Biochemistry : Biochemistry

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #1 : Other Metabolic Pathways

Which of the following cannot be directly converted to acetyl-CoA?

Possible Answers:

Alpha-keto acid

Fatty acids

Glucose

Pyruvate

All of these answers can be directly converted to acetyl-CoA

Correct answer:

Glucose

Explanation:

Pyruvate can be converted to acetyl-CoA by decarboxylation. Beta oxidation can convert fatty acids to acetyl-CoA. Transaminases can be used to make alpha-keto acids, which can be converted to acetyl-coA. Glucose cannot be directly converted to acetyl-CoA; it must be transformed into pyruvate first.

Example Question #2 : Other Metabolic Pathways

Which of the following is not an adequate alternative energy source for humans?

Possible Answers:

Fatty acids

Triglycerides

Glycogen

Cellulose

Alpha-keto acids

Correct answer:

Cellulose

Explanation:

Carbohydrates can be stored as glycogen in the liver, fats can be stored as triglycerides or fatty acids in adipose tissue, and proteins can be made into alpha-keto acids. Hence, all of these are forms of energy storage that can be used as alternative energy sources.

Cellulose is a polysaccharide that is found in plants. Humans cannot digest cellulose due to its beta-glycosidic linkages.

Example Question #2 : Enzymes

Which of the following changes will alter  of an enzyme-catalyzed reaction?

Possible Answers:

Addition of a competitive inhibitor

Addition of a non-competitive inhibitor

None of these options; cannot be changed

Increasing substrate to supraphysiological concentrations

Correct answer:

Addition of a non-competitive inhibitor

Explanation:

The only option that will alter the is to add a non-competitive inhibitor. The addition of this inhibitor will affect the amount of free enzyme available to catalyze the reaction, and thus lower the by reducing the effective enzyme concentration.

Addition of a competitive inhibitor will alter the , but not the . Increasing the substrate concentration will have no effect once saturation has been reached. 

Example Question #1 : Chemical Reactions

Which of the following is not a redox reaction?

Possible Answers:

II and III

I only

I and II

II only

III only

Correct answer:

II only

Explanation:

All of the given choices represent oxidation-reduction reactions that are important in cellular metabolism. Oxidation-reduction reactions involve the changing of oxidation states (commonly through the transfer of electrons). In the first reaction NAD+ is reduced. The second reaction shows the polymerization of two molecules of glucose via a condensation (dehydration synthesis) reaction. In the third reaction glucose is oxidized.

NADH and are important electron carriers that bring electrons to the electron transport chain and are formed during glycolysis and the Krebs cycle via reduction. The final choice represents the overall oxidation-reduction reaction that occurs for one molecule of glucose.

Example Question #1 : Protein Structure

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

Possible Answers:

None of these are examples of induced fit

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 changes the shape of the enzyme so that it fits perfectly

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

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 #1 : 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

Lysine at position 

Tryptophan at position 

Asparagine 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.

Example Question #1 : Protein Structure

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 #1 : Protein Structure

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

Possible Answers:

ionic

double

hydrogen

amino

peptide

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 #1 : Peptide Bonds

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:

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

Electronegativity differences between nitrogen and carbon

Partial double bond character of the peptide bond

Hydrogen bonding between amino acid side chains and water

The fully double bonded peptide bond

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.

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