Proteins: Videos & Practice Problems

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. Understanding these concepts is crucial for grasping protein function and interactions in biological systems.

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 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, 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.

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 '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. 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.

Answer: (D)

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.

Answer: (B)

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 five protein-related terms just tossed around and used all the time. But not everyone distinguishes between these five protein-related terms. And so here in this video we're going to specifically distinguish between these five protein-related terms. And so these five 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 on the left-hand side, and then it has the length of the amino acid chain on the right-hand side.

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.

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 fewer 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.

The fourth 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 more than 50 amino acids that are covalently linked together. And then the fifth 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 a 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.

Answer: (D)

Protein Structure

In this video, we're going to discuss protein structure. Proteins have a hierarchy of structure organized into four levels: primary, secondary, tertiary, and quaternary. Notice that each of the four levels of protein structure corresponds with the levels in our text and images. The very first level, the primary structure of protein, can be symbolized with the number one. The primary structure refers specifically to the types of amino acids, their quantity, and their specific sequence in the protein chain. Changing either these types, quantities, or the sequence will alter the primary structure. This level is arguably the most important as it determines and dictates all other levels of protein structure.

If we change the primary structure, we could potentially affect the secondary, tertiary, and quaternary structures as well. In our image, each circle represents an amino acid in the protein chain, all covalently linked together via peptide bonds. The primary structure specifies the types, quantity, and order of amino acids.

The next level is the secondary structure of protein, which involves the formation of either α-helices or β-sheets in the protein backbone. This can be symbolized with the number two. In the example image, the protein chain can fold into an α-helix, a winding staircase-type structure, or a β-sheet, an elongated zigzag structure. Thus, the secondary structure specifically refers to these formations in the protein backbone.

Moving on to the tertiary structure of protein, symbolized by the number three, which is easy to remember because the three reminds you of three-dimensional. The tertiary structure refers to the overall three-dimensional shape of the polypeptide chain. Once the backbone folds into α-helices and β-sheets, the protein chain takes on this overall shape, incorporating both α-helices and β-pleated sheets within this structure. All proteins have primary, secondary, and tertiary structures.

The quaternary structure, symbolized with the number four, occurs when a protein has multiple polypeptide chains that associate to form a single functional protein. An example provided is one protein chain with tertiary structure associating with others to form a quaternary structure. This could be a complex with four separate polypeptide chains forming a functional unit, such as hemoglobin, which is found in our red blood cells and helps transport oxygen to our tissues.

This concludes our brief lesson on protein structure, emphasizing the primary, secondary, tertiary, and quaternary levels. We’ll get some practice applying these concepts as we move forward. I'll see you all in our next video.

The specific amino acid sequence in a protein is its:

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

Answer: (A)

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.

Answer: (C)

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, examples 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.

Answer: (E)

Here’s what students ask on this topic:

What are the four levels of protein structure?

Proteins have a hierarchical structure organized into four levels: primary, secondary, tertiary, and quaternary. The primary structure refers to the sequence of amino acids in the polypeptide chain. The secondary structure involves the formation of alpha helices and beta sheets through hydrogen bonding within the backbone. The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by various interactions, including hydrogen bonds, disulfide bridges, and hydrophobic interactions. The quaternary structure occurs when multiple polypeptide chains, each with its own tertiary structure, associate to form a functional protein complex. Understanding these levels is crucial for grasping how proteins achieve their functional conformations.

What is the role of chaperone proteins in protein folding?

Chaperone proteins assist in the proper folding of other proteins, ensuring they achieve their functional three-dimensional structures. When proteins become denatured due to environmental changes like temperature or pH shifts, they lose their functional shape. Chaperone proteins help these denatured proteins refold into their correct conformations, thereby restoring their functionality. This process is vital for maintaining cellular function, as improperly folded proteins can lead to diseases and cellular dysfunction. Chaperones act as a quality control system, preventing aggregation and misfolding, which are detrimental to cell health.

What are peptide bonds and how do they form?

Peptide bonds are covalent bonds that link amino acids together in a protein. They form through a dehydration synthesis reaction, where the carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH₂) of another, releasing a molecule of water (H₂O). This bond formation results in a peptide linkage (–CO–NH–) between the amino acids. Peptide bonds are crucial for creating the primary structure of proteins, which then folds into more complex structures to become functional. Understanding peptide bonds is essential for studying protein synthesis and function.

How do changes in environmental conditions affect protein structure?

Environmental conditions such as pH, temperature, and salt concentration can significantly impact protein structure. Changes in pH can alter the ionization states of amino acid side chains, disrupting hydrogen bonds and ionic interactions. Temperature increases can cause proteins to denature, losing their three-dimensional structure and, consequently, their function. High salt concentrations can interfere with electrostatic interactions and hydrogen bonds, leading to protein precipitation or denaturation. These changes can render proteins nonfunctional, highlighting the importance of maintaining stable conditions for proper protein activity.

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

The R group, or side chain, of an amino acid is the variable part that distinguishes one amino acid from another. Each of the 20 common amino acids has a unique R group, which can be polar, nonpolar, acidic, or basic. These R groups determine the chemical properties and reactivity of the amino acids, influencing how they interact with each other and fold into proteins. The diversity of R groups allows proteins to have a wide range of structures and functions, making them versatile molecules in biological systems.