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Lesson 1: Amino Acids and Proteins

Amino Acids and Proteins

View Periodic Table

1 / 24

A new protein has been discovered in the bottom of the ocean. Researchers want to predict the folding patterns of the protein. Which of the following will the researchers most likely analyze for these predictions?

The alpha helix of the secondary structure

mRNA coding for the protein

Sequence of amino acids in polypeptide

Individual amino acids

The sequence of amino acids that form the polypeptides will determine the folding patterns and three-dimensional structure of the protein. The individual amino acid does not determine the folding patterns but rather the sequence of amino acids in the peptide.

The alpha helix structure is determined by the primary structure. mRNA does not contribute to folding patterns after protein is translated from RNA.

Reference: AK Lectures

The sequence of amino acids that form the polypeptides will determine the folding patterns and three-dimensional structure of the protein. The individual amino acid does not determine the folding patterns but rather the sequence of amino acids in the peptide.

The alpha helix structure is determined by the primary structure. mRNA does not contribute to folding patterns after protein is translated from RNA.

Reference: AK Lectures

The sequence of amino acids that form the polypeptides will determine the folding patterns and three-dimensional structure of the protein. The individual amino acid does not determine the folding patterns but rather the sequence of amino acids in the peptide.

The alpha helix structure is determined by the primary structure. mRNA does not contribute to folding patterns after protein is translated from RNA.

Reference: AK Lectures

2 / 24

A food scientist researches a new way to cook eggs. Which of the following methods will effectively denature the primary structure of egg proteins?

A change in pH

Digestive enzymes

Heat

Chemical solvents

Remember that the primary structure of proteins is built through peptide bonds, which often require specific enzymes for breakdown. Heating a protein can denature secondary, tertiary, and quarternary structure. A pH change can denature tertiary and quarternary structure. Chemical solvents can denature secondary, tertiary, and quarternary structure.

Reference: Content Review Books, Khan Academy

Remember that the primary structure of proteins is built through peptide bonds, which often require specific enzymes for breakdown. Heating a protein can denature secondary, tertiary, and quarternary structure. A pH change can denature tertiary and quarternary structure. Chemical solvents can denature secondary, tertiary, and quarternary structure.

Reference: Content Review Books, Khan Academy

Remember that the primary structure of proteins is built through peptide bonds, which often require specific enzymes for breakdown. Heating a protein can denature secondary, tertiary, and quarternary structure. A pH change can denature tertiary and quarternary structure. Chemical solvents can denature secondary, tertiary, and quarternary structure.

Reference: Content Review Books, Khan Academy

View Periodic Table

3 / 24

Due to their greater stability, antiparallel beta sheets tend to withstand greater physical and solvent-induced distortions than their parallel counterparts. This can be attributed to the fact that the polymers in an antiparallel beta pleated sheet run in ____ directions and polymers in a parallel beta pleated sheet run in the ____ directions.

same, opposite

same, same

opposite, same

opposite, opposite

Polymers (strands) in an antiparallel beta pleated sheet run in opposite directions to one another. Polymers in a parallel beta pleated sheet run in the same direction to one another. In the antiparallel arrangement, hydrogen bonds are aligned opposite to one another, making for more stable bonds.

Reference: AK Lectures

Polymers (strands) in an antiparallel beta pleated sheet run in opposite directions to one another. Polymers in a parallel beta pleated sheet run in the same direction to one another. In the antiparallel arrangement, hydrogen bonds are aligned opposite to one another, making for more stable bonds.

Reference: AK Lectures

Polymers (strands) in an antiparallel beta pleated sheet run in opposite directions to one another. Polymers in a parallel beta pleated sheet run in the same direction to one another. In the antiparallel arrangement, hydrogen bonds are aligned opposite to one another, making for more stable bonds.

Reference: AK Lectures

View Periodic Table

4 / 24

Cysteine has a thiol group as part of its side chain. Why does cysteine preferentially form disulfide bonds in the extracellular environment?

There are more peptidases within the cell membrane.

The interior space is a reducing environment; the exterior space is a oxidizing environment.

The interior space is an oxidizing environment; the exterior space is a reducing environment.

There are more oxidoreductases within the cell membrane.

The antioxidants present on the interior of the cell create a reducing environment. The lack of antioxidants on the exterior of the cell creates an oxidizing environment. Therefore, disulfide bridge formation preferentially occurs in the exterior of the cell due to the oxidizing environment needed to oxidize the sulfur atoms to form disulfide bridges.

