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Genetics and Evolution > Lecture 4 - Regulation of Gene Expression in Eukaryotes > Flashcards

Lecture 4 - Regulation of Gene Expression in Eukaryotes Flashcards

1
Q

Why is transcription and translation uncoupled in eukaryotes?

A

Eukaryotic DNA is in the nucleus, while ribosomes translate mRNA in the cytoplasm.

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2
Q

What does monocistronic mean in eukaryotes?

A

Each gene has its own promoter, and each mRNA codes for a single protein.

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3
Q

How many RNA polymerases do eukaryotes have, and what are their roles?

A

RNA Pol I: Transcribes rRNA.

RNA Pol II: Transcribes protein-coding genes.

RNA Pol III: Transcribes tRNA and other small RNAs.

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4
Q

How are eukaryotic promoters different from prokaryotic promoters?

A

Eukaryotic promoters are longer, more complex, and can include enhancers and silencers far from the transcription start site.

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5
Q

What are enhancers and silencers in eukaryotic promoters?

A

Enhancers bind activator proteins to increase transcription, while silencers bind repressors to decrease transcription.

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6
Q

What are euchromatin and heterochromatin?

A

Euchromatin: Loosely packed, active genes.

Heterochromatin: Tightly packed, silenced genes.

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7
Q

What are the key steps in mRNA processing in eukaryotes?

A

5’ capping.

3’ polyadenylation.

Splicing to remove introns and join exons.

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8
Q

What is the purpose of 5’ capping and 3’ polyadenylation?

A

They protect mRNA from degradation and help with translation initiation.

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9
Q

What is splicing, and what complex performs it?

A

Splicing removes introns and joins exons, performed by the spliceosome.

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10
Q

What is alternative splicing, and why is it important?

A

Alternative splicing allows a single gene to produce multiple protein isoforms, increasing diversity.

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11
Q

How does alternative splicing determine sex in Drosophila?

A

The doublesex gene is spliced differently in males and females, producing gender-specific transcriptional repressors.

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12
Q

What are post-transcriptional modifications?

A

Modifications like capping, polyadenylation, and splicing that occur after RNA synthesis to prepare mRNA for translation.

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13
Q

What are post-translational modifications (PTMs)?

A

Modifications like phosphorylation or ubiquitination that regulate protein function and stability after translation.

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14
Q

Why are post-translational modifications advantageous?

A

They are fast, reversible, and allow regulation without requiring new protein synthesis.

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15
Q

What is protein phosphorylation, and how is it regulated?

A

Protein phosphorylation adds a phosphate group to serine, threonine, or tyrosine using kinases and is reversible by phosphatases.

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16
Q

How does phosphorylation regulate protein-protein interactions?

A

It can either block binding (due to steric hindrance or charge repulsion) or promote binding by creating a binding site.

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17
Q

What role does ubiquitination play in protein regulation?

A

Ubiquitin marks proteins for degradation by the proteasome.

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18
Q

How do bacteria degrade proteins without ubiquitination?

A

Bacteria use signal peptides on target proteins that are recognized by adapter proteins, guiding them to specific proteases.

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19
Q

What is the spliceosome, and how does it recognize introns?

A

The spliceosome is a protein complex that identifies specific sequences at the 5’ and 3’ ends of introns for removal.

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20
Q

What is the significance of alternative splicing in gene regulation?

A

It enables differential expression and the production of tissue-specific or condition-specific proteins.

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21
Q

Why do eukaryotic promoters require additional transcription factors?

A

They have longer and more complex sequences, requiring enhancers, silencers, and other factors to regulate transcription.

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22
Q

How do histone modifications affect chromatin structure?

A

Modifications like acetylation loosen chromatin (euchromatin), while methylation tightens it (heterochromatin).

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23
Q

What is the role of RNA Pol II in eukaryotes?

A

It transcribes all protein-coding genes into pre-mRNA.

24
Q

How does polyadenylation affect mRNA stability?

A

The poly(A) tail prevents degradation but shortens over time, leading to eventual mRNA degradation.

25
Q

What are the main differences between transcription in prokaryotes and eukaryotes?

A

Prokaryotes: Coupled transcription and translation, single RNA polymerase, operons.

Eukaryotes: Uncoupled processes, three RNA polymerases, monocistronic genes, chromatin structure.

26
Q

How does phosphorylation regulate the cell cycle?

A

Cyclin-dependent kinases (CDKs) phosphorylate target proteins to control progression through specific cell cycle stages.

27
Q

How does ubiquitination limit protein activity during the cell cycle?

A

Proteins are marked with ubiquitin and degraded by the proteasome, ensuring they are present only when needed.

28
Q

What are cyclins, and how do they activate CDKs?

A

Cyclins bind to CDKs, activating their kinase activity at specific stages of the cell cycle.

29
Q

Why is PTM regulation faster than transcriptional regulation?

