Microbial Metabolism, Bacterial Genetics, and Antimicrobial Medications Flashcards

Comprehensive vocabulary flashcards covering microbial metabolism, bacterial genetics, gene regulation, and antimicrobial medications based on exam study notes.

Metabolism

Sum of all chemical reactions in a cell.

Catabolism

Degradative pathways in a cell; usually energy-yielding.

Anabolism

Biosynthetic pathways in a cell; usually energy-requiring.

ATP

Energy currency of cells; links energy-releasing reactions to cellular work.

ATP Hydrolysis

Chemical reaction where ATP breaks down into ADP and phosphate, releasing energy.

Phosphorylation

Process that adds phosphate to ADP to form ATP, storing energy in the cell.

Substrate-level Phosphorylation

Direct transfer of a phosphate from a reactive intermediate to ADP; occurs in glycolysis.

Oxidation

Loss of electrons in a chemical reaction.

Reduction

Gain of electrons in a chemical reaction.

Electron Donor

Energy source molecule that donates electrons during redox reactions.

Terminal Electron Acceptor

Molecule that receives electrons at the end of electron transfer.

Glycolysis

Metabolic stage where glucose is broken down into 2 pyruvate, producing 4 ATP and using 2 ATP for a net yield of 2 ATP and NADH.

TCA Cycle

Metabolic pathway (also known as Krebs or Citric Acid Cycle) that releases stored energy by oxidizing acetyl-CoA from pyruvate, producing 2 ATP and biosynthetic intermediates.

Electron Transport Chain

Membrane-bound system where NADH and FADH2 donate high-energy electrons, pumping $H^+$ across the membrane to create a proton motive force.

Oxidative Phosphorylation

Process where $H^+$ flows through ATP synthase to convert the energy of proton movement into chemical energy (ADP -> ATP).

Enzymes

Proteins that serve as biological catalysts to speed up reactions without being used up by lowering activation energy.

Active Site

Region of an enzyme that binds the substrate to form an enzyme-substrate complex before releasing products.

Activation Energy

The energy threshold required to start a reaction, which enzymes lower to accelerate reaction rates.

Competitive Inhibition

Enzyme inhibition where an inhibitor structurally resembles the substrate and competes for binding at the active site.

Noncompetitive Inhibition

Enzyme inhibition where an inhibitor binds to an allosteric site away from the active site, changing the enzyme's shape and decreasing activity.

Reversible Inhibition

Enzyme inhibition where the inhibitor binds temporarily and can be released, allowing enzyme activity to return.

Irreversible Inhibition

Enzyme inhibition where the inhibitor covalently binds and permanently disables the enzyme.

Sulfamethoxazole

Antibiotic that acts as a competitive inhibitor of bacterial DHPS in the folate pathway, blocking folic acid needed for DNA replication.

Penicillins

Beta-lactam antibiotics that covalently disable transpeptidase/PBPs, preventing peptidoglycan cross-linking and causing osmotic lysis and cell death.

Ciprofloxacin

Fluoroquinolone antibiotic that blocks bacterial DNA gyrase and topoisomerase IV, preventing DNA replication and transcription.

Rifampin

Antibiotic that binds the beta subunit of bacterial RNA polymerase to block RNA elongation and transcription.

Clavulanic Acid

Agent that permanently deactivates beta-lactamase to protect beta-lactam antibiotics, possessing little antimicrobial activity alone.

Central Dogma

Framework stating genetic information flows from DNA to RNA via transcription, and from RNA to protein via translation.

mRNA

Messenger RNA; a temporary copy of DNA information containing codons that specify amino acids.

Codon

Sequence of three nucleotides on mRNA that corresponds to one specific amino acid.

Start Codon

The specific codon (AUG) that signals the initiation of translation.

Stop Codons

The three specific codons (UAA, UAG, UGA) that signal the termination of translation.

tRNA

Transfer RNA; carries a specific amino acid and contains an anticodon that base pairs with an mRNA codon.

Initiator tRNA

Special tRNA carrying f-Met that pairs with the start codon AUG and occupies the P site of the ribosome during translation initiation.

Helicase

Replication enzyme that unzips the DNA double helix by breaking hydrogen bonds between nitrogenous bases.

DNA Gyrase

Topoisomerase enzyme that relieves twisting and supercoiling tension ahead of the replication fork.

SSB Proteins

Single-stranded binding proteins that keep separated DNA strands from rejoining during replication.

Primase

Enzyme that synthesizes short RNA primers required to initiate DNA synthesis.

