Week 1 HW.2: Week 2 Preparation

Homework Questions from Professor Jacobson

1. 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?

Polymerases have an initial error rate of roughly 1 in 10^4 to 10^5 nucleotides, which is extremely high compared to the ~3 billion 3 * 10^9 base pairs in the human genome. Without correction, this would lead to 100,000+ errors per cell division. Biology manages this through intrinsic proofreading exonucleases (reducing errors to 1 in 10^7 ) and post-replication mismatch repair, resulting in a final, remarkably low mutation rate of approximately 1 in 10^9 to 10^10 per base pair per generation.

2. How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?

• 20 amino acids are encoded by 61 sense codons.
• An average human protein is around ~400 amino acids long.

Assuming each amino acid has ~3 possible codons on average, the number of possible DNA sequences encoding of the same protein is around 3^400 or 10^190

Homework Questions from Dr. LeProust

1. What’s the most commonly used method for oligo synthesis currently?

Solid-phase phosphoramidite synthesis. It works by adding one nucleotide at a time in a repeating chemical cycle.

2. Why is it difficult to make oligos longer than 200nt via direct synthesis?

Because coupling efficiency is <100% meaning its error will compound over and over. Even with 99% sucess rate, it is still around 13%. This means only ~13% of the final tube is the correct full-length product.

3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Even at 99.5% efficiency per step, the result is still around  ∼0.0045% which is nearly impossible.

Homework Question from George Church

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

• Arginine, histidine, methionine, isoleucine, leucine, lysine, phenylalanine, threonine, tryptophan, and valine.
• “This forced the dinosaurs to depend on lysine supplements provided by the park’s veterinary staff. In this way, dinosaurs could never escape from the park because they would never survive long without the food supplements.”

from https://jurassicpark.fandom.com/wiki/Lysine_contingency

If negative * negative = positive, then non-synthesizable * non-synthesizable = synthesizable lysine I guess

LLM Prompt:

• calculate coupling efficiency of 2000bp genes (via direct oligo synthesis) and 200nt long oligos