2023-2024 Rickards Invitational

Microbe Mission C Exam

Student names:_____________________________________________________
School:____________________________________________________________
Team #:____

This test is sponsored by:

MONTICELLO DENTISTRY
Microbe Mission C - Microbe Mission C - Rickards Invitational Div. C SATELLITE - 11-04-2023

Instructions
Welcome to Microbe Mission C! Here are the rules:

● You have 50 minutes to take this test

● This test includes States and Nationals topics
● Only one double-sided (printed) 8.5" x 11" note sheet permitted per team, and an
acceptable calculator per participant
● Out-of-browser time will be monitored (tiered if OOB time >30 sec)

Event Supervisors: Melody Hong (Gen. Douglas MacArthur HS '25), Jad Yehia (Castro Valley HS
'24)

If you have any questions pertaining to the event/test, email us at [email protected] and
[email protected] or communicate with us via the Scilympiad chat. Have fun and good luck!

Please note that the test is divided into several loose sections based on topic. The questions within
each "section" are also mostly organized in order of increasing point value.

1. (0.50 pts)
Which of the following processes do most bacteria and archaea utilize to reproduce?
A) Gametophytes and sporophytes
B) Homogenesis
C) Heterogenesis
D) Binary fission

2. (0.50 pts)
Which of the following correctly compares spores and cysts in a bacterial context?

A) Spores tend to not be able to participate in reproductive processes but cysts can

B) Cysts are much more resistant of harsh environmental conditions

C) Only cysts are created through binary fission
D) Spores form an entirely new bacterium, while cysts only transform an existing one

3. (0.50 pts)
Which of the following is not a part of the typical eukaryotic endomembrane system?

A) Smooth Endoplasmic Reticulum

B) Lysosome
C) Nuclear membrane
D) Peroxisome
E) Golgi Apparatus

4. (0.50 pts)
Which of the following is the definition of the virusoid?

A) a single-stranded RNA molecule that depend on buddy viruses to function

B) proteins that experienced a traumatic backstory and fold incorrectly
C) viruses except they don't have the nucleocapsid
D) a single stranded RNA strand that is also a strong, independent RNA strand and doesn't need
any help

5. (0.50 pts)
For questions 5 to 8, match the correct microbial agent to its funny little about-me.

"In my human-infective stage, I grow and proliferate in hepatocytes. However, I'm also the reason
why balancing selection occurs in West Africa for the sickle-cell allele."

A) Alternaria solani
B) Plasmodium falciparum
C) Giardia duodenalis
D) Mimivirus
E) Alexandrium catenella

6. (0.50 pts)
"My phylum is known for asci, but I actually reproduce asexually. You can identify me in my host
plant by looking for leaf spots and stem lesions."

A) Alternaria solani
B) Plasmodium falciparum
C) Giardia duodenalis
D) Mimivirus
E) Alexandria catenella

7. (0.50 pts)
"If you like mussels and scallops, beware of me -- I can poison you! I'm mostly dormant during my
lifetime, but I do possess flagella if I need to be up and about."

A) Alternaria solani
B) Plasmodium falciparum
C) Giardia duodenalis
D) Mimivirus
E) Alexandrium catenella

8. (0.50 pts)
"I have two nuclei. Oh, and if you ingest me, I'll go from being a cyst to giving you some pretty bad
diarrhea.'"

A) Alternaria solani
B) Plasmodium falciparum
C) Giardia duodenalis
D) Mimivirus
E) Alexandrium catenella

9. (1.00 pts)
Viruses come in a lot of different forms. Which of the following viral structures are incorrectly
matched with their definition?

A) Capsid: the protein coat that protects the nucleocapsid

B) Envelope: a saccharide coating that originated from a previous host
C) Capsomer: the monomer proteins that form an icosahedral capsid
D) Binal symmetry: a viral structure characterized by some bacteriophages with both icosahedral
and helical structures

10. (1.00 pts)

Helminths, or a variant of parasitic worms, are not typical microorganisms. These organisms exist as
multicellular organisms that do not require a microscope to be seen, so by definition they shouldn't
be a part of microbiology or this event. Yet helminths are commonly studied as a part of
microbiology. There are even some helminths on this year's rules! How come helminths are studied
alongside other microorganisms?

11. (1.00 pts)

What is the purpose of an inclusion?

