Amino acids can be classified based on their R groups as non-ionizable or ionizable. Non-ionizable R groups are uncharged and lack acid-base reactions, having only two pKa values. In contrast, ionizable R groups can gain a charge, resulting in three pKa values. There are seven ionizable amino acids: three positively charged (arginine, histidine, lysine) and two negatively charged (aspartic acid, glutamic acid), along with cysteine and tyrosine, which are uncharged at physiological pH but can ionize at higher pH levels. Understanding these distinctions is crucial for grasping protein structure and function.
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concept
Non-Ionizable Vs. Ionizable R-Groups
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In this video, we're going to distinguish between non-ionizable and ionizable R groups. Non-ionizable R groups are basically just R groups that are uncharged. Recall that an ion is just an atom or molecule with a charge. If you are non-ionizable, it means that you are not capable of gaining a charge because these R groups lack acid-base reactions or proton transfers. They lack those, and that's why they are uncharged and non-ionizable. Amino acids that have non-ionizable R groups have only 2 pKa values, one for the amino group and one for the carboxyl group, but they do not have a third pKa value for their R group. So, their R group does not have a pKa. There are actually 13 amino acids that have non-ionizable R groups, and we'll see those in our example below.
Now, let's quickly discuss ionizable R groups. Ionizable R groups are essentially the opposite of non-ionizable R groups. Ionizable R groups are charged groups that result from acid-base reactions or proton transfers, so they do have these reactions. Because ionizable R groups are capable of ionizing and gaining a charge, amino acids with ionizable R groups have 3 pKa values because the R group does have a pKa. The ionizable R groups are all capable of forming ionic bonds, which is a significant distinction between amino acids with ionizable R groups and those with non-ionizable R groups because amino acids with non-ionizable R groups are not able to form ionic bonds. In our example, we are going to total the number of amino acids that fall into each of the indicated ionization groups. All of these groups in the color code shown on the right here. In this chart, you'll see that all the pink colored ones are positively charged amino acids at physiological pH, a pH of 7. Recall from our mnemonic, "dragons eat knights riding horses," that the knights riding horses are the positively charged, basic amino acids. There are 3 of them, so arginine, histidine, and lysine. These three are positively charged at pH 7. With the negatively charged at pH 7, we know that the dragon's eating those are the D and the E, those are the negatively charged acidic amino acids, and they are negatively charged at pH 7. And, of course, those include aspartic acid and glutamic acid, or aspartate and glutamate, shown here in yellow.
Finally, there are some amino acids that are still ionizable but are actually uncharged at physiological pH, which is why we don't have them grouped up here with our charged amino acids at physiological pH. Those 2 amino acids that can become charged but at a different pH are cysteine and tyrosine. When you add all these groups up, there are a total of 7 amino acids that are ionizable, which means, of course, that the rest of the 20 are going to be non-ionizable. Again, there are 13 amino acids that are non-ionizable and not capable of gaining a charge. Now, I want to take a look at these ionizable, but mostly uncharged at physiological pH, amino acids, which are cysteine and tyrosine. With cysteine, its three-letter code is CYS, and it has a sulfhydryl group as its R group. Cysteine's R group pKa, shown in this column over here, is 8.3. When the pH is above 8.3, cysteine's R group will donate its hydrogen and gain a negative charge. It's important to recognize how cysteine ionizes since we already know how the positive and negatively charged ones ionize. The other amino acid in this group is tyrosine, and notice tyrosine's pKa is 10.1. When the pH is above 10.1, tyrosine's R group will donate its hydrogen and gain a negative charge as well. It's important to recognize how these two ionize as we move forward in our practice problems and our next topics. This concludes our lesson on the distinction between non-ionizable and ionizable R groups, and I'll see you guys in our practice videos.
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Problem
Which pair of amino acids could form an ionic bond between the R-groups?
