Proteins - Online Tutor, Practice Problems & Exam Prep

Proteins are polymers made of amino acid monomers linked by peptide bonds, exhibiting directionality with N-terminal and C-terminal ends. There are 20 amino acids, each with common components and unique R groups. Protein structure is hierarchical, comprising primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D shape), and quaternary (multiple polypeptide chains). Denatured proteins lose functionality due to environmental changes, while chaperone proteins assist in refolding them. Understanding these concepts is crucial for grasping protein function and structure.

Proteins

In this video, we're going to begin our lesson on proteins. Now, proteins are one of the major classes of biomolecule polymers that are made up of amino acid monomers. Amino acids are the monomers that make up proteins. The covalent bonds that link adjacent amino acids together in a chain are specifically referred to as peptide bonds. We'll be able to see some examples of these peptide bonds down below in our image.

But, it's also important to note that protein polymers have directionality, meaning that in the chain of the protein polymer, one end is chemically different from the opposite end. These ends are referred to as the N-terminal end and the C-terminal end. Let's take a look at our example image down below showing the formation of proteins from amino acid monomers to get a better idea of these concepts. Notice on the far left-hand side we are showing you all of these separate individual circles which represent amino acid monomers. These amino acids are separate from each other.

Of course, if we join these amino acid monomers together in a chain like what we see here, we're building ourselves a protein polymer. Notice that the protein polymer has directionality because on one end, it's chemically different from the opposite end. The end that has the amino group, like what we see over here, is referred to as the N-terminal end because the amino group has a nitrogen atom. This other group that we see over here on the opposite end is referred to as the C-terminal end because it has a carboxyl group, which we see here. Notice that each of these separate amino acid monomers is being covalently linked together through these bonds that we see right here, and these bonds that covalently link the adjacent amino acids together are referred to as peptide bonds.

This here really concludes our introduction to proteins, and we're going to continue to talk more and more about proteins as we move forward in our course. I'll see you all in our next video.

Amino Acids

In this video, we're going to talk some more details about amino acids. Now amino acids, recall from our last lesson video, are really just the monomers of proteins. And so linking together multiple amino acids allows us to build a protein polymer. Now each individual amino acid monomer is going to contain common components that are common to all amino acids, and then they're also going to contain some unique components such as the unique R group. And we'll be able to see the common components and the unique R group down below once we get to our image.

But living organisms primarily use a total of 20 different amino acids. And once again, these different amino acids, they all have common components that we're going to talk about, but each of the 20 amino acids also has a unique R group. So let's take a look at our example down below to get a better understanding of these ideas. We're taking a look at the amino acid structure. And over here on the left, what we have is a table of the amino acid components.

Recall in our last lesson video, we were representing amino acids using these circles. And so, these circles, each of these circles has these components that we're talking about, and these components you can see over here in a more detailed chemical structure of the amino acid. Each of these amino acids is going to have common components which we have in the red box. So the red dotted box that you see here represents the common components that are found in all twenty of the different amino acids. And, down below what you'll see is a green shading which is going to be the unique region of the amino acid that will differ between all of these 20 amino acids.

When we look at the common components, notice that it starts with the central carbon atom which is also known as the alpha carbon. And so over here when we look at the chemical structure you can see that the central carbon atom is right here in the center, right in the middle. Now coming up off the top of the central carbon atom, we have a central hydrogen atom. So that would be this, hydrogen atom that we see here. And again, this is a common component found in all amino acids.

And then going to the left and going to the right of the central carbon atom, we have these 2 functional groups that you should recognize. Going to the left over here in blue, what we have is an amino group which is where the N-terminal end would be for this amino acid. And then of course going to the right over here in yellow, what we have is a carboxyl group which is going to be the C-terminal end of the amino acid. And so once again, all of these components that we talked about here are the common components found in every single amino acid. And really what makes one amino acid different from another amino acid is going to be the R group, the unique R group.

And so we can put the R group here, and the R group you can pretty much think that the R stands for the R in the rest of the molecule because the R group is going to be variable. It will change from amino acid to amino acid and it represents the rest of the molecule. Some amino acids have a really small R group with just a handful of atoms, just maybe one atom sometimes. Other amino acids have R groups that are much larger in size and have many more atoms and they're much more complicated. But the backbone, this region here is going to be common for all amino acids.

So that's important to keep in mind. Now for your biology class, you're likely not going to need to know all 20 of the different amino acids but you will need to know that there are 20. And you will need to know the common components and the fact that they all have a unique R group that has different properties. And so this here concludes our introduction to amino acids and we'll be able to get some practice applying these concepts as we move forward in our course. So I'll see you guys in our next video.

The primary building blocks (monomers) of proteins are:

• A. Glucose molecules.
• B. Lipids.
• C. Nucleotides.
• D. Amino acids.
• E. None of these.

Which two functional groups are always found in amino acids?

