Macromolecules - MCAT Biological and Biochemical Foundations of Living Systems
Card 1 of 976
Cryptosporidium is a genus of gastrointestinal parasite that infects the intestinal epithelium of mammals. Cryptosporidium is water-borne, and is an apicomplexan parasite. This phylum also includes Plasmodium, Babesia, and Toxoplasma.
Apicomplexans are unique due to their apicoplast, an apical organelle that helps penetrate mammalian epithelium. In the case of cryptosporidium, there is an interaction between the surface proteins of mammalian epithelial tissue and those of the apical portion of the cryptosporidium infective stage, or oocyst. A scientist is conducting an experiment to test the hypothesis that the oocyst secretes a peptide compound that neutralizes intestinal defense cells. These defense cells are resident in the intestinal epithelium, and defend the tissue by phagocytizing the oocysts.
She sets up the following experiment:
As the neutralizing compound was believed to be secreted by the oocyst, the scientist collected oocysts onto growth media. The oocysts were grown among intestinal epithelial cells, and then the media was collected. The media was then added to another plate where Toxoplasma gondii was growing with intestinal epithelial cells. A second plate of Toxoplasma gondii was grown with the same type of intestinal epithelium, but no oocyst-sourced media was added.
Where is the likely site of the neutralizing toxin synthesis in cryptosporidium cells?
Cryptosporidium is a genus of gastrointestinal parasite that infects the intestinal epithelium of mammals. Cryptosporidium is water-borne, and is an apicomplexan parasite. This phylum also includes Plasmodium, Babesia, and Toxoplasma.
Apicomplexans are unique due to their apicoplast, an apical organelle that helps penetrate mammalian epithelium. In the case of cryptosporidium, there is an interaction between the surface proteins of mammalian epithelial tissue and those of the apical portion of the cryptosporidium infective stage, or oocyst. A scientist is conducting an experiment to test the hypothesis that the oocyst secretes a peptide compound that neutralizes intestinal defense cells. These defense cells are resident in the intestinal epithelium, and defend the tissue by phagocytizing the oocysts.
She sets up the following experiment:
As the neutralizing compound was believed to be secreted by the oocyst, the scientist collected oocysts onto growth media. The oocysts were grown among intestinal epithelial cells, and then the media was collected. The media was then added to another plate where Toxoplasma gondii was growing with intestinal epithelial cells. A second plate of Toxoplasma gondii was grown with the same type of intestinal epithelium, but no oocyst-sourced media was added.
Where is the likely site of the neutralizing toxin synthesis in cryptosporidium cells?
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The passage specifies that the neutralizing agent is a peptide. Ribosomes synthesize peptides. Nuceloulus may have been a tempting answer, but is where ribosomes are synthesized, not peptides.
The passage specifies that the neutralizing agent is a peptide. Ribosomes synthesize peptides. Nuceloulus may have been a tempting answer, but is where ribosomes are synthesized, not peptides.
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A graduate student needs to cut a DNA plasmid using two different restriction enzymes in a buffer. He can use any two of the following enzymes in any of the four given buffers.
Enzyme Efficiency in Buffer (%) 1 2 3 4 AgeI 100 50 10 75 ClaI 10 50 50 100 PsiI 10 100 10 100
Which two enzymes and buffer should the student choose for the digestion?
A graduate student needs to cut a DNA plasmid using two different restriction enzymes in a buffer. He can use any two of the following enzymes in any of the four given buffers.
| Enzyme | Efficiency in Buffer (%) | |||
|---|---|---|---|---|
| 1 | 2 | 3 | 4 | |
| AgeI | 100 | 50 | 10 | 75 |
| ClaI | 10 | 50 | 50 | 100 |
| PsiI | 10 | 100 | 10 | 100 |
Which two enzymes and buffer should the student choose for the digestion?
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Because ClaI and PsiI both have 100% efficiency in buffer 4, that is the most ideal choice. A combination of buffers is never a valid option, as diluting the buffers fundamentally changes the composition of the reaction and the efficiency of the enzyme. In the absence of two enzymes that can function with 100% efficiency, it is best to find a combination with the greatest possible efficiency or to complete the digest sequentially in the appropriate buffers.
