Chapter 3: 3.5 Analysis of Protein Structure Flashcards
(31 cards)
True or False:
Each secondary structure has a unique set of bond rotation angles
True
What are the measurable angles of rotations in the secondary structure?
- Cα-C=O (ψ)
- Cα-NH (φ)
What is the unique set of bond rotation angles in α-helix?
- ψ: -50°
- φ: -60°
What is the unique set of bond rotation angles in β-sheet?
- ψ: +135°
- φ: -140°
Define:
Ramachandran Plots
Created by plotting the ψ angles of a protein’s amino acids on the y-axis and the φ angles on the x-axis
What does a Ramachandran Plot show?
Shows which kind of angle combinations are possible and which are not (steric hindrance)
ψ and φ angles define protein geometry, what can Ramachandran Plots define?
Protein structure
True or False:
Secondary structures show characteristic patterns on the Ramachandran plot
True
What is the speed of protein folding? What does this indicate?
- 10^3 - 10^-1 seconds
- Indicates that folding is directed
What did Anfinsen’s experiment discover?
Discovered that the primary sequence of proteins dictated the secondary and tertiary structure
What was the Anfinsen Experiment?
A series of experiments were conducted on Ribonuclease A
Angle combinations that are not possible are due to…
Steric hindrance
What is a protein’s folded state known as?
Native structure
Anfinsen Experiment rationale:
- What stabilizes a protein’s folded state?
- What should lead to the protein unfolding?
- How is this done? (protein unfolding)
- Disulfide bonds
- Reducing
- With β-mercaptoethanol
Anfinsen Experiment rationale:
When β-mercaptoethanol was applied, what happened?
Unfolding did not occur fully
Anfinsen Experiment rationale:
What had to be present in order for full protein unfolding to occur?
Urea or Guanidine
Anfinsen Experiment rationale:
Denaturing agents disrupt…
Non-covalent interactions
Anfinsen Experiment rationale:
How does urea break secondary structures?
Form H-bonds with the amino acid backbones
Anfinsen Experiment rationale:
To allow the protein to re-fold, how was urea and β-mercaptoethanol removed?
Dialysis
Anfinsen Experiment rationale:
Describe dialysis
Involves a semi-permiable membrane that allows some molecules to move from a place of high concentration to low concentration while others remain
Anfinsen Experiment rationale:
- What was the result from dialysis?
- What does this mean?
- Protein did not re-fold correctly
- Only 1% of activity was recovered
- Means there must be assisted folding
Unfolded proteins have…
- High free energy
- High entropy
What is entropy?
Measure of disorder
True or False:
There is only one possible folded state for a protein
False, there are many possible folded intermediate states
