Phosphoryl group transfers and ATP hydrolysis
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Phosphoryl group transfers and ATP hydrolysis
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[post_content] => Practice Passage (Question 1-6)
*This passage is the property of Khan Academy and has been reformatted into an AAMC-style interface in their entirety by MedLife Mastery. MedLife Mastery does not endorse and is not an affiliate of Khan Academy.
Adenosine 5’-triphosphate (ATP) serves as the main source of free energy in living cells. The energy stored by ATP can be liberated through direct hydrolysis or by group transfer. The structure of ATP is shown in Figure 1.
Figure 1 Molecular structure of ATP
Direct hydrolysis of ATP (Equation 1) consists of nucleophilic attack by H₂O at the γ phosphate position of ATP and cleavage of the γ – β phosphoanhydride bond. Direct hydrolysis of ATP liberates energy mainly in the form of heat. This heat energy can be used to cycle proteins through different conformations (for instance, in muscle contraction).
Group transfer reactions involve the covalent transfer of a portion of the ATP molecule to a substrate. Table 1 classifies the three group transfer reactions that involve ATP by the phosphate position of ATP at which nucleophilic attack occurs.
Table 1 Group transfer reactions involving ATP
Adenylyl transfer has the largest negative standard free energy change and is commonly coupled to biological reactions that have a particularly large positive standard free energy change. One example is the coupling of exergonic adenylylation of fatty acid (Equation 2) and pyrophosphatase-catalyzed pyrophosphate hydrolysis (Equation 3) to endergonic synthesis of fatty acyl-CoA (Equation 4).
[post_title] => Phosphoryl group transfers and ATP hydrolysis
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[question] => Which of the following best describes the difference between exergonic reactions (adenylylation, pyrophosphate hydrolysis) and endergonic reactions (condensation of fatty acid with coenzyme A)?
[value] => Array
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[answer] => 3
[description] => Reason for Correct Answer:
The suffix “-ergonic” is derived from the Greek word for “work,” while the prefixes “exo” and “endo” are derived from the Greek words for “outside” and “inside,” respectively.
Exergonic reactions are ones in which energy is released from the system to the outside surroundings, while endergonic reactions are ones in which energy is absorbed by the system from the outside surroundings.
Breaking chemical bonds always requires the input of energy. However, a reaction “releases” energy if the energy of the products is lower than the energy of the reactants.
The products of endergonic reactions are higher energy than the reactants, while the products of exergonic reactions are lower energy than the reactants.
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[answers] => Array
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[0] => Array
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[each_answer] => A. The bonds broken in endergonic reactions require the input of energy, while the bonds broken in exergonic reactions release energy.
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[each_answer] => B. The bonds broken in endergonic reactions release energy, while the bonds broken in exergonic reactions require the input of energy.
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[each_answer] => C. The products of endergonic reactions are higher energy than the reactants, while the products of exergonic reactions are lower energy than the reactants.
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[each_answer] => D. The products of endergonic reactions are lower energy than the reactants, while the products of exergonic reactions are higher energy than the reactants.
)
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[1] => Array
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[quiz_unique_key] => 1403770772
[question] => Which of the following perturbations of an equilibrium mixture of ATP hydrolysis reactants and products under standard conditions would NOT drive Equation 1 to the left (e.g. produce more ATP and water)?
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[answer] => 4
[description] => Reason for Correct Answer:
Le Chatelier’s principle states that a chemical system at equilibrium will self-adjust to maintain equilibrium in response to externally imposed changes to temperature, pressure, and concentrations of reactants and products.
A chemical system at equilibrium will be driven “to the left” (concentration of products will decrease and concentration of reactants will increase) if products are added to the system.
The passage states that the hydrolysis of ATP releases heat. In other words, it is exothermic and has a positive enthalpy change.
Lowering temperature (removing heat) drives exothermic reactions in the forward (rightward) direction, not towards the reactants.
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[answers] => Array
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[0] => Array
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[each_answer] => A. Addition of Pᵢ
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[1] => Array
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[each_answer] => B. Addition of ADP
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[2] => Array
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[each_answer] => C. Raising temperature
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[3] => Array
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[each_answer] => D. Lowering temperature
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[2] => Array
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[quiz_unique_key] => 1403770772
[question] => Despite having a large negative free energy change under standard conditions, fatty acid adenylation still requires the enzyme fatty acyl-coA synthetase in order to form the adenylylated fatty acid intermediate. Why is this the case?
