Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Homework Questions from Professor Jacobson: Q: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? A:Polymerase makes an error about 1 in 10⁶ DNA letters. The human genome is about 3.2×10⁹ letters, so that would be ~3,200 errors per full copy if nothing else helped. Cells fix this with proofreading during copying and mismatch repair afterward.

Subsections of Homework

Week 1 HW: Principles and Practices

Homework Questions from Professor Jacobson: Q: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? A:Polymerase makes an error about 1 in 10⁶ DNA letters. The human genome is about 3.2×10⁹ letters, so that would be ~3,200 errors per full copy if nothing else helped. Cells fix this with proofreading during copying and mismatch repair afterward.

Q: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? A:An average human protein is about 1036 bp (~345 codons). Because many amino acids have multiple codons, there are an enormous number of DNA sequences that could encode the same protein. But many don’t work well because some sequences have extreme GC%/strong RNA structures or make the RNA unstable/get cut, lowering expression.

Homework Questions from Dr. LeProust: Q:What’s the most commonly used method for oligo synthesis currently? A:Most commonly used method for oligo synthesis currently is solid-phase phosphoramidite chemical synthesis.

Q:Why is it difficult to make oligos longer than 200nt via direct synthesis? A:Because each synthesis cycle is imperfect, so errors and truncated (unfinished) products accumulate as the oligo gets longer.

Q:Why can’t you make a 2000bp gene via direct oligo synthesis? A:2000 bp is far beyond typical direct-oligo lengths, so genes that long must be built by assembling many shorter oligos/fragments.

Homework Question from George 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”? A:The 10 dietary essential amino acids commonly taught for many animals are: arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.