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.
1
Q
Which two functional groups are found in all amino acids?
A
- amine
- carboxylic acid
Each amino acid also contains a specific side chain.
2
Q
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 _________ _________.
A
alpha carbon
This is the carbon immediately adjacent to the carbonyl carbon.
3
Q
What functional group is present in all peptide bonds?
A
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.
4
Q
In a peptide bond synthesis reaction, what molecule is lost?
A
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.
5
Q
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 ___________.
A
residues
As such, a tripeptide can be said to contain three residues. Larger peptides may contain hundreds of residues or more.
6
Q
How many carbon atoms does the amino acid glycine contain?
A
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.
7
Q
How many oxygen atoms does the amino acid alanine contain?
A
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.
8
Q
The individual properties of amino acids (acidic, basic, polar, etc.) are entirely dependent on which part of the amino acid?
A
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.
9
Q
How would you characterize the side chains of alanine, valine, leucine, and isoleucine?
A
nonpolar
Specifically, they are small (<5-carbon) hydrocarbon chains.
As their names imply, leucine and isoleucine are structural isomers.
10
Q
What two elements do the side chains of valine and leucine contain?
A
- 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.
11
Q
Fill in the blank.
Both serine and glutamine contain ________ ________ side chains.
A
polar uncharged
The polar uncharged amino acids include serine, threonine, glutamine, asparagine, and cysteine.
12
Q
Between threonine and isoleucine, which contains a less polar side chain?
A
Isoleucine
Isoleucine is a nonpolar amino acid, while threonine is polar uncharged. Therefore, between the two, isoleucine has the less polar side chain.
13
Q
Of arginine, methionine, and valine, which has the most polar side chain?
A
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).
14
Q
What chemical property is shared by lysine, aspartic acid, histidine, arginine, and glutamic acid?
A
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.
15
Q
Which amino acids contain aromatic rings?
A
- 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.
16
Q
Which amino acids contain at least one -OH on their side chains, but do not contain aromatic rings?
A
- 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.
17
Q
Which amino acids have amide-containing side chains?
A
- Asparagine
- Glutamine
Both asparagine and glutamine contain an amide (carbonyl bonded to a nitrogen atom) in their side chains.
18
Q
Which amino acids contain at least one sulfur atom?
A
- Cysteine
- Methionine
Note that cysteine, but not methionine, can form disulfide bridges.
19
Q
Fill in the blank.
When two cysteine molecules connect via a disulfide linkage, the resulting structure is known as ________.
A
cystine
Note that while this looks extremely similar to the word “cysteine,” it is missing the first “e.”
20
Q
Which amino acids are acidic?
A
- 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.
21
Q
Fill in the blank.
The functional group found on the side chains of both D and E is a _________ _________.
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.
22
Q
Which amino acids are basic?
A
- 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.
23
Q
Fill in the blank.
The functional group found on the side chain of K is a(n) __________.
A
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).
24
Q
Which amino acid tends to produce turns or “kinks” in a protein’s secondary structure?
A
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.
25
Name all of the standard amino acids that **contain cyclic structures**.
## Footnote
Include any amino acid with a cyclic part of its structure, not just amino acids with aromatic side chains.
1. Tryptophan
2. Phenylalanine
3. Tyrosine
4. Histidine
5. Proline
## Footnote
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.
26
# True or false.
Since lysine is a basic amino acid, it would not be considered a polar amino acid.
False
## Footnote
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.
27
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
## Footnote
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.
28
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
## Footnote
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.
29
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
## Footnote
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.
30
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
## Footnote
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).
31
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
## Footnote
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).
32
What **name** is given to the form of glycine pictured below?
This molecule is a **zwitterion**.
## Footnote
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.
33
# True or false.
In a zwitterionic amino acid, the carboxylic acid group is typically positive.
False
## Footnote
In a standard amino acid, it is the amino group that can become positively charged, not the carboxylic acid group.
34
# Fill in the blank.
Zwitterions are \_\_\_\_\_\_\_\_, meaning that they are capable of acting as either acids or bases.
amphoteric
## Footnote
In other words, a zwitterion can be **protonated** or **deprotonated**.
35
# Fill in the blank.
All 20 standard amino acids have either \_\_\_\_\_ or \_\_\_\_\_ pKas.
## Footnote
Fill each blank with a number.
2, 3
## Footnote
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.
36
What is the approximate **pKa** of an amino acid's carboxylic acid group?
around 2
| (broadly, between 1.5 and 3)
## Footnote
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.