A) To prevent foreign influences from entering the cell

B) To create more surface area for specialized metabolic reactions
C) To store compounds for future metabolism
D) To exit the cell

12. (1.00 pts)

Which of these are correctly matched?

A) Lipoteichoic acid: stabilizes the peptidoglycan layer of gram-positive bacteria without attaching to
the cell membrane
B) Braun's lipoprotein: connects the outer membrane and the peptidoglycan layer
C) LPS: primary contributor to the negative charge distributed on bacterial surfaces
D) Porins: allow larger proteins and nucleic acids to make it through the cell via facilitated diffusion
E) Flagellum: structure that enables cellular motility, found in bacteria and fungi

13. (1.00 pts)

Close inspection of an unknown bacterial species reveals the presence of glycolipids in its
membrane as well as a high concentration of mycolic acids in its cell wall. Which of the following
statements is true about this species?
A) The Gram stain would be an effective diagnostic for this species
B) It belongs to class Betaproteobacteria
C) This species was once mistakenly grouped with the protists
D) The Ziehl-Neelsen stain would be an effective diagnostic for this species
E) This species forms cysts to survive unfavorable conditions

14. (1.00 pts)

The proteobacterial ancestor of modern mitochondria is most closely related to which of the following
species?
A) Agrobacterium tumefaciens
B) Cutibacterium acnes
C) Streptococcus pneumoniae
D) Vibrio cholerae
E) Haemophilus influenzae

15. (1.00 pts)

An acidic bacterial cell is placed in a chlorate-rich environment. Which of the following transport
methods should the bacteria use if the cell wants to expel chlorate?

A) Uniport
B) Facilitated diffusion
C) Symport
D) Antiport
E) Group Translocation

16. (1.00 pts)

You perform a Gram stain on a sample of Rickettsia rickettsii. Upon completion of the procedure,
you see that your sample is entirely violet. You're worried that you messed up at one point; which is
most likely?

A) You didn't counterstain with safranin long enough

B) You forgot the iodine
C) You forgot the ethyl alcohol
D) You added too much crystal violet
E) Nothing, this is the correct result

17. (1.00 pts)

Joey has a sample of an archaeal species that expresses the newly identified but poorly named rizz
protein, which encourages unsaturated fatty acid synthesis and insertion into the plasma membrane.
Which group is Joey's sample most likely to belong to?

A) Mesophiles
B) Psychrophiles
C) Halophiles
D) Thermophiles
E) Acidophiles

18. (1.00 pts)

Choose all the following that are studied in the field of microbiology.
(Mark ALL correct answers)
A) Lichen
B) Yeast
C) Prions
D) Algae
E) Our immune system
F) None of the above

19. (1.00 pts)

Which characteristic(s) would you typically find in archaea, but not bacteria?
(Mark ALL correct answers)
A) Some branched hydrocarbons in membrane
B) Circular chromosome
C) Formyl-methionine as the initiator amino acid for protein synthesis
D) Lack of a response to chloramphenicol
E) Polycistronic mRNAs

20. (1.00 pts)

Which characteristics are common to both PrP and amyloid beta? Select all that apply:
(Mark ALL correct answers)
A) Predominant expression in the nervous system
B) Unknown normal function
C) Difficult to crystallize
D) Implicated in the pathophysiology of numerous diseases
E) Aggregation in the form of amyloid fibrils

21. (1.00 pts)

Which of the following microbial agents would a nuclear pore inhibitor be most effective against?
Select all that apply.
(Mark ALL correct answers)
A) PrP
B) Ancylostoma duodenale
C) Taenia solium
D) Giardia duodenalis
E) The Wolbachia species

22. (1.00 pts)

Explain the relevance of the surface-volume ratio. How can a larger monocellular eukaryote still
maintain a high SA/V ratio?

(Refer to the following table for questions 23 and 24.)

You are given three unknown microbes that, however, have known characteristics, as recorded in
the following table:
23. (1.00 pts)
Which type(s) of microbe could microbe 2 be?

24. (1.00 pts)

Your friend Ben claims that microbe 1 must be a virus. State whether you agree or disagree, and
why:

25. (2.00 pts)

The French guy who made cheese safe, Pasteur, entered a competition to provide evidence that
would reject the theory of spontaneous generation. His experimental setup is shown below. Explain
what Pasteur was trying to demonstrate through this experiment and if it was successful in doing so.

