Lecture 6 DNA replication_Mutations Slides

DNA mutation

A permanent change in the DNA sequence that can be passed on through cell divisions.

DNA damage

A chemical alteration or mistake in DNA that can still be repaired before it becomes permanent.

Why is DNA repair important?

Because unrepaired DNA damage can become mutations, disrupt genes, cause disease, or lead to cancer.

Why does the cell spend lots of energy repairing DNA?

Preserving DNA information is essential for survival, so repair is worth the energy cost.

Point mutation

A mutation involving a change in one base pair.

Transition mutation

A point mutation where a purine is replaced by another purine or a pyrimidine is replaced by another pyrimidine.

Transversion mutation

A point mutation where a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine.

Purines

Adenine and guanine.

Pyrimidines

Cytosine, thymine, and uracil.

Why are transitions more common than transversions?

Transitions swap bases of similar size, so they are easier for DNA polymerase to tolerate.

Silent mutation

A mutation that changes a codon but does not change the amino acid.

Missense mutation

A mutation that changes the codon and causes a different amino acid to be added.

Nonsense mutation

A mutation that changes a codon into a stop codon.

What is the result of a nonsense mutation?

Translation stops early and usually makes a shortened, nonfunctional protein.

Insertion mutation

A mutation where one or more base pairs are added into the DNA sequence.

Deletion mutation

A mutation where one or more base pairs are removed from the DNA sequence.

Indels

Insertions and deletions grouped together.

Frameshift mutation

A mutation that shifts the reading frame of codons.

What causes a frameshift mutation?

An insertion or deletion that is not in a multiple of three nucleotides.

Why are frameshift mutations usually harmful?

They change every codon after the mutation and often create an early stop codon.

What happens if 3 bases are inserted or deleted?

One amino acid may be added or removed, but the reading frame is not shifted.

Triplet repeat expansion

A mutation where repeated three-base sequences expand in number.

Why can triplet repeat expansions be harmful?

They can disrupt gene function or protein function when the repeats become too long.

How does DNA damage become a heritable mutation?

DNA damage becomes heritable if it is not repaired before replication and the mistake is copied into daughter cells.

Why is a mismatch not automatically a mutation?

Because the cell can still repair the mismatch before the next round of replication.

When does a mismatch become a permanent mutation?

After replication copies it into a normal-looking but incorrect base pair.

What is the basic two-step process for point mutation formation?

First, a mismatch or damaged base occurs; second, replication copies it into a permanent sequence change.

Deamination

The removal of an amino group from a DNA base.

What causes spontaneous deamination?

Hydrolysis, which is damage caused by water.

Cytosine deamination

Cytosine is converted into uracil.

Why is cytosine deamination dangerous?

Uracil pairs with adenine, so unrepaired cytosine deamination can cause a C=G to T=A transition.

Adenine deamination

Adenine is converted into hypoxanthine.

What does hypoxanthine pair with?

Cytosine.

Guanine deamination

Guanine is converted into xanthine.

What does xanthine pair with?

Cytosine.

5-methylcytosine deamination

5-methylcytosine is converted into thymine.

Why is 5-methylcytosine deamination especially dangerous?

It creates thymine, which is a normal DNA base, so the damage is harder to recognize.

Why are methylated CpG sites mutation hotspots?

Because 5-methylcytosine can deaminate into thymine, creating a mismatch that may become permanent.

Depurination

The loss of a purine base from DNA.

Which bases are purines?

Adenine and guanine.

Abasic site

A DNA position where the base is missing but the sugar-phosphate backbone remains.

Why can depurination cause mutation?

DNA polymerase may insert the wrong base because the template base is missing.

Oxidative damage

DNA damage caused by reactive oxygen species.

Reactive oxygen species

Highly reactive oxygen-containing molecules that can damage DNA.

Examples of reactive oxygen species

Hydrogen peroxide, hydroxyl radicals, and superoxide radicals.

What can oxidative damage do to DNA?

It can alter bases, create abasic sites, or cause strand breaks.

8-oxoguanine

An oxidized form of guanine that can mispair with adenine.

Why is 8-oxoguanine mutagenic?

It can pair with adenine instead of cytosine.

What mutation can 8-oxoguanine cause?

A G=C to T=A transversion.

Alkylation

The addition of an alkyl group to a DNA base or DNA backbone.

Why is alkylation damaging?