37
What is the approximate **pKa** of an amino acid's amine group?
around 9
## Footnote
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.
38
Define the **isoelectric point** of an amino acid.
It is the pH at which an amino acid is **neutral** overall.
## Footnote
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.
39
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.
## Footnote
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**.
40
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.
## Footnote
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**.
41
What is the approximate **pI** of an amino acid with an **uncharged** side chain?
5.5
## Footnote
Since we're asked to approximate here, we don't even need to know which amino acid we're dealing with!
The pKas of the carboxy and amino termini are 2 and 9, respectively, so we simply must average 2 and 9 to get 5.5.
42
The three pKas for arginine are **2.17, 9.04, and 12.48**. These correspond to the carboxylic acid, the amine, and the R group, respectively. What is **arginine's pI**?
10.76
## Footnote
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.
43
# Fill in the blank.
The charge of an acidic side chain can be either \_\_\_\_\_\_\_\_ or \_\_\_\_\_\_\_\_.
neutral, negative
## Footnote
Acidic side chains contain carboxylic acid functional groups. A carboxylic acid can either be neutral (COOH) or negatively-charged (COO−).
44
# Fill in the blank.
The charge of a basic side chain can be either \_\_\_\_\_\_\_\_ or \_\_\_\_\_\_\_\_.
neutral, positive
## Footnote
Acidic side chains contain nitrogen-based functional groups, such as the amino group on lysine. These groups can either be neutral (NH2, in the case of this amino group) or positively-charged (NH3+).
45
When protonated, the side chain of **histidine** carries what charge (if any)?
positive
## Footnote
This is true for the side chains of basic amino acids in general.
46
When protonated, the side chain of the **amino acid E** carries what charge (if any)?
neutral
| It has a charge of zero.
## Footnote
E is the abbreviation for **glutamic acid**. The side chain of glutamic acid contains a carboxylic acid group, which is neutral (-COOH) when protonated.
47
What **value** can be compared to the pH to determine whether a specific group on an amino acid is **protonated**?
pKa of that group
## Footnote
Specifically, if the pH is lower (more acidic) than the pKa, that group will be protonated. If the pH is higher (more basic) than pKa, the group will be deprotonated.
48
The side chain of histidine has a pKa of around 6.00. In what **pH range** will this side chain tend to be protonated?
below 6.00
## Footnote
Remember, lower pH values correspond to a more acidic (proton-rich) solution. Thus, when the pH is lower than the pKa of a group, that group will tend to be protonated.
49
What **value** can be compared to the pH to determine whether an entire amino acid is **charged overall**?
The **isoelectric point**, or pI of the amino acid.
## Footnote
Specifically, if the pH is lower than the pI, the amino acid will be positively charged. If the pH is higher than the pI, the amino acid will be negative.
50
The pI of lysine is approximately 9.74. In what **pH range** will this amino acid tend to be **negatively charged**?
values above 9.74
## Footnote
Remember, higher pH values correspond to a more basic (less proton-rich) solution. Thus, when the pH is higher than the pI of an amino acid or protein, that amino acid or protein will tend to be negatively charged.
51
Name **two amino acids** that would be likely to interact with phosphate groups via ionic interactions at physiological pH.
1. Lysine
2. Arginine
## Footnote
Since both of these basic amino acids have side chains that are positive at physiological pH, they would be likely to interact with phosphate groups, which are negatively charged.
Note that histidine is also a basic amino acid, but its side chain tends to be neutral at physiological pH.
52
Which of the standard amino acids, if any, are **chiral**?
All except for Glycine.
## Footnote
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.
53
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)
## Footnote
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.
54
What is the relationship between **D-leucine and L-leucine**?
These two amino acids are **enantiomers**.
## Footnote
All amino acids except glycine can be found as either D or L enantiomers.
Note that only L amino acids are found in proteins. Human (and other) enzymes are stereospecific and react with the L isomer alone.
55
With regard to isomerism, what is the relationship between **leucine and isoleucine**?
These two amino acids are **structural isomers**.
## Footnote
Unlike D and L amino acids (which are enantiomers), leucine and isoleucine have different side chains with regard to the connectivity of atoms. Thus, they are structural isomers.
56
What word describes the interactions between **polar amino acids and water**?
Amino acids with polar side chains tend to be **hydrophilic**.
## Footnote
This means that they interact well with water and, in some cases, can hydrogen bond with water molecules.
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.
57
What word describes the interactions between **nonpolar amino acids and water**?
