Week 2 Pre Questions

I have answered the following questions to prepare for the lecture on DNA design and synthesis. These answers are based on the slides provided by Professor Jacobson, Dr. LeProust, and Professor Church.

Question,1

Natures 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?

My Answer: Polymerase is very accurate but it still makes mistakes. The error rate is roughly one in ten to the power of nine to ten to the power of ten per base pair. Since the human genome is about three times ten to the power of nine base pairs long, mistakes would happen every time a cell divides if there were no corrections. Biology deals with this discrepancy by using proofreading and mismatch repair systems to find and fix errors during and after the copying process.

Question,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 dont work to code for the protein of interest?

My Answer: There are many different ways to code for a single protein because the genetic code has redundancy. For an average human protein, the number of combinations can be more than ten to the power of one hundred. In practice, many of these codes do not work because of codon usage bias where certain cells prefer specific codes. Other reasons include mRNA secondary structures that block the process or sequences that are just too difficult to synthesize.

Question,3

Whats the most commonly used method for oligo synthesis currently? Why is it difficult to make oligos longer than 200nt via direct synthesis? Why cant you make a 2000bp gene via direct oligo synthesis?

My Answer: The most common method today is the phosphoramidite method. It is hard to make sequences longer than 200 bases through direct synthesis because of. the coupling efficiency. Even with a success rate of 99.5 percent at each step, the total yield for a 200 base sequence drops to about 36 percent. For a 2000 base gene, the success rate becomes effectively zero. This is why we must assemble long genes from smaller pieces instead of trying to make them all at once.

Question,4

What are the 10 essential amino acids in all animals and how does this affect your view of the Lysine Contingency?

My Answer: The ten essential amino acids are Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, and Lysine. Learning this makes me realize that the Lysine Contingency used in Jurassic Park is not a very strong safety method. Since lysine is found in many natural foods and plants, an organism could survive by finding it in the environment. This shows that we need to use synthetic amino acids that do not exist in nature to truly contain an organism.