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BIMM 120 - Microbio > Final Exam Material > Flashcards

Final Exam Material Flashcards

1
Q

Are bacterial circadian clocks functionally the same as ours?

A

YES

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2
Q

circadian clocks/rhythms in cyanobacteria are…

3 Points

A
  1. innate
  2. endogenous
  3. cannot be changed by environment, except for temp
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3
Q

why are circadian clocks important for separating oxygen rxns from nitrogen rxns?

A

photosynthesis for oxygen fixation during the day

Nitrogen fixation during the night given oxygen fixation does not occur

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4
Q

what is the the circadian-infradian rule?

A

Infradian means cycle time greater than 1 day
Thus, it makes no sense for a cell to have a circadian rhythm if its lifetime/reproduction time is shorter than 1 day

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5
Q

KaiA protein structure

A

a dimeric protein

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6
Q

KaiB protein structure

2 total

A

an inactive tetramer
an active monomer

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7
Q

KaiC protein structure

3 total

A

a hexamer

has an internal duplication leading to double-donut shape

has ATP binding motifs - core oscillator

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8
Q

which ends of KaiC are the CI/CII ring? where is the A- and B-loops?

A

Bottom donut = CI ring
–> B-loop
Top donut = CII ring
–> A-loop = C-terminus of CII ring

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9
Q

what binds to the A- and B-loops?

A

KaiB binds to phosphorylated KaiC @ the B-loops when exposed, adding another stacked toroid to KaiC

KaiA binds to A-loops when exposed, restarting the cycle

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10
Q

what aa are phosphorylated and in what order?

A
  1. Thr-432 (Threonine)
  2. Ser-431 (Serine)
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11
Q

SasA - what is it? what is its function? what is the effect on the diff classes of genes?

dont forget what happens w/ increasing phosporylation of CII

A

histidine kinase

phosphorylate TF - RpaA - that binds upstream of genes

@ day, binds to CI of KaiC and autophosphorylates, transfering its phosphate group to RpaA

more CII phosphorylation, more SasA phosphorylates RpaA

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12
Q

CikA - what is it? what is its function? what is the effect on the diff classes of genes?

A

histidine kinase + phosphatase
acts on RpaA - that binds upstream of genes

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13
Q

RpaA - what is it? what is its function? what is the effect on the diff classes of genes?

A

a responsive regulator

governs transcription from a locus that controls global changes in circadian rhythm gene expression

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14
Q

KaiABC system - @ dawn

A

Dawn: KaiC is UNphosphorylated w/ loosely connected CI/CII rings. KiaA binds exposed A-Loops

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15
Q

KaiABC system - @ morning

A

Morning: KaiA binding stimulates KaiC autokinase activity, phosphorylating Thr-432 1st

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16
Q

KaiABC system - @ daytime

A

Daytime: Phosphorylation changes KaiC structure, facilitating phosphorylation of Ser-431.

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17
Q

KaiABC system - @ dusk

A

Dusk: both residues are phosphorylated. Increased CII ring stiffness leads to stacking of CII on CI, tucking A-Loops in, hiding the KaiA binding site. B-Loop on C1 is exposed.

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18
Q

KaiABC system - @ night

what dissociates? what type of activity starts?

A

Night: KaiA dissociates due to A-Loop inaccessibility. KaiB binds the exposed B-Loop. KaiC autokinase activity ceases, and autophosphatase activity begins. Thr-432 gets dephosphorylated 1st

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19
Q

KaiABC system - @ late night

A

Late Night: Ser-431 gets dephosphorylated - The cycle restarts

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20
Q

Are TTFLs delayed-negative feedback loops?

A

YES

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21
Q

Does KaiABC act as a self-sustained PTO?

A

YES

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22
Q

Where does Ser/Thr autophosphorylation and autoDEphosphorylation occur?

A

occurs @ CII

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23
Q

about how long this whole cycle takes?

A

24 hrs to complete

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24
Q

when is CII maximally and minimally phosphorylated?

