Macromolecule Structures and Functions

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Biochemistry › Macromolecule Structures and Functions

Questions 1 - 10
1

Which of the following statements about B DNA are incorrect?

B DNA has a wide and deep major groove and a narrow and shallow minor groove

B DNA is the most commonly found double helical structure

B DNA is right handed with 10 base pairs per turn

B DNA has a diameter of

All of these are correct

Explanation

B DNA has a wide and deep major groove and a narrow and deep minor groove. All other statements regarding B DNA are true.

2

The backbone of a strand of DNA is comprised of which of these?

Sugars and phosphates

Sugars and nucleotides

Nucleotides and phosphates

Sugars only

Nucleotides only

Explanation

The backbone of DNA is made up of alternating phosphate groups and sugar groups, linked together via phosphodiester bonds. The nitrogenous bases jut off of the backbone and form bonds with nitrogenous bases on other strands of DNA to become double stranded. A nucleotide consists of a sugar, nitrogenous base, and one or more phosphate groups.

3

Which of the following lists these molecules in order of increasing permeability to a lipid bilayer?

Sodium ion, glucose, water, carbon dioxide

Carbon dioxide, water, glucose, sodium ion

Glucose, carbon dioxide, sodium ion, water

Glucose, carbon dioxide, water, sodium ion

Sodium ion, glucose, carbon dioxide, water

Explanation

Charged molecules do not permeate the lipid bilayer easily at all. So despite its small size, among our choices, a sodium ion passes least easily through. Polar molecules also have a hard (but less difficult) time passing through, and the larger the molecule, the harder that becomes, so after the sodium ion comes glucose, followed by water, which is polar but much smaller. Small, hydrophobic molecules -- such as carbon dioxide -- diffuse through most easily, because they can pass through the longest (hydrophobic) part of the membrane.

4

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.

5

If a protein is bonded to ubiquitin, this tells the cell that the protein should be __________.

degraded

activated

inactivated

elongated

shortened

Explanation

When a protein is damaged, it can be tagged with the molecule, ubiquitin. This signals to the cell that the protein is no longer functioning properly and needs to be degraded.

6

Amino terminal - Ala - Lys - Glu - Phe - Phe - Ala - Leu - carboxyl terminal.

If the above primary sequence is cleaved by trypsin, on which amino acid will the new amino terminal be?

Glu

Lys

Phe

Ala

Leu

Explanation

Trypsin will cleave the primary sequence after the lysine residue (on its carboxyl side). Thus, Lys will be the new carboxyl terminal and Glu will be the new amino terminal. Remember that a protein's primary sequence is written from N to C.

7

Sickle cell anemia is caused by a point mutation in hemoglobin, where a glutamate residue is changed to a valine. Based on this mutation mechanism, what level of protein structure is affected by sickle cell anemia?

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

Explanation

Because an amino acid has been altered in sickle cell anemia, we can say that the amino acid sequence for hemoglobin has been changed. The amino acid sequence is defined as the primary structure for a protein, so that is the level that has been altered. It should be noted that the subsequent levels of protein structure would be altered as well, but the manipulation of the amino acid sequence is a changing of the primary structure first.

8

What term is used to describe enzymes that have different chemical structures but which catalyze the same reactions?

Isozymes

Coenzymes

Apoenzymes

Holoenzymes

None of these

Explanation

The correct answer choice is isozymes, also called isoenzymes. Even though these enzymes can catalyze the same reaction, they often have differences in their kinetic parameters or in the way they're regulated. Coenzymes are a type of cofactor. They are generally complex organic molecules that are usually derived from vitamins, and they serve the purpose of assisting the enzyme to which they are bound. Examples include pyridoxal phosphate, biotin, coenzyme A, etc. Apoenzymes are enzymes that normally require a cofactor, but are in a state in which they lack that cofactor. Holoenzymes are apoenzymes that have their cofactor bound.

9

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.

10

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.

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