Protein Regulation - Online Tutor, Practice Problems & Exam Prep

Protein regulation is essential for cellular function, involving various covalent modifications. Key processes include phosphorylation, where a phosphate group alters protein activity, and glycosylation, the addition of carbohydrates. Other modifications include lipid binding, ubiquitination for degradation, and cleavage, which is irreversible. Additionally, GTP binding and hydrolysis regulate proteins like Ras, while calcium binding influences numerous proteins. Protein machines, composed of multiple proteins, require precise regulation for functionality, highlighting the complexity of protein interactions and modifications in cellular processes.

Covalent Modifications

Hi, in this topic we're going to be talking about protein regulation. Proteins need to be regulated because they don't always need to be active. Sometimes they need to change their activity based on the needs of the cell. In this video, we're going to talk about protein regulations that are caused by covalent modifications to the protein itself. Modifications to the proteins can affect their activity. Let's go through a few different types of protein modifications that exist.

The first one is going to be phosphorylation, and that's the reversible addition of a phosphate group somewhere on the protein. This brings with it two different negative charges and that can result in conformational changes. The enzymes responsible for adding or removing this phosphate are called kinases when they add it, and phosphatases when they remove it. Phosphorylation is a really big one that we're going to talk a lot more about in future topics.

A second one is called glycosylation, and that's going to be the reversible addition of carbohydrates, meaning that carbohydrates can be added or they can be removed. There are two main types of this: it's going to be N-linked if it's attached to a nitrogen, and O-linked if attached to an oxygen, which makes complete sense. Glycosylation is a big protein modifying process.

Modifications can also occur by the covalent addition of lipids. For instance, glycolipids are lipids that are linked to oligosaccharides, which are sugars, and then can be added to proteins. So, you can have lipids, you can add sugars, you can add proteins, and you can add everything to a protein essentially, and all of them have different effects. You don't necessarily need to know these types of names, but you may see them in your textbook such as palmitoylation and myristoylation, and they're all names based on their lipid type, but all of these lipids and sugars and things can be added to proteins to affect their function.

Now, there are two other types of protein modifications that I want to just highlight really quickly. One is called ubiquitination. Ubiquitination labels the protein with another protein called ubiquitin, and that protein really marks the protein to be degraded. Then you also have cleavage, and that is just sort of cutting off a section of the protein, and usually out of everything that I've talked about, cleavage is the only irreversible one. Once you chop the protein up, it's not easily put back together. Cleavage is really important for a variety of functions of the protein, including getting them to certain organelles or sort of sequestering them in one area.

So, if we look back, we can see different types of protein modifications. We have phosphorylation, which is the addition of phosphate groups; glycosylation, which is the addition of sugars or oligosaccharides to the protein; lipid binding, where sugars are attached to lipids which sort of anchor the protein inside of some type of bilayer; ubiquitination, which attaches ubiquitin for degradation; and then we also have cleavage, which you can see all these proteins are a little bigger, but then there's a section here on this one that's been cut out, and so that's going to be cleavage of the protein. These are the types of protein modifications. So now, let's move on.

GTP and Calcium Binding

So, another type of protein regulation that I really want to talk about is the GTP and calcium binding. Let's first talk about GTP binding and hydrolysis of GTP acts as a major source of protein regulation. This is because proteins can bind to GTP in a special sort of domain or binding site, the GTP binding domain. GTP is usually hydrolyzed to form GDP, and in this process, it can result in conformational changes of itself that usually inactivates its GTP form. When it does this, it can control its own self, or it can control the functions of other proteins that it might be bound to. An example of this is the Ras protein, which is a major GTP binding regulator. Interestingly, Ras is often misregulated or mutated in many cancers. Therefore, it's really important for protein regulation to manage this GTP to GDP transition effectively.

Now, let’s talk about calcium binding. Calcium can regulate a variety of proteins. Calcium concentration is generally kept very low inside the cytosol. However, if for some reason something triggers a change in that concentration, a high concentration of calcium in the cytosol can activate or inactivate a bunch of proteins that bind to calcium and respond to calcium signals. Thus, calcium is a significant protein regulator.

Continuing with the GTP example, you can see here that there is an inactive form of this protein with a GDP bound, and it becomes activated when it has GTP bound. Proteins can go back and forth between these two states, activating or inactivating themselves, or they can inactivate or activate other proteins that they might be bound to. For instance, if there is a third protein, it can inactivate or activate this protein, depending on how the particular G protein works. That covers GTP hydrolysis and calcium binding. Now, let's move on.