Reference: Khan Academy

The antioxidants present on the interior of the cell create a reducing environment. The lack of antioxidants on the exterior of the cell creates an oxidizing environment. Therefore, disulfide bridge formation preferentially occurs in the exterior of the cell due to the oxidizing environment needed to oxidize the sulfur atoms to form disulfide bridges.

Reference: Khan Academy

The antioxidants present on the interior of the cell create a reducing environment. The lack of antioxidants on the exterior of the cell creates an oxidizing environment. Therefore, disulfide bridge formation preferentially occurs in the exterior of the cell due to the oxidizing environment needed to oxidize the sulfur atoms to form disulfide bridges.

Reference: Khan Academy

View Periodic Table

5 / 24

A researcher studies the properties of amino acids at different pH levels. If the pH is equal to the pKa of the amino acid in beaker 1, which of the following is true regarding the amino acid?

Exactly ½ of the amino acid has been deprotonated.

Exactly ¾ of the amino acid has been deprotonated.

All of the amino acid has been protonated.

Exactly ⅓ of the amino acid has been protonated.

In reference to the Henderson-Hasselbach equation, when the pH=pKa, the concentration of the conjugate base and the concentration of the conjugate acid are equal, meaning that there is a 50% proportion of conjugate base, and a 50% proportion of conjugate acid.

This results in a 1:1 (deprotonated:protonated) ratio, meaning exactly half of the amino acid is deprotonated.

Reference: AK Lectures

In reference to the Henderson-Hasselbach equation, when the pH=pKa, the concentration of the conjugate base and the concentration of the conjugate acid are equal, meaning that there is a 50% proportion of conjugate base, and a 50% proportion of conjugate acid.

This results in a 1:1 (deprotonated:protonated) ratio, meaning exactly half of the amino acid is deprotonated.

Reference: AK Lectures

In reference to the Henderson-Hasselbach equation, when the pH=pKa, the concentration of the conjugate base and the concentration of the conjugate acid are equal, meaning that there is a 50% proportion of conjugate base, and a 50% proportion of conjugate acid.

This results in a 1:1 (deprotonated:protonated) ratio, meaning exactly half of the amino acid is deprotonated.

Reference: AK Lectures

View Periodic Table

6 / 24

A patient with a consistent blood glucose level greater than 300 mg/dL is determined to be in diabetic ketoacidosis (DKA). DKA patients typically have a pH below 7.4. Which of the following amino acids would not be protonated when pH falls below 6.25?

Lysine (pI=9.47)

Glutamic acid (pI=3.08)

Proline (pI=6.30)

Arginine (pI=10.76)

When pH is less than the pI of an amino acid, the solution is more acidic than the amino acid, and the amino acid becomes protonated. Because glutamic acid is the only answer choice with a pI lower than the pH of 6.25 specified in the question stem, it will not be protonated.

Reference: AK Lectures

When pH is less than the pI of an amino acid, the solution is more acidic than the amino acid, and the amino acid becomes protonated. Because glutamic acid is the only answer choice with a pI lower than the pH of 6.25 specified in the question stem, it will not be protonated.

Reference: AK Lectures

When pH is less than the pI of an amino acid, the solution is more acidic than the amino acid, and the amino acid becomes protonated. Because glutamic acid is the only answer choice with a pI lower than the pH of 6.25 specified in the question stem, it will not be protonated.

Reference: AK Lectures

View Periodic Table

7 / 24

A researcher investigates one mechanism of protein folding and solvation layer formation. The protein studied is rich in phenylalanine and leucine amino acids. When the protein is submerged in an aqueous solution, the water molecules in the solvation layer cannot form hydrogen bonds with the protein's side chain. What will most likely result from the occurrence of this phenomenon?

Nearby water molecules will rearrange themselves in order to maximize hydrogen bonding.

Water molecules will form multiple solvation layers around the protein.

The water molecules rearrange and do not hydrogen bond with the protein’s side chain.

Nearby water molecules will rearrange themselves in order to minimize hydrogen bonding.

This phenomenon occurs because phenylalanine and leucine are both hydrophobic amino acids, and will therefore orient themselves towards the interior of the protein to avoid contact with water. Nearby water molecules will rearrange themselves to form an organized structure that maximizes hydrogen bonding among themselves.

Reference: Content Review Books, AK Lectures

This phenomenon occurs because phenylalanine and leucine are both hydrophobic amino acids, and will therefore orient themselves towards the interior of the protein to avoid contact with water. Nearby water molecules will rearrange themselves to form an organized structure that maximizes hydrogen bonding among themselves.

