13.3c Protein Structure – Denaturation

13.3c Protein Structure – Denaturation


When we look at protein structure we are also worried about denaturation of proteins and the ways in which proteins can become denatured. When we look at proteins, we’ve seen that they have primary, secondary, tertiary, and quaternary structure. In order for a protein to function correctly it must maintain all four levels of structure. If any of those levels of structure are disturbed the protein can no longer do its job. For example, when we move on to enzymes, which are just proteins with a specific function, we’ll see that they cannot catalyze the necessary reaction. And so approaching denaturation occurs in several ways. In something that’s going to interfere with something about the structure of that protein. And the things that we see most often that affect that structure are the following: if we heat something up, remember those interactive forces between those parts of the protein are fairly weak, just like our intermolecular forces were fairly weak, those are weak and so it’s fairly easy, with a little bit of heat, to break them apart. Agitation will also break those apart. When you’re beating eggs you’re agitating those and what you’re really doing is starting to break down some of the proteins in that egg. If we put a heavy metal in there because it interferes with some of the interactions that are happening between different parts of the protein, a strong acid or base because it’s going to start producing H+ or OH- and water that are going to interfere with those interactions, and also the change in pH will cause some of those interactions to break. Detergent can also break those interactions. So this is why we use detergent to wash our clothes. A lot of stains that we get on our clothing are from proteins and so detergent helps break down those proteins and hopefully get them out of your clothes. And ionic compounds can also do this, so something like sodium chloride or table salt, if we add that to certain proteins it will start to break them down because in the presence of those ions they’ll dissociate and those ions, that Na+ and the Cl-, will start to interact with different portions of the proteins and interfere with those interactions. One way to think about this is a paperclip. If here on the left we have a paperclip that is perfectly formed and it functions just fine as a paperclip, if it were denature what we’d see is the paper clip starts to bend and twist around and the protein or the paper clip in this case no longer functions as it should. So even though it still has the same basic sequence, if we follow along the sequence of our paper clip we still the the basic structure, that primary structure is the same, the secondary structure and the tertiary and quaternary structure are not and therefore it’s no longer going to function correctly. And we see the same thing happening with our proteins; that when we look at denaturation we’re looking at secondary, tertiary, and quaternary structures being disrupted. So for denaturation we’re affecting these levels of structure. Remember these are peptide bonds, for secondary structure we have hydrogen bonding, and for both tertiary and quaternary structure we see things like our ionic bonds or ionic forces, we see the disulfide bridges, we see hydrogen bonding, the hydrophobic interactions. And those, which are holding together both the tertiary and the quaternary structure, are going to be disrupted or disturbed by any of those things that will result into denaturation of a protein. And the protein, like hemoglobin, depends on all levels of structure to function correctly, that if we take away just one piece of that structure it’s not going to be able to do its job correctly. So does denaturation break peptide bonds? Hopefully you said no. Remember that peptide bonds are in the primary structure, so there’s were the peptide bonds are, and when we start to look at denaturation we’re looking at breaking those interactive forces between different parts of the protein and not breaking actual chemical bonds. What levels of structure are affected by denaturation? So what we see is that our secondary, and we sometimes abbreviate this as two with the little prime there, tertiary and quaternary structure are the ones that are affected because these are the ones that are kind of assembled by those interactive forces, not by bonds. Remember that we call hydrogen hydrogen bonding, but it’s not truly a bond.

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