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?

The error rate of polymerase is 1:10^{6. The length of the human genome is about 3.2 x 10}9 base pairs. With the error rate of polymerase, just one genome replication would cause about 3,200 errors. Biology makes up for this by layering error correction: polyemerase proofreading, mismatch repair systems, and post-replication repair pathways. All together, the error rate drops to 1-3 errors per human genome replication.

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?

The average human protein length is 1036bp, about 345 amino acids. There are 64 possible codons and only about 20 amino acids, which means most amino acids have multiple synonymous codons. The number of DNA sequences that could code the same protein is therefore: very, very large. In practice, not all of these codes work to code for the protein of interest because of GC content constraints, mRNA secondary structure, coson bias, repetitive sequences, and regulatory side-effects.

Homework Questions from Dr. LeProust:

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

The most commonly used method for oligo synthesis is currently solid-phase phosphoramidite synthesis.

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

It’s difficult to make oligos longer than 200nt via direct synthesis because errors accumulate at every synthesis cycle.

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

You can’t make a 2000bp gene via direct oligo synthesis because direct chemical synthesis does not scale to kilobase lengths. Long genes are made by sythesizing short oligos, enzymatic assembly, and cloning and sequence verification.

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”?

The 10 essential amino acids: Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, arginine.

Lysine is a natural weak point in animals because they can’t make it on their own. By controlling lysine, or how its used, you can control whether an organism survives, which makes the Lysine Contingency a strong idea.