Week 2: Lecture Prep

Homework Questions

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 1:10⁶ when the throughput is 10 mS per base addition. The length of the human genome is ~3.2 giga base pairs. This means that polymerase will make errors in ~3.2 kilo base pairs for a human genome. Biological DNA Synthesis has a process called Proofreading post the copying of the DNA, where most of these discrepancies are taken care of.

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?

An average human protein would have 1036 base pairs. This means there are ~345 amino acids. If every amino acid could be coded with 1 codon, there would be exactly 1 way (not usually possible) but if every amino acid had 6 codons, there would be a maximum of 6³⁴⁵ possible ways to code the protein. In my opinion, the reasons why many of these ways fail is the energy requirement. Only the most efficient route is preferred. Secondly, the error rates must also play a role here. Additionally, many of the methods would simply not have been tried since evolution followed a specific path.

The solid phase synthesis of oligos on inorganic support (CPG) by Caruthers is the most commonly used method for oligo synthesis.

I think it is because of yield losses at each step, which results in the final product having a large efficiency loss, as the errors add up.

It would be the same reason, as the errors would pile up and the impurities will increase. The end product will not be as intended, especially with large number of base pairs (like 2000), where the number of errors at the end would also be a larger number. Hence, synthesizing smaller oligos and later assembling them is a much more viable option.

[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:
- Arginine
- Histidine
- Methionine
- Isoleucine
- Leucine
- Lysine
- Phenylalanine
- Threonine
- Tryptophan
- Valine
Lysine is a relatively rare amino acid in foods, compared to the others, so humans are in short supply of lysine with staple diets (usually relying on grains). Hence, in many parts of the world, lysine is the ’limiting’ amino acid. However, lysine also has a relatively high requirement in the body. Lysine is non-enzymatic, making it chemically vulnerable, furhtering the “lysine contingency”.