Which bonds make up different degrees of protein structure?

[kyldishgambino]

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Quick question, I'm getting mixed results on internet

what bonds dictate up second vs tertiary vs quaternary

I know (or think I know) that secondary is mainly hydrogen bonding because these dictate alpha helices and beta sheets and then tertiary is mainly disulfide bonds and salt bridges and then quaternary can be disulfide bonds to bind other subunits together. However my understanding is that salt bridges are formed via hydrogen bonds so I just want to get it all straight so when I get a question asking about beta mercaptoethanol(disrupts disulfide bridges) and what protein structure it disrupts I don't get tripped up.

I also read that increasing the salinity can have a negative effect on an enzyme because it messes up the hydrogen bonds which result is a loss of tertiary structure... which is where I get confused because I mainly think secondary structure when I read hydrogen bonds

thanks

 

[aldol16]

Salt bridges have both a hydrogen-bonding component and an electrostatic component. Basically, there is a migration of a proton which results in charge separation and thus electrostatic interactions. The migrated proton can also hydrogen bond. Disulfides will mess up whichever structures have disulfide bonds, which will be found in tertiary and quaternary structures.

You should not conceptualize each level of structure as classified by the bonds it contains. The same interactions can span multiple levels of structure. Instead, you should think about each level of structure as what is being held together. In primary structure, it's the free amino acids that are being held together. Secondary structure holds together basic 3D forms of those free amino acids such as helices and beta sheets. Tertiary structure is the sum of all the secondary structures in a unit. And quaternary structure holds multiple subunits of a protein together. The same interactions can have effects on all levels of structure.

Salts can disrupt structures because they compete with ionic protein side chains for binding. So if you have two subunits held together by a bridge between Asp and Arg, that can be disrupted at higher salt concentrations by Asp pairing with a cation and Arg pairing with an anion. That would disrupt that bridge. Similar bridges might also hold an alpha helix together, for example. In fact, if you increase the salinity of the solution by too much, you could denature the protein or cause it to crash out of solution. What happens in the latter case is the salt ions strip off the water solvation layer around the protein, causing the protein to precipitate, or salt out, from solution.