26. (1.00 pts)

Which of the following processes would a DNA-dependent RNA polymerase inhibitor most severely
affect?
A) Transcription of fungal genes
B) Insertion of HIV genes into a CD4+ cell genome
C) Transcription of bacterial genes
D) Degradation of bacterial mRNAs
E) Post-transcriptional bacterial mRNA modification

27. (1.00 pts)

Which of the following are correctly matched?

A) T4 phage: an E. coli-targeting bacteriophage that can only undergo the lysogenic cycle
B) Sigma factor: recognizes the rut site in RNA to facilitate transcriptional termination
C) Pribnow box: a segment of the Shine-Dalgarno sequence
D) Peptidyl site: follows the aminoacyl site in a ribosome
E) Shine-Dalgarno sequence: facilitates the binding of bacterial mRNA to the 50S ribosomal subunit

28. (1.00 pts)

Which of the following is false about 18S rRNA sequencing?

A) Similarity of different 18S rRNA sequences generally has to be >50% in order for them to be
grouped as an OTU (considered closely related)
B) It is a prominent marker for fungal classification
C) The V4 region of 18S rRNA has the most complete database information
D) 18S rRNA is a component of the 40S subunit in eukaryotic ribosomes
E) PCR is a common method of 18S sequence amplification for library construction

29. (2.00 pts)

Oh no! Melody's dog, Hodu, has been infected by canine parvovirus type 2 (CPV-2). It inserts the
following segment into Hodu's cells:

5'-GCA TCG GAC TTT AAG CAG-3'

How many intermediates are formed from this segment before the final mRNA, and what is the
sequence of said final mRNA?

A) 0; 5'-CUGCUUAAAGUCCGAUGC-3'
B) 0; 5'-GCAUCGGACUUUAAGCAG-3'
C) 1; 5'-GCAUCGGACUUUAAGCAG-3'
D) 1; 5'-CUGCUUAAAGUCCGAUGC-3'
E) 2; 5'-GCAUCGGACUUUAAGCAG-3'

30. (1.00 pts)

Which are true statements about Hfr and F+ bacteria? Select all that apply:
(Mark ALL correct answers)
A) Hfr bacteria have the potential to transfer chromosomal genes along with F factor genes
B) F+ bacteria can form F' cells
C) An F+ bacterium can become an Hfr bacterium
D) The F- recipient in Hfr-to-F- conjugation often ends up becoming an Hfr cell
E) An F+ bacterium would be able to transfer a mutation in a DNA polymerase over to an F- recipient
cell

31. (1.00 pts)

Kim accidentally spills an entire tub of lactose solution into the media for her E. coli, which already
contains nearly no glucose. If she were to culture E. coli on this media, what would occur within the
bacterial cells? Select all that apply.
(Mark ALL correct answers)
A) Binding of CAP to to the CAP site
B) Relatively high level of adenylyl cyclase activity
C) High rate of lac operon transcription
D) The lac repressor becomes inactive
E) Enhanced binding of RNA polymerase to the lac promoter

32. (2.00 pts)

Exposure of phage λ-infected E. coli (in the lysogenic cycle) to UV light will most likely lead to which
of the following changes (select all that apply)?
(Mark ALL correct answers)
A) Decreased initiation of transcription at the PRM promoter
B) Increased initiation of transcription at the PRE promoter
C) Cleavage of the λ repressor
D) Accumulation of cro protein
E) Expression of the O, P, and Q genes

For questions 33 to 35, consider the trp operon in E. coli. Additionally, consider the following four
possible conditions for the operation of this operon, which are listed below:

33. (1.50 pts)

Between the four conditions, rank the lengths of the final trp mRNAs produced from highest to lowest
(e.g., ABCD):

34. (3.00 pts)

Why you would find the longest mRNA in the condition (A, B, C, or D) you listed first?
35. (4.00 pts)
You introduce into each condition an agent that specifically inhibits rho factor expression. In which
condition would this agent have an effect specifically on trp operon transcription? Why?

For questions 36 to 41, refer to the following table of 6 fictional bacterial species and 4 traits. 1
denotes the presence of a trait, while 0 denotes its absence:

36. (1.00 pts)

Which is the most optimal phylogenetic tree corresponding to the above data? Choose one of the 5
trees below.
A) 1
B) 2
C) 3
D) 4
E) 5

37. (1.00 pts)

Why do we say "most accurate/probable/etc." instead of "correct" when referring to phylogenetic
trees? Give one reason why.

