Module 1 Flashcards
An absent-minded student forgets to de-stain their bacteria with alcohol during the Gram staining period. Assuming all other parts of the protocol were followed perfectly, what kind of bacteria would this forgetful student think they have? Why?
Gram positive, because the purple stain wouldn’t be washed away. If the bacteria was gram negative, the purple dye would still be in their thin peptidoglycan layer, resulting in a purple stain, where if the student had done the procedure correctly there should be a pink stain.
How do gram negative bacteria acquire resistance to β-lactams? How is this different from gram positive bacteria?
Most gram negative bacteria acquire resistance to ꞵ-lactams by acquiring genes for ꞵ-lactamases, enzymes that cleave the ꞵ-lactam antibiotic in two. Most gram positive bacteria, however, acquire resistance to ꞵ-lactams by acquiring genes that alter their transpeptidases, such that they still bind to D-alanyl D-alanine but no longer to the ꞵ-lactam antibiotics.
Why would you use augmentin to treat a β-lactam antibiotic resistant gram negative infection? Why would you not use augmentin to treat MRSA?
A gram negative bacteria that is resistant to beta lactams is likely producing lactamase into the environment, effectively neutralizing the antibiotics. However, when augmentin is added to the treatment plan, it distracts the beta lactamase enzymes. It takes up their time so that the original antibiotics can sneak past and get their job done. However, you would not use this tactic with MRSA, because its resistance isn’t based on beta lactamase. Its resistance is based on modifications to its transpeptidase, transforming into an enzyme called MecA. MecA can still form the crosslinks between peptidoglycan molecules, but it cannot bind to any beta lactam molecule, so augmentin is completely ineffective.
How are flagella different in Gram Negative vs Gram Positive bacteria?
Because gram negative bacteria have two lipid membranes making up their cell wall, the basal bodies of their flagella have two rings, one to anchor into each lipid membrane. The basal bodies of the flagella in gram positive bacteria, because they need to anchor into only one membrane, have only one ring.
Why do mycobacteria fail to stain in Gram protocols? How do we stain them instead?
Mycobacteria are coated in mycolic acid, producing a highly hydrophobic waxy coating that is impervious to many dyes, including those used in typical Gram staining protocols. Instead, we need to use an Acid-Fast Stain to visualize them. The protocol cooks the mycobacteria in the presence of carbolfuchsin, which drives the pink dye past the mycolic acid. Then the bacteria are washed with acidified hydrochloric acid. All other bacteria will give up the carbolfuchsin in the presence of acidified hydrochloric acid, but again because of its waxy mycolic acid coating, the pink dye holds fast.
Bacteria do not have organelles. What do they have instead?
Intracellular compartments, also known as microcompartments or inclusions. Some are bound by proteins, which facilitate one-way diffusion into the microcompartment/inclusion.
What is endosymbiosis and what is its significance?
Where one organism becomes a part of another organism, inside of the other, and the two mutually benefit from each other.
When our ancestral archaeal cell engulfed a bacterial cell to create the mitochondria, what advantage(s) did the archeal cell gain?
The bacterium reduced O2 to H2O via aerobic respiration.
The bacterium C. diff uses spores to access new spores. Why does this bacterium use spores, and how do these spores know when to trigger germination?
Spores aid the bacterium in accessing new hosts because the vegetative cell is Non-O2 tolerant anaerobic bacterium, yet the spore is insensitive to such harsh environments. C. diff spores ingested by a novel host are triggered to germinate by host bile acid as this signals that the spores are now past the stomach acid.
What enzyme, present in our tears in saliva, initiates bacterial lysis? How does it do this? What class of enzymes in bacteria is this similar to?
Lysozyme breaks down the beta 1-4 linkage between the NAM-NAG sugars, which weakens the cell wall enough that it causes the cells to burst. These enzymes are similar to bacterial autolysins.
How is the newly synthesized peptidoglycan monomer transported to the periplasm or extracellular environment?
The peptidoglycan monomer is attached to the lipid bactoprenol and by the action of the enzyme flippase/MurJ is transported across the periplasm or cell membrane.
Which antibiotic inhibits the bacteria’s ability to transport new peptidoglycan from the cytoplasm to the periplasm or extracellular environment?
