Module 2 Flashcards
(164 cards)
1
Q
How do sugar molecules like glucose or mannose enter a bacterial cell?
A
They must use some form of active transport, whether its simple active transport, group translocation/phosphotransferase, or ABC transporters
2
Q
What are the three different types of simple active transport and what makes them different from each other?
A
Symport - protons in, sugars in
Antiport - protons in, sodium out
Uniport - potassium in
3
Q
Compare the three different types of active transport.
A
Simple - driven by PMF
Phosphotransferase - driven by PEP, substrate is phosphorylated
ABC Transporter - driven by ATP, cargo is bound to a periplasmic or extracellular protein and transported inside, similar to Type I Secretion systems
4
Q
Why can’t most microbes ever be cultured in isolation?
A
Syntrophy
Bacteria produce waste products, and eventually they will accumulate in their environment and inhibit the bacteria that live there. They need other organisms in that environment to metabolize and get rid of those waste products.
5
Q
What kind of bug undergoes photosynthesis, reduces hydrogen sulfide for electrons, and gets its carbon from carbon dioxide?
A
A photolithic autotroph
6
Q
What kind of bug undergoes photosynthesis, gets its electrons from methane, and its carbon from glucose?
A
A photoorganotrophic heterotroph
7
Q
What kind of bug oxidizes hydrogen sulfide, gets its electrons from hydrogen sulfide, and its carbon from carbon dioxide?
A
A chemolithic autotroph
8
Q
What kind of bug oxidizes, gets its electrons, and gets its carbons from maltose?
A
A chemoorganotrophic heterotroph
9
Q
Describe the mutualistic relationship between Riftia pachyptila and their endosymbiotic thermophiles.
A
Riftia pachyptila’s endosymbiotic microbes are chemolithotrophic autotrophs. They live in deep sea hydrothermal vents, under extreme pressure and heat. R. pachyptila exchanges H2S and O2 through its gill plume, allowing the chemolithoautotrophs in its trophosomes to take in those nutrients and produce CO2 as a waste product.
10
Q
Why do bacteria need to use active transport to get their nutrients?
A
They need to use active transport because they almost never live in an environment where there are enough nutrients that they can enter the cell via simple diffusion.
11
Q
Why do bacteria need iron to survive?
A
They need it as a cofactor for their redox reactions. It’s necessary to sustain their life.
12
Q
How has our human biology evolved to take advantage of bacteria’s iron requirements? How have bacteria evolved in response?
A
We scavenge virtually all the iron out of our environment and hold it tightly in proteins in our cells. In addition to helping us for our purposes, this deprives potentially pathogenic bacteria of a necessary cofactor for their redox reactions. In response, though, the bacteria have developed their own high-iron-binding-affinity molecules, siderophores.
13
Q
How do gram negative bacteria import iron into their cells?
A
They use a cargo-specific transport protein to move the iron-bound enterobactin into the periplasm, and then they use a type of ABC transport specific to iron-bound enterobactin to move it from the periplasm to the cytoplasm.
14
Q
What happens to the iron-bound enterobactin once it enters the cytoplasm?
A
The cytoplasm is a reducing environment, so the Fe3+ is reduced with the addition of an electron to Fe2+. But enterobactin can bind only to Fe3+, so the iron is released from it, and it is now released back outside the cell.
15
Q
What are the two means of ATP production?
A
Substrate level phosphorylation and oxidative phosphorylation.
16
Q
What does catabolism generate?
A
Energy, reducing power, and precursor molecules for anabolic pathways
17
Q
Why does the cell need reducing power? What is it used for?
A
Reducing power gives the cell the ability to use electrons taken from the reduction of NADP → NADPH to construct new organic molecules. They need it for their anabolic pathways.
18
Q
What is the most common pathway bacteria use to catabolize glucose to pyruvate?
A
EMP
19
Q
How is glycolysis regulated in bacteria?
A
Pyruvate kinase, in addition to its two binding sites for ADP and PEP, has an allosteric site that binds to fructose 1,6-bisphosphate. This gives the pyruvate kinase an incentive to make pyruvate from PEP only when there’s a high presence of fructose (meaning high levels of glycolytic activity) within the cell.
20
Q
Describe the dual role PEP plays in group translocation and glycolysis.
