Lecture 7 - Protein Folding

Question 0

Name the charged amino acids that can have ionic interactions

Answer 0

Aspartate (-)
Glutamate (-)
Arginine (+)
Lysine (+)
Histidine (+)

Question 1

Name the polar amino acids that can hydrogen bond

Answer 1

Serine
Threonine
Asparagine
Glutamine

Question 2

Name the nonpolar amino acids that can have hydrophobic interactions

Answer 2

Alanine
Valine
Leucine
Isoleucine
Methionine
Tryptophan 
Phenylalanine

Question 3

What kind of interactions operate over short distances?

Answer 3

Van der Waals interactions

Attractive force is proportional to (distance)^-6

Question 4

True or false? Van der Waals interactions results from the overlap of long-lived highly fluctuating dipoles of non-bonding electron orbitals

Answer 4

FALSE.

Short-lived

Question 5

True or false? Inside the densely packed protein interior, numerous van der Waals interactions sum up and contribute to the stability of a folded protein

Answer 5

True

Question 6

What facilitates dance packing in van der Waals interactions?

Answer 6

Availability of hydrophobic side chains (R groups) of many shapes and sizes

Question 7

What kind of interaction explains why seemingly conservative substitutions of one hydrophobic side chain with another can greatly affect protein stability

Answer 7

Van der Waals

Question 8

True or false? Protein folding increases interactions between the protein and water.

Answer 8

FALSE.

decreases not increases

Question 9

True or false? Hydrogen bonding is a driving force for protein folding because H-bonds with water are broken to make intramolecular H bonds

Answer 9

FALSE

It is NOT a driving force

Question 10

True or false? H bonding changes did not affect free energy much.

Answer 10

TRUE, because the formation of extended H bond networks (especially in α-helices or β-sheets) compensate for loss of AA-water bonds

Question 11

What kind of interaction is a major contributor into protein folding and stability?

Answer 11

Hydrophobic interactions

Question 12

True or false? Proteins fold with hydrophobic residues on the interior.

Answer 12

True

Question 13

Does protein folding increase or decrease the entropy of the protein water system?

Answer 13

Protein folding increases entropy of the protein-water system because water is less ordered (ΔS is positive)

Question 14

Once a protein folds, the protein structure can be stabilized by the formation of what kind of bond?

Answer 14

Disulfide bonds (-S-S-) between sulfhydryls (-SH) of cysteine

Question 15

What is the -S-S- covalent bond energy?

Answer 15

200-800 kJ/mol

Question 16

What denatures or unfolds proteins?

Answer 16

Organic solvents, urea, detergents, and heat

Question 17

True or false? Some proteins can spontaneously refold into native 3-D structure

Answer 17

True

Question 18

True or false? Ribonuclease A can be denatured and renatured.

Answer 18

True

Question 19

Formation of some secondary structures (α-helices and β-sheets) leading to an intermediate structure

Answer 19

Nucleation

Question 20

Name the status of protein folding in model one

Answer 20

Nucleation, structural consolidation to form intermediate state, final rearrangements

Question 21

Continued formation of secondary structure and beginnings of tertiary structure to give higher level intermediate structures

Answer 21

Structural consolidation to form intermediate states

Question 22

All basic elements in place and final adjustments for a fully functional protein. What stage of protein folding?

Answer 22

Final rearrangements state

Question 23

How does protein folding occur according to the second model?

Answer 23

Formation of compact state due to hydrophobic interactions.
Compact state called “molten globule”
Structure grows out of this collapsed state

Question 24

Helper proteins that assist polypeptide folding into native structure (or prevent improper folding or aggregation)

Answer 24

Chaperonins

Question 25

Example of a molecular chaperone

Answer 25

GroEL-GroES complex

Question 26

What is spongiform encephalopathy also known as?

Answer 26

Mad cows disease

Question 27

Where is prion found?

Answer 27

In the central nervous system