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MCAT Biochemistry - OLD > Amino Acids > Flashcards

Flashcards in Amino Acids Deck (58)
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1
Q

Which two functional groups are found in all amino acids?

A

An amino acid must contain an amine and a carboxylic acid. Each amino acid also contains a specific side chain.

Amino acids that are tested on the MCAT are alpha amino acids, meaning that the amine group and the side chain are both bound to the carbon adjacent to the carbonyl carbon.

2
Q

What functional group is present in all peptide bonds?

A

Peptide bonds contain amides. In fact, they are sometimes alternatively known as amide linkages.

A peptide bond forms when the amine group of one amino acid attacks the carbonyl carbon of another. This is a nucleophilic substitution reaction.

3
Q

What name is given to the form of glycine pictured below?

A

This molecule is a zwitterion, meaning it is neutral overall but carries both positive and negative charge.

Amino acids often exist as zwitterions, depending on the pH of the surroundings. This is true because the carboxylic acid group is readily deprotonated, while the amine is readily protonated.

4
Q

What is the approximate pKa of an amino acid’s carboxylic acid group?

A

The carboxylic acid group has a pKa of around 2 (broadly, between 1.5 and 3). On average, it is protonated at a pH below that value and deprotonated at a pH above it.

In a polypeptide, the carboxylic acid that does not participate in a peptide bond is known as the carboxy terminus.

5
Q

What is the approximate pKa of an amino acid’s amine group?

A

The amine group has a pKa of around 9-10. On average, it is protonated at a pH below that value and deprotonated at a pH above it.

In a polypeptide, the amine that does not participate in a peptide bond is known as the amino terminus.

6
Q

What is the isoelectric point of an amino acid?

A

The isoelectric point, or pI, is the pH at which an amino acid is neutral overall.

When the surrounding pH is lower than the isoelectric point, the amino acid in question will have a net positive charge. When the surrounding pH is higher, its net charge will be negative.

7
Q

Explain how to calculate the pI of an amino acid with an uncharged side chain.

A

To calculate the pI, simply average the pKas of the carboxylic acid and amino groups.

For example, the two pKas of glycine are 2.34 (carboxylic acid) and 9.60 (amine). The pI of glycine is thus (2.34 + 9.60) / 2, or 5.97.

8
Q

Explain how to calculate the pI of an amino acid with a charged side chain.

A

For acidic amino acids, average the two most acidic pKas. For basic amino acids, average the two most basic pKas. Remember, do not average all three values!

For example, the three pKas of lysine are 2.18 (carboxylic acid), 8.95 (amine), and 10.53 (side chain). Since its R group is basic, its pKa is thus (8.95 + 10.53) / 2, or 9.74.

9
Q

The three pKas for arginine are 2.17, 9.04, and 12.48. These correspond to the carboxylic acid, the amine in the backbone, and the R group, respectively. What is arginine’s pI?

A

The pI of arginine is 10.76.

Arginine has a basic side chain, so its pI can be calculated by averaging its two most basic pKas. (9.04 + 12.48) / 2 = 10.76.

10
Q

What value can be compared to pH to determine whether a specific group on an amino acid is protonated?

A

The pKa of that group can be compared to the pH of the surroundings.

Specifically, if pH is less (more acidic) than the pKa, that group will be protonated. If pH is greater (more basic) than pKa, the group will be deprotonated.

11
Q

What value can be compared to pH to determine whether an entire amino acid is charged overall?

A

The isoelectric point, or pI, of the amino acid can be compared to the pH of the surroundings.

Specifically, if pH is less than the pI, the amino acid will be positively charged. If pH is greater than the pI, the group will be negative.

12
Q

Which of the standard amino acids, if any, are chiral?

A

All standard amino acids are chiral except for glycine.

Nearly all of the amino acids seen on the MCAT have at least one chiral center, the alpha carbon. Glycine is the one exception: its R group is simply a hydrogen atom, so its alpha carbon is not bound to four different groups.

