Lecture 5 Flashcards
(28 cards)
Are the residues of globular proteins in sequence?
No pattern
What are the functions of globular proteins?
Catalyze reactions, provide chemical energy, sense the environment, etc.
What is meant by “the fold” of a protein?
the way its secondary structure elements pack together and are connected (tertiary structure)
what are supersecondary structures?
simple assemblies of secondary structures that are adjacent in sequence
What are tandem repeats?
contiguous arrangement of multiple copies of a repeating structural unit in linear sequence on a protein chain
Describe the unfolded state of a protein
in solution, it has no secondary or tertiary structure and can adopt many different conformations
What is protein denaturation?
The loss of its fold
What are the three ways to unfold the protein?
increase the temperature, change the pH to extremely acidic or basic, add chaotrophic molecules
How do molecules act as chaotropes?
They can form hydrogen bonds with the protein backbone and side chains; these compete with the hydrogen bonds formed within the protein, and at high concentrations chaotropes can disrupt its structure
How do you reverse denaturation?
Lower the temperature, restore the pH, remove the chaostope
What might refolding be sensitive to?
may be sensitive to conditions such as how slowly the temperature is decreasing, and how slowly the chaotropes are removed
Describe spontaneity around delta G (gibbs free energy)
G < 0, it is spontaneous; G > 0, it is not spontaneous; G = 0 for a protein that spontaneously folds under physiological conditions
What does delta H stand for?
The heat of reaction
If delta H is negative, what does that mean for the reaction and to delta G
It is the heat released as the reaction occurs, contributes to a favourable delta G for folding
what is delta S measuring?
the randomness in a system
what happens to the process when delta S is positive vs. negative
S+, a process is favourable; S-, a process is unfavourable
Which interactions / thermodynamics are involved in the folding of proteins? (5)
- The conformational entropy of the protein chain
- Charge-charge interactions
- Hydrogen bonds
- Van der Waals interactions
- The hydrophobic effect
What does the unfolded and folded states of a protein look like?
Unfolded state (U): a random coil with many possible conformations, consists of many micro states (a high entropy state)
Folded state (F): one correct confirmation, one microstate (a low entropy state). Folding results in a loss of conformational entropy (delta S conformation) for protein
What do charge-charge interaction do for delta H for folding?
Contributes a favourable delta H for folding
What do hydrogen bonds do for delta H for folding?
Each H-bond within a protein contributes to a favourable delta H for folding
What is a clathrate?
a nonpolar molecule surrounded by a cage of water molecules
What does caging of water molecules do in clathrates to the entropy and order of the system?
increases the order of the system and is entropically unfavourable
What happens to entropy change when number of clathrates are decreased?
Increases the entropy
What is free energy change for folding?
the sum of the contributions of the different thermodynamic factors
