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 biological machinery for copying DNA, known as polymerase, has an error rate of approximately 1:10⁶. This error rate is significant when compared to the length of the human genome, which is approximately 3.2 Gbp (3.2 billion base pairs). Without additional correction, copying the entire human genome just once would result in thousands of errors. Biology deals with that discrepancy with MutH, MutL, and MutS enzyme system, which recognizes and repairs mismatched base pairs to ensure higher fidelity
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 approximately 1036 base pairs (bp) long. Because the genetic code is redundant (multiple different three-nucleotide codons can code for the same single amino acid) there are astronomically many different DNA sequences that can theoretically code for the same protein.
In practice, many of these alternative codes do not work for several reasons:
Secondary Structure Interference: Different DNA or RNA sequences result in different Minimum Free Energy (MFE) secondary structures.
Base Pairing Energetics: The stability of the genetic material is affected by its GC content.
RNA Cleavage: Specific sequences may inadvertently trigger RNA cleavage rules
Homework Questions from Dr. LeProust:
What’s the most commonly used method for oligo synthesis currently?
The most commonly used method for oligonucleotide synthesis currently is the phosphoramidite method, originally developed by Caruthers in 1981. This process typically occurs via solid-phase chemical synthesis
Why is it difficult to make oligos longer than 200nt via direct synthesis?
Direct synthesis of oligos longer than 200 nucleotides (nt) is difficult primarily due to the cumulative error rate and chemical efficiency of the synthesis cycle
Why can’t you make a 2000bp gene via direct oligo synthesis?
Direct base-by-base chemical synthesis is not used to create a 2000bp (2kb) gene because the physical and chemical limitations of the phosphoramidite process make it impossible to produce a sequence of that length with any meaningful accuracy or yield.
Homework Question from George Church:
What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
The ten essential amino acids in animals are histidine, arginine, valine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, and tryptophan. This directly relates to the concept of the “Lysine Contingency”, which emphasizes the critical role of lysine as a limiting essential amino acid for growth and survival. From my point of view, attempting to genetically modify organisms to alter these fundamental nutritional requirements is ethically questionable.