13
Q

With the exception of glycine, every amino acid can exist in two potential configurations. What names are given to these forms?

A

Amino acid configurations can either be D (dextrorotatory) or L (levorotatory). These forms are enantiomers.

These configurations are similar to those used in sugars. When drawn as Fischer projections, a D amino acid has the amino group pointing to the right, while the amino group of an L isomer points to the left.

14
Q

What is the relationship between D-leucine and L-leucine?

A

These two amino acids are enantiomers. All amino acids except glycine can be found as either D or L stereoisomers.

Note that only L amino acids are found in proteins. Human (and other) enzymes are stereospecific and react with the L isomer alone.

15
Q

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A

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16
Q

What chemical property is shared by lysine, aspartic acid, histidine, arginine, and glutamic acid?

A

These amino acids all have side chains that can be charged. More specifically, they are all classified as either acidic or basic.

Lysine, histidine, and arginine have basic side chains, which are positive when protonated. Aspartic acid and glutamic acid have acidic side chains, which are negative when deprotonated. Histidine could act as a base or an acid, making it very active for enzymes.

17
Q

What word describes the interactions between polar amino acids and water?

A

Amino acids with polar side chains tend to be hydrophilic. This means that they interact well with water and, in some cases, can hydrogen bond.

On the MCAT, hydrophilicity / hydrophobicity is often tested as a comparison. You shoud be able to look at two structures and discern which is more polar than the other.

18
Q

What word describes the interactions between nonpolar amino acids and water?

A

Amino acids with nonpolar side chains tend to be hydrophobic. This means that they interact poorly with water and generally cluster with other nonpolar groups.

On the MCAT, hydrophilicity / hydrophobicity is often tested as a comparison. You should be able to look at two structures and discern which is more polar than the other.

Note that another term for “hydrophobic” is “lipophilic.”

19
Q

Which amino acids are acidic?

A

The two acidic amino acids are aspartic acid and glutamic acid.

Since the side chains of acidic amino acids are able to be deprotonated, they tend to be negatively charged above a pH of around 4.

Note that two additional amino acids, cysteine and tyrosine, have R groups that are able to lose a proton. While these side chains do have their own pKas, they are much higher than those of aspartic and glutamic acid.

20
Q

What names are given to the deprotonated forms of glutamic acid and aspartic acid, respectively?

A

The deprotonated form of glutamic acid is known as glutamate, while the deprotonated form of aspartic acid is aspartate.

It can help to remember that in general, deprotonated carboxylic acids are called “carboxylates.”

21
Q

Which amino acids are basic?

A

The three basic amino acids are arginine, lysine, and histidine.

Since the side chains of basic amino acids are able to be protonated, they tend to be positively charged in a low to moderate pH. While you don’t need to memorize actual pKa values, note that arginine has the most basic side chain, while histidine has the least basic of the three.

22
Q

Which amino acids contain at least one sulfur atom?

A

The sulfur-containing amino acids are cysteine and methionine.

Note that cysteine, but not methionine, can form disulfide bridges. When two cysteine molecules connect with a disulfide linkage, the resulting structure is known as cystine.

23
Q

Which amino acid tends to produce turns or “kinks” in a protein’s secondary structure?

A

Proline produces kinks in secondary structures such as alpha helices and beta sheets.

This occurs because proline, unlike any other common amino acid, has an R group that is bound directly to its amino terminal in a cyclic structure.

24
Q

Which amino acids contain aromatic rings?

A

Phenylalanine, tyrosine, and tryptophan all contain aromatic side chains. Note that while histidine is classified as a basic amino acid, its structure also includes an aromatic ring.

Remember that phenylalanine is simply “phenyl” (a benzene ring) plus “alanine.” Tyrosine’s side chain involves a phenol group, while tryptophan contains a two-ring system called an indole.

25
Q

How would you characterize the side chains of alanine, valine, leucine, and isoleucine?

A

These side chains are nonpolar. Specifically, they are small (<5 carbons) hydrocarbon chains.

