MICROM 412 - Exam 2 Study Cards BALANCED

A comprehensive set of vocabulary flashcards covering signal transduction, cell envelopes, bacterial antagonism, symbiosis, nitrogen fixation, and extremophiles for MICROM 412 Exam 2.

Signal transduction

Sensing and responding to specific cellular conditions; senses environment (extra-/intracellular), allows only needed genes to be transcribed, performs logical operations, and can activate or repress transcription.

Ligand-responsive transcription factors

Proteins where ligand presence alters their DNA-binding state to either activate or repress transcription.

Ligand-inactivated transcriptional repressor

A system where repression is RELIEVED upon ligand binding; for example, the lac repressor where lactose binds the repressor to de-repress transcription.

Ligand-activated transcriptional repressor

A system where ligand binding ACTIVATES repression, often using a co-repressor; for example, the trp operon used for feedback inhibition.

Aporepressor

The inactive form of a repressor that needs to combine with a corepressor to form a functional (holo) repressor.

Holorepressor

A functional repressor formed by the complex of an aporepressor and a corepressor.

Ligand-responsive transcriptional activator

A system where ligand binding activates transcription, providing a quicker response than repression; for example, cAMP-CRP at the lac operon.

Riboswitch

Gene regulation using ONLY RNA; it forms a secondary structure that binds a ligand (often metals or metabolites) to change transcription or translation.

Two-component system (TCS)

A regulatory system consisting of a sensor kinase and a response regulator. The sensor autophosphorylates on histidine $\rightarrow$ transfers phosphate to aspartate on the response regulator $\rightarrow$ regulator binds promoters to activate or repress a regulon.

Regulon

A set of genes or operons controlled by a common regulatory protein.

Sigma factor

A component of RNA polymerase that initiates transcription by binding gene promoters.

Anti-sigma factor

A protein that holds a sigma factor inactive; it is displaced or destroyed by a signal to release the sigma factor.

ECF (Extracytoplasmic Function) sigma factors

Sigma factors that respond to changes OUTSIDE the cell, usually held at the membrane by an anti-sigma; for example, Sigma E is activated by outer membrane stress when LPS/OMPs in the periplasm cleave anti-sigma RseA.

Second messenger

A small molecule made in response to a signal that activates or represses genes or proteins.

$(p)ppGpp$ (Magic Spot / Stringent Response)

An alarmone made in response to uncharged tRNAs during starvation; it binds RNA polymerase to shut down transcription.

Cyclic di-GMP

A second messenger of 2 guanosines linked by 2 phosphodiester bonds; synthesized by DGCs and degraded by PDEs. It regulates genes for decreased motility and increased biofilm formation near stationary phase.

DGC vs. PDE

DGC (diguanylate cyclase) synthesizes c-di-GMP; PDE (phosphodiesterase) degrades it.

Cyclic di-/tri-nucleotides in phage defense

Molecules made by CD-NTases in response to phage infection; they activate proteins causing cell death (abortive infection) to save the population.

Plasmolysis

The collapse of a walled cell's cytoplasm due to a lack of water when placed in a hypertonic environment.

Peptidoglycan (murein)

A bacterial exoskeleton consisting of a single cage-like molecule of carbohydrates (NAM + NAG) and peptides (L-Ala, $\gamma$-D-Glu, meso-DAP, D-Ala).

Sacculus

The bacterial cell wall by itself when isolated.

Gram-positive cell envelope

A MONODERM (1 membrane) envelope with thick PG (~30 layers), decorated with wall teichoic acid (anionic); example: B. subtilis.

Gram-negative cell envelope

A DIDERM (2 membranes + periplasm) envelope with thin PG (1 layer); the outer leaflet of the outer membrane contains LPS (anionic); example: E. coli.

Park nucleotides

One NAG + one NAM + a pentapeptide (5 amino acids) that accumulate after penicillin treatment because penicillin blocks crosslinking.

Lipid II

The final peptidoglycan precursor consisting of NAG + NAM + pentapeptide; it is charged and linked to an undecaprenol carrier on the inner membrane.

Glycosyltransfer

The polymerization of Lipid II into long glycan chains to form the bacterial cell wall scaffold.

Transpeptidation

The formation of peptide cross-links between muramic acid residues in peptidoglycan.

Penicillin-binding proteins (PBPs)

Proteins that catalyze the final steps of PG synthesis on the inner membrane; penicillin binds them COVALENTLY and IRREVERSIBLY to inhibit crosslinking.

mur genes

Genes that synthesize peptidoglycan precursors; essential for viability.

MreB

A filament-forming protein of the ROD complex and a homolog to eukaryotic ACTIN; it recruits PG synthesis and exerts force on the membrane to direct elongation.

