- DNA questions
- Eukaryotic gene transcription: Going from DNA to mRNA
- Molecular structure of DNA
- Antiparallel structure of DNA strands
- Telomeres and single copy DNA vs repetitive DNA
- Leading and lagging strands in DNA replication
- Transcription and mRNA processing
- Speed and precision of DNA replication
- Translation (mRNA to protein)
- Differences in translation between prokaryotes and eukaryotes
- DNA repair 1
- DNA repair 2
- Semi conservative replication
- Protein modifications
- Jacob Monod lac operon
- DNA structure and function
Created by Efrat Bruck.
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- DNA Question 7 states: "An individual presenting with a mysterious disease affecting his connective tissues is found to have numerous defects in multiple regulatory proteins. If these proteins are characterized by highly abnormal patterns of glycosylation, to what structure might the patient’s disease most likely be attributed?". According to this video at6:00, the answer would be either/both the ER and the Golgi, no? Why does the question only accept "Golbi" as the right answer, and considers "ER" to be wrong?(7 votes)
- Since this is about adding to a protien already assembled, the golgi should recognize that the protien is incorrectly assembled and dispose of it instead of secreting it, for this reason the ending point lies with the golgi and not the ER.(5 votes)
- at12:27, she mentions that methylation will activate/inactivate transcription. Just to make sure, methylation would inhibit transcription, and de-methylation would activate it? Thanks!(4 votes)
- According to Science Direct (an outside source I found), methylation of a histone results in less transcription and demethylation results in more transcription.(4 votes)
- Does the Na K valve turn 180 degrees or does it hinge open?(5 votes)
- 6:15What is the purpose of a GPI anchored protein?(2 votes)
- GPI anchors allow proteins to be attached to the cell membrane and can be cleaved by phospolipase C so the protein is free-floating in the cytosol. One advantage of GPI-anchors is that they allow proteins to be near their upstream effectors. Therefore, if a membrane receptor acts on some sort of protein that is not transmembrane, it would be easier for the receptor to act on the protein if it were nearby, rather than if it were free-floating. Therefore, if the protein were attached to a GPI-anchor, then the receptor would be able to perform its actions more efficiently.(5 votes)
- @9:25She says there is a change in conformation or maybe confirmation. Would anyone be willing to explain what this means?(0 votes)
- Check out
for a nice animation, you can see the protein changing its shape(conformation)(5 votes)
- Can we think of the phosphorylation of the "pump" protein similar to the mechanism of an allosteric regulator binding to an enzyme? Or are those different processes?(2 votes)
- How is phosphorylation different from allosteric regulation? In allosteric regulation, the regulatory molecule is not covalently attached to the protein, it merely binds in a reversible manner to the protein. Phosphorylation is the covalent addition of a phosphate group to specific amino acid side chains.
Taken from oregonstate.edu/instruction/bi314/summer09/regulation.html(1 vote)
- In the ABO blood groups example for glycosylation, carbohydrates are used as markers. Are there other uses for glycosylation besides those resulting in cell markers.(2 votes)
- Does monoubiquitination mark a protein for degradation, or does polyubiquitination have to occur for a protease to be recruited?(1 vote)
- Addition of ubiquitin is highly cooperative; once one Ub is added, it becomes a signal for further (poly)ubiquitination. Target proteins are typically degraded after they've accumulated chains of 7 or more ubiquitin proteins.
