Final Review Test Questions Flashcards
1
Q
Archaea and Eukaryotic ribosomes contain 18S rRNA
A
False; archaea ribosomes are 16S
2
Q
Cells in the domains Archaea and Eukarya can have histones associated with their DNA
A
True
3
Q
Archaea and eukaryotes contain mitochondria
A
False; only eukaryotes have mitochondria
4
Q
Archaea and Eukarya lack peptidoglycan in their cell walls
A
True; only bacteria have peptidoglycan layers
5
Q
Bacteria and Archaea are more closely related based on their ribosomal RNA gene sequences
A
False; Eukarya and Archaea are more closely related
6
Q
The membrane lipids of Archaea and Bacteria contain isoprene units
A
False; bacteria do not have isoprene units
7
Q
Who used metagenomic sequencing to study the effects of lifestyle practices, such as C-section birth, on the microbiome?
A
Dominguez-Bellos
8
Q
Dominguez’s work has shown that the gut microbiome of babies born via C-section is colonized initially by the mothers __________ microbiota.
A
Skin
9
Q
Because of the babies contact with the mother’s skin via c-section, it could be inferred that the gut microbiome of these babies would contain genes supportive of these microbes thriving in a __________ environment.
A
Oxygen/salty
10
Q
When conducting gram-staining in the lab on gram-positive bacterial culture, if you forget to add the _________ which is the mordant in this procedure, your cells will stain _________.
A
iodine; pink
11
Q
Both Bacteria and Archaea can be found in biofilms
A
True
12
Q
Both Bacteria and Archaea utilize the che proteins for texis (chemo/photo)
A
True
13
Q
Both Bacteria and Archaea can grow above 100C
A
False; only archaea can
14
Q
Both Bacteria and Archaea lack a nuclear envelope
A
True
15
Q
Both Bacteria and Archaea can be cocci-shaped
A
True
16
Q
Both Bacteria and Archaea can be clinically identified by Gram staining
A
False; only bacteria
17
Q
Group Translocation in Bacteria Involves?
A
Facilitated diffusion of sugars into the cell, upon entry, these sugars are phosphorylated so that they cannot leave
18
Q
What would challenge Koch’s postulate?
A
unculturable microbes, infection without symptoms, asymptomatic carriers
19
Q
If a bacterial cell runs out of ATP….
A
the flagellum will spin CCW (run = default)
20
Q
Archaea must have ATP to spin their flagella
A
True
21
Q
Bacteria and Archaea build their flagella tip outwards
A
False; bacteria add at the base
22
Q
Bacteria indirectly use ATP to spin their flagella
A
True
23
Q
Archaea are not susceptible to penicillin
A
True; they do not have peptidoglycan layers
24
Q
Bacterial and Archaeal flagella contain the protein motA
A
False; archaea do not have motA
25
Define the role of the transpeptidase enzyme in peptidoglycan construction...
the enzyme links the amino acid chains between sugar backbones
26
A patient presents with elevated levels of endotoxin in her bloodstream, what could be true of the bacterium?
An endotoxin is an LPS subunit that is from a gram-negative bacterium, meaning the patient would have elevated TLR4 levels, and the bacterium is less likely to lyse when exposed to lysosomes
27
What is true of the resolving power of a microscope? (smaller d = better power) d = lamba/2NA
A smaller wavelength will produce a clearer image, a numerical aperture of 0.7 will produce a clearer image than a NA of 0.5
28
Which staining methods would be used to differentiate between E. coli and A. aureus
Gram-staining (-/+), simple staining (shape)
29
What methanogens are likely to be more abundant in people who consume a high fiber diet for methanogenesis?
Acetoclastic
30
How do halophilic microbes cope with osmotic stress?
Rhodopsins that transport chloride ions into the cell, accumulation of solutes as inclusions in the cell, pumps and proteins that bring in or push out salts for the cell, s-layer that maintains a more rigid cell envelope
31
What research questions could be addressed using 16S rRNA sequencing?
bacterial presence in different areas, blood samples looking for gram-negative bacteria, the population of microbes (cannot determine enzymes or function)
32
C. tenani causes muscle _________.
contraction
33
Tetanus toxin cleaves the vesicular binding protein _______________ inside a _________ neuron.
synaptobrevin; inhibitory
34
The result of tetanus is __________ release of _________ from the associated motor neurons
continued; acetylcholine
35
MotA
proton channel
36
FLIG
interacts with the proton gradient to spin the flagellum
37
MotB
binds the proton channel to peptidoglycan
38
Who is most likely to have β-lactamase?
