BIMM120 Midterm #1

October 12, 2000

Matching: each answer (A-E) can be used more than once in a section.
However, for each question, there is just one correct answer.

(1-7) Match the component to the kind of cell it is found in:

1. Lipopolysaccharide (LPS)
2. In some species, a wall made of protein
3. Outer membrane
4. Thin layer of peptidoglycan
5. Thick layer of peptidoglycan
6. A nuclear membrane
7. Lipids containing ether linkages and isoprene

A. Gram positive bacteria

B. Gram negative bacteria
C. Archaea
D. Eukaryotes
E. All of the above

(8-10) Match the following adaptations to the environmental extreme they counteract:
8. A lipid monolayer
9. Accumulation of high concentrations of internal solutes
10. Increased proportion of saturated fatty acids
A. Low temperatures
B. Very high temperatures
C. High salt concentrations
D. High pH
E. Low salt concentrations

(11-14) Match the following cell features to the functions listed in A-E.
11. Pilus
12. Flagellum
13. Capsule
14. Outer membrane
15. Peptidoglycan
A. When present, provides an excellent permeability barrier for hydrophobic
molecules, such as penicillin and detergents
B. Allows binding to surfaces or other cells
C. Determines the shape of the bacterial cell
D. Allow cells to swim (i.e.: confers motility)
E. The site of DNA replication

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(16-20) Match the terms below with the definitions listed in A-E.

16. Sterilization
17. Decontamination
18. Disinfection
19. Germicide
20. Pasteurization
A. Reduction of pathogenic bacteria to a point where they pose no risk of infection.
B. Destruction of all microbial life.
C. A compound that kills microorganisms.
D. Physically removing microbes from an instrument or surface.
E. A compound that prevents microbial growth, but does not kill microbes.

(21-25) You are performing a growth curve on your favorite bacterium, so you start a
liquid culture and periodically measure cell number. You plot time versus cell
number (which is plotted on "log" paper), and obtain the following graph:

109

108 D
A C
107
B
106

time
Match the phase of growth indicated by the letters on the graph to the corresponding
description:

21. Exponential growth.

22. The synthesis of proteins required for survival in stationary phase starts here.
23. This phase reflects the time required for stationary phase (or "old") cells to resume
growth.
24. The rate of DNA and protein synthesis is highest during this phase of growth.
25. Toxic products of metabolism may have accumulated and completely inhibited
growth.

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(26-28) Imagine that you are a bacterium that has recently been ingested by a human,
and that your goal is to colonize (i.e.: grow in) the large intestine. Select a tool from
A-E that will help you surmount the obstacles listed in 26-28, and allow you to reach
your goal:

Obstacles:
26. The detergent-like bile salts found in the stomach, which could destroy your
cytoplasmic membrane.
27. Finding the wall of the large intestine from the lumenal contents (i.e.: the partially
digested food and your competitors).
28. Movement of intestinal contents out of the human (i.e.: How can you stay put, and
thereby avoid the sewage treatment plant? )

Tools:
A. A pilus
B. An internal vacuole for the storage of nitrate
C. A flagellum and chemotaxis machinery
D. An outer membrane
E. An S-layer

Multiple choice questions

Just one answer, more than one answer scored as incorrect.

29. Which feature listed below typifies binary fission in most bacteria?
A. The resulting daughter cells are unequal in size.
B. One cell divides in one cell cycle to produce four cells.
C. The daughter cells contain approximately equal amounts of each cell component.
D. The genome is not replicated until septum formation is completed.
E. All of the cell wall material of the new cell is newly synthesized.

30. Pasteurization might be used to treat:

A. Laboratory media for the growth of bacteria
B. Beer and wine
C. Spices
D. Meat
E. All of the above

31. For which of the following applications is it necessary to completely eliminate all
microbes during treatment?
A. Surgical instruments
B. Milk
C. Treatment of drinking water
D. All of the above
E. None of the above

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32. The drug penicillin induces lysis in bacterial cells because it interferes with:
A. Linking peptidoglycan precursors to the carrier lipid bactoprenol.
B. Polymerization of the glycan chain during peptidoglycan biogenesis.
C. The selective permeability of the cell membrane.
D. Transpeptidation reaction, which is essential for cross linking of peptidoglycan.
E. None of the above.

33. Which of the following is true of the peptide cross bridges in peptidoglycan:
A. They can include a variety of amino acids, including both D- and L-isomers.
B. They are formed after the glycan chains polymerize.
C. They are formed outside the cell.
D. They can occur via a third peptide.
E. All of the above

34. Which of the following is a true of complex culture medium, but not of chemically-
defined medium?
A. Used to make solid media, for growth of bacteria in petri dishes.
B. Used to make liquid media, for growth of bacteria in flasks or tubes.
C. Contains nutrients and minerals necessary for microbial growth.
D. Contains digests of tissues, such as yeast or beef extracts.
E. All of the above are true of both types of culture media.

35. On a visit to Yellowstone National Park, you isolate a photosynthetic organism from a
60°C hot spring that is pH 3.0. Which of the following phases describes its
metabolism and growth habits:
A. Lithotroph, psychrophile, acidophile
B. Phototroph, mesophile, basophile
C. Phototroph, xerophile, alkaliphile
D. Phototroph, thermophile, acidophile
E. Organotroph, thermophile, alkaliphile

36. Which of the following categories normally used for microbes best describes the
environmental preferences of most humans?
A. Alkaliphile
B. Psychrophile
C. Mesophile
D. Barophile
E. Hyperthermophile

37. Bacteria that are spiral in shape are known as:

A. Filamentous
B. Cocci
C. Rod-shaped or bacilli
D. Spirochetes
E. Budding bacteria

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38. Which of the following is not true of a facultative organism?
A. Can tolerate exposure to oxygen.
B. Can grow both anaerobically and aerobically.
C. Is rapidly killed when exposed to oxygen.
D. Contains enzymes to detoxify oxygen and its biological side-products.
E. Is able to grow both with and without oxygen.