A
PEP powers group translocation (phosphotransferase) systems in addition to being dephosophorylated to create pyruvate and ATP in glycolysis. So if you’re a bacterium that’s starving for glucose, you’re going to use that PEP in group translocation, importing more glucose instead of breaking it down in glycolysis.
21
Q
Why is glucose favored over other sugars?
A
Because it fits directly into the glycolytic pathway. Everything else needs to be modified before it can enter glycolysis, making it less efficient.
22
Q
Why must bacteria use their reducing power?
A
Because there’s only a small pool of NAD+ in the cell. If all of that shifts to NADH and can’t be reduced back to NAD+, the oxidation in EMP glycolysis will suffer.
23
Q
How do bacteria synthesize precursor molecules for use in anabolic pathways?
A
Intermediate molecules are pulled off from the different pathways. Not every carbon that enters these pathways will go all the way through, there are siphons at different points.
24
Q
Yields of EMP
A
2 NADH, 2 ATP
25
Yields of ED
1 NADH, 1 NADPH, 1 ATP
26
Yields of PPP
2 NADPH and hella carbon skeletons, precursors for anabolic pathways
27
How does EMP generate ATP?
Substrate-level phosphorylation
28
Where are EMP, ED, and PPP found in nature?
EMP and PPP are found in all organisms, prokaryotes and eukaryotes.
ED is found only in bacteria
29
What makes PPP different from the other glycolytic pathways?
It doesn't generate energy and it doesn't involve substrate level phosphorylation
30
What’s the difference between NADPH and NADH? (not looking for biochemical differences here!)
NADPH is better at biosynthetic reactions, while NADH is better at producing energy (it does so by shoving electrons onto things, hopefully those things are the ETC)
31
If an E. coli bacterium has a high amount of ATP generated from ED, where will it send its G6P and why?
To the PPP to synthesize the precursor molecules for new amino and nucleic acids, in preparation to commence replication
32
If an E. coli bacterium is depleted of ATP, where will it send its G6P?
To the EMP to generate more ATP
33
What does fermentation do?
Regenerates NAD+
34
What happens to a bacteria if NAD is depleted? How is this problem solved?
If NAD is depleted, glyceraldehyde-3-phosphate (G3P) oxidation stops. The solution is to regenerate NAD by oxidizing NADH and reducing pyruvate.
35
Why does Strep. need to live in very nutritious environments? Another question with this same answer is “Why are strep often involved in the production of fermented foods?
Because they're not able to use the TCA cycle, they need a constant energy source, i.e. a nutritious environment.
36
How/why does our enamel decay?
The bugs in our mouth produce lactic acid as their reduced pyruvate byproduct, which is secreted out of their cells where it collects on our teeth and eats through our enamel.
37
Describe the importance of fermentation to human health.
All our dietary fiber is food for our microbiome. They eat this fiber, which we are unable to digest, and produce and secrete their fermentation end products, the most important being butyric acid. Butyric acid is the #1 energy source for all our cells in immediate contact with the microbiome, stretching from the lumen to the colon. Those cells aren’t fed by our bloodstream. They need that butyric acid to diffuse directly into their cytoplasm, where it diffuses further to their mitochondria where it’s used in our TCA cycle. Butyric acid also gets into our lamina propria and binds to G-protein coupled receptors on macrophages, dendritic cells, T-cells, etc, and promotes less inflammation in our GI tract.
38
Almost all of our cells in immediate contact with the interior of our GI tract, stretching from our lumen to our colon, aren’t fed by our bloodstream. How are they fed instead?
Butyric acid, a fermentation endproduct from microbes in our microbiomes, diffuses into those colonocytes.
39
How do high fiber diets prevent colon cancer?
The Warburg Effect.
Precancerous cells stop relying so heavily on the mitochondria and instead ramp up the glycolytic pathway, generating their ATP through substrate level phosphorylation. In shutting down the mitochondria, the butyrate diffusing into the cells is not being hydrolyzed, and as the butyrate concentration increases it inhibits histone deacetylase (HDAC) which changes the gene expression and induces apoptosis.
40
Which uses electrons more efficiently: respiration or fermentation?
Respiration
41
Compare how pyruvate is used in respiration versus fermentation.
Respiration --> pyruvate is decarboxylated to acetyl-CoA and shunted along the TCA cycle through various oxidation and reduction stops
Fermentation --> pyruvate is an electron dump
42
Describe the genesis of proton motive force.
The NADH generated by membrane proteins in TCA, PPP, and ED moves protons from the cytoplasm across the cell membrane.
