cell. The genome is docking into nuclear membrane. Then, it shows the uncoating of the dsDNA genome.

 

DIF:        Difficult                REF:       6.5          OBJ:       6.5b Categorize animal virus uncoating strategies

MSC:     Applying

 

  1. Define oncogenes and oncogenic viruses, and explain how they can be used in gene therapy.

 

ANS:

Oncogenes are genes that, when expressed, cause uncontrolled proliferation of the infected cell and ultimately cancer. These oncogenes may be activated by viral transfer of host genes to abnormal chromosome locations. Alternatively, viruses may carry these oncogenes in their genome. Viruses that lead to oncogene expression are referred to as oncogenic viruses.

In gene therapy, a virus is used as a vehicle to transfer a functional copy of a gene to an individual to “correct” a genetic defect.

 

DIF:        Difficult                REF:       6.5

OBJ:       6.5f State the conditions that favor the emergence of viral pathogens

MSC:     Applying

 

  1. What is it necessary for bacteriophage and animal virus entry into a cell? How does that differ from plant viral entry?

 

ANS:

There is a specific receptor on the host cell to which a bacteriophage or animal virus must bind to initiate viral entry into the host. There is no receptor involved in plant viral entry. It is instead gained by either contact with damaged tissues, transmission by an animal vector, or transmission through seed.

 

DIF:        Medium               REF:       6.5          OBJ:       6.5e Describe animal and plant viral defenses

MSC:     Understanding

 

  1. How is the technique displayed in the figure below used to count virions in a solution?

 

 

ANS:

Dilutions of a solution containing an unknown number of viruses is diluted and then mixed with host cells. The mixture is added to soft agar and then poured onto a plate of solid medium. When the virions infect host cells, the host cells will lyse and release more virions to infect neighboring host cells. This cycle continues until a visible clearing, a plaque, can be seen within the lawn of bacteria. The plaques can be counted and multiplied by the dilution factor to determine plaque-forming units/ml.

 

DIF:        Medium               REF:       6.6

OBJ:       6.6d Recall what plaques are and explain how they are useful to microbiologists

MSC:     Applying

 

  1. During the eclipse period of a viral infection, why are the virions undetectable in the growth medium?

 

ANS:

The virions attach to cell-surface receptors and inject their DNA. Since all or most of the virions are attached to the host-cell receptors, there are few present in the growth medium.

 

DIF:        Medium               REF:       6.6

OBJ:       6.6a Outline some of the difficulties involved in culturing viruses

MSC:     Understanding

 

  1. Why was the advent of tissue culture heralded as the end of the “monkey era”? What types of things are we able to do with it?

 

ANS:

Monkeys were being used to culture polio virus. This was very expensive and labor intensive, and it involved the use of many animals. Tissue culture affords us the option to avoid animal use. It has become the method of choice to test chemical and antibiotic reagents. It is also used to study animal and plant viruses and to develop vaccines and antiviral chemicals.

 

DIF:        Medium               REF:       6.6

OBJ:       6.6c Summarize the advantages and disadvantages of culturing animal viruses in tissue culture versus whole animals                                 MSC:     Applying

 

  1. 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.

 

ANS:

A plaque represents the area where one virus initially infected one cell. It looks like a clear zone on a lawn of uninfected cells. In the case of a lytic virus, the plaque appears because the cells lyse when the viruses are released. In the case of a nonlytic virus, the cells are not lysed, but when infected they contain components of the replicating virus. Fluorescent antibodies targeting specific viral proteins can  react with the cells.

 

DIF:        Medium               REF:       6.6

OBJ:       6.6d Recall what plaques are and explain how they are useful to microbiologists

MSC:     Applying CHAPTER 13: Energetics and Catabolism

 

MULTIPLE CHOICE

 

  1. Which of the following statements is NOT true regarding the electron donors in prokaryotic metabolism?
  2. The use of organic compounds as electron donors is known as organotrophy.
  3. Chemolithotrophy refers to the use of inorganic molecules as electron sources.
  4. Photolysis of water provides electrons to phototrophic organisms such as cyanobacteria.
  5. Electrons can be obtained from inorganic chemicals such as H2S.
  6. Oxygen can serve as an electron donor.

 

 

ANS:      E              DIF:        Easy       REF:       13.1

OBJ:       13.1b Categorize microbes based on how they acquire energy

MSC:     Remembering

 

  1. Chemoorganotrophy is a term describing microorganisms that
  2. use preformed organic compounds as a source of electrons and obtain energy through fermentations or organic respiration.
  3. obtain electrons and H via photolysis of H2O or H2S, producing O2 or S2, respectively.
  4. perform photolysis of small organic molecules.
  5. use carbon dioxide as the carbon source.
  6. pull electrons off minerals to donate to electron transport systems.

 

 

ANS:      A             DIF:        Difficult                REF:       13.1

OBJ:       13.1b Categorize microbes based on how they acquire energy

MSC:     Understanding

 

  1. 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 ________.
  2. methanogenesis; chemolithotroph
  3. respiration; heterotroph
  4. fermentation; chemoorganotroph
  5. carbon fixation; phototroph
  6. sulfur bacterium; chemolithotroph

 

 

ANS:      A             DIF:        Medium               REF:       13.1

OBJ:       13.1b Categorize microbes based on how they acquire energy

MSC:     Understanding

 

  1. The laws of thermodynamics indicate that systems tend to become less ordered and that ________, a measure of disorder or randomness of the universe, always increases.
  2. entropy d.            molecular stability
  3. enthalpy e.            activation energy
  4. Gibbs free energy

 

 

ANS:      A             DIF:        Easy       REF:       13.1

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy                MSC:     Remembering

 

  1. The Gibbs equation describes the relationship between the components of free energy change and can be generally expressed as
  2. G  G°  RT ln Keq.
  3. G  H  TS.
  4. ADP  Pi  ATP  H2O.
  5. K  T°C  273.
  6. G  2.303 RT log [C] [D] / [A] [B].

 

 

ANS:      B             DIF:        Easy       REF:       13.1

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy                MSC:     Remembering

 

  1. Which of the following statements is FALSE with respect to heterotrophic organisms?
  2. They use preformed organic compounds for biosynthesis.
  3. Most organotrophs are also heterotrophs.
  4. Along with decomposers, they are ecologically defined as consumers.
  5. Some can generate methane as an end product.
  6. They utilize glycolysis and other pathways to generate energy.

 

 

ANS:      D             DIF:        Medium               REF:       13.1

OBJ:       13.1b Categorize microbes based on how they acquire energy

MSC:     Understanding

 

  1. Hydrogen-generating reactions in Syntrophus and Syntrophomonas have G°’ > 0. Can these organisms obtain energy from hydrogen formation?
  2. No, they cannot.
  3. No—they produce energy by breaking down molecules such as benzoate or butyrate.
  4. Yes—hydrogen-producing microorganisms coexist in syntrophy with H2-consuming bacteria. Utilization of H2 (G°’  0) drives the process forward.
  5. Yes, but only when oxygen is present.
  6. Yes—this happens in sewage but never in a laboratory setting.

 

 

ANS:      C             DIF:        Difficult                REF:       13.1

OBJ:       13.1a Define catabolism, energy, enthalpy, entropy, and syntrophy

MSC:     Analyzing

 

  1. Using the table below, what is the best method for obtaining energy from catabolizing ethanol, and why?

 

  1. the catabolism of ethanol without an oxidant, because the G is almost positive
  2. the oxidation of ethanol with as the oxidant is because of the large yield of energy released
  3. the oxidation of ethanol with oxygen, because the G is the largest negative number indicating the large yield of energy released.
  4. The oxidation of ethanol yields too little biomass to be catabolized.
  5. None—ethanol can only be catabolized syntrophically.

 

 

ANS:      D             DIF:        Difficult                REF:       13.1

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy                MSC:     Evaluating

 

  1. In amphibolic pathways, enzymes do NOT
  2. function only in the biosynthetic direction.
  3. function only in the catabolic direction.
  4. function in both directions.
  5. carry out reactions that are otherwise thermodynamically impossible.
  6. have activity dependent on concentrations of reactants and products.

 

 

ANS:      D             DIF:        Medium               REF:       13.1 | 13.5

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy | 13.5g Define amphibolic reactions and describe their regulation

MSC:     Understanding

 

  1. A metabolic process allowing for anaerobic degradation of benzoate to acetate is diagrammed below. This metabolism can happen because

 

  1. benzoate contains a great deal of energy and ATP can be made.
  2. the catabolism of benzoate by the cell on the left produces hydrogen that is then used by the cell on the right to reduce sulfate.
  3. the catabolism of benzoate by the cell on the left produces hydrogen that is then used by a methanogen.
  4. the catabolism of benzoate to acetate releases so much energy that it overcomes the positive G of H2 production.
  5. the cell on the left swims away from the H2 that it produces in order to balance the thermodynamics.

 

 

ANS:      B             DIF:        Difficult                REF:       13.2

OBJ:       13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC:     Analyzing

 

  1. In most environments, the nutrient concentrations outside the cell are lower than inside the cell. If the concentration gradient is NOT favorable, a microbial cell obtains nutrients through
  2. active, energy-dependent transport. d.            forming biofilms.
  3. facilitated diffusion. e.            simple diffusion.
  4. swim and tumble.

 

 

ANS:      A             DIF:        Easy       REF:       13.2

OBJ:       13.2d Describe the relationship between energy and concentration gradients

MSC:     Remembering

 

  1. When studying an enzymatic reaction, should one consider G, G0, or G0′ when considering the thermodynamics of the reaction, and why?
  2. G0, because it considers standard conditions as well as biochemically relevant conditions such as the concentrations of substrates and products
  3. G0, because it considers standard conditions
  4. G, because it considers defined conditions such as pH
  5. G, because it considers concentrations of reactants as products.
  6. G0, because it considers entropy and enthalpy.