39. The ability of the flagellar basal body to export proteins from the cytoplasm is used to:
A. Allow growth of the flagellar filament from the tip.
B. Allow growth of the flagellar filament from the base.
C. Ensure that flagellin is not made until after the basal body is complete.
D. (A) and (C)
E. (B) and (C)

40. During a run, the flagella on the same bacterium:

A. Each turn in a different direction
B. Coalesce into bundles
C. Expand and contract
D. Melt to become a single structure
E. Fly apart, appearing disordered

41. During a tumble, the flagella on the same bacterium:

A. Each turn in a different direction
B. Coalesce into bundles
C. Expand and contract
D. Melt to become a single structure
E. Fly apart, appearing disordered

42. Which of the following statements is not true of the sterilization of a liquid with heat?
A. A longer time is required if lower temperatures are used.
B. The death of microbes occurs at an exponential rate.
C. The D-time can be determined by removing samples at different times, and determining
the number of viable microbes present.
D. A longer time is required to sterilize water than to sterilize a solution with lots of protein
(like milk).
E. Growing cells are more sensitive to heat than spores.

43. A culture was inoculated with 100 bacteria. After 10 doublings, the number of bacteria was
about 100,000. After five more doublings, the figure nearest the true number would be (use
your fingers if needed):
A. 500,000
B. 3,200,000
C. 5,000,000
D. 10,000,000
E. 100,000,000

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44. Which of the following is not true of the bacterial cell cycle?
A. The chromosomes are well-separated prior to the onset of division.
B. Chromosome replication proceeds in both directions around the chromosome (i.e.:
it is bi-directional).
C. The chromosomal origin of replication move towards the cell poles well in advance
of division.
D. DNA polymerase moves around the stationary chromosome, like a train.
E. Cell division normally occurs in the middle of the cell.

45. Which of the following is true of the final step of the bacterial cell cycle, division (i.e.:
septation)?
A. Nuclear division is complete prior to the onset of septation.
B. The tubulin-like protein FtsZ forms a ring at the division site, directing the inward
growth of the septum.
C. During division, the membrane grows inward well in advance of the cell wall
(peptidoglycan).
D. Commences after disassembly of the spindle.
E. All of the above are true.

(46-47) Answer the following questions about the first paper, "A molecular view of
microbial diversity and the biosphere” (and the first two lectures).

46. Which of the following likely contributed to the failure of conventional morphological
and nutritional criteria to provide a coherent evolutionary picture of microbial life?
A. Most microbial species cannot be grown in the laboratory.
B. There are a limited number of different cell shapes by which prokaryotes may be
classified.
C. Gene transfer events involving metabolic genes.
D. All of the above
E. None of the above

47. In which of the following ways are Archaea most similar to the Eucarya (rather than
the Bacteria) ?
A. Both the Archaea and the Eucarya have similar metabolic capabilities and diversity.
B. Both the Archaea and the Eucarya have membrane-bound organelles.
C. The Archaea and Eucarya use similar proteins for transcription and DNA
replication.
D. Both are capable of housing symbionts within their cells.
E. Both the Archaea and the Eucarya have sterols in their cytoplasmic membrane.

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(48-50) Answer the following questions from paper #2: "Dense populations of a giant
sulfur bacterium in Namibian shelf sediments".

48. According to the paper, Thiomargarita namibiensis, means:

A. Thigh-inhabiting round bacteria from Namibia.
B. Sulfur-flavored margarita of Namibia.
C. Found that sulfur bacterium, let's have a margarita in Namibia.
D. Sulfur pearl of Namibia.
E. Sulfur bacterium discovered by Margaret in Namibia.

49. Which of the following statements best explains why Thiomargarita stores its electron
acceptor (nitrate) in an internal storage vacuole?
A. The extreme competition for nitrate in the environment.
B. The rapid destruction of its electron donor (H2S), when exposed to O2 in seawater.
C. It's electron donor (H2S) and acceptor (NO3) are not found in the same environment.
D. (A) and (C)
E. (B) and (C)

50. Which of the following is responsible for the milky white appearance of the cells?
A. The storage of nitrate in the internal vacuole.
B. The large size of the cells.
C. The accumulation of elemental sulfur in the cytoplasm.
D. The mucus sheath on the outside of the cell.

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 BIMM120 Midterm #2
✩✩✩✩ November 7, 2000 ✩✩✩✩
Matching: each answer (A-E) can be used more than once in a section.
However, for each question, there is just one correct answer.

(1-5) Cultures of different organotrophic bacteria were grown in the presence and
absence of oxygen. They were shown to have the following growth responses and to
produce the following waste products:

Ability to grow: Organic waste products:

Culture Aerobically Anaerobically Aerobically Anaerobically
1 + - CO2 none
2 - + None lactate
3 + + CO2 lactate
4 - ** None CO2

5 + ** CO2 CO2
**only in the presence of nitrate
Match the above cultures (#1-5) with their metabolic capabilities:
A. Anaerobic respiration.
B. Aerobic respiration.
C. Fermentation.
D. (A) and (B).
E. (B) and (C).