Pink Stain (Gram Neg) bacteria
Cell-wall-less bacteria
motile bacteria
double-membrane bacteria
Teichoic acid bacteria
acid-fast bacteria
teichoic acid bacteria = gram positive
39
When CheA is active, the flagellum spins ________. (phototaxis)
CCW
40
CCW phottaxis moves bacteria ______ from the light
away
41
Bacteria are active when they absorb ________ light and move away
blue
42
Bacteria are inactive when they absorb ______ light and move toward
red
43
When CheA is inactive, the flagellum is spinning _______. (phototaxis)
CW
44
Streptococcus shape
cocci in chains
45
Staphylococcus shape
cocci in clusters
46
E. coli shape
bacilius
47
V. cholerae shape
comma-shaped cells
48
Robert Hooke
cells in cork
49
Louis Pasteur
spontaneous generation
50
Carl Woese
three domain system
51
Norman Pace
metagenomic sequencing
52
Shine-Delgrano Sequence
bacterial ribosomes
53
Bacilius anthracis
hyperthermophile
54
Edward Jenner
smallpox vaccine with cowpox
55
Anton van Leeuwenhoek
a lens maker
56
Onesimus
Variolation
57
PEP
group translocation
58
Mary Hunt
moldy penicillium cantaloupe
59
FepA
shuttles siderophore complex into the periplasm
60
ParA
cytoskeleton protein
61
Alexander Flemming
discovery of penicillin
62
FepB
binds siderophore complex in the periplasm
63
Basic Stain
Positively Charged
64
Acidic Stain
Negatively Charged
65
FliG
flagellum torque-generating surface
66
Botulism toxin cleaves a vesicular binding protein in the motor neuron, not the inhibitory neuron
True
67
All archaea have an S-layer
False
68
An electron microscope results in a greater distance, d, associated with a greater resolving power by manipulating the wavelength that hits the specimen
False, electron microscopes have shorter wavelengths as is
69
Hami are unique bacterial motility structures important for attachment to surfaces
False, archaea not bacteria
70
Archaea cell envelopes contain the sugar NAM
False; NAT/NAG
71
Capsular microbes have an expansive glycocalyx that is loosely attached to their cell envelopes
True; the slime layer is loosely attached, while the capsule is firmly attached
72
Without a hydrogen gradient established in the periplasm, the gram-negative bacterial flagellum would not spin.
True
73
Acellular life does not respond, grow, or metabolize
True
74
The bacterium that causes TB cannot be clinically identified by Gram staining
True, Tb is acid-fast (also M. leprae)
75
Total magnification for a typical light microscope is 1000x
True
76
Which domain contains species with monolayer membranes?
Archaea
77
In what environments would monolayers be most critical for survival?
Hyperthermic environments over 85 °C
78
Which characteristic makes Archaeal membranes inherently less reactive than Bacterial membranes?
Ether linkages are less reactive than ester linkages because it has one less highly reactive oxygen species per link
79
Which characteristic helps Archaeans maintain fluidity in their membranes?
Branched chains allow for more monolayers and more fluidity
80
Dark Phase
Rays cancel each other out, dark background
81
Under what circumstances do endospore-forming bacteria undergo sporulation?
starvation (no nutrients)
82
What is the clinical significance of endospore formation?
Endospores can be dangerous for human health. Since bacteria causing botulism or muscle paralysis are spore-forming, improper canning techniques and sterilization can allow the growth of endospores.
83
If CheY is mutated, such that it can't be phosphorylated, will the cell tumble more or less?
tumble less since CheY phosphorylation causes tumble (CW)
84
State the two possible ways a bacterium can enter into a run.
1. CheB can demethylate MCP, inducing a run
2. More attractant can bind to induce a run
85
What do you expect will happen to the flagellum spin and the movement of the bacterial cell after you enter a conc. of 2M?
Increasing concentration will inactivate CheA, no phosphorylation and no tumble, resulting in a CCW spin and a run.