 

 

ANS:      A             DIF:        Medium               REF:       13.2

OBJ:       13.2a Recall the conditions required for the standard Gibbs free energy change, DeltaG°, and the biochemical Gibbs free energy change, DeltaG°’     MSC:     Understanding

 

  1. What technique can be used to determine entropy and enthalpy changes associated with biochemical reactions?
  2. nuclear magnetic resonance d.            mass spectroscopy
  3. calorimetry e.            measurement of light levels
  4. electron microscopy

 

 

ANS:      B             DIF:        Easy       REF:       13.1

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy                MSC:     Understanding

 

  1. Which of the following phenomena is sufficient to transport nutrients to cells that lack chemotactic motility?
  2. active, ATP-dependent transport d.            quorum sensing
  3. diffusion e.            biofilm formation
  4. turbulent flow

 

 

ANS:      B             DIF:        Easy       REF:       13.2

OBJ:       13.2d Describe the relationship between energy and concentration gradients

MSC:     Understanding

 

  1. Glycolytic reactions with a near-zero G°’ can participate in the overall pathway of gluconeogenesis because they
  2. are irreversible.
  3. are reversible.
  4. contradict the laws of thermodynamics.
  5. have low energy of activation values.
  6. do not depend on concentrations of reactants and products.

 

 

ANS:      B             DIF:        Medium               REF:       13.2

OBJ:       13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC:     Understanding

 

  1. The G for a reaction can be calculated by using G0 and adding in
  2. entropy, enthalpy, and the log of the ratio of reactants to products.
  3. entropy, enthalpy, pH, and the log of the ratio of the reactants to products.
  4. the gas constant, absolute temperature, and the log of the ratio of the reactants to products.
  5. the log of the ratio of the reactants to products.
  6. the gas constant, absolute temperature, pH, and the log of the ratio of the reactants to products.

 

 

ANS:      C             DIF:        Medium               REF:       13.2

OBJ:       13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC:     Analyzing

 

  1. In their work with soil bacteria, McInerney and colleagues have found microorganisms that display metabolic pathways with net G values as small as 20 kJ/mol. This is an example of
  2. the capacity of microorganisms to conquer a wide variety of environments.
  3. microorganisms contradicting the laws of thermodynamics.
  4. growth near thermodynamic equilibrium.
  5. growth that depends on the concentration of reactants but not products.
  6. enthalpic growth.

 

 

ANS:      C             DIF:        Medium               REF:       13.2

OBJ:       13.2b Calculate the DeltaG°’ of a coupled reaction            MSC:     Evaluating

 

  1. The molecule shown below carries energy in the cell but it needs to be stabilized. It is a ________ molecule and is stabilized when it ________.

 

  1. NADPH; forms a cyclic molecule
  2. NADPH; complexes with Mg2
  3. ATP; donates its electrons to a cytochrome
  4. ATP; complexes with Mg2
  5. ATP; forms a cyclic molecule

 

 

ANS:      D             DIF:        Difficult                REF:       13.3

OBJ:       13.3c Compare and contrast ATP and NADH         MSC:     Analyzing

 

  1. In many bacteria, the electron carrier ________ is used for biosynthesis, whereas ________ feeds the electron transport system.
  2. NADPH; NADH d.            chlorophyll; NADPH
  3. FADH2; NADPH e. pyruvate; acetyl-S-CoA
  4. NADH; acetyl-S-CoA

 

 

ANS:      A             DIF:        Easy       REF:       13.3

OBJ:       13.3b Define energy carriers and provide examples         MSC:     Remembering

 

  1. All of the following are reasons to oxidize glucose in a series of steps EXCEPT to
  2. generate smaller amounts of energy in a controlled fashion and when needed.
  3. control the usage of energy in a cell by using more steps.
  4. minimize the release of heat with more small steps.
  5. control the catabolism versus biosynthetic aspects of oxidizing glucose via concentrations of reactants and end products.
  6. increase the DG of the reaction.

 

 

ANS:      E              DIF:        Medium               REF:       13.1

OBJ:       13.3a Explain why glucose is oxidized in a series of steps instead of a single step

MSC:     Understanding

 

  1. Which of the following is FALSE with respect to enzymes that use the reducing equivalents NADH and NADPH?
  2. Some enzymes only use NADH.
  3. Some enzymes only use NADPH.
  4. Some enzymes may use either NADPH or NADH.
  5. FADH2 can be used as a substitute.
  6. NADPH is more often used in biosynthesis.

 

 

ANS:      D             DIF:        Easy       REF:       13.3

OBJ:       13.3d Recall why metabolic reactions require enzymes   MSC:     Remembering

 

  1. The graph shown below diagrams the energy involved in the

 

  1. difference in activation energy of a reaction with and without an inhibitor at an allosteric site.
  2. difference in the activation energy of a reaction with and without an enzyme.
  3. activation energy needed to initiate the Embden-Meyerhof pathway.
  4. difference in synthrophic reactions with and without a hydrogen utilizing partner.
  5. difference in activation energy with NADH versus NADPH.

 

 

ANS:      B             DIF:        Difficult                REF:       13.3

OBJ:       13.3d Recall why metabolic reactions require enzymes   MSC:     Evaluating

 

  1. The base adenine forms from ________ in experiments simulating the origin of life on Earth.
  2. carbon dioxide and nitrate d.            adenosine and PO4
  3. ethanol and urea e.            ribose and RNA
  4. methane and ammonia

 

 

ANS:      C             DIF:        Medium               REF:       13.3

OBJ:       13.3b Define energy carriers and provide examples         MSC:     Remembering

 

  1. Hydrolysis of ATP with the release of pyrophosphate is the driving force of which of the following reactions?
  2. DNA and RNA synthesis
  3. peptide bond formation
  4. fatty acid synthesis
  5. transport across a membrane
  6. production of glucose-6-phosphate from glucose

 

 

ANS:      A             DIF:        Medium               REF:       13.3

OBJ:       13.3b Define energy carriers and provide examples         MSC:     Remembering

 

  1. Not all enzymes are proteins; in some enzymes, the catalytic properties depend on
  2. DNA. d.            lipids.
  3. RNA. e.            terpenoids.
  4. polysaccharides.

 

 

ANS:      B             DIF:        Medium               REF:       13.3

OBJ:       13.3d Recall why metabolic reactions require enzymes   MSC:     Remembering

 

  1. Although ATP is the main energy carrier in living organisms, other molecules may also serve as energy carriers in metabolic reactions. Which of the following molecules does NOT carry energy?
  2. nucleotides such as GTP d.            glucose
  3. phosphoenolpyruvate e.            nucleotides such as CTP and UDP
  4. creatine phosphate

 

 

ANS:      D             DIF:        Medium               REF:       13.3

OBJ:       13.3b Define energy carriers and provide examples         MSC:     Understanding

 

  1. The activity of the enzyme below is controlled in various ways using several of the binding sites shown. The two sites are the ________ site and the ________ site.

 

  1. active; inhibitor d. substrate; allosteric
  2. catalytic; inhibitor e.            catalytic; allosteric
  3. substrate; inhibitor

 

 

ANS:      E              DIF:        Medium               REF:       13.3

OBJ:       13.3d Recall why metabolic reactions require enzymes   MSC:     Analyzing

 

  1. Which of the following is NOT correct with respect to the redox pair NAD/NADH?
  2. The nicotinamide ring is a relatively stable aromatic structure.
  3. The nicotinamide ring is a heteroaromatic because it has a noncarbon atom in position 4.
  4. The nicotinamide ring may accept two electrons at carbon 1, becoming a nonaromatic ring.
  5. The reduced, nonaromatic ring of NADH is at a higher energy than the aromatic ring of NAD.
  6. NADH can accept electrons from an electron transport system.

 

 

ANS:      E              DIF:        Difficult                REF:       13.3

OBJ:       13.3b Define energy carriers and provide examples         MSC:     Analyzing

 

  1. The enzyme pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is an example of
  2. ATP synthesis by substrate-level phosphorylation.
  3. the use of a proton concentration gradient by [H]-ATPases to synthesize ATP.
  4. ATP coupled to FADH2 oxidation.
  5. a P-Type ATPase activity.
  6. oxidative phosphorylation.

 

 

ANS:      A             DIF:        Easy       REF:       13.3 | 13.5

OBJ:       13.3c Compare and contrast ATP and NADH         MSC:     Understanding

 

  1. Which of the following pairs is mismatched?
  2. Embden-Meyerhof-Parnas pathway—2 ATP, 2 NADH
  3. Entner-Doudoroff pathway—1 ATP, 1 NADH, and 1 NADPH
  4. pentose phosphate pathway—1 ATP, 2 NADPH
  5. glyoxylate bypass—2 NADH, 1 FADH2
  6. bacterial tricarboxylic acid cycle—3 NADH, 1 FADH2, 1 ATP

 

 

ANS:      D             DIF:        Medium               REF:       13.5

OBJ:       13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield     MSC:     Understanding

 

  1. The process of prioritized consumption of substrates is known as catabolite
  2. induction. d.            repression.
  3. poisoning. e.            attenutation.
  4. competition.

 

 

ANS:      D             DIF:        Medium               REF:       13.4

OBJ:       13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism        MSC:     Understanding

 

  1. Disparate animal groups, such as ruminants and humans, can digest a variety of plant fibers because they harbor cellulase-producing bacteria such as
  2. Staphylococcus aureus and Bacillus subtilis.
  3. Salmonella and Shigella.
  4. Escherichia coli and Enterococcus faecalis.
  5. Bacteroides and Ruminococcus.
  6. Escherichia chrysanthemi and Erwinia uredovora.