(6-8) Consider the following enzymes that are used for recombination between two DNA
molecules during genetic exchange in bacteria:
6. RecA
7. Transposase
8. Integrase
Which of the following statements best applies to these proteins?
A. Requires a specific, short DNA sequence on the donor DNA, but not on the
bacterial chromosome.
B. Requires a specific, short DNA sequence on the bacterial chromosome, but not on
the donor DNA.
C. Requires a specific, short DNA sequence on both the bacterial chromosome and the
donor DNA.
D. Requires large stretches of homologous (nearly identical) DNA on the chromosome
and the donor DNA
E. Does not require homology between the donor DNA and the chromosome, or a
specific recognition sequence.

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(9-11) After graduation, you accept a job at a biotech company involved in the discovery
of new antibiotics. You are given three experimental antibiotics to characterize, so you
decide to determine what affect each has on a growing culture of E. coli. You therefore
prepare four identical cultures of E. coli, and add the experimental antibiotics to three of
these cultures, while the fourth culture is your control (to which nothing is added). You
determine the number of viable cells in each culture before and two hours after adding
each antibiotic, by plating dilutions of the culture on solid medium lacking the drugs and
counting the number of colonies that form. You make the following observations:

Control culture: The number of viable cells continued to increase throughout the
experiment as the bacteria in the culture divided.

9. Drug #1: After two hours of treatment, the number of viable cells was lower than at
the start of the experiment.
10. Drug #2: The number of viable cells continued to increased throughout the
experiment at the same rate as the control culture.
11. Drug #3: The number of viable cells was the same before and after treatment, neither
increasing nor decreasing.

Match each drug with the phrase that best describes it:
A. Bacteriostatic
B. Bacteriocidal
C. Bacteriolytic
D. This drug could be either bacteriocidal or bacteriolytic.
E. This drug does not appear to inhibit growth or viability of E. coli.

(12-18) For each of the numbered items, choose the most appropriate description.
A. Transduction
B. Conjugation
C. Transformation
D. Point mutation
E. Insertion mutation
12. Change in a single DNA nucleotide (i.e.: base) within a gene.
13. Transfer of genetic material via a bacteriophage.
14. Transfer of genetic material via cell-to-cell contact.
15. Transfer of genetic material by the addition of purified DNA to a culture.
16. Addition of extra DNA within a gene.
17. Inhibited by DNase.
18. Often caused by transposons.

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Multiple choice questions
Just one answer, more than one answer scored as incorrect.

19. The aminoglycoside antibiotics, such as Streptomycin and Kanamycin, inhibit:

A. Peptidoglycan synthesis.
B. Transcription.
C. Translation.
D. DNA segregation.
E. Folic acid biosynthesis.

20. Which of the following statements best explains why penicillin is bacteriolytic?
(Note: more than one of these statements are true but only one explains why penicillin is
bacteriolytic!)
A. Penicillin inhibits cross-linking of newly-synthesized peptidoglycan, thereby
inhibiting growth.
B. Penicillin inhibits cross-linking of newly-synthesized peptidoglycan, thereby
causing lysis.
C. Penicillin inhibits peptidoglycan synthesis, thereby causing lysis.
D. Penicillin inhibits protein synthesis, thereby causing lysis.
E. Penicillin only kills growing bacteria.

21. Which of the following statements best explains the mechanism of action of
Vancomycin?
A. Vancomycin binds to transglycosylase, thereby preventing polymerization of
glycan chains in newly-synthesized peptidoglycan.
B. Vancomycin binds to N-acetylmuramic acid residues, thereby preventing
polymerization of glycan chains in newly-synthesized peptidoglycan.
C. Vancomycin binds to the Diaminopimelic Acid residues on the peptides in newly-
synthesized peptidoglycan, preventing transpeptidation.
D. Vancomycin binds to the D-Ala D-Ala residues on the peptides in newly-
synthesized peptidoglycan, preventing transpeptidation.
E. Vancomycin binds to the transpeptidase, preventing transpeptidation of newly-
synthesized peptidoglycan.

22. Which of the following is not used to maintain redox balance during fermentation?
A. Secretion of reduced inorganic waste products from the cell.
B. Secretion of reduced organic waste products from the cell.
C. Secretion of lactate from the cell.
D. Secretion of pyruvate from the cell.
E. Secretion of acetone from the cell.

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23. Which of the following statements are true of microbial fermentation reactions?
A. Fermentation reactions never generate a proton motive force (PMF), so some ATP is
always consumed to generate a PMF for other purposes.
B. Fermentation reactions must generate enough energy to make ATP by substrate-
level phosphorylation.
C. Fermentation reactions with an unfavorable (i.e.: positive) ∆Go’ cannot be used to
make energy.
D. All of the above statements are true.
E. None of the above statements are true.

24. The net result of the export of protons through the membrane during respiratory
reactions is:
A. Acidification of the cytoplasm.
B. Acidification of the outside of the cell.
C. Formation of OH- inside the cell.
D. Energization of the membrane.
E. (B), (C) and (D)

25. You have grown a microbe in a simple medium containing mineral salts, N2, H2, O2,
and CO2, in the dark. The energy yielding reaction is:
A. N2 + 3H2 à 2NH3
B. CO2 + 2 H2 à CH2O + H2O
C. 2 H2 + O2 à 2 H2O
D. N2 + H2 à 2NH
E. None of the above.

