Notes the Week 2 Lecture Prep

Gene Synthesis

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?
Nature’s machinery for copying DNA is DNA polymerase.The error rate of biological, error-correcting polymerase is approximately 1 in 10⁶ (1:10⁶) per base addition.
The human genome is about 3.2 billion base pairs (≈3.2 × 10⁹ bp). If polymerase made errors at a rate of 1 in 10⁶ without further correction, this would theoretically lead to thousands of mutations each time the genome is replicated.
Proofreading and mismatch repair reduce the overall mutation rate to a much lower level, allowing large genomes like the human genome to be copied with extremely high fidelity.

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?
An average human protein is about 1,036 base pairs long，Since each amino acid is encoded by a codon of three nucleotides, this corresponds to roughly 345 amino acids.Because most amino acids are encoded by more than one codon (there are 64 codons for 20 amino acids), each amino acid can often be chosen in several different ways. On average, there are about 3 possible codons per amino acid.

DNA Synthesis Development and Application

1.What’s the most commonly used method for oligo synthesis currently?
The most commonly used method for oligo synthesis today is the phosphoramidite solid-phase chemical synthesis method. 2.Why is it difficult to make oligos longer than 200nt via direct synthesis.
It is difficult to synthesize oligos longer than 200 nt because chemical DNA synthesis is stepwise and not perfectly efficient. Each nucleotide is added one at a time through repeated coupling cycles slides-lecture-2-leproust
Even if each step is about 99% efficient, the small loss at every cycle accumulates. After 200 steps, the overall full-length yield drops dramatically (around 13%), meaning most molecules are truncated.
Therefore，Beyond ~200 nt, the full-length yield becomes too low and error rates too high, making direct chemical synthesis inefficient and unreliable. 3.Why can’t you make a 2000bp gene via direct oligo synthesis?
It cannot synthesize a 2000 bp gene directly because chemical DNA synthesis adds one nucleotide at a time and each step is not 100% efficient

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
1.The 10 essential amino acids in all animals (cannot be synthesized de novo and must be obtained from diet) are: Histidine (H)Isoleucine (I)Leucine (L)Lysine (K)Methionine (M)Phenylalanine (F)Threonine (T)Tryptophan (W)Valine (V)Arginine (R) (essential in many animals, especially during development)
2.Because lysine is an essential amino acid that animals cannot synthesize, making an organism dependent on lysine (or a modified lysine) creates a built-in metabolic dependency.