Week 1 HW: Principles and Practices

Assignment (Week 2 Lecture Prep)

Homework Questions from Professor Jacobson: [Lecture 2 slides]

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?

Polymerase has 1:10⁶ error rate, while the human genome is 3x10⁹ base pairs. This is dealt with by exonuclease proofreading, followed by postreplication mismatch repair that looks for erros.

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?

Human proteins are around 400-500 amino acids long, and in average each amino acid can be encoded by ~3 different sequences, which would give 3⁴⁰⁰ different codes. However, some codons are actually preferred over others, bringing this number down.

Homework Questions from Dr. LeProust: [Lecture 2 slides]

1. What’s the most commonly used method for oligo synthesis currently? Solid-phase phosphoramidite method.
2. Why is it difficult to make oligos longer than 200nt via direct synthesis? The longer the oligo, the higher the chance of sequence errors.
3. Why can’t you make a 2000bp gene via direct oligo synthesis? There is a 1 in 2,000 bp error rate.

Homework Question from George Church: [Lecture 2 slides]

1. [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 are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine), and arginine. Vertebrates are not able to synthesize these amino acids, so the Lysine Contigency makes no sense since there wouldn’t be any change and the dinosaurs should be able to get Lysine with any regular diet.