A
Asp & Glu
B
Gly & Leu
C
His & Arg
D
Cys & Lys
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concept
Memorizing Amino Acids With Ionizable R-Groups
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2m
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So now that we know that there are only 7 amino acids with ionizable R groups, you might be looking for a strategy to not only memorize the 7 amino acids, but also the nature of the ionizations for those R groups themselves in terms of whether they will gain a positive charge when they're ionized or will they gain a negative charge when they're ionized? And so, the good thing is that of these 7 amino acids, it actually includes all of the charged amino acids that we already memorized in our mnemonic, "Dragons Eat Knights Riding Horses." So, it includes those 5 in addition to the 2 that we talked about in our previous lesson, tyrosine or y and cysteine or c. And so in our example, we have the mnemonic to help us memorize all 7 of those amino acids and the nature of their ionizations. And so the mnemonic is just an extension to what we already know, and it's "Yucky Crazy Dragons Eat Knights Riding Horses." And so, basically, what we've added here is Tyrosine and Cysteine with yucky and crazy. And so 'yucky' and 'crazy' are both negative words. You can't really think of something positive when it comes to yucky crazy dragons trying to eat you. And so, notice that these all have negative charges, so there's a negative charge here as well. So the only ones that have a positive charge are the ones with the knights riding horses because they again, they're noble, they're coming to save the day, and they're positive. But there's nothing positive about yucky crazy dragons trying to eat you, so they're all negative. And again, there's a distinction between the 'yucky' and the 'crazy', the tyrosine and the cysteine, from the dragons eating. Even though they're both negatively charged, there's a distinction, and that's shown by the blue shade and the yellow shade. And so with the blue shade, the difference is that these, tyrosine and cysteine, are uncharged at pH 7. At physiological pH, they're uncharged. And that's why we didn't group them originally with the charged amino acids, which are all charged around physiological pH. But even though tyrosine and cysteine, again, are uncharged at physiological pH, they are likely to be ionized and gain a charge at other pHs. And so that's why we've got this mnemonic to help us memorize them. And so hopefully, this will help you guys with a memory tool and, we'll be able to utilize it as we move along through our course. So this concludes this lesson, and I'll see you guys in our next video.
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Non-Ionizable Vs. Ionizable R-Groups
Here’s what students ask on this topic:
What are the differences between ionizable and non-ionizable R groups in amino acids?
Ionizable R groups in amino acids can gain or lose a charge through acid-base reactions, resulting in three pKa values: one for the amino group, one for the carboxyl group, and one for the R group. These R groups can form ionic bonds and are crucial for protein structure and function. Examples include arginine, histidine, lysine, aspartic acid, glutamic acid, cysteine, and tyrosine. Non-ionizable R groups, on the other hand, are uncharged and lack acid-base reactions, having only two pKa values (amino and carboxyl groups). They cannot form ionic bonds. There are 13 amino acids with non-ionizable R groups, such as glycine, alanine, and valine.
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How many amino acids have ionizable R groups, and what are they?
There are seven amino acids with ionizable R groups. These include three positively charged amino acids at physiological pH: arginine, histidine, and lysine. Two negatively charged amino acids at physiological pH are aspartic acid and glutamic acid. Additionally, cysteine and tyrosine have ionizable R groups but are uncharged at physiological pH. These amino acids can gain or lose a charge depending on the pH, which is crucial for their role in protein structure and function.
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Why do amino acids with ionizable R groups have three pKa values?
Amino acids with ionizable R groups have three pKa values because they can participate in acid-base reactions at three different sites: the amino group, the carboxyl group, and the R group. The R group can gain or lose a proton, resulting in a charge. This additional pKa value for the R group allows these amino acids to form ionic bonds and participate in various biochemical processes, making them essential for protein structure and function.
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What is the mnemonic to remember the ionizable amino acids and their charges?
The mnemonic to remember the ionizable amino acids and their charges is 'Yucky Crazy Dragons Eat Knights Riding Horses.' This helps recall the seven ionizable amino acids: Tyrosine (Y), Cysteine (C), Aspartic acid (D), Glutamic acid (E), Lysine (K), Arginine (R), and Histidine (H). 'Yucky' and 'Crazy' represent Tyrosine and Cysteine, which are uncharged at physiological pH but can ionize at higher pH levels. 'Dragons Eat' represents the negatively charged amino acids (Aspartic acid and Glutamic acid), while 'Knights Riding Horses' represents the positively charged amino acids (Lysine, Arginine, and Histidine).
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How do cysteine and tyrosine ionize at different pH levels?
Cysteine and tyrosine have ionizable R groups that are uncharged at physiological pH (7.0) but can ionize at higher pH levels. Cysteine has a pKa of 8.3 for its sulfhydryl group, meaning it will donate a proton and gain a negative charge when the pH is above 8.3. Tyrosine has a pKa of 10.1 for its phenolic hydroxyl group, so it will donate a proton and gain a negative charge when the pH is above 10.1. Understanding these ionization properties is crucial for studying protein structure and function.
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