Brock Biology of Microorganisms: Lectures 20–28 Comprehensive Review

Comprehensive practice flashcards covering Lectures 20 through 28 of Brock Biology of Microorganisms (16th Edition), focusing on regulatory RNA, cell cycle and division, antibiotic mechanisms and resistance, bacterial genetics, microbial evolution, genomics, taxonomy, and ecological methods.

Small RNA (sRNA)

A regulatory noncoding RNA molecule of $40\text{--}400\,\text{nucleotides}$ in prokaryotes and eukaryotes that regulates gene expression by base pairing directly to target mRNAs, thereby blocking or exposing the ribosome binding site (RBS) or altering susceptibility to ribonucleases.

Hfq Protein

An RNA chaperone protein that binds to both trans-sRNA molecules and their mRNA targets to facilitate base pairing across short complementary regions of $5\text{--}11\,\text{nucleotides}$.

Riboswitch

A domain within an mRNA molecule that directly binds a specific small metabolite at its aptamer region, inducing an alternate secondary structure in the downstream expression platform that regulates transcription elongation or translation initiation.

Attenuation

A transcriptional regulatory mechanism in bacteria where translation speed of a leader peptide directly influences mRNA secondary structure, causing premature transcription termination before RNA polymerase reaches the structural genes of an operon.

Feedback Inhibition

A reversible regulatory mechanism in which the final end product of a biosynthetic pathway allosterically binds to and inhibits an early or first enzyme in the pathway, shutting down intermediate generation.

Isoenzymes

Distinct enzyme variants that catalyze the exact same biochemical reaction but differ in their regulatory sensitivities to different end-product inhibitors, enabling incremental control of branched biosynthetic pathways.

$\text{P}_{\text{II}}$ Signal Transduction Proteins

A widespread family of regulatory proteins in Bacteria, Archaea, and plastids whose post-translational uridylylation by GlnD under low glutamine conditions stimulates the deadenylylation and activation of glutamine synthetase (GS).

Anti-Sigma Factor

A regulatory protein, such as RseA or SpoIIAB, that binds directly to a specific sigma factor ($\sigma^{\text{E}}$ or $\sigma^{\text{F}}$) to prevent it from interacting with RNA polymerase core enzyme until a specific environmental or developmental signal triggers degradation or release.

SeqA

A protein that binds with high affinity to hemimethylated DnaA boxes at the oriC region and the dnaA promoter following initiation of replication, sequestering the origin and repressing transcription to prevent premature re-initiation.

Multifork Replication

The phenomenon in rapidly growing bacteria where new rounds of bidirectional chromosomal replication are initiated at oriC before earlier replication forks reach the terminus, allowing cell doubling times as short as $20\,\text{minutes}$ despite a fixed replication duration of $40\,\text{minutes}$.

Par System

A bacterial chromosome and plasmid partitioning apparatus comprising ParA ATPase, ParB binding protein, PopZ anchor complexes, and a centromere-like parS sequence near oriC that directs replicated sister chromosomes to opposite cell poles.

Divisome

A multicomponent protein division apparatus that forms around the cell midpoint approximately three-quarters of the way through cell division, coordinating membrane constriction and peptidoglycan synthesis via proteins like FtsZ, ZipA, FtsA, and FtsI.

FtsZ

An essential bacterial and archaeal tubulin homolog that hydrolyzes GTP to polymerize into a ring at the cell division plane, directing septum synthesis and coordinating divisome assembly.

Lipid II

A peptidoglycan precursor composed of the $C_{55}$ polyisoprenoid alcohol bactoprenol pyrophosphate covalently bonded to N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) pentapeptide, which is translocated across the cytoplasmic membrane by flippase.

Transpeptidation

The terminal cross-linking reaction of peptidoglycan synthesis catalyzed by penicillin-binding proteins (such as FtsI), forming peptide bonds between diaminopimelic acid (DAP) on one peptide and ᴅ-alanine on an adjacent glycan chain.

Quinolones

Synthetic antimicrobial compounds that disrupt bacterial DNA unwinding and replication by specifically targeting and inhibiting DNA gyrase and topoisomerase IV.

