Bacterial Genetics and Genomics Flashcards

Vocabulary practice flashcards covering bacterial genetics, horizontal gene transfer, molecular biology techniques, and functional genomics.

Selection (in mutant isolation)

The use of specific growth conditions that favor or inhibit growth to isolate particular mutants (e.g., antibiotic plates where only resistant cells grow).

Screen (in mutant isolation)

A method that identifies mutants by phenotype without inhibiting or enhancing the growth of particular cells (e.g., visual or indicator changes).

Reporter Gene

A gene whose coding sequence (such as lacZ or GFP) is fused to a target gene's promoter to study gene regulation and expression under different environmental conditions.

Nutritional Auxotroph

A mutant strain that requires an additional nutrient for growth that the wild-type strain can synthesize on its own.

Replica Plating

A workflow where colonies are transferred from a master complete medium plate onto both a complete medium plate and a selective/minimal medium plate to identify auxotrophs (colonies that grow on complete medium but fail to grow on selective medium).

Fates of Foreign DNA

The three potential outcomes of foreign DNA entering a recipient bacterial cell: 1. Degradation by restriction enzymes or other cellular defenses; 2. Autonomous replication (if it is a plasmid); 3. Integration into the recipient chromosome via homologous recombination.

RecA Protein

The key bacterial protein required to drive homologous recombination by promoting base pairing with complementary sequences in recipient DNA to form a heteroduplex.

Natural Competence

Transformation competence involving inherent bacterial membrane permeability regulated by quorum sensing or nutrition (e.g., V. cholerae).

Artificial Competence

Transformation competence requiring laboratory manipulation via chemical treatment or electroporation to make cells permeable to DNA (e.g., E. coli).

Generalized Transduction

A process during the lytic cycle where any random fragment of the host bacterial genome is accidentally packaged into a bacteriophage head.

Specialized Transduction

A process involving the precise, rare erroneous excision of adjacent host genes alongside a prophage genome upon induction.

Conjugation

A plasmid-encoded form of horizontal gene transfer that requires direct cell-to-cell contact mediated by a conjugative pilus, followed by single-strand DNA transfer via rolling circle replication.

tra Region

A region on the F plasmid containing genes that encode transfer functions and the structural proteins required to build the conjugative pilus.

$F^+$ Cell

A bacterial cell that possesses an autonomous F plasmid separate from its chromosome and can act as a donor in conjugation.

Hfr Cell

A High frequency of recombination cell formed when the F plasmid integrates directly into the donor bacterial chromosome via insertion sequences.

Outcome of Hfr $\times$ $F^-$ Conjugation

DNA transfer initiates with part of the F plasmid followed by chromosomal DNA; chromosomal markers are transferred via recombination, but the recipient remains $F^-$ because conjugation usually interrupts early.

Sanger Sequencing

A dideoxy sequencing method that uses DNA polymerase, normal dNTPs, and fluorescently labeled chain-terminating ddNTPs, followed by capillary electrophoresis to separate and read fragment lengths by fluorescence.

Dideoxynucleotides (ddNTPs)

Nucleotides that act as chain terminators because they lack a crucial $3'\text{-OH}$ group on the ribose sugar, preventing DNA polymerase from attaching subsequent nucleotides.

Next-Generation Sequencing (NGS)

A sequencing approach that provides massively parallel high-throughput sequencing at a vastly reduced cost per base pair (dropped $>100{,}000$-fold), enabling whole genomes to be sequenced rapidly.

Genome Assembly

The computational process where algorithms identify overlapping regions of short sequenced DNA fragments and merge them into contiguous sequences called contigs.

Prokaryotic Open Reading Frame (ORF)

A predicted protein-coding region characterized by four key structural features: a ribosomal binding site (RBS), a start codon, a coding sequence, and a stop codon.

Heterologous Expression

Cloning environmental or uncultured DNA fragments into vectors, transforming them into a standard laboratory host (such as E. coli), and screening for novel traits such as antibiotic resistance.

Transposon Sequencing (Tn-seq)

A functional genomics methodology that generates a large library of random transposon insertion mutants across the genome, grows them under different conditions, and sequences insertion sites to map gene function and fitness.

Essential Genes (in Tn-seq)

Genes identified by having zero transposon insertions under a specific growth condition, indicating that the gene is required for survival because any mutation caused by an insertion was lethal.

Rolling Circle Replication (in Conjugation)

A mechanism where one strand of the plasmid is nicked and transferred to the recipient while the donor synthesizes a replacement strand, ensuring the donor retains its original plasmid copy.

Codon Bias

The statistical preference for certain codons over others for specific amino acids in a given organism, used by computer programs during genome annotation to evaluate whether a predicted ORF is likely to be genuine.