Functional Groups: Videos & Practice Problems

Functional groups are crucial in biomolecules, influencing their reactivity and properties. Key groups include methyl, hydroxyl, sulfhydryl, carbonyl, carboxyl, amino, and phosphate. These groups form linkages like ethers, esters, amides, and phosphodiester linkages, essential for macromolecules such as proteins, carbohydrates, lipids, and nucleic acids. The six major elements in living organisms—carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOPS)—constitute 97% of their mass, while trace elements play vital roles. Understanding these components is fundamental for grasping biochemical processes and molecular interactions.

Functional Groups & Linkages

We're going to do a quick recap on functional groups. So you guys already know that functional groups are very specific portions of a molecule that are abundant in biomolecules and tend to be reactive. In addition to that, they typically extend off of the carbon backbone of a molecule. Some functional groups can be further categorized as linkages because they are specific arrangements of atoms that can be used to link different kinds of molecules together. We'll be talking about functional groups and linkages throughout our entire biochemistry course, so it's important to be able to refresh and touch up on some of the common ones. In our example below, we're going to label the functional groups and linkages. We'll start with the functional groups here that we have listed, and I want to emphasize that the ending "yl" or "il" on a word is indicative that it is branching off of a chain, and you'll see that throughout our patterns when we start to label our functional groups.

The first functional group that we have is the methyl group, which of course you guys know is simply a CH₃ group branching off of a carbon chain, which is represented by R or the rest of the molecule. Our next functional group is, of course, one that you guys have seen plenty, and this is our hydroxyl group, which of course is an oxygen atom, bonded to a hydrogen atom. This is a hydroxyl group, and molecules that have hydroxyl groups are categorized as alcohols. Our next functional group is the sulfhydryl group. You can see that the "sulf" part here refers to the sulfur atom and the "hyd" refers to the hydrogen atom, and so this is simply a sulfur hydrogen atom branching off of a chain. We'll see this when we talk about some of our proteins.

The next functional group is a carbonyl group. This is a carbonyl group, which is simply a carbon atom double bonded to an oxygen atom. We'll see this plenty of times incorporated into different functional groups. In our next one, what you'll notice is that it indeed has a carbonyl group in it, but it also has a hydroxyl group. So when these atoms are arranged in this way, this makes a carboxyl group. Over here, there's another functional group that you guys are very familiar with, and this is the amino group, which consists of just a nitrogen atom and hydrogens, and we see those in proteins. Our last functional group is the phosphate group, which, of course, has a phosphorus atom in the center and it's branching off of a chain, so that makes it a little bit easy to recognize.

Now, down below we have some linkages, and notice that the linkages have R groups on either side of them. So that shows that they are able to link different types of molecules together. Our first linkage is our ether, and our next linkage is our ester. So this is our ester. Ethers and esters kinda sound similar. And you might have been wondering why this creepy little freak over here has been staring at you guys this whole video. But pretty much, what he's going to do is help us distinguish between the two. Ethers really do look like our friend over here, the ether bunny. So this is the ether bunny. Notice that he's got those cute little buck teeth and whiskers sticking out, and he's also got these big floppy ears that look just like the big floppy ears of our ether. And so, the ether really does look like the ether bunny with these big floppy ears, and the ester does not look so much like the ether bunny. And so, that can help you hopefully distinguish between the two.

Notice that esters are very similar looking to carboxyl groups. Carboxyl groups are at the end of a molecule where notice that the ester is embedded within a molecule with the two R groups on the end. The next functional group that we have is our amide linkage, which we'll see in proteins when we talk about peptide bonds. Notice that this also a derivative or a spinoff of the carboxyl group, but it has a nitrogen atom in there instead of the hydroxyl group. Our next functional group is what's called our phosphodiester linkage. Notice that it has "phospho" indicating a phosphorus atom, and it has "di" in here indicating two of something, and then it also has "ester". So really, this is essentially an ester, and notice that our esters have a double bonded oxygen here. Notice that we have the same thing with our R group and R group over here. So you can see that this is essentially an ester, and that really the only difference is that here we have a carbon atom and here we have a phosphorus atom. This is one phosphate ester linkage, but notice that on the other side, we also have another phosphate ester linkage. So this makes a phosphodiester linkage, and we'll see these when we talk about our nucleic acids in our next video.

