MCAT Biological and Biochemical Foundations of Living Systems Flashcards: 1b Dna Replication Repair

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This deck focuses on 1b Dna Replication Repair, giving you a quick way to review the definitions, rules, and examples that matter most for MCAT Biological and Biochemical Foundations of Living Systems.

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Flashcard 1: 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 2: 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 3: 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 4: 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 5: 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 6: 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 7: 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 8: What is the overall direction of DNA synthesis by DNA polymerases in all organisms?

Answer: DNA is synthesized in the $5' \to 3'$ direction. DNA polymerases add nucleotides to the growing chain's 3' end, ensuring synthesis proceeds from 5' to 3'.

Flashcard 9: 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 10: What is the direction that the DNA template strand is read by DNA polymerase?

Answer: The template is read in the $3' \to 5'$ direction. Antiparallel strand orientation requires the template to be read 3' to 5' for new strand synthesis in the 5' to 3' direction.

Flashcard 11: 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 12: 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 13: What is the immediate energy source that drives phosphodiester bond formation in DNA synthesis?

Answer: Cleavage of dNTP to dNMP with release of pyrophosphate ($PP_i$). Hydrolysis of the high-energy bonds in dNTP releases pyrophosphate, providing the energy to make the reaction exergonic.

Flashcard 14: 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 15: 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 16: 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 17: 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 18: 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 19: 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 20: 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 21: 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 22: 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 23: 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.

Flashcard 24: 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 25: Which enzymatic activity enables many DNA polymerases to proofread newly added bases?

Answer: $3' \to 5'$ exonuclease activity. This activity removes incorrectly paired nucleotides from the 3' end, allowing replacement before synthesis continues.