38. (1.50 pts)

Which groups form a polytomy (0.5)? Interpret this finding (1).
39. (1.50 pts)
16S rRNA-seq would be most effective in distinguishing between which two species?

40. (1.00 pts)

Briefly explain your answer to the previous question.

41. (1.00 pts)

Suppose we include another trait (presence of the constituent enzymes of fictional JVHR pathway)
as a column in our table:

JVHR pathway enzymes present?

A 1

B 0

C 1

D 0

E 0

F 1

The phylogenetic tree for the 6 species is reorganized to accommodate this trait. Which is now
species D's sister taxon?

A) A
B) B
C) D
D) E
E) F
F) None of the above
(Questions 42 to 44 relate to the following information.)

Matthew is studying genetic transfer between R. jickards, a (fictional) bacterial species. He has one
strain of Hfr R. jickards that is ily+lfy+tma+rso+, and one F- strain of R. jickards that is ily-lfy-tma-rso-
. Each three-letter abbreviation represents some (also fictional) necessity for R. jickards survival.
Here, + indicates that the bacteria can synthesize the indicated necessity, while - indicates that the
bacteria cannot, and requires said necessity in its medium to survive and reproduce.

He mixes the bacteria together, and interrupts them at certain time intervals with a blender. After he
interrupts their mating, he plates the bacteria on media each with a single necessity as a carbon
source and records the percentage of surviving colonies. Matthew aims to find the order of the
genes on the F plasmid in relation to the origin of transfer. Here is his data:

Minutes before interruption ily only lfy only tma only rso only

5 0 100 19 0

10 15 100 38 2

15 65 100 77 29

20 80 100 100 56

Each column represents the percentage of surviving colonies when plated with medium containing
only a certain necessity.

42. (1.00 pts)

The ily+lfy+tma+rso+ bacteria are _ for the listed necessities, while the ily-lfy-tma-rso- bacteria are
_?

___________________ ___________________

43. (1.00 pts)

Which are the possible orders of genes along the F plasmid?
(Mark ALL correct answers)
A) oriT lfy tma ily rso
B) oriT lfy tma rso ily
C) oriT ily rso tma lfy
D) oriT rso ily tma lfy
E) oriT ily rso lfy tma
44. (1.00 pts)
Explain why there are multiple answers to the previous question.

(Questions 45 to 51 relate to the following information.)

Laura has been hospitalized for nearly a month now due her recent diagnosis with renal cell
adenocarcinoma. As part of a routine hospital screening, a nasal swab sample is collected from her
and sent over for testing. It's now George the CLS's job to conduct the MRSA test.

45. (1.00 pts)

Unfortunately, George is having a bit of a brain fart and doesn't remember standard culture protocol.
However, he does know that he first has to isolate S. aureus from Laura's sample; which type of
culture and medium should he use?

A) Liquid; selective
B) Liquid; differential
C) Semi-solid; differential
D) Solid (agar); selective
E) Solid; differential

Thankfully, George's kind colleague, Kevin, reminds him of the correct protocol for isolating S.
aureus in vitro. George now proceeds to conduct an oxacillin MIC (minimal inhibitory concentration)
test on the purified, S. aureus-only sample, yielding the following results:

The MIC is the lowest concentration of an antibiotic that inhibits the growth of a given bacterial
strain. An orange well indicates bacterial growth has occurred in it, while white indicates no growth.
Additionally, George's hospital is weird, so the numbers above each column represent the negative
log of the concentration of oxacillin in each well, in g/mL. (Ex. the concentration of oxacillin in the
wells in column 2 = 10-2 g/mL.)

46. (2.00 pts)

State whether the following statement is true or false, then briefly explain why (adequate
explanation required for full credit):

Even if the S. aureus present in Laura's sample are resistant to oxacillin, they can still be treated
using cephalosporins.

47. (1.00 pts)

According to the CDC, the interpretive criteria for cefoxitin MIC tests on S. aureus are:

1. Susceptible: ≤ 4 μg/mL
2. Intermediate: N/A
3. Resistant: ≥ 8 μg/mL

Provide the MIC for the S. aureus present in Laura's sample in μg/mL and which type of S. aureus
she carries. The correct MIC is required for full credit:

48. (1.00 pts)

George thinks Laura's MIC test result is rather clear, but say he had all the time and resources in the
world. What is one measure George could take to be more secure about her test results?

