1. What is gene expression, and why is its regulation important in living organisms?
Answer:
Gene expression refers to the process by which information encoded in a gene is used to synthesize functional gene products such as proteins or RNA molecules. Regulation of gene expression ensures that genes are expressed at the right time, location, and amount, allowing organisms to respond to environmental stimuli, maintain homeostasis, and conserve energy.
2. Describe the structure and function of an operon in prokaryotes.
Answer:
An operon is a cluster of genes under the control of a single promoter and regulated together, commonly found in prokaryotes. It consists of:
- Promoter: A DNA sequence where RNA polymerase binds to initiate transcription.
- Operator: A regulatory sequence where repressors or activators bind to control gene expression.
- Structural genes: Encode proteins required for specific functions.
- Regulatory gene: Produces proteins (repressors/activators) to regulate the operon.
Example: The lac operon regulates lactose metabolism in E. coli.
3. Explain the lac operon mechanism in prokaryotes.
Answer:
The lac operon controls lactose metabolism in E. coli and functions as follows:
- In absence of lactose: The repressor binds to the operator, blocking RNA polymerase and inhibiting transcription.
- In presence of lactose: Lactose is converted to allolactose, which binds to the repressor, inactivating it. RNA polymerase transcribes the operon’s genes, leading to lactose metabolism.
4. Compare inducible and repressible operons. Provide examples.
Answer:
- Inducible Operons: Normally off but can be activated by an inducer. Example: Lac operon.
- Repressible Operons: Normally on but can be turned off by a corepressor. Example: Trp operon.
These systems allow prokaryotes to adapt gene expression to environmental changes.
5. What are enhancers and silencers in eukaryotic gene regulation?
Answer:
- Enhancers: DNA sequences that increase transcription when bound by activators. They can act at a distance and in either orientation.
- Silencers: DNA sequences that suppress transcription when bound by repressors.
Both play crucial roles in fine-tuning gene expression in eukaryotes.
6. How does chromatin structure affect gene expression in eukaryotes?
Answer:
Chromatin structure influences gene accessibility:
- Euchromatin: Loosely packed, transcriptionally active regions.
- Heterochromatin: Tightly packed, transcriptionally inactive regions.
Histone modifications (e.g., acetylation, methylation) and DNA methylation modulate chromatin structure, impacting gene expression.
7. Discuss the role of histone acetylation in gene expression.
Answer:
Histone acetylation, mediated by histone acetyltransferases (HATs), adds acetyl groups to histone tails, reducing their positive charge. This weakens their interaction with negatively charged DNA, resulting in relaxed chromatin (euchromatin) and enhanced transcription.
8. Explain the process of alternative splicing and its significance.
Answer:
Alternative splicing allows a single gene to produce multiple mRNA isoforms by including or excluding specific exons during splicing. This increases proteomic diversity, enables tissue-specific gene expression, and plays roles in development and adaptation.
9. What is RNA interference (RNAi), and how does it regulate gene expression?
Answer:
RNAi is a post-transcriptional gene regulation mechanism where small RNA molecules (e.g., miRNA, siRNA) bind to complementary mRNA, leading to mRNA degradation or translation inhibition. It is crucial for gene silencing and defense against viruses.
10. Describe the process of attenuation in the trp operon.
Answer:
Attenuation regulates the trp operon by forming alternative RNA secondary structures in the leader region:
- High tryptophan: Ribosome quickly translates the leader peptide, forming a terminator structure, halting transcription.
- Low tryptophan: Ribosome stalls, forming an antiterminator, allowing transcription to proceed.
11. How does DNA methylation affect gene expression in eukaryotes?
Answer:
DNA methylation adds methyl groups to cytosine residues in CpG islands, often leading to transcriptional repression. It plays roles in gene silencing, X-chromosome inactivation, and imprinting.
12. What are transcription factors, and how do they influence gene regulation?
Answer:
Transcription factors are proteins that bind to DNA regulatory sequences (e.g., promoters, enhancers) to activate or repress transcription. They recruit RNA polymerase, coactivators, or repressors, modulating gene expression.
