BIOB11 - LECTURE 3

Genome Change Rates

  • Factors Influencing Change: Some genome regions change faster due to less functional constraint. Non-coding regions or repetitive sequences can accumulate mutations more readily than protein-coding regions, where changes might disrupt essential functions. Additionally, certain sequences are more prone to mutation due to mechanisms like misalignment during replication in repetitive DNA.

Sequence Selection for Identification vs. Phylogenetic Trees

  1. Identifying Closely Related Individuals: Use highly variable sequences like microsatellite DNA because the number of repeats changes rapidly, making them ideal for distinguishing between closely related individuals.

  2. Constructing Phylogenetic Trees: Use slowly evolving, highly conserved sequences (e.g., ribosomal RNA genes) to trace the divergence of distantly related species. These sequences provide a stable baseline for comparison over long evolutionary timescales.

Point Mutations and SNPs

  • Point Mutation: A change in a single nucleotide base in DNA (e.g., A to G).

  • SNP (Single Nucleotide Polymorphism): A specific type of point mutation that is common in a population. SNPs can create different versions of a gene (alleles), leading to different traits.

Repetitive DNA

  1. Highly Repetitive DNA

    • Types: Satellite DNA (centromeres, telomeres), minisatellite DNA (variable number of tandem repeats), and microsatellite DNA (short tandem repeats).

    • Mechanisms of Change: Unequal crossing over, replication slippage, and transposition.

  2. Moderately/Interspersed Repetitive DNA

    • Types: SINEs (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements).

    • Mechanisms of Change: Retrotransposition, where RNA is reverse transcribed and inserted into new locations in the genome.

Synteny

  • Definition: The conserved order of genes in blocks of DNA, even when these blocks are located in different positions in different species' genomes.

  • What Studying Synteny Reveals: While nucleotide sequences of genes may diverge over time, the arrangement of genes can be more conserved. Studying synteny helps understand how genome organization changes relative to sequence evolution.

Transposon Movement

  1. Cut-and-Paste Mechanism: DNA transposons use transposase to excise the element from one location and insert it into another. Requires transposase enzyme.

  2. Copy-and-Paste Mechanism: Retrotransposons (LINEs and SINEs) are transcribed into RNA, then reverse transcriptase (often encoded by the transposon itself) converts the RNA back into DNA, which is inserted elsewhere. LINEs encode reverse transcriptase; SINEs do not and rely on LINEs for transposition.

Mechanisms for Creating New Genes/Alleles

  1. Point Mutations: Create different alleles of existing genes.

  2. Gene Duplication: Results in multigene families, where duplicated genes can evolve new but similar functions.

  3. Exon Shuffling: Mixing exons from different genes to create new proteins.

  4. Horizontal Gene Transfer: Transfer of genetic material from one organism to another.

Gene Duplication and Exon Shuffling

  • Unequal Crossing Over and Transposition: These events can lead to the duplication of genes or shuffling of exons.

  • Contribution to New Proteins: Duplication allows one copy to maintain the original function while the other copy can evolve a new function. Exon shuffling can create new proteins with novel combinations of domains.

Semi-Conservative DNA Replication

  • Explanation: Each new DNA molecule consists of one original (parent) strand and one newly synthesized strand.

  • Method to Test: The Meselson-Stahl experiment used ^{15}N and ^{14}N, heavy and light isotopes of nitrogen. The experiment showed that after one round of replication, DNA had intermediate density, and after two rounds, DNA had both intermediate and light densities, supporting the semi-conservative model.

Structural Properties of DNA for Replication

  1. Hydrogen Bonds: Allow strands to separate for use as templates.

  2. Complementary Base-Pairing: Ensures accurate nucleotide selection during replication.

  3. 3'-OH: Provides a site for the addition of new nucleotides.

Nucleotide Incorporation During DNA Replication

  • New nucleotides are added to the 3' end of the growing strand. Incoming nucleoside triphosphates pair with the template strand, and DNA polymerase catalyzes the formation of a phosphodiester bond, releasing pyrophosphate.

Error Correction During DNA Replication

  1. Proofreading by DNA Polymerase: Detects and removes mismatched nucleotides during replication.

  2. Strand-Directed Mismatch Repair (MMR): Corrects mismatches after replication by identifying and removing incorrect nucleotides from the newly synthesized strand.

Factors Influencing DNA Melting (Tm) and Renaturation (C0t)

  1. DNA Melting (T_m)

    • Factors: GC content (higher GC content increases T_m due to stronger base stacking and more hydrogen bonds) and salt concentration.

    • Plots: Melting curves show UV absorbance vs. temperature; T_m is the temperature at which half the DNA is denatured.

  2. DNA Renaturation (C_0t)

    • Factors: Genome size and repeat frequency.

    • Plots: C0t plots show the fraction of renatured DNA vs. C0t value. Smaller genomes renature faster.