49. (2.50 pts)

George recalls that his hospital has recently begun to administer ricksocin, a (fictional) novel
antibiotic that directly inhibits the synthesis of new DNA in bacterial genome replication. It is
thankfully effective against the vast majority of strains of S. aureus.

Which protein (1) and its subunit (0.5) does ricksocin most likely inhibit? How does this differ from
previously developed antibiotics that also target bacterial genome replication (1)?

50. (2.00 pts)

Laura's physician prescribes her ricksocin, which she responds to without complications. However,
when another nasal sample is collected from her within the following two weeks, George (who is
again responsible for her tests) identifies several MRSA colonies. Assuming that the original
ricksocin treatment did kill most bacteria during the first infection and Laura wasn't reinfected by
MRSA, propose a possible explanation as to how this might have occurred.
51. (1.00 pts)
Which are other potentially effective alternative treatments for Laura now? Select all that apply.
(Mark ALL correct answers)
A) A UDP-N-acetyl-D-glucosamine:chitin 4-beta-N-acetylglucosaminyl-transferase inhibitor
B) An ABC transporter inhibitor
C) T4 phage therapy
D) A catalase inhibitor
E) A reverse transcriptase inhibitor

(Questions 52 to 57 relate to the following information.)

After a long night of grinding Fermi Questions (to what avail?) in November 2023, Gerard wakes up
fatigued one morning with an intense fever and sore throat. He also struggles with walking around
his house as his body feels sore all over. However, because he lives in the very populous New York
City and today the clinic he normally visits is closed, he decides to wonder on his own what might be
afflicting him (Gerard is a curious individual). He begins by listing some likely candidates.

52. (1.00 pts)

Gerard lists the following microbes as candidate agents. Which of these can Gerard almost certainly
rule out? Hint: remember his circumstances.
(Mark ALL correct answers)
A) Corynebacterium diphtheriae
B) Poliovirus
C) SARS-CoV-2 virus
D) Influenza A virus
E) Streptococcus pneumoniae

53. (1.00 pts)

Briefly explain your choice(s) to the previous question.

54. (1.50 pts)

Gerard limits his list to the remaining candidates. While studying his choices, he thinks to himself,
"Gee, if I knew whether the agent genome contains uracil, then I'd be able to figure out which
pathogen this is in one shot!" State whether you agree or disagree with Gerard, and explain why. If
you disagree, propose an alternative characteristic that would actually allow him to determine the
pathogen without additional testing.

55. (2.00 pts)

Enough speculation -- Gerard decides to rest for the time being, and is able to land an appointment
with his physician the next day. After Gerard explains his symptoms, his physician collects a nasal
swab sample from him. Briefly explain how this swab sample will help determine which pathogen
Gerard is afflicted with.
56. (1.00 pts)
As he sits down to eat his dinner that evening, Gerard realizes that he can neither smell nor taste his
spaghetti. However, his nose doesn't feel stuffy. Which condition is he most likely afflicted with (0.5),
and what is the likely explanation for his loss of his sense of smell and taste (0.5)?

57. (1.00 pts)

Gerard sighs back in his bed as he realizes which condition he most likely has, grumbling to himself
as he's been afflicted with it before, during last December! He is also vaccinated against this
pathogen. Why then might he still have contracted this disease? Give a possible reason why.

58. (0.50 pts)

Maureen is a frustrated microbiology student wondering why she has to spend her tuition dollars on
a bioinformatics course (she dislikes computers)! Carisa reminds her that knowledge of modern
technology is important because the vast majority of microbial communities are unculturable. What is
the name of the phenomenon Carisa is referring to?

59. (1.00 pts)

Natalia desires to grow a healthy community of chemoautotrophic bacteria without the interference
of chemoheterotrophic bacterial growth in her petri dish. Which type of medium would be most
appropriate for her purposes?

