Lecture 4 - Regulation of Gene Expression in Eukaryotes Flashcards
Why is transcription and translation uncoupled in eukaryotes?
Eukaryotic DNA is in the nucleus, while ribosomes translate mRNA in the cytoplasm.
What does monocistronic mean in eukaryotes?
Each gene has its own promoter, and each mRNA codes for a single protein.
How many RNA polymerases do eukaryotes have, and what are their roles?
RNA Pol I: Transcribes rRNA.
RNA Pol II: Transcribes protein-coding genes.
RNA Pol III: Transcribes tRNA and other small RNAs.
How are eukaryotic promoters different from prokaryotic promoters?
Eukaryotic promoters are longer, more complex, and can include enhancers and silencers far from the transcription start site.
What are enhancers and silencers in eukaryotic promoters?
Enhancers bind activator proteins to increase transcription, while silencers bind repressors to decrease transcription.
What are euchromatin and heterochromatin?
Euchromatin: Loosely packed, active genes.
Heterochromatin: Tightly packed, silenced genes.
What are the key steps in mRNA processing in eukaryotes?
5’ capping.
3’ polyadenylation.
Splicing to remove introns and join exons.
What is the purpose of 5’ capping and 3’ polyadenylation?
They protect mRNA from degradation and help with translation initiation.
What is splicing, and what complex performs it?
Splicing removes introns and joins exons, performed by the spliceosome.
What is alternative splicing, and why is it important?
Alternative splicing allows a single gene to produce multiple protein isoforms, increasing diversity.
How does alternative splicing determine sex in Drosophila?
The doublesex gene is spliced differently in males and females, producing gender-specific transcriptional repressors.
What are post-transcriptional modifications?
Modifications like capping, polyadenylation, and splicing that occur after RNA synthesis to prepare mRNA for translation.
What are post-translational modifications (PTMs)?
Modifications like phosphorylation or ubiquitination that regulate protein function and stability after translation.
Why are post-translational modifications advantageous?
They are fast, reversible, and allow regulation without requiring new protein synthesis.
What is protein phosphorylation, and how is it regulated?
Protein phosphorylation adds a phosphate group to serine, threonine, or tyrosine using kinases and is reversible by phosphatases.
How does phosphorylation regulate protein-protein interactions?
It can either block binding (due to steric hindrance or charge repulsion) or promote binding by creating a binding site.
What role does ubiquitination play in protein regulation?
Ubiquitin marks proteins for degradation by the proteasome.
How do bacteria degrade proteins without ubiquitination?
Bacteria use signal peptides on target proteins that are recognized by adapter proteins, guiding them to specific proteases.
What is the spliceosome, and how does it recognize introns?
The spliceosome is a protein complex that identifies specific sequences at the 5’ and 3’ ends of introns for removal.
What is the significance of alternative splicing in gene regulation?
It enables differential expression and the production of tissue-specific or condition-specific proteins.
Why do eukaryotic promoters require additional transcription factors?
They have longer and more complex sequences, requiring enhancers, silencers, and other factors to regulate transcription.
How do histone modifications affect chromatin structure?
Modifications like acetylation loosen chromatin (euchromatin), while methylation tightens it (heterochromatin).
What is the role of RNA Pol II in eukaryotes?
It transcribes all protein-coding genes into pre-mRNA.
How does polyadenylation affect mRNA stability?
The poly(A) tail prevents degradation but shortens over time, leading to eventual mRNA degradation.
What are the main differences between transcription in prokaryotes and eukaryotes?
Prokaryotes: Coupled transcription and translation, single RNA polymerase, operons.
Eukaryotes: Uncoupled processes, three RNA polymerases, monocistronic genes, chromatin structure.
How does phosphorylation regulate the cell cycle?
Cyclin-dependent kinases (CDKs) phosphorylate target proteins to control progression through specific cell cycle stages.
How does ubiquitination limit protein activity during the cell cycle?
Proteins are marked with ubiquitin and degraded by the proteasome, ensuring they are present only when needed.
What are cyclins, and how do they activate CDKs?
Cyclins bind to CDKs, activating their kinase activity at specific stages of the cell cycle.
Why is PTM regulation faster than transcriptional regulation?
PTMs act on existing proteins, bypassing the time required for transcription and translation.
