Biochemistry : Peptide Bonds

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #3 : Macromolecule Structures And Functions

How many water molecules are lost from the condensation of 100 amino acids into a polypeptide?

Possible Answers:

Correct answer:

Explanation:

A peptide bond is formed via the condensation of one amino acid's alpha-carboxy group with the alpha-amino group of another amino acid. Thus, the joining together of two amino acids results in the loss of one water molecule. Likewise, joining three amino acids together results in the loss of two water molecules. Following this pattern, we can conclude that the number of water molecules lost is equal to the number of amino acids joined together, minus 1. Therefore, the joining together of 100 amino acids results in the loss of 99 water molecules.

Example Question #4 : Macromolecule Structures And Functions

Amino acids are connected via __________ bonds, which occur between the carboxyl group of one amino acid and the amino group of another. 

Possible Answers:

amino

peptide

hydrogen

ionic

double

Correct answer:

peptide

Explanation:

A peptide bond connects two amino acids. This is the result of a condensation reaction (water is lost) and a new nitrogen-carbon bond forms between two amino acids. Note that amino acid synthesis occurs in the  direction. Peptide bonds are covalent bonds that are responsible for the primary structure of amino acids.

Example Question #13 : Biochemistry

In how many different ways can the amino acids leucine, glutamate, and glycine be arranged?

Possible Answers:

Correct answer:

Explanation:

For this question, we are presented with three different amino acids and are asked how many possible ways they can be arranged. One way to do this is to list out all the various ways they can be connected.

1) Gly-Leu-Glu

2) Gly-Glu-Leu

3) Leu-Gly-Glu

4) Leu-Glu-Gly

5) Glu-Leu-Gly

6) Glu-Gly-Leu

Alternatively, we could use the mathematic expression  to determine the number of combinations of three separate things, which is equal to .

Example Question #1 : Peptide Bonds

What accounts for peptide bond planarity within a polypeptide?

Possible Answers:

Partial double bond character of the peptide bond

The fully double bonded peptide bond

Hydrogen bonding between amino acid side chains and water

The peptide bond is not planar, it can actually rotate relatively freely

Electronegativity differences between nitrogen and carbon

Correct answer:

Partial double bond character of the peptide bond

Explanation:

The peptide bond within a polypeptide creates planarity, while other parts of the polypeptide are free to rotate. This occurs because of a delocalization of the electrons on the nitrogen of the amino group (resonance), forming a partial double bond.

While there is a slight difference in electronegativity between carbon and nitrogen, this does not effect the planarity of a polypeptide. Additionally, while a small and insignificant amount of hydrogen bonding may occur between side chains and water, it would not effect planarity regardless.

Example Question #2 : Peptide Bonds

The cis conformation of most amino acids is virtually non-existent in nature. Which amnio acid is the exception to this rule, and has a significant amount of cis conformation present in nature?

Possible Answers:

Alanine

Tryptophan

Arginine

Glycine

Proline

Correct answer:

Proline

Explanation:

A cis conformation is so rare due to steric clashes between side chains in different amino acid residues. The Van der Waals forces are simply to great for two side chains to occupy nearby spaces. However, proline is a very unique amino acid. Proline has a unique ring structure, in which its side chain is attached to its amino backbone group. Because of this, there is actually some steric clash in the trans conformation, in addition to the cis conformation. Overall, it is estimated that 10-30% of proline exists in the cis conformation, which is far greater than any other amino acid.

Example Question #3 : Peptide Bonds

What is represented by the colored regions of a Ramachandran plot?

Possible Answers:

The amino acid residues that are permitted within a certain polypeptide chain.

The favorable angles of the bonds of an amino acid within a polypeptide chain.

The energy required to break an amide bond within a polypeptide chain.

The unfavorable angles of the bonds of an amino acid within a polypeptide chain.

The order of amino acid residues within a certain polypeptide chain.

Correct answer:

The favorable angles of the bonds of an amino acid within a polypeptide chain.

Explanation:

A Ramachandran plot, also referred to as a dihedral plot, tells us about what bond angles are favorable for an amino acid residue. The colored regions are favorable, while the uncolored (white) regions are not favorable. Additionally, each colored regions also corresponds to a different secondary structures (alpha helix, beta sheet, etc.).

These plots can't tell us much about the specific residue order within a polypeptide chain, or the energy required to break an amide bond.

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