Then the last one that we have over here is a phosphoanhydride linkage, which is represented by really two phosphate groups being connected together and also linking two different types of molecules. Again, we'll talk about functional groups and linkages throughout our course, and this is a good summary. I'll see you guys in our next video when we talk about functional groups and biomolecules.

Functional Groups in Biomolecules

So as you guys already know, functional groups are common in biomolecules, and although the structures of biomolecules vary greatly, there are consistent patterns in the functional groups and linkages and they tend to appear frequently in specific types of molecules. So down below, we have the 4 major macromolecules numbered and the numbers correspond to the numbers in the example images below. So for the first one, you guys know that amino acids and proteins have amino groups as well as carboxyl groups. And you can see that in the image below here for number 1 where an amino acid has the amino group on one end and the carboxyl group on the other.

Now, carbohydrates, you guys know have plenty of hydroxyl groups. And because of that, they are polyalcohols, and they also tend to have ether linkages. So down below in our example, you can see we have 2 different forms of the glucose molecule, a linear form and a cyclic form, and both forms have plenty of hydroxyl groups, which makes them polyalcohols. And in addition to that, the cyclic form has an ether linkage shown by this oxygen and the 2 ether "bunny ears" that are branching out to the r groups or the carbon atoms.

Now, lipids, they vary greatly in their structure, so it's a lot harder to find these consistent patterns in functional groups and linkages. But that being said, a specific type of lipid known as the fatty acids typically have methyl groups. So down below, what we'll see is that we have a specific type of lipid showing a phospholipid, and at the ends of the hydrocarbon chains, we have these methyl groups being shown. And in addition to that, you can see that there are other functional groups and linkages that we talked about previously. So you can see that we have an ether linkage here linking the glycerol molecule to the 2 hydrocarbon chains, and we also have a phosphate group up above and a phosphate ester linkage that links the phosphate group to the glycerol molecule.

Now, each nucleotide in a nucleic acid tends to have phosphate diester linkages, phosphate diester linkages. And so you can see over here in our image for number 4 that we have 2 nucleotides linking together and they're linked by a phosphate diester linkage shown here. So you can see that there's 1 phosphate ester linkage shown in the highlighted region linking this phosphate group to this nucleotide. And then on the other end, there's another phosphate ester linkage that links, this nucleotide to this phosphate group. So this is a phosphate diester linkage. And you can also see that there's an amino group on this, car on this, nitrogenous base. And over here, you have an amide linkage, shown here. And so, you can see that these functional groups appear, frequently, and we'll talk about them more as we move forward in our course. So this is a good summary, and I'll see you guys in the next video when we talk about what elements are essential to life.

Essential Elements of Life

So as you guys already know, the periodic table, which is shown below, contains all of the known elements of the universe. And of all of these known elements, only a small subset of them is found in living organisms. And actually, what's quite amazing is that about 97% of the mass of most living organisms, which is a very large percentage here, consists of just 6 elements, And those 6 elements are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. And what helps me remember that is to remember CHNOPS. And so each of the letters here in CHNOPS represents the first letter of each of these major elements as well as the element's, symbol in the periodic table below. And notice that CHNOPS is color coded in a pinkish color to correspond with the pinkish color in the periodic table here. And so the other 3% of the mass of living organisms consist of 23 other elements that can be grouped together as the trace elements. And the trace elements, of course, appear in very small amounts, but they can still have major biological roles and they are actually important for life and are required for life. And these trace elements include the 5 essential ions of life, which are sodium, chlorine, potassium, calcium, and magnesium. So, I would definitely remember the major elements of life. I would not memorize all of the 23 trace elements, but I would also remember the 5 essential ions. And so what helps me remember the essential ions is to think about, for sodium and chlorine, I think about salts, because sodium chloride makes up our salts. Bananas are a major source of potassium. Milk is a major source of calcium, and dark chocolate is a major source of magnesium. So when I think about salts, bananas, milk, and chocolate, that helps me remember all of the essential ions. And so notice that the essential ions are color coded in dark purple to correspond with the dark purple that we see below in the periodic table. Now, the light bluish color corresponds with the other trace elements. And again, the pinkish color corresponds with the major elements representing the trace elements that and this is just representing the trace elements that tend to be more prevalent than other trace elements. So the darker ones are more prevalent than the other trace elements, but I wouldn't worry about that so much in this video. And so this is a good summary of the elements of life and I'll see you guys in our practice videos.

