Past Exam Questions Flashcards
Where does peptidoglycan exist in the bacterial cell?
cell wall
Where does the phospholipid bilayer exist in a bacterial cell?
cell membrane
Where do lipopolysaccharides exist in a bacterial cell?
outer membrane
Where does the periplasm exist in a bacterial cell?
in between cell membrane and outer membrane
T/F Absolutely all functions in the cell are carried out by proteins
false
What is the basic principal of microscopy?
magnification leads to better resolution
In _____ microscopy, the light rays that are usually scattered from the object are condensed and used for visualization.
dark-field
Why do we need to coat specimens with heavy metals when using electron microscopy?
to allow the objects to absorb the electrons
Out of all microscopy types we studied, this is the only one that shows images in 3D
SEM
This component is common to both Gram negative and Gram positive bacteria
peptidoglycan
The _____ component of Gram negative bacteria is endotoxic mainly due to its _____ content.
LPS
lipid A
These are major elements required by the cell in large amounts
macronutrients
Cell membranes are ______ structures
semipermeable
You have isolated a bacterium from the rumen of a cow and wish to know how it transports the sugar “whonose” into the cell. You perform an experiment that shows that “whonose” transport dissipates the proton gradient across the membrane (that means that “whonose” transport uses the proton gradient). What is the mechanism of “whonose” transport into this cell?
coupled transport
These two types of culture media differ in whether their components are defined or not
complex and synthetic
Which structure has a thick protective coat enclosing the genome?
endospores
At the optimal growth conditions of an organism, its ____ are most functional and its _____ are intact
proteins
membranes
In these growth phases, the cell numbers do not change
lag and stationary
What is NOT a physical means to control microbes?
antiseptics
T/F Because molecules naturally flow from regions of high concentration to regions of low concentration, transport across the cell membrane is impossible against the concentration gradient
false
T/F In a eutrophic lake, nutrients are abundant
true
T/F On the ocean floor, it is common to find a psychrobarophile
true
T/F In animal guts (where conditions are usually anaerobic), we expect to find strict anaerobes, facultative anaerobes, as well as strict aerobes
false
T/F Using stains with bright field microscopy has no effect on resolution
false
T/F In the microbial world. all organisms are about the same size
false
During the phage infection cycle. what happens during the attachment stage?
phage components bind to the host cell surface receptors
During the phage infection cycle. what happens during lysogeny?
the phage integrates its genome in the host genome
During the phage infection cycle. what happens during the active replication cycle?
the phage uses the host machinery to make its own viral components
During the phage infection cycle. what happens during the genome entry phase?
the phage injects its genome inside the host cell leaving the capsid outside
During the phage infection cycle. what happens during the exit stage?
the host cell lyses and the phage progeny are released to infect new cells
What is the order of the stages in a typical virus infection cycle?
attachment
entry
replication and synthesis
assembly of virus components
exit
What do bacteriophages do during entry that differs from animal viruses?
bacteriophages “push” their genomes inside the host cells leaving the capsid outside as a ghost.
Switch from lysogeny to a lytic cycle is often triggered by host ______.
stress
What are the 4 criteria used by the ICTV for virus classifications?
viral size
capsid symmetry
genome composition
host range
T/F During lysogeny, viruses are actively directing the host cell to make their proteins
false
T/F There are some viruses that could synthesize their own proteins?
false
T/F An envelope is common to all viruses
false
What 4 forms of nucleic acids are encountered in viruses?
ssDNA
dsDNA
ssRNA
dsDNA
ss –> single stranded
ds –> double stranded
What 2 types of microscopy have a dark field?
dark-field
fluroscence
What is a main purpose of the cell membrane?
transport of molecules
Gram negative bacteria have ______ cell walls.
thin
These are trace elements required by the cell in small amounts
micronutrients
Pathogens that cause disease to human grow optimally at our body temperature. Accordingly, pathogens are most probably _________.
mesophiles
T/F Only very small molecules can pass through the cell membrane by simple diffusion through the phospholipid bilayer.
true
T/F Out of all physical means of microbial control we discussed, filtration is the only one that achieves sterilization.
false
T/F An example of a resistant form of growth that starts by attachment to surfaces is the biofilm.
true
T/F Electron microscopy can be used to resolve objects in the nanometer range.
true
When a transport move molecules along the concentration gradient, the transport is called _______ and does NOT require energy.
