- Proteins questions
- Amino acid structure
- Alpha amino acid synthesis
- Classification of amino acids
- Peptide bonds: Formation and cleavage
- Four levels of protein structure
- Conformational stability: Protein folding and denaturation
- Non-enzymatic protein function
Created by Tracy Kim Kovach.
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- At5:05when she talks about adding acid, why doesn't it disrupt secondary structure?(8 votes)
- As my friend Yverahderah mentioned earlier, the tertiary and quaternary structures are characterised by ionic bonding or salt bridge formation, whereas in secondary structure, molecules are likely to just have "affinities". To humanize it with an example:
Secondary structure is like 2 characters (opposite in nature) having a crush on each other, i.e. no interactions, just a strong affinity which cannot be broken by external force.
Tertiary and quaternary structures is if 2 people are close enough interact and form a bond (in this case commitment=ionic bond), they have something to lose by interventions from external factors, like ex-girlfriends or teachers or society.(11 votes)
- Why would tempurature not affect primary structure?(6 votes)
- Temperature only breaks down the hydrogen bonds, thus separating secondary, tertiary, and quarternary structures back into primary structures, since all those structures are held together by hydrogen bonds However, temperature cannot break the peptide bonds that hold the amino acids together in the primary structure, thus they are unaffected. Enzymes however, can break these peptide bonds.(8 votes)
- I thought the definition of denaturation was that there is a disruption to a protein shape while maintaining the peptide bonds intact?
(At least thats what i read form the MCAT 2015 review.)
So wouldn't proteins just be disrupted by extreme ph, temperature, and tonicity? and not my enzymes?(6 votes)
I would say that you are correct, as the idea of protein denaturation is the disruption of its three dimensional conformation. The pH change does not necessarily need to be extreme to change the conformation of a protein. Think of lysozymes. They are active in the pH of the lysosome, but quickly denature and inactivate should they escape into the cytosol. It is a self protective measure that the cell has evolved to not be digested should a lysozyme burst.
While enzymatic hydrolysis is not necessarily denaturation, the point of mentioning it is to show that the primary structure, i.e. the covalent bonds between aa residues are durable and are not easily broken.(4 votes)
- At6:20she says that ethanol would disrupt the H-bonds of the protein, thus disrupting the secondary through quaternary structure of the protein. Why does ethanol disrupt the H-bonds?(4 votes)
- Ethanol's chemical structure is CH3CH2OH. Hydrogen bonding occurs between the electronegative atoms Nitrogen, Oxygen, and Fluorine and the Hydrogen atoms covalently bonded to N, O, and F, making the H partially positive. Ethanol, having an -OH group is able to form hydrogen bonds, so it completes with the hydrogen bonds formed in the protein.
So you may ask, why doesn't water do this too, and I would have to go back to the inductive effect that the ethyl group CH3CH2- has on the Oxygen. The ethyl group is able to donate electron density to the oxygen atom, making it slightly more partially negative than the O in water. This is likely enough of an effect to disrupt the hydrogen bonds of the protein, while water does not. Also remember the effect of Hydrophobic packing in relation to protein folding. In water, the hydrophobic residues are tucked away on the inside of the protein and the energy to have them exposed to water is greater than the energy need to keep the protein denatured. However, ethanol is an organic solvent, and while it is a polar molecule, it also has the ethyl group which allows it to interact with the hydrophobic residues as well.(7 votes)
- Hi Tracy! Thank you SO much- your videos are so fantastic! I am so grateful!! I was just confused because I thought that the primary structure of a protein was always conserved but then at the end you mentioned that enzymes can denature the primary structure, so I was just wondering about that! Thank you so much for your time and help!! :)(3 votes)
- You are correct. Denaturation involves secondary up to quartenary structure of a protein and doesn't involve the protein's primary structure. There are proteases, like trypsin and chymotrypsin, that can cleave the peptide bond to alter the protein's primary structure. Acid with suffcient heat can also work to break amino acids apart.(5 votes)
- What does it mean when denaturation can be reversible and irreversible? Would it be possible to provide examples as well? Thank you.(2 votes)
- Successful refolding is also dependent upon the protein's size and characteristics (e.g. quaternary conformation). Some proteins can be denatured by guanidinium chloride and then refolded through dilution of the guanidinium chloride.
