Biochemistry : Primary Structure

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #1 : Protein Folding

A protein's primary structure is determined by which of the following?

Possible Answers:

The hydrophobic effect

R-group interactions

Alpha-helices

The linear sequence of specific amino acids

Beta-pleated sheets

Correct answer:

The linear sequence of specific amino acids

Explanation:

A protein's primary structure is defined solely by its amino acid sequence, and is constructred by peptide bonds between adjacent amino acid residues.

Secondary structure results from hydrogen bonding along the polypeptide backbone, resulting in alpha-helices and beta-pleated sheets. Tertiary structure results from hydrogen bonding between R groups, hydrophobic interactions, and disfulide bridges; these interactions create the three-dimensional structure of the molecule. Finally, quaternary structure arises from the joining of multiple subunits to create a functional protein complex.

Example Question #2 : Protein Folding

Sickle cell anemia results from a missense mutation that replaces a glutamic acid residue with which of the following?

Possible Answers:

Glutamine

Asparagine

Aspartic acid

Arginine

Lysine

Correct answer:

Lysine

Explanation:

A single amino acid substitution from glutamic acid to lysine is responsible for sickle cell anemia. The mutation occurs in the gene that codes for hemoglobin and causes misfolding that results in a lower oxygen affinity.

Example Question #3 : Protein Folding

The __________ structure of a protein corresponds to the linear order of amino acids in a given polypeptide chain.

Possible Answers:

Tertiary

None of these answers

Primary

Quaternary

Secondary

Correct answer:

Primary

Explanation:

With regard to protein structure, primary structure refers to the order of the amino acids, which are held together by peptide bonds. Secondary structure refers to the presence of beta pleated sheets and alpha helices within a protein. Tertiary structure refers to a protein's geometric shape as a result of the interactions between the sidechains of the amino acids in the peptide chain. Quaternary structure concerns side chain interactions within a multiple polypeptide chains.

Example Question #4 : Protein Folding

What type of bonds are found in the primary structure of a protein?

Possible Answers:

Van der Waals interactions

Peptide bonds

Sulfide bonds

Hydrogen bonds

Ionic bonds

Correct answer:

Peptide bonds

Explanation:

Primary structure consists of amino acids joined by peptide bonds. Peptide bonds are between the alpha-carboxyl of one amino acid, and the alpha-amine of the next amino acid. A peptide bond is an example of an amide bond. Hydrogen bonds are found in secondary structure, tertiary structure exhibits Van Der Waals interactions.

Example Question #1 : Protein Folding

When a protein is transferred to a solution with a pH that is much lower than its optimal range, which of the following levels of protein structure is or can be affected?

Possible Answers:

Tertiary only

Secondary, tertiary, and quaternary

Secondary only

Primary only

Primary, secondary, tertiary, and quaternary

Correct answer:

Secondary, tertiary, and quaternary

Explanation:

This question is presenting us with a scenario in which a protein is being transferred to a highly acidic solution that is outside of the protein's optimal pH range. In such a situation, we would expect the protein to undergo conformational changes that would alter its function. The question, however, is which levels of protein structure would be altered by such a change in pH.

The first level of structure worth considering is primary structure. The primary structure of a protein refers to the sequence of individual amino acids that make up the protein. Upon being transferred to an acidic solution, the protein does indeed unfold, but it doesn't break apart into individual amino acids. Therefore, the unfolded protein remains as a single, long chain, but its sequence of amino acids is still intact. Thus, there is no change in primary structure.

The secondary structure of a protein refers to local conformations found within the folded protein. Such local conformations include certain commonly found structural motifs, such as alpha-helices and beta-pleated sheets. These local conformational structures are held together by various intramolecular bonds between the amino acid residues. These intramolecular interactions include hydrogen bonding and van der Waals forces, among others. When transferred to an acidic solution, these intramolecular forces are disrupted and, as a result, cause a disruption in the protein's secondary structure.

The third level of protein structure is tertiary structure, which refers to the overall conformation of a single chain of amino acids, sometimes referred to as a polypeptide. The overall three-dimensional conformation of a polypeptide is held together by some of the same intramolecular forces involved with secondary structure, such as hydrogen bonding, van der Waals interactions, and disulfide bonds. Because a highly acidic solution interferes with these interactions, the tertiary level of protein structure is indeed affected by pH changes.

And finally, the last level of protein structure to consider is quaternary structure. Not all proteins possess this level of structure, because in order to have this level of structure, two or more polypeptide chains need to come together and interact via intermolecular bonding to form the final, finished protein. An example of this level of structure can be seen in the protein hemoglobin, in which two alpha-chains and two beta-chains come together and interact to form hemoglobin. Just as with secondary and tertiary structures, the introduction of a highly acidic solution can disrupt these intermolecular interactions, thus causing a disruption in the quaternary structure of a protein composed of two or more polypeptide chains.

Example Question #6 : Protein Folding

What is the primary structure of a protein?

Possible Answers:

The sequence of amino acids. 

The interaction of one polypeptide sub-unit with another.

Alpha and beta folding patterns created by amino acid interactions. 

The sequence of amino acids and the initial folding of the protein.

The complete folding of a protein. 

Correct answer:

The sequence of amino acids. 

Explanation:

The primary structure is only composed of the sequence of amino acids in a protein. The secondary structure is the alpha or beta folding that occurs due to amino acid interaction. The tertiary structure is the three dimensional folding that occurs within a protein. Finally, quaternary structure occurs when a protein has two or more polypeptide sub-units. A perfect example of quaternary structure is found in hemoglobin. 

Example Question #7 : Protein Folding

The formation of a peptide bond is an example of what type of reaction?

Possible Answers:

Double displacement reaction

Decomposition reaction

Condensation reaction

Hydration reaction

Combustion reaction

Correct answer:

Condensation reaction

Explanation:

The formation of a peptide bond is an example of a condensation reaction. This is because, when two amino acids come together, a water molecule is let go. 

Example Question #8 : Protein Folding

Sickle cell anemia is caused by a point mutation in hemoglobin, where a glutamate residue is changed to a valine. Based on this mutation mechanism, what level of protein structure is affected by sickle cell anemia? 

Possible Answers:

Secondary structure

Tertiary structure

Quaternary structure

Primary structure

Correct answer:

Primary structure

Explanation:

Because an amino acid has been altered in sickle cell anemia, we can say that the amino acid sequence for hemoglobin has been changed. The amino acid sequence is defined as the primary structure for a protein, so that is the level that has been altered. It should be noted that the subsequent levels of protein structure would be altered as well, but the manipulation of the amino acid sequence is a changing of the primary structure first.

Example Question #9 : Protein Folding

Which of the following describes the primary structure of a protein?

Possible Answers:

The actual amino acid residue sequence.

The assembly of subunits into a larger protein.

Hydrogen bonding between amino acid backbone groups (carboxyl and amino).

Hydrogen bonding between amino acid side chains.

None of these

Correct answer:

The actual amino acid residue sequence.

Explanation:

The primary structure of a protein is defined by the sequence of amino acid residues. It is this sequence that lays the foundation for all other higher levels of structures in a protein. Secondary structure is defined by the hydrogen bonding between the carboxyl and amino backbone of the amino acids. Tertiary is defined by amino acid side chain interactions. Finally, quaternary structure is defined by the assembly of subunits of a protein into the overall larger protein structure.

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