Lecture 7 - Protein Folding Flashcards Preview

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Flashcards in Lecture 7 - Protein Folding Deck (28):
0

Name the polar amino acids that can hydrogen bond

Serine
Threonine
Asparagine
Glutamine

1

Name the charged amino acids that can have ionic interactions

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

2

Name the nonpolar amino acids that can have hydrophobic interactions

Alanine
Valine
Leucine
Isoleucine
Methionine
Tryptophan
Phenylalanine

3

What kind of interactions operate over short distances?

Van der Waals interactions

Attractive force is proportional to (distance)^-6

4

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

FALSE.
Short-lived

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

True

6

What facilitates dance packing in van der Waals interactions?

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

7

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

Van der Waals

8

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

FALSE.
decreases not increases

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

FALSE

It is NOT a driving force

10

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

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

11

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

Hydrophobic interactions

12

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

True

13

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

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

14

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

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

15

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

200-800 kJ/mol

16

What denatures or unfolds proteins?

Organic solvents, urea, detergents, and heat

17

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

True

18

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

True

19

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

Nucleation

20

Name the status of protein folding in model one

Nucleation, structural consolidation to form intermediate state, final rearrangements

21

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

Structural consolidation to form intermediate states

22

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

Final rearrangements state

23

How does protein folding occur according to the second model?

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

24

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

Chaperonins

25

Example of a molecular chaperone

GroEL-GroES complex

26

What is spongiform encephalopathy also known as?

Mad cows disease

27

Where is prion found?

In the central nervous system