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3. Amino Acids

1

Isoelectric Point Of Amino Acids With Ionizable R-Groups

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in this video, we're gonna calculate the is electric point of amino acids with invisible are groups. So it turns out that calculating the isil electric point of amino acids with invisible are groups is just a little bit more challenging than calculating the same for amino acids with non invisible are groups. And that's because amino acids with invisible are groups have three p k A values instead of just two PK A values like those of amino acids with non ionized well, our groups. But the is electric point or the P I is still on Lee an average of just two PK a values. And that's why it's a little bit more challenging because now we have to consider the following question, which is? How do we know which PK a values toe average? So again recall that amino acids with non ionized bar groups only have two PK A values, so that makes it really easy to figure out which to PK a values we need to average to get the isil electric point. But with amino acids with ionized able are groups, they have three p k a values. So now we need to figure out which two of the three p k a values do we need to average to get Theis Electric point. And we've got these four steps to help us figure out which PK a values toe average and down below. In our example, we have the same exact four steps just listed in, um, or visual way and a diagram or a flow chart. And so when we go through each of the steps up above, if they don't quite click with you guys right away, hang on tight. Because once we get to our example and apply the steps in our exams in our example problem the steps are gonna make more sense to you guys. And as we get more and more practice utilizing the steps, the steps are gonna make Mawr and Mawr sense. And so the first step is to just know the net charge of both the person ated as well as the deep protein ated forms of ionized able are groups. And so recall from our previous lesson videos that we have in demonic to help us memorize the seven amino acids with Ryan Izabal are groups. And that demonic is just yucky crazy dragons eat nights riding horses. And so if you know this pneumonic, you know not only the seven amino acids with invisible are groups, but also the nature of the immunizations in terms of having a positive or a negative charge when they are protein ated or deep rotated. And so that's all step number one is really saying is to familiarize yourself with this pneumonic up here. Now, step number two is toe order the three p. K A. Values from smallest toe largest. And then to use the Middle Pekka as a guide and step number three. And again, this will make more sense once we get to our example down below. Now, the third step is to determine the net charge of the predominant amino acid structure at any pH that we want as long as that pH falls between adjacent PK a values. And so again, this will make more sense down below in our example. And then the fourth and final step is toe average. Of course, on Lee to PK A values the middle PK from step number two as well as another PK that needs to be determined and that PK is gonna be the one that's closest to the pH. That gives an overall neutral net charge on the predominant structure from Step number three. And again, this will make more sense in our example below. So in our example, it's asking us to calculate the is electric point of tyrosine and tire scenes. One letter code is just a Y. And so that means we know that tire scene has an ionized Volare group because it falls into our pneumonic up here of yucky crazy dragons eat nights riding horses. And so the why here stands for yucky and yucky is a negative word. And because yucky is a negative word that tells us that tyrosine, our group has a negative charge when it's ionized and really, that's all. Step number one is asking of a step. Number one wants us to know how the amino acids are groups ionized. And so just by knowing this pneumonic and knowing that tire scenes are group has a negative charge. When it's ionized, step number one is complete, so Step number two is to order the three p k A values from smallest to the greatest, and so were given thes three p k A values for Tyra scenes. Three invisible groups. And we know that Alfa Amino groups have, uh, ballpark PK a range from about 9 to 10.5. And really, there are two p. K s that fall into this potential range. So how do we know which one of these two p. K's is the one for the Alfa Amino Group? And the way that we know is because of the PKR that's here. So the PKR tells us that this is the PK of the our group. And that, of course, means that this must be the PK of the amino groups. So let's go ahead and label it as the amino Group p K. And then we can label this one over. Here is the our group PK and, of course, the one in the middle here. PK, too, must be the PK of the car Boxer group, And that's because car boxer groups have a peek a ballpark range of about two, so that falls right into that range. So now we can go ahead and fill a complete step. Number two, which is just order these P ks from smallest to largest and the smallest PK is P K two of 2.2, so we could go ahead and put that over here. The next one is PK of the Amino group, which is 9.1 that's the next smallest. And then the greatest one is the PK of the our group or the PKR, which is 10.1. And so now we've ordered them, and step number two is complete so we could go ahead and check that off. And the next step we're gonna use the middle PK or PK of the amino group as a guide and step number three and step number three just wants us to determine the net charge of predominant structures at any pH that we want as long as it falls between adjacent pairs of PKK's. And so essentially, all that saying is use the middle PK as a guide, and the region that's between these two PK is here is one region of interest, and the other region over here is another region of interest. And so what we want to do is determine the predominant structure and determine the net charge of the predominant structure and each of these two regions And so what we can do is you can either imagine or draw the predominant structure to determine the Net charges. Um, on DSO