Protein secondary structure

Alpha-helix, stick out

The polypeptide structure where it winds tightly called, … the side chains …

3.6

In a alpha-helix there is … residues per turn

Hydrogens bonds 4

Alpha helixes are stabilized by … that stretch from a carbonyl group (C=O) to a NH amine group … residues away

Right

In naturally occurring proteins the helixes of a substantial length will be … handed

- → + , - → +

The CO and NH groups roughly line up along the helix axis, when drawn the NH group has a downwards … and the CO a downwards … , starting from the electronegative atom

Small dipole, large dipole

Since the NH and CO groups roughly line up down the helix it creates a … , resulting in a … when taking into account the whole structure

Negative, positive

There is a … charge at the C-term and a … charge at N-term.

Extended

Compared to alpha-helices, beta strands and sheets are more

Antiparallel

Beta conformation where the C & N terms alternate, the side chains alternate up and down positions, where the net dipole alternates in this fashion

Paralllel

Beta conformation where the C & N terms align

Parallel

Bonds are on an angle in this beta structure making it weaker

Steric hinderance

Alpha helices and beta sheets are well defined structures where the backbone has specific angles to avoid

-60, -50,-135, 135

The phi ϕ and psi ψ angles in a alpha helix are … and … . In a beta strand the phi ϕ and psi ψ angles are … and …

A

The area on the ramachandran plot that represents beta sheets

B

The area on the ramachandran plot that represents right-handed alpha helices

Helices

Amino acids with long skinny side chains fit better in …

Beta sheets

Amino acids with larger/chunky side chains fit better in …

Proline, first turn of a helix

Amino acid … has no HN to participate in hydrogen bonding, and causes hinderance, it only fits on the …

Glycine, entropy

The amino acid … affects a helix since it allows for high flexibility making it have a high …