26. Two prokaryotic organisms that grow only together, coupling these two reactions:
Species #1: CH4 + H2O à CO2 + H2
Species #2: H2 + SO42- à H2S
are most precisely described as:
A. Lithotrophs
B. Methanotrophs
C. Phototrophs
D. Syntrophs
E. Symbiotrophs

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27. During the respiration of glucose, the citric acid cycle:
A. Catalyzes the complete oxidation of glucose to CO2.
B. Catalyzes the reduction of NAD+.
C. Synthesizes most of the ATP produced in respiratory reactions.
D. (A) and (B).
E. (A) and (C).

28. How is the reducing power necessary for carbon fixation and anabolic reactions
obtained by organisms engaged in lithotrophic metabolisms?
A. The proton motive force is used to drive the F1F0 ATPase backwards, to allow
NADH synthesis.
B. Reduced inorganic compounds and the proton motive force are used to generate
reverse electron flow through the electron transfer chain to NAD+.
C. Reduced inorganic compounds are used to "directly" reduce NAD+ (via specific
enzymes, of course!).
D. (A) and (C).
E. (B) and (C).

29. Which of the following is true of the role of H2O in oxygenic photosynthesis?
A. Early in oxygenic photosynthesis, H2O is split (into O2 and H+), allowing electrons
to flow through the photosynthetic electron transport chain.
B. H2O is split (into O2 and H+) in the final step of oxygenic photosynthesis.
C. The reducing potential of H2O is used to generate a reverse electron flow to
produce NADH.
D. Oxygenic phototrophs require a second, more highly reduced molecule, to produce
NADH.
E. None of the above statements are true.

30. Oxygenic photosynthesis occurs in:

A. The purple bacteria.
B. Plants.
C. Cyanobacteria.
D. (A) and (B).
E. (B) and (C).

31. Which of the following is necessary for carbon fixation?

A. Lots of NADH
B. Lots of NAD+
C. Lots of ATP
D. (A) and (C)
E. (B) and (C)

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32. Nitrate reduction (during anaerobic respiration) is beneficial during waste water
treatment because:
A. Nitrate reduction removes ammonia (NH3), which is toxic to many fish, from the
water.
B. Nitrate is toxic to humans, and nitrate reduction reduces its concentration to safe
levels.
C. Nitrate reduction removes available nitrogen from the water, decreasing the growth
of algae.
D. Nitrate reduction does not occur during anaerobic respiration!
E. Nitrate reduction is never beneficial!

33. An integron and/or the gene cassettes that insert into them will always have each of
these features, except:
A. A specific recombination site on the chromosome, for integration of gene cassettes.
B. A specific recombination site on the gene cassettes, for integration into the
chromosome.
C. A promoter to allow expression of genes on the cassettes.
D. A gene encoding integrase, to allow integration of the gene cassettes into the
chromosome.
E. DNA replication signals (an origin of replication), to allow replication of the gene
cassettes.

34. All of the following statements about plasmids are true, except:
A. Plasmids may be either linear or circular DNA molecules.
B. Plasmids are capable of independent replication.
C. Plasmids are extrachromosomal elements into which additional DNA may be
inserted.
D. Some plasmids can integrate into the chromosome, and then transfer almost the
entire bacterial chromosome during conjugation.
E. All of the above statements are true.

35. All of the following must occur for an F- cell to become F+ during a mating, except:
A. Transfer of the entire F plasmid.
B. Integration of the F plasmid onto the chromosome.
C. Contact between the mating pair must be initiated by the sex pilus.
D. All of the above must occur.
E. None of the above need to occur!

36. A genetic selection is different from a genetic screen because:

A. In a genetic screen, the desired mutation arises at a lower frequency than in a
genetic selection.
B. In a genetic selection, all of the bacteria are killed except those having the desired
mutation, whereas in a genetic screen, one has to devise a method to sort through
all of the mutants to identify the desired mutation.
C. In a genetic selection, transposons that encode resistance to antibiotics are used,
allowing a higher frequency of mutation.
D. (A) and (B).
E. (B) and (C).

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37. Which of the following statements are true of competence?
A. Most bacterial species are naturally competent.
B. Bacteria that are naturally competent are capable of transformation at any phase of
growth.
C. The transformation of recombinant plasmids into E. coli is an example of natural
competence.
D. Natural competence requires a nuclease, which shortens the DNA fragments to
about 10 kb (10,000 bases).
E. Natural competence is induced by treatments such as exposing the cells to CaCl2 on
ice.

38. Insertion sequences:

A. Can cause spontaneous mutations by inserting into genes.
B. Can facilitate the integration of F plasmid into the chromosome to make an HFr.
C. Can facilitate the imprecise excision of an HFr from the chromosome to make an F'
plasmid.
D. Can form a composite transposon when two identical insertion sequences flank
some useful gene.
E. All of the above.

39. Bacterial conjugation :

A. Requires genes encoded by accessory genetic elements.
B. Can be encoded by transposons, as well as plasmids.
C. Can be used to transfer DNA to Eukaryotic cells.
D. All of the above are true.
E. None of the above are true.

40. Which of the following statements are true of generalized transduction :

A. Exchange is mediated by temperate (lysogenic) phage.
B. The bacterial genes are picked up by the phage when it excises imprecisely from the
bacterial chromosome.
C. The bacterial genes transferred are part of every phage genome.
D. Exchange is mediated by virulent (lytic) phage.
E. Exchange is mediated by phage that only reproduce (i.e.: produce phage particles)
when an infected bacterial cell is stressed.

