Proteins - MCAT Biology
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Drain cleaners are a common household staple, used to open clogged drains in bathtubs and sinks. Human hair is a common culprit that clogs pipes, and hair is made predominately of protein. Drain cleaners are effective at breaking down proteins that have accumulated in plumbing. Drain cleaners can be either acidic or basic, and are also effective at breaking down fats that have accumulated with proteins.
A typical reaction—reaction 1—which would be expected for a drain cleaner on contact with human hair, would be as follows in an aqueous solution:
Another reaction that may occur, reaction 2, would take place as follows in an aqueous solution:
In reaction 1, an organic acid forms as a product of the reaction of the original protein and drain cleaner. What quality of the resulting anion contributes most to the acidity of the product?
Drain cleaners are a common household staple, used to open clogged drains in bathtubs and sinks. Human hair is a common culprit that clogs pipes, and hair is made predominately of protein. Drain cleaners are effective at breaking down proteins that have accumulated in plumbing. Drain cleaners can be either acidic or basic, and are also effective at breaking down fats that have accumulated with proteins.
A typical reaction—reaction 1—which would be expected for a drain cleaner on contact with human hair, would be as follows in an aqueous solution:
Another reaction that may occur, reaction 2, would take place as follows in an aqueous solution:
In reaction 1, an organic acid forms as a product of the reaction of the original protein and drain cleaner. What quality of the resulting anion contributes most to the acidity of the product?
The resonance of the two C–O bonds that result after deprotonation of an organic acid is the major contributor to anion stability.
The resonance of the two C–O bonds that result after deprotonation of an organic acid is the major contributor to anion stability.
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Excluding the amino acid glycine, all other amino acids found within human proteins are __________.
Excluding the amino acid glycine, all other amino acids found within human proteins are __________.
All amino acids with the exception of glycine are optically active, as they have four unique groups attached to their alpha-carbons and are situated in the L configuration (amino terminus oriented to the left and carboxyl terminus to the right of the alpha-carbon). Not all amino acids are neutral at physiologic pH, as lysine and arginine are positively charged and apartate and glutamate are negatively charged due to their respective side chains. Finally, only ten of the twenty amino acids are essential, thus, the correct answer is that the amino acids found within human proteins are of the L configuration.
All amino acids with the exception of glycine are optically active, as they have four unique groups attached to their alpha-carbons and are situated in the L configuration (amino terminus oriented to the left and carboxyl terminus to the right of the alpha-carbon). Not all amino acids are neutral at physiologic pH, as lysine and arginine are positively charged and apartate and glutamate are negatively charged due to their respective side chains. Finally, only ten of the twenty amino acids are essential, thus, the correct answer is that the amino acids found within human proteins are of the L configuration.
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What is the reasoning behind the planar geometry of peptide bonds in proteins?
What is the reasoning behind the planar geometry of peptide bonds in proteins?
The double bond character of the carbon-nitrogen bond results in a shorter bond compared to the normal length of a pure bond (
vs. 
). The double bond resonance of peptide bonds aids to increase stability, while subsequently decreasing the rotation about that bond. The partial double bond results in the amide group being planar, thus allowing for either a cis or trans conformation of a peptide bond. Due to the preference for the trans orientation over the cis orientation, there is less steric hindrance between groups attached to the alpha-carbon atoms. Thus, the correct answer is that the carbon-nitrogen bond has partial double bond character.
The double bond character of the carbon-nitrogen bond results in a shorter bond compared to the normal length of a pure bond (
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Which of the following amino acids is basic?
Which of the following amino acids is basic?
On the MCAT you must be able to recognize the following as basic amino acids: lysine, arginine, and histidine. Important acidic amino acids include aspartic acid (aspartate) and glutamic acid (glutamate). Important nonpolar amino acids include: methionine, alanine, isoleucine, proline, phenylalanine, tryptophan, valine, and leucine.