Bacitracin
According to Mark, what is the biggest difference between a gram positive and a gram negative bacteria?
Gram positive bacteria use a glycine interbridge to crosslink their peptidoglycan molecules.
How is studying thermophilic microbes useful to other scientific fields?
PCR came from thermophilic bacteria
Why is peptidoglycan synthesized with five amino acids, even though the final form has only four? What purpose does the fifth amino acid serve?
The fifth amino acid is cleaved during transpeptidation to provide the activation energy to create the crosslinking peptide bond between two peptidoglycan molecules.
How is the newly synthesized peptidoglycan monomer transported to the periplasm or extracellular environment?
The peptidoglycan monomer is attached to the lipid bactoprenol and by the action of the enzyme flippase/MurJ is transported across the periplasm or cell membrane.
What makes peptidoglycan such a unique molecule?
It is only found in bacteria. No archaea or eukaryotes have peptidoglycan
Uses both L and D isoforms of amino acids. Again, only bacteria can do this, archaea and eukaryotes can only use L isoforms
NAM isn’t found in eukaryotic cells
A lactyl group links the peptide portion of peptidoglycan to which molecule?
NAM
What specific molecule in the bacterial lipopolysaccharides performs the same function as glycerol?
NAG-Phosphate dimer
Which portion of Lipopolysaccharide is actually an endotoxic moiety?
Lipid A
Where can Lipopolysaccharide be found in the bacterial cell?
Only in the outer leaflet of the outer membrane in gram negative bacteria.
In addition to transformation between bacteria, what was Griffith demonstrating in his mouse-pneumonia experiments?
Griffith’s experiments showed the importance of the capsule to virulence. Because the rough cells didn’t have a capsule, they couldn’t avoid phagocytosis as well as the smooth strains that had the capsule.
Why are some bacteria, like coccis, round, while others, like bacilli, are rods? What about their cellular/chemical makeup determines these different shapes?
Coccis are round because they lack MreB structural proteins. Bacilli, rod shaped bacteria, will become round if they lose their genes for MreB.
What are hopanoids and how are they important to bacterial life?
Hopanoids are a diverse group of molecules, and are the most abundant organic molecule in Earth’s biomass. They are an example of parallel evolution, as they fulfill the same function and are synthesized from the same precursor molecule (isoprenes) as cholesterol, found in eukaryotes. They are stiffening agents used to increase the rigidity of bacterial cell membranes, and are so hardy that archaeologists use them to identify oil samples.
What are MotAB proteins and what are their purposes in bacterial flagella?
MotAB proteins comprise the stator and are the gates for protons to pass through to the cytoplasm.
What is the antibiotic mechanism of cycloserine?
It inhibits the alanine-racemase complex by interfering with D-alanine’s synthesis from L-alanine.
What is the antibiotic mechanism of vancomycin?
It binds to the D-alanyl D-alanine and by the nature of its enormous size blocks the peptidoglycan from entering the sacculus.
What is the antibiotic mechanism of bacitracin?
It prevents the recycling of bactoprenol by inhibiting the enzyme that catalyzes the phosphate hydrolysis that produces the activation energy necessary to take bactoprenol back across the cell membrane.
What is the antibiotic mechanism of penicillin?
Inhibits transpeptidation by binding to transpeptidase.
What does MAMPs stand for?
Mocrobial Associated Molecular Patterns
How have humans evolved to fight agains MAMPs?
We have evolved toll-like receptors on the surface of our cells, which signal the cell to release cytokines which then summon the immune system to squelch the infection.
List some examples of MAMPs
LPS, peptidoglycan, dsRNA, flagellin
What enzyme, present in our tears in saliva, initiates bacterial lysis? How does it do this? What class of enzymes in bacteria is this similar to?
Lysozyme breaks down the beta 1-4 linkage between the NAM-NAG sugars, which weakens the cell wall enough that it causes the cells to burst. These enzymes are similar to bacterial autolysins.
What are Penicillin Binding Proteins (PBPs) also known as and what is their function?
Transpeptidases. They form the crosslinks between peptidoglycan molecules.
What molecule, present in bacteria, are β-lactam antibiotics structurally similar to?