Reference: Content Review Books, AK Lectures

This phenomenon occurs because phenylalanine and leucine are both hydrophobic amino acids, and will therefore orient themselves towards the interior of the protein to avoid contact with water. Nearby water molecules will rearrange themselves to form an organized structure that maximizes hydrogen bonding among themselves.

Reference: Content Review Books, AK Lectures

View Periodic Table

8 / 24

Given that a protein is composed of nonpolar amino acids and displays typical patterns of protonation/deprotonation for neutral amino acids, which of the following amino acids is this protein most likely composed of?

Glycine, Histidine, Leucine

Aspartic acid, Glutamic acid

Alanine, Proline, Lysine

Glycine, Isoleucine, Proline

Glycine, Leucine, Isoleucine, and Proline are all nonpolar amino acids. Histidine, aspartic acid, glutamic acid, and lysine are all polar amino acids. Protein X is composed of non-polar amino acids.

Reference: Content Review Books, Amino Acid Mastery Course, Khan Academy

Glycine, Leucine, Isoleucine, and Proline are all nonpolar amino acids. Histidine, aspartic acid, glutamic acid, and lysine are all polar amino acids. Protein X is composed of non-polar amino acids.

Reference: Content Review Books, Amino Acid Mastery Course, Khan Academy

Glycine, Leucine, Isoleucine, and Proline are all nonpolar amino acids. Histidine, aspartic acid, glutamic acid, and lysine are all polar amino acids. Protein X is composed of non-polar amino acids.

Reference: Content Review Books, Amino Acid Mastery Course, Khan Academy

View Periodic Table

9 / 24

A researcher works with a protein composed of nonpolar amino acids that is found in human blood. The researcher studies the behavior of amino acids within the protein after exposure to different conditions.

Condition 1: pH = 2

Condition 2: pH = 10

Condition 3: pH = 6.8

Which of the following is true?

The COOH group is negative while the amino group is positive under condition 3.

The amino group is protonated under condition 2.

The amino group is negative and the COOH group is positive under condition 3.

Carboxylic acid side chain is deprotonated under condition 1.

A nonpolar amino acid will have a protonated amino and carboxylic acid group under condition 1. It will have a deprotonated amino and carboxylic acid group under condition 2. At physiologic pH (condition 3) the amino group is protonated (positive charge) and the carboxylic acid is deprotonated (negative charge). The charges cancel each other out resulting in a neutral charge (zwitterion).

Reference: Content Review Books, Khan Academy

A nonpolar amino acid will have a protonated amino and carboxylic acid group under condition 1. It will have a deprotonated amino and carboxylic acid group under condition 2. At physiologic pH (condition 3) the amino group is protonated (positive charge) and the carboxylic acid is deprotonated (negative charge). The charges cancel each other out resulting in a neutral charge (zwitterion).

Reference: Content Review Books, Khan Academy

A nonpolar amino acid will have a protonated amino and carboxylic acid group under condition 1. It will have a deprotonated amino and carboxylic acid group under condition 2. At physiologic pH (condition 3) the amino group is protonated (positive charge) and the carboxylic acid is deprotonated (negative charge). The charges cancel each other out resulting in a neutral charge (zwitterion).

Reference: Content Review Books, Khan Academy

View Periodic Table

10 / 24

Researchers have identified a certain prion that causes the human protein abc to misfold by affecting α-helices. When a cell is infected by this particular prion, what most likely happens to protein abc at the molecular level?

More α-helices form than normal, binding to other α-helices and causing the proteins to aggregate.

Fewer α-helices form than normal, preventing the proteins from assuming their tertiary structure and causing them to aggregate.

β-sheets replace normal α-helices, binding to other β-sheets and causing the proteins to aggregate.

α-helices replace normal β-sheets, binding to other α-helices and causing the proteins to aggregate.

Prions are infectious agents that cause the proteins of a host cell to misfold and aggregate. One well-known mechanism by which prions cause proteins to aggregate is by replacing normal α-helices with β-sheets, which have an increased likelihood of binding to one another. The β-sheets of these misfolded proteins then bind to the β-sheets of other proteins, leading to protein aggregation.

In this example, although the prion could potentially cause protein aggregation by increasing or decreasing the number of α-helices, it is more likely that β-sheets replace the α-helices. This has a higher likelihood of leading to protein aggregation.

