1. What is the main difference between prokaryotic and eukaryotic transcription?
The crucial differences between prokaryotic and eukaryotic Style transcription lie in the complexity, locations, and regulation of the process. Prokaryotic transcription occurs in the. It is relatively simplistic, requiring one RNA polymerase, and little RNA processing takes place. On the other hand, building happens in the nucleus, utilises multiple RNA polymerases, and includes much mRNA processing in eukaryotes.
2. What is the main difference between prokaryotic and eukaryotic transcription?
The main difference is the cellular location where transcription occurs. In prokaryotes, transcription happens in the cytoplasm since there's no nucleus. In eukaryotes, transcription takes place in the nucleus, where the DNA is located.
3. Why do eukaryotes need multiple RNA polymerases?
One of the features that distinguish eukaryotes from prokaryote-like Archaea is the possession of multiple RNA polymerases (I, II, III) that specialise in the transcription of different RNA types. For instance, in eukaryotes, it is RNA polymerase I that transcribes the rRNA, while RNA polymerase II synthesises mRNA. Lastly, RNA polymerase III synthesises tRNA and other small RNAs. For this reason, more fine and controlled gene expression is possible.
4. How does mRNA compare after processing in prokaryotes versus eukaryotes?
Usually, in prokaryotes, mRNA is directly transcribed and translated with no noticeable modification. In eukaryotes, mRNA undergoes intensive processing, normally the inclusion of 5' capping, splicing to remove the introns, and 3' polyadenylation. It is requisite for mRNA stability and the efficiency of translation.
5. What is the role of transcription factors in eukaryotic transcription?
Transcription factors are proteins involved in the initiation and regulation of eukaryotic transcription. They bind to specific DNA sequences, probably recruiting RNA polymerase II and other essential components to form the transcription initiation complex that goes on to control gene expression.
6. What is transcription-translation coupling, and why doesn't it occur in eukaryotes?
Transcription-translation coupling is the simultaneous occurrence of transcription and translation in prokaryotes. It doesn't occur in eukaryotes because transcription happens in the nucleus, while translation occurs in the cytoplasm, separating these processes spatially and temporally.
7. What is the function of the 5' cap in eukaryotic mRNA?
The 5' cap is a modified guanine nucleotide added to the 5' end of eukaryotic mRNA. It protects the mRNA from degradation, aids in export from the nucleus, and helps initiate translation.
8. What is the TATA box, and why is it important in eukaryotic transcription?
The TATA box is a DNA sequence found in many eukaryotic promoters. It serves as a binding site for the TATA-binding protein (TBP), which is part of the general transcription factor TFIID. The TATA box helps position the RNA polymerase II at the correct starting point for transcription.
9. What are introns, and why are they significant in eukaryotic transcription?
Introns are non-coding sequences within genes that are transcribed but removed from the mRNA during processing. They are found in eukaryotes but rarely in prokaryotes. Introns allow for alternative splicing, increasing protein diversity from a single gene.
10. What is polyadenylation, and why is it important in eukaryotic transcription?
Polyadenylation is the addition of a poly-A tail to the 3' end of eukaryotic mRNA. It helps protect the mRNA from degradation, aids in export from the nucleus, and influences translation efficiency.
11. How do the RNA polymerases differ between prokaryotes and eukaryotes?
Prokaryotes have a single type of RNA polymerase that transcribes all types of RNA. Eukaryotes have three main types of RNA polymerases: RNA polymerase I, II, and III, each responsible for transcribing different types of RNA.
12. What is the role of sigma factors in prokaryotic transcription?
Sigma factors are subunits of prokaryotic RNA polymerase that help recognize and bind to specific promoter sequences on DNA. They play a crucial role in initiating transcription by guiding the RNA polymerase to the correct starting point.
13. Do eukaryotes have sigma factors?
No, eukaryotes do not have sigma factors. Instead, they use general transcription factors (GTFs) and specific transcription factors to initiate and regulate transcription.
14. How does the initiation of transcription differ between prokaryotes and eukaryotes?
In prokaryotes, initiation is simpler and requires only the RNA polymerase and a sigma factor. In eukaryotes, initiation is more complex, involving multiple general transcription factors and RNA polymerase II for most protein-coding genes.
15. What is the significance of the -35 and -10 regions in prokaryotic promoters?
The -35 and -10 regions are conserved DNA sequences in prokaryotic promoters. They serve as recognition sites for the sigma factor, helping to position the RNA polymerase correctly for transcription initiation.
16. How does chromatin structure affect eukaryotic transcription?
Chromatin structure plays a crucial role in eukaryotic transcription. Tightly packed chromatin (heterochromatin) inhibits transcription, while loosely packed chromatin (euchromatin) allows for active transcription. This level of regulation is absent in prokaryotes.
17. What is bidirectional transcription, and how does it differ between prokaryotes and eukaryotes?
Bidirectional transcription occurs when both DNA strands are transcribed in opposite directions from a central promoter. While it occurs in both prokaryotes and eukaryotes, it's more common and often involves non-coding RNAs in eukaryotes.
