Prokaryotic Genome Organization and Regulation

These flashcards cover key concepts from prokaryotic genome organization and regulation, aimed at aiding students in understanding the principles of microbiology.

Gene

• Sequence of nucleotides where the order determines the order of monomers in  nucleic acids product and sometimes a polypeptide product

Supercoiling

Twisting of DNA caused by the action of topoisomerases, essential for proper function as a template for transcription.

Topoisomerases

Enzymes that manage the overwinding or underwinding of DNA.

Plectonemic supercoils

A type of supercoiling in DNA that involves interlinking strands.

Transposons

Genetic sequences that can change their location on a DNA molecule.

Replicative transposition

Type of transposition where one copy remains at the original site while a second copy is inserted elsewhere.

Nonreplicative transposition

Type of transposition where the transposon is physically removed from its original site and reintegrated into a new site.

Insertion sequences (IS)

The simplest transposons that consist of a transposase flanked by inverted repeats.

Composite transposons (Tn)

Transposons that contain additional genes flanked by insertion sequences.

Operons

Groups of genes organized together under a single promoter in prokaryotic genomes.

Transcriptional unit

A stretch of DNA transcribed into a molecule of RNA.

Shine-Dalgarno sequence

Base sequence on mRNA crucial for the initiation of translation in prokaryotes.

Promoter

Sequence of DNA that RNA polymerase binds to initiate transcription.

Conjugative plasmids

Plasmids that carry genes for cell-to-cell transfer.

R (resistance) plasmids

Plasmids that confer antibiotic resistance.

Degradative plasmids

Plasmids that allow the breakdown of unusual organic substrates.

Virulence plasmids

Plasmids that confer pathogenicity to bacteria.

Allosteric proteins

Proteins that change shape when binding to a molecule and influence the transcription process.

RNA polymerase

Enzyme responsible for synthesizing RNA from a DNA template.

Transcription factor

Proteins that help regulate the transcription of specific genes.

Negative control

Mechanism where transcription is inhibited by the binding of a repressor to the operator.

Positive control

Mechanism that enhances transcription by the binding of an activator to DNA.

Catabolite repression

Regulatory mechanism allowing bacteria to prioritize the use of preferred carbon sources.

cAMP (cyclic AMP)

Second messenger that participates in signaling pathways and helps regulate gene expression.

Lac operon

A model for gene regulation in E. coli that illustrates both negative and positive control.

Inducible operon

Operon that is activated only in the presence of specific substances (inducers).

Repressible operon

Operon that is normally on but can be turned off by certain molecules (co-repressors).

diauxic growth

Sequential use of two sugars by a bacterium, typically when glucose is preferred over lactose.

Global control systems

Regulatory systems that coordinate the expression of multiple operons in response to environmental changes.

Modulon

A group of genes and operons that share a common regulatory system.

Attenuation

Regulation mechanism involving the premature termination of transcription based on the level of amino acids.

Ribosomal proteins

Proteins that are integral for the structure and function of ribosomes.

Regulon

A set of genes controlled by the same regulatory protein.

Post-transcriptional regulation

Control of gene expression after the RNA is made, affecting mRNA stability and translation.

Trans-activation

The process by which a protein increases the expression of a specific gene.

Inducer exclusion

Mechanism by which the presence of a preferred carbon source inhibits the import of other sugars.

Repressor protein

Protein that inhibits gene expression by binding to the operator site on DNA.

Operator site

Region of DNA where a repressor binds to block transcription.

Polycistronic mRNA

mRNA that encodes multiple proteins, typical in prokaryotic operons.

Genetic regulation

The control of gene expression in response to environmental changes.

Regulatory gene

A gene that codes for a protein that regulates the expression of other genes.

Cistron

A segment of DNA or RNA that corresponds to a single gene coding for a specific product.

CRP (cAMP receptor protein)

Transcription factor that mediates the effects of cAMP, enhancing transcription when glucose levels are low.

Sigma factor (σ)

Protein that associates with RNA polymerase and facilitates the initiation of transcription.

Weak promoter

A promoter that is less frequently recognized by RNA polymerase, resulting in lower transcription rates.

Strong promoter

A promoter that is recognized efficiently by RNA polymerase and initiates transcription readily.

Aminoacyl-tRNA

tRNA molecule charged with a specific amino acid, necessary for protein synthesis.

Alarmones (ppGpp)

Signaling molecules produced in response to stress that regulate gene expression.

Transduction

The process by which DNA is transferred from one bacterium to another by a virus.

Transformation

The process by which a bacteria takes up naked DNA from the environment.

Conjugation

The process by which bacteria transfer DNA via direct contact.

Eukaryotic-like regulatory mechanisms

Similar control mechanisms found in prokaryotes that resemble those in eukaryotic cells.

Feedback inhibition

A regulatory mechanism wherein the end product of a metabolic pathway inhibits an earlier step.