Proteins 2 Flashcards
How is h bonding formed in an alpha helix (secondary protien structure)
The c=o of residue i accepts a H bind from residue i+4
The c=o from i+1 accepts from the nh of i+5
This makes a bend
These residues are all in a chain but then make the alpha helix due to h binding within the structure
What are the alpha helix phi and psi angles on ramachandran
-60,-60
The c=o groups point away and nh point forward
In an alpha helix structure, what is the confirmation of all of the c=o
They all point down in the structure
In an alpha helix are all c=o and amide groups h bonded to each other
All are except for the residue at the top and bottom ends of the helix
What type of shape represents the polypeptide main chain
What is sticking out
What direction and handedness is the structure
A ribbon
The r groups stick out
The ribbon is going CW. Means it’s right handed because if going cw with right hand the thumb faces down to the C terminus
What is the rise per residue of the alpha helix
What is the rotation per residue
So how many residues per rotation?
From one alpha c to another the rise is 1.5 A
the rotation is 100 degrees
360/100 degrees is 3.6 residues per rotations
What is special about the ribbon and cylinder depiction of the alpha helix
They both ignore the side chains that stick out of the helix
What do the tubes that follow the alpha helix represent
Is represents the path of the polypeptide chain when it’s not forming an alpha helix
The atoms in these tube are just primary peptides
How are beta sheets formed
Because the main chain has h binding potential, another chain can come in antiparallel and do h bonding interactions between the c=o and NH directly across from each other
The r groups alternate in and out
This causes the beta sheet
Ex.
C-N
N-C
Can beta sheets be formed from peptides parallel to each other instead of antiparallel
Yes, the bond would be a bit diagonal to each other
Can there be more than two polypeptides in a beta strand
Yes there can be sheets made of multiple strands
What is the side view pattern of a beta stand
What is the length from one down r group to the up r group in the pleated pattern
What about distance between two r groups on the same side?
Pleated (zig zag), and the r groups are of alternating side of the sheet (down, up, down , up)
3.5 (opposite)
7 (same)
What is a mixed beta sheet
Give an example of how we’d describe one
Mixed sheet are sheets that have antiparallel and parallel strands in the same sheet
Ex. Three strands top 2 para bottom 2 antiparallel
It’s a three stranded mixed beta sheet
One the arrow representation of the beta strands how would they be described
They have the arrow pointing to the C terminus
They aren’t flat, they’re usually twisted
What is a reverse turn
The third type of secondary protein structure.
This is where the c=o of residue i accepts a h-bond from the nh of residue i+3
This makes the polypeptide change direction and have a turn
