Microbiology: Bacterial Genomes, Growth, Pathogenesis, and Virology

Comprehensive practice flashcards matching key terminology, bacterial genetics, microbial growth, physiological classifications, mechanisms of pathogenesis, and viral replication characteristics covered in the lecture notes.

Genome

The total DNA sequence of a given organism, which defines the species and determines all inherited traits.

Nucleotide

The fundamental subunit of DNA, composed of a pentose sugar, a phosphate group, and a nitrogenous base.

Gene

A unit of information encoded by DNA that can be transcribed to form an RNA molecule.

Operon

A cluster of multiple genes controlled by a single promoter that function together in the same metabolic pathway or encode components of an enzymatic complex.

Plasmids

Small, circular pieces of extrachromosomal DNA in bacteria that replicate independently of the genome and often encode antibiotic resistance genes.

ESKAPE Pathogens

A group of six high-priority opportunistic bacteria known for causing severe nosocomial infections and evading antibiotics: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.

Transcription

The enzymatic synthesis of an RNA molecule from a DNA template catalyzed by RNA polymerase.

Rifamycins

A class of antibiotics that bind near the active site of bacterial RNA polymerase to sterically block the elongation stage of transcription.

Codon

A three-nucleotide sequence in mRNA that specifies a particular amino acid during ribosomal translation.

Enzyme

A biological catalyst that accelerates chemical reactions by lowering the required activation energy.

Essential Nutrients

Chemical compounds that a microbe cannot synthesize on its own and must acquire from its immediate environment to grow and replicate.

Autotrophs

Organisms that produce their own organic carbon compounds starting from inorganic carbon dioxide ($\text{CO}_2$).

Heterotrophs

Organisms that acquire organic carbon compounds by consuming nutrients produced by other organisms.

Psychrophile

A microorganism characterized by an optimal growth rate at low temperatures, typically inhabiting cold environments.

Hyperthermophile

A microorganism adapted to very high temperatures, thriving in extreme habitats such as hot springs and deep-sea hydrothermal vents.

Acidophiles

Microorganisms that grow optimally in acidic extracellular environments with a pH below $5$.

Alkaliphiles

Microorganisms that thrive in alkaline extracellular environments with a pH greater than $9$.

Reactive Oxygen Species (ROS)

Highly reactive chemical byproducts of oxygen exposure containing unpaired electrons, including superoxide anion ($\text{O}_2^-$), hydroxyl radicals ($\text{OH}^\bullet$), and hydrogen peroxide ($\text{H}_2\text{O}_2$).

Microaerophiles

Organisms that produce ATP via aerobic respiration or fermentation and require a reduced atmospheric oxygen concentration between $5\%$ and $15\%$ to grow.

Facultative Anaerobes

Organisms capable of producing ATP via aerobic respiration, anaerobic respiration, or fermentation, allowing them to grow equally well in the presence or absence of oxygen.

Aerotolerant Anaerobes

Organisms that perform anaerobic respiration and fermentation without utilizing oxygen, but can survive in its presence.

Obligate Anaerobes

Bacteria that rely exclusively on anaerobic respiration or fermentation and are killed by molecular oxygen ($\text{O}_2$) due to an inability to detoxify reactive oxygen species.

Generation Time

The doubling time required for a microbial population to double in number when grown in an environment with unlimited resources.

Binary Fission

The primary process of bacterial cell division in which an elongated parent cell divides symmetrically into two equal daughter cells.

Batch Culture

A closed liquid culture system in which bacteria grow with a finite initial supply of nutrients, leading to resource depletion and metabolic waste accumulation over time.

Chemostat

A continuous culture apparatus that maintains a bacterial population in steady-state logarithmic growth by continuously introducing fresh media while removing an equal volume of spent culture.

Biofilm

A specialized, densely packed, surface-attached microbial community that forms when nutrients are abundant.

TasA

A fibril-like amyloid protein synthesized by Bacillus subtilis that tethers individual cells and reinforces biofilm structure.

Quorum Sensing

A density-dependent cell-to-cell signaling mechanism used by bacteria to regulate coordinated group behaviors by monitoring the concentration of secreted chemical autoinducers.

Autoinducers

Signaling molecules secreted by bacteria during quorum sensing, including AI-2 in various species, short peptides in Gram-positive bacteria, and acyl-homoserine lactones (AHL) in Gram-negative bacteria.

Dysbiosis

A disruption or altered balance in the composition of the normal microbial community within the host microbiome.

Prebiotics

Non-digestible plant fibers that host enzymes cannot break down, which serve as nutritional substrates for beneficial gut microbiota.

Probiotics

Living commensal microorganisms ingested to replenish normal flora and help restore balance to the intestinal microbiome.

Fermentation

A catabolic pathway that completes nutrient breakdown without an electron transport system or exogenous terminal electron acceptor, generating ATP strictly via glycolysis.

Horizontal Gene Transfer

The movement of genetic material between non-descendant organisms, occurring through transformation, transduction, or conjugation.

Conjugation

A mechanism of bacterial horizontal gene transfer that relies on direct cell-to-cell contact mediated by a sex pilus to transfer donor DNA into a recipient.

Hfr (High Frequency of Recombination)

A bacterial donor cell carrying an F-plasmid integrated directly into its chromosomal DNA, facilitating high rates of chromosomal gene transfer to recipient cells.

Transformation

The mechanism of bacterial genetic exchange in which a competent cell imports naked, extracellular DNA fragments from its surroundings.

Transduction

The accidental transfer of bacterial host DNA from a donor cell to a recipient cell mediated by a bacteriophage infection.

Transposable Elements

Segments of DNA, also termed transposons, that possess the enzymatic capacity to excise and relocate to alternate positions within a genome or plasmid.

CRISPR

A bacterial adaptive immune system consisting of clustered regularly interspaced short palindromic repeats that capture foreign phage DNA sequences to guide endonuclease cleavage during reinfection.

16S rRNA Gene

A conserved, approximately $1500\text{ bp}$ gene present in all bacteria that serves as an evolutionary molecular clock due to its combination of invariant regions and hypervariable sequence tracts.

Pathogenesis

The biological process and sequence of events through which a pathogenic microorganism establishes infection and causes disease in a host.

Virulence Factors

Specific microbial components, such as capsules, pili, exoenzymes, or toxins, that enhance an organism's capacity to establish infection, cause host damage, or evade immune surveillance.

Adhesins

Microbial surface structures, including modified pili, fimbriae, and capsule proteins, that specifically bind to complementary receptors on host cells.

Hyaluronidase

An extracellular enzyme produced by bacteria such as Staphylococcus aureus that degrades hyaluronic acid, increasing tissue permeability and facilitating bacterial penetration.

Toxic Shock Syndrome Toxin (TSST-1)

A superantigen exotoxin synthesized by Staphylococcus aureus that cross-links T-cell receptors and MHC class II molecules, provoking an unregulated cytokine storm.

Endotoxin

The lipopolysaccharide (LPS) constituent located in the outer membrane of Gram-negative bacteria that triggers intense immune activation, hypotension, and septic shock upon release.

Hemagglutinin (HA)

An Influenza A envelope glycoprotein spike that binds to host sialic acid residues to initiate attachment and subsequently mediates endosomal membrane fusion upon acidification.

Neuraminidase (NA)

An Influenza A surface enzyme that cleaves sialic acid residues from host cell surfaces to release newly assembled virions during viral budding.

Reverse Transcriptase

A retroviral enzyme that transcribes complementary DNA from a viral single-stranded RNA template.