A

CII max phosphorylated @ dusk
CII min phosphorylated @ dawn

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25
KaiB changes form between...
a tetramer + a monomer
26
what are the 3 intertwined functions of any circadian clock?
timekeeping, entrainment, and output signaling
27
Can KaiB monomers outcompete the SasA bound to the B-loop of CI?
YES
28
What are 2 ways in which clock entrainment can be completed?
1. Through sensitivity of the phosphorylation cycle to ATP/ADP ratios - Alignment max photosynthesis w/ highest ratio 2. Through the presence of nighttime-associated photosynthetic metabolites
29
ICMs - what are they?
intracellular membranes
30
what happens when there is an accumulation of proteins?
Overproduction of protein can result in the formation of inclusion bodies
31
what are chromatophores? what are they responsible for? | via what process?
a type of ICM - a intracellular photosynthetic apparatus responsible for generating skin + eye color via catalyzing light-driven rxns including PMF-driven ATP synthesis
32
do chromatophores have a diff lipid + protein composition compared to cytoplasmic membranes? how so?
YES Some continuous, others discontinuous w/ plasma mem
33
what are magnetosomes? what are the crystals surrounded by? what does that suggest?
allow organisms to align w/ Earth’s magnetic field magnetite/greigite crystals are surrounded by a mem of lipids (similar to those of the plasma membrane) but contain unique proteins suggests they likely arose from plasma membrane invagination
34
magnetosomes: what direction do they orient to in the northern hemisphere? what direction do they swim towards? why is direction important?
NH - orient northward and swim towards the south pole of a magnet Important to search for nutrient-rich sediments
35
what are anammoxisomes?
anammoxosomes - energy-producing mitochondrion-like organelles (given their lipids) ladderanes - unusually rigid lipids bc of their inflexible ladder-like structure that contribute to energy conservation via creating a more H+ leak-proof membrane
36
what process do anammoxisomes use to establish a PMF used to make ATP?
quinone-dependent process
37
why do Anammoxosomes compartmentalize enzymes?
for catalysis of NH4+ (ammonium) oxidation, allowing for energy production to aid in anaerobic NH4+ oxidation
38
do all membranous organelles (chromatophores, magnetosomes, anammoxisomes) have unique lipid and protein compositions?
YES
39
What are ALL the ways in which bacterial OMVs can be utilized? 5 total
1. Delivery of toxins to eukaryotic cells 2. Protein + DNA transfer between bacterial cells 3. Trafficking of cell-cell signals 4. Delivery of proteases and antibiotics 5. Removal of harmful incorrectly folded proteins
40
what are acidocalcisomes? what is their function? what do they resemble?
calcium/polyphosphate rich acidic membrane-enclosed organelles (in all domains of life) function --> to store cations + polyphosphates resemble lysosomes in their size + acidic properties + contents
41
what are mesosomes? how did they arise in (+) bacteria?
intracellular extensions of the plasma membrane in (+)/(-) bacteria gram-(+) bacteria resulted from invagination of the plasma membrane
42
what happens to magnetosomes during cell division?
the chain breaks into 2, each going to 1 daughter cell
43
virulence factors of bacteria + function? | 5 total points
1. Adhesins - recognize glycolipids and glycoproteins on the surface of cells they infect 2. Invasins - adhesins that allow entry into cells 3. Cytotoxins - specific inhibitors of cellular processes 4. Proteases - modify the cell surface and destroy host cell defense functions 5. Suppression of host defense mechanisms to promote pathogen survival
44
what are the 3 types of adhesins?
1. Outer envelope proteins 2. Rigid rod-like fimbriae (pili) 3. Flexible helical fimbriae
45
what is the asymmetric division of Caulobacter crescentus?
always produces 1 motile swarm cell + a sessile stalked cell
46
what kinds of compounds are used in quorum sensing?
small, diffusible organic molecules called autoinducers
47
what is the difference between bet-hedging and division of labor?
bet-hedging: adopting phenotypic heterogeneity to deal w/ environmental fluctuations division of labor: concurrently interact with each other by exerting different functions
48
what is an examples of bet-hedging? division of labor?
BH: expression of different metabolic capacities in E. coli ex 2. presistnace DOL: energetically costly production of the T3SS of S. typhimurium
49
what is the relationship between quorum sensing and phenotypic heterogeneity?
Quorum sensing (usually a coordinator of bacterial collective behavior) can be a driver or target of phenotypic heterogeneity
50
is quorum sensing a positive feedback mechanism?
YES
51
what is public goods? private goods? cheaters? in terms of quorum sensing
PubG - primarily regulates shared features via production of energetically costly “public goods” PriG - regulate energetically costly “private goods” which are not shared, but the pop as a whole can still benefit Cheaters - invading members that don't contribute to costly production of public goods but still benefit from them, thus, a fitness advantage
52
can phenotypic heterogeneity also be caused by stochastic switching of gene expression?
YES
53
What are the basics of persisters? include transition between state characteristics. WHAT IS THE TRANSITION BETWEEN STATES???????????