13. Compare positive and negative regulation in gene expression.
Answer:
- Positive Regulation: Activators enhance transcription. Example: CAP in lac operon.
- Negative Regulation: Repressors inhibit transcription. Example: Lac repressor in lac operon.
14. How is gene expression regulated at the translational level?
Answer:
Translational regulation involves mechanisms like:
- mRNA stability and degradation.
- miRNA-mediated repression.
- Ribosomal availability and modification.
15. Explain post-translational regulation of gene expression.
Answer:
Post-translational regulation includes protein modifications like phosphorylation, ubiquitination, and acetylation, influencing protein activity, localization, and stability.
16. What is the role of CAP and cAMP in lac operon regulation?
Answer:
When glucose is low, cAMP levels rise and bind to CAP, activating it. CAP-cAMP binds near the lac operon’s promoter, enhancing RNA polymerase binding and transcription.
17. How do epigenetic modifications differ from genetic mutations?
Answer:
Epigenetic modifications alter gene expression without changing the DNA sequence, while genetic mutations involve permanent changes in the DNA sequence.
18. What is the function of insulators in eukaryotic gene regulation?
Answer:
Insulators are DNA sequences that block interactions between enhancers and promoters, ensuring specific gene regulation.
19. Discuss the role of small interfering RNAs (siRNAs) in gene silencing.
Answer:
siRNAs are double-stranded RNAs that guide the RNA-induced silencing complex (RISC) to degrade target mRNAs, silencing specific genes.
20. What is the role of riboswitches in prokaryotic gene regulation?
Answer:
Riboswitches are regulatory RNA elements that bind small molecules, altering mRNA secondary structure to regulate transcription or translation.
21. How does environmental stress affect gene expression?
Answer:
Environmental stress (e.g., heat, toxins) triggers signaling pathways, activating stress-responsive genes and adaptive mechanisms.
22. Compare cis-acting and trans-acting regulatory elements.
Answer:
- Cis-acting elements: DNA sequences near the gene, e.g., promoters, enhancers.
- Trans-acting elements: Proteins or RNAs that regulate genes from a distance, e.g., transcription factors.
23. What is the significance of TATA boxes in eukaryotic promoters?
Answer:
TATA boxes are DNA sequences in promoters where the transcription initiation complex assembles, facilitating RNA polymerase II binding.
24. Explain the role of sigma factors in prokaryotic transcription.
Answer:
Sigma factors are subunits of RNA polymerase that guide it to specific promoters, enabling transcription initiation in response to environmental signals.
25. How does quorum sensing regulate gene expression in bacteria?
Answer:
Quorum sensing is a cell-density-dependent signaling mechanism where bacteria produce and respond to autoinducers, regulating group behaviors like biofilm formation.
26. What is the difference between constitutive and regulated gene expression?
Answer:
- Constitutive Expression: Genes are continuously expressed.
- Regulated Expression: Genes are expressed under specific conditions.
27. Describe global gene regulation in prokaryotes.
Answer:
Global regulation involves transcription factors or sigma factors that simultaneously regulate multiple genes or operons in response to environmental changes.
28. How do heat shock proteins regulate gene expression?
Answer:
Heat shock proteins act as molecular chaperones, ensuring proper protein folding during stress. Heat shock genes are activated by heat shock factors (HSFs).
29. What is feedback inhibition in gene regulation?
Answer:
Feedback inhibition occurs when the end product of a metabolic pathway inhibits the pathway’s initial enzyme, regulating gene expression indirectly.
30. How is gene expression studied experimentally?
Answer:
Gene expression can be studied using techniques like:
- Northern blotting (RNA levels).
- Reporter assays (promoter activity).
- qPCR and RNA-Seq (quantitative transcript analysis).
These comprehensive questions and answers provide a detailed understanding of gene expression regulation in prokaryotes and eukaryotes.