On the MCAT you must be able to recognize the following as basic amino acids: lysine, arginine, and histidine. Important acidic amino acids include aspartic acid (aspartate) and glutamic acid (glutamate). Important nonpolar amino acids include: methionine, alanine, isoleucine, proline, phenylalanine, tryptophan, valine, and leucine.
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A depletion of amino acids in a cell would slow which immediate process?
A depletion of amino acids in a cell would slow which immediate process?
A depletion of amino acids would immediately impact protein and enzyme production in the cell. All proteins, including enzymes, are made from chains of amino acids. Lack of nutrients, such as amino acids, would eventually impact other processes listed.
A depletion of amino acids would immediately impact protein and enzyme production in the cell. All proteins, including enzymes, are made from chains of amino acids. Lack of nutrients, such as amino acids, would eventually impact other processes listed.
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Which two functional groups are included in every amino acid, and take part in amino acids binding together?
Which two functional groups are included in every amino acid, and take part in amino acids binding together?
Every amino acid contains a carboxyl group and an amino group. These two functional groups are essential for amino acid binding and breaking.
While sulfide groups contribute to higher protein structure by forming disulfide bonds, they do not exist in every amino acid.
Every amino acid contains a carboxyl group and an amino group. These two functional groups are essential for amino acid binding and breaking.
While sulfide groups contribute to higher protein structure by forming disulfide bonds, they do not exist in every amino acid.
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What are the four categories of amino acids?
What are the four categories of amino acids?
Amino acids are categorized as nonpolar, polar, acidic, or basic. The category that an amino acid is placed into gives you an idea of where you might find the amino acid within a protein. For example, polar amino acids are commonly found on the outside of proteins, where other polar molecules (water) are likely to be found.
Amino acids are categorized as nonpolar, polar, acidic, or basic. The category that an amino acid is placed into gives you an idea of where you might find the amino acid within a protein. For example, polar amino acids are commonly found on the outside of proteins, where other polar molecules (water) are likely to be found.
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A peptide bond is formed between __________.
A peptide bond is formed between __________.
Each amino acid has an N and a C terminus. The N terminus contains an amino group and the C terminus contains a carboxylic acid group. In order to make a peptide linkage (and eventually create a polypeptide), a bond must form between the amino and carboxylic groups, with water as a byproduct.
Each amino acid has an N and a C terminus. The N terminus contains an amino group and the C terminus contains a carboxylic acid group. In order to make a peptide linkage (and eventually create a polypeptide), a bond must form between the amino and carboxylic groups, with water as a byproduct.
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Integral proteins span the entire width of the plasma membrane. They are used to facilitate the diffusion of specific compounds across the membrane.
Which amino acid would you expect to find in the middle of an integral protein embedded in the phospholipid bilayer?
Integral proteins span the entire width of the plasma membrane. They are used to facilitate the diffusion of specific compounds across the membrane.
Which amino acid would you expect to find in the middle of an integral protein embedded in the phospholipid bilayer?
The middle of the phospholipid bilayer is composed of nonpolar fatty acid tails. As a result, we would expect to find a nonpolar amino acid in the middle of the bilayer as part of the integral protein. Leucine is a nonpolar amino acid, so it could be found in the middle.
All other amino acids listed are either polar or charged.
The middle of the phospholipid bilayer is composed of nonpolar fatty acid tails. As a result, we would expect to find a nonpolar amino acid in the middle of the bilayer as part of the integral protein. Leucine is a nonpolar amino acid, so it could be found in the middle.
All other amino acids listed are either polar or charged.
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What would charge would you expect on alanine when placed in a solution with a pH of 1.00?
What would charge would you expect on alanine when placed in a solution with a pH of 1.00?
Since alanine is nonpolar, we know that the only parts of the amino acid that can be charged are the N-terminus and the C-terminus.
In an acidic solution, there is an excessive amount of protons available to protonate the amino acid. As a result, the carboxylic acid end and the amine end will both be fully protonated. This will result in an overall charge of +1, due to the nitrogen having three hydrogens attached.