• A. Carbonyl and amino groups.
• B. Carboxyl and amino groups.
• C. Amino and sulfhydryl groups.
• D. Hydroxyl and carboxyl groups.

5 Protein-Related Terms

So as you guys are reading through your textbooks or sitting in class, listening to your professors, you might hear these 5 protein-related terms just tossed around and used all the time. But not everyone distinguishes between these 5 protein-related terms. And so here in this video, we're going to specifically distinguish between these 5 protein-related terms. And so these 5 protein-related terms are referring to amino acid chains that vary in their length. And so notice down below we have this table that has the protein-related terms over here on the left-hand side, and then it has the length of the amino acid chain over here on the right-hand side.

And so the first protein-related term that you all should know is, of course, amino acid, which we already talked about in our last lesson video. So, we already know that amino acids are a single protein unit or, in other words, a monomer of a protein is an amino acid. And then of course we can take these individual monomers, these individual amino acids and link them together to create a long chain of amino acids. And that's where these other four terms come into play. So the second term that we have here is going to be oligopeptide.

And so recall that the oligo prefix means a few. And so oligopeptides are going to have an amino acid chain that have just a few amino acids, somewhere between about 2 and about 20 covalently linked amino acids in the chain. So pretty short, amino acid chains are oligopeptide chains. Now the term peptide without the oligo prefix is referring to amino acid chains that have less than 50 covalently linked amino acids. And so what's important to note here is that oligopeptide and peptide at some point there's a little bit of overlap between the two terms.

Now the 4th term that we have here is polypeptide, and recall that the prefix poly means many, and so these are going to be amino acid chains that have greater than 50 amino acids that are covalently linked together. And then the 4th the 5th and final term that we have here is protein itself. And so a protein is specifically referring to just 1 or multiple polypeptide chains that are specifically in their folded or functional forms. And so when we're talking about proteins, we're talking about polypeptides that are in their folded or functional forms. And when we say folded, what we mean is that these chains don't just remain as straight linear chains, they actually fold up into themselves and create these complex three-dimensional structures.

And so really this leads us to our next lesson video which is talking about the levels of structure of protein. So I'll see you all there in that video.

What term is used for an amino acid chain that has greater than 50 covalently linked amino acids?

• A. Protein.
• B. Peptide.
• C. Amino acid.
• D. Polypeptide.

Protein Structure

In this video, we're going to introduce protein structure. And so proteins have a hierarchy of structure that's organized into four levels of structure that are conveniently labeled primary, secondary, tertiary, and quaternary levels of protein structure. And so notice that the text that we have up above for each of the four levels of structure corresponds with the image that we have down below for each of the four levels of protein structure. And so the very first level of protein structure is the primary level of structure, which we can abbreviate, with a one here. And so the primary level of protein structure specifically refers to the types, the quantity, and the specific order or sequence of amino acids in the chain.

And so by changing either the types, the quantity, or the order of amino acids in the chain, then we can change the primary level of protein structure. And so the primary level of protein structure is really, really, really important because it determines all of the other levels of structure including the secondary, tertiary, and quaternary levels of structure. And so when we take a look at our image down below over here on the left hand side, notice that each of these circles represents amino acids. And so we have this long amino acid chain here, and, the specific types, quantity, and order or sequence of these amino acids in this long chain, is going to be the primary protein structure. So we can fill in primary down below over here.

Now, the second level of protein structure is, of course, the secondary level protein structure, so we can put a 2 over here. And this is referring specifically to the formation of either alpha helices or beta sheets in the protein backbone. And so when we take a look at our image down below at the secondary protein structure, notice that the protein backbone can either take a winding, shape like what we see here which would be the alpha helix or the protein backbone could take more of a zigzag shape like what we see down here which is, the beta sheet structure. So this is more of a zigzag whereas this is more of a winding structure. And so we can say that secondary protein structure is going to be the formation of either alpha helices or beta sheets in the protein backbone.

And so this leads us to the tertiary level of protein structure which of course can be symbolized here with a 3. And so the tertiary level of protein structure is specifically referring to the overall three-dimensional shape of the polypeptide chain. And so, if we take a look at our image down below, notice that the long polypeptide chain over here, when it forms alpha helices and beta sheets, it can fold onto itself to create this complex overall three-dimensional structure. And so the tertiary protein, protein structure is specifically referring to the overall three-dimensional shape. And so embedded within the overall three-dimensional shape, you can see the alpha helices here that are in blue, and you can see the beta sheets that are, in red over here.

And so these levels of structure, they build onto each other. And so this leads us to the 4th and final level of protein structure which is the quaternary level protein structure which of course can be symbolized with a 4. And this is specifically referring to when multiple polypeptide chains are going to associate with each other to form a single functional protein. And so when we take a look at our image down below, notice that there are 2 polypeptide chains here. We have this lighter gray polypeptide chain over here, and then we have this darker gray polypeptide chain over here.

