Mutations and DNA Repair

Types of Mutations - Code's Quirky Typos

• Mutation: Permanent, heritable DNA sequence change.
• Point Mutations: Single base-pair (bp) change.

  Type	Change	Consequence	Example (Gene: AA change)
  Silent	Codon → Same AA	Usually no phenotypic effect
  Missense	Codon → Different AA	Variable; e.g., Sickle cell (HBB: Glu6Val)	Sickle cell anemia
  Nonsense	Codon → STOP (UAA, UAG, UGA)	Truncated protein 📌 Stop Nonsense!	β-thalassemia, Cystic Fibrosis
  Frameshift	Indel (not multiple of 3 bp)	Altered reading frame; new protein	Tay-Sachs, Duchenne MD

• Insertions/Deletions (Indels): Addition/removal of DNA bases; may cause frameshifts if not in multiples of 3 bp.
• Functional Effects:
  • Loss-of-function (LOF): Reduced/null protein activity.
  • Gain-of-function (GOF): New/enhanced protein activity.
  • Dominant negative: Mutant protein antagonizes wild-type.
• Somatic vs. Germline:
  • Somatic: In body cells; not inherited.
  • Germline: In gametes; heritable.

⭐ Nonsense mutations cause premature stop codons, leading to truncated, often non-functional proteins.

Mutagens & Damage - DNA's Daily Dangers

DNA faces constant threats, leading to mutations if unrepaired.

Spontaneous Damage (Endogenous):

• Deamination: C → U; A → hypoxanthine.
• Depurination: Loss of purine base (A or G), creating an AP site.
• Oxidative Damage: Reactive oxygen species (ROS) modify bases (e.g., 8-oxoG).

Induced Damage (Exogenous Mutagens):

1. Chemical Mutagens:

• Base Analogs: e.g., 5-Bromouracil (5-BU) incorporates like T, mispairs with G.
• Alkylating Agents: e.g., Ethyl methanesulfonate (EMS) adds alkyl groups (ethyl to G), causing mispairing.
• Intercalating Agents: e.g., Ethidium bromide, proflavine. Insert between base pairs, causing frameshifts.
  • 
• Deaminating Agents: e.g., Nitrous acid ($HNO_2$) converts C→U, A→hypoxanthine.

2. Physical Mutagens:

• UV Radiation (Non-ionizing): Forms pyrimidine dimers (CPDs like T-T dimers) and 6-4 photoproducts.
• Ionizing Radiation (X-rays, γ-rays): Causes single-strand breaks (SSBs) and double-strand breaks (DSBs).

⭐ UV radiation predominantly causes cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs).

Single-Strand Repair - Precision Patchwork

• Direct Repair: Directly reverses DNA damage.

  • Photolyase (not in humans): Repairs pyrimidine dimers (UV) using light.
  • MGMT ($O^6$-Methylguanine-DNA Methyltransferase): Removes alkyl groups from $O^6$-methylguanine. Suicide enzyme.

• Base Excision Repair (BER): For small, non-helix distorting lesions (e.g., uracil, oxidized/alkylated bases).

  • 📌 Mnemonic: GEL PLeASe (DNA Glycosylase, AP Endonuclease, AP Lyase, DNA Polymerase, DNA Ligase).

  ⭐ Base Excision Repair (BER) is initiated by a DNA glycosylase that recognizes and removes a specific damaged base, creating an AP site.

![Base Excision Repair pathway steps and enzymes](https://ylbwdadhbcjolwylidja.supabase.co/storage/v1/object/public/notes/L1/Biochemistry_Nucleic_Acid_Biochemistry_Mutations_and_DNA_Repair/80f40880-47bc-4632-91ad-664d6d112d6e.png)

• Nucleotide Excision Repair (NER): For bulky, helix-distorting lesions (e.g., pyrimidine dimers, bulky adducts). Excises oligonucleotide (~24-32 nt in humans).
  • Key Proteins:
    • Humans: XP proteins (XPA-XPG, part of ~30 proteins). Deficiency → Xeroderma Pigmentosum.
    • E. coli: Uvr proteins (UvrA,B,C excinuclease); excises ~12-13 nt.

![Nucleotide Excision Repair Pathways](https://ylbwdadhbcjolwylidja.supabase.co/storage/v1/object/public/notes/L1/Biochemistry_Nucleic_Acid_Biochemistry_Mutations_and_DNA_Repair/8a878069-9623-41e7-a068-e91f336606db.png)

Complex Repair & Syndromes - When Fixes Falter

• Mismatch Repair (MMR): Corrects DNA replication errors.
  • Prokaryotes: MutS, MutL, MutH.
  • Eukaryotes: MSH, MLH, PMS.
• Double-Strand Break (DSB) Repair:
  • NHEJ (Non-Homologous End Joining): Error-prone; predominant in G1.
  • HR (Homologous Recombination): Error-free; S/G2 phase (uses sister chromatid). Proteins: BRCA1, BRCA2.
• Key Repair Defect Syndromes:

  Syndrome	Defective Pathway/Gene	Key Features
  Xeroderma Pigmentosum	NER	UV sensitivity, ↑ skin cancer risk
  Lynch Syndrome (HNPCC)	MMR	↑ colorectal, endometrial, ovarian cancer risk
  Ataxia Telangiectasia	ATM (DSB sensing)	Ataxia, telangiectasias, immunodeficiency, cancer
  BRCA1/BRCA2 Cancers	HR	↑ breast, ovarian cancer risk
  Fanconi Anemia	ICL repair, HR	Pancytopenia, congenital abnormalities, cancer

⭐ Defects in Nucleotide Excision Repair (NER) are responsible for Xeroderma Pigmentosum, leading to extreme sensitivity to UV light and a high risk of skin cancer.

High‑Yield Points - ⚡ Biggest Takeaways

• Point mutations include silent, missense (altered amino acid), and nonsense (STOP codon).
• Frameshift mutations result from insertions/deletions not divisible by three, altering the reading frame.
• Mismatch Repair (MMR) corrects replication errors; defects lead to Lynch syndrome (HNPCC).
• Nucleotide Excision Repair (NER) fixes UV-induced pyrimidine dimers; defective in Xeroderma Pigmentosum.
• Base Excision Repair (BER) removes single damaged bases using DNA glycosylases.
• Double-strand breaks are repaired by NHEJ (error-prone) or Homologous Recombination (high-fidelity).
• The Ames test evaluates a chemical's mutagenic potential using bacteria_._