References: Khan Academy

Prions are infectious agents that cause the proteins of a host cell to misfold and aggregate. One well-known mechanism by which prions cause proteins to aggregate is by replacing normal α-helices with β-sheets, which have an increased likelihood of binding to one another. The β-sheets of these misfolded proteins then bind to the β-sheets of other proteins, leading to protein aggregation.

In this example, although the prion could potentially cause protein aggregation by increasing or decreasing the number of α-helices, it is more likely that β-sheets replace the α-helices. This has a higher likelihood of leading to protein aggregation.

References: Khan Academy

Prions are infectious agents that cause the proteins of a host cell to misfold and aggregate. One well-known mechanism by which prions cause proteins to aggregate is by replacing normal α-helices with β-sheets, which have an increased likelihood of binding to one another. The β-sheets of these misfolded proteins then bind to the β-sheets of other proteins, leading to protein aggregation.

In this example, although the prion could potentially cause protein aggregation by increasing or decreasing the number of α-helices, it is more likely that β-sheets replace the α-helices. This has a higher likelihood of leading to protein aggregation.

References: Khan Academy

View Periodic Table

11 / 24

A researcher is able to denature a protein by adding it to a solution with low pH. Which of the following bonds is not broken in this solution?

Peptide

Disulfide

Hydrogen

Ionic

Adding the protein to a solution with low pH will denature the protein's quaternary and tertiary structures. Disulfide, hydrogen, and ionic bonds are all utilized in the tertiary structure of proteins, and will denature at low pH. Only peptide bonds, which exist at the level of primary structure are unaffected by low pH.

References: Khan Academy

Adding the protein to a solution with low pH will denature the protein's quaternary and tertiary structures. Disulfide, hydrogen, and ionic bonds are all utilized in the tertiary structure of proteins, and will denature at low pH. Only peptide bonds, which exist at the level of primary structure are unaffected by low pH.

References: Khan Academy

Adding the protein to a solution with low pH will denature the protein's quaternary and tertiary structures. Disulfide, hydrogen, and ionic bonds are all utilized in the tertiary structure of proteins, and will denature at low pH. Only peptide bonds, which exist at the level of primary structure are unaffected by low pH.

References: Khan Academy

View Periodic Table

12 / 24

Vacuum ultraviolet circular dichroism is an experimental technique used to identify β-turns in polypeptide chains. Which of the following correctly describes the location and content of β-turns?

found on the interior of proteins, and consist of nucleotides.

found on the interior of proteins, and consist of amino acids.

found on the surface of proteins, and consist of amino acids.

found on the surface of proteins, and consist of nucleotides.

β-turns are sharp turns in the amino acid sequence that allow proteins to maintain a compact structure. They are normally located on the surface of proteins.

References: Khan Academy

β-turns are sharp turns in the amino acid sequence that allow proteins to maintain a compact structure. They are normally located on the surface of proteins.

References: Khan Academy

β-turns are sharp turns in the amino acid sequence that allow proteins to maintain a compact structure. They are normally located on the surface of proteins.

References: Khan Academy

View Periodic Table

13 / 24

Keratins are structural proteins integral to the vertebrate epidermis. The secondary structure of keratin is largely composed of α-helices. A majority of these α-helices are:

right-handed in order to increase steric hindrance between R groups.

left-handed in order to increase steric hindrance between R groups.

right-handed in order to decrease steric hindrance between R groups.

left-handed in order to decrease steric hindrance between R groups.

α-helices are a common motif in the secondary structure of proteins, and are often found in fibrous proteins such as keratin. These helices are classified as either right-handed or left-handed, depending on their axis of rotation (see above image for how to determine whether an α-helix is right-handed or left-handed). Right-handed α-helices are more common because they exhibit less steric hindrance among the R groups of the amino acids that compose them.

References: Khan Academy

α-helices are a common motif in the secondary structure of proteins, and are often found in fibrous proteins such as keratin. These helices are classified as either right-handed or left-handed, depending on their axis of rotation (see above image for how to determine whether an α-helix is right-handed or left-handed). Right-handed α-helices are more common because they exhibit less steric hindrance among the R groups of the amino acids that compose them.

References: Khan Academy

α-helices are a common motif in the secondary structure of proteins, and are often found in fibrous proteins such as keratin. These helices are classified as either right-handed or left-handed, depending on their axis of rotation (see above image for how to determine whether an α-helix is right-handed or left-handed). Right-handed α-helices are more common because they exhibit less steric hindrance among the R groups of the amino acids that compose them.