DNA Polymerase III

Main bacterial DNA polymerase that builds new DNA strands in the $5' \rightarrow 3'$ direction.

DNA Polymerase I

Enzyme that removes RNA primers and replaces them with DNA nucleotides during replication.

DNA Ligase

Enzyme that seals gaps in the sugar-phosphate backbone by joining Okazaki fragments on the lagging strand.

Topoisomerase IV

Enzyme that untangles and separates newly linked circular chromosomes at the termination of bacterial DNA replication.

Synonymous Base Substitution

A mutation where a nucleotide substitution changes a codon, but still codes for the same amino acid.

Missense Base Substitution

A mutation where a nucleotide substitution changes a codon so that it codes for a different amino acid.

Nonsense Base Substitution

A mutation where a nucleotide substitution converts an amino-acid-coding codon into a premature stop codon.

Frameshift Mutation

A mutation caused by insertion or deletion of nucleotides that shifts the translation reading frame.

Transformation

Horizontal gene transfer mechanism involving uptake of naked DNA fragments from the environment by competent bacteria.

Transduction

Horizontal gene transfer mechanism mediated by a bacteriophage virus accidentally packaging and transferring bacterial DNA.

Conjugation

Horizontal gene transfer mechanism involving direct cell-to-cell contact where a donor bacterium uses a sex pilus to transfer DNA.

Operon

Cluster of related bacterial genes sharing a single promoter and transcribed together into one polycistronic mRNA.

Promoter

DNA sequence where RNA polymerase binds to initiate transcription.

Operator

Off-switch DNA sequence in an operon where a bound repressor protein physically blocks RNA polymerase.

Repressor

Regulatory protein that binds to the operator to block RNA polymerase from transcribing structural genes.

Inducible Operon

An operon that is default OFF, but turns ON when an inducer binds and inactivates the repressor (e.g., lac operon).

Repressible Operon

An operon that is default ON, but turns OFF when an end product/co-repressor activates the repressor to bind the operator (e.g., trp operon).

Selective Toxicity

Principle that an ideal antimicrobial drug harms the microbial pathogen significantly more than the human host.

Therapeutic Index

Measurement of relative drug toxicity calculated as $\text{TD}_{50} / \text{ED}_{50}$, where a higher index indicates a better safety margin.

Bacteriostatic

Antimicrobial property that inhibits bacterial growth without directly killing cells, relying on host immune defenses to clear the infection.

Bactericidal

Antimicrobial property where the drug directly kills bacterial cells.

Broad-spectrum Antimicrobial

Antimicrobial drug effective against a wide range of bacteria, including both Gram-positive and Gram-negative species.

Narrow-spectrum Antimicrobial

Antimicrobial drug effective against only a limited range of specific bacteria.

Synergistic Interaction

Drug combination effect where one drug enhances the activity of another, resulting in greater effectiveness than either drug alone.

Antagonistic Interaction

Drug combination effect where one drug reduces the clinical effectiveness of another.

Additive Interaction

Drug combination effect where the combined response is equal to the sum of individual drug effects without enhancement or interference.

Half-life

Time required for the serum concentration of a drug to decrease by $50\%$, helping dictate dosing frequency.

Bioavailability

The fraction/amount of an administered drug that reaches systemic circulation to perform its action.

Dysbiosis

An imbalance in the body's natural microbiome caused by antimicrobial disruption of helpful normal flora.

Intrinsic Resistance

Innate, natural resistance to an antimicrobial drug inherent to a bacterial species (e.g., bacteria lacking a cell wall).

Acquired Resistance

Development of resistance in a previously sensitive bacterial population through spontaneous mutation or horizontal gene transfer.

Drug Inactivation

Resistance mechanism where bacterial enzymes destroy or chemically modify an antibiotic (e.g., beta-lactamases).

Target Modification

Resistance mechanism where genetic mutations alter a drug target protein so the antibiotic can no longer bind.

Efflux Pump

Bacterial transport protein that actively pumps antibiotics out of the cell, reducing intracellular drug concentration.

Metabolic Bypass

Resistance mechanism where bacteria use an alternate chemical pathway or scavenge environmental molecules to bypass a drug-inhibited reaction.

Minimum Inhibitory Concentration

MIC; the lowest concentration of an antibiotic that prevents visible bacterial growth in standardized dilution testing.

Kirby-Bauer Disk Diffusion Test

Standardization assay that measures the diameter of the clear zone of inhibition around an antibiotic-impregnated disk on agar to determine bacterial susceptibility.