Secondary Structures

Question 1

What is the dominant force in protein folding?

Answer 1

Van der waals repulsions

Question 2

What do VDR range from and what are they caused by?

Answer 2

Range from weak to nuclear energies- overlap of electron clouds of adjacent non covalently bonded atoms

Question 3

What is the van der waals equation?

Answer 3

(p+ n2a/v2)(v-nb)=nRT

Question 4

What are the properties of weak interactions

Answer 4

Basis of protein folding
Thermodynamically weak
Kinetically weak- low Ea with respect to thermal energy
Easily broken and reformed at cellular temperatures with typical thermal energy available
Directionality of some weak bonds can be crucial to recognition process

Question 5

What is the purpose of S-S bridges?

Answer 5

They crosslink the primary chains- extracellular

Question 6

What are some types of strong interactions?

Answer 6

Covalent bonds ( esp with C, H,N and O)
Disulphides bridges

Question 7

What are some types of weak interactions?

Answer 7

H bonding
Van der waals forces (attraction and repulsion)
Hydrophobic 
Long range electrostatic 
Salt bridge

Question 8

Describe the nature of the chain in the secondary structure

Answer 8

Chain has a regular repeating conformation
Sequence of amino acid residues along the polypeptide chain have the same phi and psi angles
They are helices

Question 9

Why are most theoretical helices not allowed?

Which are allowed?

Answer 9

VDR restrict psi and phi which means most aren’t allowed

Only alpha helix and B sheet regions are allowed secondary structures

Question 10

What helps to stabilise the secondary structure

Answer 10

H bonds and VDW attractions helps stabilise
All weak attractions must be simultaneously optimised
They are optimised at the same psi and phi angles where van der waals repulsions are minimised

Question 11

Describe the relative stability of the 3 helices

Answer 11

310 helix (i+3)- H bonds are bent so not stable 
Alpha helix (i+4)- all forces are optimised so stable 
Pi helix (i+5)- hole at centre of helix- poor van der waals attractions so not stable

Question 12

What does i mean?

Answer 12

Depicts the number of residues in the chain

Question 13

Why is the alpha helix right handed?

Answer 13

This is because on the left handed helix there is awful steric clash between cB with H atoms and oxygen of C=O
This does not happen on right handed helix