BIMM 120 Final Exam

What is time keeping?

24 hour oscillator that keeps track of day/night cycles

What is entrainment?

resetting of clock based on external factors to synchronize w/ environment

What is output signaling?

runs all temporal info from timekeeping apparatus to rest of the cell

What is the KaiABC gene cluster?

• KaiA regulates phosphorylation of KaiC

• KaiB attenuator/dephosphorylation of KaiC phosphorylation

• KaiC autophosphorylates + desphosphorylates core oscillator

What genes are activated during the day and at night?

• day = KaiA + KaiC

• night = KaiB + KaiC

What type of regulation is the KaiABC gene cluster under?

Post-translational regulation

What are the other enzymes that are involved in entrainment?

• LdpA (redox/light sensor that feeds environmental signals into clock)

• CikA (input/output factor that helps reset clock by reversing phosphorylation of RpA by SasA, senses quinone)

• Pex (protein that affects period length + clock stability)

What are the importances of supercoiling for bacterial chromosomes?

compacts chromosome, affects gene expression, facilitates replication + transcription thru ease of separation

What’s the difference between topoisomerase I and II?

• I: relaxes negative supercoils

• II: introduces negative supercoils by using ATP, DNA gyrase, essential for survival

What are bacterial nucleoids composed of?

Composed of DNA, NAPs, RNA, enzymes

Initiation, Elongation, and Termination in bacterial genome

• initiation: DNA binds to OriC -> unwinding -> DnaB helicase loads -> primase lays primers; initiation factors form complex

• elongation: DNA polymerase III synthesizes leading/lagging strands

• termination: ter sites + Tus proteins

Which processes of DNA replication are highly regulated or not?

• highly regulated = initiation

• elongation and termination are lightly regulated

Why are plasma invaginations (ICM) important in bacteria?

Increases membrane surface area + allows compartmentalization of energy-generating reactions (origin of membrane-bound organelles)

What membrane bound organelles are there in bacteria and what are their functions?

• Carboxysomes (carbon fixation)

• anammoxosomes (anaerobic ammonium oxidation)

• chromatophores (light harvesting)

• magnetosomes (magnetic navigation)

• acidocalcisomes (functions in homeostasis thru ions + metabolism)

Why is the ladderane in anammoxosomes important?

Forms extremely dense membranes (create pmf w/ quinone-dependent process or conserve energy w/ proton leak-proof membrane)

What are OMVs and what are their usages for bacteria?

Outer membrane vesicles (uses: delivery of toxins to eukaryotic cells, protein + DNA transfer btw bacterial cells, trafficking of cell-cell signals, delivery of proteases + antibiotics, removal of harmful incorrectly folded proteins)

What is quorum sensing and why is it important for bacterial communities?

Cell-density dependent communication where signaling molecules accumulate until a threshold triggers group behaviors (difs in gene expression to help community)

What processes can quorum sensing drive?

• Bet-hedging (clonal bacterial pop adapt to fluctuations w/o response to external signals)

• division of labor (individuals in clonal pop interact w/ e/o to express distinct, complementary traits)

What are indoles and how do they alter the bacterial community?

Small molecules affecting stress resistance, biofilm formation, persister formation

What QS signals do gram-positive and gram-negative bacteria release?

• Gram + = AI2; E-coli = exception to release this

• Gram - = AHLs

What are the ways bacteria can degrade QS signals?

Chemical hydrolysis, AI2 (Autoinducer 2), Indole & Indole Derivative

What 2 morphologies do Caulobacter crescentus have?

Motile swarmer and non-motile stalked cell

What is the importance of TipN?

allows for changes in morphology + ensures correct cell polarity

What are the actin nucleating proteins?

IcsA & ActA that direct motility thru animal cell/cell barriers, dependent on energy of cell (induce actin assembly -> builds actin tails at bacterial pole -> propels bacteria across cell boundaries)

How do actin nucleating proteins mediate movement of the bacterial cells?