[value] => Array
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[answer] => 4
[description] => Reason for Correct Answer:
Chemical reactions with large negative free energy changes are thermodynamically favorable. However, such reactions can still be kinetically unfavorable, requiring a large input of energy for the reaction to happen at an appreciable rate.
Enzymes affect the kinetics of reactions. They lower the activation energy of reactions to help make them more kinetically favorable.
Fatty acyl-CoA synthetase lowers the activation energy of the reaction that converts fatty acids to their adenylylated intermediates, as shown in Equation 2, making the reaction kinetically more favorable. (The enzyme also lowers the activation energy of the reverse reaction.)
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[answers] => Array
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[0] => Array
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[each_answer] => A. Fatty acyl-coA synthetase raises the activation energy for converting the adenylylated intermediate to fatty acid, making the reverse reaction less kinetically favorable.
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[each_answer] => B. Fatty acyl-coA synthetase raises the activation energy for converting the adenylylated intermediate to fatty acid, making the reaction thermodynamically more favorable.
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[each_answer] => C. Fatty acyl-coA synthetase lowers the activation energy for converting the adenylylated intermediate to fatty acid, making the reaction thermodynamically more favorable.
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[each_answer] => D. Fatty acyl-coA synthetase lowers the activation energy for converting fatty acid to the adenylylated intermediate, making the forward reaction kinetically more favorable.
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[3] => Array
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[quiz_unique_key] => 1403770772
[question] => Hydrolysis of carboxylic acid anhydrides releases greater amounts of energy than hydrolysis of phosphoanhydrides like ATP. What is the most likely explanation for why phosphoanhydrides are a better store of biological energy?
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[answer] => 3
[description] => Reason for Correct Answer:
Hydrolysis of carboxylic acid anhydrides releases more energy than hydrolysis of phosphoanhydrides; this means that the hydrolysis of carboxylic acid anhydrides has a more negative standard free energy change.
Phosphoanyhydrides like ATP are good stores of biological energy because they have relatively large negative free energies of hydrolysis while also remaining stable under physiological conditions. That is, the hydrolysis of ATP does not happen spontaneously.
Spontaneous hydrolysis of ATP does not occur under physiological conditions because ATP hydrolysis has a relatively high activation energy.
The lower activation energy of carboxylic acid anhydride hydrolysis explains why carboxylic acid anhydrides may be too reactive and not a good cellular source of energy.
)
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[0] => Array
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[each_answer] => A. Hydrolysis of carboxylic acid anhydrides has more negative standard free energy change but carboxylic acid anhydrides have more negative charge than phosphoanydrides.
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[each_answer] => B. Hydrolysis of carboxylic acid anhydrides has more negative standard free energy change but carboxylic acid anhydrides take up more physical space than phosphoanhydrides.
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[each_answer] => C. The free energy change of hydrolysis of carboxylic acid anhydrides is more negative than that of phosphoanhydrides; however, the activation energy is lower.
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[each_answer] => D. The free energy change of hydrolysis of carboxylic acid anhydrides is less negative than that of phosphoanhydrides; however, the activation energy is lower.
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[quiz_unique_key] => 1403770772
[question] => Direct hydrolysis of ATP involves breaking which bond?
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[answer] => 1
[description] => Reason for Correct Answer:
The passage states that direct hydrolysis of ATP results from a nucleophilic attack by water at the γ phosphate position.
This would look like this:
Accordingly, water becomes bonded to the γ phosphate at the end and bond A is broken. This bond would also be broken during a phosphoryl group transfer to another molecule, which often attaches the γ phosphate to an -OH group on an amino acid.
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[each_answer] => A. The bond labeled A
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[each_answer] => B. The bond labeled B
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[each_answer] => C. The bond labeled C
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[each_answer] => D. The bond labeled D
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[quiz_unique_key] => 4010399236
[question] => A pyrophosphoryl transfer from GTP would release which free molecule?
[value] => Array
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[answer] => 4
[description] => Reason for Correct Answer:
According to Table 1, a pyrpphosphoryl group transfer attaches 
to a molecule. For ATP, this would leave adenosine monophosphate behind.
For GTP, this would leave guanosine monophosphate behind.
Guanosine monophosphate is shown in Choice D. Note that these are the different bases for the nucleotides and nucleosides:
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[each_answer] => A.
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[each_answer] => B.
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[each_answer] => C.
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[each_answer] => D.
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[553953|4] => C
[553953|5] => A
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Figure 1