Identify and label the functional groups and linkages in the following molecule:

So this practice problem wants us to identify and label the functional groups and linkages in the following molecule. And so, this should look familiar to you guys, and I want to ask, what type of molecule is this? That's right. It's a nucleotide. So it has a phosphate group, a pentose sugar, and a nitrogenous base, which makes it a nucleotide. Now, is this a DNA or an RNA nucleotide? That's right. It's an RNA nucleotide, and that's because it has a ribose sugar here which has an additional hydroxyl group that the deoxyribose does not have. Now, to identify these functional groups and linkages, we'll start on the far left of the molecule and make our way through. So over here on the far left, we have a phosphate group, which is represented by this highlighted region of the molecule. Now, the phosphate group also produces a phosphate ester linkage. So you can see here's the phosphate ester, and then here's the phosphate ester linkage that connects the phosphate group to the pentose sugar or the ribose sugar. And so, in the pentose sugar, in this ribosugar, we have 2 hydroxyl groups. So we have 2 hydroxyl groups below, and then up above in the pentose sugar, we have an ether, and that's represented by this oxygen and these ether bunny ears that kinda stick out, left and right. And so, this would be our ether. Now, in the nitrogenous base above, we have an amino group, and, that's represented by this NH2. And so, what type of nitrogenous base is this? Is this a pyrimidine or is this a purine? That's right. It's a purine, and that's because it has a double ring structure, whereas pyrimidines have a single ring structure. So this is a purine, and, in fact, it's actually an adenine nitrogenous base. So this answers our practice problem here, and I'll see you guys in the next practice problem.

Which of the following elements likely make up the largest portion of the mass in an organism?

• A. Phosphorus
• B. Sodium
• C. Magnesium
• D. Fluorine

Answer: (A)

Here’s what students ask on this topic:

What are functional groups in biochemistry?

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. They are crucial in biochemistry because they determine the properties and reactivity of biomolecules. Common functional groups include methyl (CH₃), hydroxyl (OH), sulfhydryl (SH), carbonyl (C=O), carboxyl (COOH), amino (NH₂), and phosphate (PO₄). These groups often extend off the carbon backbone of a molecule and can form linkages like ethers, esters, amides, and phosphodiester linkages, which are essential for the structure and function of macromolecules such as proteins, carbohydrates, lipids, and nucleic acids.

Why are functional groups important in biomolecules?

Functional groups are important in biomolecules because they determine the chemical properties and reactivity of the molecules. They influence how biomolecules interact with each other and with other substances, which is crucial for biochemical processes. For example, the hydroxyl group (OH) makes molecules more soluble in water, while the carboxyl group (COOH) can donate a proton, making the molecule acidic. Functional groups also play a key role in the formation of linkages like peptide bonds in proteins and phosphodiester bonds in nucleic acids, which are essential for the structure and function of these macromolecules.

What are the six major elements found in living organisms?

The six major elements found in living organisms are carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S). These elements, often remembered by the acronym CHNOPS, make up about 97% of the mass of most living organisms. They are fundamental to the structure and function of biomolecules. For example, carbon forms the backbone of organic molecules, oxygen and hydrogen are key components of water and organic compounds, nitrogen is essential for amino acids and nucleic acids, phosphorus is a part of nucleotides and ATP, and sulfur is found in some amino acids and vitamins.

What is a phosphodiester linkage and where is it found?

A phosphodiester linkage is a type of covalent bond that joins a phosphate group to two alcohol groups. It is a key structural component of nucleic acids like DNA and RNA. In nucleic acids, phosphodiester linkages connect the 3' carbon atom of one sugar molecule to the 5' carbon atom of another sugar molecule, forming the sugar-phosphate backbone of the DNA or RNA strand. This linkage is crucial for the stability and integrity of the genetic material, allowing it to store and transmit genetic information.

How do functional groups affect the solubility of biomolecules?

Functional groups significantly affect the solubility of biomolecules in water and other solvents. Polar functional groups, such as hydroxyl (OH), carboxyl (COOH), and amino (NH₂), can form hydrogen bonds with water molecules, increasing the solubility of the biomolecule in water. Nonpolar functional groups, like methyl (CH₃), do not interact well with water and tend to decrease solubility. The presence and arrangement of these functional groups determine how a biomolecule interacts with its environment, influencing its biological function and behavior.