A) Defined
B) Complex
C) Reducing
D) Selective
E) Enrichment

60. (1.50 pts)

In which scenario(s) would metagenomic analysis be more appropriate than traditional culture-based
microbial genomics? Select all that apply:
(Mark ALL correct answers)
A) You want to study the bacterial species diversity of a soil sample
B) You want to study differences in the expression of a certain fungal gene between two different
environments
C) You want to identify the pathogen responsible for a patient's infectious disease
D) You want to discover novel pathogens with high sensitivity
E) You want to conduct various studies on the same community of bacteria

(Questions 61 to 77 relate to the following information.)

Joey, a microbiology major, recently got an internship at his university's laboratory. At this internship,
Joey is given a variety of samples from other labs at the university and needs to send back images
using the right microscope for the job.

61. (1.00 pts)

Before he receives any samples, Joey needs to fix the lab's primary bright field microscope. A
previous intern stated that the resolution was diminished, and objects up to 2µm were not
discernible. Which of these measures could Joey take to potentially fix the microscope?
(Mark ALL correct answers)
A) Using a Q-tip, Joey should apply a 70:30 isopropyl alcohol solution to each objective lens
B) Joey should apply a small dab of cedar oil to a microscope slide and touch the slide with each
objective lens
C) Joey should try shifting the position of the condenser lens, if the microscope allows that
D) Joey should lower the height of the stage compared the nosepiece
E) Joey should replace the ocular lens so the magnification increases to 17,000x when combined
with the maximum magnification objective lens

62. (1.00 pts)

Rank the following parts of the microscope based on its ability to adjust the magnification of a typical
brightfield microscope.
___________________ ___________________ ___________________

63. (3.00 pts)

What three factors influence the resolution of a microscope? Explain how each factor does so.

64. (1.00 pts)

The physiology department sent a living culture of one of the bacteria that cause lymphadenitis. The
researchers specifically wanted to examine the bacteria's ability to form an endospore. They
requested that the sample stays alive and that the bacteria should be highlighted against the
background. Which microscope should Joey use?
A) Brightfield
B) Phase-contrast
C) Dark-field
D) Confocal
E) TEM
F) None of the above

65. (3.00 pts)

Joey was, unfortunately, not provided an axenic culture by the department and was provided an
enrichment culture instead. The laboratory wants Joey to quantify the presence of the microbe
through MPN. Joey performs a serial dilution with the sample with the pattern 3-0-3 for the positive
tubes in each set. The third set had a concentration 1 x 10-5 of the original sample. Using the
following table, calculate the amount of microbes present in the original sample. Put your answer in
the format a x 10b, and write a and then b in the boxes below.

___________________ ___________________

66. (1.00 pts)

Dr. Coli, a biochemistry professor, is currently working on a drug that could inhibit the Epstein-Barr
virus from entering epithelial cells. What microscope could Joey use to clarify what proteins are
present in EBV's capsid?
A) SEM
B) TEM
C) Differential interference contrast
D) Cryo-EM
E) Scanning tunneling microscope
F) None of the above

67. (1.00 pts)

The economics department, after deciding to eat money to prevent inflation, is now dealing with a
novel illness. Seeking to prevent another worldwide pandemic, the epidemiology department wants
to identify the disease-causing agent and asks for Joey's help to do so.

The department has a hunch that Listeria could be the cause, but isn't confident enough to claim it
as the sole cause. Which microscope would do the best job of allowing you to confirm or deny that
conclusion?

Note: Keep in mind that Joey also can stain, treat, and culture the culture himself.

A) Bright field
B) Atomic force
C) Confocal
D) SEM
E) A mixture of the above
F) None of the above

68. (0.50 pts)

Before he observes anything via a microscope, Joey wants to at least know what type of microbe is
causing this capitalist disease. Which of the following methods are known to be used in
identification?
(Mark ALL correct answers)
A) FAME Analysis
B) FACS
C) SSU rRNA Analysis
D) Efflorescence Microscopy

69. (1.00 pts)

Joey believes an immunofluorescence assay could work here. Which of the following types of
assays are correctly matched to their mechanism?
(Mark ALL correct answers)
A) Indirect, secondary antibodies are responsible for holding flurophore
B) Direct, secondary antibodies are responsible for holding the chromophores
C) Indirect, primary antibodies are responsible for holding the flurophore
D) Direct, primary antibodies are responsible for holding the flurophore
E) Indirect tends to amplify florescence signaling more than direct
F) Indirect tends to amplify florescence signaling more than direct

70. (1.00 pts)