 

 

ANS:      D             DIF:        Medium               REF:       13.4

OBJ:       13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism        MSC:     Analyzing

 

  1. Fatty acids enter the TCA cycle after being degraded to what molecule?
  2. acetyl-phosphate d.            citrate
  3. malonyl-S-CoA e.            pyruvate
  4. acetyl-S-CoA

 

 

ANS:      C             DIF:        Easy       REF:       13.4

OBJ:       13.4b Recall the major forms of catabolism.                         MSC:     Remembering

 

  1. The figure shown below diagrams three pathways for the metabolism of glucose. Pathway ________ is most likely to be used for biosynthesis because it can be used to ________.

 

  1. 1; generate glucose
  2. 2; make carbon backbones of many lengths
  3. 3; make carbon backbones of many lengths
  4. 1; make carbon backbones of many lengths
  5. 3; generate glucose

 

 

ANS:      E              DIF:        Easy       REF:       13.5

OBJ:       13.5b Name the three main catabolic routes from glucose to pyruvate

MSC:     Understanding

 

  1. Glucose is activated by ________ phosphorylation(s) by ATP during the first stage of the Embden-Meyerhof-Parnas pathway.
  2. one d.            four
  3. two e.            Glucose is not phosphorylated.
  4. three

 

 

ANS:      B             DIF:        Easy       REF:       13.5

OBJ:       13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC:     Remembering

 

  1. In glycolysis, dihydroxyacetone phosphate is isomerized to ________, which reenters the pathway.
  2. glucose 6-phosphate d.            fructose 6-phosphate
  3. glyceraldehyde 3-phosphate e.            pyruvate
  4. phosphoenolpyruvate

 

 

ANS:      B             DIF:        Easy       REF:       13.5

OBJ:       13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC:     Remembering

 

  1. Some intestinal bacteria, such as Escherichia coli, feed on ________ from mucus secretions using the Entner-Doudoroff pathway.
  2. gluconate d.            2-oxoglutarate
  3. glucose e. oxaloacetate
  4. pyruvate

 

 

ANS:      A             DIF:        Difficult                REF:       13.5

OBJ:       13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway                MSC:     Remembering

 

  1. Bacteria synthesize ribose for nucleotides using which pathway?
  2. Embden-Meyerhof-Parnas d.            tricarboxylic acid cycle
  3. Entner-Doudoroff e.            electron transport system
  4. pentose phosphate shunt

 

 

ANS:      C             DIF:        Easy       REF:       13.5

OBJ:       13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway                MSC:     Remembering

 

  1. Which of the following molecules is responsible for the distinctive flavor of Swiss cheese?
  2. lactate d.            propionate
  3. glucose e. acetate
  4. galactose

 

 

ANS:      D             DIF:        Easy       REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Remembering

 

  1. Which of the following is NOT an end product of fermentation?
  2. carbon dioxide d.            butanol
  3. acetone e.            propionate
  4. pyruvate

 

 

ANS:      C             DIF:        Medium               REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Understanding

 

  1. The dye ________ turns ________ in the presence of acid products and is included in fermentation broth for some diagnostic tests.
  2. phenol red; yellow d.            malachite green; blue
  3. aniline blue; green e.            MacConkey; white
  4. ethidium bromide; pink

 

 

ANS:      A             DIF:        Easy       REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Understanding

 

  1. The energy yield from fermentation is lower than from respiration because
  2. fermentation uses NAD, not NADP.
  3. respiration completely oxidizes glucose to CO2, resulting in greater generation of NADH and thus ATP.
  4. respiration uses the TCA cycle, which has many steps that directly produce ATP or GTP.
  5. fermentation shunts much of the carbon from glucose to biosynthesis.
  6. fermentation relies on the glyoxylate bypass, which bypasses ATP production.

 

 

ANS:      B             DIF:        Medium               REF:       13.5

OBJ:       13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield     MSC:     Analyzing

 

  1. In the pentose phosphate shunt, glucose 6-phosphate is oxidized to 6-phosphogluconate, which is then decarboxylated to ribulose 5-phosphate. What is the main metabolic role of this pathway?
  2. production of ATP and NADH  H
  3. regeneration of NADP
  4. production of carbohydrates with three to seven carbon atoms, which can be utilized in biosynthesis
  5. production of pyruvate to feed the Krebs cycle
  6. oxidation of glucose to carbon dioxide

 

 

ANS:      C             DIF:        Medium               REF:       13.5

OBJ:       13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway                MSC:     Applying

 

  1. Clostridium acetobutylicum has been used to produce which solvents?
  2. acetate and butyrate d.            formate and ethanol
  3. acetone and butanol e.            propanol and mixed acids
  4. methanol and ethanol

 

 

ANS:      B             DIF:        Medium               REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Applying

 

  1. Which of the following is evidence that the Entner-Doudoroff (ED) route might have evolved earlier than the Embden-Meyerhof-Parnas pathway (EMP)?
  2. ED involves a larger number of reactions and produces more energy and reducing equivalents with respect to EMP.
  3. 6-phosphogluconate is dehydrated to form pyruvate and glyceraldehyde 3-phosphate, which may then reenter the EMP pathway.
  4. ED involves fewer substrate-level phosphorylations and yields less energy and fewer reductants than EMP.
  5. They are both used to catabolize glucose.
  6. They both use ATP to phosphorylate glucose.

 

 

ANS:      C             DIF:        Difficult                REF:       13.5

OBJ:       13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway                MSC:     Analyzing

 

  1. Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions. Which of the following is NOT correct with respect to “mucus farming” by bacteria?
  2. Bacteroides thetaiotaomicron and other bacteria induce the colon to produce mucus.
  3. Mucus-derived sugar acids are metabolized via the Entner-Doudoroff pathway.
  4. Sugar acids must be converted to 6-phosphogluconate in order to enter the Entner-Doudoroff pathway.
  5. The glucose derivatives are converted to glucose and degraded via the Embden-Meyerhof-Parnas pathway.
  6. This metabolism has been studied via genomics and genetic studies.

 

 

ANS:      D             DIF:        Medium               REF:       13.5

OBJ:       13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway                MSC:     Analyzing

 

  1. Ethanolic fermentation is used in making beverages such as beer, wine, and pulque. It is carried out by yeast and
  2. lactobacillus. d.            zymomonas.
  3. leuconostoc. e.            clostridium.
  4. propionibacterium.

 

 

ANS:      D             DIF:        Easy       REF:       13.5

OBJ:       13.5e Distinguish among various types of fermentation (e.g., lactic acid, ethanolic, and mixed acid)          MSC:                Remembering

 

  1. Which of the diagrammed molecules is a global signal of nutritional status?

 

  1. pyruvate d.            acetyl-CoA
  2. 2-oxoglutarate e.            acetyl-P
  3. oxaloacetate

 

 

ANS:      E              DIF:        Easy       REF:       13.6

OBJ:       13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC:     Understanding

 

  1. Amino acids can be synthesized using which one of the molecules from the diagram below?

 

  1. isocitrate d.            2-oxoglutarate
  2. succinyl-CoA e.            fumarate
  3. oxaloacetate

 

 

ANS:      D             DIF:        Easy       REF:       13.6

OBJ:       13.6b Recall the roles that the TCA cycle and the glyoxylate bypass play in cell metabolism

MSC:     Remembering

 

  1. Pyruvate dehydrogenase complex connects glycolysis to respiration. Which is a correct mechanism for how the activity of this enzyme complex is regulated?
  2. There is no need to regulate this enzyme complex.
  3. The activity is inhibited by CoA and NAD+.
  4. Gene expression is repressed by carbon starvation and low oxygen levels.
  5. The activity is inhibited by citrate.
  6. The activity is enhanced by the presence of acetyl-CoA and NADH.

 

 

ANS:      C             DIF:        Difficult                REF:       13.6

OBJ:       13.6c Describe the function and regulation of the pyruvate dehydrogenase complex

MSC:     Applying

 

  1. ________ enters the tricarboxylic acid cycle by condensing with oxaloacetate to form ________.
  2. Succinoyl-S-CoA; fumarate d.            Citrate; isocitrate
  3. Acetyl-S-CoA; citrate e.            Acetyl phosphate; citrate
  4. Pyruvate; citrate

 

 

ANS:      B             DIF:        Easy       REF:       13.6

OBJ:       13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC:     Remembering

 

  1. The greatest amount of reduced coenzyme NADH  H is produced during which stage of aerobic respiration?
  2. glycolysis d.            glyoxylate bypass
  3. pyruvate conversion to acetyl-S-CoA e.            oxidative phosphorylation
  4. tricarboxylic acid cycle

 

 

ANS:      C             DIF:        Easy       REF:       13.6

OBJ:       13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC:     Remembering

 

  1. Pathways involving both anabolic and catabolic reactions are referred to as
  2. amphibolic. d.            ambidextrous.
  3. amphipathic. e.            syntrophibolic.
  4. ambivalent.

 

 

ANS:      A             DIF:        Medium               REF:       13.5

OBJ:       13.5g Define amphibolic reactions and describe their regulation

MSC:     Analyzing

 

  1. Oxidative catabolism of benzoate and other aromatic compounds is catalyzed by
  2. 2-oxoglutarate:NADPH oxidoreductase.
  3. benzoyl-S-CoA reductase.
  4. specific dioxygenases.
  5. NADPH:ferredoxin oxidoreductase.
  6. catechol 2,3, monooxygenase.