As their names imply, leucine and isoleucine are structural isomers.

26
Q

Which amino acids contain at least one -OH on their side chains, but do not contain aromatic rings?

A

Serine and threonine contain hydroxyl (-OH) groups.

As a result, the side chains of both amino acids are classified as polar. Remember, -OH groups are not readily deprotonated, so these molecules are not acidic.

27
Q

The amino acids asparagine and glutamine are shown below. Are their R groups able to become charged?

A

No, their R groups remain uncharged. The groups present in these side chains are amides, which are neither acidic nor basic.

Do not fall for the trap of thinking that amides are basic (like amines)! The nitrogen atom of an amide is stable and unable to gain an additional proton in its usual form. Do note, however, that amides display an additional resonance structure in which the electrons from the carbon-oxygen double bond move to the carbon-nitrogen bond. In this form, the nitrogen can be positively charged.

28
Q

For aspartic acid, the pKas of the carboxy terminal, side chain, and amino terminal are 2.10, 3.86, and 9.82, respectively. Which of those groups will be protonated at a pH of 5?

A

Only the amino terminal will be protonated.

A group will be protonated at a pH lower than its pKa, and deprotonated at a higher pH. Only the amino terminal (pKa 9.82) is in a relatively more acidic solution.

29
Q

For lysine, the pKas of the carboxy terminal, side chain, and amino terminal are 2.18, 10.53, and 8.95, respectively. Which of those groups will be charged at physiological pH?

A

All three groups will be charged. The carboxy terminal will be deprotonated (negative), while the other two groups will be protonated (positive).

Be careful to discern whether a question asks about the charge or protonation state of a group. Acidic groups are only charged when deprotonated, while basic groups are charged when protonated.

30
Q

What will be the net charge on alanine at a pH of 1.2?

A

The net charge on alanine will be +1.

Since the pH is so extremely acidic here, we do not need to know the exact pKas of alanine’s two groups. The pKa of the carboxy terminal is around 2, so it will be protonated (making it a neutral COOH). The pKa of the amine is around 9-10, so it will also be protonated (making it NH3+).

31
Q

What will be the net charge on alanine at a pH of 11?

A

The net charge on alanine will be -1.

Since the pH is so extremely basic here, we do not need to know the exact pKas of alanine’s two groups. The pKa of the carboxy terminal is around 2, so it will be deprotonated (making it COO-). The pKa of the amine is around 9-10, so it will also be deprotonated (making it a neutral NH2).

32
Q

What will be the net charge on alanine at physiological pH?

A

The net charge on alanine will be zero. In other words, it will be a zwitterion and neutral overall.

Physiological pH is approximately 7.4. This is above the pKa of the carboxy terminal (leading it to be deprotonated, or COO-) but below that of the amino terminal (leading it to be protonated, or NH3+).

33
Q

At physiological pH, what is the net charge of both aspartic and glutamic acid?

A

Both amino acids will have a net charge of -1.

At physiological pH, all amino acids have deprotonated carboxy terminals (COO-) and protonated amino terminals (NH3+), so we only need to worry about the R groups. Both the molecules in question have acidic side chains, which will also be deprotonated (COO-) at a pH of 7.4.

34
Q

At physiological pH, what is the net charge of both lysine and arginine?

A

Both amino acids will have a net charge of +1.

At physiological pH, all amino acids have deprotonated carboxy terminals (COO-) and protonated amino terminals (NH3+), so we only need to worry about the R groups. Both the molecules in question have basic side chains, which will also be protonated (positive) at a pH of 7.4.

