Polar Amino Acids - Online Tutor, Practice Problems & Exam Prep

Polar amino acids, characterized by hydrophilic R groups, include serine, threonine, cysteine, asparagine, and glutamine. These amino acids can form hydrogen bonds due to electronegative atoms in their structures. Serine and threonine contain alcohol groups, while cysteine has a thiol group. Asparagine and glutamine feature amide groups, with glutamine having an additional methylene group. Understanding these structures is crucial for grasping protein interactions and functions, as they play significant roles in biochemical pathways and molecular recognition.

Polar Amino Acids

In this video, we're going to talk about our 3rd group of amino acids, the polar amino acids. So the polar amino acids all contain R groups that are hydrophilic. And recall what we mean by hydrophilic is just water-loving, and that's due to the presence of terminal electronegative atoms or electronegative atoms that are found at the very ends of the R groups and are easily able to interact with water, making them hydrophilic. Now, polar amino acids also contain hydrogen bonding groups, so the R groups of polar amino acids are capable of forming hydrogen bonds, and there are 5 amino acids that are grouped as polar amino acids, and those 5 amino acids are serine, threonine, cysteine, asparagine, and glutamine.

And so down below, we have a mnemonic to help us remember those 5 polar amino acids. So when you're thinking about the polar amino acids, you really want to be thinking about the North Pole. And who's in the North Pole? Santa, of course. And so every winter when it gets cold, Santa and his team, they craft new quilts in order to stay warm. And literally, that's our mnemonic. "Santa's team crafts new quilts," where the first letter of each of these words symbolizes the one letter code for the corresponding polar amino acids.

And so, down below, we're actually going to talk about each of these individual R groups on these amino acids in the blocks. And so in the block on the far left over here, what we have is serine. And serine's three-letter code is just SER, and its one-letter code is just an S. And so you can see how the S for serine here in our mnemonic is being represented as Santa. Now, in our next block, what we have is threonine, and threonine's three-letter code is just THR, and its one-letter code is just a T. And so you can see how the T here for threonine is being represented by the team in our mnemonic.

Now, one way to help us remember part of both serine and threonine structure is to remember that alcohol is a serious threat. And so the SER in 'serious' is for serine and the THR in 'threat' is for threonine. And so by remembering that alcohol is a serious threat, that can remind us that serine and threonine both have alcohols in their R groups, and alcohols are literally just OH groups or hydroxyl groups. And so looking up above at our image, we know that Santa here is representing serine, and notice that Santa has a little beer in his hand. He has a little bit of alcohol in his hand.

Cysteine's three-letter code is just CYS, and its one-letter code is just a C. And you can see that the C here for cysteine is being represented by the crafting hammer here. And so this crafting hammer likes to spend quiet time in the Sistine Chapel. And whenever somebody makes a noise, the Sistine is always just like "shh." And so literally, cysteine is just our leader amino acid, alanine, with an SH group, an SH group.

Asparagine's three-letter code is just ASN, and its one-letter code is just an N. And we can see that the N here for asparagine is being represented by "new" in our mnemonic. Turns out that asparagine is literally just alanine, our leader amino acid, with an amide group. And recall that an amide group is literally just when you have a carbonyl group with a nitrogen coming off of it.

Now moving on to our last amino acid in this group, we have glutamine, and glutamine's th...

Draw in the R-groups from memory for each of the polar amino acids.