 

 

ANS:      C             DIF:        Medium               REF:       13.7

OBJ:       13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC:     Understanding

 

  1. All oxidative catabolism of toluene and other benzene derivatives proceeds through
  2. benzoyl-S-CoA. d. cis, cis-muconate.
  3. aniline. e. D-gluconate.
  4. catechols.

 

 

ANS:      C             DIF:        Medium               REF:       13.6

OBJ:       13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC:     Understanding

 

  1. Species of Pseudomonas and Rhodococcus can degrade benzoate and other aromatic molecules, either aerobically or anaerobically. Which of the following is NOT correct regarding anaerobic degradation of aromatic molecules?
  2. It takes longer than aerobic degradation.
  3. It is critical because bacterial anaerobic habitats are more abundant than aerobic ones.
  4. Benzoate is activated to benzoyl-CoA prior to its degradation.
  5. It proceeds via production of catechols.
  6. The high initial investment of energy comes from either anaerobic phototrophy or anaerobic respiration.

 

 

ANS:      D             DIF:        Easy       REF:       13.6

OBJ:       13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC:     Analyzing

 

  1. Each of the following was used to elucidate the TCA cycle EXCEPT
  2. using radiolabeled acetate to determine which carbons were oxidized to CO2 .
  3. the use of crude enzyme preparations from a variety of sources such as cucumber seeds and beef liver.
  4. adding a variety of short-chain fatty acids commonly found in cells to detect activity.
  5. the use of C14-labeled carbon compounds as a source of carbon under anoxic conditions.
  6. using C13 to determine which intermediates are enriched under various growth conditions.

 

 

ANS:      D             DIF:        Medium               REF:       13.6

OBJ:       13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples              MSC:                Applying

 

SHORT ANSWER

 

  1. Define “organotroph” and “heterotroph.” Are these terms equivalent?

 

ANS:

They are not equivalent, but similar. An organotroph uses preformed organic compounds to yield energy. A heterotroph uses preformed organic compounds for biosynthesis. Most organotrophs are also heterotrophs.

 

DIF:        Easy       REF:       13.Intro

OBJ:       13.1a Define catabolism, energy, enthalpy, entropy, and syntrophy

MSC:     Analyzing

 

  1. How can a technique such as calorimetry be used to measure G?

 

ANS:

The amount of heat released by a reaction or a set of reactions, either in vitro or in a living system, can be measured by a calorimeter. If the reactions are maintained at constant temperature, the release of heat gives a measure of H. If measurements are made at different temperatures, the entropic term—TS—can be estimated from heat-release dependence on temperature. From the Gibbs-Helmholtz equation, G  H TS.

 

DIF:        Difficult                REF:       13.1

OBJ:       13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy                MSC:     Applying

 

  1. What are the differences among G, G°, and G°’?

 

ANS:

G is the change in Gibbs free energy for a reaction under defined conditions. G° is the change in Gibbs free energy for a reaction at standard conditions of temperature (298 K) and pressure (1 atm), with all reactants and products at a concentration of 1M. G°’ is similar to G°, with one other condition: that the reaction occurs at pH 7; this is commonly used in biochemistry.

 

DIF:        Easy       REF:       13.2

OBJ:       13.2a Recall the conditions required for the standard Gibbs free energy change, DeltaG°, and the biochemical Gibbs free energy change, DeltaG°’     MSC:     Understanding

 

  1. Why is magnesium an essential nutrient for all living cells?

 

ANS:

Mg2 partly neutralizes the negative changes of the phosphates in ATP, thereby stabilizing the structure in solution. Generally, any enzyme that requires ATP actually requires Mg2-ATP. As such, it is an essential nutrient.

 

DIF:        Easy       REF:       13.3        OBJ:       13.3b Define energy carriers and provide examples

MSC:     Understanding

 

  1. All nucleotide triphosphates carry energy. Provide examples of reactions that are driven by the release of energy from GTP, CTP, and TTP.

 

ANS:

GTP is specifically used in the initiation and elongation processes of protein synthesis. All nucleotide triphosphates, ATP, GTP, CTP, and TTP, as well as their corresponding deoxynucleotide triphosphates, provide the energy for their own incorporation into RNA and DNA, respectively.

 

DIF:        Medium               REF:       13.3        OBJ:       13.3b Define energy carriers and provide examples

MSC:     Understanding

 

  1. What is the phosphotransferase system (PTS) and why is the advantage for a microbial cell to have a PTS?

 

ANS:

The PTS consists of several enzymes that couple the phosphorylation of sugar molecules, such as glucose or mannose, to their transport across the cell membrane. Enzymes involved in the PTS are important in determining which nutrients from the environment (or medium) certain microorganisms can import and catabolize.

 

DIF:        Medium               REF:       13.3

OBJ:       13.3d Recall why metabolic reactions require enzymes   MSC:     Analyzing

 

  1. What is substrate-level phosphorylation? Provide two examples from bacterial metabolism.

 

ANS:

Phosphorylation of ADP at the substrate-level consists of the transfer of a phosphoryl group from a metabolic intermediate to form ATP. In glycolysis, substrate-level phosphorylation takes place when pyruvate kinase converts phosphoenolpyruvate and ADP to pyruvate and ATP. In the TCA cycle, ATP is formed when ADP is phosphorylated by succinyl-S-CoA synthetase during the conversion of succinyl-S-CoA to succinate and coenzyme A.

 

DIF:        Medium               REF:       13.3 | 13.5

OBJ:       13.3b Define energy carriers and provide examples | 13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield

MSC:     Understanding

 

  1. The catabolism of glucose is central to the overall hydrolysis of polysaccharides in an environment. Compare and contrast the analogous catabolism of polyaromatic compounds found in nature.

 

ANS:

Polyaromatic compounds found in nature include lignin found in plants and polycyclic aromatic hydrocarbons found in petroleum. As these compounds are hydrolyzed, benzene is produced just as glucose is the product from polysaccharides. Benzene will be converted to benzoate and vanillin that are converted to acetyl-CoA and hydrolyzed further via the TCA cycle. Similarly, glucose is degraded to pyruvate, then to acetyl-CoA, and further hydrolyzed via the TCA cycle.

 

DIF:        Medium               REF:       13.4

OBJ:       13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism        MSC:     Analyzing

 

  1. Define the human metagenome. Describe an example to demonstrate the importance of the metagenome.

 

ANS:

The human metagenome is composed of the human genome and the genomes of all the organisms in human gut microbiota. This is important because there are organisms present in our microbiota that we depend on to carry out reactions we cannot perform. Humans obtain some amino acids and vitamins from gut microorganisms. As such, to get a more complete picture of all the metabolic activities present in a human, the metagenome must be considered. Also, genes could be found in gut microbes that code for proteins that utilize the N-acetyl glucosamine, sialic acid and fucose found in breast milk (and not metabolized by humans).  Studies with Bacteroides and Ruminococcus sp. serve as examples. Examples may vary but can include studies examining the genes involved in digesting a variety of xyloglucan from sources such as tomatoes versus lettuce.

 

DIF:        Difficult                REF:       13.4

OBJ:       13.4c Explain how genomic studies have contributed to our understanding of microbial catabolism           MSC:                Applying

 

  1. Describe the Entner-Doudoroff (ED) pathway. What are the advantages to microorganisms that display the ED pathway?

 

ANS:

Glucose is oxidized to the sugar acid 6-phosphogluconate, a central metabolite in the Entner-Doudoroff pathway. 6-Phosphogluconate may arise from other sources, such as the bacterial catabolism of intestinal mucus, and is further oxidized to 2-oxo-3-deoxy-6-phosphogluconate, which breaks down to the glycolysis intermediates glyceraldehyde and pyruvate. Microorganisms using ED produce only one ATP, half of that produced in glycolysis, but the electrons transferred are equivalent: one NADH  H and one NADPH  H are generated in ED.

 

DIF:        Medium               REF:       13.5

OBJ:       13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC:     Understanding

 

  1. The flavor and other properties of cheeses derive from the type of fermenting microorganisms used. How do the “eyes” and the characteristic flavor of Swiss cheese originate?

 

ANS:

Fermentation of milk sugars by Propionibacterium freudenreichii produces lactate, which is further oxidized to propionate and acetate. Fermentation also produces CO2, which makes the “eyes” (holes). Other flavors come from succinate, which is formed by the reaction between lactate and two molecules of aspartate. This reaction releases CO2, which further increases the size and number of “eyes.”

 

DIF:        Difficult                REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Understanding

 

  1. What is mixed-acid fermentation? Provide examples of industrial uses of its products.

 

ANS:

Some enteric bacteria produce a series of mono- and dicarboxylic acids from pyruvate. Depending on the pH, the mixture may include succinate, lactate, acetate, or formate, plus ethanol, CO2, and H2. Regeneration of NAD and free coenzyme A also take place in the process. Some bacteria, such as Clostridium spp., possess the metabolic capability to synthesize isopropanol and butanol, which are valuable solvents. Lactic acid is part of the biochemical makeup of yogurt and cheeses. Ethanol can be used as a solvent and is found in alcoholic beverages.

 

DIF:        Difficult                REF:       13.5

OBJ:       13.5e Distinguish among various types of fermentation (e.g., lactic acid, ethanolic, and mixed acid)         MSC:                Applying

 

  1. Describe the diagnostic use of sorbitol MacConkey agar to test for the presence of E. coli O157:H7.

 

ANS:

The sugar source in this medium is sorbitol. Also present in the medium is an indicator dye that turns red in the presence of acids. An organism that ferments sorbitol produces acids, and the colony will appear red. These plates are used to screen for E. coli O157:H7 because this strain, unlike most E. coli, is incapable of fermenting sorbitol. When grown on these plates, the colonies appear pale rather than red. The appearance of pale colonies indicates a high probability of E. coli O157:H7.