Since alanine is nonpolar, we know that the only parts of the amino acid that can be charged are the N-terminus and the C-terminus.
In an acidic solution, there is an excessive amount of protons available to protonate the amino acid. As a result, the carboxylic acid end and the amine end will both be fully protonated. This will result in an overall charge of +1, due to the nitrogen having three hydrogens attached.
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Which of the following components is not found in a nucleotide?
Which of the following components is not found in a nucleotide?
Nucleotides are composed of a pentose sugar, phosphate group, and nitrogenous base. Nucleotides are the building blocks of nucleic acids, such as DNA and RNA. Phosphodiester bonds form between the phosphate group of one nucleotide and the 3' carbon of the pentose sugar on a second nucleotide to form a linkage. A nucleoside describes the molecule that is formed by a pentose sugar and nitrogenous base.
Sulfate groups are not found in nucleotides or nucleosides.
Nucleotides are composed of a pentose sugar, phosphate group, and nitrogenous base. Nucleotides are the building blocks of nucleic acids, such as DNA and RNA. Phosphodiester bonds form between the phosphate group of one nucleotide and the 3' carbon of the pentose sugar on a second nucleotide to form a linkage. A nucleoside describes the molecule that is formed by a pentose sugar and nitrogenous base.
Sulfate groups are not found in nucleotides or nucleosides.
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Which of the following amino acids contain(s) a hydrophilic functional group in its side chain?
I. Serine
II. Valine
III. Phenylalanine
IV. Tyrosine
V. Threonine
Which of the following amino acids contain(s) a hydrophilic functional group in its side chain?
I. Serine
II. Valine
III. Phenylalanine
IV. Tyrosine
V. Threonine
Serine and threonine are classified as hydrophilic amino acids and contain hydroxyl (-OH) groups in their side chains. Tyrosine, although it is considered hydrophobic, does contain a hydrophilic hydroxyl group in its side chain. The answer is I, IV, and V, as all of these contain hydrophilic functional groups.
Serine and threonine are classified as hydrophilic amino acids and contain hydroxyl (-OH) groups in their side chains. Tyrosine, although it is considered hydrophobic, does contain a hydrophilic hydroxyl group in its side chain. The answer is I, IV, and V, as all of these contain hydrophilic functional groups.
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Which of the following amino acid sequences would be found on the cytoplasm side of a transmembrane protein?
Which of the following amino acid sequences would be found on the cytoplasm side of a transmembrane protein?
Transmembrane proteins are embedded within the phospholipid bilayer of the cell membrane; therefore, the protein is exposed to the nonpolar fatty acid tails, the polar phospholipid heads, and the polar environments of the cytoplasm and extracellular space.
The questions asks which amino acids would be found facing the cytoplasm. Because the cytoplasm is polar, the amino acids interacting with the cytoplasm must also be polar. Glutamine, threonine, and tyrosine are all polar amino acids, making this the best answer. The other answers contain nonpolar amino acids (proline, leucine, cysteine, valine) causing these answers to be incorrect.
Transmembrane proteins are embedded within the phospholipid bilayer of the cell membrane; therefore, the protein is exposed to the nonpolar fatty acid tails, the polar phospholipid heads, and the polar environments of the cytoplasm and extracellular space.
The questions asks which amino acids would be found facing the cytoplasm. Because the cytoplasm is polar, the amino acids interacting with the cytoplasm must also be polar. Glutamine, threonine, and tyrosine are all polar amino acids, making this the best answer. The other answers contain nonpolar amino acids (proline, leucine, cysteine, valine) causing these answers to be incorrect.
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All amino acids have at least two pKa values, one corresponding to the carboxylic acid, and one corresponding to the amine functionality. Some amino acids with polar side chains also have a pKa associated with the sidechain functionality.
Phenylalanine has pKa values of 2.58 (carboxylic acid) and 9.24 (NH2).
Arginine has pKa values of 2.01 (carboxylic acid), 9.04 (NH2), and 12.48 (side chain).
