https://pages.htgaa.org/2026a/mariana-diaz-luna/homework/week-04-hw-protein-design-part-i/index.htmlPart A. Conceptual questions 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 has an average 20% of protein, so 500 grams of meat would have 100 grams of protein. An average amino acid mass is 100 Da (100g/mol). So, according to Avogadro’s number, in a 500 g piece of meat, we are consuming approximately 6.62x1023 molecules of amino acids. Why do humans eat beef but do not become a cow, eat fish but do not become fish? Dietary proteins are digested into individual amino acids and absorbed and reused to build proteins used for the human metabolism, processes that determine our identity, not the food we eat. Why are there only 20 natural amino acids? There are 20 natural amino acids (22 in some organisms) because the standard genetic code evolved to use this 20 structures, maybe because they were efficient for metabolism, providing sufficient chemical diversity or they were optimal in terms of evolution. Can you make other non-natural amino acids? Design some new amino acids. Using synbio it is possible to create new amino acids according to what you need or want to do, for example maybe metal-binding amino acids to coordinate metal ions, or photo-crosslinking amino acids to form bonds when exposed to light, or perhaps adding electronegative elements like Fluor to alter their electronic properties. If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? L-amino acids form right-handed helices, while D-amino acids would form a left-handed helix. Can you discover additional helices in proteins? Synbio help us explore and find new structural possibilities since protein folding is certainly a complex issue that, at present, is not fully understood. Even though they are rare, it is possible to find -helix, 310 helix, foldamers (artificial oligomers), and maybe there are more out there to be discovered. Why are most molecular helices right-handed? Because biological amino acids are L-chiral, making right-handed helices more sterically favorable and stable energetically. Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? β-sheets are made of protein strands that lie next to each other and are connected by many hydrogen bonds, forming a very flat and extended surface with many places where it can stick to another sheet, so they can easily attach and stack together. Some amino acids in proteins are hydrophobic and when the β- sheets form, these parts can be exposed. To avoid water, they stick to each other hiding from water. Aggregation happens because it is energetically favorable, so the driving forces are the hydrophobic effect, the hydrogen bonds to increase stabilization and sticking together to lower the free energy. Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? In amyloid diseases (like Alzheimer’s) some proteins misfold, losing their normal shape and refolding into β-sheet structures. Since these structures are very stable, it is hard to go back from there. These misfolded proteins then stick to each other, form long fibers (amyloid fibrils), accumulate in tissues and damage cells. Since these structures are very strong, stable and able to self-assemble, it is possible to use them as materials. Scientist are studying them for creating nanofibers, biomaterials, tissue scaffolds, and drug delivery systems. Part B. Protein Analysis and VisualizationHugoen