Chapter Four: The three dimensional structure of proteins (Includes lecture)

Question 1

What factors can cause denaturation of a protein?

Answer 1

1) Heat or cold, 2) pH extremes, 3) organic solvents, 4) Chaotropic agents (Urea and guanidium hydrochloride.

Question 2

Chaotropic agent

Answer 2

disrupts hydrogen bonds, especially in water

Question 3

Native proteins

Answer 3

Proteins in any of their functional, folded conformations.

Question 4

Why are disulfide bridges more powerful buried in a protein structure?

Answer 4

Disulfide bonds increase in strength as the move to regions with lower dielectric points. Ionic bonds are important, because they are strong and limit structural flexibility.

Question 5

The alpha helix

Answer 5

1) The simplest arrangement a polypeptide can assume that maximizes the use of internal hydrogen bonds. 2) R groups protrude outward.

Question 6

How many residues are there per turn of amino acids?

Answer 6

1) 3.6 residues per turn spanning 5.4å 2) rise for each residue 1.5å

Question 7

Which amino acid is most likely to make an alpha helix?

Answer 7

Alanine

Question 8

What two amino acids constrain the formation of the alpha helix?

Answer 8

Proline and Glycine

Question 9

What factors affect alpha helix stability?

Answer 9

1) Pro/Gly (inhibits) 2) Charge of residues (repulsion/attraction) 3) Alanine (promotes formation) 4) Positive AAs need to be at carboxyl end, Negative AAs need to be at the amino end

Question 10

Beta sheet

Answer 10

The arrangement of several segments side by side, all in the beta conformation

Question 11

B conformation

Answer 11

conformation of polpeptide chains are extended in a zig-zag rather than a helix

Question 12

Beta turns

Answer 12

connect the ends of two segments of b sheets, 180˚ turn involving four amino acid residues. Glycine and Proline are the biggest promoters of b turns. G, because it is flexible; P, because readily forms the cis configuration, which promotes the formation of b turns.

Question 13

What are the three types of secondary structures peptides form?

Answer 13

alpha helices, b conformations, b sheets.

Question 14

What are some properties that are associated with fibrous proteins?

Answer 14

insoluble in water; give strength and/or flexibility; give/have hydrophobic amino acids on exterior

Question 15

Motif

Answer 15

Fold/ super secondary structure; recognizable folding pattern involving two or more elements of secondary structure and the connections between them. example: b-a-b loop

Question 16

Domain

Answer 16

Part of a polypeptide chain that is independently stable or could undergo movements as a single entity w/respect to the entire protein.

Question 17

What are the two chaperone families?

Answer 17

Hsp70 and chaperonins

Question 18

Protein disulfide isomerase

Answer 18

PDI; catalyzes the interchange, or shuffling of disulfide bonds until the bonds of the native conformation are formed; eliminates intermediates w/ inappropriate disulfide linkages.

Question 19

Amyloid Fiber

Answer 19

Insoluble extracellular fiber; highly ordered and unbranched high degree of B sheet structure; B sheet ordered perpendicular to the axis of the fiber; in amyloidoses, aromatic amino acids are at the core region of the b sheet, alpha helix, and b turn.

Question 20

Unfolded protein response

Answer 20

goal is to manage inadequate folding. Response, increase the amount of chaperones in the ER, decrease protein synthesis.

Question 21

Autophagy

Answer 21

the process by which unfolded proteins are degraded after a vesicle engulfs it after docking with a cytosolic lysosome.

Question 22

Isoelectric point calculation

Answer 22

PI = 1/2 (Pk1 + Pk2)

Question 23

How do we calculate the amount of amino acids in a protein?

Answer 23

Divide by 110

Question 24

What are the two ways that disulfide bridges can be degraded?

Answer 24

1) Oxidation of cystine with performic acid 2) reduction by dithiothreitol