comprise individuals in a clonal, antibiotic-tolerant bacterial population that survive exposure to [high bactericidal antibiotics] Persister tolerance is temporary + Dormant/slow growing randomly determined and does not involve a genetic change + all bacteria could still have persistence
54
what does bacteria influence? how?
their environment by autoinducers
55
following bacteria influencing their environment, autoinducers then influence...
the cells
56
the progression of the asymmetric cell division of Caulobacter crescentus is controlled.......and needs to be........
sequentially; localized to a pole
57
what happens if the cell division is blocked early or late?
If blocked early, flagella and pili canNOT be assembled If blocked later, they still can be assembled
58
what is division scar?
division scar - organization centers formed during cell division that serve as markers for new cell poles
59
what are the characteristics of TipN and TipF?
TipN - marker protein for spatial and temporal differentiation TipF - a c-diGMP phosphodiesterase that regulates cell cycle
60
what are the additional functions of TipN and TipF? aka for tipN, what happens if its lacking? what can't negative TipF mutants make? what anchors TipN + TipF? what happens apon anchoring?
TipN - w/o TipN, polarity is lost and inversion sites for the new membrane is randomized TipF negative mutants cannot make flagella new septum anchors TipN, which anchors TipF anchoring lowers [c-diGMP] so the flagellum can be made
61
What does TipN localization depend on (2 things)? what does it determine + localize (3 things)? what happens if it is over expressed?
TipN localization depends on FtsZ + FtsI TipN also determines the asymmetric cell division site + localizes some regulatory proteins and actin-like proteins like MreB If TipN is overexpressed, there are many new poles w/ cell branching and each pole can then assemble a flagellum
62
What does FtsZ form? what is Ftsl?
FtsZ - septum Ftsl - septum cell wall synthesis protein
63
what are the rules of Anabaena cell division? 3 total in terms of whether you will have a large or small daughter cell
1. If a cell arises as the left (L) daughter cell its left daughter cell will be small 2. If a cell arises as the right (R) daughter cell, its right daughter will be small 3. Heterocysts always develop from a small cell. Therefore, the two daughter cells have different developmental potential
64
what are MinC/MinD/MinE? what is the purpose of the mechanism?
purpose: a mechanism that prevents separation (cell division) from occurring at the poles E - a topological specificity determinant D - an ATPase that interacts with C and E, and stimulates MinC/D release from the membrane C - a FtsZ polymerization inhibitor
65
how does Caulobacter crescentus produce either a swarmer cell or a stalked cell?
via asymmetic cell division
66
how do CheA and CheW participate in protein localization?
A conserved domain near the C-termini of the MCPs - required for polar localization - recognizes CheW + CheA
67
what is the regulation of proteolysis in Caulobacter crescentus?
proteolysis is both temporally (in the swarmer cell) and spatially (in the stalked cell) regulated
68
PleC/D? SK/RR pairs | what does it direct? what does it control? what does it initiate?
directs pilus, flagellum and MCP synthesis and controls proteolysis - initiates swarm cell biosynthesis
69
DivJ/K? SK/RR pairs
is essential for cell cycle progression
70
CckA/CrtA? SK/RR pairs
controls gene expression + silences oriC in the swarmer cell
71
what are the biofilm/planktonic state transition?
w/ c-diGMP - biofilm w/o c-diGMP - planktonic state
72
what are the factors that persistence in E. coli depend on? | 4 total
(1) the nucleotide 2 nd messenger (p)ppGpp (2) Lon protease (3) polyphosphate (P) (4) toxin/antitoxin pairs
73
what are all of the enzymes used (2 total) in ppGpp homeostasis? what are the first 4 steps?
Enzymes: RelA + SpoT 1. ppGpp activates T/AT (toxin/antitoxin) loci involving polyP + Lon 2. ppGpp inhibits exopolyphosphatase (PPX) 3. More PolyP made by polyP kinase (PPK) 4. PolyP binds w/ Lon, increasing Lon protease activity
74
what are the basics about significant plagues in history? what kind of diseases were they? 4 plagues total
***were all likely infectious diseases 430 BCE - The plague of Athens where immunity was observed Bubonic = rat-flea-man Pneumonic = man to man, coughing The Great Plague of Londone The Black Death (Bubonic Plague in Europe) w/ Buboes = lymph nodes + Hemorrhagic necrosis of the extremities
75
What are the last 4 steps (5 - 8 steps) of ppGpp homeostasis
5. Lon protease degrades eleven ATs of E. coli K12 6. More toxins (site specific RNases) are present 7. mRNA cleavage inhibits translation, which slows/stops cell growth 8. If ppGpp is low, cells revive and grow
76
what are the "thinking like bacteria" points? 2 points
Do not disfigure your host too much bc then people would know you are infected + you cannot spread the disease as much Also can use toxins to force you to cough, which then helps with the spread
77
what are Koch’s Postulates used to determine if a disease is caused by a specific microbe (3 total) and his corollary?
postulates: 1. isolate the organism from the diseased tissues 2. Grow the organism outside the host 3. Inoculate the organism into a new, healthy host 4. Reproduce the disease in the new host Corollary: you should be able to make a vaccine and prevent the disease

BIMM 120 - Microbio (6 decks)

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