lecture 4a and 4b

Question 1

Alpha-keratin:

• Describe the helices in keratin and how they are held together.
• What is the superhelix called?
• What is the repeating sequence called and what is its purpose?
• What is it found in?

Answer 1

Held together by weak vanderwaals interactions to allow stretching (alpha helices) but is strong and won’t break because of its disulphide bonds. The helix itself is formed from two right handed helices to form one left handed super helices called an alpha helix coiled coil
The heptad repeat allows interactions with complementary molecules. Found in hair and wool.

Question 2

Collagen:

• Describe the structure of the superhelices of collagen
• What is special about its pitch and rise?
• What stabilizes the helices and stabilizes the collagen?
• What AA residue is found in the center of collagen and form H-bonds to what residue?
• Why is hydroxylation crucial to collagen formation and why is vitamin C deficiency problematic?
• What is the main function of collagen?

Answer 2

• Made of 3 left handed helices to make one right handed superhelices
• The pitch and rise are double that of normal alpha helices
• Helices stabilized by steric repulsion and collagen stabilized by interchained H-bonding
• Glycine found in the middle and forms a H-bond to a proline
• Hydroxylation caused by vitamin C, if it is missing, hydroxylation (binding of proline and hydroxyproline) doesn’t occur which crucial for collagen to properly become intact, this will lead to scruvey due to fragile ECM, we can’t
• Strong and rigid, very little flexibility

Question 3

tertiary:

• Give an example
• What is it? What is folding driven by? What are some things that stabilize it?

Answer 3

• Myoglobin
• 3D globular protein formed by folding of AA residues
• Driven by hydrophobic effect: hydrophobic groups are inner and via versa, stabilized by vander waals interaction

Question 4

What are supersecondary structures? What is another name for it? Give 5 examples and give their specific function.

Answer 4

Combinations of alpha helices, beta sheets and loops, called Motifs

1) Helix-loop-helix: Ca binding protein
2) Helix- turn – helix: DNA binding proteins
3) Coiled, Helix bundle, Beta sandwhich (make a hydrophobic environment)

Question 5

Domains:

- What are they and what are their functions?

Answer 5

• Are made of combination of different motifs, have varying functions.

Question 6

Quaternary structure:

-What is a multi subunit protein called? Why are these favored for the quaternary structure? (4 reasons)

Answer 6

• called oligomers
• more stable, active sites formed, allows the 3D confirmation to change when ligand binds to it, different subunits may be shared to carry out similar functions.

Question 7

What evidence was found that proteins can refold spontaneously to native confirmation? What determines the 3D structure of peptide? Discuss the experiment that was carried out. What did this experiment prove?

Answer 7

Found that the primary structure determines the tertiary structure.
The experiment exposed Native ribonuclease to Urea and BE and it became denatured, READ THIS
Proved that primary structure determines folding and that correct folding can only occur when the protein has folded into its native conformation, also that renaturation is spontaneous.

Question 8

How does the primary sequence effect 3D structure of protein? (3 reasons)

Answer 8

• Due to the hydrophobic/philic properties, size and ability to H bond.
• Folding is highly cooperative
• Folding is done by progressive stabilization of intermediates rather than randomness

Question 9

In detail, what are the 4 forces that stabilize proteins?

Answer 9

1) Hydrophobic effect: increases entropy overall, drives hydrophobic AA to associate with themselves
2) Hydrogen bonds: contribute to cooperativity of folding
3) Vanderwaals: contribute to stability
4) Assistance from molecular chaperones: enhances correct folding.