Interestingly, monoubiquitination is a possible histone modification - it would be very bad for our DNA if every ubiquitinated histone recruited the protease!(2 votes)
- How is Phosphorylation a Post-Translational Modification of Proteins? It doesn't look like any protein was modified.(1 vote)
- Phosphorylation is a post-translational modification because it adds a phosphate group to a protein after the protein's been made. It can cause a conformation change and use this process to regulate the protein. It may be helpful to review7:30(2 votes)
- What is role of Sirituin?(1 vote)
- [Voiceover] After a polypeptide chain is formed, it's going to be folded into its secondary and tertiary structure into a very specific 3D conformation or shape. And at this point, we can start calling it a protein. But, this protein may not be ready to carry out its function just yet. There might be some additional protein modifications that need to be made to this protein before it can be functional. And those are called protein modifications. There are two different types of protein modifications. The first type is co-translational modification. And that means that these are modifications or changes that happen to the protein, or actually to the polypeptide while it's being translated. Let's say we have the ribosome right here and we have a polypeptide that's being formed. So these changes are going to happen while the polypeptide is being formed. An example of a co-translational modification is acetylation. And what happens during acetylation is, the first amino acid in the polypeptide, which is usually methionine, is going to be removed. And in its place we put an acetyl group. Let's just draw an acetyl group. And acetylation happens to 80-90% of eukaryotic proteins. But the significance of this modification is not known very well, we're actually trying to figure out what the purpose of this modification is. The other type of protein modification that happens is post-translational modification. And actually, most protein modifications fall into this category, and the examples we're going to discuss in this video are all post-translational modifications. And those modifications happen after translation. Many post-translational modifications happen in the endoplasmic reticulum and the Golgi apparatus, but not all of them. Let's go through some examples. So the first post-translational modification I want to talk about is glycosylation. Glycosylation, you can look at the word. The prefix "glyco" tells us that it has something to do with a carbohydrate. And so glycosylation is the adding of a carbohydrate to a protein. And most of the proteins in this video are all in green. And glycosylation usually happens to proteins that end up being embedded in the cell membrane. So you can see here we have a cell membrane and this protein embedded in it, and then there are these carbohydrate groups attached. So here's a carbohydrate group attached, and here's another one. Glycosylation helps to identify different types of cells. And one very common example of where we use glycosylation is in the A, B, O blood groups. Let's take four different red blood cells, and let's just say that each one of these red blood cells belongs to a different person. Red blood cells have these proteins embedded in their surface. And these proteins are going to have, many times, different carbohydrate groups attached to them. So let's say that this person right here has this particular carbohydrate group attached to it. That makes him blood type A. Let's say that this person has a different type of carbohydrate attached to the protein. Let's say it looks something like that. That makes them blood type B. Let's say that this person has both of those carbohydrates attached to his red blood cells. That would make him blood type AB. And let's say that this last person does not have any carbohydrates of this category attached to the proteins on his red blood cells, and so that makes him blood type O. So here's a very common example of how glycosylation is used in the identification of different types of cells. Let's go on to a different type of post-translational modification that's pretty similar, and that is lipidation. Lipidation is when we add a lipid to a protein, also a protein that's going to be attached to the cell membrane. And this lipid we're looking at is actually an example of a GPI anchor. And GPI anchors are lipids that help to attach or tether proteins to the cell membrane. And just to give you an idea of maybe why this would be necessary. To quickly review the structure of the cell membrane. We have these hydrophilic heads. That means that they are polar. And then we have, inside, these hydrophobic tails, and that means that they are non-polar. And so the protein has both polar and non-polar parts on it, and maybe it just doesn't attach well to the hydrophilic portion of the cell membrane. So this GPI anchor, a lipid, kind of plunges into the lipid or hydrophobic part of the cell membrane. And we know that substances that are similar, like substances that are both hydrophobic, attach very well to each other. So this lipid, which is hydrophobic, attaches very well to the inner part of the cell membrane that is also hydrophobic. And so that's how it helps to attach the protein to the cell membrane. Both glycosylation and lipidation usually do occur in the endoplasmic reticulum, or in the Golgi apparatus. Let's move on to some protein modifications that have more to do with the activity or the function of the enzyme and less with the structure. So one very, very common protein modification I want to discuss is phosphorylation. Phosphorylation is basically the adding of a phosphate group to a protein or to an enzyme. Phosphorylation comes along with dephosphorylation, is when you remove a phosphate group from the enzyme or the protein. I'm just going to make a little bit of room over here. And so, what you're looking at is this schematic diagram of the sodium-potassium pump that's found in basically every animal cell. And another name for the sodium-potassium pump, which is the enzyme that you're looking at, is the Na+ /K+ -ATPase. And so, this enzyme or protein, the sodium-potassium pump, is responsible for maintaining the proper osmolarity of sodium ions and potassium ions in and out of the cell. And so, let's see how phosphorylation regulates this protein. And again, the proteins that you're looking at, they really all represent one protein. It's just, we're going through the motions of the