 

DIF:        Medium               REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Applying

 

  1. Escherichia 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?

 

ANS:

Molecular hydrogen (H2) and CO2 are among the products of mixed-acid fermentation of the carbohydrate solution used to flush the colon. These gases can be used as energy sources for intestinal methanogenic microbes through the production of methane. However, excess H2 and CH4 may ignite during polyp removal by electrocauterization, thus causing the so-called colonic explosion.

 

DIF:        Difficult                REF:       13.5

OBJ:       13.5f Identify some food and industrial applications of microbial fermentation

MSC:     Applying

 

  1. In the pentose phosphate shunt (PPS), sugars exchange short carbohydrate moieties to form carbohydrates with varying chain lengths. What metabolic mechanisms allow these exchanges to occur? What are the metabolic advantages of the PPS pathway?

 

ANS:

Pairs of sugars exchange portions of their molecules through specific enzymatic reactions, rendering new molecules without any loss of carbon. For example, the pentose ribose 5-phosphate and xylulose 5-phosphate react to form the C3 glyceraldehyde 3-phosphate and the C7 carbohydrate sedoheptulose 7-phosphate. In turn, these sugars may be converted to the C4 erythrose 4-phosphate and the C6 fructose 6-phosphate. Some PPS intermediates are anabolic precursors. For example, ribose 5-phosphate is used for nucleotide biosynthesis, and erythrose 4-phosphate is used for aromatic amino acids. The reducing equivalent NADPH is produced by several PPS reactions and used in biosynthesis. If pathway intermediates are not used in biosynthesis, they may be converted to fructose 6-phosphate and reenter glycolysis.

 

DIF:        Difficult                REF:       13.5

OBJ:       13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC:     Analyzing

 

  1. Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.

 

ANS:

  1. pallidum’s genome encodes key enzymes for glycolysis and fermentation, but not for the TCA cycle or electron transport. Although the genome also codes for transport proteins for sugars and amino acids, there are no genes that code for any enzymes involved in either the biosynthesis or breakdown of amino acids. T. pallidum, and other obligate pathogens, therefore must depend on its host’s metabolism to supply many fundamental and essential nutrients and transport them with the transport proteins.

 

DIF:        Difficult                REF:       13.6

OBJ:       13.6b Recall the roles that the TCA cycle and the glyoxylate bypass play in cell metabolism

MSC:     Remembering

 

  1. Hans Krebs’s strategy to determine the biochemical intermediates involved in aerobic respiration was to use substrate molecules of varying lengths. What led Krebs to take this approach?

 

ANS:

Many short-chain molecules with variable numbers of carboxyl groups were known to exist in the cells of aerobic organisms. Krebs tested carboxylic acids for their capacity to induce or stimulate respiration in different animal and plant tissues and analyzed their chemical structure relationships. Feeding bacteria with 14C-radiolabeled acetate helped to determine what was the fate of carbons entering the TCA cycle and to confirm the reactions in the pathway.

 

DIF:        Difficult                REF:       13.6

OBJ:       13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples              MSC:                Remembering

 

  1. How does the efficiency of energy capture by ATP formation in bacterial tricarboxylic acid cycle compare with that of mitochondria?

 

ANS:

Whereas mitochondria are enclosed in an intracellular environment that is relatively constant, bacteria must spend energy in adapting to ever-changing environments. Although less efficient in ATP production, bacteria spend energy to achieve flexibility through keeping stable ionic potentials during extreme changes in external pH and redox conditions.

 

DIF:        Medium               REF:       13.6

OBJ:       13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC:     Analyzing

 

  1. Soils and waters become contaminated with industrial aromatic compounds and efforts are made to use bacteria to clean up these areas. Describe the experiment and finding from phenanthrene metabolism in the Antarctic.

 

ANS:

Soils from the Antarctic were incubated at a variety of temperatures. C14-labeled phenanthrene was added to the soils and a respirometer was used to collect C14-carbon dioxide. Metabolism was demonstrated in this fashion, and in fact, warmer temperatures yielded faster metabolism than lower temperatures that would be found in the Antarctic. These findings suggest that the organisms involved were psychrotrophs that could tolerate cold, not psychrophiles that thrived only in the cold.

 

DIF:        Medium               REF:       13.6

OBJ:       13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples              MSC:                Understanding

 

  1. 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?

 

ANS:

Using 13C metabolic precursors to label infected cells, it was found that M. tuberculosis uses the glyoxylate bypass to catabolize lipids. The pathogen uses much of the carbon to produce sugars and amino acids for its own biosynthetic pathways. Enzymes of the glyoxylate pathway can be used as targets in the design of new antibiotics to treat tuberculosis.

 

DIF:        Difficult                REF:       13.6

OBJ:       13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples              MSC:                Evaluating CHAPTER 21: Microbial Ecology

 

MULTIPLE CHOICE

 

  1. The instrument shown in step 5 of the figure below is used for what metagenomics step?

 

  1. DNA isolation d.            cell lysis
  2. DNA sequencing e.            sequence assembly
  3. sample filtering

 

 

ANS:      B             DIF:        Medium               REF:       21.1

OBJ:       21.1c Outline the steps required to obtain metagenomic data

MSC:     Remembering

 

  1. The Dutch microbiologist van Niel first demonstrated anoxygenic photosynthesis in soil and water bacteria. He generalized his work by hypothesizing that
  2. every molecule in nature can be used as a source of nitrogen by some microorganism.
  3. photosynthesis results in oxygen production.
  4. microbes are found in every environment on Earth.
  5. microbes cannot live deep within Earth.
  6. photosynthesis occurs deep within Earth.

 

 

ANS:      C             DIF:        Easy       REF:       21.2

OBJ:       21.2c Restate van Niel’s two hypotheses of microbial ecology

MSC:     Remembering

 

  1. What does the following rarefaction curve NOT suggest about the samples?

 

  1. More soil sequences were collected.
  2. Indoor air samples appear to be sequenced at enough depth.
  3. Water samples were not sequenced at enough depth.
  4. More sequencing should be done for these samples.
  5. Soil samples were not sequenced at enough depth.

 

 

ANS:      A             DIF:        Difficult                REF:       21.1

OBJ:       21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC:     Analyzing

 

  1. Synechococcus, a cyanobacterium, is a free-living marine organism that fixes CO2 into biomass while producing molecular oxygen utilized by swarms of heterotrophic bacteria. Which of the following is the most likely habitat of this bacterium?
  2. euphotic zone of the pelagic environment
  3. the benthos
  4. the littoral zone
  5. lake sediments
  6. aphotic zone

 

 

ANS:      A             DIF:        Medium               REF:       21.5

OBJ:       21.5a Compare the properties of the distinct regions of the marine habitat | 21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC:     Evaluating

 

  1. The following image illustrates a syntrophic relationship between an archaeon and a bacterium. The technique used to generate this image was

 

  1. light microscopy. d.            fluorescence in situ hybridization.
  2. transmission electron microscopy. e.            atomic force microscopy.
  3. metagenomics.

 

 

ANS:      D             DIF:        Medium               REF:       21.1

OBJ:       21.1f Describe techniques that circumvent the limitations of metagenomic analysis

MSC:     Understanding

 

  1. The term “metagenome” was coined by Jo Handelsman and colleagues in 1998 to refer to
  2. shotgun cloning.
  3. screening of libraries for expression of genes.
  4. the DNA sequence obtained directly from a mixture of genomes.
  5. the DNA sequence taken directly from a colony.
  6. all uncultured organisms from a community.

 

 

ANS:      C             DIF:        Easy       REF:       21.1

OBJ:       21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC:     Remembering

 

  1. A rarefaction curve is the
  2. number of sequences generated from a metagenome.
  3. number of SSU rRNA sequences found in a metagenome.
  4. number of OTUs found as a function of increasing sample size.
  5. total number of OTUs from all combined genes in a metagenome.
  6. number of organisms in an environment.

 

 

ANS:      C             DIF:        Difficult                REF:       21.1

OBJ:       21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC:     Understanding

 

  1. What does functional annotation in metagenomic analysis involve?
  2. determining the number of species in the sample
  3. calculating the %GC in the metagenome
  4. finding homologs or recurring peptide motifs that infer the function of the sequence
  5. making contigs and scaffolds and assembling the sequence
  6. analyzing the RNA sequences to see what was transcribed

 

 

ANS:      C             DIF:        Medium               REF:       21.1

OBJ:       21.1e Compare the approaches used for functional annotation

MSC:     Remembering

 

  1. Which of the following is NOT true regarding food webs in ecosystems?
  2. Primary producers assimilate minerals into biomass.
  3. Primary producers absorb energy from outside the ecosystem.
  4. Grazers convert 10% of carbon back to carbon dioxide.
  5. Consumers convert 90% of biomass carbon to atmospheric CO2.
  6. All energy gained by an ecosystem is eventually lost as heat.

 

 

ANS:      C             DIF:        Difficult                REF:       21.2

OBJ:       21.2b Explain why all ecosystems require microbes | 21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2f Distinguish different levels of consumers

MSC:     Understanding

 

  1. The availability of oxygen and other electron acceptors is the most important determinant of the types of metabolism in a habitat. Which of the following is NOT true about anaerobic environments?
  2. They have slower rates of assimilation compared to aerobic habitats.
  3. Their rates of dissimilation are slower compared to aerobic environments.
  4. Microbes sometimes use minerals such as NO2- to oxidize organic compounds.
  5. Anaerobic microbial biomass far exceeds that of the oxygenated biosphere.
  6. Respiration of organic compounds is highly dissimilatory, reducing them to CO2.

