MP 31 : Biochemistry on the MCAT – Breaking Down a Passage

Session 31

This week, we discuss a biochemistry passage where Bryan breaks down how to read the passage and look through the answers. Biochemistry is Bryan's favorite part of the MCAT and I'm not sure if the same holds true for you. They're all probably bad and biochemistry is probably the “lesser of two evils” but we're here to make it less bad for you.

[02:30] Biochemistry Passage:

Potentiometric titration is a useful means of characterizing an acid. No indicator is used. Instead, the cell potential is measured across the analyte solution. When cell potential is plotted against titrant volume added, the equivalence point is the cell potential at the inflection point, the midpoint of the steep segment of the titration curve.

For polyprotic acids, an acidic hydrogen will produce an inflection point only if it is not very weakly acidic and if its ionization constant differs from that of any other acidic hydrogen of the acid by at least a factor of 104.

Captopril (molecular weight: 217.29 g/mol), shown in Figure 1, is a competitive inhibitor of angiotensin-converting enzyme (ACE). In the figure for Captopril, we're shown two acidic Hydrogens, one on a Sulfur that has a pKa of 9.8 and another on a carboxylic acid that has a pKa of 3.7. So Captopril has two acidic protons, one at 9.8 and one at 3.7 for the pKa's.

Students studying captopril were provided the following in vivo IC50 values (the minimum plasma concentration needed to inhibit 50% of target enzyme activity). The pH range shows that below 3.7, the IC50 is 0.058. Between 3.8 – 9.5, the IC50 drops from 0.05 all the way down to 0.01 so it's much lower. Once the pH gets above 9.6, the IC50 goes back up to over 0.06. So a notable lower IC50 in the middle of the pH range.

So we've got an organic molecule Captopril with two acidic protons at a pKa of 9.8 to 3.7. The IC50, the amount of this inhibitor you need to get to 50% inhibition is really low, in between those two numbers. So it's much more powerful inhibition in that part of their pH range.

[05:00] Question #24:

If students performed an enzyme-inhibition assay using Captopril, which of the following changes in the kinetic parameters of ACE should be expected?

Answer choices: The Vmax goes up or down or is unchanged and the Km is increased or decreased or unchanged.

Bryan's Insights:

Changes in Vmax or changes in Km depend on what kind of an inhibitor it is. Going back to the passage, we know that Captopril is a competitive inhibitor. What you're expected to walk into the test is that as a competitive inhibitor, it doesn't change the Vmax. So it's unchanged. That then narrows us down to choices (C) and (D).

In order to get to the Vmax, you have to add a lot more substrate and flood out the inhibition with tons of the natural substrate. This means that the Km (the substrate concentration required to reach 1/2 Vmax) goes up.

So Captopril as a competitive inhibitor, Vmax is unchanged, Km is increased. And that leads us to answer choice (D).

[06:36] Pure Outside Knowledge

This is a question where about 70% of the students get right. So this is somewhere between easy to medium level of difficulty. But it's important that for questions like this, make sure you're keeping up with the crowd. This means you need to find places where you can do better than other premeds. At the bare minimum, on the more straightforward questions like this, you really need to be keeping up with the pack. So competitive inhibitor, Vmax unchanged, Km increased.

This is strictly a matter of knowledge. It's a common style of questioning on the MCAT. Every passage is basically going to have one or two questions like this where you have to look up a single fact from the passage, in this case, the Captopril was a competitive inhibitor. Other than that, it is just pure outside knowledge.

[07:50] Question #25:

Which of the following protonation states of the Captopril thiol and Carboxyl groups is required to maximize Captropril's inhibition of ACE?

We have to decide whether to have the thiol group be protonated or deprotonated and have the carboxylic acid group either protonated or deprotonated.

Bryan’s Insights:

Going back to the table, the extra little step of reasoning we have to apply here is that if you want to maximize the inhibition, you want to minimize the IC50 (the amount of inhibitor needed to get to 50% inhibition). So if you're a really strong inhibitor doing your job really well, you don't need to add much. A little dab will get you to half inhibition. Based on the table, it was the pH range in the middle, between 3.8 and 9.5. Unsurprisingly, this drug does its best work at a normal physiological pH (around 7 to 7.3).

Looking at the Figure for Captopril, if your pH is in the middle of the pH range, the carboxylic acid is going to be deprotonated, which means you have to strip the proton off that since the pKa for that is only 3.7. If the pH is over the pKa (the pH is really high and you're in a really basic environment relative to that group or molecule), you deprotonate it. So you deprotonate the carboxyl group.

The hydrogen and the sulfur to the thiol group had a pKa of 9.8 so we're below that. Relative to 9.8, being a neutral pH is actually relatively acidic from the Sulfur's point of view. The sulfur would then be protonated.