35
Q

What are the one-letter abbreviations for:

  • arginine?
  • cysteine?
  • histidine?
  • glutamine?
  • tryptophan?
A
  • arginine = R
  • cysteine = C
  • histidine = H
  • glutamine = Q
  • tryptophan = W
36
Q

What are the one-letter abbreviations for:

  • leucine?
  • asparagine?
  • tyrosine?
  • proline?
  • glycine?
A
  • leucine = L
  • asparagine = N
  • tyrosine = Y
  • proline = P
  • glycine = G
37
Q

What are the one-letter abbreviations for:

  • phenylalanine?
  • serine?
  • isoleucine?
  • glutamic acid?
  • methionine?
A
  • phenylalanine = F
  • serine = S
  • isoleucine = I
  • glutamic acid = E
  • methionine = M
38
Q

What are the one-letter abbreviations for:

  • threonine?
  • aspartic acid?
  • valine?
  • alanine?
  • lysine?
A
  • threonine = T
  • aspartic acid = D
  • valine = V
  • alanine = A
  • lysine = K
39
Q

Of the amino acids K, L, and R, which will have a net charge of zero at physiological pH?

A

L (leucine) will have a zero charge. The other amino acids, K (lysine) and R (arginine) have basic side chains, which will be positively charged at a pH of 7.4.

Remember that L is the abbreviation for leucine, not lysine!

40
Q

A peptide has the amino acid sequence DIFELGA. How many acidic residues does it contain?

A

It contains two acidic residues, D (aspartic acid) and E (glutamic acid).

I is the abbreviation for isoleucine, while F is phenylalanine, L is leucine, G is glycine, and A is alanine.

41
Q

What are the three-letter abbreviations for:

  • glutamic acid?
  • glycine?
  • glutamine?
A
  • glutamic acid = Glu
  • glycine = Gly
  • glutamine = Gln

Note that most three-letter abbreviations are simply the first three letters of the amino acid, but be careful with ones as similar as those above.

42
Q

What are the three-letter abbreviations for:

  • asparagine?
  • arginine?
  • aspartic acid?
A
  • asparagine = Asn
  • arginine = Arg
  • aspartic acid = Asp

Note that most three-letter abbreviations are simply the first three letters of the amino acid, but be careful with ones as similar as those above.

43
Q

What are the three-letter abbreviations for:

  • isoleucine?
  • tryptophan?
A
  • isoleucine = Ile
  • tryptophan = Trp
44
Q

Which amino acid will be more negatively charged at a pH of 5, Gln or Glu?

A

Glu (glutamic acid) will be more negative. Its side chain contains a carboxylic acid, which will be deprotonated at pH values above its pKa (approximately 4).

Gln stands for glutamine, which has a neutral side chain.

45
Q

Which peptide is less polar: LeuPheAlaVal or TyrCysGlyAsp?

A

LeuPheAlaVal is less polar (more hydrophobic). Its residues are leucine, phenylalanine, alanine, and valine, which all contain fairly nonpolar hydrocarbon side chains.

The other peptide has residues of tyrosine (somewhat polar), cysteine (polar due to its sulfur atom), glycine (nonpolar), and aspartic acid (very polar due to its ability to carry a negative charge).

46
Q

What separation technique is used to isolate amino acids based on their isoelectric points?

A

Isoelectric focusing is used to separate amino acids by pI.

This process involves an anode, or positive terminal, and a cathode, or negative terminal. Any amino acid with a net charge will migrate toward one terminal until it reaches the region with the same pH as its own isoelectric point.

47
Q

In isoelectric focusing, what charge is given to the anode?

A

The anode is positively charged.

Isoelectric focusing, or gel electrophoresis in general, resembles an electrolytic cell. As in any cell, electrons move from anode to cathode. However, electrolytic cells are nonspontaneous, meaning that they require outside power input. Such energy input is necessary because electrons are being forced off of a positive terminal (the anode) and onto a negative one (the cathode).

48
Q

During isoelectric focusing, an amino acid migrates toward the anode until it stops at a region of pH 2.7. What is the pI of this amino acid?

A

This amino acid must have a pI of 2.7.

Isoelectric focusing is a technique that separates amino acids by their isoelectric points. An AA will migrate until it reaches a section of the gel with a pH equal to its pI.

49
Q

During isoelectric focusing, an amino acid migrates toward the anode until it stops at a region of pH 2.7. What was its net charge during the migration and at the end of the experiment, respectively?