Aminoglycosides

A class of antibiotics, including streptomycin, that bind directly to the $16\text{S}\text{ rRNA}$ of the bacterial $30\text{S}$ ribosomal subunit, causing faulty codon reading and mistranslated, error-filled proteins that arrest cell growth.

Daptomycin

A cyclic lipopeptide antibiotic that binds specifically to phosphatidylglycerol residues within the bacterial cytoplasmic membrane, inducing rapid pore formation, membrane depolarization, and cell death.

Auxotroph

A mutant microorganism that has acquired an additional nutritional growth requirement not present in the wild-type parental strain (prototroph), commonly identified via replica plating onto selective minimal media.

Frameshift Mutation

A genetic mutation caused by the insertion or deletion of one or two base pairs in a coding region, which alters the triplet reading frame of mRNA downstream and leads to a completely scrambled, nonfunctional polypeptide.

RecA

An essential bacterial recombination protein that binds single-stranded DNA and catalyzes strand invasion into homologous double-stranded DNA during homologous recombination and DNA repair.

Horizontal Gene Transfer (HGT)

The unidirectional, asymmetrical transfer of genetic information between organisms that are not parent and offspring, occurring through transformation, transduction, or conjugation.

Transduction

The transfer of host bacterial genetic material from a donor cell to a recipient cell mediated by a bacteriophage encapsidating host DNA instead of viral DNA, occurring via generalized or specialized modes.

Hfr Strain

A high-frequency of recombination bacterial donor cell in which an F plasmid is integrated into the host chromosome via insertion sequences, enabling rolling-circle transfer of chromosomal genes through a conjugation bridge.

RNA World Hypothesis

The evolutionary model proposing that early self-replicating biological systems relied entirely on RNA to perform catalytic activities (ribozymes), genetic information storage, and template-directed protein synthesis before the evolution of DNA and proteins.

Last Universal Common Ancestor (LUCA)

The hypothetical organism existing approximately $3.8\text{--}3.7\,\text{billion years ago}$ that was anaerobic, thermophilic, and chemolithotrophic in a sulfur- and iron-rich environment, from which all extant cellular life (Bacteria and Archaea) descended.

Banded Iron Formations

Laminated marine sedimentary geological deposits composed of oxidized iron ($\text{Fe}^{3+}$) oxides precipitated when biogenic oxygen produced by early phototrophs reacted with dissolved ferrous iron ($\text{Fe}^{2+}$) during the Great Oxidation Event approximately $2.4\,\text{billion years ago}$.

Last Eukaryotic Common Ancestor (LECA)

The ancestral chimeric cell of all modern eukaryotes that possessed approximately $4,000\,\text{genes}$ along with mitochondria, a nucleus, endomembranes, cytoskeleton, and spliceosome machinery.

Endosymbiotic Theory

The theory stating that eukaryotic organelles originated through mutualistic engulfment, where mitochondria evolved from an engulfed aerobic respiring bacterium and chloroplasts evolved from an engulfed cyanobacterium.

Genetic Drift

A stochastic, random evolutionary mechanism that causes allele frequencies in a population to fluctuate independently of natural selection, exerting its strongest effects in small populations and following genetic bottlenecks.

Molecular Clock

An evolutionary tool that uses the rate of accumulation of neutral nucleotide sequence changes in homologous genes over time to estimate the chronological point of evolutionary divergence between taxa.

Orthologs

Homologous genes found in different species that evolved directly from a single ancestral gene following a speciation event and retain the exact same biological function.

Paralogs

Homologous genes within an organism that originated via ancestral gene duplication and have accumulated mutations to evolve distinct functional roles.

Pan Genome

The comprehensive set of all genes present across every strain of a single microbial species, including both the core genome shared by all strains and the dispensable accessory genes found in only some isolates.

Pathogenicity Islands

Horizontally acquired chromosomal gene clusters flanked by inverted repeats and integrases that exhibit atypical $\text{GC content}$ and codon usage, encoding multiple virulence determinants in pathogenic bacteria.

Polyphasic Taxonomy

The integrated framework of microbial systematics that combines phenotypic traits (morphology, metabolism, physiology), genotypic characteristics ($\text{\%GC}$, genome size, ANI), and phylogenetic analysis (SSU rRNA and housekeeping gene sequences) to define taxa.

