Microbial Genetics and Biotechnology Flashcards chap 12,10,16

Vocabulary practice flashcards covering gene regulation, operon mechanisms, two-component systems, quorum sensing, horizontal gene transfer, recombinant DNA cloning, CRISPR-Cas systems, and microbial genomics.

Constitutive Genes

Genes that are continuously expressed ("turned on") under all conditions because their products are essential for basic cellular processes.

Inducible Genes

Genes whose expression is normally turned off and only activated ("turned on") when their products are specifically needed by the cell.

Operon

A transcriptional unit in bacterial DNA containing a cluster of genes controlled by a single promoter and regulatory elements, typically encoding proteins involved in the same metabolic pathway.

Promoter

A specific DNA sequence bound by RNA polymerase that directs the initiation of transcription.

Activator

A regulatory protein that binds to an activator binding site on DNA to assist RNA polymerase binding to the promoter, increasing the initiation of transcription.

Repressor

A regulatory protein that binds to the operator region of DNA to inhibit or block transcription by RNA polymerase.

Operator

The specific DNA site within or near an operon's promoter that is recognized and bound by a repressor protein.

Effector

A small regulatory molecule that binds to activator or repressor proteins, altering their conformation and gene-regulating activity.

Inducer

An effector molecule that stimulates transcription by either enabling an activator protein or disabling a repressor protein.

Corepressor

An effector molecule that decreases transcription by binding to an inactive repressor protein and enabling it to bind to the operator.

Feedback Inhibition

A post-translational regulatory mechanism in which the final product of an enzymatic pathway binds to an allosteric site on an upstream enzyme to inhibit pathway activity.

Precursor Activation

A post-translational regulatory mechanism in which an initial substrate binds to an allosteric site on a downstream enzyme to activate the pathway.

Sigma-70 ($\sigma^{70}$)

The standard sigma factor in Escherichia coli that directs RNA polymerase holoenzyme to recognize the vast majority of normal bacterial promoters.

Alternative Sigma Factors

Specialized sigma subunits (such as $\sigma^{54}$ for nitrogen utilization, $\sigma^{32}$ for heat-shock response, and $\sigma^{38}$ for general stress response) that redirect RNA polymerase to specific sets of promoters.

Two-Component Regulatory System

A bacterial signal transduction system consisting of a membrane-bound sensor kinase (typically histidine protein kinase) and an intracellular response regulator that modulates gene transcription in response to environmental stimuli.

Histidine Protein Kinase (HPK)

The transmembrane sensor component (Component 1) of a two-component regulatory system that autophosphorylates a transmitter domain using ATP upon binding an external signal.

Response Regulator

The intracellular component (Component 2) of a two-component regulatory system that receives a transferred phosphate group onto its receiver domain to activate an output domain that regulates transcription.

VirA / VirG System

A two-component regulatory system in Agrobacterium tumefaciens where the VirA sensor detects sugars and phenolic compounds at low pH near plant wound sites, subsequently phosphorylating the VirG regulator to activate Ti plasmid virulence genes.

Quorum Sensing

A mechanism of bacterial cell-cell communication that regulates gene expression in response to changes in local population cell density.

Acyl-Homoserine Lactone (AHL)

A diffusible autoinducer signaling molecule synthesized by LuxI in Aliivibrio fischeri that accumulates at high cell density and binds LuxR to trigger transcription of the lux operon.

Luciferase

The bioluminescent enzyme, encoded by luxA and luxB in Aliivibrio fischeri, that catalyzes light emission when induced by quorum sensing in the light organ of the Hawaiian bobtail squid.

HapR

The master regulator in Vibrio cholerae that represses virulence genes and whose repression by LuxO is relieved at high cell density to promote mucosal exit and inflammation.

Auxotroph

A mutant microorganism that has lost the ability to synthesize an essential nutrient or organic compound required for its growth on defined minimal media.

