Eukaryotic Gene Regulation and Molecular Mechanisms

Vocabulary flashcards covering mechanisms of eukaryotic gene regulation, including specific transcription factors (HIF 1 alpha, p53, steroid hormones, Bicoid, Pax6), metabolic shifts, cell cycle control, and post-transcriptional mechanisms like RNAi, CRISPR, and translational repression.

HIF 1 alpha

A eukaryotic specific transcription factor sensitive to oxygen levels; it is hydroxylated and degraded under normoxia, but translocates to the nucleus under hypoxia to activate gene transcription.

VHL

An E3 ubiquitin ligase that binds hydroxylated HIF 1 alpha under normal oxygen levels, targeting it for ubiquitination and proteasomal degradation.

Hypoxia response element (HRE)

The specific enhancer sequence to which stabilized HIF 1 alpha binds in the nucleus during hypoxic conditions to activate downstream transcription.

PDK1

Pyruvate dehydrogenase kinase 1, an enzyme upregulated by HIF 1 alpha that inhibits pyruvate dehydrogenase, halting pyruvate oxidation and accumulating pyruvate.

Warburg metabolism

A metabolic state wherein pyruvate is converted to lactate and exported from the cell instead of undergoing regular cellular respiration, yielding 2 ATP per glucose.

GLUT1

A glucose transport protein translated by bound ribosomes and upregulated by HIF 1 alpha to increase glucose uptake into the cell.

p53

A constitutively expressed tumor suppressor and transcription factor that is stabilized by phosphorylation during genotoxic stress to direct cell cycle arrest or apoptosis.

MDM2

The E3 ubiquitin ligase that interacts with p53 under normal homeostatic conditions to cause its ubiquitination and degradation by the proteasome.

p21

A cell cycle regulator upregulated by p53 that inhibits cyclins and cyclin-dependent kinases to block the cell cycle at the G1 to S restriction point.

BAX

A proapoptotic gene and protein controlled by p53 that inserts into the mitochondrial membrane to release mitochondrial contents and enable apoptosis.

Western blot

An experimental technique used to identify specific protein expression patterns extracted from cells.

Steroid hormones

Lipid signaling molecules such as testosterone, cortisol, and estradiol that diffuse through the plasma membrane, bind cytoplasmic receptors, and function as specific transcription factors in the nucleus.

Bicoid

A maternal transcription factor positioned in high concentrations at the anterior end of the Drosophila embryo to specify head formation along the anterior-posterior axis.

Caudal

A maternal transcription factor localized in high concentrations at the posterior end of the Drosophila embryo to direct tail development along the anterior-posterior axis.

Pax6 (Eyeless)

An evolutionarily conserved master regulatory transcription factor responsible for eye development across distant species, designated eyeless in Drosophila and Pax6 in vertebrates.

Necessity

A molecular biology criterion demonstrated when a loss-of-function experiment results in the absence of a particular structure or function.

Sufficiency

A molecular biology criterion demonstrated when a gain-of-function experiment, altering spatiotemporal expression, shows that a single molecule alone can produce a structure or function.

Spatiotemporal expression

The controlled regulation of gene expression specifying both the physical location (spatio) and the developmental timing (temporal) in which a gene is active.

RNA interference (RNAi)

A naturally occurring cellular defense and regulatory mechanism initiated by double-stranded RNA that targets cytoplasmic mRNA for degradation or translational downregulation.

RISC

A cytoplasmic protein complex that binds one strand of processed double-stranded RNA and guides it to target complementary mRNA molecules for degradation or sequestration.

CRISPR-Cas9

A system using regulatory guide RNA to direct the Cas9 enzyme to introduce double-stranded breaks into specific DNA sequences, regulating gene expression at the transcriptional level.

3' UTR

The three prime untranslated region of an mRNA molecule located downstream of the stop codon that serves as a regulatory binding platform for translational repressors.

Translational repressors

Proteins that bind to mRNA sequences (often the 3' UTR) and interact with cap-binding proteins to block the small ribosomal subunit from binding to the 5' cap.