1. What is the major difference between prokaryotic from eukaryotic DNA replication?
The chief difference is in prokaryotic replication, which prudently contains one origin of replication, while eukaryotic replication contains multiple origins.
2. How is the rate of DNA replication different between prokaryotes and eukaryotes?
Basically, prokaryotic replication is much faster since it contains less regulatory apparatus and its replication machines are simple in design.
3. Why is there more than one origin of replication in eukaryotic cells?
The replication in eukaryotic cells is more complex, making it necessary to have multiple origins to complete the process on time.
4. What is the function of telomeres in the eukaryotic DNA-replicating process?
Telomeres are discrete, non-coding, repetitive sequences located at the linear chromosomes' terminal. They save the ends of linear chromosomes from degradation and prevent them from being recognised as damaged DNA.
5. How is replication accuracy maintained in prokaryotes vs. eukaryotes?
While proofreading is an intrinsic property of DNA polymerases in all living organisms, both prokaryotes and eukaryotes, the latter have additional repair pathways brought about by the complexity of their genomes.
6. What is the role of histones in eukaryotic DNA replication?
Histones play a crucial role in eukaryotic DNA replication by packaging DNA into nucleosomes. During replication, histones must be removed to allow the replication machinery access to the DNA, and then reassembled on the newly synthesized DNA to maintain chromatin structure.
7. What role do cyclins and cyclin-dependent kinases play in eukaryotic DNA replication?
Cyclins and cyclin-dependent kinases (CDKs) regulate the timing of DNA replication in eukaryotes by controlling the activation of replication origins. They ensure that replication occurs only once per cell cycle by phosphorylating key replication proteins.
8. Why is DNA replication in eukaryotes restricted to the S phase of the cell cycle?
Eukaryotic DNA replication is restricted to the S phase to ensure that the genome is replicated only once per cell cycle. This tight regulation prevents errors that could lead to genomic instability and is coordinated with other cellular processes like mitosis.
9. How does the presence of introns in eukaryotic genes affect DNA replication?
The presence of introns in eukaryotic genes doesn't directly affect DNA replication, as the entire gene, including introns, is replicated. However, it does impact the overall genome size and complexity, which influences the need for multiple replication origins and longer replication times in eukaryotes.
10. Why is coordinating leading and lagging strand synthesis more challenging in eukaryotes?
Coordinating leading and lagging strand synthesis is more challenging in eukaryotes due to their larger genomes, multiple replication origins, and the need to maintain chromatin structure. This requires more complex machinery to ensure efficient and accurate replication.
11. Why don't prokaryotes need telomeres?
Prokaryotes don't need telomeres because they have circular chromosomes. The circular structure eliminates the end-replication problem that linear chromosomes face, as there are no free ends to be lost during replication.
12. How does the number of origins of replication differ between prokaryotes and eukaryotes?
Prokaryotes typically have a single origin of replication on their circular chromosome, while eukaryotes have multiple origins of replication distributed along their linear chromosomes. This allows eukaryotes to replicate their larger genomes more efficiently.
13. How does the process of termination differ between prokaryotic and eukaryotic DNA replication?
In prokaryotes, termination occurs when the two replication forks meet at a specific termination site opposite the origin. In eukaryotes, termination happens when replication forks from adjacent origins meet, or when a fork reaches the end of a chromosome.
14. Why is DNA proofreading more extensive in eukaryotes compared to prokaryotes?
DNA proofreading is more extensive in eukaryotes because they have larger genomes and longer generation times. This makes it crucial to minimize mutations that could accumulate over time. Prokaryotes can afford a slightly higher mutation rate due to their rapid reproduction and simpler genomes.
15. How does the licensing of replication origins differ between prokaryotes and eukaryotes?
In eukaryotes, replication origins must be "licensed" during the G1 phase before they can be activated in the S phase. This involves the assembly of pre-replication complexes. Prokaryotes, with their single origin, don't require this complex licensing process.