SDS is a harsh detergent (labeled "sodium lauryl sulfate" on your soap products) that unravels proteins and confers a dominant negative charge. Protein mixtures will migrate on SDS-PAGE solely based on the proteins' molecular weights, rather than a combination of their MW's, individual shapes and charges.(5 votes)
- Are there situations in with the primary structure is disrupted? Can you provide an example?
Also, this was probably answered when you discussed Alzhiemer's but are there ways to regenerate proteins once they have become denatured?
This is a third, and semi unrelated question... Since you provided us with the example of the egg, I began to think about the nutritional value of the egg/other foods, and the point at which they start to lose their "nutritional value". Does that refer to proteins as wells as vitamins and minerals? Thanks.
- I understand your concerns regarding nutritional value, Danielle.
The nutritional value of the egg does not lower when you cook it. It only makes it easier for your cells to digest the protein. If you just broke the egg and drank the yolk (btw do not do try this at home cause its yuck and gross) the exact same amount of vitamins and minerals will go in to your digestive system, but it will take longer for you to digest the content, because your stomach will have to degrade every albumin (the egg protein) and vitamin to its basic form, and this will cause your stomach to try harder and increase its pH level, then act on the egg with its enzyme. This will cause you a little gastric distress. but either way you'll degrade the protein to its most basic units. so basically. If you cook it right, there will be no loss of nutrition, what so ever.(2 votes)
- what is the chemical structure of enzymatic protein(2 votes)
- Tracy, you mentioned that increasing a temperature destroys all but the primary structure of the protein. What about decreasing a temperature?(2 votes)
- This is a really neat question!
I'm pretty sure you would have unfolding/denaturation as well.
The cold temperature causes the polypeptide chains to unfold, and causes non-polar groups to interact with water. Thus, hydrophobic groups that are normally hidden in protein structure are exposed to the water. This causes aggregation of the chains and precipitation.(2 votes)
- Adding a chemical to a protein should be able to change its primary structure right? (Depending on the chemical)(2 votes)
- If that chemical cleaves the amino acids, then yes it will change its primary structure ( Common examples are Trypsin, Chymotrypsin, Elastase). However, a chemical will change its primary structure only if it cleaves are substitutes amino acids (cleavage is much more common).(1 vote)
Let's talk about conformational stability and how this relates to protein-folding and denaturation. So first, let's review a couple of terms just to make sure we're all on the same page. And first, let's start out with the term conformation. And the term confirmation just refers to a protein's folded, 3D structure, or in other words, the active form of a protein. And next we can review what the term denatured means when you're talking about proteins. And denatured proteins just refer to proteins that have become unfolded, or inactive. So all conformational stability is really talking about are the various forces that help to keep a protein folded in the right way. And these various forces are the four different levels of protein structure, and we can review those briefly right here. So recall that the primary structure of a protein just refers to the actual sequence of amino acids in that protein, and this is determined by a protein's peptide bonds. And then next, you have secondary structure, which just refers to the local substructures in a protein. And they are determined by backbone interactions held together by hydrogen bonds. Then you have tertiary structure, which just talks about the overall 3D structure of a single protein molecule. And this is described by distant interactions between groups within a single protein. And these interactions are stabilized by van der Waals interactions, hydrophobic packing, and disulfide bonding, in addition to the same hydrogen bonding that helps to determine secondary structure. And then quaternary structure just describes the different interactions between individual protein subunits. So you have the folded-up proteins that then come together to assemble the completed, overall protein. And the interaction of these different protein subunits are stabilized by the same kinds of bonds that help to determine tertiary structure. So all of these levels of protein structure help to stabilize the folded-up, active confirmation of a protein. So why is it so important to know about the different levels of protein structure and how they contribute to conformational stability? Well, like I said, a protein is only functional when they are in their proper conformation, in their proper 3D form. And an improperly folded or degraded, denatured, protein