Microbiology: Genetics, Biotechnology, Archaea, and Environmental Microbiology

Vocabulary practice flashcards covering bacterial genetics, gene-editing technologies, parasitology, archaeal physiology, and environmental biogeochemical cycles.

Selection (Genetic)

A laboratory cultivation condition that selectively favors or inhibits the growth of microorganisms possessing a particular genotype or phenotype, allowing only desired mutants to survive.

Screen (Genetic)

An experimental approach that permits the identification and differentiation of organisms based on phenotype or genotype without selectively inhibiting or enhancing the growth of non-mutant cells.

Auxotroph

A mutant bacterial strain that has acquired an additional nutritional requirement beyond that of the wild-type parental strain.

Replica Plating

A screening technique in which colonies are transferred from a master plate to both complete and selective media using a sterile transfer tool (such as velvet or toothpicks) to detect nutritionally deficient mutants.

Horizontal Gene Transfer (HGT)

The non-genealogical movement and exchange of genetic material between cells that are not direct descendants of one another, occurring via transformation, transduction, or conjugation.

RecA Protein

A crucial bacterial protein that binds single-stranded DNA and catalyzes strand invasion and complementary base pairing during homologous recombination, forming a heteroduplex intermediate.

Bacterial Transformation

The horizontal gene transfer process by which competent bacterial cells take up free, naked foreign DNA fragments from their extracellular environment.

Electroporation

A laboratory technique that applies short, high-voltage electrical pulses to permeabilize bacterial cell membranes, facilitating the artificial uptake of plasmid or chromosomal DNA.

Generalized Transduction

A bacteriophage-mediated gene transfer event occurring during the lytic cycle wherein random fragments of the host chromosome are packaged mistakenly into the progeny capsid at a low frequency ($1/10^6\text{--}10^8$).

Specialized Transduction

A highly efficient but selective viral gene transfer process wherein an integrated temperate prophage (such as lambda) excises aberrantly from the host chromosome, carrying adjacent bacterial genes into new virions.

F Plasmid (Fertility Factor)

A conjugative circular DNA element containing a $tra$ region that encodes transfer proteins and the conjugative pilus, facilitating cell-to-cell contact and DNA transfer via rolling circle replication.

Hfr (High Frequency of Recombination) Strain

A bacterial donor cell carrying an F plasmid integrated directly into the host circular chromosome, resulting in the high-frequency transfer of chromosomal markers to an $F^-$ recipient.

Sanger Sequencing (Dideoxy Method)

A DNA sequencing method that relies on chain-terminating dideoxynucleoside triphosphates (ddNTPs) lacking a $3'\text{-OH}$ group, halting polymerase extension at specific fluorescently tagged bases.

Open Reading Frame (ORF)

A stretch of prokaryotic DNA bounded by a ribosomal binding site (RBS), a start codon, a protein-coding nucleotide sequence, and a stop codon that can be translated into a functional polypeptide.

Transposon Sequencing (Tn-seq)

A genome-wide functional genomics technique combining massive random transposon insertion libraries with high-throughput sequencing to determine gene fitness and essentiality under defined growth conditions.

Polymerase Chain Reaction (PCR)

An in vitro molecular biology method used to exponentially amplify specific target DNA sequences through repeated cycles of thermal denaturation ($90\text{--}100^\text{o}\text{C}$), primer annealing ($30\text{--}65^\text{o}\text{C}$), and enzymatic extension ($72^\text{o}\text{C}$).

Gel Electrophoresis

An analytical method that applies an electric field across an agarose matrix to migrate negatively charged nucleic acids toward the positive anode, separating fragments primarily based on molecular weight.

pUC19 Vector

A standard bacterial cloning plasmid possessing an ampicillin resistance marker ($amp^R$) and a multiple cloning site (MCS) embedded within the $lacZ'$ gene to facilitate blue-white recombinant screening.

Recombineering

A molecular cloning and genomic engineering technique utilizing homologous recombination driven by specialized phage recombinases (such as the lambda Red system) rather than restriction endonucleases.

Cassette Mutagenesis

A targeted mutation procedure in which an entire section of a gene is excised with restriction enzymes and replaced with a synthetic DNA cassette, such as an antibiotic resistance marker to produce a knockout.

CRISPR/Cas9 System

An adaptive immune system from Streptococcus pyogenes engineered for gene editing; Cas9 endonuclease is targeted by a synthetic guide RNA (sgRNA) to create double-stranded DNA cuts at specific loci.

PAM (Protospacer Adjacent Motif)

A conserved short sequence motif ($5'\text{-NGG-}3'$ in S. pyogenes) directly adjacent to the non-target strand of the protospacer, strictly required for Cas9 binding, DNA unwinding, and nucleolytic cleavage.

Non-Homologous End Joining (NHEJ)

An error-prone DNA double-strand break repair mechanism that joins broken DNA ends directly without a template, often introducing insertions or deletions that disrupt the open reading frame.