SSU rRNA ($16\text{S}\text{ rRNA}$)

The small subunit ribosomal RNA molecule whose gene is universally conserved across all Bacteria and Archaea, serving as the gold standard for microbial phylogenetic classification and evolutionary distance measurement.

Homoplasy

The occurrence of similar phenotypic or sequence traits resulting from convergent evolution or recurrent mutations rather than direct descent from a common ancestor, complicating phylogenetic tree reconstruction.

Average Nucleotide Identity (ANI)

A genome-wide pairwise sequence comparison metric that aligns approximately $1,000\,\text{bp}$ homologous genomic segments; values greater than $96\%$ indicate that two isolates belong to the same species, whereas values below $93\%$ denote distinct species.

Multilocus Sequence Analysis (MLSA)

A high-resolution taxonomic approach that sequences multiple conserved protein-encoding housekeeping genes (such as recA and gyrB) to resolve closely related species that share nearly identical $16\text{S}\text{ rRNA}$ gene sequences.

Candidatus

A provisional taxonomic prefix assigned to well-characterized, taxonomically distinct microorganisms that have been identified and described using molecular methods but have not yet been successfully cultivated in pure culture.

Pseudomonadota

The phylum formerly known as Proteobacteria, representing the largest and most metabolically diverse group of gram-negative bacteria, divided into six classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, and Zetaproteobacteria.

Pelagibacter

An extremely abundant oligotrophic genus of marine Alphaproteobacteria possessing one of the smallest and most streamlined bacterial genomes known, optimized for scavenging scarce nutrients in open ocean waters.

Enterobacteriales

A major order within the Gammaproteobacteria comprising facultatively aerobic, gram-negative rod-shaped enteric bacteria that ferment glucose via either mixed-acid fermentation (e.g., Escherichia) or 2,3-butanediol fermentation (e.g., Enterobacter).

Bacillota

The bacterial phylum formerly called Firmicutes, characterized by low $\text{G+C content}$ and predominantly monoderm (gram-positive) cell envelopes, encompassing endospore formers (Bacillus, Clostridium) and lactic acid bacteria (Lactobacillus, Streptococcus).

Tenericutes (Mycoplasmas)

A group of diminutive bacteria lacking cell walls and peptidoglycan, resulting in pleomorphic cell shapes and intrinsic resistance to $\beta$-lactams and other cell wall-directed antibiotics.

Actinomycetota

The bacterial phylum formerly known as Actinobacteria, comprising high $\text{G+C content}$ gram-positive organisms ranging from pleomorphic rods to mycelial filament formers like Streptomyces that produce the majority of known clinical antibiotics.

Enrichment Bias

The experimental distortion where lab culture media disproportionately favor fast-growing, opportunistic 'weed' species ($r\text{-strategists}$) over ecologically dominant, slow-growing oligotrophic organisms ($K\text{-strategists}$).

Winogradsky Column

A glass cylinder containing mud, water, cellulose, and sulfate salts that functions as a self-sustaining mixed microbial ecosystem, establishing oxygen and hydrogen sulfide gradients to enrich anoxygenic phototrophs, cyanobacteria, and sulfate reducers.

Viability Staining

A differential fluorescence microscopy technique using a mixture of fluorophores, such as green-fluorescing Syto-9 (permeates intact membranes) and red-fluorescing propidium iodide (penetrates only damaged membranes), to assess cell membrane integrity and viability.

Fluorescent In Situ Hybridization (FISH)

A culture-independent visualization method using fluorescently labeled single-stranded oligonucleotide probes targeting specific ribosomal RNA sequences to identify, locate, and quantify microbes directly within natural or clinical samples.

Denaturing Gradient Gel Electrophoresis (DGGE)

An electrophoretic profiling technique that separates PCR amplicons of identical length based on differential strand melting behavior determined by $\text{\%GC content}$ along a linear gradient of urea and formamide.

Alpha Diversity

The measure of microbial species richness and evenness within a single defined community or sample, evaluated through mathematical metrics such as the Shannon or Chao indices.

Beta Diversity

The comparative measure of species composition turnover or ecological dissimilarity between different microbial communities, commonly analyzed using Bray-Curtis distance and principal component analysis.