Chapter 6: Protein Folding, Tertiary Structure, Fibrous Proteins Flashcards
what does it mean to say that a molecule is a ‘dimer’?
it means the molecule or molecular complex consists of two identical molecules linked together.
what is a globular protein?
a compact (relatively spherical) protein that is water soluble and usually involved in stuff like metabolism.
what secondary structures can a globular protein fold into?
alpha helix
beta sheet
what protein/enzyme did Christian Anfinsen study?
Ribonuclease A (RNase A)
Why does Dr Shimko wish Anfinsen had studied a different protein instead of RNase A?
Because the (RNase A) protein that Anfinsen picked is one of the few proteins that has disulfide bonds (and this extra feature makes them harder for students to learn about)
what is a chaotrope?
a small molecule that denatures proteins
what do we use instead of chaotropes?
SDS Page
what are 2 of the common chaotropes?
Urea and Guanidinium chloride
How do chaotropes work?
They steal attention/attraction away from water
water breaks bonds with protein to join the chaotrope; this causes the protein to lose its shape
Do chaotropes work at any old concentration?
No! They must be present at high concentrations.
What was the gist of Anfinsen’s experimental method (in 2 sentences)?
Anfinsen used chaotropes to denature proteins. When he removed the chaotropes, the proteins spontaneously refolded.
What were the 2 major conclusions of Anfinsen’s Denaturation Experiments?
- Proteins spontaneously fold into their native conformation, without facilitation from the cell
- The native conformation of a folded protein is the most thermodynamically favored form
(If the functional state of the protein is the state you arrive at when the protein is at it’s lowest energy, the functional state must be the native state)
what causes proteins to fold?
the hydrophobic effect
what causes proteins to adopt any given shape?
hydrogen bonding
Why did Anfinsen choose RNase A for his protein experiment?
given the tech he had, RNase A was the easiest to work with:
it was easy to get in its natural abundance (from cow pancreas)
it was easy to identify
it was easy to purify into high yields
its activity was easy to detect (experimentally)
What does RNase A do?
it hydrolyzes RNA
it splits up RNA/nucleotide chains into their individual nucleotides by breaking the RNA’s phosphodiester backbone
How did Anfinsen detect the activity of his RNase A?
He’d look to see how thick or thin the RNase A appeared.
RNase A looks thick/viscous when it’s Inactive.
RNase A looks thin when it’s active (the work of breaking up nucleotide chains makes it look thin)
What question was Anfinsen trying to answer when he did his RNase A experiments?
Can proteins fold on their own or do structures/machinery in the cell make them fold?
What were the main 4 steps in Anfinsen’s protein folding experiment?
- purify the protein (outside of the cell)
- denature the protein (with chemicals)
- check the protein’s activity (by thickness)
- try to get the inactive protein to be active again without putting it back in the cell
Why does the RNase A from Anfinsen’s experiment have disulfide bonds?
Because RNase A is a secreted protein that exists outside the cell (in the oxidizing environment) and subsequently has disulfide bonds that other proteins we study do not have.
Is RNase A particularly stable?
Yes. This is part of the reason Anfinsen used it in his experiments
Are Urea and Guanidinium chloride polar chaotropes or NON polar chaotropes?
VERY polar
Why did Anfinsen have to do a control experiment?
To prove that the inactive proteins he renatured really were inactive.
What is a/the hydrophobic collapse?
It’s what happens when a protein gets to be a certain size and its hydrophobic start coming together into what will become the protein’s hydrophobic core.
This process releases caged water
How do proteins fold?
The protein gets made, the hydrophobic effect causes the hydrophobic collapse create the beginning of a hydrophobic core, the molten globule state is adopted, and then the final, most energetically favorable shape is settled upon.
what is a molten globule?
Molten globules are partially folded proteins that have some characteristics of both folded. (or ‘native’) and unfolded proteins.
They represent a transition state between unfolded and fully folded protein
When you see the (y) energy axis of a protein folding funnel, does it represent the energy of the protein or the energy of the system?
BOTH! It represents/INCLUDES the energy of the protein and the system.
What does a protein folding funnel show you?
the thermodynamics of protein folding
Why is the overall energy (of the total system) so high when the protein is completely unfolded?
The caged water around the protein’s exposed hydrophobic regions make the energy high
(more caged water = less entropy)