Dependency on ATP of cell

What is sporulation?

Developmental process producing endospore

Why do cells undergo the process of sporulation?

Nutrient limitation or stress in isogenetic communities

What are the stages of sporulation and what occurs at each stage?

• 0-1: pre-septation; vegetative growth + chromosome condensation/axial filament formation

• 2: asymmetric septation; spore divides

• 3: engulfment; naked forespores engulfed by mother cell for protection/nutrients

• 4: cortex formation/deposited inside membrane

• 5-6: coat formation/maturation mother cell turns into coat to mature into proper coat; deposited outside + resistance to environmental stresses develops to completion

• 7: lysis; forespore kills mother cell to release mature spore

How is sporulation activated?

phosphorelay system (KinA (cascade of kinases phosphorylates histidine residues) -> Spo0F (phosphate transferase, receiver domain phosphorylated on aspartate residue) -> Spo0B (histidine domain phosphorylated; phosphate transferase) -> Spo0A aspartate domain (N) gets phosphorylated triggers C domain to bind to OA boxes/DNA motif, activation/repression of genes (response regulator leads to sporulation, competence, or cannibalism)

What genes are important for sporulation?

SpoIIIE (DNA translocation pump at septum for segregation, full complement of genetic material + mediation of chromosome translocation in generating + maintaining shape) and Spo0A (transcription factor that starts/regulates sporulation; regulates w/ repressing AbrB synthesis)

Know the nomenclature of sporulation gene mutations. What does IIIIBC mean?

Blockage at stage III, 2nd operon, 3rd gene

Which correspond to the mother and forespore?

• Sigma F = early forespore

• Sigma E = early mother cell

• Sigma G = late forespore

• Sigma K = late mother cell

What is the order of their activation?

Sigma F -> Sigma E -> Sigma G -> Sigma K

What is σH and σK?

Sigma H controls sporulation/competence, entry into stationary phase while Sigma K is late mother-cell activity, coat formation, protease cascade

What motility is observed in Myxobacteria?

A (adventurous/single-cell gliding) vs S motility (social/type IV pili in large groups)

What is the C-signal?

Capability of motility + aggregation but deficient in rippling, mound formation, fruiting, sporulation

What stages do the concentrations of C-signal correspond to?

• low = rippling

• medium = mound formation

• high = fruiting body + sporulation

What are transposons?

DNA elements that can move (jumping DNA elements that can move independently of other genetic elements; can give rise to gene activations + mutations)

Where are transposons inserted at higher frequencies?

AT-rich, non-essential regions; highly transcribed areas, regulatory regions upstream of structural genes

glpFK operon

• found in E. coli (encodes glycerol utilization genes)

• regulated by glycerol repressor (controls expression of operon + dehydrogenase)

• repressor = GlpR

• activator = CRP-cAMP

Phases of Myxococcus xanthous life cycle

• multicellular development

  • cells become starved + cell undergoes developmental process to produce upright fruiting bodies -> segregation into subpops that show division of labor, starvation to trigger (p)ppGpp to accumulate to cause this to occur

  • starvation → fruiting bodies

• cooperative predation

  • presence in nutrients as cells move in coordinated manner to form biofilms + take in metabolites -> adventurous gliding + social twitching -> predation

  • swarm attacks prey

What is the importance of ECM in motility?

slime matrix needed for S-motility and coordinated aggregation + adhesion

What is the developmental order of fruiting body formation?

Swarming -> aggregation -> starvation -> fruiting bodies -> spores

What is the A-signal and what life phase does it correspond to?

Controls entry into development if pop density/quorum sensing + nutrients are sufficient (multicellular development)

What are the broad effects on the gut microbiome due to chronic alcohol consumption?

• liver disease/ALD

• decreases in microbial diversity

• intestinal bacterial overgrowth

• promotes inflammation + stress

• disrupts balance of gut microbiota → breakdown of tight junctions in intestinal epithelial cells