86
Based on what you know about these mechanisms, which wavelength would likely promote maximum ATP production using archaerhodopsin?
red
87
What happens to the conformation of the rhodopsin molecule when it absorbs light?
before trans confirmation, after light cis confirmation (more energy)
88
With the conformational change, describe the mechanism by which it produces ATP?
light energy changes the conformation changing the structure to allow for H+ to leave the cell, increasing the concentration gradient outside, then ATP synthase uses the gradient to shuttle H+ back through to synthesize ATP
89
For bacteria and archaea the domain name and kingdom name are the same
True
90
Which domains of life contain unicellular organisms?
bacteria, archaea, eukarya
91
Bacterial ETCs produce less ATP than mitochondrial ETCs
True
92
Bacterial cells can conduct transcription and translation simultaneously
True
93
Eukaryotic cells do not carry out fermentation
False
94
ATP synthase functions the same way in bacterial and eukaryotic cells
True
95
Eukaryotic cells are inherently resistant to cephalosporins
True; they are a β-lactam antibiotic
96
When an alcohol swab is used to clean your shoulder prior to receiving a vaccine...
bacterial membranes are being dissolved, bacterial enzymes are being denatured, and is a type of antiseptic
97
During the cytosolic stage of peptodoglycan synthesis, the enzyme, _____________, uses phosphoenolpyruvate to convert UDP-NAG to UDP-NAM.
Enol pyruvate transferase
98
During conjugation, if the relaxase enzyme is dysfunctional...
The DNA will not be shuttled to the secretion system since relaxase cleaves DNA and then transfers it
99
What antimicrobials exert their antimicrobial effects via competitive inhibition of an enzyme?
sulfonamides, amoxicillin, trimethoprim
100
A missense conservative mutation will...
be a different DNA and protein sequence than the wild type, but the function of the protein will be the same as the WT
101
Factors that affect whether an antimicrobial agent is effective against a pathogen...
size of population, length of exposure, environment, concentration of agent, contact time
102
Nitrosomonas
a facultative anaerobe, beneficial to add to an aquarium tank to cope with high levels of ammonia
103
P. denitrifcans
can oxidize organic compounds and deplete the surrounding environment of usable nitrogen
104
What is true of F' bacteria?
produce a sex pilus, encode a relaxase enzyme for conjugation, transfer the ability to carry out F-factor-mediated conjugation, and produce recombinant bacteria
105
What antibiotic is ineffective if there is a mutation in the large ribosomal subunit?
Macrolides
106
Vancomycin and penicillin are most effective in the _________ stage.
extracellular
107
Boil water notices were released after fire for possible contamination of the water with _________.
coliform
108
Coliform ferment ___________.
lactose
109
Fermentation of lactose produces acidic by-products that result in a drop in pH, wherein only ____________ will be able to thrive.
acidophiles
110
E. coli uses a branched ETC for __________ respiration.
aerobic
111
During log phase growth ___ branch is used.
bo
112
Consuming a low fiber diet...
produces fewer SCFA, gut will be populated with more microbes that do not ferment complex carbohydrates, inflammation may increase
113
Stages of Biofilm Formation
1. Substratum preconditioning
2. Microbe deposition
3. Microbe replication and growth
4. Polysaccharide release from microbes
5. Microbe sloughing into the surrounding environment
114
If the MIN system is dysfunctional ...
chromosomes may not be paritioned before separtion takes place
115
High conc. of V. fisheri cells will instigate the diffusion of AHLs from the ______________ to the __________, instigating a _________ in LUXR expression.
extracellular space; cytosol; increase
116
During _________ transduction, a __________ integrated into the bacterial genome de-integrates incorrectly.
specialized; prophage
117
Tannins
phenolic compound
118
Luxl
AHLs
119
ParM
plasmid partitioning
120
Missense nonconservative
new amino acid
121
Rhodopsin
phototrophy
122
qPCR
non-culture based
123
FtZ
septation
124
Lysogenic cycle
Prophage
125
Azoles
ergosterol
126
Type IV secretion system
Conjugation
127
Lytic Cycle
mature phage
128
Frederick Griffith
Transformation
129
Paul Ehrlich
syphilis
130
Lipid II
peptidoglycan
131
Colony Forming Units
culutre-based
132
Autoclave
sterilization
133
Chemolithotroph
eats rocks
134
Persister Microbes
Biofilms
135
More lysol will likely be required to kill a microbe in a moist drain compared with a dry surface
True
136
When a microbe receives the gene that encodes β-lactamase, this microbe will grow if plated on media containing vancomycin
False; penicillin
137
A bacterial cell that becomes infected with a prophage is a recombinant cell
True
138
If you know the number of cell divisions a microbe has undergone during a segment of time, you can calculate that microbe's growth rate
True
139
An antibiotic with a therapeutic index of 5 is more selectively toxic than one with 10
False
140
Aldehydes target bacterial ribosomes
False; cell wall
141
The goal of fermentation is to produce more NAD+
True
142
The human microbiome consists mostly of mesophiles
True
143
An F' cell was once unable to produce F- F-cells via conjugation
True
144
E. coli will present as a narrow stab line in a SIM media tube
False; E. coli is motile
145
Both spontaneous and induced mutations can occur on plasmids and chromosomes
True
146
The proton motive force produced in a mitochondrial ETC is much smaller than the proton motive force produced by P. denitrificans aerobic ETC>
False
147
A mutation in 16S will not make a microbe resistant to a macrolide
True; 50S large subunit
148
Three types of HGT
1. Conjugation (cell-cell)
2. Transformation (uptake of free DNA)
3. Transduction (phage-mediated through lytic/lysogenic)
149
Mechanism for Acetate
Increased Acetate -> Increased Lung Epithelium -> Increased binding -> Decreased HDAC -> Decreased DNA acetylation -> More DNA expressed Foxp3 -> Decreased inflammation -> Up reg of T-reg pop
150
What short-chain fatty acid is most abundant in the gut?
