Amino Acids Flashcards
Take any practice exam and you'll notice the same trend: amino acid questions appear constantly. From their structures and abbreviations to titration curves and isoelectric focusing, these cards will help you master amino acids as they appear on the MCAT.
Which two functional groups are found in all amino acids?
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.
What functional group is present in all peptide bonds?
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.
What name is given to the form of glycine pictured below?
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.
What is the approximate pKa of an amino acid’s carboxylic acid group?
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.
What is the approximate pKa of an amino acid’s amine group?
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.
What is the isoelectric point of an amino acid?
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.
Explain how to calculate the pI of an amino acid with an uncharged side chain.
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.
Explain how to calculate the pI of an amino acid with a charged side chain.
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.
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?
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.
What value can be compared to pH to determine whether a specific group on an amino acid is protonated?
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.
What value can be compared to pH to determine whether an entire amino acid is charged overall?
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.
Which of the standard amino acids, if any, are chiral?
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.
With the exception of glycine, every amino acid can exist in two potential configurations. What names are given to these forms?
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.
What is the relationship between D-leucine and L-leucine?
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.
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What chemical property is shared by lysine, aspartic acid, histidine, arginine, and glutamic acid?
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.
What word describes the interactions between polar amino acids and water?
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.
What word describes the interactions between nonpolar amino acids and water?
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.”
Which amino acids are acidic?
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.
What names are given to the deprotonated forms of glutamic acid and aspartic acid, respectively?
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.”
Which amino acids are basic?
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.
Which amino acids contain at least one sulfur atom?
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.
Which amino acid tends to produce turns or “kinks” in a protein’s secondary structure?
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.