passive
The smallest distance by which two objects can be separated and still be distinguished:
resolution
The sudden introduction of large quantities of a previously limited nutrient in a system:
eutrophication
The time it takes for a population to double:
generation time
The apparent increase in the size of an abject
magnification
The phase of growth where stress response is tun=rned on in anticipation of lack of nutrients:
stationary phase
The phase of growth where cells are actively growing and dividing:
log phase
The phase where cells are preparing to grow:
lag phase
You see two species growing on a MacConkey agar plate. One is pink growth, one is yellow growth. Is the medium selective or differential? Does the plate contain a pure culture?
differential
no
In order to avoid any detrimental scenarios that could occur during DNA replication prior to cell division, the process of replication happens in a _________ manner where each of the daughter cells will receive a double stranded DNA where one strand is old and the other is newly made.
semi-conservative
In translation, there are 64 possible ______. ______ of them don’t code for any amino acids and are used as ______ .
codons; 3; stop codons
Why do cells need to import DNA (3)?
to use it as food
to fix a damaged genome
to adapt to new environments
T/F Gene transfer by conjugation between two unrelated cells is a form of vertical gene transfer.
false
horizontal gene transfer
T/F Gene transfer is known to occur between different cells in an environment. There is only one way for this to occur.
false
multiple ways for gene transfer to occur and between many different specimens
This type of mutation where one nucleotide is switched to another…
point
If the point mutation from T to A leads to calling the same amino acid during translation…
silent mutation
The point mutation from T to A leads to calling a different amino acid during translation…
missense
The point mutation from T to A caused a switch of the codon to a stop codon…
nonsense
Mutation where a couple of bases are added…
insertion
Mutation where a couple of bases are removed…
deletion
Insertion and/or deletion would lead to a _____ mutation in the protein product.
frameshift
From a gene to mRNA is called…
transcription
From mRNA to a protein is called…
translation
A cell can control gene expression at the level of process A (that means controlling gene expression before the mRNA product is made) by manipulating the activity and/or the amount _______ available in the cell.
sigma factor
Regulatory proteins could either be ______, that bind to the DNA and prevent process A form starting, or ______, that bind to the DNA and stimulate process A to start.
repressor
activator
A process starts with the DNA in a relaxed state (the circle) and then introduces twists (one of them is shown). Going through this process several times would produce a(an) _____ molecule. Enzymes that increase and decrease this state are known as _______.
supercoiled
topoisomerases
In the process of DNA replication for a double strand, the _____ is replicated continuously, while the ______ strand is replicated in fragments. This is because the replication enzyme can only work in one direction 5’ to 3’.
leading
lagging
What type of bond connects the phosphorus chain in DNA?
phosphodiester
In DNA structure, _____ on one strand binds to ______ on the opposite strand via _____ H-bonds.
C; G; three
What pathway produces more ATP from the breakdown of 1 glucose?
EMP
ED and EMP have this in common
they both produce 2 pyruvates from 1 glucose
Ethanol is a byproduct of _______ and ________ fermentations.
ethanolic and heterolactic
During respiration, which step(s) produce(s) NADH?
both PDC and TCA produce NADH
If the ETS is halted (i.e. stopped working) during respiration, for example, when the cell runs out of an electron acceptor, what would be the other way of recycling the NADH?
Fermentation
The proton motive force drives the following process in bacteria:
- ATP biosynthesis
- flagellar rotation
- nutrient uptake by couple transport
Sulfide oxidizers are organisms that have an ETS in their membrane, and they can use H2S as their electron donor and O2 as their electron acceptor. Based on this information, what kind of process do sulfide oxidizers carry?
aerobic lithotrophy
From your knowledge about electron acceptors, which of these do you think could not be an electron acceptor?
- H2
- O2
- Sulfate (SO4)
- Nitrate (NO3)
H2
Water can act as an electron donor to the ETS. But since water is a very stable molecule, energy from light is required to release the electrons from water. What would this make organisms that use water as an electron donor?
phototrophs
In class, Dr. Youssef told us that the majority of lithotrophs use CO2 as their carbon source. What would this make the majority of lithotrophs?
autotrophs
Carbon is an essential element for biosynthesis. What are the possible forms of C used in biosynthesis?