18. How does the concept of supercoiling affect prokaryotic transcription?
DNA supercoiling affects prokaryotic transcription by influencing the accessibility of promoter regions. Negative supercoiling generally facilitates transcription initiation, while positive supercoiling can inhibit it.
19. What is the significance of the nucleolus in eukaryotic transcription?
The nucleolus is a subnuclear structure in eukaryotes where ribosomal RNA genes are transcribed by RNA polymerase I. It's a specialized region for the production of ribosomal components, highlighting the compartmentalization of transcription in eukaryotes.
20. What is the significance of the C-terminal domain (CTD) of RNA polymerase II in eukaryotes?
The CTD of RNA polymerase II in eukaryotes undergoes phosphorylation changes during transcription. These modifications help recruit factors involved in RNA processing and chromatin modification, coordinating transcription with other nuclear processes.
21. What is the role of the mediator complex in eukaryotic transcription?
The mediator complex in eukaryotes acts as a bridge between transcription factors bound to enhancers and the RNA polymerase II at the promoter. It helps integrate regulatory signals and stimulate transcription initiation.
22. What is the role of non-coding RNAs in regulating eukaryotic transcription?
Non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs, play important roles in regulating eukaryotic transcription. They can interact with chromatin, transcription factors, and other regulatory elements to modulate gene expression.
23. What is the role of topoisomerases in transcription, and how does it differ between prokaryotes and eukaryotes?
Topoisomerases help relieve DNA supercoiling during transcription in both prokaryotes and eukaryotes. However, eukaryotes have additional types of topoisomerases and their action is often coupled with chromatin remodeling.
24. What is the significance of transcription-coupled DNA repair in both prokaryotes and eukaryotes?
Transcription-coupled DNA repair is a process where DNA damage in actively transcribed genes is repaired more quickly. While it occurs in both prokaryotes and eukaryotes, the mechanisms and proteins involved can differ.
25. What are enhancers, and why are they more relevant in eukaryotic transcription?
Enhancers are DNA sequences that can increase transcription of a gene, even when located far from the promoter. They are more common and important in eukaryotes due to the complex regulation of gene expression in these organisms.
26. How does the concept of gene looping differ between prokaryotes and eukaryotes?
Gene looping, where the promoter and terminator regions of a gene come into close proximity, occurs in both prokaryotes and eukaryotes. However, in eukaryotes, it can involve long-range interactions and is often associated with transcriptional memory and efficient re-initiation.
27. How does the concept of transcription factories apply to eukaryotic transcription?
Transcription factories are nuclear subcompartments where multiple active genes cluster for efficient transcription. This concept is specific to eukaryotes and helps explain how complex genomes can be efficiently transcribed.
28. What is the significance of RNA polymerase pausing in eukaryotic transcription?
RNA polymerase pausing, particularly near the promoter, is an important regulatory mechanism in eukaryotes. It allows for checkpoints in gene expression and can facilitate the assembly of factors needed for efficient elongation.
29. How does the concept of transcriptional bursting apply to both prokaryotic and eukaryotic transcription?
Transcriptional bursting, where genes switch between active and inactive states resulting in pulses of mRNA production, occurs in both prokaryotes and eukaryotes. However, the mechanisms and timescales can differ between the two.
30. How does the concept of transcriptional memory differ between prokaryotes and eukaryotes?
Transcriptional memory, where past transcriptional states influence future gene expression, exists in both prokaryotes and eukaryotes. In eukaryotes, it often involves chromatin modifications and nuclear positioning, while in prokaryotes it may involve DNA methylation or specific regulatory proteins.
31. How does the concept of transcriptional noise apply to prokaryotic and eukaryotic gene expression?
Transcriptional noise, or variability in gene expression among genetically identical cells, occurs in both prokaryotes and eukaryotes. However, eukaryotes have additional mechanisms to buffer this noise, such as nuclear export and mRNA decay.
32. How does the structure of prokaryotic and eukaryotic promoters differ?
Prokaryotic promoters are simpler, typically containing two conserved sequences: the -35 and -10 regions. Eukaryotic promoters are more complex, often containing a TATA box, initiator element, and various upstream regulatory elements.
33. How does the process of elongation differ between prokaryotes and eukaryotes?
Elongation is similar in both, involving the addition of nucleotides to the growing RNA chain. However, in eukaryotes, elongation is often coupled with RNA processing events like capping and splicing, which don't occur in prokaryotes.
34. How does termination of transcription differ between prokaryotes and eukaryotes?
In prokaryotes, termination often involves specific sequences that form hairpin structures in the RNA, causing the polymerase to stop. In eukaryotes, termination is more complex, involving specific sequences and proteins that signal the end of transcription and trigger RNA processing.
35. How does RNA processing differ between prokaryotes and eukaryotes?
Eukaryotic RNA undergoes extensive processing, including 5' capping, 3' polyadenylation, and splicing. Prokaryotic RNA generally doesn't require such processing, although some modifications may occur.
36. Why don't prokaryotic mRNAs have a 5' cap?
Prokaryotic mRNAs don't need a 5' cap because they don't have a nucleus, so there's no need for nuclear export. Additionally, prokaryotic ribosomes can bind directly to the mRNA without the need for a cap structure.
