MODULE C3: DNA Metabolism, part 2

These flashcards cover key concepts in DNA replication, repair mechanisms, and recombination as discussed in Chapter 25.

What are the key topics covered in Chapter 25 of DNA Metabolism?

DNA replication, DNA repair, DNA recombination.

What is DNA repair and its significance?

DNA repair involves correcting changes in the structure of DNA strands; its failure can lead to mutations, which are correlated with cancer.

What types of damage can DNA sustain?

Chemical reactions and physical processes can damage DNA, such as mismatches from incorrect nucleotides and pyrimidine dimers from UV light.

How does methylation of DNA in bacteria affect replication?

In E. coli, DNA is fully methylated at GATC sites before replication; this distinguishes parent strands from newly synthesized strands and ensures accurate replication.

What role does the MutL/MutS complex play in DNA repair?

It binds to mismatched base pairs to initiate the methyl-directed mismatch repair process by cleaving the unmethylated strand.

What is base-excision repair?

A repair mechanism where DNA glycosylases recognize and remove damaged bases, creating an abasic site for repair.

What occurs during nucleotide-excision repair?

Excinuclease hydrolyzes phosphodiester bonds around a lesion, followed by DNA polymerase filling in the gap and DNA ligase sealing it.

What is the function of DNA photolyases?

They use absorbed light to directly repair cyclobutane pyrimidine dimers caused by UV light.

What is translesion DNA synthesis (TLS)?

An error-prone repair process that allows DNA replication to continue past extensive damage, but increases mutation rates.

Describe homologous genetic recombination.

A process involving exchange between two DNA molecules sharing nearly identical sequences, significant for DNA repair and genetic diversity.

What are transposons and their significance?

Segments of DNA that can move within the genome, playing a key role in genetic diversity and can potentially carry antibiotic resistance.

What are the roles of immunoglobulin genes in recombination?

Recombination of gene segments allows for the production of a vast diversity of antibodies despite a limited number of genes.

What is the Holliday model in homologous recombination?

A model describing how a double-stranded break leads to crossover structures and the eventual formation of recombinant DNA.

What is the importance of DNA replication?

DNA replication is essential for cell division, ensuring that each new cell receives an accurate copy of the DNA.

What mechanisms do cells use to prevent mutations?

Cells utilize proofreading during DNA replication, DNA repair mechanisms, and apoptosis (programmed cell death) to prevent mutations.

What are the differences between prokaryotic and eukaryotic DNA replication?

Prokaryotic replication is generally faster and occurs at a single origin, while eukaryotic replication is more complex with multiple origins and additional regulatory mechanisms.

How does the structure of DNA influence its replication?

The antiparallel structure of DNA strands and complementary base pairing facilitate accurate replication by allowing various enzymes to function effectively.

What role do helicases play in DNA replication?

Helicases are enzymes that unwind the double-stranded DNA to allow access to the template strands for replication.

What is the significance of ligases in DNA repair?

DNA ligases are crucial for sealing nicks and joining Okazaki fragments during DNA replication and repair processes.

What is the significance of telomeres in DNA replication?

Telomeres protect the ends of chromosomes from deterioration and prevent fusion with neighboring chromosomes, critical during cell division.

What is non-homologous end joining?

A DNA repair process that directly joins broken DNA ends without the requirement of a homologous template, often leading to insertions or deletions.

What is the role of DNA polymerase in DNA replication?

DNA polymerase synthesizes new DNA strands by adding nucleotides complementary to the template strand, playing a crucial role in DNA replication.

What is the function of primers in DNA replication?

Primers are short RNA sequences that provide a starting point for DNA polymerases to begin DNA synthesis during replication.

What is the difference between leading and Lagging strands in DNA replication?

Leading strands are synthesized continuously in the direction of the replication fork, while lagging strands are synthesized in short segments (Okazaki fragments) away from the fork.

What is the function of topoisomerases in DNA replication?

Topoisomerases alleviate torsional strain in the DNA helix ahead of the replication fork by cutting and rejoining the DNA strands.

What is the significance of the origin of replication?

The origin of replication is the specific location on the DNA where replication begins, allowing DNA to be copied accurately and efficiently.