Because ClaI and PsiI both have 100% efficiency in buffer 4, that is the most ideal choice. A combination of buffers is never a valid option, as diluting the buffers fundamentally changes the composition of the reaction and the efficiency of the enzyme. In the absence of two enzymes that can function with 100% efficiency, it is best to find a combination with the greatest possible efficiency or to complete the digest sequentially in the appropriate buffers.
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Which amino acid has a side chain that can form covalent bonds?
Which amino acid has a side chain that can form covalent bonds?
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Cysteine has a sulfide (-SH) in its side chain, which can form covalent disulfide bonds. These bonds are often integral in creating protein tertiary structures.
Cysteine has a sulfide (-SH) in its side chain, which can form covalent disulfide bonds. These bonds are often integral in creating protein tertiary structures.
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A supercoiled helix is described by which level of peptide structure?
A supercoiled helix is described by which level of peptide structure?
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Secondary peptide structure refers to alpha-helices and beta-sheets, which are formed by hydrogen bonding. A supercoiled helix is due to the secondary structure of a peptide. Primary structure is the sequence of amino acids, tertiary structure is the three-dimensional arrangement of the protein, and quatenary structure arises when more than one peptide subunit interacts.
Secondary peptide structure refers to alpha-helices and beta-sheets, which are formed by hydrogen bonding. A supercoiled helix is due to the secondary structure of a peptide. Primary structure is the sequence of amino acids, tertiary structure is the three-dimensional arrangement of the protein, and quatenary structure arises when more than one peptide subunit interacts.
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Disulfide linkages are connections made between polypeptide chains to increase the cohesion of a protein. These bonds fall into the category of .
Disulfide linkages are connections made between polypeptide chains to increase the cohesion of a protein. These bonds fall into the category of .
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Disulfide bonds are covalent attachments created between two sulfur atoms. Cysteine is usually the amino acid that creates these connections.
Disulfide bonds are covalent attachments created between two sulfur atoms. Cysteine is usually the amino acid that creates these connections.
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Pepsin is an enzyme found within the stomach. As a physiologist you are setting up an experiment to study the properties of pepsin. You place pepsin enzymes into a solution and notice that the pH of the solution is 4.
Which of the following would you add in order to maximize the enzyme's ability to function normally?
Pepsin is an enzyme found within the stomach. As a physiologist you are setting up an experiment to study the properties of pepsin. You place pepsin enzymes into a solution and notice that the pH of the solution is 4.
Which of the following would you add in order to maximize the enzyme's ability to function normally?
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Pepsin is used to break down protein in the stomach by hydrolyzing some peptide bonds. Pepsin can operate best at a pH of 2 (same pH as the stomach). Adding HCl to the solution will bring the solution's pH closer to this optimal pH.
Pepsin is used to break down protein in the stomach by hydrolyzing some peptide bonds. Pepsin can operate best at a pH of 2 (same pH as the stomach). Adding HCl to the solution will bring the solution's pH closer to this optimal pH.
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Which of the following is FALSE concerning enzymes?
Which of the following is FALSE concerning enzymes?
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Enzymes will increase the rate of a chemical reaction, but will not alter the equilibrium of a reaction. As a result, the amount of product is not affected by enzymes. The same amount of product will be made; it will just be made at a faster rate.
Enzymes will increase the rate of a chemical reaction, but will not alter the equilibrium of a reaction. As a result, the amount of product is not affected by enzymes. The same amount of product will be made; it will just be made at a faster rate.
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The functional properties of an enzyme are dependent on the pH of the body as well as temperature. Each protein has specific conditions at which it will function optimally. These conditions can help predict where a protein will be found in the body.
In what area of the cell would you expect to find an enzyme that functions best in acidic conditions?
The functional properties of an enzyme are dependent on the pH of the body as well as temperature. Each protein has specific conditions at which it will function optimally. These conditions can help predict where a protein will be found in the body.
In what area of the cell would you expect to find an enzyme that functions best in acidic conditions?
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Lysosomes are responsible for the degradation of macromolecules, and typically have an internal pH of 5. They contain acid hydrolases: enzymes that function optimally in an acidic environment.
Lysosomes are responsible for the degradation of macromolecules, and typically have an internal pH of 5. They contain acid hydrolases: enzymes that function optimally in an acidic environment.
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Diisopropylflourophosphate (DFP) is an example of an enzyme inhibitor. It covalently binds to a serine residue in the active site of a serine protease, thus inactivating the enzyme.
