week 04 hw: protein design-part-I
- Amino Acid Count in 500g Meat: Meat is roughly 20% protein by mass. (Human Nutrition - Protein, Vitamins, Minerals | Britannica, n.d.)
- 500g meat x 0.20 = 100g protein.
- Using an average mass of 100 Daltons (Da) per amino acid: 100g / 100 Daltons (or g/mol) = 1 moles of amino acids
- 1x 6.022 x 1023 = 6.022 x 1023 molecules /1 mole.
- Why we don’t become cows: When we eat protein, our digestive system breaks it down into individual amino acids. Our body then uses its own DNA information to reassemble those amino acids into human proteins. The information which is coded by the sequence of AA is destroyed, but the building blocks or AA are reused.
- Why only 20 amino acids: In nature, the use of 20 amino acids is often explained as a “frozen accident” that originated in the early RNA World. This set worked well very early in Earth’s history and then became fixed. These 20 amino acids were good enough to build strong and functional proteins. Even though many other amino acids exist, this small group provides enough variety to perform many functions while remaining simple, stable, and efficient for cells to use. (Doig, 2017)
- Non-natural amino acids: Yes, scientists can make non-natural (unnatural) amino acids. They do this using chemical methods and special genetic tools that allow new amino acids to be added to proteins. These new amino acids can give proteins new properties that natural amino acids do not have. (Young & Schultz, 2010) For example, A new amino acid could be made by taking a normal amino acid, like alanine, and adding a fluorine atom to its side chain. This fluorinated amino acid would make proteins more stable and less likely to break down, which is useful for drug design. (Adhikari et al., n.d.)
- Pre-life origins of amino acids: According to Gutiérrez-Preciado, Romero, and Peimbert (2010) Before enzymes and living organisms existed, amino acids were probably formed naturally on early Earth. Energy from lightning, UV light, and volcanic heat helped simple gases react to make amino acids. Some amino acids were also brought to Earth by meteorites and comets. Together, these processes created a “primordial soup” of basic organic molecules. (Amino Acids, Evolution | Learn Science at Scitable, n.d.)
- D-amino acid α-helix: In nature, L-amino acids form right-handed helices. If you used only D-amino acids, the stereochemistry would be mirrored, resulting in a left-handed $\alpha$-helix. (Zotti et al., n.d.)
- Additional helices: Yes, additional helical structures besides the standard α-helix can be found in proteins. Studies show that other types of helices occur in many proteins, but they are often overlooked or mistaken for small distortions in α-helices. These helices are especially common in membrane proteins and are found in a significant number of known protein structures.(Vieira-Pires & Morais-Cabral, 2010)
- Why right-handed helices: because this shape is the most stable for the natural building blocks of life. L-amino acids and D-sugars fit together best in a right-handed twist, which allows strong hydrogen bonds and reduces crowding between atoms. Left-handed helices are usually less stable or hard to form. (Right-Handed Alpha-Helix - an Overview | ScienceDirect Topics, n.d.)
- β -sheet aggregation: β-sheets tend to aggregate because their edges have exposed hydrogen-bonding groups that easily stick to other β-strands. The main driving forces are hydrogen bonding between strands and the hydrophobic effect, which together make the stacked β-sheet structure very stable and allow fibrils to form.(Gsponer & Vendruscolo, 2006)