BLOCK 3: MBG: (3.2) DNA REPLICATION

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Questions and Answers

What is the main function of DNA polymerases in prokaryotic cells?

To synthesize RNA primers for DNA replication

To remove RNA primers after replication

To unwind the DNA double helix prior to replication

To catalyze the formation of phosphodiester bonds during DNA synthesis (correct)

Which statement best describes the role of topoisomerases during DNA replication?

They relieve the tension created by the unwinding of DNA (correct)

They form the RNA primers necessary for initiating replication

They ligate Okazaki fragments on the lagging strand

They add nucleotides to the growing DNA strand

What consequence arises from the end-replication problem in linear chromosomes?

High frequency of mutations occurs in the coding regions

Replication forks stall and cannot complete the leading strand

Telomeres gradually shorten with each round of replication (correct)

All genes are replicated completely, but at a slower rate

How are RNA primers removed during DNA replication in eukaryotic cells?

They are replaced by DNA polymerase using a specific mechanism Signup and view all the answers

Which DNA polymerase is primarily involved in the synthesis of the leading strand in eukaryotes?

DNA polymerase ε Signup and view all the answers

What is the main function of DNA polymerase in prokaryotic replication?

To synthesize new DNA strands Signup and view all the answers

How do eukaryotic DNA polymerases differ from prokaryotic DNA polymerases?

Eukaryotic polymerases have multiple types with specialized functions Signup and view all the answers

What role do topoisomerases play during DNA replication?

They relieve strain ahead of the replication fork Signup and view all the answers

What is the end-replication problem primarily related to?

Inability to fully replicate linear chromosomes Signup and view all the answers

What mechanism is employed for primer removal during DNA replication?

Exonuclease activity of DNA polymerase Signup and view all the answers

Which of the following is true regarding the replication fork during DNA synthesis?

One strand of DNA is continuously synthesized while the other is synthesized in fragments Signup and view all the answers

What is the purpose of RNA primers during DNA replication?

To initiate DNA synthesis with a free 3’-OH group Signup and view all the answers

Why do eukaryotic cells require multiple origins of replication?

To efficiently replicate larger genomes with multiple linear chromosomes Signup and view all the answers

What is the primary role of DNA Pol III in prokaryotes?

Elongation of the DNA strand Signup and view all the answers

Which function is primarily associated with the eukaryotic DNA polymerase Pol ε?

Leading strand elongation Signup and view all the answers

How do Type I topoisomerases manage DNA supercoiling?

Cut one strand and rotate it around the second strand Signup and view all the answers

What is the primary function of telomeres at the ends of linear chromosomes?

Preventing loss of genetic information Signup and view all the answers

Which enzyme is responsible for processing the flap created during RNA primer removal on the lagging strand?

DNA2 Signup and view all the answers

Which of the following is NOT a subunit of DNA Pol III in prokaryotes?

Delta (δ) Signup and view all the answers

What critical role does the 3' OH group play in DNA synthesis?

Essential for strand elongation Signup and view all the answers

What occurs if topoisomerases fail to function during DNA replication?

Accumulation of supercoiling and tension Signup and view all the answers

What is the function of Flap Endonuclease (FEN1) in the context of DNA replication?

Cleaves long RNA primers Signup and view all the answers

In which situation does the end-replication problem primarily occur?

In linear chromosomes Signup and view all the answers

What is the primary challenge faced by DNA polymerases during the synthesis of lagging strands?

Many RNA primers must be synthesized Signup and view all the answers

Which of the following correctly describes the role of DNA pol I in prokaryotes?

Eliminates RNA primers and fills gaps Signup and view all the answers

Which statement accurately describes the structure of telomeres?

Repetitive DNA sequences Signup and view all the answers

What is the main reason for the formation of Okazaki fragments during DNA replication?

Direction of the replication fork movement Signup and view all the answers

What impact can a gain of function mutation have on a gene?

It can be beneficial if it enhances gene activity. Signup and view all the answers

How can mutations in germline cells affect future generations?

They can potentially pass the mutation to offspring. Signup and view all the answers

What is a consequence of a loss of function mutation in a gene like P53?

It may result in deleterious changes affecting cellular regulation. Signup and view all the answers

What distinguishes spontaneous mutations from induced mutations?

Induced mutations are caused by environmental factors beyond one's control. Signup and view all the answers

What does 'benign' imply about a beneficial mutation?

It confers an advantage without negative recessive traits. Signup and view all the answers

What is the primary role of exonuclease activity in DNA replication?

To remove RNA primers from the DNA Signup and view all the answers

Which of the following statements best describes the significance of polymerases in the replication process?

They facilitate the copying of genetic material across all organisms. Signup and view all the answers

What is the main function of primers during DNA replication?

To provide a necessary starting point for polymerases Signup and view all the answers

What does the term 'highly conserved process' imply in the context of DNA replication?