is inactive. So in addition to the four levels of protein structure that I just reviewed, there is also another force that helps to stabilize a protein's conformation. And that force is called the solvation shell. Now, the solvation shell is just a fancy way of describing the layer of solvent that is surrounding a protein. So say I have a protein who has all these exterior residues that are overall positively charged. And picture this protein in the watery environment of the interior of one of our cells, then the solvation shell is going to be the layer of water right next to this protein molecule. And remember that water is a polar molecule, so you have the electronegative oxygen atom with a predominantly negative charge leaving a positive charge over next to the hydrogen atoms. The same is true for each of these water molecules. So now, as you can see, the electronegative oxygen atoms are stabilizing all the positively charged amino acid residues on the exterior of this protein. So as you can see, the conformational stability of a protein depends not only on all of these interactions that contribute to primary, secondary, tertiary, and quaternary structure, but also what sort of environment that protein is in. And all of these interactions are very crucial for keeping a protein folded properly, so that it can do its job. Now, what happens when things go wrong? How does a protein become unfolded and thus inactive? Well, remember that this is called denaturation. And this can be done by changing a lot of different parameters within a protein's environment, including changing the temperature, the pH, adding chemical denaturants, or even adding enzymes. So let's start with what happens if you alter the temperature around a protein. And we can use the example of an egg when we put it into a pot of boiling water, because an egg, especially the white part, is full of protein, and this pot of boiling water is representing heat. And remember that heat is really just a form of energy. So when you heat an egg, the proteins gain energy and literally shake apart the bonds between the parts of the amino acid chains. And this causes the proteins to unfold. So increased temperature destroys the secondary, tertiary, and quaternary structure of a protein, but the primary structure is still preserved. So the take-away point is that when you change the temperature of a protein by heating it up, you destroy all of the different levels of protein structure except for the primary structure. So now, let's say you were to take an egg and then add vinegar, which is really just an acid. The acid in the vinegar will break all the ionic bonds that contribute to tertiary and quaternary structure. So the take-away point when you change the pH surrounding a protein is that you have disruption of ionic bonds. And if we think about this a little bit more deeply, it kind of makes sense, because ionic bonds are dependent upon the interaction of positive and negative charges. So when you add either an acid or a base, which in the case of an acid is just like adding a bunch of positive charges, you kind of disrupt the balance between all these interactions between the positive and negative charges within the protein. So now let's look at how chemicals denature proteins. Chemical denaturants often disrupt the hydrogen bonding within a protein. And remember that hydrogen bonds contribute to secondary, tertiary, all the way up to quaternary structure. So all these levels of protein structure will be disrupted if you add a chemical denaturant. So let's take our same example of a protein with an egg, and say, if you were 21 years or older, you got your hands on some alcohol, and you added this to the egg. Then, all the hydrogen bonds would be broken up, leaving you with just linear polypeptide chains. And then finally, let's take our hard-boiled egg from the temperature example, and let's eat it. So here's my beautiful drawing of a person, representing you, eating this hard boiled egg. Once the egg enters our digestive tract we have enzymes that break down the already denatured proteins in the egg even further. They take the linear polypeptide chain, whose primary structure is still intact. And they break the bonds between the individual amino acids, the peptide bonds, so that we can absorb these amino acids from our intestines into our bloodstream. And then we can use them as building blocks for our own protein synthesis. And that's how enzymes can alter a protein's primary structure and thus the protein's overall conformational stability. So what did we learn? Well, we learned that the conformational stability refers to all the forces that keep a protein properly folded in its active form. And this includes all the different levels of protein structure, as well as the salvation shell. And we also learned that a protein can be denatured into its inactive form by changing a variety of factors in its environment, including changing the temperature, the pH, adding chemicals, or enzymes.