Week 1 HW: Week 2 Lecture Prep

Questions from Professor Jacobson:

  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?
  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?

Answer:

  1. The error rate is one in a million. Compared to a human genome, which has approximately 3 billion base pairs. Any mispaired bases in DNA replication are detected by DNA polymerase through a process called proofreading and replaced with the correct base pairs through a process called mismatch repair.
  2. Because of the codon usage bias. Codon usage bias is the preferential use of certain synonymous codons in an organism. It occurs because different codons are decoded by tRNAs that exist at different cellular abundances. Codons corresponding to abundant tRNAs are translated faster and more accurately, so they are favored, especially in highly expressed genes. Conversely, genes that contain codons corresponding to rare tRNAs are translated more slowly and are more prone to ribosome pause and translational errors.

Homework Questions from Dr. LeProust:

  1. What’s the most commonly used method for oligo synthesis currently?
  2. Why is it difficult to make oligos longer than 200nt via direct synthesis?
  3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Answer:

  1. Solid Phase Synthesis.
  2. Direct chemical DNA synthesis is limited by cumulative coupling efficiency. Each nucleotide addition step has about ~99% success, but a 200-nt oligo requires 200 consecutive successful reactions. The probability of obtaining a full-length product is therefore ~0.99²⁰⁰ ≈ 13%, meaning most synthesized molecules are truncated because they failed to extend during earlier cycles. These truncated strands differ from the correct product by only one or a few nucleotides, making purification difficult. Techniques such as HPLC or denaturing PAGE have limited resolution at longer lengths, so separating 200-nt DNA from 199-nt DNA results in low recovery and contamination.
  3. The reasoning is similar to my answer to Question 2. During chemical DNA synthesis, each nucleotide addition (coupling step) has about a 99% efficiency. Because the process is stepwise, the probability of obtaining a full-length product decreases multiplicatively with every cycle. For a 2000 bp sequence, the probability of producing a correct molecule is approximately 0.99²⁰⁰⁰ ≈ 0.000000186%. This means essentially none of the synthesized molecules will be the correct full-length gene. Instead, it is more practical to synthesize shorter oligonucleotides (e.g., ~100 nt each) and assemble them into a full gene using methods such as Gibson assembly or overlap-extension PCR, which bypass the chemical synthesis length limitation.

Homework Question from George Church:

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

Answer:

  1. Animals require ten essential amino acids in their diet: arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are termed “essential” because animals cannot synthesize them and must obtain them from dietary protein. Though Arginine can be considered conditionally essential.

    Although I have not watched the Jurassic Park or Jurassic World films, I read about the “lysine contingency” used as a biological containment strategy devised by Dr. Wu. The idea is that the dinosaurs were engineered to be unable to synthesize lysine and would die without lysine supplementation. However, this would not be an effective containment mechanism. Lysine is an essential amino acid for all animals, meaning the dinosaurs (like any other animal, including humans) would naturally obtain it by consuming protein sources in their environment. In fact, this trait would not be unique to the dinosaurs, because all animals already lack the ability to synthesize lysine.

ChatGPT Prompts:

• What is lysine contingency?