Amino Acid Properties Flashcards
Take any practice exam and you'll notice the same trend: amino acid questions appear constantly. (In fact, they make up a huge fraction of BOTH the C/P and B/B sections.) From their structures and chemical behavior to titration curves and isoelectric focusing, these cards will help you thoroughly master amino acids.
Which two functional groups are found in all amino acids?
- amine
- carboxylic acid
Each amino acid also contains a specific side chain.
Fill in the blank.
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 _________ _________.
alpha carbon
This is the carbon immediately adjacent to the carbonyl carbon.
What functional group is present in all peptide bonds?
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.
In a peptide bond synthesis reaction, what molecule is lost?
water
(H2O)
Since water is lost in this reaction, it (in addition to being a nucleophilic substitution reaction) can also be termed a dehydration synthesis reaction.
Fill in the blank.
When amino acids are incorporated into a peptide (that is, when multiple amino acids have joined together via peptide bonds), those amino acids are termed ___________.
residues
As such, a tripeptide can be said to contain three residues. Larger peptides may contain hundreds of residues or more.
How many carbon atoms does the amino acid glycine contain?
There are two carbons in an amino acid:
- alpha carbon
- carbonyl carbon
Since glycine is the simplest amino acid, this question is essentially asking for the minimum number of carbons that can be present in an amino acid in general. The answer is two: the alpha carbon and the carbonyl carbon.
How many oxygen atoms does the amino acid alanine contain?
There are two oxygen atoms in alanine:
- One in the carboxyl group’s C=O bond
- One in the hydroxyl (-OH) of the carboxyl group
While you don’t need to memorize the structure of every amino acid, this question can be answered by knowing the backbone common to all standard amino acids. Alanine’s side chain is a methyl group, which contains no oxygen.
The individual properties of amino acids (acidic, basic, polar, etc.) are entirely dependent on which part of the amino acid?
side chain
Since all amino acids share a common backbone (consisting of an amino terminal, an alpha carbon, and a carboxylic acid terminal), their varying properties are entirely dependent on their individual side chains.
How would you characterize the side chains of alanine, valine, leucine, and isoleucine?
nonpolar
Specifically, they are small (<5-carbon) hydrocarbon chains.
As their names imply, leucine and isoleucine are structural isomers.
What two elements do the side chains of valine and leucine contain?
- carbon
- hydrogen
Valine and leucine (along with alanine and isoleucine) are nonpolar amino acids with simple hydrocarbon side chains. Hydrocarbons consist of carbon and hydrogen.
Fill in the blank.
Both serine and glutamine contain ________ ________ side chains.
polar uncharged
The polar uncharged amino acids include serine, threonine, glutamine, asparagine, and cysteine.
Between threonine and isoleucine, which contains a less polar side chain?
Isoleucine
Isoleucine is a nonpolar amino acid, while threonine is polar uncharged. Therefore, between the two, isoleucine has the less polar side chain.
Of arginine, methionine, and valine, which has the most polar side chain?
Arginine
Arginine is a basic amino acid, which means that its side chain is capable of becoming positively charged. As such, it is more polar than either methionine or valine (both of which are considered nonpolar amino acids).
What chemical property is shared by lysine, aspartic acid, histidine, arginine, and glutamic acid?
side chains that can become 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.
Which amino acids contain aromatic rings?
- Phenylalanine
- Tyrosine
- Tryptophan
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.
Which amino acids contain at least one -OH on their side chains, but do not contain aromatic rings?
- Serine
- Threonine
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.
Which amino acids have amide-containing side chains?
- Asparagine
- Glutamine
Both asparagine and glutamine contain an amide (carbonyl bonded to a nitrogen atom) in their side chains.
Which amino acids contain at least one sulfur atom?
- Cysteine
- Methionine
Note that cysteine, but not methionine, can form disulfide bridges.
Fill in the blank.
When two cysteine molecules connect via a disulfide linkage, the resulting structure is known as ________.
cystine
Note that while this looks extremely similar to the word “cysteine,” it is missing the first “e.”
Which amino acids are acidic?
- Aspartic acid
- Glutamic acid
The side chains of acidic amino acids can be deprotonated and 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.
Fill in the blank.
The functional group found on the side chains of both D and E is a _________ _________.
carboxylic acid
D and E refer to aspartic acid and glutamic acid. Both of these acidic amino acids have carboxylic acids on their side chains.
Which amino acids are basic?
- Arginine
- Lysine
- Histidine
The side chains of basic amino acids can be protonated and tend to be positively charged at 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.
Fill in the blank.
The functional group found on the side chain of K is a(n) __________.
amine
K, or lysine, is a basic amino acid and has an amine on its side chain. The other basic amino acids, histidine (H) and arginine (R), also have nitrogen-containing side chains (specifically, an imidazole ring on H and a guanidino group on R).
Which amino acid tends to produce turns or “kinks” in a protein’s secondary structure?
Proline, such as:
- alpha helices
- 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.
Name all of the standard amino acids that contain cyclic structures.
