Biochemistry : Active Site

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #1 : Active Site

Which of the following describes induced fit regarding enzyme/substrate binding?

Possible Answers:

Upon binding to the enzyme, the substrate changes the shape of the enzyme so that it fits perfectly

Upon binding to the enzyme, the substrate changes its own shape so that it fits perfectly

All of these are examples of induced fit

Upon binding to the enzyme, the substrate already fits perfectly into the active site

None of these are examples of induced fit

Correct answer:

Upon binding to the enzyme, the substrate changes the shape of the enzyme so that it fits perfectly

Explanation:

The induced fit model explains one method by which an enzyme's active site can accept some specific substrate. Initially, the active site might not be a perfect match for the substrate, however, when the substrate enters into the site, it can change the conformation of the enzyme just enough that it now fits perfectly and can be acted upon by the enzyme.

Example Question #2 : Active Site

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?

Possible Answers:

Aspartate at position 

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

Asparagine at position 

Tryptophan at position 

Lysine at position 

Correct answer:

Lysine at position 

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.

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