Amino acids with nonpolar side chains tend to be **hydrophobic**.
## Footnote
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."
58
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**.
* The deprotonated form of aspartic acid is **aspartate**.
## Footnote
It can help to remember that in general, deprotonated carboxylic acids are called "carboxylates."
59
Most amino acids that tend to become **phosphorylated** are those that contain which side-chain functional group?
Hydroxyl
| (-OH)
## Footnote
All three OH-containing amino acids (serine, threonine, and tyrosine) are able to become phosphorylated, meaning that a phosphate group is attached to their structure in the place of the hydroxyl hydrogen atom.
60
A five-residue sequence in the middle of a large protein has the sequence DRSGP. Which position of that **sequence** is most likely to be phosphorylated?
serine (S) residue
## Footnote
Of the five amino acids listed (aspartic acid, arginine, serine, glycine, and proline), serine is the only one likely to become phosphorylated, as serine contains a hydroxyl (-OH) group.
61
# Fill in the blank.
In a phosphorylated threonine residue, phosphorus is connected to the alpha carbon via an atom of \_\_\_\_\_\_\_\_\_\_\_\_.
oxygen
## Footnote
For this question, it's helpful to be familiar with the structure of phosphate.
In a phosphate ion, the central phosphorus atom is bonded only to oxygen atoms. Therefore, an oxygen atom (specifically, the O atom from threonine's side-chain hydroxyl group) must connect that phosphorus atom to the alpha carbon.
62
The amino acids asparagine and glutamine are shown below. Are their **R groups** able to become **charged**?
No
## Footnote
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.
63
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?
Only the **amino terminal** will be protonated.
## Footnote
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 (lower-pH) solution.
64
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**?
**All three groups** will be charged.
## Footnote
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.
65
What will be the net charge on alanine at a **pH of 1.2**?
+1
## Footnote
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+).
66
What will be the net charge on alanine at a **pH of 11**?
-1
## Footnote
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).
67
What will be the net charge on alanine at **physiological pH**?
zero
## Footnote
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+).
68
At physiological pH, what is the net charge of both **aspartic** and **glutamic** acid?
-1
## Footnote
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.
69
At physiological pH, what is the net charge of both **lysine** and **arginine**?
+1
## Footnote
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.
70
What **separation technique** is used to isolate amino acids based on their isoelectric points?
**Isoelectric focusing** is used to separate amino acids by pI.
## Footnote
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.
71
In isoelectric focusing, what **charge** is given to the anode?
positive
## Footnote
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).
72
In **isoelectric focusing**, will positively-charged molecules migrate toward the anode or the cathode?
cathode
## Footnote
In isoelectric focusing (which has charge designations similar to an electrolytic cell), the cathode is negative. Therefore, positive molecules will migrate toward it.
73
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?
While the AA was migrating, its net charge was **negative**. It comes to a stop when that charge becomes **neutral**.
## Footnote
In isoelectric focusing, the anode is positive. Amino acids that migrate toward it therefore 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.
74
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?
2.7
## Footnote
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.
75
During **isoelectric focusing**, which will migrate nearer the cathode: arginine or alanine?
arginine
## Footnote
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.
76
Consider the amino acids glycine, tryptophan, and lysine.
At pH 7.4, which is most likely to **bind negatively** charged groups?
Lysine
## Footnote
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.
77
Consider the amino acids glycine, tryptophan, and lysine.
Which is **least** likely to rotate plane-polarized light?
Glycine
## Footnote
It 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.
78
Consider the amino acids glycine, tryptophan, and lysine.
Which would migrate **farthest** toward the cathode during isoelectric focusing?
Lysine
## Footnote
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.
79
Name **two areas** of a protein that are likely to contain a high proportion of nonpolar amino acids.
1. The **interior** of a globular protein
2. The portion of a transmembrane protein **adjacent to the lipid bilayer**
## Footnote
These areas do not face the aqueous surroundings. Therefore, nonpolar residues tend to cluster there.
80
Name at least **two areas** of a protein that are likely to contain a high proportion of polar amino acids.
1. The **exterior** of a globular protein
2. The portion of a transmembrane protein facing the **exterior of the cell**
3. The portion of a transmembrane protein facing the **interior of the cell**
## Footnote
These areas are in direct contact with the aqueous surroundings. Therefore, polar residues tend to be oriented there.
81
Of valine, phenylalanine, and serine, which is most likely to be found on the **extracellular** face of a protein?
serine
## Footnote
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.
