Control of Gene Expression in Bacteria and Eukaryotes

A comprehensive set of vocabulary flashcards covering the control of gene expression in bacterial and eukaryotic systems based on Chapters 16 and 17 of the lecture transcript.

Operon

A group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription, producing a single mRNA molecule that encodes several proteins.

Regulator gene

A DNA sequence that encodes a protein or RNA molecule—often a DNA-binding protein—that interacts with other DNA sequences and affects the transcription or translation of those sequences.

Structural genes

Genes that encode proteins used in metabolism or biosynthesis or that play a structural role in the cell.

Constitutive genes

Structural genes that encode essential cellular functions, such as housekeeping genes, and are expressed continually rather than being regulated.

Regulatory elements

DNA sequences that are not transcribed but play a role in regulating other sequences to which they are physically linked.

Negative control

A mechanism of gene regulation in which a regulatory protein, called a repressor, binds to DNA and inhibits transcription.

Positive control

A mechanism of gene regulation in which a regulatory protein, called an activator, binds to DNA and stimulates transcription.

Inducible operon

An operon in which transcription is normally off and must be turned on by a specific event or molecule.

Repressible operon

An operon in which transcription is normally on and must be turned off by a specific event or molecule.

Inducer

A small molecule that binds to a repressor protein, causing an allosteric change that renders the repressor unable to bind to the operator, thereby turning on transcription.

Corepressor

A small molecule that binds to an inactive repressor protein to make it capable of binding to the operator, thereby inhibiting transcription.

Allosteric proteins

Proteins that change shape upon binding to another molecule, such as the lac repressor which changes shape when bound to allolactose.

Coordinate induction

The simultaneous synthesis of several proteins—such as the products of the lacZ, lacy, and lacA genes—stimulated by a specific inducer molecule.

Catabolite repression

A system in which bacteria like Escherichia coli preferentially metabolize glucose, causing genes involved in the metabolism of other sugars to be turned off.

Catabolite activator protein (CAP)

A regulatory protein that, when complexed with $cAMP$, binds to or near the lac promoter to stimulate the binding of RNA polymerase, facilitating positive control.

3',5'-cyclic adenosine monophosphate (cyclic AMP or cAMP)

A modified nucleotide involved in cellular signaling whose concentration in Escherichia coli is inversely proportional to the level of available glucose.

Motif

Characteristic structures within the binding domain of a regulatory protein, such as the helix-turn-helix or zinc-finger, that fit into the major groove of the DNA double helix.

DNase I hypersensitive sites

Regions typically located about $1000$ nucleotides upstream of a transcription start site that are highly sensitive to DNase I, indicating that chromatin has assumed an open configuration.

Chromatin-remodeling complexes

Transcription factors and proteins that use energy from the hydrolysis of $ATP$ to reposition nucleosomes, making DNA more accessible to the transcription machinery without directly altering histone chemical structure.

Histone code

The collective modifications of histone tails—including the addition of phosphate, methyl, or acetyl groups—that encode information affecting how genes are expressed.

Histone acetyltransferases

Enzymes that add acetyl groups ($CH_3CO$) to histone proteins, destabilizing chromatin structure and usually stimulating transcription.

DNA methylation

The modification of cytosine bases to form $5\text{-methylcytosine}$, often associated with the long-term repression of transcription in vertebrates and plants.

Epigenetics

Alterations to DNA and chromatin structure, such as DNA methylation and histone modification, that affect traits and are inherited but are not caused by changes in the DNA base sequence.

General transcription factors

Proteins that bind to the core promoter and are part of the basal transcription apparatus, which includes RNA polymerase and other proteins necessary for the initiation of transcription.

Mediator

A complex of proteins within the basal transcription apparatus that interacts with RNA polymerase and transcription factors bound to regulatory promoters or enhancers.

Enhancers

Regulatory DNA sequences that affect the transcription of distant genes by causing DNA to loop, bringing transcription factors into contact with the basal transcription apparatus.

Insulators

Also known as boundary elements, these DNA sequences block the action of enhancers in a position-dependent manner when they lie between an enhancer and a promoter.

Response elements

Short regulatory sequences shared by several eukaryotic genes that allow them to be coordinately expressed in response to the same stimulus.

Alternative splicing

A posttranscriptional process that allows a single pre-mRNA to be spliced in multiple ways to produce different proteins in different tissues or at different developmental stages.

RNA interference (RNAi)

A mechanism triggered by $miRNAs$ or $siRNAs$ that leads to the degradation of mRNA, inhibition of translation, or transcriptional silencing through chromatin modification.

Dicer

An enzyme that cleaves and processes double-stranded RNA to produce single-stranded $siRNAs$ or $miRNAs$ that are approximately $21$ to $25$ nucleotides long.

RNA-induced silencing complex (RISC)

A complex formed by small RNA molecules and proteins that pairs with complementary sequences in mRNA to either cleave the mRNA or inhibit its translation.

P bodies

Specialized cytoplasmic complexes that serve as sites for RNA degradation and the temporary storage of mRNA molecules.

Competing endogenous RNAs (ceRNAs)

RNA molecules, such as $lncRNAs$, that compete for shared $miRNA$ binding sites, creating a regulatory network known as RNA crosstalk.