Biochemistry : Biochemistry

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #3 : Primary Structure

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

Possible Answers:

Double displacement reaction

Hydration reaction

Decomposition reaction

Combustion reaction

Condensation 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 #4 : Primary Structure

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:

Quaternary structure

Secondary structure

Tertiary 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 #2 : Primary Structure

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

Possible Answers:

The assembly of subunits into a larger protein.

None of these

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

Hydrogen bonding between amino acid side chains.

The actual amino acid residue sequence.

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.

Example Question #1 : Protein Folding

An alpha-helix is formed by hydrogen bonding between the hydrogen of an amine group and the backbone carbonyl group how many amino acids upstream of it?

Possible Answers:

Two

Three

Four

Five

Six

Correct answer:

Four

Explanation:

Alpha-helices are formed by hydrogen bonding involving an alpha carbon-bound amine group's hydrogen and the carbonyl group attached to the amino acid four amino acids upstream.

Example Question #2 : Secondary Structure

Which of the following best describes a characteristic of a protein motif?

Possible Answers:

A commonly occurring arrangement made up of multiple secondary structures

A unique arrangement made up of secondary structures found only in a single protein

A family of proteins with similar functions

A commonly occurring arrangement made up of tertiary structures

A unique arrangement made up of tertiary structures found only in a single protein

Correct answer:

A commonly occurring arrangement made up of multiple secondary structures

Explanation:

A protein motif (aka supersecondary structure) is a defined arrangement of secondary structures within a protein. It is commonly occurring enough to have an identified structure. An example would be the beta-alpha-beta loop. While the arrangement is made up of secondary structure, the overall motif itself can be considered supersecondary or possibly even tertiary, though its components are secondary structures. Motif's do not necessarily have a defined function across different proteins. Protein domains on the other hand, do.

Example Question #1 : Secondary Structure

What type of bonds are the "backbone" of secondary protein structure?

Possible Answers:

Amide bonds

Hydrogen bonds

Amino acid bonds

Peptide bonds

Van der Waals interactions

Correct answer:

Hydrogen bonds

Explanation:

Hydrogen bonds stabilize interactions among the amide and carboxyl groups in the main chain of the polypeptide. These interactions may induce the formation of alpha-helices and/or beta-pleated sheets.

Example Question #2 : Secondary Structure

Which of the following amino acids is least likely to be found in the middle of an alpha helix?

Possible Answers:

Proline

Methionine

Serine

Glutamic acid

Correct answer:

Proline

Explanation:

Proline is bound to two alkyl groups thus giving it a planar configuration, giving the nitrogen only the ability to accept hydrogen bonds not donate them. While this is not a problem at the beginning of an alpha helix this can disturb the bonds if place further down the chain. Thus proline is often referred to as the "alpha helix buster."

Example Question #2 : Secondary Structure

The stabilization of secondary structure in polypeptides is conferred by which of the following?

Possible Answers:

Metal cations

Disulfide bonds

The R-groups of the amino acids

The amino acid backbones

The phosphate groups

Correct answer:

The amino acid backbones

Explanation:

Alpha helices and beta sheet, the dominant secondary structural motifs in polypeptides are formed by hydrogen bonds between the carbonyl and amino groups of the amino acid backbone.

Example Question #3 : Secondary Structure

Why are antiparallel beta sheets more stable than parallel beta sheets? 

Possible Answers:

The hydrogen bonding angle is optimized by antiparallel sheets

The hydrogen bond angle is 150 degrees

There are more covalent interactions between its amino acids

There are more hydrophobic interactions between its amino acids

The antiparallel sheets are composed of more stable amino acids

Correct answer:

The hydrogen bonding angle is optimized by antiparallel sheets

Explanation:

In an antiparallel beta sheet, the hydrogen bonding angle is 180 degrees and optimal; this is the most stable angle. In parallel sheets, it is a less stable 150 degrees. Whether a sheet is parallel or antiparallel does not tell us anything about what amino acids it is composed of, so each of the other answers is incorrect.

Example Question #1 : Secondary Structure

In a sequence of amino acids within an alpha helix, between which amino acids in the sequence does hydrogen bonding occur (i.e. every how many amino acids)?

Possible Answers:

1 and 5, so every 5 amino acids

1 and 4, so every 4 amino acids

1 and 6, so every 6 amino acids

1 and 6, so every 4 amino acids

1 and 3, so every 3 amino acids

Correct answer:

1 and 4, so every 4 amino acids

Explanation:

In an alpha helix, hydrogen bonding occurs every four amino acids, starting from the 1st binding to the 4th in the sequence; the 2nd amino acid binds to the 6th, the 3rd to the 7th, and so on. 

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