Week 2 Lecture Prep

Homework Week 1, Lecture Prep

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?

Error rate = 1x10⁴ from Slide 15

Length: If the human genome is 3 billion bp, then that would be approximately 3x10⁵ errors.

Discrepancy: This is dealt with by repair mechanisms

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?

Different ways to code: With 61 codons coding for 21 amino acids there are a large number of ways to code for the average protein.

In practice why doesn’t this work: tRNA availablity, mRNA secondary structure, co-translation folding errors.

Citation: Gemini Ai prompt: ‘why do alternate codes for protein coding fail, list the most often reasons and provide scientific backing’

Homework Questions from Dr. LeProust:

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

The most common method of oligo syntesis is solid phase synthesis with the phosphoramidite method.

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

Errors accumulate and the sequence becomes inaccurate.

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

The error rate of such a process is too high to be feasible. Typically you would use smaller fragments and join them with Gibson or another method of nucleotide assembly.

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.

[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”?

Phenylalanine, Valine, Threonine - PVT Tryptophan, Isoleucine, Methionine - TIM Histidine, Arginine, Leucine, Lysine - HALL

The lysine contingency, from the film jurassic park, is not a good contingency considering all animals have to get these 10 amino acids from their diet anyways. It’s not like the parks managers were very good with any of their ethical considerations or failsafe systems though. Life finds a way.

Citations: I just directly Google searched the question ‘What are the 10 essential amino acids in all animals’ and ‘Lysine Contingency’

[Given slides #2 & 4 (AA:NA and NA:NA codes)] What code would you suggest for AA:AA interactions? n/a

[(Advanced students)] Given the one paragraph abstracts for these real 2026 grant programs sketch a response to one of them or devise one of your own: n/a https://arpa-h.gov/explore-funding/programs/boss https://www.darpa.mil/research/programs/smart-rbc https://www.darpa.mil/research/programs/go