A

PTMs act on existing proteins, bypassing the time required for transcription and translation.

30
Q

What is the proteasome, and how does it function?

A

The proteasome is a barrel-shaped complex that degrades polyubiquitinated proteins.

31
Q

Why are eukaryotic promoters more complex than prokaryotic promoters?

A

Eukaryotic promoters include sequences like enhancers and silencers that can be far from the transcription start site, requiring additional regulatory factors.

32
Q

What is the role of transcription factors in eukaryotic transcription?

A

They bind to promoter regions and enhancers/silencers to recruit or inhibit RNA polymerase activity.

33
Q

What is the role of the TATA box in transcription?

A

It is a conserved sequence in eukaryotic promoters (-30 position) recognized by transcription factors to initiate RNA polymerase binding.

34
Q

How does chromatin structure impact gene expression in eukaryotes?

A

Euchromatin: Open structure, accessible for transcription.

Heterochromatin: Condensed structure, transcriptionally silent.

35
Q

What are exons and introns?

A

Exons: Coding regions of a gene.

Introns: Non-coding regions spliced out during RNA processing.

36
Q

How does alternative splicing contribute to proteome diversity?

A

By producing multiple mRNA variants from a single gene, allowing the generation of different protein isoforms.

37
Q

How is the spliceosome able to recognise introns?

A

It identifies conserved sequences at the 5’ and 3’ splice sites and the branch point within introns.

38
Q

Why do eukaryotic genes often appear much longer than bacterial genes?

A

Eukaryotic genes contain introns, which increase gene length but are removed during splicing to produce shorter mRNA.

39
Q

What is 5’ capping, and what are its functions?

A

The addition of a methylated guanosine to the 5’ end of mRNA to protect it from degradation and assist in translation initiation.

40
Q

What is the purpose of the poly(A) tail in mRNA?

A

It stabilizes mRNA, facilitates nuclear export, and aids in translation.

41
Q

Why is alternative splicing considered a regulatory mechanism?

A

It allows cells to produce different proteins from the same gene based on developmental stage, tissue type, or environmental signals.

42
Q

What are some examples of post-translational modifications (PTMs)?

A

Phosphorylation
Ubiquitination
Methylation
Acetylation
Glycosylation

43
Q

How does ubiquitination target proteins for degradation?

A

Ubiquitin chains are attached to lysine residues on a protein, marking it for recognition and degradation by the proteasome.

44
Q

Why is phosphorylation a common regulatory mechanism?

A

It is reversible and can rapidly alter protein activity, localization, or interactions.

45
Q

What are cyclins, and why are they important in the cell cycle?

A

Cyclins regulate the cell cycle by activating cyclin-dependent kinases (CDKs) at specific checkpoints.

46
Q

How does phosphorylation regulate DNA replication in the cell cycle?

A

CDKs phosphorylate replication machinery proteins to initiate replication in the S phase and deactivate them afterward.

47
Q

What happens to cell cycle proteins after their function is complete?

A

They are either dephosphorylated or degraded via ubiquitination to ensure their activity is temporary.

48
Q

How do bacteria achieve proteolysis without ubiquitination?

A

They use signal peptides exposed on target proteins, which are recognized by adapter proteins and delivered to specific proteases.

49
Q

What is euchromatin, and how does it appear under a microscope?

A

Euchromatin is the less dense, transcriptionally active form of chromatin, appearing light in color when stained.

50
Q

What are the benefits of regulating gene expression post-translationally?

A

Rapid response to changes

Reversible regulation

Allows fine-tuning of protein activity

51
Q

What is the role of the proteasome in protein turnover?

A

The proteasome degrades polyubiquitinated proteins into peptides, regulating protein levels and removing damaged or misfolded proteins.

52
Q

What is the significance of introns in eukaryotic genes?

A

Introns allow for alternative splicing, increasing the diversity of the proteome and enabling tissue-specific or developmental regulation.

53
Q

How does chromatin remodelling impact transcription?

A

Chromatin remodelling complexes reposition nucleosomes, making DNA more or less accessible to transcription factors.

54
Q

What are RNA-binding proteins (RBPs), and how do they regulate mRNA?

A

RBPs bind to mRNA to regulate stability, localization, and translation efficiency.

55
Q

How is transcription regulated at enhancers and silencers?

A

Enhancers increase transcription by recruiting activators, while silencers decrease transcription by recruiting repressors.

56
Q

What are the main differences between transcription in prokaryotes and eukaryotes?

A

Prokaryotes: Coupled transcription-translation, single RNA polymerase, operons.

Eukaryotes: Uncoupled processes, three RNA polymerases, monocistronic genes, chromatin regulation.

57
Q

Why is the lac operon a good example of gene regulation?

A

It demonstrates both positive (CAP-cAMP activation) and negative (LacI repression) regulation, allowing bacteria to prioritise glucose over lactose.

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