- Amino acids and proteins questions
- Central dogma of molecular biology
- Central dogma - revisited
- Peptide bonds: Formation and cleavage
- Special cases: Histidine, proline, glycine, cysteine
- Amino acid structure
- Isoelectric point and zwitterions
- Classification of amino acids
- Four levels of protein structure
- Conformational stability: Protein folding and denaturation
- The structure and function of globular proteins
Different bonds/interactions contribute to the stability of each level of protein structure. Let's explore some common ones such as peptide bonds, hydrogen bonds, and disulfide bonds. By Tracy Kovach. . Created by Tracy Kim Kovach.
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- If I put fish meat for example of atlantic salmon in a machine thats divide the meat into very small pieces, what will happend to the proteins?(4 votes)
- Answer: It depends. Probably they won't be affected because proteins are working at a chemical or cellular level, and are not affected by the whole piece of meat being divided.
Think about it like a bag of marbles. The bag is the fish, and each marble is a protein. If you split the bag in half, you have two separate piles of marbles, but each individual marble (protein) is not affected.(13 votes)
- Aren't van-der-waals forces and hydrophobic interaction the same thing?
what about ionic bonds between -COO- and -NH3+ groups in the side chains?(2 votes)
- They are not. VDWF are interactions between the subatomic particles of the atoms. For example, if the distance between molecules is minimized enough, the nuclei will repel one another, but at just the right distance, the maximum attraction between molecules is attained. VDWF are extremely weak, and usually only transient. Usually VDWF are generated by very small distortions in the electrons about an atom. This may result in very small partial positive and negative charges which may attract another molecule with distorted electrons. Hydrophobic interactions are the result of hydrophobic groups trying to avoid contact with hydrophiles like water. Take for example, Phenylalanine, the most hydrophobic AA. Why does L-Phe exist usually on the inside of globular proteins? It is b/c the inside of soluble proteins does not touch water (L-Phe hates water). Inside the protein, you might also find other hydrophobes like Leucine, Isoleucine, Valine, and Methionine. This is due to their attempt to avoid water. On the outside of the protein, you might find Glutamate, Aspartate, and Lysine. They have polar side chains and can H-bond with water. It's all about stability. If polar touches non-polar the Gibbs energy differential,Delta G, gets more positive, singalling unfavorability. When unfavorable interactions are minimized, the Delta G is negative, and stability is high. IN conclusion, VDWF are due to electronic distortions in the atoms of adjacent molecules. Hydrophobic interactions are attempts to minimize unfavorable interactions, and are the actual driving force of protein folding. In fact, hydrophobic interactions are why cell membranes have the glycerol and phosphate of the phospholipids facing the watery environment and the hydrophobic fatty acyl chains away from all water.(17 votes)
- So pH only denatures the tertiary and quaternary layers of a protein? But if the pH changes then the protonation of the amino acid could change which could, therefore, affect hydrogen bonding. Wouldn't pH changes also affect the secondary structure as well then? I'm referring to the 3 and 4 crossed out at the bottom of the screen at6:00.(7 votes)
- When we have a pH decrease, shouldn't that disrupt H-bonding in the secondary structure since we are increasing the concentration of hydrogen ions in the environment?(3 votes)
- Hydrogen ions are positively charged and therefore and disrupt the balance between positive charges and negative charges which means addition of acids can disrupt 3rd, 4th structures. However, hydrogen bonds are not formed by hydrogen ions but between electronegative atoms such as NOF and H atoms that are connected to NOF.(0 votes)
- In the video about peptide bonds it's said that peptide bonds can be destroyed by heat (unspecific hydrolysis). The primary structure is about peptide bonds, so why isn't it denatured by the temperature?(2 votes)
- Peptide bonds are extremely stable, which means they are harder to break. In general, the peptide bonds in the primary structure can only be broken by hydrolysis where acid and heat are used in conjunction with one another (or via proteolysis). This is because the primary structure of proteins loses a molecule of water for every pair of amino acids joined together; the acid hydrolysis gives back this water molecule allowing the original amino acid conformations to result. If heat alone is applied, then the denaturation of interactions such as hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions occur on the secondary, tertiary, and quaternary structure levels.(2 votes)
- Denaturation is a reversible process but coagulation is not? is that right?(1 vote)
- Denaturation can be reversible in some situations - typically though, Denaturation and coagulation are irreversible. Denaturation occurs when the secondary/tertiary polypeptides are "unfolded" down to the primary/linear form. When this happens, the amino acids (which are variably hydrophilic and hydrophobic) are exposed to the solution and/or H2O. This unfolding can be due to heat, change in pH, addition of detergents, change in salt concentration etc. This unfolding is the denaturation.
Coagulation is when solution/H2O molecules are attracted (and subsequently trapped) on the a.a.. Because of the solution, the hydrophilic areas have nowhere to hide and are subjected to bombarding of the solution. As the solution is attracted to the a.a., the solution molecules continue to attract more of itself, pulling the linear polypeptide chain in unnatural ways. This traps (coagulates) solution molecules. This is also typically irreversible (cooking/making jello, eggs, bread rising). You could reverse the process but would not get the same initial materials.(5 votes)
- So does adding enzymes Denature a protein or not? Because I thought Enzymes can only work on the primary structure due the need for an active site being available which seems unlikely if secondary, tertiary and quaternary structures are preserved. So you would have to add heat/change pH/add chemical in order to disrupt 2,3,4 structures which is the only way to Denature (by definition) a protein and THEN you could add an enzyme to go to work on the primary structure resulting in a fully disrupted protein which is now a bunch of residues. Or am I understanding it incorrectly?(2 votes)
- If the food isn't heated up or cooked so that the food is reduced to its primary structure will the enzyme still reduce the food to its primary structure? So can enzymes still act on quaternary structures?(2 votes)
- Do the proteins already need to be denatured for enzymes to break the protein down? Or can enzymes work on a whole/conformation protein?(1 vote)
- What are the ionic bonds between amino acids that contribute to the tertiary and quarternary structures of the proteins? Does she mean truly ionic or just highly polar?(1 vote)
- You could get ionic bonds contributing to tertiary structure. An example could be an ionic bond between an NH3+ and a COO- from different amino acid residues. Imagine the R group from a Lysine lying next to the R group from aspartic acid.
Notice how the COO- group on the aspartic acid must be deprotonated and carry a full negative charge for it to work. That helps explain why an acidic solution might disrupt the ionic bond by protonating the COO-(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 we'll start out with the term conformation. And the term "conformation" 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 that 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 conformation 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 and 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 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 of 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 takeaway 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 takeaway 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 makes sense, because ionic bonds are dependent upon the interaction of positive and negative charges. So when you add either acid or base, which in the case of an acid is just like adding a bunch of positive charges, you disrupt the balance between all of 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 of 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 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 lets 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 of the different levels of protein structure as well as the solvation 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.