Regulation of Gene Expression in Eukaryotes (1B) - Bio & Biochem

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

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

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

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

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

   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.

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

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

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

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

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

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

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

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

8. What is alternative splicing in eukaryotes?

   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.

9. What is the mediator complex in eukaryotic transcription regulation?

   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.

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

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

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

    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.

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

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

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

    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.

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

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

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

    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.

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

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

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

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

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

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

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

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

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

    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.

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

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

22. What is a silencer element in eukaryotic gene regulation?

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

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

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

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

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

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