changes that happen to this one protein. It's not like we're looking at six different proteins in the membrane. So here's our first step. And when you look at this enzyme, you can see that there are three receptor sites for a particular ion, this is the sodium ion. Represented by these dark blue circles. And then there are two receptor sites that look kind of more squarish, and those are receptor sites for the potassium ions, and those are represented by these light blue squares. So those are the potassium ions. And so, back to the first step, and what's happening here. The sodium ions will attach to the receptor sites on the enzyme. And just to clarify, this is the intracellular space, so this is basically the cytoplasm. And so these sodium ions are coming from the cytoplasm. And then out here is the extracellular space, the outside of the cell. Back to our first step. So the sodium ions attach to the receptor site. When the receptor sites are full, it's going to cause something to happen. It's going to cause an ATP molecule, adenosine triphosphate, to break down into ADP, adenosine diphosphate, plus phosphate. And then this phosphate will attach itself to the protein, and that is phosphorylation. And so when this protein gets phosphorylated, when the phosphate group is attached to it, it causes there to be some sort of change in the conformation of the protein. And that change in conformation causes the protein to turn itself around by 180 degrees and face the outside of the cell. That's what you're looking at right over here. So our protein is still phosphorylated. I know I drew it in a different place, but just keep in mind that there's still a phosphate group attached to that protein. And then the protein releases the sodium ions into the extracellular space. So the next step is number four. And again, we are still phosphorylated, there's still a phosphate group attached to our protein. And so in the next step, the potassium ions on the outside of the cells will attach themselves to the protein on the receptor sites. Take note, there are three receptor sites for sodium but only two for potassium. When the potassium receptor sites are full, it's going to cause a different change to happen. This phosphate group is going to be removed. And that is called dephosphorylation. That phosphate group ends up in the inside of the cell, and it gets recycled in some other way. And when this protein is dephosphorylated, when that protein is removed, it's going to cause a different change in the conformation of the protein. And that change in conformation causes the protein now to turn around again by 180 degrees and it faces the inside of the cell. So that's our fifth step, you can see the protein is facing the inside of the cell. And in the last step, the potassium ions are released into the inside part of the cell. And then we're back to our first step. And so you can see that the phosphorylation and dephosphorylation basically regulates the activity of this protein. And the end result that we're trying to get to is that we want there to be, on the outside of the cell, a rather high concentration of sodium, and a rather low concentration of potassium. And on the inside of the cell we want there to be a rather low concentration of sodium, and a relatively high concentration of potassium. That's accomplished by the fact that for every three sodiums that are pumped out, two potassiums are pumped in. And so here's an example, a very common example of how phosphorylation regulates a protein. And this doesn't happen just in the sodium-potassium pump, it happens in many, many enzymes and proteins in our bodies and in cells. Let's move on to two other protein modifications that also have to do with regulating an enzyme or something similar to that. So the next protein modification I want to talk about is methylation. And in particular, the methylation of certain proteins called histones. And those are these green circles that you're looking at. Histones are these proteins around which DNA wraps itself. So they're found in the chromosomes, and they help to package DNA in a very tight and organized manner. And sometimes histones are methylated, so let's put some methyl groups on our histones. Methylating and demethylating histones helps to turn certain genes on and off. And so here's another example of, a protein modification helps to regulate activity, but in this case we're regulating the activity of genes as opposed to proteins. Another protein modification I want to bring up is proteolysis. And by looking at this word, "proteo" means protein and "lysis" means to break something down, or to cut something. Proteolysis is sometimes to take a protein and activate it, we need to cut it. And in fact, the insulin has to be cut twice before it's activated. So let's cut this protein twice. You may have actually heard of the term zymogen. A zymogen is an inactive form of an enzyme. And sometimes the way to activate a zymogen is by cutting it, and that's proteolysis. There's one more protein modification I want to discuss. And that is, sometimes we add a protein, ubiquitin, to another protein. So that protein I just added is ubiquitin. And this process is called ubiquitination. And what ubiquitination does is, it basically marks this green protein for degradation, or for breakdown. So within a short while of being ubiquinated, this protein is going to be destroyed and the different parts are going to be recycled. Let's just quickly review the post-translational modifications that we discussed. So we talked about glycosylation and lipidation. Those are two protein modifications that generally happen to proteins that end up being embedded in the cell membrane. So glycosylation was the adding of a carbohydrate group which helps to identify certain cells, and lipidation is when you add a lipid to a protein, and that generally helps to anchor a protein to the cell membrane. Then we talked about phosphorylation, methylation and proteolysis. And these all had to do with activating or deactivating an enzyme or genes. So phosphorylation, we brought the example of the sodium-potassium pump, which is basically regulated with phosphorylation and dephosphorylation. Then we spoke about methylation, which basically helps to turn on or turn off certain genes. And proteolysis is a way in which many enzymes are activated. And the last post-translational modification we talked about was ubiquitination. And ubiquitination marks a protein for degradation, and then the various parts are recycled.