82
Of isoleucine, threonine, and aspartic acid, which is most likely to be found in the **interior** of a membrane-embedded protein?
isoleucine
## Footnote
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.
83
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**.
## Footnote
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.
84
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
## Footnote
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.
85
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
## Footnote
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.
86
On a titration curve, plateaus (flat portions) generally correspond to which **points**?
half-equivalence points
## Footnote
This applies to any titration curve, whether in the context of biochemistry (amino acids) or general chemistry.
87
On a titration curve, sharp, steep portions generally correspond to which **points**?
equivalence points
## Footnote
Equivalence points refer to pH levels at which a given position has become fully protonated/fully deprotonated.
88
When aspartic acid is fully titrated with NaOH, how many **equivalence points** will appear on the titration curve?
three
## Footnote
Titration curves always contain the same number of equivalence points as the number of pKas on the molecule, which in the case of aspartic acid is three. (The same is true for half-equivalence points.)
89
# True or false.
When a nonpolar amino acid is titrated with NaOH, the first equivalence point corresponds to the pI of the molecule.
True
## Footnote
In fact, this is true for any amino acid with an uncharged side chain. The first equivalence point falls halfway between the two pKas of the molecule. In other words, it falls at the pH that represents the average of those two pKas.
90
# True or false.
As a basic amino acid, arginine could never be titrated with NaOH.
False
## Footnote
This statement might seem accurate given that bases are typically reacted with acids (and not other bases). However, what an amino acid is titrated with depends on its starting protonation state, not on whether its side chain is acidic or basic. Arginine could easily be kept at an initial pH of 1 (at which all three of its groups would be protonated) and then titrated with NaOH.
91
Of the amino acids K, L, and R, which will have a net charge of **zero** at physiological pH?
L
| (Leucine)
## Footnote
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!
92
A peptide has the amino acid sequence DIFELGA. How many **acidic residues** does it contain?
two
## Footnote
* D (aspartic acid)
* E (glutamic acid)
I is the abbreviation for isoleucine, while F is phenylalanine, L is leucine, G is glycine, and A is alanine.
93
A peptide has the amino acid sequence EFKWYG. How many **aromatic residues** does it contain?
three
## Footnote
* F (phenylalanine)
* W (tryptophan)
* Y (tyrosine)
These are actually all three of the amino acids typically classified as aromatic amino acids.
94
The amino acid Q is fully titrated. How many **half-equivalence points** are expected to appear on the titration curve?
two
## Footnote
As a polar uncharged amino acid, glutamine has only two pKas. Since each pKa corresponds to a half-equivalence point, the titration curve of glutamine will have two such points.
95
Which amino acid will be **more negatively charged** at a pH of 5: Gln or Glu?
Glu
| (glutamic acid)
## Footnote
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.
96
Which peptide is **less polar**, LeuPheAlaVal or TyrCysGlyAsp?
LeuPheAlaVal
| (more hydrophobic)
## Footnote
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).
97
The side chain of histidine has a pKa of approximately 6.00. At physiological pH, would a **histidine residue** be positively charged, negatively charged, or neutral?
neutral
## Footnote
As a basic amino acid, histidine has a side chain that can either be positive (if protonated) or neutral (if deprotonated). Since physiological pH—7.4—is higher than its pKa of 6.00, the side chain will be deprotonated, or neutral.
98
What is the **average molecular weight** of an amino acid, in daltons (Da)?
110
## Footnote
Remember this value! The AAMC has been known to ask this question, or more complex questions that require this knowledge, in their practice materials.
99
# Fill in the blank.
A 150-residue peptide would have a molecular weight of approximately \_\_\_\_\_\_ \_\_\_.
16,500 Da
| 16.5 kDa
## Footnote
The math here is relatively simple: 150 residues × 110 Da/residue. You can either write out this math *or* you can realize that 150 × 100 is 15,000 and 150 × 10 is 1,500, so 150 × 110 must be equal to 15,000 + 1,500.
On a multiple-choice MCAT question, it's also likely that you could get the correct answer by simply deducing that you are looking for a value slightly above 15,000.
100
A protein homodimer has an overall molecular weight (MW) of 44 kDa. Approximately how many **amino acid residues** are in each monomer?
200 residues
## Footnote
If the dimer (two-subunit protein) has an MW of 44 kDa, each monomer must have an MW of 22 kDa, or 22,000 Da. If we recall that the average MW of one amino acid residue is 110 Da, we can do the following math:
22,000 Da × (1 residue / 110 Da) = 200 residues
