MCAT Biological and Biochemical Foundations of Living Systems Flashcards: 1b Gene Regulation Eukaryotes

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This deck focuses on 1b Gene Regulation Eukaryotes, giving you a quick way to review the definitions, rules, and examples that matter most for MCAT Biological and Biochemical Foundations of Living Systems.

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Flashcard 1: What is the direct effect of histone acetylation on chromatin structure?

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

Flashcard 2: What enzyme class adds acetyl groups to histone tails to promote transcription?

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

Flashcard 3: What is RNA interference (RNAi) in the context of post-transcriptional gene regulation?

Answer: 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.

Flashcard 4: Which histone modification is most strongly associated with increased transcription: acetylation or deacetylation?

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

Flashcard 5: What is ubiquitination most commonly used for in regulating eukaryotic protein levels?

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

Flashcard 6: Identify the typical outcome of near-perfect siRNA base pairing to an mRNA target.

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

Flashcard 7: What is genomic imprinting in terms of allele-specific gene expression?

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

Flashcard 8: What is alternative splicing in eukaryotes?

Answer: 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.

Flashcard 9: What is the mediator complex in eukaryotic transcription regulation?

Answer: 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.

Flashcard 10: What is chromatin remodeling in the context of transcription regulation?

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

Flashcard 11: Identify the main role of general transcription factors (GTFs) for RNA polymerase II.

Answer: 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.

Flashcard 12: What is the function of the $5'$ cap on eukaryotic mRNA in gene expression?

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

Flashcard 13: What is X-inactivation and what noncoding RNA is central to it?

Answer: 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.

Flashcard 14: What is the function of the poly(A) tail on eukaryotic mRNA in gene expression?

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

Flashcard 15: What is the typical role of a promoter in eukaryotic transcription regulation?

Answer: 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.

Flashcard 16: What is the defining feature of heterochromatin with respect to transcriptional activity?

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

Flashcard 17: What enzyme class removes acetyl groups from histone tails to repress transcription?

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

Flashcard 18: Which DNA modification at CpG islands is classically associated with transcriptional repression?

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

Flashcard 19: Which complex uses miRNA or siRNA to direct mRNA silencing in eukaryotes?

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

Flashcard 20: What is the molecular basis of a transcription factor DNA-binding domain's specificity?

Answer: 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.

Flashcard 21: What is a eukaryotic enhancer in terms of distance, orientation, and function?

Answer: DNA element that increases transcription independent of distance/orientation. Enhancers bind activators that loop DNA to interact with promoters, boosting transcription regardless of position.

Flashcard 22: What is a silencer element in eukaryotic gene regulation?

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

Flashcard 23: Which spliceosomal small nuclear RNAs are core components of the major spliceosome?

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

Flashcard 24: What is the defining feature of euchromatin with respect to transcriptional activity?

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