43
List the three most important things PMF can do.
1. Generate rotation for the flagella
2. Drive active transport
3. Gated across ATP synthase, drives oxidative phosphorylation to create ATP from phosphates free in the environment
44
What metabolic type of organism are E. coli? What does that mean for their biochemistry?
Facultative anaerobes. This means that they use oxygen to the exclusion of any other electron acceptor, until all their oxygen is gone.
45
What happens if E. coli is placed in an oxygen-deprived environment?
They will continue respiration by reducing nitrate or other forms of nitrogen to nitrate. However, less PMF is generated from this, which is why they spend so much of their resources making a branched ETC so they can use every bit of oxygen.
46
How and why does our atmosphere maintain its 78% N2(g) state? Why isn’t our planet’s nitrogen tied up in organic material?
Our atmosphere maintains its N2(g) state because N2 is the final endproduct of the ETC in soil-microbe Paracoccus denitrificans. These bug respirate anaerobically and can use all different forms of nitrogen, including NO3, NO2, NO, N2O. Once it finishes with one product, unless it has reached its final-final endproduct, N2, it can shunt that nitrogen molecule back into its ETC until it is finally reduced down to N2.
47
Who are the true masters of the glycolytic pathways?
Salmonella
48
How does Salmonella enterica mediate infectious population growth?
They use their Type III secretion systems to directly inject proteins into our cells. These proteins (re: toxins) change our epithelial cell’s cytoskeleton and cause the salmonella to be engulfed by the cell. Salmonella induces its own uptake. From there, our host cells sense danger and release cytokines to attract help from the white blood cells. The WBCs arrive and release ROS to try and kill the salmonella, but salmonella are incredibly resistant to ROS so all it really does is kill other competing bacterial species. They intentionally induce inflammation to kill competing microbes.
The end goal of this is to change sulfates into tetrathionate, which the salmonella can use as a terminal electron acceptor, allowing them to do anaerobic respiration, which is more efficient than fermentation and allows the salmonella to multiply quite rapidly.
49
How do bugs that lack electron transport chains drive their active transport and flagella (if they have them)?
They rotate their ATP synthase proteins backwards to pump protons out. It burns the ATP generated in glycolysis, but the PMF gained is more advantageous.
50
Which energy production method, fermentation or aerobic respiration, is better? Why?
Aerobic respiration.
Uses electrons more efficiently
51
Why does E. Coli, a facultative anaerobe, have a branched Electron Transport chain rather than simply shifting to the use of NO3 when O2 becomes limiting?
Less PMF is generated from reducing nitrate than from branching the ETC to continue reducing oxygen.
52
What is a branched electron transport chain?
The protein that reduces oxygen in normal ETC can work only when oxygen levels are high. A branched electron chain solves this problem. The branching occurs when a new protein is substituted for the old one when oxygen levels are low, allowing for PMF to continue being produced, albeit at lower levels.
53
What makes a microbe a facultative anaerobe?
The ability to use oxygen to the exclusion of any other electron acceptor, until all the oxygen is gone.
54
What would happen if a mutant e. Coli lost its ability to use O2 as a terminal electron acceptor? What if it lost its ability to use NO3 as an electron acceptor instead? If one of each of these two mutants were in an environment with adequate supplies of both O2 and NO3, what would happen?
The mutant that can’t use oxygen will use nitrate as its terminal electron acceptor.
The mutant that can’t use nitrate will use oxygen as its terminal electron acceptor, and in the absence of oxygen it will use other terminal electron accepts such as nitrite, TMAO, DMSO, etc.
The mutant that can use oxygen will proliferate and thrive more than the mutant that can’t, as it will be able to generate more PMF and will have and advantage over the other.
55
Why don’t infectious cells secrete toxins at all times? Why do they wait until their population has reached a certain size?
Many infectious cells don’t want to start secreting toxins until they’ve reached a large enough population size because if they did, they’d risk attracting the host’s immune system while their population is still small enough to be easily wiped out.
56
Where would you find higher levels of AHL, inside the cell wall or outside the cell wall? Why?
Neither.
The acyl side chain allows the molecule to diffuse freely across membranes, so there should be equal concentrations of AHL inside and outside the cell.
57
How do AHL levels regulate gene expression?
When AHL levels become high, they bind to LuxR, a transcription factor, activating them. Once activated, LuxR changes conformation and becomes dimers that bind to specific genes coding for quorum-dependent proteins and increases the transcription of AHL synthase, which drastically increases AHL levels.
