Chapter 1: Approaches to Studying Biology at the Molecular Level

Approaches to Addressing Biological Questions at the Molecular Level

Genetic Approach

Studying/Altering genes to learn about function of gene products in vivo

  • Forward Genetics: Find mutant and identify what causes phenotype
  • Reverse Genetics: Find gene of interest and create mutant (using introduction of additional sequences: transgenes) and observe phenotype
  • Transgenes: Genetic material transferred to an organism which may alter phenotype
  • Silence Genes: miRNA and siRNA complementary to target mRNA and 2 products will anneal and produce ds RNA which is degraded by RNase because it looks like viral RNA reduce expression of target genes to see impact


  • Mutagenize using mutagens such as chemicals, radiation or genetic element (CRISPR, transposon)
  • Substitution – Single Nucleotide Polymorphism SNP
  • Small Insertion or Deletion – called indels, can result in frameshift mutations
  • Larger Insertions of Deletions or Inversions
  • Screen (look at each individual and identify altered) or Select (mutant has growth advantage)

Biochemical Approach

Studying proteins or metabolites in vitro

  • Prepare an assay mix with enzyme/protein in active state, can learn optimal temp/pH, rxn rate, pI, structure
  • Extract: Homogenized tissue via sonicator/blender/mortar pestle/ bead breaker (yeast)
  • Assay: Quantitative measure of protein/enzyme activity or developmental trait

Bioinformatic Approach

creation of databases of large data and mining data to make predictions/models in silico

  • Before other approaches, the combination of biology and computer science involving collection of protein and nucleic acid into searchable databases for comparative analysis
  • Gene Sequencing of mutant may reveal other family members, similar genes, sites of mutation
  • Scan complete genome sequence for genes encoding related enzymes, number of copies of enzyme gene, amino acid structure

Model Organisms

Organisms used to represent a population, these are much simpler than the ones they represent and less complex

  • Sequence complexity: one copy of each repeat sequence + length of unique sequence not same as length

Common traits for model organisms (E. Coli, Saccharomyces cerevisiae, Drosophila melanogaster, Xenopus laevis)

  • Smaller genome size: fewer genes to search through, map, sequence
  • Low amount of repetitive DNA: Repetition in DNA complicates hybridization experiments & sequencing
  • Diploid (not all): hard to pinpoint and mutate genes (too many copies of gene)
  • Short life cycle: helps high generation #, see how the gene is regulated and its impact on next generation
  • Small, cheap: can house many in small space and perform higher # of samples
  • Transformable: allows for gene manipulation


  • Share data, cost effective
  • Validate results
  • Share techniques/research moves faster
  • Aid large scale experiments & benefit whole community


  • Too competitive
  • Model organisms may not have specific trait
  • All organisms raised in artificial environments

Species can't accurately represent whole population

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