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3. Hemoglobin Secondary Structure
  Most of the amino acids in hemoblogin form alpha helices, connected by short loops (white) that are neither helical nor beta strands. Hemoglobin has no beta strands and no disulfide bonds. Here is shown a single beta chain (146 amino acids). Alpha chains (141 amino acids each) have similar secondary structure.
  A rainbow coloring scheme from the N-terminus to the C-terminus helps to discern how the separate alpha helices fold into a compact protein domain.
N               C
  This is a ribbon or "cartoon" representation.
  We'll focus on a single alpha helix.
  Here is the isolated alpha helix (17 amino acids: 59-75 of chain B in 1hho).
  The backbone trace connects alpha carbon positions in this alpha helix.
  Here are the atoms and covalent bonds of the alpha helix backbone or "main chain". The backbone is made up of 3-atom repeats: NCC, namely Nitrogen, Alpha-Carbon, Carboxy-Carbon (with its Oxygen). The backbone trace is translucent.
  Here we have added hydrogens (white) and removed the translucent backbone trace. Alpha helices (and beta strands) are favored conformations of polypeptides because they avoid steric clashes. An interactive Ramachandran Principle tutorial shows clashes forming and receding as phi and psi angles rotate.
   Here are the hydrogen bonds (broken white lines) that stabilize alpha helices. Hydrogen bonds are non-covalent.
  When the hydrogen bonds are shown schematically against the backbone alpha-carbon trace, you can see how they stabilize the helix.
  Now the amino acid sidechains are shown radiating from each alpha-carbon.
  Now the sidechain chemical elements are identified: C N O. (Hydrogens are not shown.)

         

What Do You See?
  1. What protein secondary structures make up each chain of hemoglobin?
  2. What kind of chemical bonds stabilize the conformation of an alpha helix?
  3. Are those chemical bonds covalent or non-covalent?

Get immediate feedback at the practice quiz.

Why are alpha helices common? See an interactive Ramachandran Principle tutorial that shows atomic clashes forming and receding during rotation of the phi or psi bonds.

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