Some of the students in the biology department, Pinky and Petunia, have an interesting obsession
with amoebas, so much so that they keep them as pets! The sisters want a video observing the
motion of these amoeba to make a microbial thirst trap on TikTok. What should Joey, reluctantly, do
to accomplish this?
A) Treat the amoebas with a stain that highlights them against the background of a bright field
microscope
B) Treat the amoeba to chemically fix them to the stage for better observation
C) Utilize a microscope with florescence to make the amoeba's internal features appear brighter
D) Utilize a microscope like DIC that makes the amoeba appear to pop out from the slide
E) Simply load the sample into the brightfield and take the video
F) Tell the "amoeba" sisters that it isn't possible

71. (0.50 pts)

The amoeba sisters also want to observe the motion of the pseudopod via florescent microscopy.
Which cytoskeletal monomer should the fluorophores bond to?

A) Tubulin
B) Actin
C) Intermediate Filaments
D) Dynein
E) None of the above

72. (0.50 pts)

If the amoeba sisters wanted to observe how the nuclear lamina shifts throughout the amoeba's
movement, which cytoskeletal element should also be tagged?

A) Microtubules
B) Myosin
C) Actin
D) Intermediate Filaments

73. (1.00 pts)

After a long day at his internship, Joey decides to use one of the microscopes to take some images
of the microorganisms that live in his saliva. He uses a Q-tip to swab the inside of his mouth and
wipes the Q-tip on a microscope slide. Here's one of the more interesting organisms he found.

Which type of microscope was used to take this image?

A) Brightfield
B) Confocal
C) DIC
D) Phase-contrast
E) Cryo-EM
F) None of the above

74. (2.00 pts)

What type of microbe is this? If this organism grows in concentration, what should Joey do (or
should he do anything)?

75. (1.00 pts)

Joey reports taking a lot of antibiotics prior to swabbing. Explain if this fact is correlated to the
appearance of this organism and if so, how. If not, explain how it might impact other microbes in his
swab.

76. (1.00 pts)

Joey, in his spare time, likes to grow bacterial colonies for funsies. One day, his evil roommate adds
something to his favorite colony and the next day, Joey sees this! What did they add?

___________________

77. (1.00 pts)

What causes the black spots to appear?

A) The death of a lot of bacteria

B) The overabundance of certain bacteria
C) The introduction of an antimicrobial compound
D) Bacteria that mutated or transformed morphologically

Joey was also tasked with organizing the journals of the previous intern. In each image, identify what
type of stain the intern used and the bacterial shape observed.
78. (1.00 pts)

___________________ ___________________

79. (0.50 pts)

The intern behind this image noted that they treated the backdrop with a purple stain. What type of
staining is this?
A) Positive
B) Basic
C) Negative
D) Acidic

80. (1.00 pts)

___________________ ___________________

81. (0.50 pts)

The intern noted applying a mordant to the bacteria sample before they stained them with fuchsin.
What is the purpose of the mordant?

A) To chemically fix the flagella so they don't flail around

B) To weaken the structure so the flagella can move freely
C) To weaken the structure of the flagella so the stain can puncture through
D) To thicken the flagella so the stain actually appears

82. (0.50 pts)

What type of flagella distribution is this?

A) monotrichous
B) amphitrichous
C) lophotrichous
D) peritrichous

83. (1.00 pts)

Note: This is an example of the Ziehl-Neelsen method, which uses heat the fix the microorganisms.

___________________ ___________________

84. (0.50 pts)

Which of the following features does the group marked A have?
(Mark ALL correct answers)
A) More easily targeted by cephalosporins
B) A large layer of peptidoglycan
C) Lipopolysaccharides with endotoxic abilities
D) Mycolic acid in the cell wall
E) A periplasmic space

85. (0.50 pts)

These microbes are organized in a specific manner. What is the name of the organization pattern?
(Hint: an example of one of these patterns would be streptobacillus.)

___________________

After flipping through all of those logs, Joey seems to have caught some sort of respiratory illness.
He believes it's from a virus.
86. (0.50 pts)
Desperate to understand his ailment, Joey researches how viruses even work and encounters a lot
of virus-esque terms. Which of the following define the new viruses being formed from previous
viruses in Joey's poor cells?
A) Viroid
B) Virion
C) Virusoid
D) Phage

87. (0.50 pts)

Joey believes he's caught a case of influenza. He finds a SEM photograph of the influenza molecule
and notices that this virus tends to be enveloped. What is covering the virus, and where does it
come from?
A) Proteins, created from the host cell's ribosomes
B) Lipid bilayer, forms from the plasma membrane of a previous host
C) Glycocalyx, formed from gluconeogenesis and other processes
D) Proteins, formed using the enzymes present inside the capsid

88. (1.00 pts)

Influenza has noticeable spikes on its envelope, including ones made of hemagglutinin. Describe the
purpose of these spikes.