FtsZ

A filament-forming protein of the DIVISOME and a homolog to TUBULIN; it forms polymeric filaments at the division site to recruit PG synthesis and exert force on the membrane.

Min system

A system that positions the Z-ring at the midcell; Min proteins oscillate pole-to-pole to spend the LEAST time at midcell.

MinC

A divisome inhibitor that blocks FtsZ ring formation where present.

Competitive Index formula

(Ratio of Strain 1 / Strain 2 AFTER) / (Ratio of Strain 1 / Strain 2 BEFORE). A value $>1$ means Strain 1 outcompetes Strain 2.

MIC (Minimum Inhibitory Concentration)

The lowest concentration of antibiotic that completely inhibits bacterial growth.

Bactericidal vs. Bacteriostatic

Bactericidal KILLS bacteria (irreversible); bacteriostatic INHIBITS GROWTH (reversible, allowing the immune system to clear the infection).

NRPS (Nonribosomal Peptide Synthases)

Modular enzymes that make polypeptide antibiotics; each PCP domain is charged with specific AMINO ACIDS.

PKS (Polyketide Synthases)

Modular enzymes that make polyketide antibiotics using ACYL-CoA THIOESTERS (like acetyl-CoA) in a process similar to fatty acid synthesis.

Siderophores

Diverse small molecules that chelate $Fe^{3+}$ to make it water-soluble for uptake.

Bacteriocins

Secreted PROTEINS (30-60 amino acids) toxic to bacteria; ribosomally produced and post-translationally modified (RiPPs); narrow-spectrum.

Tailocins

Phage tail-like structures (~1 MDa) that collapse the PMF in target cells; homologous to phage tails and produced via cell lysis.

Type VI Secretion System (T6SS)

A Gram-negative secretion machinery related to contractile phage tails that delivers toxins via cell-cell contact.

Contact-Dependent Inhibition (CDI)

A "toxin on a stick" system encoding CdiB (secretion), CdiA (filament/toxin), and CdiI (immunity); delivers ONE toxin molecule per contact.

Bdellovibrio bacteriovorus

A predatory bacterium that replicates in the PERIPLASM of Gram-negative prey, digesting the host for raw materials.

Myxococcus xanthus

A predatory bacterium that travels in multi-cellular swarms ("wolfpacks") and forms fruiting bodies with dormant spores under starvation.

Riftia (Giant tube worms)

Animals in chemosynthesis-based deep-sea symbioses that harbor sulfide-oxidizing bacteria in a trophosome; they have no gut.

Buchnera

An obligate symbiont that lives in specialized aphid cells called MYCETOCYTES to produce essential amino acids and vitamins.

Wolbachia

An intracellular parasite in arthropods known as a "reproductive parasite" that promotes female survival via cytoplasmic incompatibility (CI).

Cytoplasmic Incompatibility (CI)

A phenomenon where infected males' sperm cannot successfully fertilize uninfected females' eggs, driven by the cifA (antidote) and cifB (toxin) gene pair.

Diazotroph

A microbe capable of fixing nitrogen ($N_2 \rightarrow NH_3$).

N assimilation Mechanism 1

A process used when $NH_3$ is HIGH; uses the enzyme glutamic dehydrogenase ($\alpha$-ketoglutarate + $NH_3 \rightarrow$ glutamic acid).

N assimilation Mechanism 2

A process used when $NH_3$ is LOW; uses glutamine synthetase (GS) and GOGAT to produce glutamate with high affinity.

Heterocyst

A specialized cell in Anabaena for N fixation with a gas-impermeable envelope, inactivated PSII (no $O_2$ produced), and no Calvin cycle.

PatS

A small peptide inhibitor of heterocyst differentiation that diffuses to set heterocyst spacing.

Haber-Bosch process

An industrial method for nitrogen fixation requiring high heat ($~450^{\circ}C$) and high pressure ($~500\,atm$).

Leghemoglobin

A plant-made protein that acts as an $O_2$ sponge to protect nitrogenase while delivering $O_2$ to the electron transport chain in root nodules.

Flavonoids

Plant signals made by legume root hairs that attract bacteria and promote nod gene expression.

Nod factors

Bacterial signaling molecules (chitin-like sugar backbone) detected by plant receptors to stimulate root hair curling and plant cell division.

Bacteroid

The differentiated intracellular form of Rhizobium within a root nodule that lacks a cell wall and performs nitrogen fixation.

Psychrophiles

Microorganisms with growth optima at LOW temperatures.

Extremophile high-temp adaptations

Increased saturated fatty acids, reverse gyrase (positive supercoils), archaeal histones, and heat-stable proteins with more H-bonds and ionic bonds.