Enzymes and Protein Binding - Online Tutor, Practice Problems & Exam Prep

Protein binding is essential for protein function, involving specific interactions at binding sites with ligands. Key characteristics include specificity, affinity, and the role of non-covalent bonds. Antibodies, or immunoglobulins, are proteins that bind to antigens at specific regions called epitopes, showcasing high specificity. Enzymes catalyze reactions by binding substrates at active sites, lowering activation energy and facilitating chemical transformations. Understanding these interactions is crucial for grasping biochemical processes and drug design.

Protein Binding

Hi. In this video, we're going to be talking about protein binding. So, in order to exert their functions on the cells, proteins have to be able to interact with other proteins or other molecules to perform their functions. I'm going to talk to you a little bit about protein binding basics. All proteins have to bind to some other type of molecules, generally through a site called the binding site, which is the region where proteins bind to other molecules or proteins. Let me tell you a few terms, specifics, and characteristics about the binding site that you will need to know:

1. The binding site is highly specific. So it usually only binds to one or a few particles.
2. The substance binding the protein at the binding site is called a ligand.
3. Affinity is a measurement of how strongly the ligand and protein are interacting. High affinity implies a strong interaction, while low affinity indicates a weak interaction.

The interactions between proteins and other molecules are primarily held together by non-covalent bonds. Some of you may see the term "molecular complementarity" in your textbook or in lecture. If you don't see it, don't worry about it; but if you do, it refers to the properties on the ligand and the protein that allow them to interact strongly. This could mean that their shapes fit together like puzzle pieces, they could have opposite charges that attract, or they could be either all polar or all non-polar. These properties enable them to interact effectively. Typically, molecular complementarity, or how well the protein and ligand interact, is due to the number of complimentary or non-covalent bonds that can be formed between them.

Another factor impacting protein-ligand binding is the surface conformation of the protein binding site, which provides a certain chemistry. For instance, sometimes proteins have little channels where the binding sites are located. The ligand enters the channel, but once inside, the channel restricts elements like water or other molecules, preventing, for instance, the formation of hydrogen bonds on the ligand. Another scenario is if the binding site is on the surface of the protein surrounded by polar amino acids, which would attract a lot of water and lead to substantial hydrogen bond formation. The surface conformation of the binding site significantly affects what the ligand can do.

Now, regarding the types of protein-protein or protein-molecule binding, I've italicized these terms as it's unlikely you'll need to know these exact terms, but understanding their interactions is important:

• In the surface strain model, a protein with a large surface interacts with another polypeptide chain.
• The helix-helix interaction involves two helices coming together.
• Surface-surface interaction occurs between two surfaces.
• A molecular channel is formed if a protein creates a channel, and the ligand goes inside to interact with the protein.
• Interaction with a small molecule happens when the protein interacts directly with a small molecule embedded within it.

That's an overview of protein binding. Let's now move on.

Antibodies

So in this video, we're going to talk about antibodies. And the reason we're talking about antibodies in the protein binding section is because antibodies are proteins, and their entire function is to bind to other things for destruction or recognition. So, antibodies are proteins. They're sometimes called immunoglobulin proteins, and they're produced by the immune system. Thus, antibodies are really responsible for helping the body defend and respond to molecules, viruses, bacteria, or whatever it might be. They recognize what's known as an antigen, which is any foreign molecule. That could be a foreign amino acid, for instance, or a foreign protein, a foreign bacteria or cell wall, or any of these structures that aren't naturally produced by animal cells, for example, human cells when we talk about it. These antibodies are really specific. Generally, they don't recognize the entire antigen; they recognize a portion of the antigen called an epitope. So, that's going to be a very small specific region that the antibody binds to on the antigen. The antibody binds the antigen's epitope.

Antibodies are shaped. We're looking at what the shape of the protein is like a Y. It has heavy and light chain segments. You don't need to necessarily know this, you will if you ever take immunology, but right now, we don't need to know about this. Generally, the regions that recognize the antigen are called variable regions. There are two kinds of segments here. There is a variable region, but then there is also a constant region. The constant region is constant among all the groups of antibodies, with the variable region changing based on the antigen's epitope. So, antibodies are extremely precise, and they actually have the ability to tell the difference between a single amino acid. If there was a single amino acid change, that antibody is not going to bind. These are super specific. So, if we look at what an antibody looks like, you can see here it's the Y shape, and you have this antigen-binding site here, which is the variable region. And then all of these blue parts down here will be the constant region. And this is where the antigen binds, which you can see this antigen binding here. And you have all these different antigens, for instance, and each one of them is going to bind a different antibody. They are really really specific. So that's about antibodies, so now let's move on.

