Week 2 Lecture Prep: DNA, Read, Write, and Edit

h1 Heading ‘Assignment W2 Lecture Prep’

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? It depends on the species and cell type, but DNA polymerases exhibit an error rate of approximately 10⁻⁵ to 10⁻⁶ errors per nucleotide during DNA replication. With the help of other proofreading enzymes they can reduce it to ~10⁻⁸ to 10⁻¹⁰ errors per nucleotide, increasing its accuracy, additional repair mechanisms pathways exist to correct these errors and maintain genomic integrity. The human genome contains roughly 3 billion base pairs (3x10⁹), so even with an error rate of 10⁻⁸, there could be several errors during each DNA replication event.
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? Multiple codons can code for the same amino acid, where there are 64 possible codons, but only 20 standard amino acids. There is also codon redundancy since multiple codons will code for the same amino acid. Many of these sequences do not work well because of codon bias, limited availability of certain tRNAs, effects on mRNA structure and stability, unintended regulatory signals, or problems with translation efficiency and accuracy.

What’s the most commonly used method for oligo synthesis currently? The most commonly used method is solid-phase phosphoramidite chemical synthesis.
Why is it difficult to make oligos longer than 200nt via direct synthesis? Each step of chemical synthesis is slightly imperfect. As the oligo gets longer, small inefficiencies accumulate, leading to more truncated or incorrect sequences and a lower fraction of full-length product.
Why can’t you make a 2000bp gene via direct oligo synthesis? Direct synthesis of very long DNA suffers from too many errors and very low yield. Long genes are made by synthesizing shorter oligos (100-200bp) and then assembling them into the full-length gene using enzymatic methods, which helps correct errors and increases overall accuracy.

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 Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and Arginine. As lysine is an essential amino acid, its availability likely shaped species/animals dietary habits and metabolism, due to reliance on external sourses, becoming a critical in evolutionary adaptation.