Week 4 HW: Protein Design Part I

1. Why are there only 20 natural amino acids?

• There aren’t only 20 amino acids. There are just 20 that biology standardized early on in evolution. Proteins are built using translation. Once that system had evolved changing it was difficult because every protein in every organism depended on it. That creates evolutionary lock-in often referred to as a “frozen standard.” The current amino acids were selected due to their component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. There are reasons for the selection of every amino acid.

2. Where did amino acids come from before enzymes that make them, and before life started?

• Abiotic chemistry on early Earth. Amino acids are chemically natural products when carbon, nitrogen, hydrogen, oxygen, and energy mix. Meteorites can also contain amino acids, therefore, some could have come to Earth from space. Geochemical environments like hydrothermal vents, mineral surfaces, metal ions, heat gradients, and pH differences can drive reactions that form amino acids from simpler molecules. Before enzymes chemistry did the job.

3. If you make an α-helix using D-amino acids, what handedness (right or left) would you expect?

• A helix made from D-amino acids will form a left-handed α-helix.

4. Can you discover additional helices in proteins?