acetate
151
T. aquaticus, the microbe from which we isolate Taqp for PCR, likely thrives at around 72 degrees C
True
152
What are the components of the index PCR reaction?
Taq polymerase, dNTPs, Index Primers, Template DNA
153
If a phage mutates enough such that the original crRNA no longer aligns to it...
the bacterium will most likely die because this crRNA will likely not hybridize to this mutated phage
154
Viral proteins that are likely to be made on the rough ER are__________.
spike, hemagglutinin
155
What is the most likely outcome if you use genomic DNA rather than 16S-enriched DNA in the index PCR reaction?
no bands on gel
156
What is true of a +sense ssRNA virus?
the virus will not enter the nucleus to replicate its genome, the viral genome is translated by host ribosomes immediately upon entry into the cytosol
157
SSC
granuality
158
FSC
size
159
Steps in illumination library preparation and NGS that involve DNA are..
sequencing by synthesis, bridge amplification, 16S enrichment, indexing
160
Massively Parallel
all clusters on the flow cell are sequenced simultaneously
161
During CRISPR RNA biogenesis...
crRNA will only transcribe for phages the bacterium has been previously infected with
162
What organism would be identifiable from a sample using Illumina NGS DNA sequencing?
HSV-1, HIV
163
During HSV-1 infection, which of the following viral proteins would be amongst the first to be translated from the viral genome?
DNA polymerase
164
Cas enzyme
cleaves phage DNA, processes pre-crRNA into mature crRNA, and cleaves what hybridizes to their associated mature crRNA
165
What gene must be transcribed prior to gp55 transcription?
T4's motA gene
166
Viral uncoating
low pH
167
- gel electrode
larger DNA fragment
168
+ gel electrode
smaller DNA fragment
169
CAS-9
gene editing
170
Tamiflu
flu
171
Docosanol
HSV-1
172
T4 bacteriophage
LPS
173
Innate immune cells
early/first immune responders
174
Adaptive immune cells
later immune response
175
Higher Ct value
lower gene expression/abundance
176
BSL-1
V. fischeri
177
BSL-4
smallpox
178
HPV
oncogenic virus
179
CCR5
HIV
180
To study T4 bacteriophages in the gut microbiome of humans, you would need to conduct 16S targeted amplicon next-generation sequencing
False; bacteriophages are viruses and cannot be studied by NGS
181
A sample with 3500 ASVs is likely less diverse than one with 1000s ASV
False; Amplicon sequence variant when larger is more diverse
182
CAS enzymes are going to be most effective at interfering during the lytic cycles of phage infection
True
183
If it takes 40 cycles or more of qPCR to see fluorescence for both markers of covid then this person is considered negative for covid
True
184
CAS enzymes target viruses with complex shaped capsids
True
185
HIV and Influenza enter animal cells through receptor-mediated endocytosis
False; HIV uses a fusion mechanism
186
Cytotoxic T-cells are susceptible to HIV infection
False; only Helper T-cells
187
A sequencer that can carry out 300 cycles of sequence-by-synthesis will result in greater breadth compared with a sequencer that can carry out 400 cycles of sequence-by-synthesis
False; breadth is the number of nucleotides, not the number of cycles
188
A bacterium with 10 spacer regions in its CRISPR region has survived more phage infections than a bacterium with 5 spacer regions
True
189
A virus that infects cells faster will produce fewer plaques on the plate
False
190
There are no -sense RNA viruses that enter the nucleus during virion production
False; flu
191
If a dog has a homologous receptor to CD4; it most likely can be infected with HIV
True
192
The flu virus _________ protein binds ________ on epithelial cells of the gut and respiratory system
HA; SA
193
Where in the cell does the virus make its first mRNA?
nucleus
194
Name one advantage and one disadvantage of NGS when compared to culture-based techniques used to study bacteria
NGS is more comprehensive but there is a lack of viability information