Knowing that the thiol is going to be protonated and the carboxylic group is going to be deprotonated, this would then lead us to answer choice (B).

[10:18] The Paradox in Biochemistry

It's a common style of reasoning in biochemistry where they something like, “This is variable is the amount of x needed to get to y.” Seeing that, you'd say, “Lower amounts of x, it's a powerful molecule so you don't need as much x to get the job done.” It's this weird paradoxical thing in biochemistry where smaller numbers have more oomph to whatever you're looking at.

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Transcript

Introduction

Dr. Ryan Gray: The MCAT Podcast is part of the Med Ed Media network at www.MedEdMedia.com. Now part of the Med Ed Media network is The Short Coat Podcast at www.TheShortCoat.com. The Short Coat Podcast is a broadcast from the amazing and intense world of medical school from the students at the University of Iowa Carver College of Medicine. Go check them out at www.TheShortCoat.com and check out everything that we're doing at www.MedEdMedia.com.

This is The MCAT Podcast, session number 31.

A collaboration between the Medical School Headquarters and Next Step Test Prep, The MCAT Podcast is here to make sure you have the information you need to succeed on your MCAT test day. We all know that the MCAT is one of the biggest hurdles, and this podcast will give you the motivation and information that you need to know to help get you the score you deserve so you can one day call yourself a physician.

As I mentioned at the beginning, the Short Coat Podcast is now part of the Med Ed Media network. Go check out everything that we do at www.MedEdMedia.com.

If this is your first time joining us here at The MCAT Podcast, I usually do not sound like this, I just got back from a conference and my voice is shot, but we push on. Today we're going to dig in and talk about biochemistry.

Bryan, welcome back for another MCAT Podcast. Are you so excited today?

Bryan Schnedeker: Very excited, I'm also happy to do biochemistry, it is my favorite part of the MCAT.

Dr. Ryan Gray: I don't know if ‘favorite' is the right word for the majority of students listening, but we'll let you have this one.

Bryan Schnedeker: Sure. Yeah it's a weird place to have favorites, right? What would be your favorite place on your body to get punched? It kind of isn't really a good choice.

Dr. Ryan Gray: Yes I would agree with that. It's like- I hate to compare it to elections, but it's one of those ‘it's the lesser of two evils' kind of things. They're all bad, you've just got to dive in and go.

Biochemistry Passage Question #1

Bryan Schnedeker: Well we're here to make it a little less bad for you. So we're looking at a biochem passage today. As always if you're on the website and can print out the handout, that would be great. This is a relatively short passage so I'm actually just going to go ahead and read it for the listeners. So it says, ‘Potentiometric titration is a useful means of characterizing an acid, no indicator is used. Instead, cell potential is measured across the [Inaudible 00:02:42] solution. When cell potential is plotted against titrant volume added, the equivalence point is the cell potential inflection point, the midpoint or the steep segment of the titration curve. For polyprotic acids an acidic hydrogen will produce an inflection point only if it's not very weakly acidic and if its ionization constant differs from that of any other acidic hydrogen by a factor of at least ten to the fourth. Captopril, which is pictured in figure one, so it's a small organic molecule. Captopril is a competitive inhibitor of angiotensin converting enzyme, ACE. It's a very clinically important enzyme. So Captopril is a competitive inhibitor of ACE. In the figure for Captopril, we're shown two acidic hydrogens, one on a sulfur that has a PKA of 9.8, and another on a carboxylic acid that has a PK of 3.7. So Captopril has two acidic protons, one at 9.8, one at 3.7 for their PKAs. Students studying Captopril were provided the following in vivo IC50 values. The minimum plasma concentration needed to inhibit 50% of the target enzyme activity. So the IC50 is the amount needed to get to 50% inhibition. And the PH range shows us that below 3.7, the IC50 is 0.058. Between 3.8 and 9.5, the IC50 drops from 0.05 all the way down to 0.01, much lower. And then once the PH gets about 9.6, the IC50 goes back up to over 0.06. So a notably lower IC50 in the middle of the PH range there. So we've got again, an organic molecule Captopril with two acidic protons at a PKA of 9.8 and 3.7, and the IC50, the amount of this inhibitor that you need to get to 50% inhibition is really low in between those two numbers. So it's much more powerful inhibition in that part of the PH range. So now the questions we want to look at here. So first, question number 24, ‘If students perform an enzyme inhibition assay using Captopril, which of the following changes in the kinetic parameters of ACE should be expected?' The Vmax goes up or down or is unchanged, and the Km is increased or decreased or unchanged. So looking at the answer choices there Ryan, we know that changes in Vmax or changes in Km, those depend on what kind of an inhibitor it is. So this is one where we need to go back to the passage just to refresh our memory really quickly, and see what kind of inhibitor we were told Captopril is. And in this case we were told it is a competitive inhibitor. And so Ryan, do you remember what competitive inhibitors do to the Vmax?