Both of these forms of C could possibly be used for biosynthesis depending on the organism [organic forms of C and CO2]
N is another essential element for biosynthesis. Easily accessible N in ______ can be used by virtually all organisms as a source of N.
ammonia
In biosynthesis of purines and pyrimidine, which of these is made first?
ribonucleotides
Green plants carry out a type of photosynthesis that produces O2 as a by-product. Which bacteria did we talk about that also share the same type of photosynthesis with green plants?
Cyanobacteria
What do Nitrogen fixation and CO2 fixation have in common?
- they both are energy-intensive processes
- They both require a large input of reducing power in the form of NADPH
- they both are carried out by only a handful of organisms (i.e. they are not widespread processes)
What receives electrons from NADH during fermentation?
pyruvate
What is a terminal electron acceptor in anaerobic respirations?
nitrate and sulfate
In class, we talked about how electrons cannot “fly” or “swim” and that for them to move from one substrate to the next, they need to be carried on electron carriers. Accordingly, how many forms does an electron carrier have?
two
One way that CO2 is fixed is through _______
the calvin cycle
In amino acid biosynthesis, the amino group can be transferred between molecules in a process known as ______
transamination
T/F Lithoautotrophs can use substrate level phophorylation to make ATP
False
T/F While it is beneficial to have the ETS components embedded in a membrane, they don’t necessarily need to be present in the membrane
False
T/F The difference between anaerobic respiration and anaerobic lithotrophy is in the nature of the electron acceptor
false
T/F Phototrophs use an ETS
true
T/F The main goal of respiration or fermentation is to make ATP
false
T/F Chemotrophs organize their light-absorbing pigments (chlorophylls) in the form of antenna complexes to maximize light absorption
false
T/F Catabolism is defined as the breakdown of large complex molecules into smaller ones to produce energy
True
T/F Electron acceptors are oxidized molecules while electron donors are reduced molecules
true
T/F In fermentation, all carbon in the original carbon source will eventually be released as CO2
false
T/F In a strictly fermenting cell, pyruvate would be further broken down by the PDC (pyruvate dehydrogenase complex) and the TCA (tricarboxylic acid or Kreb’s Cycle)
false
What is the CO2 fixation key enzyme?
Rubisco
What is N2 fixation key enzyme?
Nitrogenase
What is Fatty acid synthesis key enzyme
fatty acid synthase
What organism uses H2 as the electron source, CO2 as the carbon source, and does not require light to grow
Chemo-litho-auto-troph
What organism uses H2O as the electron source, CO2 as the carbon source, and requires light to grow
Photo-litho-auto-troph
What organism uses NADH as the electron source, glucose as the carbon source, and does not require light to grow
Chemo-organo-hetero-troph
Where does Carboxysome occur?
CO2 fixation in Cyanobacteria
Where does Heterocyst occur
Nitrogen fixation in Cyanobacteria
What occurs at the cell membrane?
Electron transport systems in prokaryotes
What occurs at the cytoplasm
EMP pathway in prokaryotes
Order the steps of respiration starting from pyruvate
step 1: PDC (or PDH)
step 2: TCA cycle
step 3: ETS or ETC
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
How many net molecules of ATP will be produced from the metabolism of these 20 molecules of glucose using the EMP pathway?
40
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
What type of phosphorylation is this?
Substrate level
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
In order for this cell to be able to eat more glucose molecules, it will need to have its electron carrier (the NAD/NADH pair) recycled back to the _______ form.
oxidized
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
This recycling could occur by either one of two processes, a less efficient way known as __________, and a more efficient way known as _________
fermentation, respiration
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
Assume the cell went through the more efficient way for recycling the electron carrier and that this cell is aerobic, what will be the electron acceptor in the process?
O2
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
After the completion of this more efficient process for electron carrier recycling, protons are present in a higher concentration outside than inside the cell. The cell is said to have created a/an ______ across the membrane.
PMF
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
The cell can then let these protons back in through an enzyme that will use the motion of the protons to make ATP. What is the name of this enzyme?
ATP synthase
A bacterial cell has an energy source that consists of 20 glucose molecules that are available for use. It also has all the enzymes needed for carrying out the EMP pathway. Based on what you know about this pathway.
This ATP production that was just created using the enzyme in the previous blank is known as ________ phsophorylation
Oxidative
This is a picture of a process that happens in the cell membrane of some bacteria. It involves electrons being transferred from an electron donor eventually to a terminal electron acceptor. What is the name of this system?