Valine has pKa values of 2.29 (carboxylic acid) and 9.72 (NH2).
For this problem, consider a molecule made of up of three amino acids, as described below.
HO-phenylalanine-arginine-valine-NH2
What would the overall charge of this molecule be at a pH of 7?
All amino acids have at least two pKa values, one corresponding to the carboxylic acid, and one corresponding to the amine functionality. Some amino acids with polar side chains also have a pKa associated with the sidechain functionality.
Phenylalanine has pKa values of 2.58 (carboxylic acid) and 9.24 (NH2).
Arginine has pKa values of 2.01 (carboxylic acid), 9.04 (NH2), and 12.48 (side chain).
Valine has pKa values of 2.29 (carboxylic acid) and 9.72 (NH2).
For this problem, consider a molecule made of up of three amino acids, as described below.
HO-phenylalanine-arginine-valine-NH2
What would the overall charge of this molecule be at a pH of 7?
Phenylalanine:
Since the phenylalanine residue is at the C-terminus end of the molecule, only its carboxylic acid pKa is relevant, as its amine is involved in a peptide bond with arginine. At a pH of 7 (well above the carboxylic acid pKa of 2.58), the C-terminus carboxylic acid would be deprotonated and have a charge of 
.
Arginine:
For the middle amino acid, arginine, the only relevant pKa is that of its side chain since both its carboxylic acid and amino groups are involved in peptide bonds with neighboring amino acids. Since the side chain of arginine would be protonated at a pH of 7 (well below the sidechain pKa of 12.48), this amino acid would have a charge of 
.
Valine:
Finally, for valine, the relevant pKa to consider is the NH2 pKa of 9.72. At pH 7, this would also be protonated, resulting in a charge of 
.
The overall charge of the molecule at pH 7 would be 
.
Phenylalanine:
Since the phenylalanine residue is at the C-terminus end of the molecule, only its carboxylic acid pKa is relevant, as its amine is involved in a peptide bond with arginine. At a pH of 7 (well above the carboxylic acid pKa of 2.58), the C-terminus carboxylic acid would be deprotonated and have a charge of
Arginine:
For the middle amino acid, arginine, the only relevant pKa is that of its side chain since both its carboxylic acid and amino groups are involved in peptide bonds with neighboring amino acids. Since the side chain of arginine would be protonated at a pH of 7 (well below the sidechain pKa of 12.48), this amino acid would have a charge of
Valine:
Finally, for valine, the relevant pKa to consider is the NH2 pKa of 9.72. At pH 7, this would also be protonated, resulting in a charge of
The overall charge of the molecule at pH 7 would be
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Which of the following amino acids is considered basic?
Which of the following amino acids is considered basic?
Basic amino acids are those containing an amine group, while acidic contain a carboxylic acid group.
The basic amino acids are lysine (the correct answer), arginine, and histidine.
The acidic amino acids are glutamic acid (glutamate) and aspartic acid (aspartate).
Basic amino acids are those containing an amine group, while acidic contain a carboxylic acid group.
The basic amino acids are lysine (the correct answer), arginine, and histidine.
The acidic amino acids are glutamic acid (glutamate) and aspartic acid (aspartate).
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Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.
Which of the following proteins would be least affected by the introduction of mercaptoethanol?
Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.
Which of the following proteins would be least affected by the introduction of mercaptoethanol?
Disulfide bonds are disrupted by the introduction of mercaptoethanol. Disulfide bonds are created by the interaction of two cysteine amino acids on different parts of the amino acid chain during the development of tertiary protein folding. As a result, a protein with few to no cysteine amino acids would be least affected by mercaptoethanol.
Alpha-helices are linked to secondary structure, and do not involve disulfide bonds. Similarly, quaternary structure is not determined by disulfide bonds; a protein without quaternary structure could still have disulfide bonds, which would be disrupted by mercaptoethanol. Proline is not involved in disulfide bonds, and its frequency would not affect the potency of mercaptoethanol to the protein.
