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 common amino acids, each with unique R groups that determine their properties. 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 to regain their active forms.

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. And so amino acids are the monomers that make up proteins. Now, the covalent bonds that link adjacent amino acids together in a chain are specifically referred to as peptide bonds. And 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 the protein polymers are actually going to have directionality, meaning that in the chain of the protein polymer one end is going to be chemically different than the opposite end. And so we refer to these ends as the N-terminal end and the C-terminal end. And so let's take a look at our example image down below at the formation of proteins from amino acid monomers to get a better idea of these concepts. And so notice over here on the far left-hand side, we're showing you all of these separate individual circles which represent amino acid monomers. And so these are amino acids that are separate from each other. But of course, if we join these amino acid monomers together in a chain like what we see here, then we're building ourselves a protein polymer. And notice that the protein polymer has directionality because on one end over here, it's chemically different than the opposite end over here. And so 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. And then 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, over here. And then notice that each of these separate amino acid monomers are 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. And so, 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. And so 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 in the unique R group down below once we get to our image. But living organisms, they 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, so each 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 so over here on the left, what we have is a table of the amino acid components. And so 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. So 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 20 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.

So 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. So 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 '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 really small R group with just a handful of atoms, just maybe one atom sometimes. And other amino acids have R groups that are much much larger in size and have many many more atoms and they're much, 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.

• 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.

• 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 has 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 one 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.

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

Protein Structure

In this video, we're going to introduce protein structure. Proteins have a hierarchy of structure that's organized into four levels of structure, conveniently labeled primary, secondary, tertiary, and quaternary levels of protein structure. Notice that the text above for each of the four levels of structure corresponds with the image we have below for each of these levels. The very first level of protein structure is the primary level, which we can abbreviate with a 1 here. 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. By changing either the types, the quantity, or the order of amino acids in the chain, we can alter the primary level of protein structure. This level is crucial because it determines all of the other levels of structure, including the secondary, tertiary, and quaternary levels.

Looking at our image on the left-hand side, notice that each of these circles represents amino acids. We have this long amino acid chain here, and the specific types, quantity, and order of these amino acids in this long chain define the primary protein structure. Next, the second level of protein structure is, of course, the secondary level, symbolized as 2. This refers specifically to the formation of either alpha helices or beta sheets in the protein backbone. In the image showing secondary protein structure, the protein backbone can either take a winding shape, which would be the alpha helix, or a zigzag shape, which is the beta sheet structure.

Moving on to the tertiary level of protein structure, symbolized by a 3, it specifically refers to the overall three-dimensional shape of the polypeptide chain. The long polypeptide chain, when it forms alpha helices and beta sheets, can fold onto itself to create a complex overall three-dimensional structure. Embedded within the overall three-dimensional shape, you can see the alpha helices in blue and the beta sheets in red. These levels of structure build onto each other.

This leads us to the fourth and final level of protein structure, the quaternary level of protein structure, symbolized with a 4. This level specifically refers to when multiple polypeptide chains associate with each other to form a single functional protein. Looking at our image below, there are two polypeptide chains: a lighter gray chain and a darker gray chain. When these two separate polypeptide chains come together and associate to form a single functional protein, that is referred to as the quaternary protein structure. This introduction to protein structure concludes here, and we'll discuss more about it in our next lesson video. 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.

• 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.

• 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. And so what's important for you all to note is that a protein's structure and shape is actually really critical for its proper function. And so what this means is that a protein will not be able to properly function or properly work if it loses or changes its structure and shape. And so it's really the structure and shape that dictates the protein's function. And this idea leads us directly to the term denatured protein, and that is because a denatured protein is a protein that is nonfunctional, a nonfunctional protein that has altered its shape. And so, once again, by altering or changing the shape of a protein, that will change its function and make it nonfunctional. Now, denatured proteins can result from changes to the environment. And so, examples of changes in the environment that could lead to a denatured protein include changes such as 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 things can lead to the change of a protein shape and therefore lead to a nonfunctional protein, a denatured protein. Now, on the other hand, proteins that have lost their shape can sometimes regain their original shape by the help of what are known as chaperone proteins. Chaperone proteins are proteins themselves that help other proteins reform their original shapes or renature, if you will. And so let's take a look at our example image down below to get a better understanding of denatured proteins and chaperone proteins. And so what you'll need to notice is over here on the left-hand side, we're starting with a functional protein, which is this shape right here, this red structure. And, what's important to note is that it has a very, very specific shape. However, if the functional protein is heated, if the temperature changes in the environment, recall that the temperature is just one of the changes in the environment that can cause a functional protein to denature and lose its shape. And so if we heat up the protein, that can change the shape of the protein. And so notice here, the protein has changed its shape in comparison to the functional form of the protein. And so what this means is, of course, 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 that we call chaperone proteins. And so this structure that you see here throughout is referring to the chaperone protein. And so the chaperone protein can take the denatured protein and basically help it reform its original structure. And so once the protein has regained its original shape and structure, it becomes a functional protein once again. And so chaperone proteins are good for cells to have to make sure that their proteins are properly folded. And so this here 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.

• 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 in cells?

Chaperone proteins assist in the proper folding of other proteins within the cell. They help prevent misfolding and aggregation that can occur during protein synthesis. Chaperones can also aid in refolding denatured proteins that have lost their functional shape due to environmental changes such as heat, pH shifts, or changes in salt concentration. By ensuring proteins achieve and maintain their correct conformation, chaperones play a crucial role in maintaining cellular function and homeostasis.

How do peptide bonds form between amino acids?

Peptide bonds form between amino acids through a dehydration synthesis reaction. This reaction occurs when the carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH₂) of another, releasing a molecule of water (H₂O) and forming a covalent bond. The resulting bond, known as a peptide bond, links the carbon atom of the carboxyl group to the nitrogen atom of the amino group, creating a continuous chain of amino acids in a protein.

What causes proteins to denature?

Proteins can denature due to changes in their environment, such as alterations in pH, temperature, or salt concentration. These changes can disrupt the non-covalent interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces) that maintain a protein's structure. When these interactions are disrupted, the protein loses its specific three-dimensional shape, rendering it nonfunctional. Denaturation is often irreversible, but in some cases, chaperone proteins can help refold denatured proteins back to their functional forms.

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

The R group, or side chain, of an amino acid is significant because it determines the amino acid's unique properties and its role in protein structure and function. The R group can vary in size, shape, charge, hydrophobicity, and reactivity. These variations influence how amino acids interact with each other and with their environment, affecting the folding, stability, and activity of the protein. The diversity of R groups among the 20 common amino acids allows for the vast array of protein structures and functions observed in living organisms.