Enzymes

Okay. So in this video, we're going to talk about enzymes. We've talked about enzymes a lot, but I'm going to bring them up and mention them again here because enzymes are extremely important examples of protein binding. Enzymes are proteins that help to catalyze or speed up reactions. How they do that is they actually bind to what's known as a substrate. This substrate is going to be a special ligand that binds to enzymes. It also binds to an active site, which is very similar to the binding site. It's exactly the same; it's just an enzyme, so we call it an active site, on the enzyme. Once it binds to this active site, that stabilizes the state, allows the energy to lower, and that speeds up the chemical reaction, allows the chemical reaction to take place. So, many pharmaceutical drugs target this and sort of inhibit enzymes in order to exert their effects because that's going to affect protein binding in some way.

And so, if we look at enzyme binding, what you can see, here is a model where you have an enzyme here. It's bound to a substrate, and it causes some type of chemical reaction to take place where the substrate is released and changes. It's some type of chemical reaction that changes the substrate. And so here, you can see it interacts with it at a binding site, this active site here, which is in blue. Site. And, that's where the enzyme is interacting with its substrate or ligand. Enzymes are a really great example of protein binding. So now, let's move on.

Which of the following is not a form of protein binding?

• A. Helix-helix
• B. Surface-string
• C. Surface-surface
• D. Surface-helix

The region of a molecule that an antibody binds is called what?

• A. Antigen
• B. Epitope
• C. Ligand
• D. Substrate

The binding site of a protein is highly specific for one or a few ligands

• A. True
• B. False

Here’s what students ask on this topic:

What is the role of the binding site in protein function?

The binding site is crucial for protein function as it is the region where proteins interact with other molecules, known as ligands. This interaction is highly specific, meaning the binding site typically binds to only one or a few types of ligands. The strength of this interaction is measured by affinity, with high affinity indicating a strong interaction. Non-covalent bonds, such as hydrogen bonds and ionic interactions, primarily hold these interactions together. The surface conformation of the binding site also affects how the ligand interacts, influencing the protein's overall function.

How do antibodies recognize and bind to antigens?

Antibodies, or immunoglobulins, are proteins produced by the immune system to recognize and bind to antigens, which are foreign molecules. They bind to specific regions on the antigen called epitopes. Antibodies have a Y-shaped structure with variable regions that bind to the epitope and constant regions that remain the same across different antibodies. This binding is highly specific, allowing antibodies to distinguish even a single amino acid difference in the antigen. This specificity is crucial for the immune system to target and neutralize foreign invaders effectively.

What is the difference between a binding site and an active site in enzymes?

Both binding sites and active sites are regions on proteins where interactions with other molecules occur. In enzymes, the active site is a specialized binding site where substrates bind. The active site not only binds the substrate but also catalyzes the chemical reaction, lowering the activation energy required for the reaction to proceed. While a binding site can refer to any region where a protein binds a ligand, the term active site is specific to enzymes and their catalytic function.

What factors influence the affinity between a protein and its ligand?

Affinity between a protein and its ligand is influenced by several factors. The primary factor is the complementarity of the binding site and the ligand, which includes shape, charge, and hydrophobic/hydrophilic properties. Non-covalent bonds, such as hydrogen bonds, ionic interactions, and van der Waals forces, also play a significant role. The surface conformation of the binding site can either facilitate or hinder these interactions. Additionally, environmental conditions like pH and temperature can affect the affinity by altering the protein's structure or the ligand's properties.

How do enzymes speed up chemical reactions?

Enzymes speed up chemical reactions by binding to substrates at their active sites. This binding stabilizes the transition state of the reaction, lowering the activation energy required for the reaction to proceed. By reducing the activation energy, enzymes increase the reaction rate, allowing biochemical processes to occur more efficiently. This catalytic function is essential for various cellular processes, including metabolism, DNA replication, and signal transduction.