41. Salmonella bacteria are capable of switching between the H1 and H2 flagellins at a
high frequency, by a process known as phase variation. Which of the following
statements are not true of the switch from H1 production to H2 production?
A. Phase variation helps the bacteria avoid the immune system during an infection.
B. Phase variation requires a protein (H1 repressor) that inhibits synthesis of H1.
C. Phase variation requires the action of a site-specific recombinase known as H-
invertase.
D. Phase variation involves inversion of the gene encoding H1, so that the H1
promoter transcribes an "anti-sense" H1 mRNA that does not encode H1 flagellin.
E. Phase variation involves inverting the promoter for H2, so that it transcribes away
from the H2 gene (such that no H2 mRNA is made).

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42. Imagine two bacterial cultures separated by a filter that allows the passage of
anything smaller than the bacteria themselves. Which of the following will be impaired by
this arrangement:
A. Mutation in either culture.
B. Transformation.
C. Conjugation.
D. Transduction.
E. Replication of plasmids.

43. Which of the following statements is true of bacterial genetics, but not eukaryotic
genetics?
A. Genetic exchange in bacteria represents an equal mixing of parental chromosomes.
B. In bacteria, genetic exchange usually involves the exchange of segments of DNA,
not of entire chromosomes.
C. In bacteria, genetic exchange is always unequal, with one cell receiving genetic
information from another.
D. (A) and (B).
E. (B) and (C).

Answer the following questions about paper #1: “A molecular view of microbial
diversity.." Pace, Science 276:734-739.

44. The Bacteria and Archaea from the most ancient lineages (i.e.: those most closely
related to the progenote) are thermophilic and share what type of metabolism?
A. Oxygenic photosynthesis.
B. Anoxygenic photosynthesis.
C. Organotrophy.
D. Lithotrophy.
E. Heterotrophy.

45. The communities of Bacteria and Archaea that can be found several kilometers
beneath the earth's crust must depend on which of the following metabolic types for their
productivity:
A. Phototrophy and autotrophy.
B. Heterotrophy.
C. Organotrophy.
D. Lithotrophy and autotrophy.
E. Lithotrophy and heterotrophy.

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Answer the following questions about paper #4: “A role for excreted quinones…..”
Newman and Kolter, Nature 405:94-97.

46. It is unclear how bacteria are able to use insoluble electron acceptors (such as Fe3+
compounds) for respiratory reactions. What mechanisms do the authors propose to
explain this ability?
A. The release of NADH from the cell.
B. The release of a menaquinone-related redox-active molecule from the cell.
C. The export of free protons from the cell.
D. The export of free electrons from the cell.
E. None of the above.

47. In Figure 2, the authors demonstrate that the wild type bacteria can produce a
compound that diffuses through the medium and allows the menC mutants to reduce the
humic acid analogue AQDS. What are the possible explanations for this observation?
A. The wild type releases a diffusible electron carrier that the menC mutants can use,
but not make themselves.
B. The wild type releases an intermediate in the biogenesis of a diffusible electron
carrier that the menC mutants cannot make themselves, but which they can convert
to the mature electron carrier.
C. Either (A) or (B) are possible explanations.
D. None of the above are possible.

Answer the following questions about paper #5: “A bacteriophage encoding a

pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria” Karaolis et
al., Nature 399:375-379.

48. The authors made use of a strain of Vibrio cholerae that contained the CTX phage
(which encodes cholera toxin), but which did not have VPI (which encodes pilin). Which
of the following statements describes the most likely origin of this strain?
A. The strain initially lacked both phage (and was therefore non-pathogenic), then
obtained CTX phage, and now needs only VPI phage in order to be fully
pathogenic.
B. The strain must have once had both CTX phage and VPI phage, but has since lost
the VPI phage.
C. The strain must have obtained point mutations in VPI which prevented phage
production.
D. None of the above provides a likely explanation for the origin of this strain.

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49. Which of the following observations led the authors to propose that VPI might be a
phage, and therefore to initiate the experiments described in the paper?
A. They observed that some genes on VPI encoded proteins similar to phage and viral
proteins.
B. They observed transfer of the pilin genes on VPI to a new strain of Vibrio cholerae in
an infected human.
C. They knew that cholera toxin was also encoded on a phage.
D. (A) and (B).
E. (A) and (C).

50. Following their demonstration of filamentous particles in the culture supernatant that
bound TcpA antibodies (by immunoelectron microscopy), the authors performed an
experiment to demonstrate that VPI DNA and pilin (TcpA) were in the same particle, and
therefore, that the VPI phage capsid contained pilin. Which of the following experiments
did they perform to allow this conclusion?
A. They showed that VPI DNA encoded pilin.
B. They purified VPI DNA, and then showed that the pilin protein (TcpA) was present
in the DNA preparations (i.e.: the pilin co-purified with the DNA).
C. They purified the pilin protein (TcpA), then showed that VPI DNA was also
purified (i.e.: the DNA co-purified with the pilin).
D. All of the above experiments were performed in order to demonstrate that the
phage particle contained pilin.
E. None of the above experiments were performed.

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 BIMM120 final exam
December, 2000
True (A) or False (B)?
1. In a single genetic exchange event, bacteria can become resistant to several antibiotics.
2. Food that has been pasteurized is sterile.
3. Archaeal transcription, translation and DNA replication is more similar to that of the
Eukarya than that of Bacteria.

4. Organotrophy is likely to have been the first type of metabolism on earth.

5. Catabolism is the type of metabolism that involves using various chemicals to produce
energy.

6. The energy used by bacterial flagella during chemotaxis comes from ATP.
7. Hyperthermophiles can grow in frozen lakes.
8. Precursors of peptidoglycan are synthesized within the cell and transported to the
outside of the cell.

9. Gram-positive bacteria have outer membranes surrounding their cell walls.

10. Glycine is the only amino acid that makes crosslinks (or bridges) in bacterial cell walls.
11. Bacterial endospores, such as those from the genus Bacillus, can survive boiling
temperatures and are highly resistant to chemical disinfectants.