Include any amino acid with a cyclic part of its structure, not just amino acids with aromatic side chains.
- Tryptophan
- Phenylalanine
- Tyrosine
- Histidine
- Proline
Tryptophan, phenylalanine, and tyrosine all contain aromatic rings in their side chains. Histidine, a basic amino acid, has a ring in its side chain. Proline’s structure includes a ring between the side chain and the amino nitrogen atom.
True or false.
Since lysine is a basic amino acid, it would not be considered a polar amino acid.
False
Basic (and acidic) amino acids are polar! An amino acid can fall into multiple groups. Often, sources will specifically refer to “polar uncharged” amino acids to indicate polar amino acids that are not acidic or basic.
A researcher is attempting to identify an amino acid. Given the information below, which amino acid is being described?
The amino acid is known to contain an -SH group.
Cysteine
It is the only standard amino acid to contain an -SH group. Note that methionine does contain a sulfur atom, but that atom is bonded only to carbon, not to hydrogen.
A researcher is attempting to identify an amino acid. Given the information below, which amino acid is being described?
The amino acid is aromatic, but it has a lower molecular weight than tyrosine.
Phenylalanine
The aromatic amino acids are phenylalanine, tyrosine, and tryptophan. While you do not need to be able to draw these structures atom-for-atom, you should have a general idea that of the three, only phenylalanine (the simplest aromatic amino acid) is smaller than tyrosine.
A researcher is attempting to identify an amino acid. Given the information below, which amino acid is being described?
The amino acid lacks D- and L-isomers.
Glycine
For an amino acid to lack D- and L-isomers, it must be achiral (in other words, not chiral).
It is the only achiral amino acid.
A researcher is attempting to identify an amino acid. Given the information below, which amino acid is being described?
The amino acid is aromatic and has a side chain that contains an OH group.
Tyrosine
This is the only standard amino acid that is both aromatic and OH-containing (that is, its side chain contains a hydroxyl, or -OH, group).
A researcher is attempting to identify an amino acid. Given the information below, which amino acid is being described?
The amino acid’s side chain can act as a stronger base than the side chain of lysine.
Arginine
For the MCAT, it can be helpful to know that arginine is the strongest base of the basic amino acids, while histidine is the weakest. Thus, arginine is the only basic amino acid that can act as a stronger base than lysine (which falls in the middle of the three with regard to basicity).
What name is given to the form of glycine pictured below?
This molecule is a zwitterion.
It is neutral overall but carries both positive and negative charges.
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.
True or false.
In a zwitterionic amino acid, the carboxylic acid group is typically positive.
False
In a standard amino acid, it is the amino group that can become positively charged, not the carboxylic acid group.
Fill in the blank.
Zwitterions are ________, meaning that they are capable of acting as either acids or bases.
amphoteric
In other words, a zwitterion can be protonated or deprotonated.
Fill in the blank.
All 20 standard amino acids have either _____ or _____ pKas.
Fill each blank with a number.
2, 3
Specifically, amino acids with uncharged side chains have only 2 pKas (one for the amino and one for the carboxy terminal). Amino acids with charged side chains have one additional pKa, for the side chain.
What is the approximate pKa of an amino acid’s carboxylic acid group?
around 2
(broadly, between 1.5 and 3)
On average, it will be 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.
What is the approximate pKa of an amino acid’s amine group?
around 9
On average, it will be 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.
Define the isoelectric point of an amino acid.
It 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.
Explain how to calculate the pI of an amino acid with an uncharged side chain.
Simply average the pKa values of the carboxyl and amino groups, then divide it by 2.
For example:
- The two pKa values 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.
Explain how to calculate the pI of an amino acid with a charged side chain.
- For acidic amino acids, average the two most acidic pKa values.
- For basic amino acids, average the two most basic pKa values.
Remember, do not average all three values!
For example:
- The three pKa values of lysine are 2.18 (carboxylic acid), 8.95 (amine), and 10.53 (side chain). Since its R group is basic, its pI is thus (8.95 + 10.53) / 2, or 9.74.
With the exception of glycine, every amino acid can exist in two potential configurations. What names are given to these forms?
- D (dextrorotatory)
- 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.
The amino acids asparagine and glutamine are shown below. Are their R groups able to become charged?
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.
Consider the amino acids glycine, tryptophan, and lysine.
At pH 7.4, which is most likely to bind negatively charged groups?
Lysine
As a basic amino acid, lysine has a side chain that is able to become positively charged (NH3+). At physiological pH, then, lysine will have a net positive charge. This makes it prone to binding to negative groups.
Of valine, phenylalanine, and serine, which is most likely to be found on the extracellular face of a protein?
serine
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.
Of isoleucine, threonine, and aspartic acid, which is most likely to be found in the interior of a membrane-embedded protein?
isoleucine
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.
What positions on a titration curve correspond to the pKas of an amino acid?
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.
The curve below shows the titration of glutamic acid with NaOH. At the position marked, what will be the amino acid’s net charge?
-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.
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?
1.5
To answer this question, first consider how many positions are protonated at the very beginning of the titration (two: 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.
