DNA Damage and Repair I

Title: DNA Damage and Repair I
Presented by: Anna Potter, PhD, Assistant Professor
Date & Time: September 19, 2025, 2:10 - 3:00 PM
Location: Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University
Contact: apotter1@nova.edu
Course: Medical Biochemistry COM 5021, Lecture #45
Institution: Tampa Bay Regional Campus

List possible causes of DNA damage.
List the types of DNA mutations at the sequence level.
Describe the types of DNA mutations or epigenetic modifications at the chromosomal level.
Describe deletion syndromes.

DNA in Cells:
- Every second, the DNA in each cell is being damaged through various processes, including:
- Breaking of chemical bonds.
- Snapping of DNA strands.
- Loss of nucleotide bases.
- At body temperature, over 10,000 bases are lost per day per cell due to spontaneous breakdown.
- Many cells are also dividing, risking errors during DNA copying.
- Exposure to carcinogens intensifies DNA damage and mutation occurrences.

Definition of Mutation:
- A mutation is defined as any change made to the DNA sequence or chromosome structure.
- Key Properties of Mutations:
1. Not inherently good or bad - can lead to diseases but also allows for evolution by creating new alleles.
2. Permanent changes - mutations cannot be removed or repaired (distinguished from DNA damage).
3. Random occurrences - they do not occur selectively.

By Size:
- Chromosomal Mutations: Involves large segments that are deleted, inverted, moved, or duplicated.
- Gene Mutations: Smaller changes in DNA sequence involving one or a few nucleotides.
By Cause:
- Spontaneous Mutations: Occur naturally due to biochemical events.
- Induced Mutations: Caused by external factors such as chemicals, radiation, or viruses.
**By Cell Type:
- Somatic Mutations: Occur in somatic cells and are not inherited.
- Germ-line Mutations: Occur in gamete-forming tissues and can be passed to offspring.

Defined as mutations that arise without known mutagens.
Causes of Spontaneous Mutations:
- Errors during replication of undamaged DNA.
- Mutagenic nucleotide substrates.
- Endogenous DNA lesions.

Base Alteration: Changes in the base structure.
Base Deletion: Loss of a nucleotide base.
Sugar Alteration: Changes in the sugar molecule of DNA.
Strand Break: Physical breaking of a DNA strand.
Ineffective repair or replication prior to repair can cause these lesions to become permanent mutations.

Depurination:
- The sugar-base bond is broken resulting in an apurinic site.
- Occurs frequently (~10,000 times per day).
Deamination:
- Loss of an amino group from cytosine or adenine, leading to incorrect base pairing.
- Example: Conversion of cytosine to thymine due to deamination.
Tautomeric Shifts:
- Nitrogenous bases can exist in different structural isomers leading to abnormal base pairing.
- Normally, bases pair as A-T and C-G, rare forms can lead to mismatches during replication.

All possible nucleotide mutations fall into two categories:
- Transitions: A purine is changed into another purine or a pyrimidine to another pyrimidine (e.g., A ↔ G, C ↔ T).
- Transversions: A purine is substituted for a pyrimidine or vice versa.

Base Analogs:
- Chemicals resembling regular nucleotides that can incorporate during replication.
- Example: 5-bromouracil replacing thymine.
Alkylating Agents:
- Chemicals that add alkyl groups to nucleotides, altering base pairing (e.g., Ethyl guanine pairs with thymine).
- Example: Mustard gas used in WWI causes severe health issues.
Intercalating Agents:
- Planar molecules that insert themselves between base pairs, causing distortions.
- Result in insertion or deletion mutations.
UV Light and Low-Energy Radiation:
- Alters DNA structure creating pyrimidine dimers, preventing normal replication and can lead to cell apoptosis.
High-Energy Radiation (Ionizing Radiation):
- Causes double-stranded breaks and generation of free radicals, leading to extensive DNA damage.
- Historical examples include the Chernobyl disaster and Fukushima disaster.

Base-Pair Substitutions:
- Changes a nucleotide; outcomes include:
  - Silent Mutation: No effect on amino acid sequence.
  - Missense Mutation: Leads to a different amino acid, potentially altering the protein's shape.
  - Nonsense Mutation: A codon is altered to a stop codon, truncating the protein.
Insertions/Deletions (Indels):
- Addition or loss of a nucleotide causes frameshifts altering the entire downstream protein coding sequence.
- Example: "THE DOG BIT THE MAN" becomes "THE DOB ITT HEM AN" due to deletion.
Expansion of Trinucleotide Repeats (TNRE):
- An increase in the copy number of a trinucleotide sequence which can lead to diseases like Huntington's.
- Copy numbers may worsen in subsequent generations.

Aneuploidy:
- An organism ends up with extra or missing chromosomes (e.g., Monosomy, Trisomy).
- Example: Down syndrome is a trisomy of chromosome 21, resulting in various phenotypical traits.
Polyploidy:
- Presence of multiple sets of chromosomes, rare in humans; usually occurs in specific tissues.
- Triploidy: 69 chromosomes due to polyspermy, often detrimental to health.

Williams Syndrome:
- Caused by a deletion of 26-28 genes on chromosome 7 (including elastin).
- Symptoms include short stature, learning disabilities, and unique social behaviors.
Cri-du-Chat Syndrome:
- Caused by a deletion on chromosome 5.
- Symptoms include developmental delays, a characteristic high-pitched cry, and various physical abnormalities.