16. What is the main difference between prokaryotic and eukaryotic DNA replication?
The main difference is that prokaryotic replication occurs in the cytoplasm with a single origin of replication, while eukaryotic replication takes place in the nucleus with multiple origins of replication. This allows eukaryotes to replicate their larger genomes more efficiently.
17. Why do prokaryotes have a circular chromosome while eukaryotes have linear chromosomes?
Prokaryotes have circular chromosomes to maximize efficiency in their simple cellular structure. Linear chromosomes in eukaryotes allow for more complex genome organization and regulation, which is necessary for their more sophisticated cellular processes.
18. How does the speed of replication differ between prokaryotes and eukaryotes?
Prokaryotic replication is generally faster, occurring at about 1000 nucleotides per second, while eukaryotic replication is slower at about 50 nucleotides per second. This difference is due to the more complex nature of eukaryotic genomes and the additional regulatory steps involved.
19. What are Okazaki fragments and why are they more significant in eukaryotic replication?
Okazaki fragments are short DNA segments synthesized during lagging strand replication. They are more significant in eukaryotic replication because eukaryotic chromosomes are linear and much longer, resulting in more frequent and longer lagging strands that require more Okazaki fragments.
20. How do telomeres solve the end-replication problem in eukaryotes?
Telomeres are repetitive DNA sequences at the ends of eukaryotic chromosomes. They solve the end-replication problem by providing a buffer zone that can be shortened during each replication cycle without losing essential genetic information. Telomerase can also add new telomeric sequences to maintain chromosome length.
21. What is the significance of the MCM complex in eukaryotic DNA replication?
The MCM (Mini-Chromosome Maintenance) complex serves as the main helicase in eukaryotic DNA replication. It is loaded onto origins during G1 phase as part of the pre-replication complex, playing a crucial role in origin licensing and the initiation of DNA synthesis.
22. How does the process of primer removal differ between prokaryotes and eukaryotes?
In both prokaryotes and eukaryotes, RNA primers are removed and replaced with DNA. However, eukaryotes use more specialized enzymes like FEN1 (Flap Endonuclease 1) to remove primers, especially those from Okazaki fragments, due to the more frequent priming events in their lagging strand synthesis.
23. How does the presence of a nuclear membrane in eukaryotes affect DNA replication?
The nuclear membrane in eukaryotes compartmentalizes DNA replication, keeping it separate from other cellular processes. This requires specialized mechanisms for importing replication proteins into the nucleus and coordinating replication with nuclear envelope breakdown during cell division.
24. What is the significance of replication factories in eukaryotic cells?
Replication factories are specialized nuclear regions where multiple replication forks cluster. They allow for more efficient replication by concentrating necessary enzymes and factors, and may help coordinate the replication of different chromosomal regions in eukaryotes.
25. How does the presence of heterochromatin in eukaryotes affect DNA replication?
Heterochromatin in eukaryotes presents a challenge for DNA replication as it is more condensed and less accessible. Special mechanisms are required to temporarily loosen heterochromatin structure to allow replication machinery access, adding complexity to the eukaryotic replication process.
26. What is the significance of bidirectional replication in both prokaryotes and eukaryotes?
Bidirectional replication, where two replication forks move in opposite directions from the origin, allows for faster and more efficient DNA replication in both prokaryotes and eukaryotes. This is especially important for eukaryotes with their larger genomes.
27. What is the role of topoisomerases in prokaryotic and eukaryotic DNA replication?
Topoisomerases relieve DNA supercoiling during replication in both prokaryotes and eukaryotes. However, eukaryotes require additional types of topoisomerases to deal with the more complex DNA topology resulting from chromatin structure and longer chromosomes.
28. How does the complexity of the replication machinery differ between prokaryotes and eukaryotes?
Eukaryotic replication machinery is more complex than prokaryotic machinery. Eukaryotes have additional proteins involved in the process, such as those required for chromatin remodeling, checkpoint controls, and coordinating replication with the cell cycle.
