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

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

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

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

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

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

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. At the same time, water molecules surrounding the protein will orient themselves to maximize contact with hydrophobic residues in order to maximize hydrogen bonding. 

Reference: Content Review Books, AK Lectures

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

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 

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

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

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

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 

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 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

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

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

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

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

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

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

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

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

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

Reference:  Khan Academy