Protein Machines

Hi, in this video, we're going to be talking about protein machines. Protein machines are protein complexes that contain 10 or more proteins. These machines generally have interchangeable or dynamic parts, meaning that the parts are constantly coming in, moving around, and being replaced. So these protein machines are actively moving protein machines. In order for these protein machines to have a function, each part has to be specific or positioned in a very specific way so that the protein can exert its function.

Control of these machines, or how these machines are regulated, depends on the control of each individual part. Remember, this is a protein regulation topic. If there's one protein missing, that protein machine isn't going to work. Each protein of these 10 or more proteins has to be positioned correctly and regulated independently so that they all can come together and work as a single machine.

If you were to look at what this looks like, this is an example of one. You don't need to know anything about this right now, or what all these proteins are. Just get an overall view here that there's a bunch of proteins involved in this protein machine and each one of them has to be independently regulated to arrive here at the right time for the right function. Protein machines are super important and a big part of protein regulation so that they can exert their function.

So now let's move on.

Which of the following is not a protein modification that allows for protein regulation?

• A. Ubiquitination
• B. Phosphorylation
• C. Glycosylation
• D. Noncovalent interactions in the binding site

Hydrolysis of GTP to GDP causes what to occur to a GTP-Binding protein

• A. It marks it for degradation
• B. It cleaves it
• C. It activates it
• D. It inactivates it

To regulate large protein complexes there is a single, powerful regulator of the entire complex.

• A. True
• B. False

Here’s what students ask on this topic:

What is protein phosphorylation and how does it regulate protein activity?

Protein phosphorylation is the reversible addition of a phosphate group (PO₄^3-) to a protein, typically on serine, threonine, or tyrosine residues. This process is catalyzed by enzymes called kinases, while phosphatases remove the phosphate group. The addition of the phosphate group introduces two negative charges, causing conformational changes in the protein structure. These changes can either activate or inactivate the protein, thereby regulating its function. Phosphorylation is crucial in many cellular processes, including signal transduction, cell division, and metabolism.

What is glycosylation and what role does it play in protein regulation?

Glycosylation is the covalent addition of carbohydrate groups to a protein. This modification can occur in two main forms: N-linked glycosylation, where the carbohydrate is attached to a nitrogen atom in the amino acid asparagine, and O-linked glycosylation, where it is attached to an oxygen atom in serine or threonine. Glycosylation affects protein folding, stability, and cell signaling. It can also influence protein interactions and localization within the cell. This modification is essential for the proper function of many proteins, including those involved in immune responses and cell-cell communication.

How does GTP binding and hydrolysis regulate protein activity?

GTP binding and hydrolysis are critical mechanisms for regulating protein activity. Proteins with GTP-binding domains can bind guanosine triphosphate (GTP), which often activates the protein. The hydrolysis of GTP to guanosine diphosphate (GDP) usually inactivates the protein. This cycle of binding and hydrolysis induces conformational changes that regulate the protein's activity. An example is the Ras protein, which is involved in cell growth and differentiation. Mutations in Ras that affect GTP hydrolysis are linked to various cancers, highlighting the importance of this regulatory mechanism.

What is ubiquitination and how does it affect protein function?

Ubiquitination is the process of attaching ubiquitin, a small regulatory protein, to a target protein. This modification typically marks the protein for degradation by the proteasome, a protein complex responsible for breaking down unneeded or damaged proteins. Ubiquitination involves a series of enzymatic steps, including activation by E1 enzymes, conjugation by E2 enzymes, and ligation by E3 enzymes. This process is crucial for maintaining cellular homeostasis, regulating protein levels, and controlling various cellular processes such as cell cycle progression and DNA repair.

What are protein machines and how are they regulated?

Protein machines are complexes composed of multiple proteins, often ten or more, that work together to perform specific cellular functions. These machines are dynamic, with parts that can be interchanged or replaced as needed. Each protein within the machine must be precisely regulated and positioned to ensure the complex functions correctly. Regulation can involve various modifications, such as phosphorylation, glycosylation, and ubiquitination, to control the activity, stability, and interactions of the individual proteins. Proper regulation of protein machines is essential for processes like DNA replication, transcription, and cellular transport.