Regulation of Gene Expression in Eukaryotes (1B) - MCAT Biological and Biochemical Foundations of Living Systems

Condensed chromatin that is generally transcriptionally silent. Heterochromatin's tightly packed form restricts access of transcription factors and RNA polymerase, inhibiting gene expression.

Open chromatin that is generally transcriptionally active. Euchromatin's less condensed structure allows greater accessibility for transcription machinery, promoting gene expression.

Histone acetylation. Acetylation neutralizes positive charges on histones, loosening their interaction with DNA to facilitate transcription.

Decreases histone-DNA affinity, opening chromatin. Acetyl groups reduce the electrostatic attraction between histones and DNA, promoting a more open structure for gene activation.

Histone acetyltransferases (HATs). HATs transfer acetyl groups to lysine residues on histones, which relaxes chromatin and enhances transcriptional activity.

Histone deacetylases (HDACs). HDACs remove acetyl groups, restoring positive charges on histones that tighten chromatin and suppress gene expression.

DNA methylation of cytosine (5-methylcytosine). Methylation at CpG sites recruits repressive proteins and condenses chromatin, leading to gene silencing.

Parent-of-origin monoallelic expression via epigenetic marks. Epigenetic modifications like methylation silence one parental allele, resulting in expression from only the other allele.

Silencing of one X chromosome; mediated by XIST lncRNA. X-inactivation equalizes X-linked gene dosage in females by coating one X chromosome with XIST RNA to induce heterochromatin formation.

DNA site where RNA polymerase II and factors assemble. Promoters contain core sequences like TATA box where general transcription factors recruit RNA polymerase II for initiation.

DNA element that decreases transcription when bound by repressors. Silencers recruit repressor proteins that inhibit transcription factor assembly or promote chromatin condensation.

Form the preinitiation complex and enable basal transcription. GTFs recognize promoter elements and facilitate RNA polymerase II binding to form the complex for minimal transcription levels.

Coactivator that links activators at enhancers to RNA polymerase II. Mediator acts as a bridge, transmitting regulatory signals from enhancer-bound activators to the basal transcription machinery.

ATP-dependent nucleosome repositioning to alter DNA accessibility. Chromatin remodelers use ATP hydrolysis to slide, evict, or exchange nucleosomes, exposing DNA for transcription factors.

Recognition of specific DNA sequences via major groove contacts. DNA-binding domains use motifs like helix-turn-helix to form hydrogen bonds with specific bases in the major groove.

Different exon combinations from one pre-mRNA to produce isoforms. Alternative splicing allows exon skipping or inclusion, generating protein diversity from a single gene transcript.

U1, U2, U4, U5, and U6 snRNAs. These snRNAs form the spliceosome core, recognizing splice sites and catalyzing intron removal in pre-mRNA processing.

Promotes stability, nuclear export, and translation initiation. The 7-methylguanosine cap protects against exonucleases, aids in export via nuclear pores, and recruits initiation factors.

Increases mRNA stability and enhances translation efficiency. Polyadenylation protects the 3' end from degradation and interacts with poly(A)-binding proteins to stimulate translation.

Small RNAs guide silencing complexes to inhibit target mRNAs. RNAi uses miRNAs or siRNAs to base-pair with target mRNAs, leading to translational repression or degradation.

RNA-induced silencing complex (RISC). RISC incorporates guide RNAs to recognize complementary mRNAs, triggering cleavage or translational inhibition.

Endonucleolytic cleavage and degradation of the target mRNA. Perfect complementarity allows Argonaute in RISC to cleave the mRNA, followed by exonucleolytic degradation.

Targeting proteins for degradation by the $26$S proteasome. Ubiquitin chains signal the proteasome to unfold and degrade proteins, controlling levels of regulatory factors.