29. Why is the replisome more complex in eukaryotes compared to prokaryotes?
The eukaryotic replisome is more complex because it must deal with a larger genome, chromatin structure, and multiple regulatory mechanisms. It includes additional proteins for unwinding DNA, coordinating leading and lagging strand synthesis, and maintaining genomic stability.
30. Why is replication initiation more tightly regulated in eukaryotes compared to prokaryotes?
Replication initiation is more tightly regulated in eukaryotes to prevent re-replication of DNA within a single cell cycle. This is crucial for maintaining genomic stability in complex eukaryotic genomes, whereas prokaryotes can tolerate some re-replication due to their simpler genome organization.
31. How do checkpoint mechanisms differ between prokaryotic and eukaryotic DNA replication?
Eukaryotes have more extensive checkpoint mechanisms that can halt replication in response to DNA damage or replication stress. These checkpoints are less developed in prokaryotes, which rely more on rapid repair and replacement of damaged cells.
32. How does the organization of replicated DNA differ between prokaryotes and eukaryotes?
In prokaryotes, replicated DNA is quickly segregated into daughter cells. In eukaryotes, replicated DNA is organized into sister chromatids, which remain attached until mitosis. This allows for more complex regulation of chromosome segregation in eukaryotes.
33. How does the coupling of transcription and replication differ between prokaryotes and eukaryotes?
In prokaryotes, transcription and replication can occur simultaneously due to the lack of a nuclear membrane. In eukaryotes, these processes are generally separated, with replication occurring in the S phase and transcription regulated throughout the cell cycle.
34. Why is the regulation of replication timing more complex in eukaryotes?
Replication timing in eukaryotes is more complex because different regions of the genome replicate at different times during S phase. This temporal program is linked to gene expression, chromatin state, and nuclear organization, factors that are less relevant in prokaryotic replication.
35. How does the mechanism of dealing with replication fork stalling differ between prokaryotes and eukaryotes?
Eukaryotes have more sophisticated mechanisms for dealing with stalled replication forks, including specialized checkpoint responses and repair pathways. Prokaryotes rely more on restarting replication from the origin or using recombination-based mechanisms to overcome fork stalling.
36. What is the role of PCNA in eukaryotic DNA replication and how does it differ from the β-clamp in prokaryotes?
PCNA (Proliferating Cell Nuclear Antigen) in eukaryotes and the β-clamp in prokaryotes both serve as sliding clamps that increase DNA polymerase processivity. However, PCNA has additional roles in eukaryotes, including coordinating various DNA repair processes and chromatin remodeling.
37. How does the mechanism of replication fork progression differ between prokaryotes and eukaryotes?
In prokaryotes, replication fork progression is relatively straightforward due to the circular chromosome and simple cellular organization. In eukaryotes, fork progression must navigate through complex chromatin structures and deal with potential conflicts with transcription machinery, requiring additional regulatory mechanisms.
38. Why is the coupling of DNA replication and histone synthesis important in eukaryotes?
The coupling of DNA replication and histone synthesis in eukaryotes is crucial for maintaining chromatin structure. As DNA is replicated, new histones must be synthesized and deposited onto the newly formed DNA to recreate nucleosomes, ensuring proper chromosome structure and gene regulation.
39. How does the presence of multiple chromosomes in eukaryotes affect the replication process?
The presence of multiple chromosomes in eukaryotes requires coordinated replication of all chromosomes within the S phase. This involves the activation of multiple origins on each chromosome and mechanisms to ensure that all chromosomes complete replication before entering mitosis.
40. What is the significance of replication timing domains in eukaryotes?
Replication timing domains in eukaryotes are large chromosomal regions that replicate at similar times during S phase. These domains are important for organizing the replication of the large eukaryotic genome efficiently and are often correlated with gene activity and chromatin state.
41. How does the process of DNA replication contribute to epigenetic inheritance in eukaryotes?
During eukaryotic DNA replication, epigenetic marks such as DNA methylation and histone modifications must be accurately copied to maintain cell identity. This process, known as epigenetic inheritance, requires specialized mechanisms coupled to DNA replication that are not present in prokaryotes.