It can change base-pairing behavior, block replication, or distort DNA structure.

Benzo[a]pyrene

A DNA-damaging chemical found in cigarette smoke, wood smoke, and coal tar.

How does benzo[a]pyrene damage DNA?

It is metabolized into a reactive form that forms bulky DNA adducts.

DNA adduct

A chemical group covalently attached to DNA.

Nitrogen mustard

An alkylating agent that can form DNA cross-links.

DNA cross-link

Damage where DNA bases become covalently linked, blocking normal DNA separation or replication.

Mutagen

A substance that increases the rate of mutation.

Carcinogen

A substance that promotes cancer formation.

Genotoxic compound

A compound that damages genetic material.

Why can DNA-damaging agents cause cancer?

They can create mutations that disrupt cell cycle control or DNA repair.

Why can some DNA-damaging agents be used in chemotherapy?

At high doses, they can damage DNA so severely that rapidly dividing cancer cells die.

Why do chemotherapy DNA-damaging agents mainly affect dividing cells?

The damage is most harmful when cells are trying to replicate their DNA.

Ames test

A bacterial test used to identify chemicals that cause mutations.

What organism is used in the Ames test?

Salmonella typhimurium.

What kind of Salmonella strain is used in the Ames test?

A histidine auxotroph that cannot make histidine.

Histidine auxotroph

A mutant cell that cannot synthesize histidine and needs histidine in the medium to grow.

What is the purpose of the Ames test?

To determine whether a chemical is mutagenic.

What medium is used in the Ames test?

Medium lacking histidine.

Why can the Ames test bacteria not normally grow without histidine?

They have a mutation that prevents histidine synthesis.

Reversion mutation

A mutation that restores a lost function.

What does a positive Ames test mean?

Many bacterial colonies grow, meaning the chemical likely caused mutations.

What does more colony growth mean in the Ames test?

More mutations occurred, so the chemical is more mutagenic.

Why are liver enzymes sometimes added to the Ames test?

Some chemicals only become mutagenic after being metabolized by the liver.

Why is the Ames test useful?

It is a quick and inexpensive way to screen chemicals for mutagenicity.

UV radiation damage

DNA damage caused by ultraviolet light.

Pyrimidine dimer

A UV-induced cross-link between adjacent pyrimidines, usually thymine bases.

Thymine dimer

A type of pyrimidine dimer where two adjacent thymine bases become linked.

Why are pyrimidine dimers harmful?

They distort DNA and stall replication machinery.

What happens if pyrimidine dimers are not repaired?

DNA replication can stall, which can lead to cell death or mutation.

Single-strand nick

A break in one strand of the DNA backbone.

Why is a single-strand nick easier to repair?

The opposite strand can still be used as a template.

Double-strand break

A break through both DNA strands.

Why is a double-strand break more dangerous than a nick?

There may be no intact template strand at the break site.

What repairs double-strand breaks?

Homologous recombination or non-homologous end joining.

Homologous recombination repair

A repair pathway that uses a homologous DNA sequence as a template.

Non-homologous end joining

A repair pathway that directly joins broken DNA ends without needing a homologous template.

Mismatch repair

A DNA repair pathway that fixes incorrect base pairs made during replication.

What type of damage does mismatch repair fix?

Replication errors, such as single-base mismatches and small insertion/deletion loops.

Why is mismatch repair needed if DNA polymerase proofreads?

Some replication mistakes escape proofreading, so mismatch repair provides another correction system.

What is the main challenge of mismatch repair?

The cell must know which strand is the new incorrect strand and which strand is the correct parent template.

How does E. coli identify the parent strand during mismatch repair?

The parent strand is methylated at GATC sites.

Dam methylase

The enzyme that methylates adenine in GATC sequences in E. coli.

Hemimethylated DNA

DNA where the parent strand is methylated but the newly synthesized strand is not yet methylated.

Why is hemimethylation useful for mismatch repair?

It lets the cell distinguish the old template strand from the new strand.

Which strand gets repaired in E. coli mismatch repair?

The newly synthesized unmethylated strand.

Which strand is used as the correct template in E. coli mismatch repair?

The methylated parent strand.

MutS

A mismatch repair protein that recognizes the mismatch.

MutL

A mismatch repair protein that helps coordinate the repair process.

MutH

A mismatch repair protein that cuts the unmethylated daughter strand.

What does MutS recognize?

DNA distortion caused by a mismatch.