Lecture 4: tert. structure and protein purification Flashcards
which structure determines the complete 3D structure of a polypeptide chain?
tertiary structure
most influential factor in protein folding
hydrophobic effect
what types of H-bonds stabilize the tertiary structure? (3)
H-bonds between:
- side chain-to-side chain groups
- side chain-to-backbone group
- backbone group-to-backbone group
how does the hydrophobic effect stabilize the tertiary structure?
- interior packing of hydrophobic residues contributes to favorable ∆S and ∆H
- ∆S (+) because water is at a higher concentration than the protein and water is boss
- ∆H (-) = favorable enthalpy from VDW interactions helps develop a -∆G
removing urea from a protein allows ____
allows for VDW and H-bonding interactions to take over and complete protein folding
what order results in correct protein folding? (of oxidizing and removing urea)
remove urea first then oxidize
what does oxidation do to a denatured protein?
oxidizing reforms disulfide bonds
protein in the denatured state is (high/ low) entropy and (high/ low) entropy in the folded state
protein in the denatured state is high entropy and low entropy in the folded state
how do you remove the targeted protein in affinity chromotography?
adding free histidine or imidazole will displace the protein
SDS is a ___ molecule and does what?
SDS is an amphipathic molecule and allows proteins to be separated based on approximate mass
why do you use a reducing agent in SDS PAGE process?
break disulfide bonds
for SDS PAGE: no matter what the charge was before, the protein completely unfolds and becomes ____ charged
becomes negatively charged
for SDS PAGE: larger will stop at the ____, smaller at the ____; which moves through faster?
larger will stop at the top, smaller will stop at the bottom; smaller proteins will move through faster
for gel filtration chromatography: what are the rates that proteins pass through the column?
big proteins go through faster, smaller proteins move slower