Homology-Directed Repair (HDR)

A high-fidelity DNA repair pathway that uses a homologous donor DNA template to repair double-stranded cuts, allowing precise genomic sequence modification or foreign gene insertion.

Protozoan Parasites

Single-celled eukaryotic microorganisms capable of multiplying inside human hosts, often transmitted via arthropod vectors or the fecal-oral route.

Helminths

Large, multicellular parasitic worms (such as nematodes/roundworms and platyhelminths/flatworms) that cause chronic pathology in humans but generally do not replicate in their adult form within the host.

Malaria

A protozoan parasitic disease caused by species of Plasmodium (P. falciparum, P. vivax, P. ovale, P. malariae, P. knowlesi) and transmitted through the bite of infected female Anopheles mosquitoes.

Apicoplast

A non-photosynthetic relict plastid organelle found in intraerythrocytic Plasmodium parasites that is targeted therapeutically by antibacterial agents like doxycycline, azithromycin, and clindamycin.

Hemozoin

An insoluble biocrystal synthesized by intraerythrocytic malaria parasites inside the digestive vacuole to sequester toxic free heme, which is inhibited by 4-aminoquinolines (chloroquine) and quinolinemethanols (quinine).

16S rRNA Molecule

A ubiquitous component of the small ribosomal subunit of prokaryotes containing alternating conserved and hypervariable regions, serving as the standard phylogenetic marker established by Carl Woese.

Asgard Archaea

An uncultured superphylum of Archaea (including Lokiarchaeota) containing eukaryotic signature proteins (actin homologs, small GTPases, ESCRT proteins), supporting a two-domain tree of life.

Ether Linkage in Archaeal Lipids

The covalent ether bond joining glycerol carbons to branched isoprenoid side chains (phytanyl or biphytanyl), conferring greater chemical stability than the bacterial/eukaryotic ester linkage.

Pseudomurein

A structural polysaccharide found in cell walls of specific methanogenic Archaea containing $N$-acetylglucosamine and $N$-acetyltalosaminuronic acid linked by $\beta(1,3)$-glycosidic bonds, rendering it insensitive to lysozyme.

Methanogenesis

An obligately anaerobic chemolithoautotrophic pathway in which Archaea reduce $\text{CO}_2$ with $\text{H}_2$ to yield methane ($\text{CH}_4$), utilizing enzymes like Mtr and MCR to pump $\text{Na}^+$ and establish an ion gradient.

Reverse DNA Gyrase

A specialized topoisomerase enzyme unique to hyperthermophilic organisms that introduces positive supercoiling into double-stranded DNA to prevent heat denaturation above $80\text{--}90^\text{o}\text{C}$.

Great Oxidation Event (GOE)

The geological epoch approximately $2.4\text{--}3.0\times 10^9$ years ago triggered by cyanobacterial oxygenic photosynthesis, precipitating dissolved oceanic ferrous iron ($\text{Fe}^{2+}$) into insoluble ferric ($\text{Fe}^{3+}$) oxides and forming the ozone layer.

Winogradsky Column

A classical enrichment model that sets up vertical gradients of oxygen and hydrogen sulfide in a mud cylinder to stratify diverse phototrophic, chemotrophic, aerobic, and anaerobic microbial niches.

Nitrogenase

An oxygen-sensitive metalloenzyme complex consisting of an Fe protein and a MoFe protein, encoded by $nif$ genes, that reduces atmospheric $\text{N}_2$ to $2\text{NH}_3$ using 16 ATP.

Nitrification

An aerobic, chemolithotrophic microbial process consisting of the sequential oxidation of ammonia ($\text{NH}_4^+$) to nitrite ($\text{NO}_2^-$) by AOB (e.g., Nitrosomonas) followed by nitrite oxidation to nitrate ($\text{NO}_3^-$) by NOB (e.g., Nitrobacter).

Denitrification

An anaerobic respiratory process performed by facultative bacteria wherein oxidized nitrogen species are sequentially reduced: $\text{NO}_3^- \rightarrow \text{NO}_2^- \rightarrow \text{NO} \rightarrow \text{N}_2\text{O} \rightarrow \text{N}_2$.

Anammox (Anaerobic Ammonium Oxidation)

An anaerobic process exclusive to the phylum Planctomycetota in which ammonium is oxidized with nitrite to produce dinitrogen gas ($\text{NH}_4^+ + \text{NO}_2^- \rightarrow \text{N}_2 + 2\text{H}_2\text{O}$) through a hydrazine ($\text{N}_2\text{H}_4$) intermediate.

The Great Plate Count Anomaly

The observation in environmental microbiology where microscopic direct cell counts from natural habitats exceed viable colony-forming units on agar plates by a factor of 100 to 1,000.

Shotgun Metagenomics

A culture-independent sequencing technique that fragments and sequences total environmental community DNA without gene-specific PCR, enabling reconstruction of metagenome-assembled genomes (MAGs).

Metatranscriptomics

The comprehensive sequencing and functional profiling of total messenger RNA (mRNA) isolated directly from an environmental microbial community to quantify active gene expression and in situ metabolic activity.