In the last video we talked about the structure of a general amino acid and we mentioned the variable group which we call the R group. Recall that there are 20 different versions of this R group which means there are 20 different amino acids that are available to build proteins. Of all of the components of an amino acid, R groups are the most important because they give each amino acid different defining properties.
For example, R groups can be either hydrophilic or hydrophobic, which dictates how they interact with other R groups that are part of the amino acid chain. Looking deeper into the hydrophilic amino acids, a few are polar, without a net charge while others can be charged by acting as an acid, by giving up a proton which gives them a negative charge, or a base, by accepting a proton granting a positive charge. You do not need to know any specific examples or R-group structures for the exam, but you do need to understand that R-groups are the parts of amino acids that make the molecules chemically diverse and heavily influence how it functions and interacts with other molecules. The specific three-dimensional structure of a protein is based on the order and number of amino acids it has in its chain.
When an amino acid chain is being built, each amino acid is added one at a time until the process is done. This early version of the chain, when amino acids simply exist in a straight line, is called its primary structure. At this point, very early on, it is unfolded. And again, the thing to remember here is that the order of the amino acids will dictate the conformation, or folding, of the final structure.
And it is the conformation of the protein that determines its function. So in essence, everything leads back to that primary structure. A different sequence of amino acids will result in a different conformational structure, which results in a different function.
Let's talk about the next few levels of protein organization to see what types of conformational patterns are seen within protein folding. The primary structure of a protein involves many amino acids connected by peptide bonds. As we saw in the last video, a peptide bond removes a water molecule via the condensation of the carboxyl and amine groups, leaving a bond between the carbon and nitrogen. But there are still other structures branching off of the carbon and nitrogen within that peptide bond, which is a double bond to an oxygen from the carbon and a single bond to a hydrogen from the nitrogen. Both of these hydrogen and oxygen atoms are polar, and when the primary structure of a protein is created, these atoms can interact via the formation of hydrogen bonds.
This results in the oxygen of one amino acid being attracted to the hydrogen of another amino acid somewhere else along the same chain. And if this happens to a lot of them, certain structures can be created that are relatively strong. Two common structures seen created from these hydrogen bonds are the alpha helix and the beta pleated sheet.
Both of these involve different orientations of those hydrogen bonds between the atoms of the base amino acid molecule. This is commonly the first type of folding that occurs after the primary structure of the protein is built, which is why we call it the secondary structure. So remember that the straight chain of amino acids is the primary structure, and the initial hydrogen bond interactions between the oxygen and hydrogen atoms of the peptide bond create alpha helices and beta pleated sheets, which are the secondary structure. We have looked at the primary and secondary structures of proteins.
But as we discussed on the first slide, those R groups are able to bond and create folds within the protein structure. When that happens, and more structures within the amino acid chain interact with each other, it creates a protein tertiary structure. This has many more folds and interactions than just the alpha helices and beta pleated sheets from the secondary structure.
With the tertiary structure, there are specific examples of interactions and bonds that you need to know about for the IB exam. Let's go through each one. Hydrogen bonds can occur between R groups of different amino acids as we see here with asparagine and serine. Ionic bonds can be created as seen here with lysine and aspartic acid.
This occurs because both amine and carboxyl groups that are part of R group structures can become positively or negatively charged by the binding or dissociation of hydrogen atoms. With their charged states, ionic bonds can be formed. Next, both hydrophilic and hydrophobic interactions can take place.
as seen here. And lastly, a specific type of bond can be created between two cysteine amino acids, called a disulfide bond or disulfide bridge. This is the only example that you need to know the actual names of the amino acids for, which again are both cysteine. It is called a disulfide bond because the R groups of cysteine contain sulfur, and to create the bond, two sulfur from each amino acid end up bound together.
which is where the di and the sulfide within the name originate from. Again make sure you know about all of these for the IB exam in relation to the tertiary structure of a protein. We talked earlier about how amino acids can be polar and nonpolar based on their variable group. This polarity property directly impacts the tertiary structure of proteins, and you need to know about two examples of how this can occur.
Some proteins take on tertiary shapes that look like a sphere, or are all globbed up together. which we call globular proteins. These proteins take on this shape because of the dichotomy between polar and nonpolar amino acids. Many of these proteins carry out functions within the cytoplasm, which is a water-based solution.
To achieve this tertiary shape, the polar amino acids are oriented towards the outer part of the sphere that comes in contact with water, which is perfect because the water is also polar, and the nonpolar amino acids clump together in the middle of the structure where they are away from water. These interactions therefore directly impact the final shape of the protein, making it that globular shape. Another example of how polarity impacts proteins can be seen in integral proteins, which are found embedded in the cell membrane.
These proteins contain polar and nonpolar amino acids on different parts of the molecule. Recall that the cell membrane contains phospholipid tails that are nonpolar within its core. For these reasons, transmembrane sections of proteins contain amino acids that are also nonpolar, to be able to attract to those tails and embed themselves into the cell membrane.
We would then find polar amino acids that make up the other ends of the protein, as water is found both in the cytoplasm inside of the cell and outside of the cell in the exterior space. The last level of protein structure is called quaternary structure. This is when two or more separate protein chains bind together to make a larger protein structure.
There are two different versions of this that scientists classify. which are called conjugated and non-conjugated quaternary proteins. This is describing if other structures that are not proteins are also bound to the protein which can alter its form and function.
An example of a non-conjugated protein, meaning it does not have any other additional structures that are not proteins, is insulin. Insulin is created by joining two protein chains together via a disulfide bridge, meaning this structure is now quaternary because it has more than one chain. An example of a conjugated protein would be hemoglobin. Hemoglobin is a quaternary protein made up of four separate tertiary proteins that are linked together. Each of the tertiary proteins contains a heme group, which are not amino acids, you can see the structure here, making it a conjugated protein.
This heme group, which contains a central iron atom, helps it perform its function of picking up and transporting oxygen around the body. As we have been discussing for pretty much this entire video, the structure of a protein is very important when it ends up determining how that protein functions. To put this in plain words that you will see in most biology textbooks across many different topics throughout the curriculum, we can say that form fits function. The form of a protein directly impacts its function. To go through more examples, we can take a look at the difference between insulin, which is a non-conjugated globular protein, compared to collagen, which is a non-conjugated fibrous protein.
As we discussed earlier, insulin has a globular shape making it round as amino acids interact and fold the protein structure in. This makes the structure very stable and allows it to create a conformation that can easily move around and bond with insulin receptors, sending important signals that help with controlling blood sugar levels. Collagen, on the other hand, is a fibrous protein and has amino acid chains that create long rope-like structures. For collagen, that involves three protein chains wound together into a helix, which is different from the alpha helix secondary structure we discussed earlier.
This long chain form gives the protein a high amount of tensile strength, which is why it is used for structural support within many cells and tissues in the body.