It signifies an essential and effective mechanism across all organisms. Signup and view all the answers

Which of the following enzymes is primarily responsible for synthesizing the new DNA strand in prokaryotes?

DNA polymerase III Signup and view all the answers

How does the presence of helicases contribute to DNA replication?

By unwinding the double-stranded DNA helix Signup and view all the answers

Why is it necessary to remove RNA primers during DNA replication?

To allow for accurate and continuous DNA synthesis Signup and view all the answers

Which of the following best describes the relationship between leading and lagging strands during DNA replication?

The lagging strand is synthesized in fragments while the leading strand is continuous. Signup and view all the answers

What is the primary function of DNA in the cell?

To provide instructions for making proteins Signup and view all the answers

How does the organization of DNA depend on proteins?

Proteins make DNA more compact and stable Signup and view all the answers

What aspect influences the efficiency of cellular functions regarding protein synthesis?

The availability of DNA to produce proteins efficiently Signup and view all the answers

What characteristic best defines the ideal genetic material?

Being capable of moderate change based on environmental needs Signup and view all the answers

What happens if a cell lacks the necessary supplies to synthesize proteins?

It will become reliant on external sources for all functions Signup and view all the answers

How can a cell transmit and replicate genetic information?

By being capable of copying and changing the genetic material Signup and view all the answers

In terms of job efficiency, how is a cell's functionality determined?

By the instructions encoded in DNA and available materials to fulfill them Signup and view all the answers

What role do proteins play in relation to DNA synthesis?

Proteins provide machinery for replication and transcription of DNA Signup and view all the answers

What is the main reason for the existence of two leading strands during DNA replication?

Synthesis is bidirectional, allowing for two strands. Signup and view all the answers

How does a polymerase know which direction to move during DNA synthesis?

By identifying the available 3' hydroxyl group. Signup and view all the answers

What is indicated by the concept of an 'imaginary rope' in lagging strand synthesis?

Polymerase must continually catch up to helicase. Signup and view all the answers

Why does the lagging strand require continuous synthesis despite the simultaneous unwinding of DNA?

It needs to continuously access 3' hydroxyls which are moving away. Signup and view all the answers

What characteristic of DNA synthesis is emphasized by stating it occurs from 5' to 3'?

New nucleotides are always added to the 3' end. Signup and view all the answers

In what scenario would the unidirectional synthesis model apply incorrectly to DNA replication?

When viewing both leading and lagging strands together. Signup and view all the answers

What implication does bidirectional synthesis have on the efficiency of DNA replication?

Allows simultaneous synthesis, reducing replication time. Signup and view all the answers

What might occur if a polymerase encounters a 5' end while attempting to synthesize in the direction of the replication fork?

The process will be halted, preventing further synthesis. Signup and view all the answers

How does the accessibility of genetic information vary between different cell types?

Different cells have differing levels of accessibility to specific genes based on their function. Signup and view all the answers

What is the role of origins of replication in transcriptionally active genes?

They are positioned to avoid disrupting the gene they replicate. Signup and view all the answers

What happens to the origins of replication when a gene is not actively transcribed?

They become randomly organized. Signup and view all the answers

What are the two main steps involved in the initiation of DNA replication?

Licensing and firing. Signup and view all the answers

Which component is involved in the recognition of origin sites during DNA replication?

Origin recognition complex (ORC). Signup and view all the answers

Why is it important that all origins are found at the same time during replication?

To ensure rapid cellular response to replication needs. Signup and view all the answers

What determines the timing of origin firing during DNA replication?

Transcriptional activity of the cell. Signup and view all the answers

What kind of organization is observed in the origins of replication for yeast cells compared to other organisms?

Yeast have strict sequence-defined origins. Signup and view all the answers

Study Notes

Replication Regions

Late Replication regions are dependent on various factors across different organisms.
In yeast, specific sequences have been identified for late replication regions.
The functions of these sequences in other eukaryotes are currently under investigation.

Early vs Late Replication

DNA replication is not uniform throughout the genome.
Replication Timing Program is cell type specific and established during G1 phase.
Early replication regions are associated with active gene transcription.
Late replication regions are associated with lower gene transcription levels.
Early replication origins are often located between genes or at distinct locations.
Late replication origins are distributed more randomly.

Initiation of Replication

There are two stages of replication initiation in yeast: Origin Licensing and Origin Firing.
Origin Licensing is a regulatory process that controls the location of replication origins.
Origin Firing is the activation of origins for replication.
The Pre-Replication Complex (Pre-RC) plays a crucial role in replication licensing.
Pre-RC contains the Origin Recognition Complex (ORC), which promotes the binding of Cdc6, Cdt1, and MCM helicase.
MCM helicase binding initiates replication licensing.
The Pre-Initiation Complex (Pre-IC) is formed after origin licensing.
Transcription influences DNA replication and can contribute to genomic instability.

