Week 2 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?

A: Polymerase error rate appprox. 1 in 10^6 base pairs, vs. human genome approx. 3.2 billion base pairs. This leads to thousands of errors per replication. Biology deals with that discrepancy by proofreading polyerases, and through post-replication mismatch repair systems and evolutionary selection.

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: There are approximately 10^165 different DNA sequences in which a human protein can be encoded. In practice, most of these sequecees are not functional because DNA and RNA are physical molecules subject to physical constraints such as translation-dependent protein folding. As a result, only a small subset of possible sequences can produce functional proteine expressions.

Homework Questions from Dr. LeProust:

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

A: solid-phase phosphoramidite chemical synthesis.

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

A: Chemical DNA is stepwise and imperfect, and small inefficiencies at each nucleotidic addition accumulae exponentially with length. Therefore, beyond 200nt, the yield of full-length error-free molecules becomes extremely unlikely due to errors.

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

A: Genes are built by assembling short oligos because direct chemical synthesis does not scale. therefore a 2000bp gene would require thousands of sequential chemical coupling steps, causing error rates. So genes are therefore not directly synthesized, but assembled hierarchically from any shorter oligos using enzymatic processes such as PCR.

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”?

A: The 10 essential amino-acids are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine.

The “lysine Contingency” presents lysine as a point of dependency since it is not synthesizable by animals, and must obtain it externally. This concept is already deeply embedded in biological environments such as with microbes, and in food chains