Bacterial Physiology & Metabolism (W1-W15) Practice Flashcards

Comprehensive practice flashcards covering bacterial lifestyles, stress responses, transport systems, cell envelope structure, motility, and central metabolism based on MICR 3162/6262 lecture materials.

Binary Fission

The classical model of bacterial reproduction where a cell undergoes division to produce two identical daughter cells that act independently.

Quorum Sensing

Communal behavior in bacteria where individuals coordinate gene expression based on the density of the population.

Biofilm

Recalcitrant bacterial communities encased in an extracellular matrix comprised of DNA and/or polysaccharide, which provides resistance to toxic molecules.

Endospores

Specialized dormant, metabolically inactive cells resistant to stressors such as heat, UV, and chemicals, produced by some bacteria like Bacillus and Clostridium.

Stressor

Any condition that leads to cellular damage or disruption of cellular processes, such as DNA damage or unfolded proteins.

Fenton Reaction

The chemical reaction expressed as $Fe(II) + H_2O_2 \rightarrow Fe(III) + HO^{\cdot} + OH^-$ involved in oxidative stress.

Siderophore

A small microbially produced metal-binding molecule specifically used by microbes to obtain iron under starvation conditions.

Autoinducer-2 (AI-2)

A boronated furanone compound described as a universal signal that allows bacteria from divergent species to communicate.

Bacterial Luciferase

An expensive enzyme used for light production in Vibrio fischeri that costs ATP and $2 \, NADH$, approximately 6,000 to 60,000 ATP equivalents per second.

Thiolactone

The chemical nature of the modified peptide Autoinducing Peptide (AIP) produced by the Agr system in Staphylococci.

Type IV Pili

Dynamic bacterial appendages that mediate twitching motility, host cell adhesion, and DNA uptake; assembled by a motor complex driven by ATP.

Chemotaxis

The process by which bacteria achieve directional movement toward an attractant or away from a repellent by altering the frequency of swimming and tumbling.

MCP (Methyl-accepting Chemotaxis Proteins)

Sensors in the chemotaxis system that exist as a trimer of dimers to evaluate the presence of ligands.

Sigma Factor

A component of the RNAP holoenzyme that controls the sequence of DNA it will bind to, regulating the timing of complex processes like flagellar assembly.

Sec System

The general secretory system that transports over 90% of periplasmic and membrane proteins using a translocon ($SecEYG$), a chaperone ($SecB$), and an ATPase ($SecA$).

Tat System (Twin Arginine Translocation)

A Sec-independent system that exports already folded proteins using the PMF as an energy source, recognizing a signal sequence with two arginine residues.

SRP (Signal Recognition Particle)

A ribonucleoprotein complex (Ffh protein and 4.5S RNA in E. coli) that helps insert proteins into the cytoplasmic membrane co-translationally.

PTS (Phosphotransferase System)

An active transport system for sugars where the substrate is phosphorylated as it enters the cell using Phosphoenolpyruvate (PEP) as the energy donor.

Efflux Pump

Membrane proteins that transport toxic molecules, including antibiotics, out of cells; tripartite structures in Gram-negatives can pump drugs across both membranes.

S-layer

A repeating lattice of one abundant protein found outside the peptidoglycan or outer membrane that provides an additional layer of protection.

Teichoic Acids

Negatively charged linear carbohydrates (WTA or LTA) anchored to the PG or membrane in Gram-positive bacteria, often modified with D-alanine to modulate surface charge.

Elongasome

Also called the Rod Complex; a system involving MreB and RodA that inserts peptidoglycan at dispersed sites throughout the cell cylinder to maintain rod shape.

Divisome

Also called the Septal Ring; a machine involving FtsZ and PBP3 that inserts peptidoglycan at the midcell during constriction.

FtsZ

A tubulin homolog that forms short filaments at the midcell, recruiting other division proteins and moving via treadmilling.

Sacculus

The single, covalently closed bag-shaped peptidoglycan molecule that surrounds the bacterial cell to provide shape and protect against osmotic lysis.

mDAP (meso-Diaminopimelic Acid)

An unusual amino acid found in the peptidoglycan peptide sidechain that provides a terminal amino group for crosslinking.

Lipid II

A key peptidoglycan intermediate consisting of a disaccharide-pentapeptide attached via a pyrophosphate linkage to a $C_{55}$ lipid carrier.

Penicillin-binding Proteins (PBPs)

Enzymes that polymerize glycan strands (transglycosylation) and crosslink peptides (transpeptidation) in cell wall synthesis.

Lipopolysaccharide (LPS)

An endotoxin unique to the Gram-negative outer membrane consisting of Lipid A, a core polysaccharide, and an O-specific polysaccharide.

Anaerobic Respiration

An energy-yielding pathway that uses an external electron acceptor other than oxygen, such as Fe(III), $NO_3^-$, or sulfate.

Methanogens

Archaea that perform anaerobic respiration using $H_2$ as an electron donor and $CO_2$ as an electron acceptor to produce $CH_4$.

Chemoautotroph

An organism that obtains energy from inorganic electron donors and fixes $CO_2$ as its only carbon source.

Proton Motive Force (PMF)

The electrochemical potential ($\Delta P$) across a membrane comprised of an electrical component ($\Delta \psi$) and a chemical component ($\Delta pH$).

F0F1 ATPase

A membrane-bound motor that uses the PMF to drive ATP synthesis ($ADP + P_i \rightarrow ATP$) or runs in reverse to create a PMF.

Uncouplers

Acidic aromatic compounds, like DNP, that carry protons across the membrane to collapse the PMF and inhibit oxidative phosphorylation.

Glyoxylate Shunt

A variation of the TCA cycle that skips CO2-releasing steps, allowing bacteria to grow using acetate or two-carbon compounds as a sole carbon source.

Fermentation

A cytosolic oxidation-reduction pathway where an organic compound produced by the pathway is used as an electron sink to reoxidize $NADH$ to $NAD^+$.

Stickland Reaction

A fermentation process used by some Clostridia where one amino acid is oxidized and another is reduced.

Allosteric Regulation

Modulation of protein activity driven by the non-covalent interaction of a regulatory molecule at a site other than the active site.

Gluconeogenesis

The metabolic process of synthesizing glucose or precursors from non-carbohydrate sources, essentially running glycolytic pathways in reverse.