References: Khan Academy

View Periodic Table

14 / 24

Ser108 and Gln114 are residues in the same α-helix of an antibody. A hydrogen bond:

will not form between these two residues.

will form between the R groups of Ser108 and Gln114.

will form between the amino group of Ser108 and the carbonyl of Gln114.

will form between the amino group of Gln114 and the carbonyl of Ser108.

Amino acids in α-helices form hydrogen bonds with the amino acid 4 residues ahead of them. The amino group of one residue forms a hydrogen bond with the carbonyl of another residue.

In this problem, Ser108 and Gln114 are more than 4 residues apart. They will not form a hydrogen bond.

References: Khan Academy

Amino acids in α-helices form hydrogen bonds with the amino acid 4 residues ahead of them. The amino group of one residue forms a hydrogen bond with the carbonyl of another residue.

In this problem, Ser108 and Gln114 are more than 4 residues apart. They will not form a hydrogen bond.

References: Khan Academy

Amino acids in α-helices form hydrogen bonds with the amino acid 4 residues ahead of them. The amino group of one residue forms a hydrogen bond with the carbonyl of another residue.

In this problem, Ser108 and Gln114 are more than 4 residues apart. They will not form a hydrogen bond.

References: Khan Academy

View Periodic Table

15 / 24

What is the correct amino acid sequence for this polypeptide? (See image)

Question Image

S-D-K-P-V-G-C

S-E-K-F-V-G-C

C-G-V-P-K-D-S

C-G-V-F-K-E-S

Amino acid sequences are written starting from the N-terminus and ending with the C-terminus. The amino acid at the N-terminus of this polypeptide is Serine (S), and the second amino acid is Glutamate (E). This eliminates all other answer choices.

References: Khan Academy; Amino Acid Mastery Course

Amino acid sequences are written starting from the N-terminus and ending with the C-terminus. The amino acid at the N-terminus of this polypeptide is Serine (S), and the second amino acid is Glutamate (E). This eliminates all other answer choices.

References: Khan Academy; Amino Acid Mastery Course

Amino acid sequences are written starting from the N-terminus and ending with the C-terminus. The amino acid at the N-terminus of this polypeptide is Serine (S), and the second amino acid is Glutamate (E). This eliminates all other answer choices.

References: Khan Academy; Amino Acid Mastery Course

View Periodic Table

16 / 24

High levels of cyclin-dependent kinase activity have been implicated in tumorigenesis. Which of the following amino acids' R groups would likely remain unchanged in the presence of a kinase?

W

Y

S

T

W (Tryptophan) is the only one of the choices that does not include a hydroxyl (-OH) group. A kinase adds on a phosphate group to a molecule by removing a hydrogen and creating a bond between the Oxygen of the hydroxyl group and the phosphate of the phosphate group (O-P).

References: Content Review Books, Amino Acid Mastery Course

W (Tryptophan) is the only one of the choices that does not include a hydroxyl (-OH) group. A kinase adds on a phosphate group to a molecule by removing a hydrogen and creating a bond between the Oxygen of the hydroxyl group and the phosphate of the phosphate group (O-P).

References: Content Review Books, Amino Acid Mastery Course

W (Tryptophan) is the only one of the choices that does not include a hydroxyl (-OH) group. A kinase adds on a phosphate group to a molecule by removing a hydrogen and creating a bond between the Oxygen of the hydroxyl group and the phosphate of the phosphate group (O-P).

References: Content Review Books, Amino Acid Mastery Course

View Periodic Table

17 / 24

A scientist shines plane polarized light through various amino acids. Which amino acid will not show optical activity?

G

T

E

R

Glycine (G, Gly) is the only amino acid that does not rotate the plane of plane-polarized light because glycine is an achiral compound, making it optically inactive.

References: Content Review Books; Amino Acid Mastery Course

Glycine (G, Gly) is the only amino acid that does not rotate the plane of plane-polarized light because glycine is an achiral compound, making it optically inactive.

References: Content Review Books; Amino Acid Mastery Course

Glycine (G, Gly) is the only amino acid that does not rotate the plane of plane-polarized light because glycine is an achiral compound, making it optically inactive.

References: Content Review Books; Amino Acid Mastery Course

View Periodic Table

18 / 24

The amino acid histidine is often found in the active site of several enzymes. Which of the following best explains why this is true?

Its side chain is nonpolar, allowing it to bind nonpolar substrates.

