There's reasons for why proteins go from nice long strands of stuff to more compact folded things. The first part of it is conformational entropy... The -deltaS in this case makes a positive contribution because you're going from a very random thing to a much less random thing, which means entropy is technically working against folding.
But despite that, the thing still folds. That means deltaG must still be negative. So that means this happens because deltaH must be very negative, which comes from the nice interactions that happen between the amino acid side chains in the folded thing.
Another thing going on in protein folding is charge-charge interactions. This comes from charged side chains that might form bridges. However, if pH changes, the side chains might lose their charge, breaking the ionic bonding between them, which would then contribute to denaturing the folded thing.
The next factor to look at is internal hydrogen bonding between side chain. Side chains with OH, NH2, etc are the ones that can participate in non-covalent *technically* bonding interactions.
If we go back far enough in our biochemistry memory map, we can maybe remember that neutral-neutral interactions (induced dipoles) are the strongest if the interaction is physically close enough, which is what I guess happens here. The non polar groups in the protein, when they pack in densely enough, will contribute to a more stable protein. The folding up of the protein also reduces any favorable interactions that the chains may have with solvent...the unfolded chain may have residues that CAN interact nicely with water.
So, looking at the enthalpy changes going from unfolded to folded, we see that the type of non covalent bonding changes..you go from interactions between the open chain and the solvent to interactions within the chain.
*Sort of * along those lines, there's disulfide bonds. They're usually the only covalent bonds that are going to form when a protein folds up, and the sentence is BLUE is very important because although disulfide bonds contribute to enthalpy, they have more entropic effects.
Final consideration for us is the hydrophobic effect. Myoglobin is actually stabilized by it.
When you have hydrophobic residues in contact with the solvent in open chain form, you get those CLATHRATES that we talked about in chapter...3? 2? oh, who remembers?
Anyway, when you form clathrates, water gets ordered around stuff that it doesn't really want to be around, which is bad for entropy.
So when you have an unfolded protein with lots of crappy clathrates going to a folded thing where all the hydrophobic shit is inside...I'd say that frees up some of those unhappy water molecules. That's pretty good times.
Disulfide bonds are like the one girlfriend you had in high school..you're going to keep talking about her. In Bovine pancreatic trypsin inhibitor, we have three of them. BPTI is pretty hard to denature but putting it in really acidic stuff at temperatures above 100degreesC is going to get the job done. Eventually.
HOWEVER. If you cleave just ONE of those little suckers, you can start denaturing that shit at like...
...a much lower temperature !
In short, if you have disulfide bonds, you've got less conformational entropy in your unfolded state than if you don't have disulfide bonds....there's just less shapes for you to be in when you're all connected like that. Disulfide bonds are typically found in proteins that get taken out of the cell (RNase, BPTI, Insulin...)... In the cell you've got a reducing environment ... which...HELLO? Would reduce that shit. But outside the cell, you've got an oxidizing environment which is actually going to help stabilize those -S-S-'s
Chaperones keep proteins from getting into trouble..
Like this mess of an example..
A summary of what happens.
A short summary slide to help you remember which amino acids are going to be predominantly present in which things. I'm especially proud of the vampires.
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