42. Why is the coordination between DNA replication and cell cycle checkpoints more critical in eukaryotes?
Coordination between DNA replication and cell cycle checkpoints is more critical in eukaryotes due to their complex genomes and longer cell cycles. Checkpoints ensure that replication is complete and error-free before allowing cell division, preventing genomic instability in these complex organisms.
43. How does the mechanism of dealing with DNA damage during replication differ between prokaryotes and eukaryotes?
Eukaryotes have more sophisticated mechanisms for dealing with DNA damage during replication, including specialized translesion synthesis polymerases and complex DNA damage response pathways. Prokaryotes rely more on rapid repair and tolerance mechanisms due to their simpler genomes and faster replication cycles.
44. What is the role of dormant origins in eukaryotic DNA replication?
Dormant origins in eukaryotes are backup replication start sites that can be activated if nearby active origins fail. This provides a failsafe mechanism to ensure complete genome replication, especially in regions where replication forks may stall or collapse, a complexity not found in prokaryotic systems.
45. How does the process of replication-transcription conflicts resolution differ between prokaryotes and eukaryotes?
In prokaryotes, replication and transcription occur simultaneously in the same compartment, requiring mechanisms to resolve direct conflicts. Eukaryotes generally separate these processes temporally and spatially, but still need complex mechanisms to deal with conflicts in highly transcribed regions or during stress conditions.
46. Why is the regulation of origin firing more complex in eukaryotes compared to prokaryotes?
Origin firing regulation is more complex in eukaryotes because they have multiple origins that must be activated in a coordinated manner throughout S phase. This involves a two-step process of origin licensing and activation, controlled by various factors including CDKs, which is not necessary in the simpler prokaryotic system.
47. How does the process of replication fork reversal differ between prokaryotes and eukaryotes?
Replication fork reversal, a mechanism to deal with replication stress, occurs in both prokaryotes and eukaryotes. However, in eukaryotes, this process is more tightly regulated and involves more factors due to the complexity of their genomes and the need to maintain genomic stability across larger chromosomes.
48. What is the significance of replication factories in eukaryotes and why are they not observed in prokaryotes?
Replication factories in eukaryotes are nuclear sites where multiple replication forks cluster, allowing for efficient use of replication machinery. They are not observed in prokaryotes due to the simpler organization of prokaryotic cells and their single replication origin, which doesn't require such spatial organization.
49. How does the process of replication-coupled nucleosome assembly differ between prokaryotes and eukaryotes?
Replication-coupled nucleosome assembly is a eukaryotic-specific process where newly synthesized histones are deposited onto replicated DNA to reform chromatin structure. Prokaryotes do not have nucleosomes, so this process is not relevant to their DNA replication.
50. Why is the regulation of replication origin spacing more important in eukaryotes compared to prokaryotes?
Regulation of replication origin spacing is more important in eukaryotes because they have multiple origins on each chromosome. Proper spacing ensures efficient replication of the entire genome within S phase. Prokaryotes, with their single origin, do not require this level of spatial regulation.
51. How does the mechanism of dealing with replication fork barriers differ between prokaryotes and eukaryotes?
Eukaryotes have more complex mechanisms for dealing with replication fork barriers, including specialized proteins that help the fork navigate through difficult-to-replicate regions. Prokaryotes rely more on recombination-based mechanisms to overcome barriers, reflecting their simpler genome organization.
52. What is the role of the pre-RC (pre-replication complex) in eukaryotic DNA replication and why is it not necessary in prokaryotes?
The pre-RC is crucial in eukaryotes for licensing origins before S phase, ensuring that each origin fires only once per cell cycle. This complex licensing system is not necessary in prokaryotes due to their single origin and simpler cell cycle regulation.
53. How does the process of replication termination contribute to genome stability differently in prokaryotes and eukaryotes?
In prokaryotes, replication termination occurs
