Protein Structure and Functions
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Biochemistry › Protein Structure and Functions
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.
Which of the following best explains a quaternary structure of a protein?
Hydrogen and disulfide bonds, two or more polypeptide chains
Hydrogen bonds, alpha-helices and beta-pleated sheets
Linear sequence of amino acids
Disulfide bonds, single polypeptide chain
Collagen and myoglobin
Explanation
Primary structure: linear sequence of amino acids
Secondary structure: hydrogen bonds, alpha-helices and beta-pleated sheets
Tertiary structure: disulfide bonds, single polypeptide chain
Myoglobin is a monomer, and is made of a single polypeptide chain. Thus, its highest level of protein structure is tertiary. While collagen does contain different polypeptide chains, it is an example of a protein with quaternary structure, not an explanation of what this means.
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.
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.
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.
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.
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.
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.
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.
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.