How does urea disrupt the secondary structure of proteins?

[sillyjoe]

In labs, why do they use urea to denature proteins? By what mechanism?

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[pepocho]

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[sillyjoe]

MCAT-wise, who cares? mechanism are not important for the MCAT, unless provided to you, I doubt you will need to know why it does so. Just implant it in your memory that it does so.

However, if you are truly curious, I am sure someone knows 😉

I do not mean mechanism in the orgo sense. I mean how does it do it.

 

[pepocho]

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[sillyjoe]

Oh sorry, I hope I understood what you meant. Urea screws up hydrogen bonds within the protein, causing changes in the secondary and tertiary structure.

A good tip is just to remember that when they say denature a protein, they mean that the secondary and tertiary structure has been messed up, which more than likely means that the hydrogen bonds have been messed up (pretty sure there is more ways to mess up secondary structures, but I cannot recall from the top of my head, hydrogen bonds is by the far the most important though)

But how though, what about the structure of urea causes it to denature?

 

[Chrisz]

In labs, why do they use urea to denature proteins? By what mechanism?

I do not know how exactly why they use urea in the lab to denature protein but I would like to take a guess. Urea has a pKa of 0.1. It would certainly dissolve some dergree in water to lower its pH. One the pH is lowered to a certain degree, some of its side groups which were not protonated at a neutral pH and get protonated at a lower pH. This would definitely change the structure of the protein.

 

[pepocho]

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[deleted647690]

In labs, why do they use urea to denature proteins? By what mechanism?

Urea is used to disrupt hydrogen bonding; thus, it disrupts the secondary structure; the hydrogen bonds between the amides and carbonyls of the backbone

 

[aldol16]

@acetylmandarin has the right thinking here. Think of backbone H-bonding. You learn that H-bonding is mediated by the backbone amide N-H protons. Urea contains four such amidic protons and a carbonyl to accept H-bonds. So it'll basically replace backbone-backbone interactions with backbone-urea interactions, which unfolds the protein.

 

[Lawpy]

@acetylmandarin has the right thinking here. Think of backbone H-bonding. You learn that H-bonding is mediated by the backbone amide N-H protons. Urea contains four such amidic protons and a carbonyl to accept H-bonds. So it'll basically replace backbone-backbone interactions with backbone-urea interactions, which unfolds the protein.

Yeah this is accurate. For further information, see:

Protein denaturation by urea: Slash and bond

Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group