Biochemistry
Lecture 4
1.0 PROTEIN FOLDING
1.1 What is the central dogma in molecular biology?
DNA > RNA > protein > function
1.2 What is Anfinsen's dogma?
Protein 3D structure is encoded in the sequence. Primary structure contains all tertiary
structure
Information.
1.3 What are the driving forces for folding?
secondary structure: many H-bonds
compact fold: Vanderwaals interactions
perhaps some ion bonds
1.4 If we consider the equilibrium between unfolded and folded state,
which of these states is favored by the interactions above?
Folded
1.5 Is this force entropic or enthalpic in nature?
Enthalpic -> living cell produces heat to compensate lack of entropy.
1.6 Which state has a larger multiplicity (i.e., equivalent microscopic
states with the same macroscopic appearance)?
The unfolded state
1.7 Which state is entropically more favorable?
The unfolded state
1.8 Explain why the unfolded state is favorable in q1.7 and q1.8
S = Kb ln W
In an unfolded state the W is greater. Since the chains can adopt many shapes, thus W > 1. If
they were folded it would be W = 1. This shows that the unfolded state is entropically favored.
,1.9 Why does a disulfide bond stabilize a protein?
Disulfide bonds reduce the number of conformations that the protein can adopt, by forming
bonds. This will cause for a protein that can't adopt other forms because they are fixed to their
conformation that they got from the disulfide bonds.
What happens to the entropy when disulfide bonds form ? It reduces since disulfide bonds
cause W = 1 to be
2.0 THE HYDROPHOBIC EFFECT IN PROTEINS
2.1 Which state has the largest contact area with water?
The unfolded state
Why? At an unfolded state water molecule can easily reach the molecules of the protein.
2.2 Which state has more hydrophobic side chains exposed to water?
The unfolded state
Why? Due to hydrophobic effect the hydrophobic chains will be in the interior of the protein
in an aqueous environment. However, when it is unfolded it means that these molecules are
exposed to water.
2.3 Which state is favored by the hydrophobic effect?
The folded state
Why? The folded state, since the hydrophobic effect causes hydrophobic chains not to be in
contact with water. So, they will be folded and thus not be in contact with water.
2.4 Is the hydrophobic effect entropic or enthalpic in nature?
Entropic
Why? Entropic, since it influences (increase) the entropy of the protein molecules
2.5 What is the effect of the hydrophobic effect in protein folding?
Hydrophobic effect causes the hydrophobic sidechains to be located in the center of the
protein, shielded from the water. Only few are found at the surface, why?
Surrounding water molecules force the hydrophobic side chains to the center and interact
with polar side chains at the surface.
2.6 What is the hydration shell?
Layer of bound water molecules on the protein (side chains)
2.7 What is the energy balance of protein folding?
∆G = ∆H -T∆S; must be negative for spontaneous folding
, ∆H<0 = Internal interactions favor folding (release of heat during folding). -> due to
hydrophobic effect
-T∆S>0 = Conformational entropy is lost during folding (protein loses freedom). ∆S<0
Hydrophobic effect: less water trapped on folded protein surface. Bulk water has more
freedom, entropy is increased during folding. ∆S>0, hence -T∆S<0.
Thus, ∆G is negative
3.0 PROTEIN (UN)FOLDING
3.1 How can a protein be de-activated?
Rising temperature: denaturation. This implies that the stability of folded protein is
temperature dependent.
3.2 What can be said about H-bonds in proteins?
The strength of one internal H-bond is in the order of 20 kJ/mol. The net stability of an entire
protein is thus only in order of 2-3 H-bonds!
3.3 How does denaturation work?
Entropy has for most proteins a net force working against folding (if chain entropy exceeds
hydrophobic effect).
The larger T, the larger this force.
At some temperature, the unfolded state is more
favorable, and the protein unfolds.
This is why you boil your food! Unfolded proteins are easier to digest into small peptides.
3.4 EX. Once you have boiled your egg and allow it to cool down, why
don’t the egg proteins refold to their native state?
If one protein molecule is unfolded, it can
refold spontaneously (most of them).
If all proteins are in an extended, unfolded state, they get entangled. They all interact with
many other protein chains. Because of the exposure of hydrophobic side chains that are
supposed to be inside the protein= aggregation
3.5 How does a fever work?
Higher body temperature causes reduced stability of proteins at higher temperature sets
limits on cells.
3/6 How does our digestive system denature/unfold the proteins that we
eat?
acid: pH 1-2 in the stomach
Acid = Causes all negative charges to disappear, the protein only contains positive charges
that repel.
3.7 What is Levinthal's paradox?
His experiment shows that the random search for the correct conformation would take
longer that the lifetime of the universe.