12. The enzyme transposase mediates the insertion of transposons into a specific site in the
bacterial chromosome (the attachment site).

13. The enzyme RecA is required for HFr mediated genetic exchange.
14. Type III secretion is a device used by some pathogenic bacteria to introduce proteins
into host cells.

15. Unlike Type III secretion, flagellar synthesis does NOT depend on the removal of a
protein that inhibits the expression of genes encoding the relevant proteins.

16. Pili are seldom involved in the adhesion of bacteria to animal cells.
17. The symptoms of some diseases, such as cholera, can be induced by giving purified
exotoxin to volunteers.

18. The walls of Archaea can be made of pseudopeptidoglycan or protein.

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19. All prokaryotic organisms have a cell wall.
20. Rhizobium bacteriods are strict anaerobes, and die rapidly when exposed to oxygen.
21. The purpose of decontamination efforts is to sterilize the object or surface under
question.

22. Some bacteria form multicellular aggregates that can either form hunting swarms or
develop into fruiting bodies.

23. Multicellular development is limited to the Eukarya.

24. Insertion sequences do not encode the enzyme transposase.
25. In generalized transduction, virtually any gene can be transferred from a donor to a
recipient.

26. In some symbiotic relationships, the symbiont is transmitted vertically (from parent to
offspring).

Matching: each answer can be used more than once in a section. However,
for each question, there is just one correct answer.

(27-33) Match the cell component listed in 27-33 to the type of Bacterial cell (A-D) in
which it is likely to be found:
A. Gram positive bacteria
B. Gram negative bacteria
C. Both
D. Neither
27. Lipid A
28. Thin layer of peptidoglycan
29. Thick layer of peptidoglycan
30. O-specific polysaccharides
31. Cytoplasmic membrane
32. Lipids containing ether linkages
33. Porins (channels that allow passage of molecules below a certain size limit across a
membrane)

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(34-37) Match the steps in pathogenesis listed in 34-37 with the bacterial factors listed in
A-D that mediate each step.
A. Injected proteins that cause a transient rearrangement of the host cytoskeleton.
B. Injected proteins that induce apoptosis (death) of macrophages.
C. Chelators that scavenge iron for the bacterium.
D. Leghemoglobin.
E. Pili.
34. Binding to the host cell surface.
35. Entry into the host cell.
36. Multiplication within the host.
37. Avoiding the host immune response.

(38-41) Match the statements in 38-41 to A-D.

A. Exotoxins
B. Endotoxins
C. Both
D. Neither
38. Soluble proteins
39. Non-antigenic
40. Made only by Gram negative bacteria
41. Responsible for some of the most evident manifestations of infection

(42-47) Match the statements in 42-47 to A-D.

A. The actinomycetes (i.e.: Streptomyces species)
B. The endospore-forming bacteria (i.e.: Bacillus and Clostridium species)
C. The budding bacteria (i.e.: Caulobacter sp.)
D. Species of Rhizobium, Sinorhizobium, and Bradyrhizobium
42. Their cells are often unusually shaped, with cytoplasmic extensions known as stalks
or prosthecea.
43. Cell division is required only during spore formation, but not during vegetative
growth.
44. During their development, one bacterial cell engulfs a second bacterial cell, in a
process similar to eukaryotic phagocytosis.
45. Their developmental pathway requires the production of surfactants to allow the
developing cells to rise from the substrate.
46. Their developmental pathway is cell-cycle dependent and essential.
47. Their developmental pathway results in the formation of spores that are not
particularly resistant to UV light or disinfectants, and whose primary purpose is
dispersal.

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Multiple choice questions: Just one answer, more than one
answer scored as incorrect.

48. Identification of the three domains of life (Bacteria, Archaea and Eukarya) has
primarily resulted from:
A. Advanced methods of morphological examination (i.e.: better microscopes).
B. Analysis of the preferred environments of various organisms.
C. Analysis of metabolic pathways
D. Sequencing of genes encoding metabolic enzymes.
E. Sequencing of ribosomal RNA genes.

49. Functions of the cell wall include:

A. Creating a permeability barrier
B. Providing energy using the proton motive force
C. Preventing osmotic lysis
D. Anchoring pili to the cell surface
E. All of the above

50. You need to know how much time at high temperatures is required to kill a particular
bacterial species. If you were to compare the time required to kill 90% of the bacteria at
75°C and 65°, which of the following results would you expect?
A. Less time would be required at 65°C.
B. More time would be required at 65°C.
C. The same time would be required at 65°C.
D. Impossible to tell.

51. Similarities between nitrogen fixation and carbon fixation include:

A. Both require lots of ATP.
B. Both require lots of reducing potential (directly, rather than simply to make ATP).
C. Both are sensitive to Oxygen.
D. (A) and (B)
E. (B) and (C)
Any answer OK (question discarded)

52. Autotrophs use which of the following to make ATP?

A. Reduced inorganic compounds (such as H2)
B. Reduced organic compounds (such as carbohydrates)
C. Light
D. A and B are correct
E. A and C are correct

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53. Which of the following can occur in the absence of oxygen?
A. Fermentation reactions
B. Anaerobic respiration
C. Anoxygenic photosynthesis
D. Carbon Fixation
E. All of the above.

54. Which of the following statements is false?

A. The flagellum is inefficient, and lots of energy is lost as heat, rather than being
converted to movement.
B. Flagella can rotate in both directions.
C. The basal body acts as a channel for the export of flagellin.
D. The basal body acts as a motor to spin the flagellum.
E. Flagellin is the protein that assembles into the long flagellar filament.

