DNA Damage and Repair Notes

DNA Damage and Repair I

Kiran C. Patel College of Osteopathic Medicine
Nova Southeastern University Medical Biochemistry
COM 5021 Lecture #45
Date: 9/19/25
Time: 2:10-3:00 pm
Instructor: Anna Potter, PhD, Assistant Professor
Email: apotter1@nova.edu
Campus: Tampa Bay Regional Campus
Office: #3614

Learning Objectives

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

Constant Threats to DNA

  • The DNA in each cell of the body is under continuous threat, experiencing various forms of damage.
  • Damage types include:
    • Breaking of chemical bonds in nucleotides.
    • Snapping of DNA strands.
    • Loss of nucleotide bases.
  • Each cell loses more than 10,000 bases per day due to spontaneous breakdown at normal body temperature.
  • Cells during division face risks associated with DNA copying errors.
  • External exposure to carcinogens amplifies DNA injury, contributing to mutations that can lead to diseases like cancer.

Possible Causes of DNA Damage: Mutations

Definition of Mutation

  • Mutation: Any alteration in the DNA sequence or chromosome structure.
  • Key properties of mutations:
    1. They are not inherently beneficial or harmful; they can lead to disease or death but also to new alleles, contributing to evolution.
    2. Mutations are permanent changes that cannot be removed or repaired.
    3. Mutations occur randomly and do not have a preferential occurrence.

Classification of Mutations

Mutations can be classified based on various criteria:

  1. Size:

    • Chromosomal mutations: Significant alterations such as deletions, inversions, relocations, or duplications of large chromosome segments.
    • Gene mutations: Smaller changes involving one or few nucleotides.

  2. Cause of Mutation:

    • Spontaneous mutations: Result from natural biochemical events.
    • Induced mutations: Caused by artificial factors such as chemicals, radiation, or viruses.

  3. Cell Type Containing Mutated DNA:

    • Somatic mutations: Arise in somatic (non-germ) cells, not passed to the next generation.
    • Germ-line mutations: Occur in gamete-forming tissues and can be transmitted to offspring.

Spontaneous Mutations

  • Spontaneous mutations occur in the absence of known mutagens and can arise from:
    • Errors during replication of undamaged template DNA.
    • Mutagenic nucleotide substrates and endogenous DNA lesions.
    • Spontaneous DNA lesions may include:
    • Base alterations.
    • Base deletions.
    • Sugar alterations.
    • Strand breaks.
  • Faulty replication before repair, or ineffective repair, can lead to permanent mutations.
Causes of Spontaneous Damage
  • Depurination:
    • The bond between sugar and base is severed, resulting in an apurinic site (a missing base).
    • Occurs about 10,000 times per day.
  • Deamination:
    • Loss of amino groups from cytosine or adenine, disrupting normal hydrogen bonding and leading to mispairing during replication (e.g., C -> T).
Tautomeric Shifts
  • Nitrogenous bases can exist in alternate structural forms (tautomers).
  • Normal Pairing: A-T, C-G
  • Rare (Abnormal) Pairing: May lead to mismatches (e.g., T-H bonds with G).
  • Rare isomerization is a factor potentially leading to DNA replication errors.

Types of Nucleotide Mutations

  1. Transitions:

    • Changes a purine (two-ring) to another purine (A

  2. Transversions:

    • Substitution of a purine with a pyrimidine or vice versa (e.g., A

  3. Oxidative Damage:

    • Reactive oxygen species (ROS) formed during metabolism result in DNA damage.
    • Free radicals can alter DNA structure, which poses significant risks during replication, associated with aging and cancer development.

  4. Transposons (Jumping Genes):

    • DNA segments that can move within a genome, either by “cutting and pasting” (transposons) or “copying and pasting” (retrotransposons).
    • Can disrupt gene expression and contribute to chromosomal alterations.
Induced/Exogenous DNA Damage
  • A variety of environmental factors can induce DNA damage:

  1. Base Analogs:

    • Chemicals resembling normal nucleotides which can be misincorporated during replication (e.g., 5-bromouracil).

  2. Alkylating Agents:

    • Chemicals that add alkyl groups to nucleotides, causing abnormal base pairing (e.g., mustard gas).

  3. Intercalating Agents:

    • Molecules that insert between base pairs, distorting DNA structure (e.g., acridine orange, ethidium bromide).

  4. UV Light and Low Energy Radiation:

    • Alters DNA structure by creating pyrimidine dimers, disrupting replication.

  5. High-Energy Radiation (Ionizing):

    • X-rays and gamma rays can directly break phosphodiester bonds in DNA, leading to severe mutations.

Types of Possible DNA Mutations at the Sequence Level

1. Base-pair Substitutions

  • A single nucleotide is altered.
    • Silent Mutation: No effect; often third nucleotide in a codon changes.
    • Missense Mutation: Change results in a different amino acid.
    • Nonsense Mutation: Results in a premature stop codon, truncating the protein.

2. Insertions/Deletions

  • Addition or loss of nucleotides.
    • Results in a frameshift mutation affecting all subsequent amino acids.

3. Expansion of Trinucleotide Repeats (TNRE)

  • Seen when the number of repeat triplets in a mutated gene exceeds the normal levels.
    • Can lead to diseases such as Huntington’s and Fragile X syndrome, and typically become more severe with successive generations.

Chromosomal Level Mutations

1. Alterations in Chromosome Number

  • Changes in the number of chromosomes:
    • Aneuploidy: Loss or gain of one or more chromosomes.
    • Monosomy: One chromosome missing (e.g., Turner Syndrome - XO).
    • Trisomy: One extra chromosome (e.g., Down Syndrome - Trisomy 21).
    • Polyploidy: Multiple sets of chromosomes.
    • Triploidy (3n) and Tetraploidy (4n) are forms mostly non-viable in humans.

2. Examples of Aneuploid Disorders

  • Down Syndrome: Caused by Trisomy 21, leading to a range of phenotypes including intellectual disabilities and health issues.

Deletion Syndromes

Williams Syndrome

  • Resulting from the deletion of 26-28 genes from the long arm of chromosome 7.
  • Symptoms include:
    • Short stature, learning disabilities, wide mouth, and unique personality traits.
    • At the cellular level, affected individuals exhibit reduced tissue elasticity and elevated blood calcium levels.

Cri-du-Chat Syndrome (5p-Syndrome)

  • Caused by a deletion on the short arm of chromosome 5.
  • Characterized by:
    • High-pitched cry, intellectual disabilities, low birth weight, and distinct facial anomalies.
    • The majority of cases are sporadic.