Its side chain has an aromatic ring, allowing it to remain stable while catalyzing reactions.

Its side chain is polar, allowing it to bind polar substrates.

Its side chain has a pKₐ similar to physiological pH, allowing it to protonate and deprotonate easily.

Histidine's R group has a pKₐ of ~ 6.5, the closest of all amino acid side chains to the physiological pH of 7.3 - 7.4. Therefore, Histidine protonates and deprotonates more easily than other amino acids, allowing it to stabilize/destabilize substrates in the active site.

References: Khan Academy; Amino Acid Mastery Course

Histidine's R group has a pKₐ of ~ 6.5, the closest of all amino acid side chains to the physiological pH of 7.3 - 7.4. Therefore, Histidine protonates and deprotonates more easily than other amino acids, allowing it to stabilize/destabilize substrates in the active site.

References: Khan Academy; Amino Acid Mastery Course

Histidine's R group has a pKₐ of ~ 6.5, the closest of all amino acid side chains to the physiological pH of 7.3 - 7.4. Therefore, Histidine protonates and deprotonates more easily than other amino acids, allowing it to stabilize/destabilize substrates in the active site.

References: Khan Academy; Amino Acid Mastery Course

View Periodic Table

19 / 24

Zwitterions are amphoteric, meaning that they can act as both acids and bases. At what pH are amino acids predominantly in their Zwitterion form?

2 < pH < 9

pH = 7

8 < pH < 12

1 < pH < 4

Zwitterions are dipolar molecules, meaning they possess both a positive and negative charge. They do not necessarily have a net neutral charge.

The pKₐ of an amino acid's carboxyl terminus is ~ 2, at which point the carboxylic acid is deprotonated and left with a negative charge. The amino terminus remains positively charged until its pKₐ at pH ~ 9-10. Therefore, between pH = 2 and pH = 9, amino acids are usually found with a negatively charged carboxyl terminus and a positively charged amino terminus, making them Zwitterions.

References: Khan Academy; Amino Acid Mastery Course

Zwitterions are dipolar molecules, meaning they possess both a positive and negative charge. They do not necessarily have a net neutral charge.

The pKₐ of an amino acid's carboxyl terminus is ~ 2, at which point the carboxylic acid is deprotonated and left with a negative charge. The amino terminus remains positively charged until its pKₐ at pH ~ 9-10. Therefore, between pH = 2 and pH = 9, amino acids are usually found with a negatively charged carboxyl terminus and a positively charged amino terminus, making them Zwitterions.

References: Khan Academy; Amino Acid Mastery Course

Zwitterions are dipolar molecules, meaning they possess both a positive and negative charge. They do not necessarily have a net neutral charge.

The pKₐ of an amino acid's carboxyl terminus is ~ 2, at which point the carboxylic acid is deprotonated and left with a negative charge. The amino terminus remains positively charged until its pKₐ at pH ~ 9-10. Therefore, between pH = 2 and pH = 9, amino acids are usually found with a negatively charged carboxyl terminus and a positively charged amino terminus, making them Zwitterions.

References: Khan Academy; Amino Acid Mastery Course

View Periodic Table

20 / 24

A researcher wishes to introduce a mutation to an enzyme that utilizes Threonine to bind reactants in its active site. Which of the following amino acids would replace threonine in such a way to inhibit the activity of the enzyme?

Tryptophan

Aspartate

Tyrosine

Serine

The distinguishing characteristic of Threonine is the -OH group on its side chain. Therefore, in order to inhibit this enzyme's active site, the researcher must replace Threonine with an amino acid that lacks a similar -OH group.

Serine and Tyrosine both contain alcohols in their R groups, giving them similar bonding capabilities to Threonine.

Aspartate is too similar to Threonine due to the carboxylic acid in its R group.

Tryptophan is the best answer because it does not have an -OH group in its side chain.

References: Content Review Books, Amino Acid Mastery Course

The distinguishing characteristic of Threonine is the -OH group on its side chain. Therefore, in order to inhibit this enzyme's active site, the researcher must replace Threonine with an amino acid that lacks a similar -OH group.

Serine and Tyrosine both contain alcohols in their R groups, giving them similar bonding capabilities to Threonine.

Aspartate is too similar to Threonine due to the carboxylic acid in its R group.

Tryptophan is the best answer because it does not have an -OH group in its side chain.

