Biochemistry : Macromolecule Structures and Functions

Study concepts, example questions & explanations for Biochemistry

varsity tutors app store varsity tutors android store

Example Questions

← Previous 1 3 4 5 6 7 8 9 19 20

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 already fits perfectly into the active site

All of these are examples of induced fit

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

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

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:

Asparagine at position 

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

Aspartate at position 

Lysine at position 

Tryptophan 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 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 #1 : 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

ionic

hydrogen

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 #1 : Protein Structure

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:

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

Partial double bond character of the peptide bond

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.

Example Question #1 : 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:

Proline

Alanine

Tryptophan

Glycine

Arginine

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 #2 : Protein Structure And Functions

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 order of amino acid residues within a certain 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 favorable angles of the bonds of an amino acid within a 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.

Example Question #1 : Globular And Fibrous Proteins

Which proteins are generally water-soluble?

Possible Answers:

Globular proteins

Neither globular nor fibrous proteins

Fibrous proteins

Both globular fibrous proteins

Correct answer:

Globular 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.

Example Question #1 : Globular And Fibrous Proteins

Which of the following is false about actin filaments?

Possible Answers:

They are made up of G-actin

Nucleotide hydrolysis promotes dissociation of actin filaments

2 microfilaments combine to make a coiled filament

They require GTP for assembly

Growth of the actin chain occurs at the plus (+) end

Correct answer:

They require GTP for assembly

Explanation:

Actin chain growth occurs at the (+) end of the chain, and nucleotide hydrolysis promotes dissociation of actin chains. 2 microfilaments of G-actin monomers make 1 filament of F-actin. However, actin filament assembly is powered by ATP, not GTP. 

← Previous 1 3 4 5 6 7 8 9 19 20
Learning Tools by Varsity Tutors