mutation and repair

Mutation

  • A mutation is defined as any change in the DNA sequence of an organism's genome.

    • Can occur naturally during DNA replication or be induced by external factors (radiation, chemicals, viruses).
    • Can affect:
    • A single nucleotide,
    • Large sections of DNA, or
    • Entire chromosomes.
    • Effects can be:
    • Neutral
    • Beneficial
    • Harmful

  • Types of Mutations:

    • Somatic Mutations: Mutations in non-reproductive cells.
    • Germline Mutations: Mutations in germ cells that can be transmitted to offspring.

Point Mutation

  • A point mutation affects a single nucleotide in the DNA sequence.

    • Types:
    1. Silent Mutations: No change in the resulting amino acid sequence.
    2. Missense Mutations: Substitution of one amino acid for another in a protein.
    3. Nonsense Mutations: Introduce a premature stop codon, resulting in truncated proteins.

  • Mutant: An organism, cell, or gene containing a mutation, often exhibiting altered traits compared to the wild-type.

Gene

  • A gene is a DNA segment that contains instructions for making a specific protein or RNA molecule and determines traits by coding for proteins affecting characteristics.

Allele

  • An allele is a specific version or variant of a gene, with organisms typically having two alleles for each gene (one from each parent).

Heterozygote vs. Homozygote

  • Heterozygote: Individual with two different alleles for a specific gene.
  • Homozygote: Individual with two identical alleles for a specific gene.

Architectural Components of a Gene

  1. Regulatory Regions (Control Gene Expression):

    • Promoter:
      • Upstream DNA sequence, serves as a binding site for RNA polymerase to initiate transcription.
      • May contain a TATA box (eukaryotes), or -10 and -35 sequences (prokaryotes).
    • Enhancers and Silencers:
      • Enhancers: Increase transcription when bound by activator proteins.
      • Silencers: Decrease transcription when bound by repressor proteins.
      • Can be located distantly.
    • Operator (Prokaryotes Only):
      • Binding site for repressor proteins affecting transcription.

  2. Coding Region:

    • Exons (Eukaryotes): Protein-coding sequences that remain in mature mRNA.
      • Consist of codons that specify amino acids during translation.
    • Introns (Eukaryotes): Non-coding sequences removed from pre-mRNA before translation.
    • Start Codon: Marks the beginning of translation (AUG, Methionine).
    • Stop Codon: Signals end of translation (UAA, UAG, UGA).

  3. Termination Region:

    • Terminator Sequence: Signals RNA polymerase to stop transcription.
    • In prokaryotes: Intrinsic or Rho-dependent termination.
    • In eukaryotes: Polyadenylation signals (AAUAAA).

Genetic Information Flow in Central Dogma

  1. Replication (DNA → DNA):

    • Purpose: To copy DNA before cell division; involves DNA polymerase.
    • Process:
      • DNA unwinds (helicase).
      • Each strand serves as a template (semi-conservative replication).
      • DNA polymerase adds complementary nucleotides (A-T, G-C).
      • Results in two identical DNA molecules.
    • Occurs in the nucleus (eukaryotes) or cytoplasm (prokaryotes).

  2. Transcription (DNA → RNA):

    • Purpose: Convert genetic information into mRNA.
    • Enzyme: RNA polymerase.
    • Process:
      • Binds to promoter region.
      • Unwinds DNA and synthesizes RNA complementary to DNA template.
      • Uses Uracil (U) instead of Thymine (T).
      • Processes RNA (splicing, 5' cap, poly-A tail in eukaryotes).
    • Occurs in the nucleus (eukaryotes) or cytoplasm (prokaryotes).

  3. Translation (RNA → Protein):

    • Purpose: Convert mRNA into a functional protein.
    • Main Players: mRNA (carries genetic code), tRNA (transfers amino acids), ribosomes (protein factories).
    • Process:
      • Ribosome binds to mRNA.
      • tRNA carries amino acids matching mRNA codons.
      • Amino acids linked into polypeptide chain.
      • Translation halts at a stop codon (UAA, UAG, UGA).
    • Occurs in the cytoplasm at ribosomes (eukaryotes and prokaryotes).

Point Mutation Consequences

a) Promoter Mutations
  • Affect gene expression rather than protein structure.
  • Effects on gene expression:
    • Upregulating (Gain-of-function):
    • Increases promoter activity → higher transcription → more mRNA → more protein.
    • Downregulating (Loss-of-function):
    • Decreases promoter activity → lower transcription → less mRNA → less protein.
    • Abolishing Expression:
    • Mutation completely blocks transcription.
    • Ectopic Expression:
    • Causes expression in the wrong tissue, time, or developmental stage.
b) Coding Mutations

  • Affect protein product.

  • Types of functional effects:

    • Loss-of-function mutation: Reduces or abolishes protein activity.
    • Gain-of-function mutation: New or enhanced activity, often seen in oncogenes.
    • Dominant-negative mutation: Mutant protein inhibits normal protein activity.
    • Neutral (Silent) mutation: No significant impact on protein function.

  • Descriptors based on amino acid effect:

    • Silent mutation: No amino acid change due to genetic code redundancy.
    • Missense mutation: One amino acid replaced; effects vary.
    • Nonsense mutation: Codon changes to stop codon leading to non-functional protein.

Defective Repair

  • Balance Between Damage and Repair:

    • Cells accumulate DNA damage from endogenous and exogenous sources.
    • Balance between DNA damage and repair mechanisms is crucial; failure can lead to disease (e.g., cancer).

  • Repair Strategy:

    Repair PathwayTarget Damage
    Base Excision Repair (BER)Small, non-helix-distorting lesions (e.g., oxidative damage)
    Nucleotide Excision Repair (NER)Bulky, helix-distorting lesions (e.g., UV-induced thymine dimers)
    Mismatch Repair (MMR)Replication errors (mismatched bases)
    Homologous Recombination (HR)Double-strand breaks — error-free repair
    Non-Homologous End Joining (NHEJ)Double-strand breaks — quicker but error-prone

  • Mutation Effects Due to Defective Repair:

    • Deleterious Mutation: Disrupts gene function, leads to diseases (e.g., BRCA1/2 mutations reduce repair efficiency).
    • Beneficial Mutation: Enhances survival/adaptation, drives evolutionary change (e.g., Sickle cell trait confers malaria resistance).
    • Neutral Mutation: No significant effect; often in non-coding regions or causes silent changes.

Selection of Mutations

  • The fate of mutations in populations is influenced by natural selection:
    • Positive Selection: Favors beneficial mutations, increasing their frequency.
    • Example: Lactase persistence in adults.
    • Purifying Selection (Negative Selection): Removes deleterious mutations, maintaining gene function integrity; highly conserved sequences are often under strong purifying selection.