Chapter 3: 3.5 Analysis of Protein Structure

Question 1

True or False:

Each secondary structure has a unique set of bond rotation angles

Answer 1

True

Question 2

What are the measurable angles of rotations in the secondary structure?

Answer 2

1. Cα-C=O (ψ)
2. Cα-NH (φ)

Question 3

What is the unique set of bond rotation angles in α-helix?

Answer 3

• ψ: -50°
• φ: -60°

Question 4

What is the unique set of bond rotation angles in β-sheet?

Answer 4

• ψ: +135°
• φ: -140°

Question 5

Define:

Ramachandran Plots

Answer 5

Created by plotting the ψ angles of a protein’s amino acids on the y-axis and the φ angles on the x-axis

Question 6

What does a Ramachandran Plot show?

Answer 6

Shows which kind of angle combinations are possible and which are not (steric hindrance)

Question 7

ψ and φ angles define protein geometry, what can Ramachandran Plots define?

Answer 7

Protein structure

Question 8

True or False:

Secondary structures show characteristic patterns on the Ramachandran plot

Answer 8

True

Question 9

What is the speed of protein folding? What does this indicate?

Answer 9

1. 10^3 - 10^-1 seconds
2. Indicates that folding is directed

Question 10

What did Anfinsen’s experiment discover?

Answer 10

Discovered that the primary sequence of proteins dictated the secondary and tertiary structure

Question 11

What was the Anfinsen Experiment?

Answer 11

A series of experiments were conducted on Ribonuclease A

Question 12

Angle combinations that are not possible are due to…

Answer 12

Steric hindrance

Question 13

What is a protein’s folded state known as?

Answer 13

Native structure

Question 14

Anfinsen Experiment rationale:

1. What stabilizes a protein’s folded state?
2. What should lead to the protein unfolding?
3. How is this done? (protein unfolding)

Answer 14

1. Disulfide bonds
2. Reducing
3. With β-mercaptoethanol

Question 15

Anfinsen Experiment rationale:

When β-mercaptoethanol was applied, what happened?

Answer 15

Unfolding did not occur fully

Question 16

Anfinsen Experiment rationale:

What had to be present in order for full protein unfolding to occur?

Answer 16

Urea or Guanidine

Question 17

Anfinsen Experiment rationale:

Denaturing agents disrupt…

Answer 17

Non-covalent interactions

Question 18

Anfinsen Experiment rationale:

How does urea break secondary structures?

Answer 18

Form H-bonds with the amino acid backbones

Question 19

Anfinsen Experiment rationale:

To allow the protein to re-fold, how was urea and β-mercaptoethanol removed?

Answer 19

Dialysis

Question 20

Anfinsen Experiment rationale:

Describe dialysis

Answer 20

Involves a semi-permiable membrane that allows some molecules to move from a place of high concentration to low concentration while others remain

Question 21

Anfinsen Experiment rationale:

1. What was the result from dialysis?
2. What does this mean?

Answer 21

• Protein did not re-fold correctly
• Only 1% of activity was recovered
• Means there must be assisted folding

Question 22

Unfolded proteins have…

Answer 22

1. High free energy
2. High entropy

Question 23

What is entropy?

Answer 23

Measure of disorder

Question 24

True or False:

There is only one possible folded state for a protein

Answer 24

False, there are many possible folded intermediate states

Question 25

Which folded state has the lowest free energy?

Answer 25

The native structure

Question 26

The energy difference between transition states and native strucutre…

Answer 26

Large

Question 27

Transition states are the —– in the graph

Answer 27

Peaks

Question 28

What does the large energy gap between transition states and native structure ensure?

Answer 28

Ensures protein unfolding does not occur

Question 29

True or False:

Proteins smoothly fold

Answer 29

False, they can get “stuck” in energy wells

Question 30

What assists in protein folding? How?

Answer 30

Chaperones
* Bind to exposed hydrophobic areas

Question 31

What do chaperone proteins ensure?

Answer 31

• Ensure that improperly folded proteins don’t aggregate
• Mis-folded proteins are degraded by the proteosome