Week 1 HW: Pre-Prep Week 2

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?

The error rate of polymerases depends on their type, as Human DNA has mechanisms for proofreading that other organisms’ DNA lacks. The error rate for DNA polymerase is 1 in every 10^{7 base pairs. As compared to the human genome size of 6 X 10}9 base pairs. The mechanisms include mismatch repair, base excision repair, nucleotide excision repair, NHEJ, HR, damage checkpoint, and some tolerance mechanisms. This is how biology deals with discrepancies via multiple mechanism before-during-after DNA replication and the cell cycle.

Prompts - What is the length of human DNA base pairs? what the different ways in which DNA is proffread nd repaired?

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?

As each amino acid has 3 codons mostly and proteins are made of a combination of 20 amino acids. With a lot of amino acids with multiple codons , the ways to code are astronomically huge.
Codes at times fail to work as the amino acids might not form the protein folding form, mRNA fold, tRNA, ribosome as the same ones required in the cells. That is where protein design and coding gets complex to gain the exact intended expression.
https://doi.org/10.3390/biom14010132

1. What’s the most commonly used method for oligo synthesis currently?

phosphoramidite chemistry

2. Why is it difficult to make oligos longer than 200nt via direct synthesis?

As error accumulates on every nucleotide addition , so instead assembling enzymatically i better.

3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Again error rates decrease final yields and limit purification, which also leads to yield loss.

10 AA in animals and What do you think about Lysine Contingency?

The ten essential amino acids in animals are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine;
“lysine contingency” means the biological dependence of animals on external lysine supply due to the absence of lysine biosynthetic pathways. This creates a dependency that can be exploited in evolution and synthetic biology for metabolic control and biocontainment.

My take on Lysine Contingency is - This can certainly be a powerful tool to implement biocontainment when we decide to inhabit or spread bioforms on extraterrestrial land. But it also threatens the very existence of human & animal bodies, in turn showing our dependency on plants. It certainly makes me further appreciate the importance of the food chain and the evolutionary process of life forms. Prompts : 10 amino acids in all Animals? What does Lysine Contingency mean?