Protein Structure

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Biochemistry › Protein Structure

Questions 1 - 10
1

Suppose that the active site of an enzyme contains amino acid residues at the following positions:

Residue - Arginine

Residue - Valine

Residue - Glutamate

Residue - Glycine

Which of the following amino acid substitutions would be least likely to affect the activity of this enzyme?

Lysine at position

Aspartate at position

Tryptophan at position

Asparagine at position

A substitution at any of these positions would render the enzyme inactive

Explanation

To answer this question, we need to have a general understanding about amino acid properties. For instance, at physiological pH, some amino acid side chains will carry a negative charge, some will carry a positive charge, and others will be neutral. Thus, we'll need to take note of which amino acid characteristics each position has, and then evaluate each answer choice to see if the new amino acid being substituted has different characteristics.

At position is arginine, which carries a positive charge. At position is valine, which has an aliphatic side chain that is neutral and relatively hydrophobic. At position is the amino acid glutamate, which is negatively charged due to the carboxyl group on its side chain. Finally, we have glycine at position , which contains a lonely hydrogen atom as its side chain.

Now that we have the characteristics of the amino acid residues in the enzyme, let's compare them to the substitutions listed in the answer choices.

Substituting an aspartate residue into position would mean replacing valine (neutral) with a positively charged amino acid. Hence, this would likely result in disruption of enzyme activity.

Substituting a tryptophan residue into position would replace glycine. In contrast to the extremely small side chain of glycine, the side chain of tryptophan is very large. This great size discrepancy could potentially lead to steric effects that could interfere with the binding of substrate to the enzyme.

Substitution of an asparagine residue into position would replace glutamate. Because glutamate is negatively charged, whereas asparagine is neutral, this substitution would likely interfere with enzyme activity.

Finally, let's consider the substitution of arginine at position with a lysine. In this case, a positively charged arginine would be replaced by another positively charged amino acid, lysine. Because of the similarity between these two amino acids, this substitution would be the least likely to cause a disruption in the enzyme's activity.

2

Which proteins are generally water-soluble?

Globular proteins

Fibrous proteins

Both globular fibrous proteins

Neither globular nor fibrous proteins

Explanation

In a globular protein, the amino acid chain can twist in a way that polar groups lie at the protein's surface. This allows the protein to interact with water and enhances the protein's solubility in water. This does not occur in fibrous proteins, so fibrous proteins are insoluble in water.

3

An O-linked glycoprotein has a sugar attached to an oxygen atom on what amino acid(s)?

Serine or threonine

Serine only

Methionine only

Methionine or threonine

Threonine only

Explanation

An O-linked glycoprotein is a protein that has a sugar attached to it. It is called O-linked because the sugar is attached to an oxygen atom on either a threonine residue or a serine residue within the protein.

4

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

peptide

ionic

hydrogen

double

amino

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.

5

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

peptide

ionic

hydrogen

double

amino

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.

6

An O-linked glycoprotein has a sugar attached to an oxygen atom on what amino acid(s)?

Serine or threonine

Serine only

Methionine only

Methionine or threonine

Threonine only

Explanation

An O-linked glycoprotein is a protein that has a sugar attached to it. It is called O-linked because the sugar is attached to an oxygen atom on either a threonine residue or a serine residue within the protein.

7

Which proteins are generally water-soluble?

Globular proteins

Fibrous proteins

Both globular fibrous proteins

Neither globular nor fibrous proteins

Explanation

In a globular protein, the amino acid chain can twist in a way that polar groups lie at the protein's surface. This allows the protein to interact with water and enhances the protein's solubility in water. This does not occur in fibrous proteins, so fibrous proteins are insoluble in water.

8

Suppose that the active site of an enzyme contains amino acid residues at the following positions:

Residue - Arginine

Residue - Valine

Residue - Glutamate

Residue - Glycine

Which of the following amino acid substitutions would be least likely to affect the activity of this enzyme?

Lysine at position

Aspartate at position

Tryptophan at position

Asparagine at position

A substitution at any of these positions would render the enzyme inactive

Explanation

To answer this question, we need to have a general understanding about amino acid properties. For instance, at physiological pH, some amino acid side chains will carry a negative charge, some will carry a positive charge, and others will be neutral. Thus, we'll need to take note of which amino acid characteristics each position has, and then evaluate each answer choice to see if the new amino acid being substituted has different characteristics.

At position is arginine, which carries a positive charge. At position is valine, which has an aliphatic side chain that is neutral and relatively hydrophobic. At position is the amino acid glutamate, which is negatively charged due to the carboxyl group on its side chain. Finally, we have glycine at position , which contains a lonely hydrogen atom as its side chain.

Now that we have the characteristics of the amino acid residues in the enzyme, let's compare them to the substitutions listed in the answer choices.

Substituting an aspartate residue into position would mean replacing valine (neutral) with a positively charged amino acid. Hence, this would likely result in disruption of enzyme activity.

Substituting a tryptophan residue into position would replace glycine. In contrast to the extremely small side chain of glycine, the side chain of tryptophan is very large. This great size discrepancy could potentially lead to steric effects that could interfere with the binding of substrate to the enzyme.

Substitution of an asparagine residue into position would replace glutamate. Because glutamate is negatively charged, whereas asparagine is neutral, this substitution would likely interfere with enzyme activity.

Finally, let's consider the substitution of arginine at position with a lysine. In this case, a positively charged arginine would be replaced by another positively charged amino acid, lysine. Because of the similarity between these two amino acids, this substitution would be the least likely to cause a disruption in the enzyme's activity.

9

What accounts for peptide bond planarity within a polypeptide?

Partial double bond character of the peptide bond

The fully double bonded peptide bond

Electronegativity differences between nitrogen and carbon

Hydrogen bonding between amino acid side chains and water

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

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.

10

What accounts for peptide bond planarity within a polypeptide?

Partial double bond character of the peptide bond

The fully double bonded peptide bond

Electronegativity differences between nitrogen and carbon

Hydrogen bonding between amino acid side chains and water

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

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.

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