58
Can a bacterium recognize the AHSL produced by another species? Why or why not?
Sometimes, mostly no. Each species produces its own unique AHSL molecules, and recognizes the molecule based on those minor structural variations. A bacterium of one species is effectively blind to the AHSL molecules from other species. However, there are some specific cases in which two AHSL molecules are similar enough that the can confuse other populations.
59
What feature of quorum sensing demonstrates its importance to bacterial survival?
The fact that it evolved twice: once in gram negative bacteria, and again in gram positive bacteria.
It hadn’t evolved yet when the ancestral prokaryotes split into gram positive and gram negative domains, but it became so important to survival that all bacterial species needed to evolve some sort of population density sensing mechanism to survive, hence why it evolved twice.
60
Describe the life cycle of Vibrio fisherii within the Hawaiian Bobtail Squid.
Vibrio fisherii live in a mutualistic relationship with the nocturnal Hawaiian Bobtail Squid. During the day, the HBS buries itself into the sand and sleeps. During this time V. fisherii populations within its stomach increase until they reach quorum. At night, the HBS wakes up and enters the water column, the bioluminescence now being produced by the V. fisherii now at quorum in the stomach protects the HBS from predators. The predators sense their prey by sensing decreases in moonlight from fish swimming in front of the moon, casting a shadow. That bioluminescence prevents the HBS from casting a shadow, allowing it to survive the night. When morning comes, and the HBS goes back into the sand to sleep, the stomach is full of waste product, so it squeezes its stomach and expels 95% of its stomach contents, leaving behind only a small amount of the V. fisherii to spend the day growing and reaching quorum once again.
61
Describe the AHSL levels present extracellularly of a bacterial population during its different life/growth phases.
Lag Phase → Low AHSL levels
Log Phase → Increasing AHSL levels
Stationary Phase → High AHSL levels
Death Phase → Decrease AHSL levels
62
What phenotype do Vibrio fisherii present when LuxR levels are low? Why?
No bioluminescence. When LuxR proteins are low, the population is likely low, so there wouldn’t be enough AHSL to interact with the LuxR to turn on the bioluminescence.
63
What phenotype do Vibrio fisherii present when LuxR levels are high? Why?
Bioluminescence. When LuxR levels are high, there is enough to interact with the AHSL to turn on the bioluminescence.
64
What’s the difference between chemotaxis and response regulators?
Chemotaxis → changes protein function
Response regulators (aka quorum sensing) → changes gene expression
65
Why/how can prokaryotic species survive and thrive at much higher temperatures than us multicellular eukaryotes?
The more complex you are, the more ways there are for heat to kill you.
66
What kind of microorganism prefers to live in environments at or below 15 degrees Celsius?
Psychrophiles
67
What kind of microorganism prefers to live in environments between 20 and 30 degrees Celsius?
Psychrotrophs
68
What kind of microorganism prefers to live in environments between 20 and 45 degrees Celsius?
Mesotrophs
69
What kind of microorganism prefers to live in environments between 55 and 65 degrees Celsius?
Thermophiles
70
What kind of microorganism prefers to live in environments between 80 and 105 degrees Celsius?
Hyperthermophiles
71
What life/growth phase is a bacterial population in when an equal number of their population are “dying” and reproducing (when the birth and death rate are the same)? What does “dying” mean in this case?
Stationary phase. “Dying” in this case means that the microbes are incapable of replicating, senescence.
72
What life/growth phase is a bacterial population in when its total population is the lowest?
Lag phase
73
What life/growth phase is a bacterial population in when the medium they are in is high in nutrients and low in waste products?
Log phase
74
What life/growth phase is a bacterial population in when the rate at which its population is changing is negative?
Death phase
75
Why are archaea more closely related to us eukaryotes than bacteria?
Archaeal transcription is far more alike to eukaryotic transcription than bacterial transcription, indicating that they are closer relatives to us eukaryotes than our bacterial friends. Like us eukaryotes, they use more than one RNA Polymerase during transcription, and while they aren’t identical to ours (i.e. they aren’t the same molecules), they do share some homologous polymerases with us, in addition to their own unique polymerases.
76
What’s the difference between the core enzyme and the holoenzyme?
The core enzyme is the portion of RNAP that can synthesize mRNA.
