Smoother Rotation         Center Clicked
5. Hydrophobicity, Polarity & Charge

In this chapter, all views show only one beta chain, which is one of the 4 chains in the complete hemoglobin tetramer.

  In this single beta chain, amino acids have been divided into two categories, based on their sidechains: Hydrophobic, Polar. Heme. Also shown are the oxygens of the tightly bound water molecules.

About half of the surface amino acids are polar.

Check Cut in Zoom/Cut at the bottom of this window. This slices down the middle of the molecule, hiding the front portion.

At Cut≈50%, you can see that the core of the folded protein chain is hydrophobic. All the polar amino acids are on the surface, where they can form hydrogen bonds with water. The buried portion of heme is hydrophobic.

When you rotate the molecule with Cut ON, the cutting plane remains parallel to the screen.

  Here are all the charged amino acid sidechains: Positive, Negative. Using Cut, you can see that the charged sidechains are all on the surface of this protein domain.
  Histidine sidechain nitrogens have partial positive charges in the slightly acidic, CO2 rich environment of tissues. Histidine is nearly uncharged in the higher pH of the lungs.
  Now only salt bridges have their charges colored. Salt bridges occur when positive and negative charges are within 4.0 Å of each other, enabling a strong electrostatic non-covalent bond.

         

What Do You See?
  1. How do the core and the surface of each protein chain differ?
  2. What drives that difference?
  3. How does a slightly acidic pH affect charge?
  4. What is a "salt bridge"?

Get immediate feedback at the practice quiz.

Want bigger text?
View the Text Size Instructions
Zoom / Cut     Zoom = 100%