DNA Synthesis and Repair

Flashcards covering key concepts of DNA synthesis and repair from the lecture.

In what direction does DNA synthesis always proceed?

DNA always grows 5' to 3', by adding nucleotides to the 3' hydroxyl group of the existing strand.

How is the leading strand synthesized compared to the lagging strand?

The leading strand is synthesized continuously, while the lagging strand is synthesized in short discontinuous fragments called Okazaki fragments.

What are the three major classes of proteins that unwind DNA in eukaryotic replication?

DNA helicases (unwind DNA), Topoisomerases (relieve upstream tension), Single-stranded DNA-binding proteins (stabilize unwound DNA).

How is DNA organized in eukaryotic cells?

DNA is wound around histone proteins and organized into structures called nucleosomes.

Which enzyme is specific to eukaryotic DNA replication?

Telomerase, which extends the ends of linear chromosomes in eukaryotes to prevent loss of genetic material.

What is the most common form of spontaneous replication error?

Tautomeric shifts — rare forms of bases cause incorrect base pairing during replication.

Can DNA damage occur outside of replication?

Yes — DNA damage can occur due to spontaneous events, chemical exposure, or radiation, not just replication errors.

What is strand slippage?

Strand slippage occurs in repetitive DNA regions, causing extra copies to be made and leading to genetic disorders.

What are two common types of spontaneous DNA hydrolysis?

Depurination: loss of a purine base (adenine or guanine), and Deamination: removal of an amino group from a base (e.g., cytosine → uracil).

What kind of DNA damage does UV radiation cause?

Pyrimidine dimer formation — covalent bonds form between adjacent thymine bases, distorting the helix.

What repair pathway removes damaged DNA from chemical or radiation sources?

Nucleotide excision repair, which cuts out and replaces damaged or distorted DNA segments.

What does base excision repair target and fix?

It removes damaged or modified individual bases (like uracil or depurinated bases) and replaces them with the correct base.

What happens when cytosine is deaminated?

Deamination converts cytosine to uracil, which mispairs with adenine.

How is uracil removed and fixed in DNA?

Uracil DNA glycosylase removes the uracil and restores the correct base.

Why does DNA use thymine instead of uracil?

DNA uses thymine to help cells identify uracil as a mistake, allowing deamination errors to be repaired.

How do mismatch repair proteins distinguish between original and new DNA strands?

The new strand is not methylated; mismatch repair proteins use this to identify and fix errors.

What is the SOS system in E. coli?

It’s a last-resort DNA repair system that activates RecA and bypass polymerases to replicate past damaged DNA.

Why is the SOS response risky for the cell?

It skips over damaged DNA, increasing the chance of mutations and genomic instability.

What allows repair proteins to distinguish abnormal from correct base pairs?

The new strand is unmethylated, while the original is methylated.

What makes SOS repair the most error-prone DNA repair system?

It uses bypass polymerases to skip over unfixable DNA damage, risking mutations instead of correcting them.