Protein Folding and Denaturation

Define Protein folding:

Process by which amino acid chains develop secondary, tertiary, or quaternary structures.

In reference to protein folding, define Native state, :

Refers to a fully folded protein; proteins are usually most functional in their native state. Native state does NOT mean the initial state (that would be a peptide chain).

Native state is largely determined by what?

The amino acid sequence (encodes bonding).

In relation to protein folding, what are Chaperones and what are their purpose?

Chaperones are proteins that assist in protein folding. They stabilize folding and prevent aggregation (crowding/clumps/anything that might threaten the natural function and shape of the protein).

So, it's not so much that the chaperones are queued into how the protein ultimately has to be configured, it's more like they are buffers on the side of the road. They prevent the protein from going astray, or clumping with other proteins, or with its own chains.

Chaperones are (specific or nonspecific).

Nonspecific. They assist multiple types of proteins.

Is protein folding a spontaneous or non-spontaneous reaction?

Spontaneous reaction.

Spontaneous reactions are defined in cases where the ΔG free energy is (positive or negative).

Negative.

Negative ΔG means the reactants have (more or less) free energy than the products.

More free energy. So the unfolded protein has more free energy than the folded protein (or the process does not require additional energy to occur).

1. Define Enthalpy:

2. Define Entropy:

1. Enthalpy is the heat content of a system. The enthalpy change of a reaction is equivalent to the amount of energy lost or gained during the reaction.

2. Entropy refers to the measure of the level of disorder in a thermodynamic system.

Write the ΔG equation:

ΔG = ΔH - T * ΔS

ΔG = Gibbs Free Energy (kJ/mol)

T = Temperature (Kelvin)

H = Enthalpy (kJ/mol)

S = Entropy (J/K*mol)

1. In the protein folding process you see (positive or negative) values for both ΔH and ΔS.

2. Does that make the reaction endothermic or exothermic?

1. Negative.

2. It means the process is exothermic.

What does a negative ΔS value mean?

It means negative entropy, so there is less disorder in the system by the time a protein folds.

Why does the value of ΔH need to be greater than the value of ΔS?

Because we know that the ΔG has to be negative, and we're subtracting a negative value, i.e. ΔG = ΔH - T * ΔS.

Example: let's say we have a ΔH = -800J and a ΔS = -2J/K, the equation would look as follows:

1. -800J - (-2J/K)300K

2. ΔG = -800J + 600J

3. ΔG = -200J

In relation to protein folding, define Denaturation:

Unfolding. It's where proteins lose their secondary, tertiary, and quaternary structures.

Denaturing can refer to partial-denaturation, in which a protein could go from tertiary down to secondary, and not all the way to primary.

What causes denaturation of a protein?

Changes in the environment, such as:

-pH.

-Temperature.

-Certain chemical exposures (e.g., alcohol).

-Radiation.

Why do proteins lose most or all of their function when they denature?

Because both the hydrophobic and hydrophilic regions become exposed.

True or false: Once denatured, proteins can't be refolded.

False. Proteins can undergo renaturation in some cases.

1. Proteins are recycled by what?

2. Do they just denature?

1. Lysosomes.

2. No, they just kind of break apart into pieces.

In reference to part 2 of the previous question, what is the exception in which proteins do denature?

When a cell dies, its proteins do denature.