Chapter Four: The three dimensional structure of proteins (Includes lecture) Flashcards
What factors can cause denaturation of a protein?
1) Heat or cold, 2) pH extremes, 3) organic solvents, 4) Chaotropic agents (Urea and guanidium hydrochloride.
Chaotropic agent
disrupts hydrogen bonds, especially in water
Native proteins
Proteins in any of their functional, folded conformations.
Why are disulfide bridges more powerful buried in a protein structure?
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.
The alpha helix
1) The simplest arrangement a polypeptide can assume that maximizes the use of internal hydrogen bonds. 2) R groups protrude outward.
How many residues are there per turn of amino acids?
1) 3.6 residues per turn spanning 5.4å 2) rise for each residue 1.5å
Which amino acid is most likely to make an alpha helix?
Alanine
What two amino acids constrain the formation of the alpha helix?
Proline and Glycine
What factors affect alpha helix stability?
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
Beta sheet
The arrangement of several segments side by side, all in the beta conformation
B conformation
conformation of polpeptide chains are extended in a zig-zag rather than a helix
Beta turns
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.
What are the three types of secondary structures peptides form?
alpha helices, b conformations, b sheets.
What are some properties that are associated with fibrous proteins?
insoluble in water; give strength and/or flexibility; give/have hydrophobic amino acids on exterior
Motif
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
Domain
Part of a polypeptide chain that is independently stable or could undergo movements as a single entity w/respect to the entire protein.
What are the two chaperone families?
Hsp70 and chaperonins
Protein disulfide isomerase
PDI; catalyzes the interchange, or shuffling of disulfide bonds until the bonds of the native conformation are formed; eliminates intermediates w/ inappropriate disulfide linkages.
Amyloid Fiber
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.
Unfolded protein response
goal is to manage inadequate folding. Response, increase the amount of chaperones in the ER, decrease protein synthesis.
Autophagy
the process by which unfolded proteins are degraded after a vesicle engulfs it after docking with a cytosolic lysosome.
Isoelectric point calculation
PI = 1/2 (Pk1 + Pk2)
How do we calculate the amount of amino acids in a protein?
Divide by 110
What are the two ways that disulfide bridges can be degraded?
1) Oxidation of cystine with performic acid 2) reduction by dithiothreitol
