Why do humans eat beef but do not become a cow, eat fish but do not become fish?
During digestion, proteases break down the cow/fish proteins down into their constituent free amino acids and small peptides. These are then
absorbed as monomers. Your ribosomes then reassemble them according to your own mRNA instructions.
Why are there only 20 natural amino acids?
Likely a combination of three things. First, once the genetic code co-evolved around these 20 amino acids, any change would catastrophically
mis-translate the entire proteome, so those 20 were ’locked in’. Second, the 20 cover the necessary chemical space (charged, polar,
hydrophobic, aromatic, etc). Third, the simplest amino acids (Gly, Ala, Asp, Glu, Val…) are exactly the ones most readily produced
abiotically, so the code evolved around what was chemically accessible early on. Selenocysteine and pyrrolysine as the “21st and 22nd” amino
acids show the code can expand, but only under very constrained circumstances.
Where did amino acids come from before enzymes that make them, and before life started?
They form spontaneously from simple chemistry. Amino acids are thermodynamically reasonable products.
The Miller-Urey experiment showed electric discharge through CH₄, NH₃, H₂O and H₂ produces Gly, Ala, Asp and others.
Hydrothermal vents provide mineral catalysts and redox gradients. Meteorites (like Murchison) contain over 70 amino acids synthesized in
space, confirming abiotic production is universal wherever C, N, O, H and energy coexist.
If you make an α-helix using D-amino acids, what handedness (right or left) would you expect?
The 3₁₀-helix is tighter (i→i+3 H-bonds), more strained, and common at helix termini.
The π-helix is wider (i→i+5 H-bonds) and surprisingly prevalent at functional sites — maybe 15% of proteins contain at least one π-turn.
The polyproline II (PPII) helix has no intramolecular H-bonds at all, is left-handed, and is extremely common in disordered regions,
collagen, and signaling domains (SH3 recognition).
The collagen triple helix is three intertwined PPII-like chains stabilized by interchain H-bonds.
New folds continue to emerge from cryo-EM and AlphaFold-era structural biology, so the catalogue is probably not closed.
Why are most molecular helices right-handed?
Most molecular helices are right-handed because all biological amino acids are L-form, so their bond geometry naturally favors coiling
clockwise when chained together.
Why do β-sheets tend to aggregate?
Edge strands have unpaired backbone NH and C=O groups pointing outward (they’re basically unsatisfied H-bond donors and acceptors, which
makes them inherently “sticky.”)
Flat hydrophobic surfaces on sheet faces also drive stacking through the hydrophobic effect.
Side chains interdigitate into a tight steric zipper, which is favorable in both enthalpy and entropy, and thus very hard to prevent without
chaperones or proline residues.
Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials?\
For many disease-associated sequences (Aβ in Alzheimer’s, α-synuclein in Parkinson’s, IAPP in type II diabetes), the amyloid state is
actually thermodynamically more stable than the native fold. Stress, concentration increases, mutations, or metal ions can nucleate
conversion, after which elongation proceeds rapidly like crystal growth. The resulting cross-β architecture is extraordinarily stable,
resistant to heat, detergent, and proteases.
As materials, amyloid fibrils are definitely useful. They can have a Young’s modulus of 1–20 GPa (similar to silk), high aspect ratio,
and nanoscale precision. Functional amyloids already exist naturally (curli fibers in bacterial biofilms, yeast prions as regulatory
switches). Proposed applications include conductive nanowires (metallized with silver or gold), hydrogels for drug delivery, tissue
engineering scaffolds, and even food technology(whey protein amyloids are already used commercially as emulsifiers).
Protein Analysis and Visualization
Insulin is a small hormone produced by the pancreas that regulates blood glucose levels. I chose it because of its fascinating history as a therapeutic protein. Decades of protein engineering have produced analogs like insulin lispro and glargine, where just one or two amino acid changes dramatically alter how the drug behaves in the body. I wanted to explore the structure underlying a protein that has been so deliberately and successfully redesigned.
this specific insulin protein is in the broader insulin family
Protein Structure Page
The structure was released on February 24, 2009. (Note: While the very first insulin structure was solved in 1969, this version (3E7Y) is
the modern high resolution reference for the native human protein).
The quality is excellent - 1.60 Å
There are other molecules in the solved structure of the protein, as this classic structure represents the storage form (hexamer). It
contains zinc ions, chloride ions, and water molecules
This protein is the defining member of the Insulin-like superfamily.
3D Structure
cartoon
ribbon
sticks
secondary structure: the protein has more helices than sheet
protein surface: the distribution of hydrophobic (orange) vs hydrophillic (cyan) residues follows as expected. Most of the surface residues are hydrophillic, and the hydrophobic residues line the binding pockets