References: Content Review Books, Amino Acid Mastery Course

The distinguishing characteristic of Threonine is the -OH group on its side chain. Therefore, in order to inhibit this enzyme's active site, the researcher must replace Threonine with an amino acid that lacks a similar -OH group.

Serine and Tyrosine both contain alcohols in their R groups, giving them similar bonding capabilities to Threonine.

Aspartate is too similar to Threonine due to the carboxylic acid in its R group.

Tryptophan is the best answer because it does not have an -OH group in its side chain.

References: Content Review Books, Amino Acid Mastery Course

View Periodic Table

21 / 24

A certain protein is 8 amino acids in length. How many different amino acid sequences are possible for this protein?

2.56 ⋅ 10¹⁰

1,600

160

1.15 ⋅ 10¹⁸

To determine the total number of amino acid sequences that are possible for this protein, we must take the number of naturally occurring amino acids (20) and raise it by the number of amino acids in this sequence (8).

20⁸ = 20 × 20 × 20 × 20 × 20 × 20 × 20 × 20

= 400 × 400 × 400 × 400

= 160,000 × 160,000

= 25,600,000,000

= 2.56 ⋅ 10¹⁰ possible sequences

References: Khan Academy; High-speed Math Mastery Course

To determine the total number of amino acid sequences that are possible for this protein, we must take the number of naturally occurring amino acids (20) and raise it by the number of amino acids in this sequence (8).

20⁸ = 20 × 20 × 20 × 20 × 20 × 20 × 20 × 20

= 400 × 400 × 400 × 400

= 160,000 × 160,000

= 25,600,000,000

= 2.56 ⋅ 10¹⁰ possible sequences

References: Khan Academy; High-speed Math Mastery Course

To determine the total number of amino acid sequences that are possible for this protein, we must take the number of naturally occurring amino acids (20) and raise it by the number of amino acids in this sequence (8).

20⁸ = 20 × 20 × 20 × 20 × 20 × 20 × 20 × 20

= 400 × 400 × 400 × 400

= 160,000 × 160,000

= 25,600,000,000

= 2.56 ⋅ 10¹⁰ possible sequences

References: Khan Academy; High-speed Math Mastery Course

View Periodic Table

22 / 24

An unspecified virus uses RNA as its genetic material. This viral RNA could possibly lead to the synthesis of which of the following?

I. cDNA

II. mRNA

III. Proteins

I and III only

I, II, and III

I only

II only

Viruses use a living host cell to replicate their own genetic material.

Retroviruses are a subtype of virus that use the enzyme reverse transcriptase to create a strand of cDNA from an mRNA template strand. The cDNA is then incorporated into the host cell's DNA, where it is eventually replicated.

RNA viruses also use mRNA as a template strand. However, unlike retroviruses, RNA viruses use a host cell's machinery to carry out translation or RNA replication. This results in new proteins and mRNA, respectively.

References: Khan Academy

Viruses use a living host cell to replicate their own genetic material.

Retroviruses are a subtype of virus that use the enzyme reverse transcriptase to create a strand of cDNA from an mRNA template strand. The cDNA is then incorporated into the host cell's DNA, where it is eventually replicated.

RNA viruses also use mRNA as a template strand. However, unlike retroviruses, RNA viruses use a host cell's machinery to carry out translation or RNA replication. This results in new proteins and mRNA, respectively.

References: Khan Academy

Viruses use a living host cell to replicate their own genetic material.

Retroviruses are a subtype of virus that use the enzyme reverse transcriptase to create a strand of cDNA from an mRNA template strand. The cDNA is then incorporated into the host cell's DNA, where it is eventually replicated.

RNA viruses also use mRNA as a template strand. However, unlike retroviruses, RNA viruses use a host cell's machinery to carry out translation or RNA replication. This results in new proteins and mRNA, respectively.

References: Khan Academy

View Periodic Table

23 / 24

The Strecker synthesis is often conducted to produce racemic mixtures of methionine. Which of the following is not a starting component for the Strecker synthesis?

Grignard Reagent

Potassium cyanide

Ammonia

Aldehyde or ketone

Remember that The Strecker Synthesis is a preparation of α-aminonitriles, which are versatile intermediates for the synthesis of amino acids via hydrolysis of the nitrile.

Ammonia is used as the precursor for the amino group. Potassium cyanide is the precursor for the carboxylic acid group, An aldehyde or ketone serves as a scaffold for the amino and carboxylic acid groups. The Grignard reagent is the only thing listed not needed for a strecker synthesis reaction.

