Biology 2153: Principles of Genetics - 4a

This set of flashcards covers bacterial and eukaryotic gene regulation methods, including operons (lac, ara, trp, lux), two-component systems, sigma factors, and RNA interference.

Regulated genes

Inducible and repressible genes in bacteria whose expression is controlled by the needs of the cell as it responds to its environment to increase mass and divide.

Constitutive genes

Also known as housekeeping genes, these are generally continuously expressed and include genes involved in protein synthesis and glucose metabolism.

Operons

Clusters of genes undergoing coordinated transcriptional regulation by a shared regulatory region; they are co-transcribed and produce polycistronic mRNA.

Riboswitch

A sequence of mRNA that can interact with a small molecule (ligand), resulting in a conformational change that alters the production of the protein encoded by that mRNA.

Sensor kinase

A protein in the cytoplasmic membrane that binds to a signal molecule and activates itself via autophosphorylation as part of a two-component signal transduction system.

Cytoplasmic response regulator (CRR)

A protein that takes a phosphate from a sensor kinase, binds to DNA, and alters the transcription rate of genes.

Alternative sigma factors

In bacteria, use of different factors to direct RNA polymerases to certain genes, such as using $\sigma-32$ instead of $\sigma-70$ under heat stress to activate specialized response genes.

Operator site

A DNA sequence adjacent to a gene where activated repressors bind to block transcription initiation (negative control).

Activator binding sites

DNA sequences where activator protein binding facilitates RNA polymerase binding at promoters to help initiate transcription at a high level (positive control).

Effectors

Small molecules that bind to activator or repressor proteins to modify their gene regulation activity; include inducers and corepressors.

Inducer

An effector that increases transcription by enabling an activator or disabling a repressor.

Corepressor

An effector that decreases transcription by enabling a repressor.

lacZ

A structural gene in the lac operon that encodes $\beta-$galactosidase, which hydrolyzes the $\beta, 1-4$ linkage of lactose into glucose and galactose.

lacY

A structural gene in the lac operon that encodes lactose permease, a membrane protein using the proton motive force to transport lactose into the cell.

lacA

A structural gene in the lac operon that encodes galactoside transacetylase, which uses acetylCoA to acetylate specific galactosides to prevent them from re-entering the cell after excretion.

lacI

A gene outside the lac operon that encodes the Lac repressor protein.

Allolactose

A molecule converted from lactose that acts as an inducer by binding allosterically to the Lac repressor, reducing its affinity for the operator site.

cAMP (cyclic adenosine monophosphate)

A molecule synthesized from ATP by adenylyl cyclase that forms a complex with CRP to allow RNA polymerase to bind tighter to DNA for high-level transcription.

CRP (cAMP receptor protein)

Also called CAP (catabolite activator protein), this activator protein must form a complex with cAMP to bind to DNA and facilitate high-level expression of the lac operon.

Diauxic growth

Growth pattern characterized by the presence of two sugars in a medium where one sugar (e.g., glucose) is metabolised easier and preferred over another (e.g., lactose).

Catabolite repression

A mechanism where the presence of one catabolite, such as glucose, inhibits the transcription of genes for an alternative catabolite, such as lactose.

AraC

A regulatory protein dimer that, in the absence of arabinose, binds two DNA sites to create a loop preventing RNA polymerase binding; in the presence of arabinose, it undergoes an allosteric shift to enhance transcription.

trp operon

A repressible operon containing five structural genes ($trpA$ through $trpE$) responsible for the biosynthesis of tryptophan.

Feedback inhibition

A process where the end product of a metabolic pathway inhibits an enzyme near the beginning of that pathway.

Attenuation

A second method for regulating the trp operon besides the repressor protein, involving premature termination of transcription.

Quorum Sensing

A chemical signaling system used for communication between microbes, where cells release autoinducer molecules to detect population density and regulate gene expression.

Lux operon

A prototypical quorum-sensing system in Vibrio fischeri that controls the production of luciferase for bioluminescence based on the concentration of AHL.

Luciferase

An enzyme produced by bacteria like Vibrio fischeri that emits light.

AHL (N-acyl-homoserine lactone)

An autoinducer molecule; its synthesis is catalyzed by LuxI and it is detected by LuxR to turn on the Lux operon at high cell density.

Mediator

A large multiprotein coactivator complex important for the functioning of RNA pol. II in eukaryotes.

Histone acetyltransferase (HAT)

A coactivator that adds an acetyl group to histone proteins, removing the positive charge ($$+$) to increase gene expression through chromatin remodeling.

Histone deacetylase (HDAC)

An enzyme that removes acetyl groups from histone proteins, exposing the positive charge ($$+$) to decrease gene expression.

RNA interference (RNAi)

A regulatory mechanism using endoribonucleases Dicer and Drosha to cleave RNA into siRNAs or miRNAs to trigger mRNA degradation or repress translation.

Dicer

An endoribonuclease that cleaves double-stranded RNA molecules into small interfering RNAs (siRNAs).