for now, I would say Get more practice drawing the structure since you guys are kind of new to that. But aside, you get better and better. At these practice problems, you'll be able to save a lot of time by just imagining the structures rather than just drawing them out. And so the way that we determine the predominant structures recall is Thio. Compare the pH to all of the P K A values. So let's go ahead and let's do this yellow region first. So the yellow region here corresponds with this region here between these two PKs and this blue region corresponds with this region between these two be gays. And so let's check the yellow region first just because we normally do things from left to right. But it doesn't matter which region you decide to check first so we can choose any pH that we want as long as it falls between these two values. So let's just go ahead and choose a Ph of five, and so now we need to do is compare the pH to each of the individual PK. So let's start with the PKK of the amino group. So the PK of the amino group is greater than the Ph of five. And so that means the pH is less than the PK PK. So pH is less than the p k A. For the amino group. And with that recall from our previous lesson videos that when the pH is less than the PK, this means that the conjugate acid form predominates, and so that the conjugate acid form of the amino group is going to be an NH three plus. And so it's gonna have a positive charge on it. And so down below, we've pre John in the structures for most of tire scenes. Um, structure, Uh, except for the ionized able groups. So we can go ahead and fill in the amino group NH within NH three plus for this yellow region. So now we could do the same for the Car Boxer group. The car boxer groups PK is 2.2, which is smaller than the pH. This time the pH is greater, so the pH is greater than the PK this time. And when the pH is greater than the PK, the conjugate base form predominates and the college get base form of the car. Boxer Group is gonna be a deep protein ated car, Boxley and I and so Seo minus or over here, we could just put in the O minus. And so we've got that group. Now we can do is fail in our final ionized well, group, which is gonna be the hydroxyl group down below. On our, um, Tyra, scenes are group, and so the PKR is 10.1 and 10.1 is greater than ph of five. And so the pH is smaller. So when the pH is smaller, thin the PK or the PKR, that means that the conjugate acid is gonna predominate. And the kind of get acid of the our group here is gonna be a protein ated our group or one that has the hydrogen on it. So it's gonna be a hydroxyl group with the hydrogen. It's gonna be neutral. And so what you'll see is that this charge here cancels out with this charge over here. And the overall net charge of the structure is going to be a net charge of zero. And that's exactly what we were looking for. We were looking for the region that gives us the net charge of zero. So we did it. We chose the right region by choosing this yellow region. But if we had chosen this blue region by accident, we just decided to choose that one. Then we would do a similar process. We would pick any pH between these two, and so we could pick a Ph of say, I don't know, 9.5. It falls right between these two, and then we would do the same exact thing. Compare the Ph to each of the P. K. S and notice that the Onley thing that changes is that now the PK of the Amino group is smaller than the pH appear. But everything else is gonna be exactly the same. So what that means is that the amino group is gonna be the only one to change. And the amino group was protein ated over here. But because this time the pH is greater than the PK here, that means that the amino group is gonna be in its conjugate base form And that means the Amino group is gonna b NH two instead of, uh, NH three plus. So it's gonna be neutral, and all of the other groups are gonna be exactly the same as they were over here on the left. And so what you'll see is that this structure over here is gonna have a net charge of negative one. And so once we really, if we had chosen this blue region first we would have realized it had a negative one charge, and then we would have realized that's the wrong region. It doesn't have a neutral net charge, so we need to check a different region and we would have checked this yellow region. And so now that we've chosen this correct region, that we move on to our fourth step, which is to just average calculate the p I by averaging the middle PK with the other PK, that's sandwiching the predominant structure that has a neutral net charge. So the middle PK would be this PK right here PK of 9.1. So we'll highlighted, agreed on then the one that sandwiching the structure that has a neutral that charge the neutral that charge was found in this yellow region. And so the PK that's sandwiching that region is gonna be this one. So all we need to do is average these two PKs and green to get the is electric points. So the is electric point is gonna be 9.1 plus 2.2, divided by two. So this comes out to 11.3, divided by two, which comes out to 5.65 Which means that this answer right here corresponds with answer option D, and that d here is our is electric point. And we can cross off all of the other options which are incorrect. And so we'll be able to get a lot more practice in our next couple of videos. Calculating the isil electric point of amino acids with invisible are groups. So I'll see you guys in those videos.

2

Problem

What is the pI of His?

A

7.59

B

6.58

C

3.91

D

5.5

3

Problem

Electrophoresis separates molecules by migration through a gel only if they have a net charge. How do you expect an amino acid to migrate during electrophoresis when the pH = pI?

A

Migrate from the (-) end to the (+) end.

B

Migrate from the (+) end to the (-) end.

C

No migration.

4

Problem

Draw Glu and calculate its isoelectric point. pK_{a1} = 9.67. pK_{a2} = 2.19. pK_{R} = 4.25.

A

7.48

B

3.22

C

6.96

D

5.93

5

Problem

Calculate Cys’s pI.

A

2.3

B

3.14

C

5.05

D

6.05

6

Problem

Calculate the pI of Arg. pK_{a1} = 9. pK_{a2} = 2.2. pK_{R} = 12.5.

A

1.9

B

10.75

C

3.6

D

12.5

7

Problem

Calculate the pI of Asp.

A

1.4

B

3

C

5.95

D

6.85

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