In-Depth Notes on SNPs and DNA Extraction

Overview of Genetic Material

  • Genomic DNA is responsible for carrying genetic information essential for organismal development and function.

  • Functions of genetic DNA:

    • Contains complete information for cell structure and function.

    • Codes for processes vital for life, including protein synthesis.

    • Replicates accurately to maintain genetic consistency in progeny.

    • Allows for variation through meiosis, pivotal for evolution.

  • Most organisms possess double-stranded DNA; some viruses may use single-stranded DNA or RNA.

Chemical Composition of DNA

  • Structure: DNA is a linear polymer composed of nucleotides.

  • Components of Nucleotide:

    1. Deoxyribose: A pentose sugar with 5 carbon atoms.

    2. Nitrogenous Bases: Four types - Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

    3. Phosphate Group: Connects to the 5’ carbon of the sugar.

Structure of Pentose Sugar

  • Carbon Numbering: Carbons are numbered 1' to 5' in the sugar ring.

  • Comparison with RNA:

    • DNA: 2’ carbon connected to hydrogen (H).

    • RNA: 2’ carbon connected to hydroxyl (OH).

  • Nitrogenous bases attach to the 1' carbon; phosphate groups attach to the 5' carbon.

Nitrogenous Bases

  • Types in DNA:

    1. Pyrimidines (Single Ring): Cytosine (C), Thymine (T).

    2. Purines (Double Rings): Adenine (A), Guanine (G).

  • Types in RNA:

    1. Pyrimidines: Cytosine (C), Uracil (U).

    2. Purines: Adenine (A), Guanine (G).

Polynucleotide Chains and Bonding

  • Formation of DNA Strands: Nucleotides link via covalent bonds called phosphodiester bonds.

  • Directionality: Chains built from the 5’ end to the 3’ end.

  • The first nucleotide has a free 5’-phosphate end, and the last has a free 3’-hydroxyl end.

Single Nucleotide Polymorphism (SNP)

  • Definition: A SNP is a variation in a single nucleotide that occurs in more than 1% of a population.

  • Characteristics:

    • Represents the simplest form of genetic variation.

    • Can result in phenotypic changes and associate with diseases.

Genetic Variations Related to SNPs

  • Types of Genetic Variation:

    1. Genetic Polymorphism: Variations in DNA sequences among individuals (>1%).

    2. Genetic Mutation: Less common changes in chromosomal structure or number (<1%).

Classification of SNP Effects

  • Synonymous (Silent Mutation): Does not change the amino acid.

  • Non-Synonymous: Results in an amino acid change.

    • Missense: Changes one amino acid in the protein sequence.

    • Nonsense: Creates a premature stop codon.

    • Nonstop: Changes a stop codon to an amino acid codon.

Taste Perception and SNPs

  • Taste Types: Sweet (energy detection), Salt (electrolyte balance), Sour & Bitter (warning against toxins), Umami (protein detection).

  • PTC (Phenylthiocarbamide): A bitter compound that interacts with receptors encoded by the TAS2R38 gene.

    • Inherited tasting ability can be phenotypically classified as taster (T) or non-taster (t) based on SNPs.

Objectives for DNA Extraction Experiment

  • Understand molecular biology techniques for isolating genomic DNA.

  • Materials Used:

    • Cheek cells, saline solution, DNeasy kit.

Procedures for DNA Extraction

  1. Swab cheek and add to saline solution.

  2. Vortex and centrifuge to pellet cells.

  3. Add lysis buffer and proteinase K to release DNA from cells.

  4. Mix with ethanol to precipitate DNA.

  5. Wash with buffers and elute DNA from silica membrane.

Conclusion

  • The study of SNPs provides insights into genetic diversity and associated traits, as exemplified in PTC tasting ability. Understanding molecular techniques such as DNA extraction from cheek cells illustrates fundamental biological processes and applications in genetics research.