Topic 6: Secondary Structures of Proteins

Question 1

Describe the 4 levels to protein structure?

Answer 1

-Primary structure - amino acid linear sequence
- Secondary structure - regions of regularly
repeating conformations of the peptide chain,
such as a-helices and b-sheets
-Tertiary structure - describes the shape of the
fully folded polypeptide chain
-Quaternary structure - arrangement of 2 or
more polypeptide chains into a multi-subunit
molecule

Question 2

Common structures in the secondary level

Answer 2

𝛼-helix
Β-sheets
Loops or random coils and turns

Question 3

Describe the structure of an alpha helix

Answer 3

The alpha helix structure is much like the coils of a wired telephone. Protein helices are always right-handed
The hydrogen bonding stabilizes the structure
There are 3.6 ≅ 4 amino acids per turn
Say the first residue is n, and n+4 is the last residue of the turn. Hydrogen bonds form between the n and n+4 residues, and so forward, occurring between the hydrogen of the amino group in the first residue and the oxygen of the carbonyl group in the 4th residue
Ionizable amino acids like glutamate and lysine which are charged at certain conditions are not great to have in successive sequences in a polypeptide due to the electrostatic repulsion that can occur

Question 4

Which amino acids are alpha helix breakers and why

Answer 4

Glycine and proline are denoted as 𝛼-helix breakers

Glycine is too small, and introduces kinks into the alpha helix, disrupting the structure
Proline is too rigid, introducing kinks into the alpha helix and also has a secondary alpha-amine grorup, which becomes tertiary when a peptide bond is formed, meaning it lacks the hydrogen bonds that allow it to stabilize the alpha helix
These molecules are often found at the boundaries of alpha-helices and in turns

Question 5

Describe the structure of a beta pleated sheet

Answer 5

In beta pleated sheets, the repeating units, called beta strands, lie one on top of the other, and are stabilized by hydrogen bonding (the hydrogen bonding depends on if the strands are parallel or antiparallel), and are often looped together with beta turns

Question 6

Describe the structure of beta turns

Answer 6

They generally consist of 4 amino acid residues. Often, glycine and proline are found in these turns due to the flexibility they offer
Beta turns are frequently found at the ends of beta strands in beta sheets, where they help to reverse the direction of the polypeptide chain and enable the formation of an antiparallel beta sheet.
Like the alpha-helix turn, it is the n+3 amino acid which forms the hydrogen bond with.
The carbonyl of the nth amino acid forms the hydrogen bond with the amine of the n+3 amino acid