Topic 8: DNA Replication and Repair - BIOL 211

Practice questions covering the mechanisms of DNA replication, the Meselson-Stahl experiment, enzymatic functions, telomeres, and various DNA repair pathways based repair mechanisms.

Which model of DNA replication did the Meselson and Stahl experiment support?

The semiconservative model.

Why did the mixture contain only heavy DNA when bacteria were grown in a medium containing $N^{15}$?

Because $N^{15}$ is a heavy nitrogen isotope, causing the DNA to sink to the bottom during centrifugation.

In the Meselson and Stahl experiment, what was the composition of the DNA after one round of replication in the $N^{14}$ medium?

$100\%$ hybrid DNA ($N^{15}\text{-}N^{14}$).

What is the ratio of DNA types after two rounds of replication in the $N^{14}$ medium in the Meselson and Stahl experiment?

$50\%$ hybrid DNA ($N^{15}\text{-}N^{14}$) and $50\%$ light DNA ($N^{14}\text{-}N^{14}$).

In which direction does DNA polymerase synthesize a new DNA strand?

$5'$ to $3'$ direction.

What specific chemical group is required at the end of the existing strand for DNA polymerase to add a new nucleotide?

A free $3'\text{-OH}$ group.

What is the term for the specialized DNA sequences at the ends of eukaryotic chromosomes that consist of non-coding repeats?

Telomeres.

What is the specific repeat sequence of human telomeres?

$$5'\text{-TTAGGG-}3'$$

Which enzyme is responsible for unwinding the DNA double helix at the origin of replication?

Helicase.

What is the function of Single-stranded binding proteins (SSBs)?

They bind to the separated DNA strands to keep them from re-annealing into a double helix.

Which enzyme relieves the strain in the DNA double helix during unwinding?

Topoisomerase.

What is the role of Primase in DNA replication?

It generates an RNA primer that provides the free $3'\text{-OH}$ needed for DNA polymerase to begin synthesis.

Why does lagging strand synthesis occur discontinuously?

Because DNA polymerase can only synthesize in the $5'$ to $3'$ direction, and the lagging strand template is oriented in the opposite direction ($5'$ to $3'$) relative to the replication fork's movement.

What are the short segments of DNA produced on the lagging strand called?

Okazaki fragments.

Which enzyme replaces RNA primers with DNA nucleotides?

DNA polymerase I.

What is the function of DNA ligase during replication?

It seals the nicks between DNA fragments to create a continuous daughter strand.

What is the 'End Replication Problem' in linear chromosomes?

The requirement for an RNA primer means the $3'$ ends of linear chromosomes cannot be fully replicated, leading to additive loss of DNA after each cell division.

Which enzyme is active in stem cells and gametes to maintain telomere length by extending the $3'$ overhang?

Telomerase.

What is Theta ($\theta$) replication?

The process of DNA replication in prokaryotes involving a circular genome, one origin of replication, and a replication bubble with two forks.

How does DNA Polymerase III perform proofreading during replication?

It uses $3'$ to $5'$ exonuclease activity to remove mispaired nucleotides before resuming synthesis.

In the Mismatch Repair (MMR) pathway, which protein nicks the daughter strand?

MutH endonuclease.

What is the role of DNA glycosylase in Base Excision Repair (BER)?

It removes a modified or damaged nitrogenous base, forming an AP site (apurinic/apyrimidinic site).

Which specific type of DNA damage is caused by UV radiation?

Thymine Dimers (covalent links between adjacent pyrimidines).

What enzyme complex in prokaryotes performs Nucleotide Excision Repair (NER) by removing a segment of $12$ or $13$ nucleotides?

UvrABC exinuclease.

What is Imetelstat?

A telomerase inhibitor used as an anticancer therapeutic.

Which chemical agent from Page 31 modifies guanine to prevent replication?

Aflatoxin $B_1$.