Disulfide bonds are disrupted by the introduction of mercaptoethanol. Disulfide bonds are created by the interaction of two cysteine amino acids on different parts of the amino acid chain during the development of tertiary protein folding. As a result, a protein with few to no cysteine amino acids would be least affected by mercaptoethanol.
Alpha-helices are linked to secondary structure, and do not involve disulfide bonds. Similarly, quaternary structure is not determined by disulfide bonds; a protein without quaternary structure could still have disulfide bonds, which would be disrupted by mercaptoethanol. Proline is not involved in disulfide bonds, and its frequency would not affect the potency of mercaptoethanol to the protein.
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Which of the following forms of valine would be expected to exist under extremely acidic conditions?
Which of the following forms of valine would be expected to exist under extremely acidic conditions?
At low pH levels, we expect amino acids to exist in their cationic form. At a pH level equal to the isoelectric point (pI) we expect amino acids to exist as zwitterions, and at high pH levels we expect them to exist in their anionic forms.
Low pH causes protonation of the amino groups; high pH causes deprotonation of the carboxyl groups.
At low pH levels, we expect amino acids to exist in their cationic form. At a pH level equal to the isoelectric point (pI) we expect amino acids to exist as zwitterions, and at high pH levels we expect them to exist in their anionic forms.
Low pH causes protonation of the amino groups; high pH causes deprotonation of the carboxyl groups.
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How many moles of base are required to fully deprotonate glutamic acid in its most acidic form (shown below)?
How many moles of base are required to fully deprotonate glutamic acid in its most acidic form (shown below)?
One mole is base is required to deprotonate each carboxylic acid or amine, until the amino acid exists in its most deprotonated and basic form. First, two moles of base would be needed to deprotonate the two acid groups on glutamic acid (one depicted on each end). Next, a third mole would be needed to deprotonate the amine to its neutral state. Three total moles is the correct answer.
One mole is base is required to deprotonate each carboxylic acid or amine, until the amino acid exists in its most deprotonated and basic form. First, two moles of base would be needed to deprotonate the two acid groups on glutamic acid (one depicted on each end). Next, a third mole would be needed to deprotonate the amine to its neutral state. Three total moles is the correct answer.
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Polypeptides are molecules that contain multiple __________.
Polypeptides are molecules that contain multiple __________.
Polypeptides are made from individual amino acids through formation of peptide bonds.
Monosaccharides are the fundamental units for carbohydrates, while fatty acids come together to form lipids. Nucleotides and phosphates are key components of the nucleic acids, RNA and DNA.
Polypeptides are made from individual amino acids through formation of peptide bonds.
Monosaccharides are the fundamental units for carbohydrates, while fatty acids come together to form lipids. Nucleotides and phosphates are key components of the nucleic acids, RNA and DNA.
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What type of amino acid will have an isoelectric point above 7?
What type of amino acid will have an isoelectric point above 7?
The isoelectric point is the pH where the amino acid solution is electrically neutral. In acidic conditions, the carboxylic acid and amino terminus will both be protonated. This results in a positive charge (due to the amine being protonated). In basic conditions, both ends are deprotonated, resulting in a negative charge.
If an amino acid is basic, that means that the pH must be above 7 in order to deprotonate the amine in the side chain. Only then will the amino acid be electrically neutral. All basic amino acids (three of them) have an isoelectric point above a pH of 7. All other amino acids have an isoelectric point at a pH below 7.
The isoelectric point is the pH where the amino acid solution is electrically neutral. In acidic conditions, the carboxylic acid and amino terminus will both be protonated. This results in a positive charge (due to the amine being protonated). In basic conditions, both ends are deprotonated, resulting in a negative charge.
If an amino acid is basic, that means that the pH must be above 7 in order to deprotonate the amine in the side chain. Only then will the amino acid be electrically neutral. All basic amino acids (three of them) have an isoelectric point above a pH of 7. All other amino acids have an isoelectric point at a pH below 7.
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