Based on this information, what type of enzyme inhibitor is DFP?
Diisopropylflourophosphate (DFP) is an example of an enzyme inhibitor. It covalently binds to a serine residue in the active site of a serine protease, thus inactivating the enzyme.
Based on this information, what type of enzyme inhibitor is DFP?
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Whenever you read that an enzyme inhibitor has covalently bonded to an enzyme, you can conclude that it is an irreversible inhibitor. Both competitive and noncompetitive inhibitors bind noncovalently to the target enzyme.
Whenever you read that an enzyme inhibitor has covalently bonded to an enzyme, you can conclude that it is an irreversible inhibitor. Both competitive and noncompetitive inhibitors bind noncovalently to the target enzyme.
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Which of the following is not an example of positive feedback?
Which of the following is not an example of positive feedback?
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Negative feedback provides the body with a method for shutting down a reaction once sufficient product has been created. Parathyroid hormone (PTH) is responsible for increasing blood calcium levels, but once the level is sufficient, the parathyroid glands detect the sufficient calcium level and no longer produce PTH. PTH works in coordination with calcitonin to maintain this balance via its negative feedback loop.
Positive feedback, in contrast, involves the exponential increase of a reaction upon detection. Very few examples of positive feedback exist in the body, though oxytocin follows this model during childbirth.
Negative feedback provides the body with a method for shutting down a reaction once sufficient product has been created. Parathyroid hormone (PTH) is responsible for increasing blood calcium levels, but once the level is sufficient, the parathyroid glands detect the sufficient calcium level and no longer produce PTH. PTH works in coordination with calcitonin to maintain this balance via its negative feedback loop.
Positive feedback, in contrast, involves the exponential increase of a reaction upon detection. Very few examples of positive feedback exist in the body, though oxytocin follows this model during childbirth.
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In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:
In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.
The enzyme PERK is a kinase. Which of the following is not true of all kinases?
In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:
In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.
The enzyme PERK is a kinase. Which of the following is not true of all kinases?
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Kinases are protein enzymes that add phosphate groups to targets. These targets can be diverse, however, and are not always translation factors.
Kinases are protein enzymes that add phosphate groups to targets. These targets can be diverse, however, and are not always translation factors.
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In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:
In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.
We do not know the exact action of eIF2 after it has been acted upon by PERK, and therefore cannot draw conclusions about the phosphorylation or dephosphorylation of transcription factors.
Which of the following is most likely the molecular event that causes repression of translation, based on the information in the passage?
In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:
In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.
We do not know the exact action of eIF2 after it has been acted upon by PERK, and therefore cannot draw conclusions about the phosphorylation or dephosphorylation of transcription factors.
Which of the following is most likely the molecular event that causes repression of translation, based on the information in the passage?
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The diagram in the passage shows the kinase PERK, which must phosphorylate its substrate, acts on eIF2. Based on its kinase nature and the diagram, phosphorylation of eIF2 is the most likely answer that would lead to propagation of the signal shown.
The diagram in the passage shows the kinase PERK, which must phosphorylate its substrate, acts on eIF2. Based on its kinase nature and the diagram, phosphorylation of eIF2 is the most likely answer that would lead to propagation of the signal shown.
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Which of the following statements about enzymes is false?
Which of the following statements about enzymes is false?
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While enzymes do not change the amount of product formed in a reaction (no change to Keq) they do speed up the rate of reaction. It is also true that under certain conditions pH and/or heat can denature an enzyme.
During a reaction, an enzyme does not get used up and is regenerated; enzymes are a type catalyst. Essentially, the enzyme is both a reactant and a product of the reaction it catalyzes.
While enzymes do not change the amount of product formed in a reaction (no change to Keq) they do speed up the rate of reaction. It is also true that under certain conditions pH and/or heat can denature an enzyme.
During a reaction, an enzyme does not get used up and is regenerated; enzymes are a type catalyst. Essentially, the enzyme is both a reactant and a product of the reaction it catalyzes.
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Enzymes are proteins that catalyze the biological reactions in the body. Every enzyme has a unique set of conditions in which it functions optimally. The function of an enzyme can be plotted on a graph, with the functionality of the enzyme on the y-axis, and the factor being manipulated on the x-axis.
