Lecture 7 - Protein Folding Flashcards
Name the charged amino acids that can have ionic interactions
Aspartate (-) Glutamate (-) Arginine (+) Lysine (+) Histidine (+)
Name the polar amino acids that can hydrogen bond
Serine
Threonine
Asparagine
Glutamine
Name the nonpolar amino acids that can have hydrophobic interactions
Alanine Valine Leucine Isoleucine Methionine Tryptophan Phenylalanine
What kind of interactions operate over short distances?
Van der Waals interactions
Attractive force is proportional to (distance)^-6
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
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
What facilitates dance packing in van der Waals interactions?
Availability of hydrophobic side chains (R groups) of many shapes and sizes
What kind of interaction explains why seemingly conservative substitutions of one hydrophobic side chain with another can greatly affect protein stability
Van der Waals
True or false? Protein folding increases interactions between the protein and water.
FALSE.
decreases not increases
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
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
What kind of interaction is a major contributor into protein folding and stability?
Hydrophobic interactions
True or false? Proteins fold with hydrophobic residues on the interior.
True
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)
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
What is the -S-S- covalent bond energy?
200-800 kJ/mol
What denatures or unfolds proteins?
Organic solvents, urea, detergents, and heat
True or false? Some proteins can spontaneously refold into native 3-D structure
True
True or false? Ribonuclease A can be denatured and renatured.
True
Formation of some secondary structures (α-helices and β-sheets) leading to an intermediate structure
Nucleation
Name the status of protein folding in model one
Nucleation, structural consolidation to form intermediate state, final rearrangements
Continued formation of secondary structure and beginnings of tertiary structure to give higher level intermediate structures
Structural consolidation to form intermediate states
All basic elements in place and final adjustments for a fully functional protein. What stage of protein folding?
Final rearrangements state
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