DNA Synthesis

DNA is composed of phosphodiester bonds.
The 3' hydroxyl group is essential for DNA synthesis.
Cleavage of the 3' hydroxyl group prevents strand elongation.
DNA synthesis occurs in a 5' to 3' direction.
Leading strand synthesis occurs continuously in the same direction as helicase movement.
Lagging strand synthesis is fragmented due to polymerase moving against the helicase direction and results in Okazaki fragments.

Rolling Circle Replication

In circular dsDNA, one strand is cut by a nuclease, creating a 3'OH group.
DNA polymerase extends the 3'OH group.
The newly synthesized strand displaces the original template strand.
The displaced strand acts as a template for the complementary DNA strand.

Single-Stranded DNA Virus Replication

Circular ssDNA viruses utilize rolling circle replication.
Linear ssDNA viruses use rolling hairpin replication.
Initial dsDNA circularization is achieved by host polymerases.

DNA Polymerases

Prokaryotes have five different DNA polymerases.
DNA polymerase I removes the RNA template during lagging strand synthesis and elongates the strand afterwards.
DNA polymerase III is the primary elongation enzyme.
DNA polymerase III is a complex enzyme with multiple subunits (alpha, epsilon, theta, beta, tau, gamma, chi, psi).
Eukaryotes have 15 different DNA polymerases.
Pol alpha is a polymerase-primase that synthesizes RNA primers.
Pol delta is the main polymerase for lagging strand synthesis and primer removal.
Pol epsilon is the main polymerase for leading strand synthesis.
Pol beta and other polymerases play roles in DNA repair.

Topoisomerases

Topoisomerases are enzymes that unwind DNA to facilitate strand separation.
Type I topoisomerases cut one strand, rotate it around the other strand, and seal the break.
Type II topoisomerases cut both strands of DNA.

The End-Replication Problem and Telomeres

Linear chromosomes cannot be fully replicated.
Limitations of DNA polymerases and the requirement for RNA primers lead to the End Replication Problem.
Telomeres are repetitive DNA sequences located at the ends of chromosomes that protect against genetic loss during replication.

Primer Removal: Pol Delta and Flap Endonuclease

RNA primers must be removed during DNA replication.
Pol delta displaces the RNA primer, forming a flap structure.
DNA2 processes long flaps into shorter flaps.
Flap Endonuclease (FEN1) cleaves the shorter flaps.
DNA ligase seals the gaps in the DNA backbone.

Bidirectional DNA Replication

DNA is synthesized in both directions simultaneously from a single origin of replication.
Polymerases moving in opposite directions are bound to an imaginary line that actually represents the helicase, opening the DNA in one direction.
The polymerase on the leading strand moves in the same direction as the helicase, continuously adding nucleotides to the 3' end.
The lagging strand polymerase moves in the opposite direction of the helicase, synthesizing short Okazaki fragments that are later joined together.

DNA and Proteins

DNA influences protein synthesis by providing genetic instructions for building them.
The cell relies on DNA for essential functions, such as synthesizing the necessary materials for tasks.
DNA's organization is dependent on proteins like histones and the replication and transcription machineries.

Genetic Information

The best genetic material can copy and change to adapt to environmental needs.
Viruses often rely on host cells for their replication machinery.
Polymerases have specific functions, such as exonuclease activity for removing RNA primers.

DNA Replication in Prokaryotes vs. Eukaryotes

Prokaryotes use DNA polymerase III for replicating DNA.
DNA replication in both prokaryotes and eukaryotes occurs bidirectionally, with leading and lagging strands.
Eukaryotes have more complex polymerases than prokaryotes but still use the same basic mechanism.

Primers and Origins of Replication

Primers are short RNA sequences that are used to initiate DNA synthesis.
They provide a 3’ hydroxyl group required for polymerase binding.
Origins of replication are organized differently depending on the gene's importance.
Important genes have origins outside their reading frames to ensure continuous replication.

Licensing and Firing

The origin recognition complex (ORC) identifies all origins of replication simultaneously.
Licensing involves binding of ORC, helicase, CDT1, and CDC6 to the origin.
Firing is the initiation of replication at the licensed origins.

Mutations

Mutations can be beneficial, neutral, or deleterious depending on the gene and function affected.
Beneficial mutations improve gene function, while deleterious mutations reduce or eliminate function.
Mutations in somatic cells affect only the individual, while mutations in germ cells can be passed to offspring.

Induced vs. Spontaneous Mutations

Spontaneous mutations occur due to errors in DNA replication.
Induced mutations are caused by external factors, such as radiation or chemicals.

DNA Repair

DNA repair is essential for maintaining the integrity of the genome.
Replication errors and induced mutations cause damage to DNA, which needs to be repaired.
DNA repair mechanisms are highly conserved across organisms, reflecting the importance of this process.

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Description

Explore the intricacies of DNA replication timing in eukaryotic cells with this quiz. Understand the differences between early and late replication regions, their association with gene transcription, and the initiation processes specific to organisms like yeast. Test your knowledge on how these mechanisms function across various cell types.