https://pages.htgaa.org/2026a/selin-erdem/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? Meat is approximately 20% protein by mass. So, 500g of meat contains about 100g of protein. Given that the average mass of an amino acid is 100 Daltons ($1.66 \times 10^{-22}$ grams), we can calculate the total number of molecules:$100g / (100 \times 1.66 \times 10^{-24}g) \approx 6 \times 10^{24}$ amino acid molecules. That is roughly 10 moles. Why do humans eat beef but do not become a cow, eat fish but do not become fish? This is because our digestive system breaks down the proteins we eat into their individual building blocks: amino acids. Our body doesn’t use the cow or fish proteins directly; it uses these free amino acids to assemble “human” proteins based on the instructions in our own DNA. Why are there only 20 natural amino acids? This is often described as a “frozen accident” in evolution. While there are many more possible amino acids, these 20 provided enough chemical diversity (acidic, basic, hydrophobic, etc.) to build complex 3D structures and catalyze reactions. Once life became complex, changing this fundamental toolkit would have been too disruptive. Can you make other non-natural amino acids? Design some new amino acids.Yes, scientists can synthesize non-natural amino acids (ncAAs) by adding unique side chains. For my project on schizophrenia, I could design an amino acid with a fluorescent “sensor” side chain that changes color when it interacts with high concentrations of dopamine. This would allow us to visualize “dopamine storms” in real-time. Where did amino acids come from before enzymes that make them, and before life started? Amino acids likely formed through abiotic synthesis. The Miller-Urey experiment showed that early Earth’s atmospheric gases (methane, ammonia, water vapor) could react with electrical discharges (lightning) to create amino acids. They might have also been delivered to Earth via meteorites. Why are most molecular helices right-handed? This is due to the “chirality” of L-amino acids. Because all life uses L-amino acids, the right-handed $\alpha$-helix is the most energetically stable conformation that avoids steric clashes (physical bumping) between the side chains. Why do $\beta$-sheets tend to aggregate? What is the driving force? The main driving forces are hydrogen bonding and the hydrophobic effect. The edges of a $\beta$-sheet have “unsatisfied” hydrogen bond donors and acceptors. This makes them very “sticky,” leading them to stack with other $\beta$-sheets to achieve a lower energy state. Why do many amyloid diseases form $\beta$-sheets? Can you use them as materials? Amyloid $\beta$-sheets are incredibly stable and resistant to degradation. In diseases like Alzheimer’s, proteins misfold into this “energy well” from which they cannot escape.As materials: Yes! Amyloid fibers are stronger than steel for their size. They can be engineered as ultra-stable nanowires or drug-delivery scaffolds. Design a $\beta$-sheet motif that forms a well-ordered structure. A well-ordered motif can be designed using an “alternating” pattern: (Val-Lys-Val-Glu)n. In this sequence, the hydrophobic Valine residues face one side while the charged Lysine and Glutamate residues face the other. This creates a “Janus-faced” sheet that is oily on one side and water-loving on the other, allowing it to assemble into perfect layers. Part B: Protein Analysis and Visualization 1. Briefly describe the protein you selected and why you selected it. I want to select DRD2(the Human Dopamine D2 Receptor) protein because this protein provided to enter the doapamin in the cell. Also ın neurodejenaretif diseases such as in schzophrenia this receptor protein is overexpressing therefore dopamin enter the cell more than normal and this leads to hallucination. Therefore this protein plays important role in brain.Hugoen