Week 02 Pre HW:

Homework Questions from 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?

DNA polymerases used to amplify targets during PCR cloning are high fidelity enzymes with error frequencies typically in the range of 10^6 mutations/bp amplified

Ref: McInerney P, Adams P, Hadi MZ. Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase. Mol Biol Int. 2014;2014:287430. doi: 10.1155/2014/287430. Epub 2014 Aug 17. PMID: 25197572; PMCID: PMC4150459.

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?

I will have to understand this in more detail to answer this question.

Homework Questions from Dr. LeProust:

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

Phosphoramidite based synthesis process

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

  • Time-consuming
  • Expensive
  • Energy and processes

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

Making 2000bp gene via direct oligo synthesis - there is a potential for increased error rate

  • Purification from mixture

Homework Question from George Church:

Choose ONE of the following three questions to answer; and please cite AI prompts or paper citations used, if any.

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

Essential amino acids - histidine, isoleucine, leucine, lysine, methionine,, threonine, tryptophan, valine (Google search)

Lysine contingency: Lysine is an essential amino acid and given that humans and animals do not have gene to make lysine, they have to be dependent on food source to acquire lysine. If this is the case then how would lysine contingency be true? Or did dinosaurs had an ability to make lysine? as an exceptional case?