And when you have these 2 separate polypeptide chains that come together and associate to form a single functional protein, that is what we refer to as the quaternary protein structure. So it's when multiple amino acid chains come together. And so this here concludes our introduction to protein structure. And we'll be able to talk a little bit more about protein structure in our next lesson video. So I'll see you all there.

The specific amino acid sequence in a protein is its:

• A. Primary structure.
• B. Secondary structure.
• C. Tertiary structure.
• D. Quaternary structure.

Which of the following is true of protein structure?

• A. Peptide bonds are formed by hydrolysis.
• B. Peptide bonds join the amine group on one amino acid with the R group of another amino acid.
• C. Secondary protein structures are caused by hydrogen bonding between atoms of the peptide backbone.
• D. Tertiary protein structure emerges when there is more than one polypeptide in a protein.

Denatured Proteins & Chaperones

In this video, we're going to introduce denatured proteins and chaperones. It's important for you all to note that a protein's structure and shape are critical for its proper function. This means that a protein will not be able to properly function or work if it loses or changes its structure and shape. It's really the structure and shape that dictates the protein's function. This idea leads us directly to the term denatured protein, which is a protein that is nonfunctional, a nonfunctional protein that has altered its shape.

By altering or changing the shape of a protein, that will change its function and make it nonfunctional. Denatured proteins can result from changes in the environment. Examples of changes in the environment that could lead to a denatured protein include changes in the pH of the solution, changes in the temperature of the environment, or changes in the salt concentration of the environment as well. All of these factors can lead to the change of a protein's shape and therefore lead to a nonfunctional protein, a denatured protein. On the other hand, proteins that have lost their shape can sometimes regain their original shape with the help of what are known as chaperone proteins.

Chaperone proteins are proteins themselves that help other proteins reform their original shapes or renature. Let's take a look at our example image below to get a better understanding of denatured proteins and chaperone proteins. Notice that we're starting with a functional protein on the left hand side, represented by a red structure with a very specific shape. However, if the functional protein is heated, which is just one of the changes in the environment that can cause a functional protein to denature and lose its shape, its shape will change. Notice here, the protein has changed its shape in comparison to the functional form of the protein. As a result, we have a denatured protein here that has lost its shape and therefore lost its function. It will no longer work when it's lost its shape.

However, proteins can regain their shapes with the help of other proteins called chaperone proteins. The structure you see represents the chaperone protein. The chaperone protein can take the denatured protein and help it reform its original structure. Once the protein has regained its original shape and structure, it becomes a functional protein once again. Chaperone proteins are beneficial for cells to ensure that their proteins are properly folded. This concludes our introduction to denatured proteins and chaperones, and we'll be able to get a little bit of practice applying these concepts as we move forward in our course.

So I'll see you all in our next video.

What is the role of a chaperone protein?

• A. Assist in RNA and DNA folding.
• B. Assist in membrane transport.
• C. Assist in protein denaturation.
• D. Assist in dehydration synthesis reactions.
• E. Assist in protein folding or re-naturing.

Here’s what students ask on this topic:

What are the four levels of protein structure?

The four levels of protein structure are primary, secondary, tertiary, and quaternary. The primary structure is the sequence of amino acids in a polypeptide chain. The secondary structure refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone, such as alpha helices and beta sheets. The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by interactions between R groups. The quaternary structure is the arrangement of multiple polypeptide chains into a single functional protein complex.

What is the role of chaperone proteins?

Chaperone proteins assist in the proper folding of other proteins. They help prevent misfolding and aggregation that can occur during protein synthesis. Chaperones can also aid in refolding denatured proteins, restoring their functional shapes. This is crucial because a protein's function is highly dependent on its structure. By ensuring proteins fold correctly, chaperones maintain cellular function and prevent diseases related to protein misfolding.

How do peptide bonds form between amino acids?

Peptide bonds form through a dehydration synthesis reaction between the amino group of one amino acid and the carboxyl group of another. This reaction releases a molecule of water (H₂O) and creates a covalent bond between the nitrogen atom of the amino group and the carbon atom of the carboxyl group. The resulting bond is called a peptide bond, and it links amino acids together in a polypeptide chain.

What causes protein denaturation?

Protein denaturation is caused by changes in the protein's environment, such as alterations in pH, temperature, or salt concentration. These changes can disrupt the non-covalent interactions (hydrogen bonds, ionic bonds, hydrophobic interactions) that maintain the protein's structure, leading to the loss of its three-dimensional shape and, consequently, its function. Denatured proteins are nonfunctional and can sometimes be refolded with the help of chaperone proteins.

What is the significance of the R group in amino acids?

The R group, or side chain, of an amino acid is what makes each of the 20 amino acids unique. The R group determines the chemical properties and reactivity of the amino acid, influencing how it interacts with other amino acids and how it contributes to the protein's overall structure and function. R groups can be polar, nonpolar, acidic, or basic, and these properties play a crucial role in the folding and stability of proteins.