55. In the bacterial world, a gene located on which of the following would be the least
likely to be transferred during genetic exchange?
A. The chromosome.
B. A lysogenic phage.
C. A conjugative transposon.
D. An F’ or R plasmid.

56. Which of the following is true?

A. Symbiotic relationships are never species-specific.
B. Some symbiotic relationships involve the invasion of host cells by the symbiont.
C. The symbiont and the host cell are never capable of independent growth (i.e.:
growth without their partner).
D. None of the above statements are true (all are false).

57. In the symbiotic relationship between Rhizobium and legumous plants, nitrogen is
fixed in the:
A. Infection tube
B. Root hair
C. Bacteroid
D. Growing bacterial cells
E. Plant leaves

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58. Which of the following is involved in species specificity in the relationship between
Rhizobium and legumes?
A. Only the correct species of Rhizobium is able to bind the root hair surface.
B. The bacterium makes Nodulation factors that are recognized only by the correct
species of plant.
C. The plant secretes specific compounds (flavanoids) that are recognized only by the
correct species of Rhizobium.
D. (A) and (B)
E. (B) and (C)

59. Consider the following statements about the metabolic exchanges between Rhizobium
and legumous plants in the root nodule:
(1) The plant provides fixed nitrogen (in the form of amino acids) to Rhizobium.
(2) The plant provides fixed carbon (in the form of organic acids/citric acid cycle
intermediates) to Rhizobium.
(3) The plant provides fixed carbon (in the form of glucose) to Rhizobium.
(4) Rhizobium provides fixed carbon (in the form of organic acids/citric acid cycle
intermediates) to the plant.
(5) Rhizobium provides fixed nitrogen (in the form of ammonia) to the plant.

Which two statements most accurately describes this relationship?

A. (1) and (4)
B. (2) and (4)
C. (2) and (5)
D. (3) and (4)
E. (3) and (5)

60. All of the following require site-specific, element-encoded recombination enzymes,

except:
A. Genetic exchange following conjugation between closely related HFr and F- strains.
B. Integration of a lysogenic phage into the attachment site on the bacterial
chromosome (attB).
C. Integration of new gene cassettes into an integron.
D. Transposition of an insertion sequence from one chromosomal site to another.
E. Phase variation of Salmonella flagella.

61. You have isolated an organism from a marine environment, and found that it requires
a saline environment for growth. The organism is called a:
A. Xerophile
B. Halophile
C. Psychrophile
D. Barophile
E. Thermophile

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62. One defining characteristic of the cyanobacteria is:
A. They are the only kingdom of bacteria capable of anoxygenic photosynthesis.
B. They are the only kingdom of bacteria capable of oxygenic photosynthesis.
C. They are the only kingdom of bacteria that can fix nitrogen.
D. They are the only kingdom of bacteria that can fix carbon.
E. They are the only kingdom of bacteria with an outer membrane.

63. A cell component used by bacteria to attach to non-living surfaces is:

A. Lipopolysaccharide
B. Exopolysaccharide
C. Peptidoglycan
D. Injectisome
E. Flagellum

64. What cell surface structure is used both during biofilm formation to allow the
monolayer of cells to aggregate to form a microcolony, and during fruiting body
formation to allow aggregation of the cells?
A. The flagellum
B. The type III protein export apparatus (the injectisome)
C. A specific type of pilus
D. The exopolysaccharide
E. None of the above

65. Which of the following accounts for the difficulty in treating certain bacterial
infections in which the bacteria are in a biofilm?
A. Some bacteria are not growing, and so are resistant to certain antibiotics
B. The biofilm releases motile cells that can colonize distant parts of the body.
C. The exopolysaccharide layer protects the cells from the host immune system.
D. (A) and (C)
E. None of the above, such infections are easily treated.

66. Listeria makes an enzyme, LISTERIOLYSIN, that when purified is capable of forming
pores in (and lysing) any membrane. During an infection, the enzyme is involved in the
passage of Listeria from the phagocytic vacuole into the cytoplasm of infected cells, where
the organisms grow. Listeriolysin has 27 amino acids at one end that targets the enzyme
for degradation by proteases. Which of the following makes the most sense in this
context?
A. Listeriolysin synthesized by intracellular bacteria makes pores in both the
membrane of the phagocytic vacuole and the plasma membrane.
B. Listeriolysin synthesized by intracellular bacteria makes pores in the
host’s plasma membrane, but not in the phagocytic vacuole.
C. Listeriolysin is degraded within the phagocytic vacuole.
D. Listeriolysin is degraded in the cytoplasm to prevent damage to the host cell.
E. Listeriolysin is degraded outside the host cell to prevent damage to surrounding
cells.

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67. All the listed mechanisms are used by pathogenic microorganism to directly protect
themselves from the host's ANTIBODY RESPONSE EXCEPT:
A. Antigenic variation
B. Intracellular existence
C. Immunosuppression
D. Making capsules
E. Making proteases that cleave antibodies

68. Properties of bacterial pili include:

A. Acting as adhesins
B. Killing neutrophils
C. Both
D. Neither

69. Which statements about BACTERIAL LIPOPOLYSACCHARIDES (LPS) is correct:

A. They are more toxic on a weight basis than exotoxins
B. They can be inactivated by proteolytic enzymes
C. They are part of the bacterial cytoplasm
D. They do not act as immunostimulants
E. They are antigenic

70. The best defense of the body against BACTERIAL EXOTOXINs:

A. Activated macrophages
B. Antibodies
C. Helper T cells
D. Complement activation
E. Lysozyme

71. In a person completely lacking the complement system (due to a genetic defect):
A. Antibodies do not effectively neutralize toxins.
B. If phagocytized by phagocytes, sensitive bacterial will not be killed.
C. Bacteria will not be taken up effectively by phagocytes.
D. Antibodies will not circulate in the blood.
E. The most common infections will be due to typically intracellular bacteria.