The holoenzyme is the core enzyme with the addition of sigma factor, which is necessary to recognize the promoter sequence.
77
Describe the structure and function of the six protein subunits that make up the holoenzyme.
Two 𝜶 subunits
One 𝝱 subunit → binds to the DNA
One 𝝱’ subunit → largest gene and largest protein bacteria have. It’s intrinsically disordered region makes it more prone to conformation changes and denaturation
One 𝞈 subunit → maintains the structure of 𝝱’, keeps the holoenzyme functional
One 𝞼 subunit → provides the promoter-specific recognition site
78
A student in your dorm is diagnosed with a severe case of bacterial meningitis (not to worry, they survive and make a full recovery). As a prophylactic measure, everyone in your building is treated with Rifampin. Why should you not be worried about Rifampin harming your nascent eukaryotic cells?
Rifampin binds to the 𝝱 subunits of bacterial RNAP and inhibits mRNA synthesis. Since its target molecule is only found in bacteria, rifampin won’t harm our eukaryotic cells.
79
How would a bacteria acquire resistance to Rifampin?
Usually through mutations altering one or a few amino acids in the 𝝱 subunit, which decreases rifampin’s binding affinity to those 𝝱 subunits.
80
What would happen to transcription if 𝞼 factor isn’t removed from the holoenzyme?
Promoter escape won’t happen and the holoenzyme won’t be able to leave the promoter.
81
What would happen to transcription if 𝞼 factor isn’t present?
The core enzyme won’t be able to recognize and bind to the promoter sequence, so transcription wouldn’t occur.
82
What would happen to transcription if 𝞈 is absent?
𝝱’ would be more prone to conformational changes or denaturation, so it may become dysfunctional, preventing transcription
83
What would happen to transcription if DNA gyrase is absent?
The positive supercoils put into the DNA by the replication bubble wouldn’t be relaxed, which would stop transcription.
84
What makes Ciprofloxacin lethal to bacteria? Why is it lethal only to bacteria?
Ciprofloxacin kills bacteria by inhibiting DNA gyrase, which inhibits transcription. It is lethal only to bacteria because DNA gyrase isn’t found in eukaryotic cells.
85
Why can bacteria make more than one protein from a single piece of mRNA?
Because their ribosomes can bind to more than one region in a single piece of mRNA. Wherever there’s a Shine-Dalgarno sequence, their ribosomes can bind and initiate translation of a new protein. This is very different from our ribosomes, which can bind only to the 5’ cap on the end of each mRNA strand.
86
How do bacterial ribosomes differ from eukaryotic ribosomes?
Bacterial ribosomes can bind to Shine-Dalgarno sequences internally, anywhere in the mRNA strand, allowing them to make more than one protein from one mRNA strand. Eukaryotic ribosomes can make only one protein from each mRNA as they can bind only to the 5’ cap at the front end of each mRNA strand.
87
How does transcription work in eukaryotic mitochondria?
The same way it does in bacteria
88
What happens to E. coli’s 𝞼 factors when it moves from exponential phase to stationary phase?
When a population moves from exponential phase to stationary phase, each individual bacterium’s transcription profile needs to change to meet the new environment. So, E. coli’s pool of 𝞼 factors transitions from 𝞼70 to 𝞼38.
89
How do bacteria use 𝞼 factors to adapt to different environmental conditions?
They have different 𝞼 factors for different types of promoters, and subsequently different types of genes. For a bacterium, shifting one’s pool of 𝞼 factors from one type to another allows them to express different types of genes and proteins that are more advantageous in their new environment.
90
How does salmonella regulate the synthesis of its flagella?
Through regulation of sigma and anti-sigma factors, specifically 𝞼28 and FlgM. Most of the time, 𝞼28 is not free floating in the cytosol, it’s bound to FlgM. As the bug begins to synthesize flagellar basal bodies, the basal body acts as a secretion system and rips the FlgM outside the cell. Once enough FlgM has been ripped away, enough 𝞼28 is now free floating to bind to the genes that code for the flagellar motors and initiate their transcription.
91
How does clostridium regulate their 𝞼 factors? Put another way, how do they shift their pool of 𝞼 factors?
Most of the time, clostridium’s 𝞼 factors are bound to CBM domains anchored in the cell wall. When polysaccharides are present extracellularly, they bind to the extracellular receptor of the CBM which changes its conformation and releases the 𝞼 factor. Those 𝞼 factors are then free to bind to promoters for the genes coding for cellulosomal proteins, the enzymes that are secreted to break the polysaccharides down.
