L9: Proteins - Self Assembly, Interactions

Question 1

Describe the hydrophobic effect in terms of proteins.

Answer 1

• When a protein goes from unfolded (less stable) to folded (more stable).
• Spontaneous reaction
• Gibbs Free energy < 0, thus energetically favourable.

Question 2

What is denaturation?

Answer 2

• Unfolding of proteins

- Not all proteins can “re-nature” and re-gain function

Question 3

What is denaturation a result of?

Answer 3

• Disruption of non-covalent interaction

- Can happen by changing pH, temperature, etc.

Question 4

What makes a protein more stable?

Answer 4

• Strong interactions between side chains = more stable protein.
• Weaker interactions = less stable protein

Question 5

What role do non-covalent interactions have in folded polypeptide chains?

Answer 5

• Hold the polypeptide chain into the correct structure.

Question 6

What is the key concept in regards to non-covalent interactions in proteins?

Answer 6

• The interactions can be easily broken.

Question 7

Why is it important that the non-covalent interactions can be easily broken?

Answer 7

• For different protein functions.
• Changing shape is important for it to be able to accomplish the many tasks it has within the cell (ex. catalyzing reactions, binding a substrate, etc.)

Question 8

What are integral membrane (transmembrane) proteins?

Answer 8

• Proteins that cross through the lipid bilayer.

Question 9

What are peripheral proteins?

Answer 9

• Associated w/ the lipid bilayer on either side

- DOES NOT span the lipid bilayer

Question 10

What are the side groups of the proteins that are exposed to extracellular fluid?

Answer 10

• Charged/hydrophilic

Question 11

What are the side groups of the proteins that are within the protein?

Answer 11

• Hydrophobic

Question 12

What are the side groups of the proteins that are in the protein channel?

Answer 12

• Charged/hydrophilic

Question 13

List the non-covalent interactions from strongest to weakest.

Answer 13

• Ionic
• Ion-PD
• PD-PD
• PD-ID
• ID-ID

Question 14

What factors may impact non-covalent interactions?

Answer 14

• Size of side chain
• Hydrophobic (ID-ID) interactions (lots of interactions make them very strong)
• Location in the protein (interior vs. exterior, charged and polar side chains tend to interact w/ water vs. nonpolar side chains)