D-alanyl D-alanine
Why are eukaryotic cells much less biochemically and metabolically diverse than prokaryotic cells?
Eukaryotes arose from the fusion of one bacteria and one archeon. All of the metabolic diversity that existed before the advent of eukaryotes was kind of lost, or at least wasn’t present in the genomes of eukaryotes. That diversity still existed, just not in eukaryotes. It didn’t get transferred to eukaryotes. Classic bottleneck effect.
Why are eukaryotic cells much more structurally and functionally diverse than prokaryotic cells?
Eukaryotes all have mitochondria, often multiple mitochondria in each cell. This excessive surplus of usable energy can be put to maintaining complex structures and unique functions.
Why are bacteria so small?
As a sphere increases in size, its volume increases at a much greater rate than its circumference. Because bacteria rely on diffusion across their membrane, their circumference, to obtain nutrients necessary to feed its inner volume, as the bacteria increases in size it becomes harder and harder to obtain enough nutrients to sustain its inner volume. At a certain point, if bacteria grow too large, the enzymes and reactions in the center of the cell may not receive nutrients at all, and the waste products, of which there would be more of, would have farther to travel to diffuse out of the cell membrane.
What are some advantages to being small?
Higher metabolic rate, which allows for faster replication and therefore faster evolution
Better or more efficient exchange of nutrients and waste products
No neural circuitry is required between their MCP receptors and basal bodies. Simple diffusion transmits the signals almost instantly.
What are some disadvantages to being small?
Cannot sense a spatial chemical gradient, instead are forced to use temporal gradients.
Explain how the Earth became oxygenated and its significance for the genesis of eukaryotic organisms.
Earth’s oxygenation created an immense evolutionary pressure. It caused a mass extinction of microbes, providing a wealth of new niches for the aerobic eukaryotes to grow into.
What is the bacterial homolog to tubulin?
FtsZ
What is the bacterial homolog to intermediate filaments?
Crescentin
What is the bacterial homolog to actin?
MreB
What is the bacterial homolog to cholesterol?
Hopanoids
Why can bacteria and archaea withstand much higher temperatures than eukaryotes?
The larger and more complex an organism is, the more ways there are to die from heat.
Additionaly, positive supercoiling in the genome and a monolipid bilayer.
The bacterium C. diff uses spores to access new environments. Why does this bacterium use spores, and how do these spores know when to trigger germination?
Spores aid the bacterium in accessing new hosts because the vegetative cell is Non-O2 tolerant anaerobic bacterium, yet the spore is insensitive to such harsh environments. C. diff spores ingested by a novel host are triggered to germinate by host bile acid as this signals that the spores are now past the stomach acid.
What is an endospore and when does its formation commence?
Formation commences when bacterial growth ceases due to nutrient deprivation.
How do bacteria control the Earth’s climate?
The sun provides energy in the form of light for photosynthetic phytoplankton, which produce DMSP as a byproduct. Bacteria love to consume DMSP, and release DMS as a byproduct. Once released into the atmosphere, the DMS is reduced to SO2 in the presence of sunlight. Water droplets in the atmosphere then condense around the SO2 molecules, forming clouds. As enough cloudcover forms, the sunlight is blocked from reaching the photosynthetic phytoplankton, who stop producing DMSP, forming a feedback loop that modulates Earth’s rain and temperature.
Why did it take so long for us to demonstrate that TB is a bacterial infection?
Tuberculosis are mycobacteria, meaning that they are coated in a highly hydrophobic waxy envelope. They do not show up at all in classic Gram staining protocols, so for a long time we couldn’t prove that TB was caused by a bacterium at all. Instead, we had to develop a new staining protocol that would get the dye past the mycolic acid coat.
How are flagella different in eukaryotes and prokaryotes?
Eukaryotes:
Driven by ATP hydrolysis
Moves in a wave
Covered by a membrane
9+2 tubulin structure
Prokaryotes
Powered by H+ passing through motor proteins
Rotary movement
What is the default direction of rotation in peritrichous bacteria, and what is its purpose?
CCW. When all the flagella in a peritrichous bacteria are rotating, they move in unison and form what looks like a rope/braid that functions as one large flagella. It produces great force to move the bacteria forwards.