92
How does salmonella regulate their 𝞼 factors? Put another way, how do they shift their pool of 𝞼 factors?
Most of the time, 𝞼28 is not free floating in the cytosol, it’s bound to FlgM. As the bug begins to synthesize flagellar basal bodies, the basal body acts as a secretion system and rips the FlgM outside the cell. Once enough FlgM has been ripped away, enough 𝞼28 is now free floating to bind to the genes that code for the flagellar motors and initiate their transcription.
93
What happens to the levels of 𝞼 factor within a clostridium when polysaccharides are present extracellularly?
𝞼 levels increase.
94
What happens to the levels of 𝞼 factor within a clostridium when polysaccharides are absent?
𝞼 levels decrease.
95
Why do salmonella wait to build their flagellar motors?
If the flagella are fully formed before they’re needed for chemotaxis, the salmonella would just be burning through and wasting PMF.
96
Compare and contrast factor dependent transcription termination with factor independent transcription termination.
Factor Dependent - uses exogenous proteins, NusA and Rho. Unique to prokaryotes.
Factor Independent - no exogenous proteins involved, intrinsic to RNA's structure and encoded within the DNA
97
What will happen to RNAP if it encounters a stem-loop structure with no poly-uracil tail at the end?
It will pause
98
What will happen to RNAP if it encounters a stem-loop structure with a poly-uracil tail?
It will stop and drop off.
99
How are stem-loop structures formed? What kinds of sequences have an affinity for forming stem-loop structures?
Inverted repeats can form stem-loop structures.
100
What would happen to transcription if RNAP encounters a stem-loop structure when NusA isn’t bound?
It will continue, or pause briefly then continue.
101
What would happen to transcription if RNAP bound to NusA encounters a stem-loop structure?
Rho will catch up and kick RNAP off the DNA.
102
What does it mean when we say that picornaviruses express over 12 distinct functional proteins despite the fact that the viral genome possesses only one gene?
Their genomes are polycistronic. One gene can code for multiple different proteins because the ribosomes that translate those genes can bind intrinsically, anywhere with a promoter sequence, regardless of the location within the genome.
103
What is factor independent transcriptional termination and what is required for it to work/be activated/induced?
Factor Independent transcription termination, aka intrinsic transcription termination, happens when the RNAP meets a section of RNA that has formed a stem-loop structure with the addition of a poly-uracil tail. This structure makes the RNAP fall off. Both the stem-loop and the poly-uracil tail are required for the RNAP to fall off.
104
What features of a DNA sequence make it more likely to be a factor independent transcriptional terminator?
Inverted repeats
105
Why can Factor Dependent transcriptional termination not function in a eukaryotic cell?
Because it is dependent on transcription and translation happening in the same place at the same time.
106
Why are inverted repeats so effective as binding sites in operators and activator sites?
The DNA binding proteins have a binding affinity for one specific sequence. If that sequence is repeated, such as in an inverted repeat, an additional DNA binding protein can bind and strengthen the repression of transcription. The additional protein-protein interactions strengthen the protein’s repression.
107
How have bacteria divided transcriptional responsibilities without having multiple different RNA polymerases?
One RNAP synthesizes all the RNA, however the labor is divided by using alternative sigma factors. The sigma factors have different affinities for different types of genes. Genes will only be expressed if their respective sigma factors are predominant or at least present in the cell.
108
What process can change the length of the poly T tract of a DNA sequence? What kind of change in gene expression does this lead to?
Slipped Strand Mispairing, can lead to a change in reading frame, and depending on how many nucleotides were inserted or deleted could lead to insertion or deletion of amino acids, a change in all amino acids downstream of the mutation, or the revealing of a cryptic stop codon, truncating the protein.
109
What is Slipped Strand Mispairing (SSM), and what features of a DNA sequence would make it susceptible to this phenomenon?
SSM happens when repetitive DNA sequences dissociate and form a loop during replication, either elongating or shortening the DNA strand and causing a change in the reading frame. Repetitive sequences are susceptible to this phenomenon.
110
What causes frameshift mutations and how do they affect translation and protein synthesis?