What shape would you expect the graph for an enzyme to look like with temperature as the factor being manipulated?
Enzymes are proteins that catalyze the biological reactions in the body. Every enzyme has a unique set of conditions in which it functions optimally. The function of an enzyme can be plotted on a graph, with the functionality of the enzyme on the y-axis, and the factor being manipulated on the x-axis.
What shape would you expect the graph for an enzyme to look like with temperature as the factor being manipulated?
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Keep in mind that enzymes are proteins. They will increase in efficiency as temperature increases, but eventually too much heat will start to denature the protein. As a result, the graph will climb to maximum effeciency at a specific temperature. After that peak, it will decrease due to the denaturing of the enzyme.
Very low temperatures result in very low functionality. Mid-range temperatures result in maximum functionality. Very high temperatures result in very low functionality. As a result, the graph will be shaped like a bell-curve.
Keep in mind that enzymes are proteins. They will increase in efficiency as temperature increases, but eventually too much heat will start to denature the protein. As a result, the graph will climb to maximum effeciency at a specific temperature. After that peak, it will decrease due to the denaturing of the enzyme.
Very low temperatures result in very low functionality. Mid-range temperatures result in maximum functionality. Very high temperatures result in very low functionality. As a result, the graph will be shaped like a bell-curve.
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Enzymes are proteins that catalyze the biological reactions in the body. Every enzyme has a unique set of conditions in which it functions optimally. The function of an enzyme can be plotted on a graph, with the functionality of the enzyme on the y-axis, and the factor being manipulated on the x-axis.
What will be the shape of a graph with enzyme reaction rate on the y-axis, and substrate concentration on the x-axis?
Enzymes are proteins that catalyze the biological reactions in the body. Every enzyme has a unique set of conditions in which it functions optimally. The function of an enzyme can be plotted on a graph, with the functionality of the enzyme on the y-axis, and the factor being manipulated on the x-axis.
What will be the shape of a graph with enzyme reaction rate on the y-axis, and substrate concentration on the x-axis?
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As substrate concentration is increased, the reaction rate will increase accordingly; however, let's think about the extreme case where there is an extremely large amount of substrate. Eventually, every binding site of every molecule of enzyme will be filled. Substrate molecules will have to wait in order to be catalyzed by the enzyme. When this happens, we say that the enzyme is saturated. At this point, the graph will begin to level off and look like a horizontal line.
In summary, the graph will rise quickly in the beginning, but will eventually level off as substrate concentration becomes excessive compared to the available enzyme in solution.
As substrate concentration is increased, the reaction rate will increase accordingly; however, let's think about the extreme case where there is an extremely large amount of substrate. Eventually, every binding site of every molecule of enzyme will be filled. Substrate molecules will have to wait in order to be catalyzed by the enzyme. When this happens, we say that the enzyme is saturated. At this point, the graph will begin to level off and look like a horizontal line.
In summary, the graph will rise quickly in the beginning, but will eventually level off as substrate concentration becomes excessive compared to the available enzyme in solution.
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Sulfanilamide is an antibiotic that resembles the intermediate, 4-aminobenzoic acid (PABA), in the metabolic pathway to create folic acid. It binds to the active site of the enzyme that normally binds to PABA, and inhibits the binding of PABA temporarily. Since folic acid is necessary for bacterial growth, this antibiotic helps inhibit the spread of infection in humans.
Based on this information, what type of inhibitor is sulfanilamide?
Sulfanilamide is an antibiotic that resembles the intermediate, 4-aminobenzoic acid (PABA), in the metabolic pathway to create folic acid. It binds to the active site of the enzyme that normally binds to PABA, and inhibits the binding of PABA temporarily. Since folic acid is necessary for bacterial growth, this antibiotic helps inhibit the spread of infection in humans.
Based on this information, what type of inhibitor is sulfanilamide?
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Competitive inhibitors block substrates by binding noncovalently to the active site on enzymes. This prevents the substrate from entering the active site.
Noncompetitive inhibitors, in contrast, will act on regions outside of the active site to prevent binding. Uncompetitive inhibition is a specialized form of noncomptitive inhibition in which the inhibitor binds to the enzyme complex after the substrate has entered the active site. Irreversible inhibitors form covalent bonds, and fall outside the common inhibitor classifications.