What is the proteasome, and how does it function?
The proteasome is a barrel-shaped complex that degrades polyubiquitinated proteins.
Why are eukaryotic promoters more complex than prokaryotic promoters?
Eukaryotic promoters include sequences like enhancers and silencers that can be far from the transcription start site, requiring additional regulatory factors.
What is the role of transcription factors in eukaryotic transcription?
They bind to promoter regions and enhancers/silencers to recruit or inhibit RNA polymerase activity.
What is the role of the TATA box in transcription?
It is a conserved sequence in eukaryotic promoters (-30 position) recognized by transcription factors to initiate RNA polymerase binding.
How does chromatin structure impact gene expression in eukaryotes?
Euchromatin: Open structure, accessible for transcription.
Heterochromatin: Condensed structure, transcriptionally silent.
What are exons and introns?
Exons: Coding regions of a gene.
Introns: Non-coding regions spliced out during RNA processing.
How does alternative splicing contribute to proteome diversity?
By producing multiple mRNA variants from a single gene, allowing the generation of different protein isoforms.
How is the spliceosome able to recognise introns?
It identifies conserved sequences at the 5’ and 3’ splice sites and the branch point within introns.
Why do eukaryotic genes often appear much longer than bacterial genes?
Eukaryotic genes contain introns, which increase gene length but are removed during splicing to produce shorter mRNA.
What is 5’ capping, and what are its functions?
The addition of a methylated guanosine to the 5’ end of mRNA to protect it from degradation and assist in translation initiation.
What is the purpose of the poly(A) tail in mRNA?
It stabilizes mRNA, facilitates nuclear export, and aids in translation.
Why is alternative splicing considered a regulatory mechanism?
It allows cells to produce different proteins from the same gene based on developmental stage, tissue type, or environmental signals.
What are some examples of post-translational modifications (PTMs)?
Phosphorylation
Ubiquitination
Methylation
Acetylation
Glycosylation
How does ubiquitination target proteins for degradation?
Ubiquitin chains are attached to lysine residues on a protein, marking it for recognition and degradation by the proteasome.
Why is phosphorylation a common regulatory mechanism?
It is reversible and can rapidly alter protein activity, localization, or interactions.
What are cyclins, and why are they important in the cell cycle?
Cyclins regulate the cell cycle by activating cyclin-dependent kinases (CDKs) at specific checkpoints.
How does phosphorylation regulate DNA replication in the cell cycle?
CDKs phosphorylate replication machinery proteins to initiate replication in the S phase and deactivate them afterward.
What happens to cell cycle proteins after their function is complete?
They are either dephosphorylated or degraded via ubiquitination to ensure their activity is temporary.
How do bacteria achieve proteolysis without ubiquitination?
They use signal peptides exposed on target proteins, which are recognized by adapter proteins and delivered to specific proteases.
What is euchromatin, and how does it appear under a microscope?
Euchromatin is the less dense, transcriptionally active form of chromatin, appearing light in color when stained.
What are the benefits of regulating gene expression post-translationally?
Rapid response to changes
Reversible regulation
Allows fine-tuning of protein activity
What is the role of the proteasome in protein turnover?
The proteasome degrades polyubiquitinated proteins into peptides, regulating protein levels and removing damaged or misfolded proteins.
What is the significance of introns in eukaryotic genes?
Introns allow for alternative splicing, increasing the diversity of the proteome and enabling tissue-specific or developmental regulation.
How does chromatin remodelling impact transcription?
Chromatin remodelling complexes reposition nucleosomes, making DNA more or less accessible to transcription factors.
What are RNA-binding proteins (RBPs), and how do they regulate mRNA?
RBPs bind to mRNA to regulate stability, localization, and translation efficiency.
How is transcription regulated at enhancers and silencers?
Enhancers increase transcription by recruiting activators, while silencers decrease transcription by recruiting repressors.
What are the main differences between transcription in prokaryotes and eukaryotes?
Prokaryotes: Coupled transcription-translation, single RNA polymerase, operons.
Eukaryotes: Uncoupled processes, three RNA polymerases, monocistronic genes, chromatin regulation.
Why is the lac operon a good example of gene regulation?
It demonstrates both positive (CAP-cAMP activation) and negative (LacI repression) regulation, allowing bacteria to prioritise glucose over lactose.
