Amino Acid Discussion and High-Yield Discretes

Session 151

Today, we highlight some of the key concepts for Amino Acids. We’re joined once again by Clara from Blueprint MCAT (formerly Next Step Test Prep)

Check out the review I made on the MCATCourseReview.com to find out more about their course and what students say about them.

High-Yield Topic in Biochemistry: Amino Acids

[01:50] Why Amino Acids Are So Important

Amino acids are huge on the MCAT. Interestingly, they weren’t tested at all prior to 2015. Amino acids are relevant to diseases and their fundamental role in proteins. They’re relevant to biology, general chemistry, organic chemistry, etc.

'You can almost ask about everything on the MCAT in relation to amino acids.'Click To Tweet

[03:55] Question 1

An unknown amino acid is titrated with 1 M NaOH according to the following titration curve. (The titration curve has three points labeled 2.18, 8.95, and 10.53. It’s a totally standard titration curve but we need to figure out what this means.)

Based on the given curve, the unknown amino acid is most likely:

Ser.
Asp.
Lys.
Ala.

Clara’s insights:

There are so many steps to amino acid questions. The first step is knowing what the abbreviations mean. Ser. is Serine. Asp. is Aspartic acid or Aspartate. (Aspargine has an abbreviation of Asn.) Lys. is Lysine and Ala. is Alanine.chfhn

If you can’t get past this step, you’re in big trouble. But even once you get past this step, you still have a lot more to do.

The next step is to look at the titration curve. There are three numbers listed on it. Even if you don’t remember much about titrations, you should know that there are three equivalence points.

This means our amino acid has three acidic or basic groups. Amino acids are either two or three. Serine or Alanine only have two because their side chains are not acidic or basic. They have two groups that can be protonated or deprotonated but they only have two. They don’t have a third one. So these two are out.

We’re now down between Asp. and Lys. Aspartic acid is acidic so its side chain does have a half-equivalence point. Lysine is basic so its side chain has one as well.

Now, you have to look at the numbers themselves to tell which is the right answer. The first point (2.18) is the standard pKA for a carboxylic acid. Every single amino acid you see on the MCAT is going to have around 2.0 and one of these pKAs.

The second one (8.95) is a standard PKA for an amino group, which every amino acid also has. This doesn’t help us.

But the third one here at 10.53 is a really high pKa. When you see high pKa’s with amino acids, think basic just like you would think high pH is basic. And we’re looking for a basic amino acid here so the answer is Lysine.

[08:55] A Basic Rundown of Amino Acids

The most important thing to know about every amino acid is the abbreviation. There’s the one-letter abbreviation and the three-letter abbreviation. The former tends to be harder and they’re used more frequently so you should focus on that.

The next thing you need to know is the status of each side chain. Amino acids all have the same background structure. Their side chains are what is different. Whether an amino acid is acidic or nonpolar or uncharged, this would be all in relation to the side chain.

All that being said, you need to know every one of the 20 amino acids and what word essentially describes its side chain. Is it polar, nonpolar, etc?

Then understand how those side chains interact with acid-base chemistry. In this case, three pKa’s would mean it’s either basic or acidic amino acid. This is the next conceptual level that you should go up.

A lot of biochemistry classes will tell people to memorize the exact structures of all the amino acids. You don’t need to do this for the MCAT. If you want to draw them, that’s fine. But you won’t be asked to draw them. You just need to know the abbreviation and whether they’re acidic or basic. What does it mean for general chemistry?

[11:35] Question 4

The alpha helix is a common form of secondary structure in proteins. It is a compact, right-handed helical structure that is stabilized by tight packing, as well as hydrogen bonding between backbone C=O and amino groups. Based on this information, the incorporation of which amino acid would most disrupt the alpha helix?

(A) Alanine

(B) Aspartic acid

(D) Proline

Clara’s insights:

The correct answer here is Proline.

A handful of amino acids have weird characteristics. And this is a fact you should memorize. Proline has a really interesting structure. Its amino group is actually attached to its side chain.

Because of this, it’s bent in a way that a regular amino acid isn’t. It introduces kinks in alpha helices. So proline is just the amino acid that disrupts alpha helices and this is something you should know about.

As mentioned, Proline disrupts alpha helices. Methionine and Cysteine have sulfur in them. There are always these simple facts that you should know about.

[16:00] Question 6

Which of these statements describe(s) the amino acid W at physiological pH?

It has no net electrical charge.
It is not a zwitterion.

III. It is neither acidic nor basic.

(A) II only

(B) III only

(D) I, II, and III

Clara’s insights:

W is Tryptophan. In fact, it’s the one with the weirdest abbreviation. But there’s actually a trick for this. Look at its structure and it will really stand out as having these two rings that are next to each other. And W is like two V’s next to each other, so Tryptophan has these two rings right next to each other.

As long as you know what Tryptophan’s side chain is like then you’d be in pretty good shape. It has a side chain that cannot become charged. So it’s neither basic nor acidic. It doesn’t become protonated or deprotonated.

Based on this, you can pick the right answer. As soon as you know that a side chain doesn’t become protonated or deprotonated, we know that III is right. (This makes us get rid of answer choice A).

Know that for all of those amino acids, they’re all zwitterions at physiological pH. They’re basically a species of molecule that has equal numbers of positive and negative charges. So even if they’re charged, they still come out as neutral. And Tryptophan is one of those at physiological pH. II is out then since it’s a zwitterion.

I (no electrical charge) is characteristic of a zwitterion and this holds true to all zwitterions. They always have no net charge. Hence, I is correct.

Therefore, the correct answer here is C.