How does DNA replication ensure fidelity?

DNA replication ensures fidelity through proofreading mechanisms by DNA polymerases and mismatch repair systems that correct errors after replication.

What are the roles of accessory proteins in DNA replication?

Accessory proteins, like clamp loaders and sliding clamps, help stabilize the DNA polymerase and ensure efficient and processive DNA synthesis during replication.

What is the importance of maintaining genome integrity during DNA replication?

Maintaining genome integrity is crucial to prevent mutations, which can lead to diseases such as cancer and ensure proper cellular function across generations.

What is the function of nucleotides in DNA structure?

Nucleotides are the building blocks of DNA; they consist of a sugar, a phosphate group, and a nitrogenous base, which determine the genetic information.

What is the significance of the 5' to 3' direction in DNA replication?

DNA strands are antiparallel, and the 5' to 3' direction is essential for DNA polymerases to synthesize new strands by adding nucleotides.

What is the role of RNA in DNA replication?

RNA primers are necessary for DNA polymerases to initiate synthesis of new DNA strands, as DNA polymerases cannot start from scratch.

How does the process of DNA methylation affect gene expression?

DNA methylation usually represses gene expression by inhibiting the binding of transcription factors to the DNA.

What types of enzymes are involved in DNA replication, and what are their specific functions?

Key enzymes include helicases (unwind DNA), primases (synthesize RNA primers), DNA polymerases (synthesize DNA), and ligases (join Okazaki fragments).

What is the difference between homologous and non-homologous recombination?

Homologous recombination occurs between similar sequences, while non-homologous recombination joins dissimilar DNA ends directly.

What is the role of single-strand binding proteins (SSBs) in DNA replication?

SSBs bind to single-stranded DNA during replication to prevent it from re-annealing or forming secondary structures.

What are the consequences of mutations during DNA replication?

Mutations can lead to changes in protein function, which may cause genetic disorders or contribute to the development of cancer.

Describe the function of exonucleases in DNA repair.

Exonucleases remove nucleotides from DNA ends to correct errors during replication and participate in DNA repair mechanisms.

What mechanism do cells utilize to repair double-strand breaks in DNA?

Cells can use homologous recombination for accurate repair or non-homologous end joining for quick fix with possible mutations.

What are the key features of prokaryotic DNA replication?

Prokaryotic DNA replication typically occurs in the cytoplasm, is faster than eukaryotic replication, and involves a single circular chromosome with one origin of replication.

What is the role of DNA ligase in DNA replication?

DNA ligase joins Okazaki fragments on the lagging strand and seals nicks in the sugar-phosphate backbone of the DNA.

What is the significance of Okazaki fragments?

Okazaki fragments are short segments of DNA synthesized on the lagging strand during DNA replication, allowing for discontinuous synthesis.

How do cells fix mismatched bases after DNA replication?

Cells utilize the mismatch repair system, which identifies and corrects errors in base pairing after replication, often involving the MutS and MutL proteins.

What are the roles of clamp loaders and sliding clamps in DNA replication?

Clamp loaders help assemble the sliding clamp onto DNA, which then stabilizes DNA polymerase for efficient and processive DNA synthesis.

What is the function of topoisomerases during DNA replication?

Topoisomerases relieve the torsional strain in the DNA helix that occurs ahead of the replication fork by cutting and rejoining the DNA strands.

What is the effect of UV light on DNA, and how is it repaired?

UV light causes the formation of pyrimidine dimers in DNA, which are repaired by nucleotide excision repair mechanisms using excinucleases and repair polymerases.

What are the mechanisms cells use for proofreading during DNA replication?

Proofreading during replication is primarily performed by DNA polymerases, which can remove incorrectly paired nucleotides immediately after insertion.

What is the significance of the origin of replication in eukaryotic cells?

The origin of replication is a specific sequence where DNA replication begins in eukaryotic cells, ensuring that the DNA is duplicated accurately across multiple origins.

What roles do helicases play in the initiation of DNA replication?

Helicases unwound the double-stranded DNA at the replication fork, allowing the template strands to be accessed by other enzymes involved in replication.