Alpha helices are a helix-helix structure
Which of the following best describes an alpha helix?
Ridges are formed by side chains with troughs in between
Ridges are formed by the peptide bonds and the amino acid side chains form the troughs
Helix-helix packing can be shown by highlighting every _ residues?
Alpha helices must follow particular rules when packing together
Describe the ridges of the following proteins
i + 4
i + 2
i + 3
The angle between two packed helices depends on which type of ridges pack into which troughs.
The troughs of one alpha helix will be filled by the 'backbone' of another
Beta sheets twist slightly _ each other
The angle between two beta sheets is approx....?
Where in the plane is each color (ignore green)
Yellow- above plane
White- below plane
White- above plane
Yellow- below plane
The amino acids will point in opposite directions
The strands of beta sheets are held together by backbone hydrogen bonding
The angle between sheets is determined by their...
Right handed twist
Left handed twist
Amino acid side chains
How are the aa side chains arranged in beta sheets?
The amino acid residue side chains of one beta sheet pack between the spaces between side chains on the adjacent beta sheet
The amino acids on one beta sheet will have no residue where the other beta sheet has one (they're removed)
The amino acids with residues attached will alternate between beta sheets
When an alpha helix and a beta sheet pack together, the groove the beta sheet lies in tends to be made by amino acids how far apart?
Name three things that can be used in protein folding to encourage correct folding?
Non-native interactions (as long as they are reversible)
Pinching (isolates subdomains for folding)
The removal of a domain for folding, before it's re-addition
Negative Free Energy is less favorable
Concerning entropy- less order is more favorable
Which of the following is the equation for the free energy change of a folded protein
ΔG = ΔH - TΔS
ΔH = ΔG x TΔS
TΔS = ΔH + ΔG
Hydrogen bonds are the least common type of bond in proteins
What's the enthalpy change of a H bond formation?
-4 to -30 kJmol
-4 to -3 kJmol
-40 to -30 kJmol
A hydrophobic core in water is entropically favorable
Why is hydrophobic cores in water _favorable?
They make the water molecules more ordered, decreasing entropy
They make the water molecules less ordered, increasing entropy
Why do hydrophobic proteins fold?
Folded proteins have a reduced surface area, leading to a reduced number of organised water molecules, leading to a lower decrease of entropy
Folded proteins have a reduced surface area, leading to a reduced number of organised water molecules, leading to a lower increase of entropy
As water ordering decreases, entropy decreases
Why is energy needed to maintain the folding of a (hydrophobic) protein (i.e. from hydrogen bonds etc.)?
Because the unfolded state of the protein is more entropically favorable than the folded state
Because though the folded protein is more entropically favorable, it's folding decreases entropy, which is unfavorable
So energy must be produced to maintain the fold
Heating denatures a protein because it breaks the bonds required to offset the negative change in entropy caused by the protein folding i.e, it makes ΔH less negative
In protein folding, ΔH is negative, and -TΔS is positive