Insertion or deletion of one or more nucleotides via Slipped strand Mispairing causes frameshift mutations. If the insertion or deletion is in a multiple of three, one amino acid will be added or removed respectively. If the insertion or deletion is not in a multiple of three, every amino acid downstream of the mutation will change, and the shift in reading frame may reveal a cryptic stop codon, truncating the protein.
111
What is phase variation, and what features of a DNA sequence would make it capable of phase variation during replication?
Occurs at the population level. A gene under phase variation expresses two phenotypes within a population: on and off. Repetitive sequences make genes susceptible to PV, as they are more likely to undergo the SSM required for PV.
112
How do bacteria prevent the translation+transcription of genes that have been affected by a frameshift mutation?
If the frameshift mutation exposes a cryptic stop codon, the ribosome translating the mRNA will stop. Because the ribosome and RNAP are attached (remember that transcription isn’t separate from translation in bacteria), Rho will catch up to the ribosome and kick RNAP off the DNA, preventing the translation of a useless gene.
113
How do bacteria manipulate the probability of single-nucleotide insertion frameshift mutations? What aspect of bacterial genetics makes this process easier?
Bacteria tend to use repetitive sequences that are NOT in replicates of three, causing more impactful frameshift mutations. It sets up a situation where some cells in a expressing one protein one way and some cells the other way, so if their environment shifts and one allele becomes more advantageous than the other, the allele frequency in that population will shift.
114
What is the outcome of backwards slippage in slipped strand mediation?
Insertion
115
What is the outcome of forwards slippage in SSM?
Deletion
116
What is the difference between Antigenic Variation (AV) and Phase Variation (PV)?
PV is the expression of two phenotypes of one gene in a population, with those phenotypes being on and off.
AV is the expression of only one of multiple genes within a population at a time.
117
Why haven’t we been able to develop a vaccine against Neisseria gonorrhoeae?
Because there are too many pilus protein antigenic variants. The recombination their pilS genes undergoes creates an almost unlimited number of variants, too many to create an effective vaccine against.
118
What is a regulon?
A series of unconnected genes controlled by one regulatory protein
119
What is an operator?
DNA sequences that bind to repressor proteins to hold back and/or decrease transcription.
120
Why is ssDNA an indicator of DNA damage?
Lesions, such as pyrimidine dimers, cause replication to pause, leaving ssDNA free floating for longer than usual. When there’s too much ssDNA free floating or the ssDNA has been out for a long time, that’s a sign that the damage is severe.
121
What happens when RecA initiates LexA’s self-destruction?
There’s less LexA to bind to the operator sequences of the uvrABC repair system, allowing those genes to be transcribed to then find and replace the damaged DNA.
122
What happens when LexA levels drop?
More and more repair pathways in the SOS response system will be transcribed.
123
What is the last gene to be expressed in SOS response? Why is this one last?
umuDC. It codes for DNA Polymerase IV, the “sloppier copier.” This DNAP fixes lesions with very poor fidelity, however unlike more fidelous polymerases it can actually fix those lesions. Fixing the larger problems is worth the bp mistakes.
124
What signal detected inside a bacterium initiates the activation of the SOS response? What molecule detects this signal? What does this molecule then do?
Single stranded DNA. that’s the abnormal situation inside the cell, it's usually a rare commodity. When replication forks can’t be resolved, that's when there's problems, so the ssDNA really is the SOS signal.
125
Why are DNA binding proteins almost always sequence specific to inverted repeats?
Because the inverted repeat allows for a second DNA binding protein to bind and strengthen the repressing power through protein-protein interactions in addition to DNA-protein interactions.
126
Why is it a good thing that the lac operon’s repressor isn’t 100% effective?
If the repressor was 100% effective, there’d be no expression of 𝝱-galactosidase, permease, and transacetylase, (especially permease!) which means the cell wouldn’t be able to import lactose should tumble into a pocket of it.
127
What is the true inducer of the lac operon?
Allolactose, an isomer of lactose
128
What happens to β-galactosidase when its cellular levels are high?
It stops isomerizing lactose to allolactose and instead hydrolyzes lactose into glucose and galactose.
129
What happens to β-galactosidase when its cellular levels are low?
It isomerizes lactose into allolactose to induce allolactose.
130
How does cAMP control the lac operon?
It allosterically modifies CAP, allowing it to bind to the promoter and activates transcription. CAP binds to the activator site that promotes the transcription of the lac operon.
131
What happens to lac operon transcription levels when glucose is absent and lactose is present?
Transcription is high
132
What happens to lac operon transcription levels when glucose and lactose are present?
