Week 04 HW: Protein Design Part 1

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)

No. of AA molecules in 500gm of meat = Proteins consist of amino acids linked by peptide bonds, losing ~18 Da (water) per bond, so ~0.9–1 g protein yields ~1 mol amino acid residues (using your ~100 Da average residue weight). Protein in 500 g meat: ~120 g average (24% protein content). Moles of amino acids: 120 g / 100 g/mol = 1.2 mol. Molecules: 1.2 mol × 6.022 × 10²³ = ~7.2 × 10²³ (adjusts to ~2.3 × 10²⁴ if using precise 110 Da avg

  1. Why do humans eat beef but do not become a cow, eat fish but do not become fish? Because the proteins consumed are broken down into amino acids and are used to manufacture human proteins as dictated by our DNA codes.

  2. Why are there only 20 natural amino acids? These amino acids have been enough to support and compose life, so there is no need for more yet.

  3. Can you make other non-natural amino acids? Design some new amino acids. Yes, we can. We can use any amino acid’s molecular structure to make synthetic AAs.Eg. changing ethanol’s structure by adding a hydroxyl group.

  4. Where did amino acids come from before enzymes that make them, and before life started? The formations of amino acids before enzymes are thought to be due to extreme reactive environment. During the early days of earth, it was full of reactive ammonia, gydrogen, methane with energy from sun & lightning. These created conditions required for complex AA formation like thermodynmic & kinetic energy.

  5. If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? D-amino acids means dextro that is anti-clockwise. So it will make left handed amino acid helix.

  6. Can you discover additional helices in proteins? Helical structures can be discovered using various method like NMR spectroscopy, X-ray crystallography, computational protein modelling.

  7. Why are most molecular helices right-handed? As proteins are primarily made of right-handed AA causing stable hydrogen bonding.

  8. Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? B-sheets have strong intermolecular bonding of hydrogen with peptide backbone. Their side chains are hydrophobic causing stable sheet via van der Waals interaction forming agregations.

  9. Why do many amyloid diseases form β-sheets? Amyloid dieade tend to be due to accumulation of insoluble fibril agregates. These are in fact beta sheets that disrupt cell function.

  10. Can you use amyloid β-sheets as materials? Yes