 

 

ANS:      E              DIF:        Difficult                REF:       21.2

OBJ:       21.2h Describe the contributions of oxygen levels, pH, salinity, and temperature to metabolic processes                MSC:     Analyzing

 

  1. Culturing methods often detect organisms that may be rare in the environment but prevail when nutrients appear. What are these typically called?
  2. weed organisms d.            OTUs
  3. protists e. microbial dark matter
  4. rhizobia

 

 

ANS:      A             DIF:        Medium               REF:       21.1

OBJ:       21.1b Propose questions that can only be answered with a metagenomics approach

MSC:     Remembering

 

  1. Which of the following are the main consumers of biomass in the ocean?
  2. multicellular organisms d.            heterotrophic bacteria
  3. fish and tube worms e.            fungi
  4. protists and viruses

 

 

ANS:      C             DIF:        Difficult                REF:       21.2

OBJ:       21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2g Compare the importance of microbial producers and consumers to that of multicellular producers and consumers in both marine and terrestrial ecosystems

MSC:     Remembering

 

  1. The algal and fungal interaction within a lichen would best be described as
  2. mutualism. d.            amensalism.
  3. synergism. e.            parasitism.
  4. commensalism.

 

 

ANS:      A             DIF:        Easy       REF:       21.3

OBJ:       21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism | 21.3b Distinguish among mutualism, synergism, commensalism, amensalism, and parasitism                MSC:     Remembering

 

  1. Lichens consist of an intimate mutualistic symbiosis between a fungus, an alga, and/or cyanobacteria. What is one primary role of the cyanobacteria in this association?
  2. protection of the symbionts d.            recycling of waste products
  3. nitrogen fixation e.            degradation of lignin
  4. decomposition of toxic compounds

 

 

ANS:      B             DIF:        Medium               REF:       21.3

OBJ:       21.3c Identify the partners present in lichens      MSC:     Understanding

 

  1. Which step is NOT common for metagenomic processing and analysis?
  2. FISH d.            contig assembly
  3. binning e. scaffold assembly
  4. functional annotation

 

 

ANS:      A             DIF:        Medium               REF:       21.1

OBJ:       21.1c Outline the steps required to obtain metagenomic data | 21.1e Compare the approaches used for functional annotation          MSC:     Understanding

 

  1. The relationship among endosymbiotic microbes in the termite gut that results in complex metabolic fluxes with a negative G, which would NOT happen for individual members, is called
  2. mutualism. d.            predation.
  3. parasitism. e.            syntrophy.
  4. exothermic association.

 

 

ANS:      E              DIF:        Medium               REF:       21.4

OBJ:       21.4a Define holobiont and syntrophy | 21.4b Describe the organisms in and functions of the termite hindgut microbiome                        MSC:     Understanding

 

  1. Metatranscriptomics is the study of ________ obtained from an environmental community.
  2. lipids d.            DNA
  3. proteins e.            RNA
  4. organisms

 

 

ANS:      E              DIF:        Easy       REF:       21.1

OBJ:       21.1f Describe techniques that circumvent the limitations of metagenomic analysis

MSC:     Remembering

 

  1. The ________ is a set of conditions, including its habitat, resources, and relations with other species of the ecosystem, that enable an organism to grow and reproduce.
  2. benthos d.            metagenome
  3. environment e.            resource requirement
  4. niche

 

 

ANS:      C             DIF:        Easy       REF:       21.2

OBJ:       21.2a Define niche, biomass, and trophic levels  MSC:     Remembering

 

  1. In wetlands, Beggiatoa oxidize H2S for energy. Removal of H2S enables growth of other microbes for which H2S is toxic. However, Beggiatoa derives no benefit from these microbes. This interaction is an example of
  2. syntrophy. d.            amensalism.
  3. mutualism. e.            synergism.
  4. commensalism.

 

 

ANS:      C             DIF:        Medium               REF:       21.3

OBJ:       21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism | 21.3b Distinguish among mutualism, synergism, commensalism, amensalism, and parasitism                MSC:     Understanding

 

  1. The reactions on the right side of the following table occur only

 

  1. under thermophilic conditions. d.            under aerobic conditions.
  2. under anaerobic conditions. e.            in the euphotic zone.
  3. deep within Earth’s crust.

 

 

ANS:      B             DIF:        Easy       REF:       21.2

OBJ:       21.2h Describe the contributions of oxygen levels, pH, salinity, and temperature to metabolic processes                MSC:     Remembering

 

  1. Nonphotosynthetic ________ provide minerals and protection for lichen symbiotic partners.
  2. plankton d.            fungi
  3. proteobacteria e.            cyanobacteria
  4. algae

 

 

ANS:      D             DIF:        Easy       REF:       21.3

OBJ:       21.3c Identify the partners present in lichens      MSC:     Remembering

 

  1. Thousands of species of microbes in the cow ________ ferment and break down plant material to small particles.
  2. rumen d.            reticulum
  3. stomach e.            intestine
  4. omasum

 

 

ANS:      A             DIF:        Easy       REF:       21.4

OBJ:       21.4c Recall the names and functions of the four chambers of the rumen gut

MSC:     Remembering

 

  1. Which region of marine habitat refers to the microscopic interface between water and air?
  2. pelagic zone d.            aphotic zone
  3. neuston e.            benthic zone
  4. euphotic zone

 

 

ANS:      B             DIF:        Easy       REF:       21.5

OBJ:       21.5a Compare the properties of the distinct regions of the marine habitat

MSC:     Remembering

 

  1. The depth of the photic zone at the coastal shelf of marine habitats is
  2. 100–200 m. d.            about 0.1 m.
  3. 10–20 m. e.            about 2 m.
  4. about 1 m.

 

 

ANS:      C             DIF:        Medium               REF:       21.5

OBJ:       21.5a Compare the properties of the distinct regions of the marine habitat

MSC:     Understanding

 

  1. Animal intestinal microbiota typically yields ________, which the host animal can absorb and digest to completion through aerobic respiration.
  2. celluloses d.            polysaccharides
  3. CO2 e.            short-chain fatty acids
  4. oligosaccharides

 

 

ANS:      E              DIF:        Difficult                REF:       21.4

OBJ:       21.4d Compare and contrast the termite, cow, and human gut microbiomes

MSC:     Understanding

 

  1. Much of the microbial fermentation in humans occurs in the
  2. stomach. d.            small intestine.
  3. colon. e.            esophagus.
  4. rumen.

 

 

ANS:      B             DIF:        Medium               REF:       21.4

OBJ:       21.4e State some contributions of the commensal gut microbiome to human health

MSC:     Remembering

 

  1. A holobiont is defined as an
  2. organism that benefits while providing no benefit or a hidden benefit to its host.
  3. interaction that harms one partner nonspecifically without an intimate symbiosis.
  4. organism that forms an intimate relationship with another, where both benefit.
  5. entity composed of multiple types of organisms, including microbes.
  6. intimate relationship in which one member benefits while harming a host.

 

 

ANS:      D             DIF:        Difficult                REF:       21.4

OBJ:       21.4a Define holobiont and syntrophy                    MSC:     Understanding

 

  1. Which of the following plays an important role in keeping the water column clear enough for the penetration of light?
  2. algae d.            invertebrates
  3. bacteria e.            viruses
  4. fish

 

 

ANS:      E              DIF:        Difficult                REF:       21.5

OBJ:       21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC:     Remembering

 

  1. All of the following are likely to be found among the benthic microbes EXCEPT
  2. barophiles. d.            phototrophs.
  3. psychrophiles. e.            methanogens.
  4. thermophiles.

 

 

ANS:      D             DIF:        Medium               REF:       21.5

OBJ:       21.5a Compare the properties of the distinct regions of the marine habitat

MSC:     Analyzing

 

  1. The flame-like vertical forms and breakaway pieces of mat in ice-covered Antarctic lakes are caused by

 

  1. limited light penetration in the lake. d.            oxygen production.
  2. denitrification. e.            freeze-thaw cycles.
  3. sulfur-reducing bacteria.

 

 

ANS:      D             DIF:        Medium               REF:       Special Topic 21.1

OBJ:       21.5g Recall the properties of the different regions of freshwater habitats

MSC:     Understanding

 

  1. The ________ region of an oligotrophic lake extends to about 10 meters below the surface.
  2. neuston d.            hypolimnion
  3. benthic e. euphotic
  4. epilimnion

 

 

ANS:      C             DIF:        Medium               REF:       21.5

OBJ:       21.5g Recall the properties of the different regions of freshwater habitats

MSC:     Understanding

 

  1. Which of the following refers to the zone of a lake with higher relative oxygen concentrations?
  2. neuston d.            hypolimnion
  3. epilimnion e.            benthos
  4. thermocline

 

 

ANS:      B             DIF:        Easy       REF:       21.5

OBJ:       21.5g Recall the properties of the different regions of freshwater habitats

MSC:     Understanding

 

  1. Lakes that have dilute concentrations of nutrients are termed
  2. eutrophic. d.            oligotrophic.
  3. syntrophic. e.            atrophic.
  4. aphotic.

 

 

ANS:      D             DIF:        Easy       REF:       21.5

OBJ:       21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes                MSC:     Remembering

 

  1. Eutrophic lakes typically support ten times the microbial concentrations of an oligotrophic lake. Which of the following statements is NOT true of eutrophic lakes?
  2. Biochemical oxygen demand is high.
  3. Population of aquatic animals is high.
  4. Nitrogen and phosphorous levels are usually high.
  5. Photosynthetic activities are altered.
  6. Algal blooms are common.