This suggests that There must be local favorable interactions that, once formed, remain quite
stable. -> hierarchical guided process
Pathways for protein folding
Lecture 4
1.0 PROTEIN FOLDING
1.1 What is the central dogma in molecular biology?
DNA > RNA > protein > function
1.2 What is Anfinsen's dogma?
Protein 3D structure is encoded in the sequence. Primary structure contains all tertiary
structure
Information.
1.3 What are the driving forces for folding?
secondary structure: many H-bonds
compact fold: Vanderwaals interactions
perhaps some ion bonds
1.4 If we consider the equilibrium between unfolded and folded state,
which of these states is favored by the interactions above?
Folded
1.5 Is this force entropic or enthalpic in nature?
Enthalpic -> living cell produces heat to compensate lack of entropy.
1.6 Which state has a larger multiplicity (i.e., equivalent microscopic
states with the same macroscopic appearance)?
The unfolded state
1.7 Which state is entropically more favorable?
The unfolded state
1.8 Explain why the unfolded state is favorable in q1.7 and q1.8
S = Kb ln W
In an unfolded state the W is greater. Since the chains can adopt many shapes, thus W > 1. If
they were folded it would be W = 1. This shows that the unfolded state is entropically favored.
,1.9 Why does a disulfide bond stabilize a protein?
Disulfide bonds reduce the number of conformations that the protein can adopt, by forming
bonds. This will cause for a protein that can't adopt other forms because they are fixed to their
conformation that they got from the disulfide bonds.
What happens to the entropy when disulfide bonds form ? It reduces since disulfide bonds
cause W = 1 to be
2.0 THE HYDROPHOBIC EFFECT IN PROTEINS
2.1 Which state has the largest contact area with water?
The unfolded state
Why? At an unfolded state water molecule can easily reach the molecules of the protein.
2.2 Which state has more hydrophobic side chains exposed to water?
The unfolded state
Why? Due to hydrophobic effect the hydrophobic chains will be in the interior of the protein
in an aqueous environment. However, when it is unfolded it means that these molecules are
exposed to water.
2.3 Which state is favored by the hydrophobic effect?
The folded state
Why? The folded state, since the hydrophobic effect causes hydrophobic chains not to be in
contact with water. So, they will be folded and thus not be in contact with water.
2.4 Is the hydrophobic effect entropic or enthalpic in nature?
Entropic
Why? Entropic, since it influences (increase) the entropy of the protein molecules
2.5 What is the effect of the hydrophobic effect in protein folding?
Hydrophobic effect causes the hydrophobic sidechains to be located in the center of the
protein, shielded from the water. Only few are found at the surface, why?
Surrounding water molecules force the hydrophobic side chains to the center and interact
with polar side chains at the surface.
2.6 What is the hydration shell?
Layer of bound water molecules on the protein (side chains)
2.7 What is the energy balance of protein folding?
∆G = ∆H -T∆S; must be negative for spontaneous folding
, ∆H<0 = Internal interactions favor folding (release of heat during folding). -> due to
hydrophobic effect
-T∆S>0 = Conformational entropy is lost during folding (protein loses freedom). ∆S<0
Hydrophobic effect: less water trapped on folded protein surface. Bulk water has more
freedom, entropy is increased during folding. ∆S>0, hence -T∆S<0.
Thus, ∆G is negative
3.0 PROTEIN (UN)FOLDING
3.1 How can a protein be de-activated?
Rising temperature: denaturation. This implies that the stability of folded protein is
temperature dependent.
3.2 What can be said about H-bonds in proteins?
The strength of one internal H-bond is in the order of 20 kJ/mol. The net stability of an entire
protein is thus only in order of 2-3 H-bonds!
3.3 How does denaturation work?
Entropy has for most proteins a net force working against folding (if chain entropy exceeds
hydrophobic effect).
The larger T, the larger this force.
At some temperature, the unfolded state is more
favorable, and the protein unfolds.
This is why you boil your food! Unfolded proteins are easier to digest into small peptides.
3.4 EX. Once you have boiled your egg and allow it to cool down, why
don’t the egg proteins refold to their native state?
If one protein molecule is unfolded, it can
refold spontaneously (most of them).
If all proteins are in an extended, unfolded state, they get entangled. They all interact with
many other protein chains. Because of the exposure of hydrophobic side chains that are
supposed to be inside the protein= aggregation
3.5 How does a fever work?
Higher body temperature causes reduced stability of proteins at higher temperature sets
limits on cells.
3/6 How does our digestive system denature/unfold the proteins that we
eat?
acid: pH 1-2 in the stomach
Acid = Causes all negative charges to disappear, the protein only contains positive charges
that repel.
3.7 What is Levinthal's paradox?
His experiment shows that the random search for the correct conformation would take
longer that the lifetime of the universe.
This suggests that There must be local favorable interactions that, once formed, remain quite
stable. -> hierarchical guided process
Pathways for protein folding
