Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
I. Biological Engineering Application or Tool - MechaVita My idea is to create a pseudo living robot in a sense. Living cells (in an organism) will be programmed by humans. The living cells will be provided mechanical exoskeletons to survive in unfavourable conditions. These cells will be able to perform their assigned functions (a specific purpose with which they are created). They will function like living organisms with metabolic processes but utilise mechanical enhancements to aid their purpose.
Week 2 HW: DNA Read, Write and Edit
Part 1: Firstly, I made the enzyme list on Benchling, containing the mentioned enzymes: Secondly, I tried playing around with the restriction enzymes to make some kind of resemblance to artwork. I finally made something satisfactory, and had to make the other symmetrical half.
Homework Questions I. From Professor Jacobson 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 polymerase is 1:106 when the throughput is 10 mS per base addition. The length of the human genome is ~3.2 giga base pairs. This means that polymerase will make errors in ~3.2 kilo base pairs for a human genome. Biological DNA Synthesis has a process called Proofreading post the copying of the DNA, where most of these discrepancies are taken care of. 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 would have 1036 base pairs. This means there are ~345 amino acids. If every amino acid could be coded with 1 codon, there would be exactly 1 way (not usually possible) but if every amino acid had 6 codons, there would be a maximum of 6345 possible ways to code the protein. In my opinion, the reasons why many of these ways fail is the energy requirement. Only the most efficient route is preferred. Secondly, the error rates must also play a role here. Additionally, many of the methods would simply not have been tried since evolution followed a specific path. II. From Dr. LeProust What’s the most commonly used method for oligo synthesis currently? The solid phase synthesis of oligos on inorganic support (CPG) by Caruthers is the most commonly used method for oligo synthesis. Why is it difficult to make oligos longer than 200nt via direct synthesis? I think it is because of yield losses at each step, which results in the final product having a large efficiency loss, as the errors add up. Why can’t you make a 2000bp gene via direct oligo synthesis? It would be the same reason, as the errors would pile up and the impurities will increase. The end product will not be as intended, especially with large number of base pairs (like 2000), where the number of errors at the end would also be a larger number. Hence, synthesizing smaller oligos and later assembling them is a much more viable option. III. From Professor George Church [Using Google & Prof. Church’s slide #4] 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:
Python Script Having no prior experience in python, I decided to use TA Donovan’s website. I chose the mRFP1 Bacteria to design the Transformers Autobots logo on the agar plate. I manually drew the desired shape and manipulated using only the cursor. I ended up with the following: After making the logo of one faction, I decided it would be fun to attempt again with the Transformers Decepticons logo, as well. I chose the Azurite bacteria for this one. Again after careful trial and error (especially to make diagonal lines), I finished with the following:
Week 4 HW: Protein Design Part I
Part A 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Meat contains ~20% protein (Kenneth Carpenter et al. Britannica, 2026). In 500 grams of meat, ~100 grams is protein. That is equivalent to 100 grams of amino acids. By the mol formula, the number of mols of amino acids = Mass/RMM = 100 grams/100 Daltons = 100 grams/100 gram mol-1 = 1 mol Therefore, number of molecules = Number of mols x Avogadro’s Number = 1 mol x 6.02214076×1023 mol−1 = 6.02214076×1023 Hence, 6.02214076×10^23 molecules of amino acid are present in 500 grams of meat. 2. Why do humans eat beef but do not become a cow, eat fish but do not become fish?
Week 5 HW: Protein Design Part II
Part A Part 1 I added the protein sequence from UniProt after mutating it, and changed the parameters, as needed. The Sequence: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I ended up with these 4 results. I added the given peptide sequence and calculated the Pseudo Perplexity for the same. Part 2