37. How does the concept of operons apply to prokaryotic transcription?
Operons are clusters of genes under the control of a single promoter, common in prokaryotes. This allows for coordinated regulation of multiple genes involved in a single metabolic pathway, which is less common in eukaryotes.
38. What is the role of histone modifications in eukaryotic transcription?
Histone modifications, such as acetylation and methylation, can alter chromatin structure and accessibility. These modifications can either promote or inhibit transcription, providing an additional layer of regulation in eukaryotes.
39. How does the speed of transcription compare between prokaryotes and eukaryotes?
Prokaryotic transcription is generally faster than eukaryotic transcription. This is partly due to the simpler genome organization in prokaryotes and the lack of extensive RNA processing steps.
40. How do transcription factors differ between prokaryotes and eukaryotes?
Prokaryotic transcription factors are generally simpler and often regulate specific operons. Eukaryotic transcription factors are more diverse and can act over long distances, often working in combination to fine-tune gene expression.
41. How does the presence of a nuclear membrane affect eukaryotic transcription?
The nuclear membrane in eukaryotes separates transcription from translation, allowing for more complex regulation. It necessitates mechanisms for RNA export and enables post-transcriptional modifications before translation begins.
42. How does the presence of histones affect eukaryotic transcription?
Histones in eukaryotes package DNA into nucleosomes, which can inhibit transcription by blocking access to DNA. Histone modifications and chromatin remodeling complexes help overcome this barrier, providing an additional layer of transcriptional regulation.
43. How does the concept of transcriptional interference apply to prokaryotic and eukaryotic genomes?
Transcriptional interference, where transcription from one gene affects the transcription of a neighboring gene, can occur in both prokaryotes and eukaryotes. However, it's often more significant in the compact genomes of prokaryotes.
44. What is the role of RNA-binding proteins in eukaryotic transcription and post-transcriptional regulation?
RNA-binding proteins in eukaryotes can influence transcription by interacting with the nascent RNA and the transcription machinery. They also play crucial roles in post-transcriptional processes like splicing, export, and mRNA stability.
45. What is the significance of antisense transcription in both prokaryotes and eukaryotes?
Antisense transcription, where RNA is produced from the opposite strand of a gene, occurs in both prokaryotes and eukaryotes. It can regulate gene expression by interfering with sense transcription or producing regulatory RNAs, but the mechanisms and prevalence differ between the two domains.
46. What is the role of nuclear pore complexes in eukaryotic transcription?
Nuclear pore complexes in eukaryotes not only facilitate the export of mRNA to the cytoplasm but can also influence transcription. Some actively transcribed genes are recruited to the nuclear periphery, which can affect their expression.
47. How does the concept of transcriptional amplification apply to eukaryotic gene regulation?
Transcriptional amplification in eukaryotes refers to the phenomenon where activators can increase the expression of a gene beyond what would be expected from increased recruitment of RNA polymerase alone. This often involves enhancing multiple steps of the transcription process.
48. What is the significance of transcription start site heterogeneity in eukaryotes?
Many eukaryotic genes have multiple transcription start sites, leading to transcripts with different 5' ends. This heterogeneity can affect mRNA stability, translation efficiency, and even protein function, providing an additional layer of gene regulation.
49. How does the process of transcriptional proofreading differ between prokaryotes and eukaryotes?
Both prokaryotic and eukaryotic RNA polymerases have some ability to proofread and correct errors during transcription. However, eukaryotes have additional factors that enhance this process, particularly during the early stages of transcription.
50. What is the role of phase separation in eukaryotic transcription regulation?
Phase separation, where proteins and nucleic acids form condensates within the nucleus, is emerging as an important concept in eukaryotic transcription regulation. It can concentrate transcription factors and other regulatory molecules, potentially enhancing or repressing transcription.
51. How does the concept of transcriptional adaptation apply to prokaryotes and eukaryotes?
Transcriptional adaptation, where cells adjust their gene expression in response to environmental changes, occurs in both prokaryotes and eukaryotes. However, the mechanisms are often simpler and faster in prokaryotes, while eukaryotes may involve more complex signaling cascades and chromatin remodeling.
52. What is the significance of promoter-proximal pausing in eukaryotic transcription?
Promoter-proximal pausing, where RNA polymerase II pauses shortly after initiating transcription, is a common regulatory mechanism in eukaryotes. It allows for rapid induction of genes and can serve as a checkpoint for proper transcript processing.
53. How does the concept of transcriptional bursting relate to gene expression noise in prokaryotes and eukaryotes?
Transcriptional bursting, where genes are transcribed in pulses rather than at a constant rate, contributes to gene expression noise in both prokaryotes and eukaryotes. However, the timescales and regulatory mechanisms of these bursts can differ between the two domains.
54. What is the role of enhancer RNAs (eRNAs) in eukaryotic transcription regulation?
Enhancer RNAs are non-coding RNAs transcribed from enhancer regions in eukaryotes. They can play active roles in gene regulation by facilitating enhancer-promoter interactions, recruiting transcription factors, or modulating chromatin structure.
