Week 4 HW: Protein Design
Part A – Conceptual Questions
- How many amino acid molecules are in 500 g of meat?
A typical amino acid has a mass of about 100 g per mole.
If you have 500 g, that corresponds to roughly 5 moles.
Since one mole contains about 6 × 1023 molecules, 5 moles would contain about 3 × 1024 amino acid molecules.
This shows how enormous molecular numbers are, even in everyday amounts of food.
- Why don’t we turn into a cow when we eat beef?
When we digest food, proteins are broken down into individual amino acids.
Our body does not keep cow proteins intact.
Instead, we reuse those amino acids to build new proteins based on instructions from our own DNA.
So what we eat provides building blocks, not the identity of the organism.
- Is it possible to create new, artificial amino acids?
Yes. Chemists can synthesize amino acids that do not occur naturally.
These can include unusual side chains, special reactive groups, or atoms like fluorine.
Such modified amino acids are used in research to design proteins with new properties.
- Where did amino acids originate before life existed?
Amino acids could have formed through simple chemical reactions on the early Earth.
Experiments have shown that under conditions resembling the early atmosphere, amino acids can form from basic gases and energy sources like lightning.
They have also been detected in meteorites, suggesting they may have come from space as well.
- What happens if you build an α-helix from D-amino acids?
Natural proteins use L-amino acids and form right-handed helices.
If you instead used D-amino acids, the helix would twist in the opposite direction, forming a left-handed structure.
- Are there other types of helices beyond the common ones?
Yes. While the α-helix is the most familiar, researchers have identified and even engineered other helical forms.
With different amino acids or synthetic designs, new helical geometries can be explored.
- Why do β-sheets often clump together? What drives this?
β-strands align side by side and form hydrogen bonds.
When these sheets are exposed, they can easily bind to other β-strands.
Aggregation is mainly driven by:
- Hydrogen bonding between strands
- Hydrophobic side chains packing together
- The flat, extended shape of β-sheets that allows stacking
These features make β-sheets prone to sticking together.
- Why are β-sheets common in amyloid diseases? Could they be useful?
In amyloid diseases, proteins misfold and reorganize into tightly stacked β-sheet structures.
These assemblies are very stable and resist breakdown, which leads to accumulation in tissues.
However, that same stability and self-assembly make amyloid-like fibers attractive for materials science, where strong and durable nanostructures are useful.
- Propose a β-sheet sequence that forms an ordered structure.
A repeating pattern that alternates hydrophobic and polar residues can promote organized packing, for example:
Val–Thr–Val–Thr–Val–Thr
This arrangement allows one face of the sheet to interact with water while the other packs tightly against neighboring sheets, helping create a stable and ordered structure.