CHAPTER 6 — DNA REPLICATION & REPAIR

DNA replication (semiconservative)

DNA replication is semiconservative, meaning each daughter DNA molecule contains one parental strand and one newly synthesized strand.

Double helix

The DNA double helix consists of two antiparallel strands held together by complementary base pairing (A–T, C–G) and hydrogen bonds.

Antiparallel DNA

DNA strands run in opposite directions: one strand runs 5’→3’, the other runs 3’→5’.

Replication origin

A replication origin is a specific DNA sequence where replication begins. It is recognized by proteins such as ORC.

Origin Recognition Complex (ORC)

ORC is a protein complex that binds replication origins and prepares DNA for replication initiation.

Cdc6

Cdc6 binds to ORC and helps assemble the replication machinery, preparing DNA for replication.

Replication fork

A replication fork is the Y-shaped region where DNA is unwound, and replication occurs in both directions.

DNA helicase

DNA helicase unwinds the DNA double helix by breaking hydrogen bonds between strands.

DNA polymerase

DNA polymerase synthesizes new DNA strands using a template and performs proofreading to maintain accuracy.

Primase

Primase synthesizes short RNA primers that provide a starting point for DNA polymerase.

DNA ligase

DNA ligase joins DNA fragments by forming phosphodiester bonds, especially between Okazaki fragments.

Topoisomerase

Topoisomerase relieves twisting tension ahead of the replication fork by cutting and rejoining DNA strands.

Leading strand

The leading strand is synthesized continuously in the same direction as the replication fork.

Lagging strand

The lagging strand is synthesized discontinuously in short segments due to opposite orientation relative to the fork.

Okazaki fragments

Okazaki fragments are short DNA pieces synthesized on the lagging strand that are later joined together.

Nucleotide triphosphates

Nucleotide triphosphates provide energy for DNA synthesis through hydrolysis of phosphate bonds.

Proofreading

DNA polymerase removes incorrect nucleotides and replaces them with correct ones to ensure accuracy.

DNA damage

DNA damage can result from radiation, chemicals, replication errors, or metabolic byproducts.

Mismatch repair

Mismatch repair corrects errors by removing incorrect bases, resynthesizing DNA, and sealing it with ligase.

Nonhomologous end joining

A repair mechanism that joins broken DNA ends directly but may introduce mutations.

Homologous recombination

A precise repair mechanism using a homologous DNA sequence as a template.

Telomerase

Telomerase extends chromosome ends to solve the end replication problem.

Phosphodiester bond

A phosphodiester bond is a covalent bond that links nucleotides together within a DNA strand, forming the sugar-phosphate backbone.

Hydrogen bonds in DNA

Hydrogen bonds hold the two DNA strands together by linking complementary bases (A–T and C–G), allowing strands to separate during replication.

Replication fork direction

Replication forks move outward from the origin in both directions along the DNA molecule.

Relationship between fork movement and synthesis

DNA synthesis always occurs 5’→3’, but replication forks move bidirectionally, creating leading and lagging strands.

Asymmetrical replication fork problem

Because DNA strands are antiparallel and DNA polymerase works only 5’→3’, one strand must be synthesized discontinuously.

Solution to asymmetrical replication

The lagging strand is synthesized in short Okazaki fragments that are later joined together.

Replication machine

A multi-protein complex that includes helicase, primase, DNA polymerase, ligase, and topoisomerase working together at the replication fork.

Supercoiling problem

As DNA unwinds, tension builds ahead of the replication fork, causing supercoiling.

Topoisomerase function (expanded)

Topoisomerase resolves supercoiling by temporarily breaking DNA strands, allowing rotation, and then resealing them.

Types of DNA damage

DNA damage includes base mismatches, chemical modifications, thymine dimers, and double-strand breaks.

Single-strand damage

Damage affecting only one DNA strand, which can be repaired using the complementary strand as a template.

Mismatch repair (step 1)

The incorrect nucleotide is recognized and identified.

Mismatch repair (step 2)

A nuclease removes the section of DNA containing the error.

Mismatch repair (step 3)

DNA polymerase fills in the gap using the correct strand as a template.

Mismatch repair (step 4)

DNA ligase seals the repaired strand.

Nonhomologous end joining (expanded)

A repair process that directly joins broken DNA ends without a template, often introducing mutations.

Homologous recombination (expanded)

A repair process that uses an intact homologous DNA sequence as a template, making it more accurate.

Mutation

A permanent change in DNA sequence that can affect protein function and lead to disease.

Consequences of unrepaired DNA damage

Can lead to mutations, cell death, or diseases such as cancer.

Template strand

The original DNA strand used to guide synthesis of a new complementary strand.

Nascent strand

The newly synthesized DNA strand formed during replication.

Base-pairing rules

Adenine pairs with thymine, and cytosine pairs with guanine.