Transcription is low
133
What happens to lac operon transcription levels when glucose and lactose are absent?
Transcription is low
134
What happens to lac operon transcription levels when glucose is present and lactose is absent?
Transcription is low
135
What happens to trp operon transcription levels when tryptophan levels are high?
Transcription is low
136
What kind of control regulates the trp operon?
Negative control
137
What happens to trp operon transcription when tryptophan levels are low?
Transcription is high
138
Why is attenuation unique to prokaryotes?
Because it is dependent on transcription and translation happening in the same place at the same time.
139
What about the tryptophan attenuation gene makes it a barometer for cellular tryptophan levels?
It contains a leader gene with two trp amino acids in a row. If the ribosome has to stall and wait for a trp-charged tRNA, that’s an indicator that cellular tryptophan levels are low and the cell needs to make more.
140
What is the role of the leader peptide in the process of tryptophan synthesis?
Leader peptide has no role. The question is whether it can be made or not. It's a barometer if a bacterium can make that leader peptide easily, it means that trp is present at high level so it doesn’t need to make more. Not enough tryptophan charged tRNA, and it will struggle to make the peptide if trp levels are low.
141
How does a ribosome affect transcription of the tryptophan operon?
Attenuation.
The attenuation gene contains two trp codons in a row → if the ribosome stalls when translating this transcript, Rho will catch up to the ribosome and terminate transcription. That transcript’s protein won’t be made, and the absence of this protein signals that cellular trp levels are low and that the trp operon needs to be transcribed.
142
What kind of control regulates the maltose operon?
Positive control
143
What is the general idea of enzyme repression?
The presence of a pathway’s end products decreases the transcription of the genes in that pathway.
144
How does enzyme repression work in the context of arginine repression?
Arginine binds to the repressor protein and changes its conformation, allowing it to bind to the operator and preventing the transcription of the arginine operon.
145
Is enzyme repression an example of positive or negative control?
Negative control
146
How does enzyme induction work in the context of the lac operon?
Allolactose allosterically modifies the repressor protein, changing its conformation and preventing it from binding to the operator, allowing transcription to proceed.
147
What's the difference between enzyme repression and enzyme induction?
Repression - allosteric modification allows the repressor to bind to the operator, represses transcription
Induction - allosteric modifier prevents the repressor from binding to the operator, induces transcription
148
What is the most used GRS in E. coli?
Catabolite repression
149
List some different types of GRS in E. coli.
SOS response, catabolite repression, oxidative stress, aerobic respiration, anaerobic respiration, etc.
150
Why do E. coli use glucose to the exclusion of every other carbon source?
Because it is more efficient. It fits directly into the glycolytic pathway. All other sugars need to be modified before entering glycolysis, making it less efficient.
151
Why is catabolite repression sometimes called “the glucose effect”?
Because glucose mediates the catabolite’s repression. It ensures that nothing is wasted making things to break down alternative carbon sources when glucose is present, it ensures that the cell uses its resources efficiently.
152
How does cAMP control the lac operon?
cAMP binds to CAP, allowing it to bind to the promoter, inducing transcription.
153
What is the function of Catabolite Activator Protein (CAP)?
CAP ensures that genes for the catabolism of less favorable energy sources remain untranscribed until more favorable energy sources are depleted.
154
How does the Phosphotransferase System (PTS), aka Group Translocation, dictate sugar use?
With glucose-specific EIIA phosphorylation. When glucose is present, EIIA’s PO4 is transferred to make G6P. When glucose is absent, EIIA’s pool becomes predominantly phosphorylated, and then induces adenyl cyclase to stop inducer exclusion of other sugar options.
155
What happens to EIIA when glucose is present?
Its pool shifts to being predominantly nonphosphorylated.
156
What happens to EIIA when glucose is absent?
Its pool shifts to being predominantly phosphorylated.
157
What happens to adenyl cyclase when glucose is present?
It is inactive.
158
What happens to adenyl cyclase when glucose is absent?
It is active
159
Autotrophs
Carbon source is CO2
160
Heterotrophs
Carbon source is reduced, preformed, or organic molecules from other organisms
161
Phototrophs
Energy source is light
162
Chemotrophs
Energy source is the oxidation of some molecule, organic or inorganic
163
Lithotrophs
Electron source is reduced inorganic molecules
164
Organotrophs
Electron source is organic molecules