89. (2.00 pts)

These spikes are known to mutate incredibly quick! The mutation of the two main sub-units of the
protein were responsible for the reemergence of the virus in past pandemics. Why did a change in a
single spike protein cause new pandemics?

90. (1.50 pts)

Match the following microbes to their respective industrial application:

1. Saccharomyces cerevisiae A. Potential source of biofuel

2. Lactobacillus nagelii B. Baker's yeast

3. Pseudomonas putida C. Kombucha production

 4. Genus Chlorella D. Treatment for bacterial
dysentery

5. Shigella phages E. Yogurt production

6. Lactobacillus bulgaricus F. Aromatic compound

degradation

Fill in the letters for microbes #1-3 below (#4-6 in the next question).

___________________ ___________________ ___________________

91. (1.50 pts)

Fill in the letters for microbes #4-6 below.

___________________ ___________________ ___________________

92. (0.50 pts)

Interspecies hydrogen transfer is a well-studied phenomena that occurs specifically between anoxic
methanogenic archaea and other anaerobes in aquatic ecosystems. Anaerobes, since they cannot
use oxygen, tend to use which of the following elements in the end product of the ETC?

A) Sulfur
B) Phosphorous
C) Nitrogen
D) Hydrogen

93. (1.50 pts)

The methanogenic archaea utilize the electron acceptor of anaerobes and carbon dioxide to produce
methane, which boosts how exergonic the electron transport chain is. Explain the reasoning behind
why this happens and how it benefits the bacteria.

94. (0.50 pts)

The previous question describes which type of microbial interaction?

A) Amensalism
B) Syntrophy
C) Lithotrophy
D) Antagonism
E) None of the above

95. (2.00 pts)

Explain why a fully sealed jar of kimchi can be left in the fridge for months but a sealed beer keg will
eventually explode.

(Questions 96 to 100 relate to the following information.)

Consider the function

which is a logistic model for the population of a certain bacteria P with respect to time t (in hours). In
our case, L and k are constants where L = the carrying capacity of the population, t0 = the time at
which the population is at half of its theoretical maximum, and k = the per capita growth rate.

The differential form of this logistic model is expressed as

Note P here represents P at some time t. The output of this form of the logistic is the derivative of
the population size P with respect to time in hours t, or the slope of the line tangent to the point
(t,P(t)) along the original function P(t).

96. (1.00 pts)

The logistic model is a mathematically handy function to approximate bacterial population growth,
though it doesn't entirely capture the bacterial growth curve on its own. Name one of its limitations:

97. (3.00 pts)

For our purposes, let L = 105 cells/mL, t0 = 6 hours and k = 4/hour. Substituting these values in for L
and k, respectively, determine the maximum value of the differential form of the logistic with the
correct units (2). Interpret it with respect to the population being modeled (1).

98. (2.00 pts)

With respect to t, when does the maximum from the previous question occur?
99. (2.00 pts)
The empirical Monod equation is another model that describes microbial growth, expressed in the
form

where μ = the specific growth rate (expressed per time), μmax is the maximum specific growth rate
(expressed per time) for the culture, S is the limiting substrate concentration (expressed as
mass/volume), and Ks is the half-saturation constant (mass/volume). It is clearly very different from
the logistic model. In which scenario would the Monod equation theoretically be more appropriate
than the logistic?

A) You desire to study the growth rate of a bacterial community simply as a function of biomass
B) You desire your growth model to include a lag phase
C) You would like to compare fungal growth between when water is the limiting nutrient and when
carbon is the limiting nutrient
D) You are unsure of the accuracy of your substrate measurements in your microbial growth
experiment
E) You are having difficulty making precise measurements of ambient environmental conditions,
such as pH

100. (2.00 pts)

Select one of the four remaining choices from the previous question, and describe why the logistic
model would -- at least theoretically -- be more appropriate to use than the Monod in that scenario.