ETS
What is the name of component A
initial oxidoreductase
what is the name of component b
mobile electron carrier
what is the name of component c
terminal oxidase
in the process what acted as the electron donor
ammonia
what acted as the terminal electron acceptor
O2
based on the nature of the electron donor and the type of electron acceptor, this process is taking place in an _________________ cell.
aerobic lithotrophic
In the ETS, what is the most likely source of carbon?
inorganic CO2
Organisms diverge from a common ancestor by several mechanisms. Which of these refer to divergence by losing unwanted genes?
reductive evolution
Horizontal gene transfer refers to the transfer of _____ between _____ species.
a piece of DNA containing a gene or a group of genes
unrelated
A symbiotic relationship between two or more unrelated species where all partners benefit is referred to as _____.
mutualism
The chloroplast in green plants has its own genome. On the chloroplast genome, some genes are still encoded including genes for small subunit rRNA. Based on your knowledge of the endosymbiotic origin of organelles, which of these do you think the chloroplast small subunit rRNA will be most closely related to?
cyanobacteria
Related to the question above, what other genes are still encoded on the chloroplast genome but are essential to the host (host here refers to green plants or algae)? 3 things
the gene encoding for Rubisco
genes for photosynthesis
genes for CO2 fixation
Firmicutes and Actinobacteria are two of the bacterial phyla we studied. What do members of these phyla have in common?
they both have Gram positive cell walls
One of the classes of Proteobacteria harbors organisms that can use sulfate as their electron acceptor. Which one is it?
delta
Not all bacteria belonging to the Firmicutes phylum make endospores. Which of these is (are) non-spore formers?
staphylococcus
streptococcus
One of the examples of archaea we studied is the “halophilic archaea”. They have characteristics that would make their survival in one of these habitats highly unlikely. Which one of these habitats is highly unlikely to harbor halophilic archaea?
the ocean
These two fungal phyla harbor edible (i.e. can be consumed as food) fungi.
Ascomycota
Basidiomycota
Bacteria and methanogens are present in the termite gut and aid with wood digestion. What is the relationship of bacteria and methanogens TO EACH OTHER?
syntrophic
Bacteria and methanogens are present in the termite gut and aid with wood digestion. What is the relationship of bacteria and methanogens collectively TO THE TERMITE?
endosymbionts
In the ocean, you would expect to find phototrophs in the ________ zone.
euphotic
aphotic
In soil, you would expect to find methanogens in
the lower anoxic zones
Elements can take several forms with different oxidation states (remember the table on your slides?). The form of an element with the most positive oxidation state is the most ______, and so can only act as electron ______.
oxidized
acceptor
This reservoir is the fastest to recycle for C and has the major amount of N.
atmosphere
Eutrophic lakes have ____ biochemical oxygen demand (BOD)
high
Out of the three elemental cycles we studied, this element has the most oxidation states.
N
In the S cycle, this can act only as an electron donor.
H2S (hydrogen sulfide)
The reservoir of an element is the part of the biosphere that contains significant amounts of that element. A reservoir can be ____ (2 things)
a source for the element for these processes using the element
a sink of the element for those processes producing this element
T/F The central dogma that genes are transcribed to mRNA which then get translated into proteins is a common feature of all domains of life.
true
T/F When comparing Bacteria and Archaea, they both have very similar metabolism. However, there are metabolic processes that are exclusive to only one of these domains but not the other.
true
T/F Microbial ecologists classify microorganisms into different taxa. In the taxa hierarchy, phylum is at a lower taxonomic level than species.
false
species is lower
T/F Carbonate rock (or the Earth’s crust) is the largest reservoir of C.
true
T/F In wastewater treatment plants, O2 is continually supplied to the system. Accordingly, it is impossible to use methanogens in wastewater treatment.
false
betaproteobacteria
T/F The major decomposers in the ocean are viruses.
true
T/F A form of an element with an oxidation state of 0 (zero) could either be reduced or oxidized.
true
What domain of life has cell walls and contains pathogens?
bacteria
What domain of life harbors methanogens?
archaea
What domain of life harbors a breathtaking array of diversity and includes animals and plants?
eukaryotes
All domains of life share some properties including a __________ DNA, and a cellular architecture encompassing an aquous cytoplasm surrounded by a _________.
double-stranded
cell membrane
Out of the three domains of life, ____ are prokaryotic.
