Molecular Biology - DNA Replication & Repair Mechanisms Flashcards

Question 1

In what direction does DNA polymerase synthesize new DNA strands?

Accepted Answer

DNA polymerase can only add nucleotides to the $3'$ hydroxyl end of a growing strand, meaning synthesis always proceeds in the $5' 	o 3'$ direction.

Question 2

What is semi-conservative DNA replication?

Accepted Answer

The process where each new DNA molecule consists of one original (parental) strand and one newly synthesized strand. This mechanism ensures genetic continuity and was famously demonstrated by Meselson and Stahl.

Question 3

What is an Origin of Replication (Ori)?

Accepted Answer

A specific sequence of DNA where replication is initiated. Prokaryotes typically have one origin, while eukaryotes have multiple origins along each chromosome.

Question 4

Describe a replication fork.

Accepted Answer

The Y-shaped structure formed when the double-stranded DNA unwinds during replication, creating two single strands that serve as templates for new DNA synthesis.

Question 5

What is the primary function of DNA helicase in replication?

Accepted Answer

DNA helicase unwinds the double-stranded DNA helix by breaking the hydrogen bonds between complementary base pairs, separating the two strands to create the replication fork.

Question 6

What is the role of Single-Strand Binding Proteins (SSBPs)?

Accepted Answer

SSBPs bind to the separated single DNA strands, preventing them from re-annealing and protecting them from degradation, thus keeping the template strands accessible for replication.

Question 7

What is the function of topoisomerase (DNA gyrase) during DNA replication?

Accepted Answer

Topoisomerase (specifically DNA gyrase in prokaryotes) relieves the torsional stress (supercoiling) that builds up ahead of the replication fork due to unwinding by helicase, by cutting and rejoining DNA strands.

Question 8

What is the function of primase in DNA replication?

Accepted Answer

Primase is an RNA polymerase that synthesizes short RNA primers (5-10 nucleotides long) on the DNA template. These primers provide the free $3'$-OH group required for DNA polymerase to initiate DNA synthesis.

Question 9

Describe the main functions of DNA Polymerase III in prokaryotic DNA replication.

Accepted Answer

DNA Polymerase III is the primary enzyme responsible for synthesizing new DNA strands. It has $5' 	o 3'$ polymerase activity (adding nucleotides) and $3' 	o 5'$ exonuclease activity (proofreading, removing incorrectly paired nucleotides).

Question 10

What are the key functions of DNA Polymerase I in prokaryotic DNA replication?

Accepted Answer

DNA Polymerase I has three activities: $5' 	o 3'$ polymerase activity (filling gaps), $3' 	o 5'$ exonuclease activity (proofreading), and crucially, $5' 	o 3'$ exonuclease activity (removing RNA primers).

Question 11

What is the function of DNA ligase in DNA replication?

Accepted Answer

DNA ligase catalyzes the formation of a phosphodiester bond between adjacent nucleotides, sealing nicks in the DNA backbone. It is essential for joining Okazaki fragments on the lagging strand and repairing DNA.

Question 12

Describe leading strand synthesis.

Accepted Answer

The leading strand is synthesized continuously in the $5' 	o 3'$ direction, moving towards the replication fork. Only one RNA primer is needed to initiate its synthesis, and DNA polymerase III extends it without interruption.

Question 13

Describe lagging strand synthesis.

Accepted Answer

The lagging strand is synthesized discontinuously, in short fragments (Okazaki fragments), in the $5' 	o 3'$ direction, moving *away* from the replication fork. Multiple RNA primers are required.

Question 14

What are Okazaki fragments?

Accepted Answer

Short DNA segments (100-200 nucleotides in eukaryotes, 1000-2000 in prokaryotes) synthesized on the lagging strand during DNA replication. Each fragment requires its own RNA primer.

Question 15

What is a replisome?

Accepted Answer

A complex molecular machine that carries out DNA replication. It consists of DNA helicase, primase, DNA polymerase (III in prokaryotes), and other associated proteins working together at the replication fork.

Question 16

Why are DNA repair mechanisms crucial for genomic integrity?

Accepted Answer

DNA is constantly exposed to damaging agents and replication errors. Repair mechanisms correct these errors and damage, preventing mutations that can lead to genetic diseases, cancer, and cell death, thus maintaining genomic stability.

Question 17

Explain the Mismatch Repair (MMR) mechanism.

Accepted Answer

MMR corrects errors that escape proofreading during replication, such as incorrect base pairings (e.g., A-C). It identifies the newly synthesized strand (often by methylation patterns in prokaryotes) and excises the mismatched nucleotide, which is then replaced by DNA polymerase and sealed by ligase.

Question 18

Describe the Base Excision Repair (BER) pathway.

Accepted Answer

BER repairs small, non-helix-distorting lesions, such as damaged or modified bases (e.g., deaminated cytosine to uracil). A DNA glycosylase removes the damaged base, creating an AP site. AP endonuclease then cuts the backbone, DNA polymerase fills the gap, and ligase seals it.

Question 19

Explain the Nucleotide Excision Repair (NER) mechanism.

Accepted Answer

NER is a versatile repair pathway that removes bulky, helix-distorting lesions, such as pyrimidine dimers caused by UV radiation or chemical adducts. An excinuclease complex recognizes the distortion, cuts the damaged strand on both sides, removes the oligonucleotide, and DNA polymerase fills the gap, followed by ligase.

Question 20

What is direct repair, and provide an example.

Accepted Answer

Direct repair mechanisms reverse DNA damage without removing and resynthesizing a segment of DNA. An example is photoreactivation, where DNA photolyase uses light energy to directly break pyrimidine dimers. Another is alkyltransferases removing alkyl groups.

Question 21

What is Non-Homologous End Joining (NHEJ)?

Accepted Answer

NHEJ is a major pathway for repairing double-strand breaks (DSBs) in DNA. It directly ligates the broken ends together, often with some loss of nucleotides at the break site, making it an error-prone but efficient repair mechanism.

Question 22

Describe Homologous Recombination (HR) in DNA repair.

Accepted Answer

HR is an accurate pathway for repairing double-strand breaks (DSBs) that uses an undamaged homologous DNA molecule (e.g., sister chromatid) as a template to precisely repair the break, ensuring no loss of genetic information.

Molecular Biology - DNA Replication & Repair Mechanisms

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