Lecture 3 Protein Structure and Folding

How was the secondary structure of protein discovered?

It was a major example of structure prediction before direct experimental protein structures. Pauling, Corey, and Branson had used basic chemistry (planar peptide bonds, bond angles, atomic distances, and hydrogen bonding) to propose the alpha-helix.

What are the components of the alpha helix?

- It starts at the N-terminus and ends at the C-terminus.

- The repeating protein backbone atoms (N - C alpha - C = O) coil around the central axis and form the central axis.

- The R groups/side chains project away from the helix, where they can interact with water, membranes, or other parts of the protein.

- Hydrogen bonds stabilize the helix.

Which backbone groups of the alpha helix form hydrogen bonds?

C=O of one residue and N-H of another residue.

Why does the backbone of a alpha helix twist in to a helix?

Because that shape allows many C=O and N-H groups to line up and form, stabilizing the hydrogen bonds without major steric clashes.

Which direction does an alpha helix turn?

Right-handed, where R groups protrude away from the backbone. (Most common)

Left-handed, found in bacteria cell wall. (Very rare)

Why is the alpha helix turn right-handed?

Proteins are made mostly from L-amino acids, whose geometry favors a right-handed alpha helix because it avoids steric clashes and allows good backbone hydrogen bonding.

What does homochirality mean?

Living systems mostly use one handedness of biological molecules instead of random mixture of both mirror-image forms.

Lecture 3. Slide 8.