 

 

ANS:      B             DIF:        Medium               REF:       21.5

OBJ:       21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC:     Understanding

 

  1. The high biological oxygen demand that accompanies algal bloom in eutrophic lakes increases the span of the ________ zone.
  2. oxygenic epilimnion d.            anoxic benthic
  3. anoxic hypolimnion e.            oxygenic neuston
  4. coastal shelf

 

 

ANS:      B             DIF:        Medium               REF:       21.5

OBJ:       21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC:     Understanding

 

  1. Compared to eutrophic lakes, the biochemical oxygen demand, or BOD, of oligotrophic lakes is
  2. low. d.            unpredictable.
  3. similar. e.            extremely high.
  4. high.

 

 

ANS:      A             DIF:        Medium               REF:       21.5

OBJ:       21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC:     Remembering

 

  1. A graduate student filtered a liter of seawater using a Millipore filter membrane of 2 m pore size. Her filtrate
  2. is sterile. d.            contains nanoplankton.
  3. contains microplankton. e.            contains all plankton.
  4. contains picoplankton.

 

 

ANS:      C             DIF:        Difficult                REF:       21.5

OBJ:       21.5e Contrast the different ways of measuring planktonic community population size

MSC:     Understanding

 

  1. Bacteria found growing in between crystals of solid bedrock as deep as 3 km below Earth’s surface are called
  2. endophytes. d.            decomposers.
  3. symbionts. e.            saprophytes.
  4. endoliths.

 

 

ANS:      C             DIF:        Medium               REF:       21.6

OBJ:       21.6b State the properties of the different soil horizons; include microbes typically found in each layer   MSC:                Remembering

 

  1. Which of the following is responsible for the characteristic odor of soil?
  2. Vibrio sp. d.            Staphylococcus sp.
  3. Bacillus sp. e.            Pseudomonas sp.
  4. Streptomyces sp.

 

 

ANS:      C             DIF:        Easy       REF:       21.6

OBJ:       21.6a Justify the importance of understanding the soil and plant microbial communities

MSC:     Remembering

 

  1. Which term represents the region of soil influenced by plant roots?

 

  1. stele d.            rhizoplane
  2. cortex e.            rhizosphere
  3. root cap

 

 

ANS:      E              DIF:        Easy       REF:       21.6

OBJ:       21.6c Outline the relationships in the soil food web          MSC:     Remembering

 

  1. Fungi play a much larger and more significant role in the decomposition of terrestrial biomass than they do in marine ecosystems. This is because fungi
  2. do not thrive in a marine environment.
  3. outcompete bacteria in terrestrial habitats.
  4. can degrade the abundant lignin in terrestrial habitats.
  5. decompose leghemoglobin rapidly.
  6. degrade human waste faster than bacteria.

 

 

ANS:      C             DIF:        Difficult                REF:       21.6

OBJ:       21.6c Outline the relationships in the soil food web | 21.6h Categorize different types of fungus–plant interactions                                MSC:     Understanding

 

  1. Lignin decomposition forms
  2. arbuscules. d.            humus.
  3. detritus. e.            rhizopus.
  4. fruiting bodies.

 

 

ANS:      D             DIF:        Easy       REF:       21.6

OBJ:       21.6c Outline the relationships in the soil food web          MSC:     Remembering

 

  1. Most forest trees require mycorrhizae for growth because
  2. forest soils are rich in phosphorous.
  3. mycorrhizae limit toxic metal uptake.
  4. the mycorrhizal form an ammensalic association.
  5. mycorrhizae significantly increase the uptake of nutrients.
  6. forest trees do not have deep roots.

 

 

ANS:      D             DIF:        Medium               REF:       21.6

OBJ:       21.6h Categorize different types of fungus–plant interactions

MSC:     Understanding

 

  1. Rhizosphere bacteria benefit their host plant by
  2. degrading plant lignin.
  3. attracting symbiotic nematodes.
  4. improving water uptake.
  5. producing large amounts of photosynthate.
  6. discouraging growth of plant pathogens.

 

 

ANS:      E              DIF:        Medium               REF:       21.6

OBJ:       21.6h Categorize different types of fungus–plant interactions

MSC:     Understanding

 

  1. Vascular abuscular mycorrhizae (VAM) are an example of which of the following?
  2. ectomycorrhizae d.            lignin decomposer
  3. endomycorrhizae e.            nitrogen fixer
  4. free-living fungus

 

 

ANS:      B             DIF:        Difficult                REF:       21.6

OBJ:       21.6d Compare and contrast ectomycorrhizae and endomycorrhizae

MSC:     Remembering

 

  1. One of the most important ecological roles of the Florida Everglades is that
  2. it is home to beautiful birds.
  3. it filters much of the water supply for Florida communities.
  4. many bacteria reside in it.
  5. nutrients can easily be leached to the lakes.
  6. tourists come to see it in large numbers.

 

 

ANS:      B             DIF:        Medium               REF:       21.6

OBJ:       21.6g Explain why wetlands are among the most productive ecosystems

MSC:     Understanding

 

  1. Which of the following organisms forms a specific mutualistic association with legumes?
  2. rhizobia d.            morels
  3. agrobacteria e.            Vibrio sp.
  4. E. coli

 

 

ANS:      A             DIF:        Easy       REF:       21.6

OBJ:       21.6e Recall the benefits endophytes provide to plants and how endophytes impact humans | 21.6f Summarize the colonization of legumes by rhizobia         MSC:     Remembering

 

  1. In the legume-rhizobium symbiosis, nitrogen fixation is carried out in nodules by
  2. bacteroids that lack a cell wall.
  3. intact rhizobia in the plant cortex.
  4. plant cells in the presence of symbiotic bacteria.
  5. bacteroids in oxygen-rich nodules.
  6. photosynthetic bacteroids in plants.

 

 

ANS:      A             DIF:        Medium               REF:       21.6

OBJ:       21.6e Recall the benefits endophytes provide to plants and how endophytes impact humans | 21.6f Summarize the colonization of legumes by rhizobia         MSC:     Remembering

 

  1. Bacteroids remain sequestered within a sac of plant-derived membrane known as the
  2. flavonoid. d.            nucleosome.
  3. infection thread. e.            symbiosome.
  4. Nod factor.

 

 

ANS:      E              DIF:        Easy       REF:       21.6

OBJ:       21.6f Summarize the colonization of legumes by rhizobia

MSC:     Remembering

 

  1. Which of the following require endosymbiotic protists and bacteria to digest plant material such as lignin and cellulose?
  2. termites d.            humans
  3. cattle e.            microplankton
  4. gorillas

 

 

ANS:      A             DIF:        Medium               REF:       21.4

OBJ:       21.4b Describe the organisms in and functions of the termite hindgut microbiome

MSC:     Remembering

 

SHORT ANSWER

 

  1. Explain at least three ways in which metagenomes may overlook organisms in the environment.

 

ANS:

Possible answers include the following: the sample was not sequenced enough to catch all the microbes in the environment and may miss the “rare biosphere.” The sample was not properly filtered or DNA extracted from all organisms in the sample. The PCR primers may not be general enough and may miss microbes with very divergent sequences.

 

DIF:        Medium               REF:       21.1

OBJ:       21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC:     Remembering

 

  1. What are the benefits and limitations of different environmental sequencing methods? Explain why ribosomal gene sequencing can be used as an initial screen.

 

ANS:

SSU rRNA gene sequence libraries generated with primers may miss microbes with 16S rRNA sequences very different than known microbes. An advantage of 16S rRNA amplicon sequencing is that we may quickly identify many taxa present in a community, including relatively rare members that do not yield full genomes when large-scale sequencing is performed. SSU rRNA gene similarity is used to define OTUs. Direct metagenome sequencing can identify those organisms not amplified with traditional SSU rRNA gene primers, but also sequences other genes than SSU rRNA. Metagenomes require large amounts of computational analysis and are typically much more expensive than targeted sequencing technologies.

 

DIF:        Difficult                REF:       21.1

OBJ:       21.1d Identify limitations of SSU rRNA sequencing and metagenomic analysis

MSC:     Understanding

 

  1. Describe the steps in sequencing a metagenome.

 

ANS:

You first sample the microbial target community and either separate it from its surroundings (in the case of terrestrial samples) or filter the sample (in the case of water samples) to only include the organisms of interest. You lyse the cells to extract the DNA and then clone the DNA fragments or amplify them by PCR. The DNA is then sequenced typically via next-generation sequencing such as Illumina. The sequences are then assembled and contigs can be analyzed by computational pipelines.

 

DIF:        Medium               REF:       21.1

OBJ:       21.1c Outline the steps required to obtain metagenomic data

MSC:     Understanding

 

  1. Explain the difference between assimilation and dissimilation.

 

ANS:

Assimilation refers to processes by which organisms acquire an element, such as carbon from CO2, to build into cells. Common kinds of assimilation include carbon dioxide fixation and nitrogen fixation. Dissimilation is the process of breaking down organic nutrients to inorganic minerals such as CO2 and NO2, usually through oxidation. Microbial dissimilation releases minerals for uptake by plants and other microbes, but microbial dissimilation can decrease habitat quality by removing organic nitrogen.

 

DIF:        Easy       REF:       21.2        OBJ:       21.2d Contrast assimilation and dissimilation

MSC:     Remembering

 

  1. Name two factors that differentiate aquatic and terrestrial ecosystems and explain how they affect food cycles in these systems.

 

ANS:

A major difference appears between marine and terrestrial ecosystems. In the oceans, the smallest inhabitants, phototrophic bacteria, perform most of the CO2 fixation and biomass production. The main consumers are protists and viruses. Viruses are the most numerous replicating forms in the ocean—and they lyse most marine cells before any multicellular predators get a chance to consume them. In terrestrial ecosystems, by contrast, the major primary producers and fixers of CO2 are multicellular plants. Plants generate detritus, discarded biomass such as leaves and stems, that requires decomposition by fungi and bacteria. While viruses are important, multicellular consumers such as worms and insects play a greater role in decomposition.