Reference: Khan Academy

Remember that The Strecker Synthesis is a preparation of α-aminonitriles, which are versatile intermediates for the synthesis of amino acids via hydrolysis of the nitrile.

Ammonia is used as the precursor for the amino group. Potassium cyanide is the precursor for the carboxylic acid group, An aldehyde or ketone serves as a scaffold for the amino and carboxylic acid groups. The Grignard reagent is the only thing listed not needed for a strecker synthesis reaction.

Reference: Khan Academy

Remember that The Strecker Synthesis is a preparation of α-aminonitriles, which are versatile intermediates for the synthesis of amino acids via hydrolysis of the nitrile.

Ammonia is used as the precursor for the amino group. Potassium cyanide is the precursor for the carboxylic acid group, An aldehyde or ketone serves as a scaffold for the amino and carboxylic acid groups. The Grignard reagent is the only thing listed not needed for a strecker synthesis reaction.

Reference: Khan Academy

View Periodic Table

24 / 24

Gabriel synthesis is often used in the preparation of primary aromatic amines, which can be used as a starting material in the manufacture of dyes. What type of reaction occurs in Gabriel synthesis?

E1

SN1

E2

SN2

This is a basic recall question. The Gabriel synthesis pathway involves alkylation in a SN2 reaction.

Reference: Khan Academy

This is a basic recall question. The Gabriel synthesis pathway involves alkylation in a SN2 reaction.

Reference: Khan Academy

This is a basic recall question. The Gabriel synthesis pathway involves alkylation in a SN2 reaction.

Reference: Khan Academy

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These recommendations are directly from the AAMC Content Outline module available on the MCAT Official Prep Hub. All of their text recommendations have been incorporated into our free e-course, with their respective learning objectives listed in parentheses.

Do textbook chapters and AAMC Content Outline match up perfectly?

The Kaplan Books, Princeton Books, AAMC Content Outline texts, and Khan Academy Videos were all produced by different authors. For this reason, there are some chapters in the Kaplan Book or Princeton Book that are not even found in the Khan Academy Videos or AAMC Content Outline and vice versa. For instance, the Kaplan and Princeton Books have chapters that cover certain experimental procedures that the Khan Academy Videos do not cover.

Our goal in matching up the AAMC Content Outline with the lessons was to correlate the content as best as possible while also covering ALL the content from every resource. For this reason, when nothing in the Kaplan Books matched up with one of the video playlists, instead of leaving the reading assignment for Kaplan blank, we inserted material that did not fit in anywhere else (i.e. one of those chapters on an experimental procedure that was not covered by Khan Academy). So, when the assignment doesn’t appear to match up right, please know that this was intentional.

*If you follow the reading assignments outlined, you will finish the entire AAMC Content Outline by the time you finish all 10 content modules.

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If the sections assigned in our eCourse do not match up with the sections contained in your content review book, you may have a different edition. The sections should still match up the large majority of the time, but in the rare instance that they don’t, I’d recommend simply reading sections that do match up and saving the ones that do not for a future lesson.

Which books do the lessons match up with?

The books we use in each lesson are linked below. We plan to stick with these older editions of the books since very little has changed and the older editions are much more affordable:

First Edition of the Kaplan 7-book Series
First Edition of the Princeton 7-book Series

Do the chapters match up perfectly?

The Kaplan Books, Princeton Books, and Khan Academy Videos were all produced by different authors. For this reason, there are some chapters in the Kaplan Book or Princeton Book that are not even found in the Khan Academy Videos and vice versa. For instance, the Kaplan and Princeton Books have chapters that cover certain experimental procedures that the Khan Academy Videos do not cover.

Our goal in matching up the books with the videos was to correlate the content as best as possible while also covering ALL the content from every resource. For this reason, when nothing in the Kaplan Books matched up with one of the video playlists, instead of leaving the reading assignment for Kaplan blank, we inserted material that did not fit in anywhere else (i.e. one of those chapters on an experimental procedure that was not covered by Khan Academy). So, when the assignment doesn’t appear to match up right, please know that this was intentional.

*If you follow the reading assignments outlined, you will finish the entire Kaplan 7-book series and/or Princeton 7-book series by the time you finish all 10 content modules.

Do the sections match up perfectly?

If the sections assigned in our eCourse do not match up with the sections contained in your content review book, you may have a different edition. The sections should still match up the large majority of the time, but in the rare instance that they don’t, I’d recommend simply reading sections that do match up and saving the ones that do not for a future lesson.