72. As opposed to non-encapsulated bacteria, bacteria with capsules are usually endowed with:
A. Lower virulence
B. Greater motility
C. Lesser resistance to antibiotics
D. Greater resistance to phagocytosis
E. Greater ability to make exotoxin

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73. The most likely reason why there is no successful vaccine for gonorrhea at present is:
A. Most gonococcal proteins are poorly antigenic.
B. The gonococcus does not come in contact with the immune system during infection.
C. Patients with gonorrhea are usually immunosuppressed, thus cannot make
antibodies effectively.
D. One of the most promising antigens for a vaccine, the pilus protein, can undergo
rapid molecular rearrangements that result in antigenic variation

74. The reason why gonococcal pilin (the main proteins of pili) changes into a huge
number of antigenic type:
A. The number of genes for pilin is the same as that of possible antigenic types.
B. Extensive recombination can take place between the expressed pilin gene, and the
silent (unexpressed) pilin genes.
C. Each gene for pilin has its own promoter.
D. The pilin protein is intrinsically unstable and can change its amino acid. sequence
when exposed to specific antibodies.

75. The following are valid reasons for wanting to test all possible sexual contacts of a
gonorrhea patient EXCEPT:
A. Gonococci are hard to grow in the laboratory, thus the test is unreliable
B. Asymptomatic patients can transmit the gonococcus to partners.
C. Females contacts are at risk of pelvic inflammatory disease and ectopic pregnancy.
D. Many people with gonococcal infection show no symptoms.

76. Which is the WRONG answer?

All by itself, the activation of complement results in the formation of....:
A. Opsonins (proteins that facilitate phagocytosis)
B. Chemotaxins (proteins that recruit phagocytes)
C. Antibodies
D. The membrane attack complex (proteins that make pores in membranes)
E. Anaphylatoxins (compounds that promote the enlargement of blood vessels,
leading to lowering of blood pressure)

77. Which of the following statements is CORRECT?

A. The innate defenses of the body help the establishment of the induced defenses.
B. The induced defenses are always activated to their full potential.
C. Each species of pathogenic bacteria must overcome a different and specific set of
innate defenses in order to cause disease.
D. The induced defenses of the body are made up of soluble proteins only.
E. The innate defenses of the body are made up of soluble proteins only.

78. Ways that pathogenic microbes avoid the INNATE responses of the human body
include:
A. Superantigens (inducers of non-specific antibodies)
B. Proteins that cleave (i.e.: degrade) or inhibit chemotaxins

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 C. Proteases that cleave antibodies
D. Antigenic variation
E. Inhibitors of cell-mediated immunity

79. Which of the following characteristics of development are found in

the Eukarya, but not the Bacteria?
A. Multicellular development.
B. Development that is induced in response to environmental signals.
C. The production of terminally differentiated cell types, that cannot resume
growth.
D. All of the above features are limited to the Eukarya.
E. None of the above features are limited to the Eukarya.

Answer the following questions about Paper #6: "Supramolecular structure of the
Salmonella typhimurium Type III protein secretion system", Science 280:602-605.

80. Why did the authors use a mutant of Salmonella typhimurium that lacked the ability to
assemble flagellar basal bodies in their experiments?
A. Because it would have been difficult for them to perform experiments on motile
bacteria.
B. Because they needed to prevent the export of flagellin from the flagellar basal body.
C. Because the flagellar basal body would have been labeled with their antibodies to
the Type III export system in their immunoelectron microscopy experiments.
D. Because they wanted to be certain that any structures visualized on the cell surface
(by electron microscopy) were related to the Type III export system, and were not
simply flagellar basal bodies.

81. Which of the following statements is true of the needles assembled by the Type III
secretion system?
A. The needles span only the cytoplasmic (inner) membrane, and allow export of
proteins from the cytoplasm to the periplasm.
B. The needles span the bacterial outer membrane, and allow export of proteins from
the periplasm to the outside of the bacterial cell and into a host cell.
C. The needles span both bacterial membranes (the cytoplasmic and outer
membranes), allowing export of proteins from the cytoplasm to the outside of the
cell and into a host cell.
D. None of the above.

Page 27
(82-84) Answer the following questions about Paper #7: "Fungus growing ants use...",
Nature 398:701-704.

82. Attine ants have a complex symbiotic relationship that involves a fungus and a
bacterium from the genus ________.
A. Mycoplasma
B. Bacillus
C. Streptomyces
D. (A) and (B)
E. (B) and (C)

83. The symbiotic bacteria associated with the fungus-growing ants is transmitted
_________ to new ant colonies, and is found ___________ the ant cells.
A. vertically, outside
B. vertically, inside
C. horizontally, outside
D. horizontally, inside

84. The authors found that the bacterial symbiont produced one or more compounds
that:
A. inhibits the growth of all fungi tested, except for that grown in the fungal gardens
(i.e.: the fungal mutualist).
B. inhibits the growth of fungal parasites from the genus Escovopsis, but does not
inhibit the growth of most other fungi.
C. inhibits the growth of all bacteria, except for the bacterial symbiont itself.
D. promotes the growth of the bacterial symbiont.

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