All flashcards
Flashcard 1: What is the core function of telomerase in eukaryotic cells?
Answer: Extends the 3′ end of telomeres using an internal RNA template (reverse transcriptase). As a ribonucleoprotein with reverse transcriptase activity, telomerase adds repeats to prevent telomere shortening.
Flashcard 2: What chemical group provides the nucleophile that attacks the incoming dNTP during elongation?
Answer: The primer strand 3′-OH group. The 3'-OH attacks the alpha phosphate of the incoming dNTP, forming a phosphodiester bond during chain elongation.
Flashcard 3: What is the direction that the DNA template strand is read by DNA polymerase?
Answer: The template is read in the 3′→5′ direction. Antiparallel strand orientation requires the template to be read 3' to 5' for new strand synthesis in the 5' to 3' direction.
Flashcard 4: What is the overall direction of DNA synthesis by DNA polymerases in all organisms?
Answer: DNA is synthesized in the 5′→3′ direction. DNA polymerases add nucleotides to the growing chain's 3' end, ensuring synthesis proceeds from 5' to 3'.
Flashcard 5: What is the immediate energy source that drives phosphodiester bond formation in DNA synthesis?
Answer: Cleavage of dNTP to dNMP with release of pyrophosphate (PPi). Hydrolysis of the high-energy bonds in dNTP releases pyrophosphate, providing the energy to make the reaction exergonic.
Flashcard 6: What is the replication fork “leading strand” defined by relative to fork movement?
Answer: The strand synthesized continuously in the same direction as fork movement. It allows continuous elongation toward the replication fork without interruption as the helix unwinds.
Flashcard 7: What is the replication fork “lagging strand” defined by relative to fork movement?
Answer: The strand synthesized discontinuously as Okazaki fragments. Synthesis occurs in short segments away from the fork due to the antiparallel nature of DNA strands.
Flashcard 8: What is the primary function of helicase during DNA replication?
Answer: Unwinds the parental double helix at the replication fork. Helicase uses ATP hydrolysis to separate DNA strands, creating single-stranded templates for polymerase access.
Flashcard 9: What is the primary function of single-strand binding proteins (SSB) in replication?
Answer: Stabilize ssDNA and prevent reannealing or secondary structure formation. SSBs coat exposed single strands to maintain their accessibility and prevent unwanted structures during replication.
Flashcard 10: What is the primary function of topoisomerases during DNA replication?
Answer: Relieve supercoiling/torsional strain ahead of the replication fork. They introduce temporary strand breaks to relax positive supercoils generated by unwinding at the fork.
Flashcard 11: What is the key mechanistic difference between topoisomerase I and topoisomerase II?
Answer: Topo I cuts 1 strand; topo II cuts 2 strands (ATP-dependent). Type I relaxes supercoils via single-strand nicks without ATP, while type II passes strands through double-strand breaks using ATP.
Flashcard 12: What is the function of primase during DNA replication?
Answer: Synthesizes short RNA primers to provide a free 3′-OH. Primase, an RNA polymerase, creates RNA segments that DNA polymerase extends, as it cannot start chains de novo.
Flashcard 13: What is the function of DNA ligase in replication and repair?
Answer: Seals nicks by forming phosphodiester bonds between adjacent DNA ends. It catalyzes the ATP-dependent formation of phosphodiester bonds to join Okazaki fragments or repair breaks.
Flashcard 14: What is the role of the sliding clamp (e.g., PCNA in eukaryotes) in DNA replication?
Answer: Increases processivity by tethering DNA polymerase to DNA. The clamp encircles DNA and binds polymerase, enhancing its ability to synthesize long stretches without dissociating.
Flashcard 15: Which enzymatic activity enables many DNA polymerases to proofread newly added bases?
Answer: 3′→5′ exonuclease activity. This activity removes incorrectly paired nucleotides from the 3' end, allowing replacement before synthesis continues.
Flashcard 16: What is the key limitation of DNA polymerases that necessitates a primer?
Answer: They cannot initiate synthesis de novo; they require a preexisting 3′-OH. DNA polymerases can only extend existing chains, requiring an RNA primer to supply the initial 3'-OH group.
Flashcard 17: In bacteria, which DNA polymerase primarily performs chromosomal DNA elongation?
Answer: DNA polymerase III. Pol III is the highly processive replicative enzyme responsible for most nucleotide addition during bacterial replication.
Flashcard 18: In bacteria, which DNA polymerase primarily removes RNA primers and fills in DNA?
Answer: DNA polymerase I. Pol I uses its 5' to 3' exonuclease to excise RNA primers and polymerase activity to replace them with DNA.
Flashcard 19: What is the “end-replication problem” that occurs in linear eukaryotic chromosomes?
Answer: After primer removal, the terminal lagging-strand segment cannot be fully replicated. Lagging strand synthesis leaves a gap at the 5' end after RNA primer removal, as no upstream 3'-OH is available for filling.
Flashcard 20: What is semiconservative DNA replication?
Answer: Each daughter duplex contains one parental strand and one newly synthesized strand. This mechanism, proven by Meselson-Stahl, preserves genetic information by using each parental strand as a template.
Flashcard 21: What is the specific base-pairing rule that stabilizes DNA during replication and repair?
Answer: A pairs with T; G pairs with C (Watson–Crick base pairing). Specific hydrogen bonds between purines and pyrimidines ensure fidelity in template-directed synthesis and repair.
Flashcard 22: What is mismatch repair (MMR) primarily responsible for correcting after replication?
Answer: Base-base mismatches and small insertion/deletion loops that escape proofreading. MMR detects and excises errors like mismatches or loops post-replication, using strand discrimination to guide repair.
Flashcard 23: What is base excision repair (BER) primarily used to fix in DNA?
Answer: Small, non-bulky base lesions (e.g., deamination, oxidation) via DNA glycosylase. BER initiates with glycosylase removing altered bases, followed by strand incision and gap-filling for subtle damage.
Flashcard 24: What is nucleotide excision repair (NER) primarily used to fix in DNA?
Answer: Bulky, helix-distorting lesions (e.g., thymine dimers) by excising an oligonucleotide. NER excises a short single-stranded segment containing the lesion, then synthesizes a replacement using the intact strand.
Flashcard 25: Identify the most accurate classification of UV-induced thymine dimers as DNA damage.
Answer: Bulky, helix-distorting lesions typically repaired by NER. UV light causes covalent bonds between adjacent thymines, distorting the helix and triggering NER for removal.