A

While the AA was migrating, its net charge was negative. It comes to a stop when that charge becomes neutral.

In isoelectric focusing, the anode is positive. Amino acids that migrate toward it, then, must be negative. These AAs stop moving when the surrounding pH is equal to their pI values, at which point they exist as neutral zwitterions.

50
Q

During isoelectric focusing, which will migrate nearer the cathode: arginine or alanine?

A

Arginine will migrate nearer the cathode.

As a basic amino acid, arginine has a side chain that can be protonated to gain a positive charge. Alanine, in contrast, has a neutral side chain. Since the cathode is negative, the amino acids that are most positive will move closest to that terminal.

51
Q

Consider the amino acids glycine, tryptophan, and lysine.

At pH 7.4, which is most likely to bind negatively charged groups?

A

Lysine will bind negative ligands most readily.

As a basic amino acid, lysine has a side chain that is able to become postively charged (NH3+). At physiological pH, then, lysine will have a net positive charge. This makes it prone to binding to negative groups.

52
Q

Consider the amino acids glycine, tryptophan, and lysine.

Which is least likely to rotate plane-polarized light?

A

Glycine is least likely to display such optical activity, since it is achiral. Its alpha carbon is bound to two hydrogen atoms.

All other amino acids that appear on the MCAT contain at least one chiral center.

53
Q

Consider the amino acids glycine, tryptophan, and lysine.

Which would migrate farthest toward the cathode during isoelectric focusing?

A

Lysine would migrate farthest toward the cathode.

Since isoelectric focusing is performed with electrolytic cells, the anode is positive while the cathode is negative. Lysine, a basic amino acid, has a side chain that can be positively charged and will thus migrate toward a negative pole. The other two molecules have neutral side chains.

54
Q

Of valine, phenylalanine, and serine, which is most likely to be found on the extracellular face of a protein?

A

Serine is most likely to be located on a protein’s exterior.

For questions like this, simply assess whether the amino acid in question has a hydrophilic or hydrophobic side chain. Serine, a polar amino acid, is relatively hydrophilic and tends to be positioned facing the cytosol or extracellular fluid.

55
Q

Of isoleucine, threonine, and aspartic acid, which is most likely to be found in the interior of a membrane-embedded protein?

A

Isoleucine is most likely to be embedded within a protein’s interior.

For questions like this, simply assess whether the amino acid in question has a hydrophilic or hydrophobic side chain. Isoleucine, which has a nonpolar R group, is relatively hydrophobic. It tends to cluster away from water and near other nonpolar groups.

56
Q

What positions on a titration curve correspond to the pKas of an amino acid?

A

The pKas of an amino acid, like those of any acid, are equal to the pH values at the half-equivalence points.

According to the Henderson-Hasselbalch equation, pH = pKa at the half-equivalence point of a titration. While amino acids are polyprotic and thus have two or more pKa values, the principle holds true.

57
Q

The curve below shows the titration of glutamic acid with NaOH. At the position marked, what will be the amino acid’s net charge?

A

The net charge on a glutamic acid molecule will be -1.

The position shown on the titration curve is the second equivalence point. Here, both the carboxy group and the side chain will be fully neutralized (deprotonated) by the base, but the amino group will retain its proton. If you couldn’t tell that this was an equivalence point, simply look at the pH, which is between 7 and 8. This pH is high enough to deprotonate the side chain of any acidic AA.

58
Q

The curve below shows the titration of phenylalanine with NaOH. At the position marked, how many acidic protons will be present on the average phenylalanine molecule?

A

The average molecule will have 1.5 acidic protons.

To answer this question, first consider how many positions are protonated at the very beginning of the titration (2: the carboxylic acid and the amine). The position shown is the first half-equivalence point, or the pKa of the carboxylic acid. Here, that first acidic proton is “half neutralized,” meaning that half of the molecules retain it and half do not. Since all molecules still have a protonated amine, this averages out to 1.5.