 

DIF:        Difficult                REF:       21.2

OBJ:       21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2f Distinguish different levels of consumers | 21.2g Compare the importance of microbial producers and consumers to that of multicellular producers and consumers in both marine and terrestrial ecosystems                                            MSC:     Analyzing

 

  1. How do microbes live if their metabolic process to generate energy has a positive G?

 

ANS:

They live in association with another organism in a relationship known as syntrophy, or “feeding together.” This typically happens when a product from the positive G is removed fast enough by another organism, resulting in a favorable reaction or a community-balanced negative G.

 

DIF:        Difficult                REF:       21.4        OBJ:       21.4a Define holobiont and syntrophy

MSC:     Evaluating

 

  1. Describe the interaction of Vibrio cholerae with copepods. How did sari cloth help decrease the incidence of cholera in Bangladesh?

 

ANS:

Vibrio cholerae is a mutualist on the surfaces of the small, invertebrate copepods. The copepods have come to rely on the bacteria to eat through the chitin of their egg cases to release their young. Anwar Huq found that if the Bangladesh people filtered their water through several layers of sari cloth, the incidence of cholera decreased.

 

DIF:        Medium               REF:       21.3

OBJ:       21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism            MSC:     Understanding

 

  1. How do metatranscriptomics and metaproteomics address functional limitations of metagenomics?

 

ANS:

Metatranscriptomics, the study of the RNA transcripts (or RNAseq) obtained from an environmental community, and metaproteomics, the study of proteins synthesized by environmental samples, both identify genes that are actually expressed by the target community. These techniques address a major limitation in metagenomics regarding the actual function of microbes in the environment.

 

DIF:        Medium               REF:       21.1

OBJ:       21.1d Identify limitations of SSU rRNA sequencing and metagenomic analysis | 21.1e Compare the approaches used for functional annotation             MSC:     Analyzing

 

  1. Propose a method to measure biomass production in terms of DNA synthesis. What are the limitations?

 

ANS:

The rate of DNA synthesis is determined by the uptake of 14C radiolabeled thymidine. A limitation is that addition of the radiolabeled substrate may raise a nutrient concentration to artificially high levels that distort the naturally occurring rates of activity. Another limitation is that not all growing cells incorporate exogenous thymidine into their DNA.

 

DIF:        Medium               REF:       21.5

OBJ:       21.5e Contrast the different ways of measuring planktonic community population size

MSC:     Evaluating

 

  1. Compare and contrast the photic zones of freshwater lake and pelagic ecosystems.

 

ANS:

The photic zone in the marine habitat is called the euphotic zone and is up to 200 meters deep except near the coastal shelf. In lakes, the epilimnion reaches only about 10 meters in depth, making it much shallower than the marine euphotic zone. Both regions are oligotrophic and contain a wide diversity of phototroph primary producers.

 

DIF:        Medium               REF:       21.5

OBJ:       21.5a Compare the properties of the distinct regions of the marine habitat | 21.5g Recall the properties of the different regions of freshwater habitats               MSC:     Understanding

 

  1. Explain how metagenomics and metatranscriptomics have been used to assess ocean diversity.

 

ANS:

A 2015 study led by Shinichi Sunagawa showed that the abundant Prochlorococcus and Synechococcus constitute only a small fraction of the microbes present. Abundant heterotrophs included Proteobacteria, many of which have proteorhodopsins for photoheterotrophy. Also abundant were the Thaumarchaeota, which oxidize ammonia released by fish and other organisms.

 

Metatranscriptomes were compared to those amplified from metagenomic DNA of the same microbial community. The most highly expressed genes included those encoding functional elements of photosynthesis, such as light-harvesting proteins and Rubisco. Genes for DNA repair were also highly expressed, presumably to correct UV damage in the open ocean. But the most highly expressed genes were some of the rarest in the metagenomes, and 40% of all expressed genes had no counterpart in the metagenome.

 

DIF:        Difficult                REF:       21.5

OBJ:       21.5d Evaluate the role of metagenomic approaches to understanding the marine microbial community                MSC:     Understanding

 

  1. The net biomass of a population does not indicate productivity within an ecosystem. Explain.

 

ANS:

At each trophic level above the producers, about 90% of biomass is consumed for energy generation. Biomass is a small fraction of productivity because it misses the amount of carbon cycled through respiration.

 

DIF:        Difficult                REF:       21.5

OBJ:       21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC:     Understanding

 

  1. Explain how viruses select for increased diversity of microbial plankton in the oceans.

 

ANS:

Recent studies indicate that cell lysis by viruses breaks down about half of microbial biomass. Virus particles represent a significant sink for carbon and nitrogen. They accelerate the return of minerals to producers and necessitate a larger base of producers to sustain the ecosystem. Some marine viruses are highly host specific, infecting only certain species of dinoflagellates or cyanobacteria. Their presence selects for diverse communities containing numerous scattered species. Other viruses attack many hosts—and they transfer genes from one host to another, such as the genes encoding photosystems. Thus, marine viruses are a dominant force determining community species distribution and genome content.

 

DIF:        Difficult                REF:       21.5

OBJ:       21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC:     Understanding

 

  1. Define BOD, and explain why it can be used to measure the pollution level of lakes. Describe how effluents carrying high levels of nutrients can cause eutrophication.

 

ANS:

BOD is an abbreviation for biochemical oxygen demand, which is the amount of oxygen removed from water by aerobic respiration. A eutrophic lake is one in which the upper layers have become depleted of oxygen as a consequence of an overgrowth of microbial producers. Problems arise when effluents entering a lake carry high concentrations of nutrients, relieving nitrogen limitation and causing an overgrowth of phototrophs. The cell mass of the phototrophs sinks to the bottom, where an overgrowth of heterotrophs then depletes oxygen.

 

DIF:        Medium               REF:       21.5

OBJ:       21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC:     Applying

 

  1. Explain how endoliths derive energy inside bedrock, where there is no sunlight.

 

ANS:

Endoliths are chemilithotrophs. It is believed that radioactive decay of uranium may be the energy source for these bacteria. Uranium-238 decay generates hydrogen radicals that combine to form hydrogen gas. The hydrogen gas combines with CO2 from carbonate rock, providing an electron donor and a carbon source for methanogens and other endolithic lithotrophs.

 

DIF:        Medium               REF:       21.6

OBJ:       21.6b State the properties of the different soil horizons; include microbes typically found in each layer   MSC:                Understanding

 

  1. Describe the initiation process for legume-rhizobium symbiosis.

 

ANS:

The legume exudes signaling molecules called flavonoids into its rhizosphere. The flavonoids are detected by rhizobial bacteria, which respond by chemotaxis, swimming toward the root surface. Flavonoids then induce bacterial expression of Nod factors. The bacterial Nod factor induces the root hair to curl around it and ultimately surround the bacterium with plant cell envelope. The bacterium then induces growth of a tube poking into the plant cell. As the tube grows, bacteria proliferate, forming a column of cells that projects down the tube.

 

DIF:        Medium               REF:       21.6

OBJ:       21.6f Summarize the colonization of legumes by rhizobia

MSC:     Remembering

 

  1. In any environment, pathogens are always outnumbered by a vast community of neutral or helpful microbes. Describe some beneficial as well as devastating incidences of plant pathogens.

 

ANS:

Answers may vary. A plant virus is associated with the production of striped tulips, which are much admired by tulip fanciers. Agrobacterium tumefaciens causes crown gall tumors on plants. It is applied widely for commercial plant engineering as a natural genetic transformation system. Ophiostoma novo-ulmi, a fungus carried by bark beetles, which bore into the xylem of elm trees, damaging the tree’s transport vessels and allow access for fungal spores.

 

DIF:        Difficult                REF:       21.6

OBJ:       21.6h Categorize different types of fungus–plant interactions

MSC:     Analyzing

 

  1. Describe the process of haustorial parasitism.

 

ANS:

Some fungal pathogens generate specialized structures to acquire nutrients from plants. A hypha grows across the plant’s epidermis, penetrating the cell wall and generating an ingrowth of a bulbous extension called a haustorium. The haustorium never penetrates the plant cell membrane, instead it causes the membrane to invaginate, while expanding into the volume of the plant cell. The haustorium takes up nutrients such as sucrose, generated by adjacent chloroplasts. Depending on the species of fungus, haustorial parasitism can lead to mild growth retardation, or it can rapidly kill the plant.

 

DIF:        Difficult                REF:       21.6

OBJ:       21.6h Categorize different types of fungus–plant interactions

MSC:     Understanding

 

  1. Describe the technique pioneered by Robert Hungate of the University of California at Davis to study anaerobic microbiology of the rumen. What types of questions can be answered with this technique?

 

ANS:

Robert Hungate pioneered the use of the fistulated, or cannulated, cow to study anaerobic microbes of the rumen. A fistulated cow is a cow in which an artificial connection is surgically made between the rumen and the animal’s exterior. Samples may be taken from the rumen to determine what types of microbes are present, and different foods can be put into the rumen to determine what changes occur.

 

DIF:        Easy       REF:       21.4

OBJ:       21.4c Recall the names and functions of the four chambers of the rumen gut

MSC:     Understanding

 

  1. What is coral bleaching? What is its possible cause?

 

ANS:

Coral bleaching occurs when coral zooxanthellae symbionts die or are expelled from the coral. The zooxanthellae are photosynthetic protists that are sensitive to climate change and pollution. Upon losing the endosymbionts, the coral turns white and soon dies, unless its symbionts return.

 

DIF:        Medium               REF:       21.3

OBJ:       21.3d Describe the relationship between corals and zooxanthellae

MSC:     Applying