Competitive inhibitors block substrates by binding noncovalently to the active site on enzymes. This prevents the substrate from entering the active site.
Noncompetitive inhibitors, in contrast, will act on regions outside of the active site to prevent binding. Uncompetitive inhibition is a specialized form of noncomptitive inhibition in which the inhibitor binds to the enzyme complex after the substrate has entered the active site. Irreversible inhibitors form covalent bonds, and fall outside the common inhibitor classifications.
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What would you predict would happen to pancreatic enzymes if they were introduced to the stomach?
What would you predict would happen to pancreatic enzymes if they were introduced to the stomach?
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The efficiency of an enzyme is dependent on the pH (as well as other features) of the environment in which it acts. The pancreatic digestive enzymes are typically secreted into the small intestine, which has a pH of about 6. As a result, the acidic pH of the stomach (about 2) would significantly reduce the efficiency of the pancreatic enzymes.
Remember that, though the stomach contents is highly acidic, it is neutralized in the duodenum before continuing through the small intestine, thus allowing these enzymes to function.
The efficiency of an enzyme is dependent on the pH (as well as other features) of the environment in which it acts. The pancreatic digestive enzymes are typically secreted into the small intestine, which has a pH of about 6. As a result, the acidic pH of the stomach (about 2) would significantly reduce the efficiency of the pancreatic enzymes.
Remember that, though the stomach contents is highly acidic, it is neutralized in the duodenum before continuing through the small intestine, thus allowing these enzymes to function.
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Which term is used to refer to an inactive enzyme precursor?
Which term is used to refer to an inactive enzyme precursor?
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Zymogen is the correct term for the inactive precursor of an enzyme. Zymogens are cleaved by other enzymes in order to become active. The zymogen form can help prevent improper action of the enzyme in different regions of the body. For example, trypsinogen is a zymogen released from the pancreas. It is transported to the small intestine before become active trypsin to prevent the trypsin from accidentally digesting and damaging the pancreatic cells.
Apoenzymes refer to enzymes without cofactors, while holoenzymes are enzymes bound to their cofactors. Inhibitors bind to enzymes to block their activity.
Zymogen is the correct term for the inactive precursor of an enzyme. Zymogens are cleaved by other enzymes in order to become active. The zymogen form can help prevent improper action of the enzyme in different regions of the body. For example, trypsinogen is a zymogen released from the pancreas. It is transported to the small intestine before become active trypsin to prevent the trypsin from accidentally digesting and damaging the pancreatic cells.
Apoenzymes refer to enzymes without cofactors, while holoenzymes are enzymes bound to their cofactors. Inhibitors bind to enzymes to block their activity.
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Which of the following changes could lead to loss of enzymatic function?
Which of the following changes could lead to loss of enzymatic function?
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Enzymes are pH and temperature sensitive., and only function in optimal ranges of these conditions. Certain enzymes will only function in acidic environments, while others require basic conditions.
The overall free energy and enthalpy of the reaction, activation energy, and enzyme concentration do not have a bearing on enzymatic activity.
Enzymes are pH and temperature sensitive., and only function in optimal ranges of these conditions. Certain enzymes will only function in acidic environments, while others require basic conditions.
The overall free energy and enthalpy of the reaction, activation energy, and enzyme concentration do not have a bearing on enzymatic activity.
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Which of the following strategies of enzymatic inhibition is used by noncompetitive inhibitors?
Which of the following strategies of enzymatic inhibition is used by noncompetitive inhibitors?
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Noncompetitive inhibitors of enzymes function by binding to a site other than the active site on the enzyme, known as an allosteric site. This causes the enzyme to go through a conformational shift and inhibits binding of the substrate.
Competitive inhibitors bind to the enzyme active site to prevent substrate action. Uncompetitive inhibitors are a sub-category of noncompetitive inhibitors, and bind to an allosteric site only after the substrate has entered the active site, thus preventing the substrate from leaving.
Noncompetitive inhibitors of enzymes function by binding to a site other than the active site on the enzyme, known as an allosteric site. This causes the enzyme to go through a conformational shift and inhibits binding of the substrate.
Competitive inhibitors bind to the enzyme active site to prevent substrate action. Uncompetitive inhibitors are a sub-category of noncompetitive inhibitors, and bind to an allosteric site only after the substrate has entered the active site, thus preventing the substrate from leaving.
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