Dr. Ryan Gray: I have no idea.

Bryan Schnedeker: Yeah it's one of those things that you remember for the MCAT and then promptly forget. So you're expected to walk into the test, just from outside knowledge, knowing a competitive inhibitor doesn't change the Vmax, it's unchanged, so that narrows us down to choices C and D. But that in order to get to the Vmax you have to add a lot more substrate. You would have to flood out the inhibition with tons of the natural substrate. What that means is the Km, which is the substrate concentration required to reach one half Vmax, it's the definition of Km, the Km goes up. So a competitive inhibitor, Vmax is unchanged, Km is increased, and that leads us to answer choice D. Now that's a question that about 70% of students get right, so it's somewhere between kind of a medium and easy difficulty question, but it's real important on questions like that to make sure you're keeping up with the crowd. The MCAT is a real competitive environment, like a lot of kind of premed life, very competitive. Fortunately not once you get to med school, much more cooperative in med school. And what that means is of course you need to be finding places where you can do better than other premeds, and at the bare minimum on the more straightforward questions like this, you really do need to be keeping up with the pack. So competitive inhibitor, Vmax unchanged, Km increased.

Dr. Ryan Gray: Is this one where it's strictly this is just something you know about competitive inhibitors? Or are students trying to figure something out and that's where they're getting it wrong?

Bryan Schnedeker: It's a matter strictly of knowledge. The very common style of question on the MCAT, basically every passage is going to have one or two questions like this where really you have to look up a single fact from the passage, in this case the Captopril was a competitive inhibitor, and then other than that it is just pure outside knowledge.

Dr. Ryan Gray: Okay.

Biochemistry Passage Question #2

Bryan Schnedeker: Yeah. Alright let's do one more from this passage, number 25. Which of the following protonation states of the Captopril thiol and carboxyl groups is required to maximize Captopril's inhibition of ACE? And we have to decide to either have the thiol group be protonated or deprotonated, and have the carboxylic acid group either protonated or deprotonated. And so for this again, we would go back to the table. The question said to maximize the inhibition, and so the extra little step of reasoning we have to apply here is that if you want to maximize the inhibition, you want to minimize the IC50, the amount of inhibitor needed to get to 50% inhibition. So if you're a really strong inhibitor, doing your job really well, you don't need to add much, just a little dab will do you- will get you to half inhibition. And so we said when we saw this in the table that it was the PH range right in the middle between 3.8 and 9.5. So unsurprisingly, this drug does its best work at a normal physiological PH, right around 7.0, 7.3. Looking at the figure for Captopril, if your PH is in the middle of the PH range, a carboxylic acid is going to be deprotonated. You're going to strip the proton off that because the PKA for that is only 3.7, and if the PH is over the PKA, that is the PH is really high, you're in a really basic environment relative to that group or molecule, you deprotonate it. So we're deprotonating the carboxyl group and then the hydrogen on the sulfur, the thiol group, had a PKA of 9.8 so we're below that. Relative to 9.8 being that kind of a neutral PH is actually relatively acidic from the sulfur's point of view, so the sulfur would then be protonated. So knowing that the thiol is going to be protonated and the carboxylic group is going to be deprotonated would send us there to answer choice B.

Dr. Ryan Gray: Makes sense. So this one you obviously need to understand what you had said, looking at that table and going, ‘Okay maximum Captopril inhibition, I need that middle value on the table, the lowest IC50,' and then looking at those PK values or PKA values and figuring out what happens there.

Bryan Schnedeker: Yeah that's a common style of reasoning in biochemistry where they say something like, ‘This variable is the amount of X needed to get to Y,' whatever it is. And so when you see that you know oh okay, so lower amounts of X mean it's a more powerful molecule because I didn't need as much X to get the job done. So it's this weird little kind of paradoxical thing in a lot of this biochemistry reasoning where smaller numbers means a more oomph to whatever you're looking at.

Final Thoughts

Dr. Ryan Gray: Alright there you go, biochemistry broken down by the magical Bryan from Next Step Test Prep. If you are still unsure about how you are going to prepare for the MCAT, go check out everything that Next Step Test Prep is doing over at www.NextStepTestPrep.com. They are known for their one-on-one tutoring but they now have an amazing course- online course that you can take that includes not only all of the content that you need, but also office hours with the people that created the content. Go check out their course and everything they're doing and use the code MCATPOD all capital letters, MCATPOD, to save some money.

I hope you enjoyed the show today. If you did I'd love for you to tell somebody about it. Go tell your advisor, your classmate, your mom, your dad, whoever, just go tell someone. And don't forget to check us out next week here at The MCAT Podcast and Med Ed Media.

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