Secondary Structures

Question 1

What type of alpha helices are more common and how is this used to check the correctness of X-Ray crystallography?

Answer 1

Helices are almost exclusively right handed allowing the correctness of x-ray crystallography to be checked through the ramachan plot

Question 2

What occurs to the amino acids in an alpha helixes?

Answer 2

Each amino acid rises by 1.5 Armstrong and is rotated by 100 degrees to give 3.6 residues per turn

Question 3

How long is the average alpha helix in globular proteins?

Answer 3

<45 Armstrongs

Question 4

What is the helix dipole?

Answer 4

All of the dipole moments in an alpha helix are aligned, reinforcing each other, this results in the C terminal having a partial negative charge and the N terminal having a partial positive charge which may or maynot be reinforced by charged amino acids
For this reason the ends of helices are often bound to ions

Question 5

What are the different types of helices, and how could they give an indication of the proteins location?

Answer 5

Hydrophobic could be in the cell membrane or buried inside the protein core
Amphipathic could be involved in solvent shielding

Question 6

What is an example of an all alpha helical protein?

Answer 6

Ferritin which stores iron

Question 7

How are Beta sheets formed?

Answer 7

Hydrogen bonds between amino acid sidechains which may be distant in the protein sequence but 3.5 armstrongs close in the protein structure
Side chains point in opposite directions

Question 8

What are the different types of beta sheet?

Answer 8

Parallel, antiparallel, mixed sheet, twisted sheet