2
archaea
bacteria
The prokaryotic domain(s) is/are different from the eukaryotic domain(s) in having the nuclear material packed in the form of _______, and in having a ________ chromosome.
nucleoid
circular
The prokaryotic domain(s) also exhibit(s) some forms of metabolism that are completely absent from the eukaryotic domain(s). These include _______.
nitrogen fixation
Surprisingly, one of the three domains of life lacks any pathogens. This is the domain _____
archaea
Which fungal phylum we studied harbors anaerobic members that associate with animals and have a major role in the digestion of plant material in herbivorous ruminant animals, e.g. cows?
chytridiomycota
Members of this fungal phylum are usually present in the largest chamber in ruminant animal stomachs known as the ____.
rumen
Which fungal phylum we studied is known to associate with plant roots by penetrating inside the plant root cells where it forms arbuscular (tree-like) structures?
zygomycota
This fungus-root mutualistic relationship is known as ______.
endomycorrhizae
Since both fungi live inside the bodies of their hosts, the mutualistic relationships can be classified as _____.
endosymbiosis
N2 gas is converted to NH3. This process is known as _____. Some Bacteria belonging to the ______ class of Proteobacteria can carry out this process in soil. The most common example is ________. This genus is known to associate with leguminous plant roots
N2-fixation
alpha
rhizobium
NH3 is oxidized to Nitrate. This process is known as _________. Some Bacteria belonging to the _______ class of Proteobacteria can carry out this process. A very common example is _______ This genus is a lithotroph using ammonia as its electron donor.
nitrification
beta
nitrosomonas
Nitrates are reduced back to N2 gas. This process is known as _________. Some bacteria belonging to the ________ class of Proteobacteria can carry out this process. A very common example is ______. This bacterium is a very common inhabitant of our gut.
denitrification
gamma
e.coli
N2 is returned back to the atmosphere by the oxidation of NH3 to N2, also known as the________ process.
anammox
Two processes return N2 gas back to the atmosphere. Both of these processes are ________, but one of them recycles the majority of N2 back to the atmosphere. This process is ________.
anaerobic
anammox
In the aerobic carbon cycle, which of these processes would take CO2 to organic carbon?
oxygenic photosynthesis
In the aerobic carbon cycle, which of these processes would take organic carbon back to CO2?
aerobic respiration
In an anaerobic carbon cycle, which of these processes would take CO2 to organic carbon?
anaerobic lithoautotrophy
In an anaerobic carbon cycle, which of these processes would take organic carbon back to CO2?
fermentation
The process of methanogenesis will take CO2 to ________ and only occurs in the ______ carbon cycle.
methane
anaerobic
Oxygenic photosynthesis and aerobic respiration are examples of ______, while anaerobic lithoautotrophy and fermentation are examples of ________. Accordingly, oxygenic photosynthesis and anerobic lithoautotrophy are carried out by __________, while aerobic respiration and fermentation are carried out by _______.
assimilation
dissimilation
primary producers
consumers and decomposers
Help keep the H2 concentration down to ensure the completion of wood digestion…
termite gut methanogens
Aid in the breakdown of wood to simple nutrients that the termite can absorb…
termite gut bacteria
Help keep the H2 concentration down to ensure the completion of complex plant fiber digestion…
rumen methanogens
Aid in the breakdown of complex plant fibers to simple nutrients that the cow can absorb…
rumen bacteria and fungi
Provide photosynthesis-rich nutrients (or in other words carry out photosynthesis and CO2 fixation and provide the fixed C to the other partner)
any green partner
Protection of the system…
fungus in lichens
Extend to meters away and provide nutrients to the plant (especially P)…
fungus in mycorrhizae
Provides fixed nitrogen in the form of NH3…
bacteroid inside the leguminous plant root cells
Help keep the H2 concentration down to ensure the completion of wastewater treatment…
methanogens in wastewater flocs
Does the majority of organic load breakdown to CO2 in the secondary stages of wastewater treatment…
aerobic heterotrophs in wastewater flocs
Anaerobic endospore-forming firmicutes…
clostridium
Non-mycelial actinobacteria…
mycobacteria
The only prokaryotic phylum capable of oxygenic photosynthesis…
cyanobacteria
Aerobic endospore-forming firmicutes…
bacillus
Mycelial actinobacteria…
streptomyces
Evolution of two species in response to one another…
co-evolution
The intimate association of two unrelated species…
symbiosis
A group of species that share a common ancestor…
clade
The description of distinct life-forms and their organization into different categories with shared traits…
taxonomy