Plasmid

A small, circular, extrachromosomal DNA molecule capable of autonomous replication that typically carries non-essential accessory genes, such as those conferring antibiotic resistance or virulence traits.

Restriction Endonuclease

A bacterial defense enzyme that recognizes and cleaves specific, often palindromic, double-stranded DNA sequences ($4\text{–}8\text{ bp}$) by breaking phosphodiester bonds.

Sticky Ends

Short, staggered single-stranded complementary overhangs produced on DNA fragments following cleavage by certain restriction enzymes such as EcoRI, BamHI, or HindIII.

Multiple Cloning Site (MCS)

A short, engineered region within a cloning vector containing multiple unique restriction enzyme recognition sites, allowing the insertion of foreign DNA fragments.

Blue-White Screening

A visual screening technique using X-gal and the lacZ' gene where non-recombinant vectors form blue colonies ($\beta$-galactosidase active) and recombinant vectors with inserted foreign DNA form white colonies due to insertional inactivation.

Horizontal Gene Transfer (HGT)

The lateral movement and acquisition of genetic information between distinct organisms or across species boundaries, separate from vertical descent from parent to offspring.

Transformation

The horizontal gene transfer process whereby a competent bacterial cell takes up free, naked extracellular DNA from its environment and integrates it via recombination.

Conjugation

The direct transfer of genetic material (often a plasmid, such as the F factor) from a donor cell to a recipient cell through a sex pilus and mating bridge.

Transduction

The horizontal transfer of bacterial host DNA from a donor bacterium to a recipient bacterium mediated by a packaging error in a bacteriophage.

Insertion Sequence (IS)

The simplest type of transposable element, encoding only the transposase enzyme flanked on either end by inverted repeats (IR).

Transposon (Tn)

A mobile genetic element that contains inverted repeats and a transposase gene, plus additional genes such as those conferring antibiotic resistance.

CRISPR-Cas System

An adaptive, heritable prokaryotic defense system consisting of Clustered Regularly Interspaced Short Palindromic Repeats and Cas proteins that protects cells against invading bacteriophages and plasmids.

crRNA (CRISPR RNA)

Small, mature RNA fragments derived from the transcription and Cas-mediated cleavage of the pre-crRNA transcript that guide Cas surveillance complexes to destroy matching viral targets.

Biorefinery

A facility that uses microbial processes to convert renewable biomass and waste products (such as sawdust, straw, and grease) into fuels, bioplastics, chemical feedstocks, and fine chemicals.

Polyhydroxybutyrate (PHB)

A natural, biodegradable polyester belonging to the polyhydroxyalkanoate (PHA) class produced and accumulated intracellularly by bacteria as an energy reserve.

Genomics

The comprehensive field of study focused on mapping, sequencing, analyzing, and comparing the entire DNA sequence and structural content of an organism's genome.

Sanger Sequencing

A classical DNA sequencing method that uses chain-terminating dideoxynucleotides (ddNTPs lacking a 3' OH group) labeled with fluorescent tags to determine sequence fragments one read at a time.

Illumina Sequencing

A high-throughput, sequencing-by-synthesis method that simultaneously sequences millions of short fragments ($150\text{–}300\text{ bp}$) using reversible fluorescently labeled nucleotides on a flow cell.

Transcriptome

The complete collection of all RNA transcripts, including mRNA and functional non-coding RNAs, present within a cell at a specific time or condition.

Proteome

The entire complement of proteins expressed, modified, and functioning within a cell, tissue, or organism under specified conditions.

Comparative Genomics

The analysis and comparison of whole genome sequences across different species or strains to evaluate evolutionary relationships, gene gains, gene losses, and structural variations.

Metagenomics

The direct sequencing and analysis of total genomic DNA extracted from uncultured microbial communities within an environmental or clinical sample to assess taxonomic diversity and metabolic potential.

Metatranscriptomics

The direct sequencing and profiling of total RNA extracted from a mixed microbial community to quantify active gene expression across the entire community.