Biochemistry : Biochemistry

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #6 : Tertiary Structure

2-mercaptoethanol is a chemical agent used in denaturing proteins. Its primary method of denaturing involves separating disulfide bonds. Based on this method of denaturation, what is the lowest level of protein structure affected by 2-mercaptoethanol?

Possible Answers:

Primary structure

Secondary structure

Quaternary structure

Tertiary structure

Correct answer:

Tertiary structure

Explanation:

A disulfide bond is created by two cysteine residues coming together and creating a sulfur-sulfur linkage. This type of linkage contributes to the tertiary structure of proteins. It can also be seen in quaternary structure between peptide subunits, but tertiary structure is the first level where this force can be observed.

Example Question #7 : Tertiary Structure

Which of the following statements are true about protein domains?

I. Polypeptide chains longer than 200 amino acids in length have multiple domains.

II. Domains are tertiary structural components of proteins.

III. Different domains are encoded by different exons of a gene.

IV. Each domain in a protein has a specific function.

Possible Answers:

II, III, and IV

I, II, and III

I and IV

I, II, III, and IV

II and IV

Correct answer:

I, II, III, and IV

Explanation:

Domains are tertiary structures that have motifs (a supersecondary structure) as their components. Domains are independent (functionally and structurally) from each other.

Example Question #1 : Quaternary Structure

Which of these macromolecules has quarternary structure?

Possible Answers:

Chymotrypsin

Lactose

Myoglobin

Hemoglobin

Sucrose

Correct answer:

Hemoglobin

Explanation:

Hemoglobin is the only available example of a macromolecule composed of multiple subunits. Hemoglobin has frou subunits, each capable of binding and transporting one molecule of oxygen in the blood.

Chymotrypsin and myogblobin are both simple proteins, each consisting of a single polypeptide. These proteins do not have multiple subunits; thus their highest level of structure is tertiary (three-dimensional). Lactose and sucrose are disaccharides, each composed of two carbohydrate monomers (monosaccharides).

Example Question #1 : Quaternary Structure

Hemoglobin is a protein that possesses more than one polypeptide subunit, therefore it has a __________ structure.

Possible Answers:

complex

tertiary

primary

secondary

quaternary

Correct answer:

quaternary

Explanation:

Hemoglobin is a tetramer that possesses a quaternary structure containing multiple folded polypeptide structures (tertiary structures). A tertiary protein will commonly contain a single polypeptide chain with one or more secondary structures.

Example Question #41 : Protein Folding

Which of the following is true about quaternary structure?

Possible Answers:

When ligands bind to proteins, their 3D-structures sometimes change

A protein with multiple identical subunits does not have a quaternary structure.

The main forces holding together oligomeric subunits are disulfide bonds

None of these

Correct answer:

When ligands bind to proteins, their 3D-structures sometimes change

Explanation:

A protein with multiple identical subunits does indeed have a quaternary structure; in these cases, dimers and tetramers are common. The main forces holding together oligomeric subunits are weak, non-covalent interactions, specifically, hydrophobic ones, as well as electrostatic forces. Subunits do not necessarily form separate domains within a protein; in a potassium channel protein, for example, there are identical subunits which come together to form the single channel. Proteins’ 3D-structures do indeed sometimes change when ligands bind; this change help regulate the proteins’ biological activity.

Example Question #3 : Quaternary Structure

Which of the following proteins do not have quaternary structure?

Possible Answers:

p53

DNA polymerase

Myoglobin

Hemoglobin

Correct answer:

Myoglobin

Explanation:

Quaternary structure of a protein involves the assembly of subunits. Hemoglobin, p53 and DNA polymerase are all composed of subunits, while myoglobin is a functional single sequence. Since myoglobin does not have multiple subunits, it does not have quaternary structure.

Example Question #41 : Protein Folding

Which of the following best describes the quaternary structure of a protein?

Possible Answers:

How the polypeptide chains fit together

The four parts of a protein's amino acid sequence

The polypeptide chain's complete 3-D structure

The layout of alpha-helices and beta-sheets

The sequence of nucleic acids

Correct answer:

How the polypeptide chains fit together

Explanation:

Quaternary structure describes how polypeptide chains fit together to form a complete protein. Quaternary protein structure is held together by hydrophobic interactions, and disulfide bridges. The sequence of amino acids is known as primary structure; helices, sheets, and similar features are part of the secondary structure; and the 3-D organization is tertiary structure. "The four parts of a protein's amino acid sequence" does not refer to anything in particular.

Example Question #1 : Quaternary Structure

Which of the following best explains a quaternary structure of a protein?

Possible Answers:

Hydrogen bonds, alpha-helices and beta-pleated sheets

Linear sequence of amino acids

Collagen and myoglobin 

Disulfide bonds, single polypeptide chain

Hydrogen and disulfide bonds, two or more polypeptide chains

Correct answer:

Hydrogen and disulfide bonds, two or more polypeptide chains

Explanation:

Primary structure: linear sequence of amino acids

Secondary structure: hydrogen bonds, alpha-helices and beta-pleated sheets

Tertiary structure: disulfide bonds, single polypeptide chain

Myoglobin is a monomer, and is made of a single polypeptide chain. Thus, its highest level of protein structure is tertiary. While collagen does contain different polypeptide chains, it is an example of a protein with quaternary structure, not an explanation of what this means.

Example Question #2 : Quaternary Structure

What form of protein structure includes disulfide bonds?

Possible Answers:

Only secondary structure

Only primary structure

Only tertiary structure

Only quaternary structure

Tertiary and quaternary structures

Correct answer:

Tertiary and quaternary structures

Explanation:

In this question, we're asked about how disulfide bonds relate to protein folding. Let's go through each form of structure.

Primary structure refers to the sequence of amino acids in the polypeptide, from the N-terminal end to the C-terminal end.

Secondary structure refers to local conformations of protein folding. There are a number of commonly found motifs that have been recognized, such as alpha-helices and beta-pleated sheets. These motifs are stabilized by intermolecular interactions between amino acid side-chains and also between alpha-carboxy and alpha-amino groups of the peptide backbone. Some of these intermolecular interactions include hydrogen bonding, van der Waals interactions, dipole interactions, and ionic bonding.

Tertiary structure refers to the overall three-dimensional structure of the folded polypeptide. This form of structure relies on the same intermolecular interactions found in secondary structure. In addition, tertiary structure also includes disulfide bonds that are found between cysteine residues.

Quaternary structure refers only to proteins that are composed of multiple polypeptides. These separate polypeptides are held together by the same intermolecular forces found in secondary and tertiary structures. In addition, disulfide bonds are also found in quaternary structure, just like in tertiary structure.

Thus, tertiary and quaternary structure both include disulfide bonds.

Example Question #42 : Protein Folding

What is the primary driver of protein folding on a macro level?

Possible Answers:

Covalent bonding

Entropic force

Hydrogen bonding

Van der Waals forces

Ionic bonding

Correct answer:

Entropic force

Explanation:

While covalent bonds create the primary structure of a protein, and hydrogen bonding and Van der Waals forces have a large impact on the secondary structure of a protein, they are not the main contributors to overall folding of a protein. This has more to do with solvation costs, hydrophobicity, and entropy. The hydrophobicity and hydrophobic portions of the protein must fold to minimize entropic costs.

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