So this practice problem wants us to draw in the R groups from memory for each of the polar amino acids. So when we think about the polar amino acids, we think about the North Pole and we think about our mnemonic for memorizing the 5 polar amino acids, which is Santa's team crafts new quilts. And so we know that even though Santa and his team know that alcohol is a serious threat, where the 'serious' here is for serine and the 'thre' is for threonine, that Santa and his team can have alcohol in moderation while they're crafting their new quilts and it's totally fine. And so that helps us remember that both serine and threonine are the only 2 amino acids of these 5 that actually have alcohol groups in their R groups. And so what you'll recognize is that because S here, serine, is the first amino acid of this group, it's the leader amino acid of this group. And so, serine is really going to be following our leader amino acid, alanine. And so serine is literally just alanine or, CH2 here with an alcohol group branching off of it. And so, it will have an OH group and really, that is it for serine's structure. Next, we have is TNT is for threonine, and we know that threonine is also going to have an alcohol group. And really, threonine's structure is based right off of serine's structure. So, they feed off of each other here. And so threonine is really going to look just like serine here with the alcohol group coming down. But instead of having 2 hydrogens, it's only going to have 1 hydrogen coming off, and then on the other side, it's going to have a methyl group, a CH3 group. And so we can remember that threonine has three parts surrounding its central carbon atom in its R group. And so the 3 groups are the hydrogen, the alcohol group, and the methyl group. And so that is it for threonine's structure. Next, we have is the C, and the C is for cysteine. And in our mnemonic, we know that cysteine is really a hammer, and we know that it's actually, standing for crafting. It's that crafting hammer. And that crafting hammer spends a lot of quiet time in the Sistine Chapel, which is a church. So when we think about the North Pole, we think about Santa Claus, we think about Christmas, and we think about church. And then, we know that Sistine spends a lot of quiet time in the Sistine Chapel. And so whenever somebody makes a noise, cysteine is always like, Shhh. And so literally cysteine is just our leader amino acid alanine, so CH2, with an SH group coming off. And so literally, this is cysteine's structure. Moving on, next what we have is the N, and the N is specifically for asparagine. And so asparagine's R group, we know has an amide group in it. And so we can, remember that because its one letter code, the N, has these 2 parallel lines in it, and those two parallel lines remind us of a double bond. The nitrogen that's present, tells us that there's a double bond with a nitrogen, and that reminds us of the amide group. And so, literally, asparagine is just our leader amino acid alanine with an amide group coming off. And so, we can draw alanine, and it's going to have an amide group branching off, which is a C double bond O with an NH2 group. And so this here is our amide group, and you can see that it's essentially just alanine with an amide group branching off, and that is it for asparagine's structure. Next, we have is the Q, and the Q is for glutamine. And glutamine's structure is really based right off of the asparagine's structure, kind of like how threonine's structure is based off of serine's structure. And so with glutamine, because it has the 'glute' in it, the 'glute' reminds us of our gluteus maximus or our butt section. And so if you're missing the butt section, you're going to be a little bit shorter, but because glutamine actually has the 'glute' in it, it's going to have an extra butt section or an extra CH2. And so, essentially it's going to be exactly the same as asparagine, but it's going to have an extra CH2. So we can go ahead and start to draw its structure over here, so it's going to be a CH2, we know that it's going to have an extra CH2, and then it's going to have the amide group at the very bottom. And so this is it. So an NH2. Let's make that a little bit clearer here. Perfect. So this is it for a glutamine structure. You can see we have the amide group at the bottom, and it has an extra CH2 that asparagine doesn't have because glutamine has that extra 'glute' in it. And so that is it for glutamine's structure. And so that concludes this practice problem, and hopefully, that helped you guys refresh a lot of those memory tools that we learned in our previous lesson video, and we'll be able to get even more practice utilizing all of these concepts and memory tools as we move along through our course. So I'll see you guys in our next video.

Here’s what students ask on this topic:

What are the polar amino acids and their characteristics?

Polar amino acids are characterized by hydrophilic R groups, which means they are water-loving due to the presence of electronegative atoms. The five polar amino acids are serine, threonine, cysteine, asparagine, and glutamine. Serine and threonine contain alcohol groups (OH), cysteine has a thiol group (SH), and asparagine and glutamine feature amide groups (CONH2). Glutamine has an additional methylene group (CH2) compared to asparagine. These structures enable polar amino acids to form hydrogen bonds, playing crucial roles in protein interactions and biochemical pathways.

How can I remember the structures of polar amino acids?

A useful mnemonic to remember the five polar amino acids is 'Santa's Team Crafts New Quilts,' where each word's first letter corresponds to the one-letter code of the amino acids: Serine (S), Threonine (T), Cysteine (C), Asparagine (N), and Glutamine (Q). Additionally, serine and threonine can be remembered by the phrase 'alcohol is a serious threat,' indicating their alcohol groups. Cysteine can be linked to a 'crafting hammer' (SH group), asparagine to 'new' (amide group), and glutamine to 'quilts' (extra CH2 group).

What is the difference between serine and threonine structures?

Serine and threonine both contain alcohol groups in their R groups, but they differ in their structures. Serine's R group is CH2OH, making it essentially alanine with an added hydroxyl group. Threonine, on the other hand, has an additional methyl group, making its R group CH(OH)CH3. This means threonine has three parts on its central carbon: a hydrogen atom, an alcohol group, and a methyl group, whereas serine has only two parts: a hydrogen atom and an alcohol group.

Why are polar amino acids important in protein interactions?

Polar amino acids are crucial in protein interactions because their hydrophilic R groups can form hydrogen bonds with water and other molecules. This property allows them to participate in various biochemical pathways and molecular recognition processes. For example, the hydrogen bonding capability of serine and threonine's alcohol groups, cysteine's thiol group, and the amide groups in asparagine and glutamine facilitate the formation of stable protein structures and interactions with other biomolecules, enhancing the protein's functionality and stability.

How do the structures of asparagine and glutamine differ?

Asparagine and glutamine both feature amide groups in their R groups, but they differ in the presence of an additional methylene group in glutamine. Asparagine's R group is CH2CONH2, while glutamine's R group is CH2CH2CONH2. This extra methylene group in glutamine makes it slightly larger and more flexible, which can influence its interactions and role in proteins compared to asparagine.