Week 1 HW: Week 2 Lecture Prep

Lecture Prep: My approach was to view the slides, then seek direct answers via ChatGPT, then review the slides to find corresponding answers. It is allowing me to begin to comprehend the depth of the subject matter. I look forward to the reinforcing live presentations.

  • Professor Jacobson

    • Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?
      • 1:106
      • In contrast, the human genome is 3:109 or many magnitudes higher.
    • How many different ways are there to code (DNA nucleotide code) for an average human protein?
      • Average human protein length ≈ 400 amino acids
    • In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
      • Because DNA is not just a protein recipe. The sequence carries many layers of information beyond amino acids.

  • Dr. LeProust

    • What’s the most commonly used method for oligo synthesis currently?
      • Phosphoramidite solid-phase synthesis
    • Why is it difficult to make oligos longer than 200nt via direct synthesis?
      • small per-base imperfections compound exponentially, and the chemistry has no way to “fix” them once they happen.
    • Why can’t you make a 2000bp gene via direct oligo synthesis?
      • Because chemical oligo synthesis breaks down long before you reach that length, for fundamental probabilistic, chemical, and practical reasons. A 2000 bp gene is two orders of magnitude beyond what direct synthesis can support.

  • Professor Church

    • [Using Google & Prof. Church’s slide #4] What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
    • The 10 essential amino acids

Histidine

Isoleucine

Leucine

Lysine

Methionine

Phenylalanine

Threonine

Tryptophan

Valine

Arginine

My view is now informed by the concept that “No lysine available → the organism stops functioning”.