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Energy input during ATP Dephosphorylation?

Energy input during ATP Dephosphorylation?


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What is the energy input needed to break the phosphor bond during ATP Dephosphorylation? How and when this will occur?

Many thanks for your answers.

Edit 1: I know how much free energy (∆G) is released with the hydrolysis of ATP, but I dont know how much energy is needed to start the hydrolysis of ATP.

Updated Question/s: To break the phosphorus bond of ATP, must there be some input energy? What is the amount of this energy? Else how can break any bond of ATP without the supplement any energy?


It sounds like you are asking about the activation energy of the ATP hydrolysis reaction. This paper estimates the activation at 35--39 kcal / mol, depending on details of the reaction mechanism. So yes, energy is needed to break the phosphate bond; this ensures that ATP does break down spontaneously (which would make it a rather useless molecule for cells).

Note that this concerns ATP hydrolysis without enzymatic catalysis. Enzymes that break the phosphate bond of ATP to drive reactions lower this reaction energy substantially.


Dephosphorylation

In biochemistry, dephosphorylation is the removal of a phosphate (PO4 3− ) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP and inorganic phosphate.

Dephosphorylation employs a type of hydrolytic enzyme, or hydrolase, which cleaves ester bonds. The prominent hydrolase subclass used in dephosphorylation is phosphatase, which removes phosphate groups by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl (-OH) group.

The reversible phosphorylation-dephosphorylation reaction occurs in every physiological process, making proper function of protein phosphatases necessary for organism viability. Because protein dephosphorylation is a key process involved in cell signalling, [1] protein phosphatases are implicated in conditions such as cardiac disease, diabetes, and Alzheimer's disease. [2]


Phosphorylation

Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each other on the enzyme, forming an intermediate complex. An intermediate complex is a temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily react with each other in reactions involving ATP, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (

P). This is illustrated by the following generic reaction:

A + enzyme + ATP → [A − enzyme −

P] → B + enzyme + ADP + phosphate ion

When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism.

Figure 2. In phosphorylation reactions, the gamma phosphate of ATP is attached to a protein.


6.4 ATP: Adenosine Triphosphate

In this section, you will explore the following questions:

  • Why is ATP considered the energy currency of the cell?
  • How is energy released through the hydrolysis of ATP?

Connection for AP ® Courses

Adenosine triphosphate or ATP is the energy “currency” or carrier of the cell. When cells require an input of energy, they use ATP. An ATP nucleotide molecule consists of a five-carbon sugar, the nitrogenous base adenine, and three phosphate groups. (Do not confuse ATP with the nucleotides of DNA and RNA, although they have structural similarities.) The bonds that connect the phosphate have high-energy content, and the energy released from the hydrolysis of ATP to ADP + Pi (Adenosine Diphosphate + phosphate) is used to perform cellular work, such as contracting a muscle or pumping a solute across a cell membrane in active transport. Cells use ATP by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions, with ATP donating its phosphate group to another molecule via a process called phosphorylation. The phosphorylated molecule is at a higher energy state and is less stable than its unphosphorylated form and free energy is released to substrates to perform work during this process. Phosphorylation is an example of energy transfer between molecules.

Information presented and the examples highlighted in the section support concepts and Learning Objectives outlined in Big Idea 2 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.
Enduring Understanding 2.A Growth, reproduction and maintenance of living systems require free energy and matter.
Essential Knowledge 2.A.1 All living systems require constant input of free energy.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow, and to reproduce.

Teacher Support

It is easy to say that ATP carries energy and transfers it to chemicals to fuel reactions. The hard part is in answering the question, how? All three phosphates are negatively charged and naturally repel each other. Energy is needed to keep them together. Line them up and the repelling forces increase and makes it difficult to get the third phosphate attached. This requires much more energy and creates an unstable bond. Energy is stored in this easily broken bond and can be passed on when the third phosphate is used to phosphorylate another compound. It brings the energy with it and losses some in the transfer, creating wasted energy as heat.

The Science Practices Assessment Ancillary contains additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 2.2][APLO 4.14][APLO 2.7][APLO 2.35]

Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate , or ATP . ATP is a small, relatively simple molecule (Figure 6.13), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in much the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.

Teacher Support

Figure 6.13 is useful in illustrating the structure of ATP and why it is easy to detach the gamma phosphate that is hanging out at the end of the structure. Figure 6.14 is useful in illustrating the use of ATP in the sodium-potassium pump that is in every cell membrane.

As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure 6.13). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds ( phosphoanhydride bonds ) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. The reason that these bonds are considered “high-energy” is because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place with the use of a water molecule, it is considered a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following reaction:

Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction regenerates ATP from ADP + Pi. Indeed, cells rely on the regeneration of ATP just as people rely on the regeneration of spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. The formation of ATP is expressed in this equation:

Two prominent questions remain with regard to the use of ATP as an energy source. Exactly how much free energy is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, it would be expected that a different value exists under cellular conditions. In fact, the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: -14 kcal/mol (−57 kJ/mol).

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question posed above, that is, how the energy released by ATP hydrolysis is used to perform work inside the cell, depends on a strategy called energy coupling . Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na + /K + pump) drives sodium out of the cell and potassium into the cell (Figure 6.14). A large percentage of a cell’s ATP is spent powering this pump, because cellular processes bring a great deal of sodium into the cell and potassium out of the cell. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K + ions), one molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate doesn’t simply float away, but is actually transferred onto the pump protein. This process of a phosphate group binding to a molecule is called phosphorylation. As with most cases of ATP hydrolysis, a phosphate from ATP is transferred onto another molecule. In a phosphorylated state, the Na + /K + pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na + to the outside of the cell. It then binds extracellular K + , which, through another conformational change, causes the phosphate to detach from the pump. This release of phosphate triggers the K + to be released to the inside of the cell. Essentially, the energy released from the hydrolysis of ATP is coupled with the energy required to power the pump and transport Na + and K + ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation.

Visual Connection

The illustration depicts a sodium-potassium pump, which uses energy derived from ATP hydrolysis. The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy (ΔG = −7.3 kcal/mol of energy). If it takes 2.1 kcal of energy to move one Na + across the membrane (ΔG = +2.1 kcal/mol of energy), what is the maximum number of sodium ions that could be moved by the hydrolysis of one ATP molecule?

Often during cellular metabolic reactions, such as the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a molecule of the sugar glucose is broken down in the process of glycolysis. In the first step of this process, ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to be converted to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for the phosphorylation of another molecule, creating an unstable intermediate and powering an important conformational change.

Link to Learning

See an interactive animation of the ATP-producing glycolysis process at this site.


ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group (Figure 4.14). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine di phosphate (ADP) the addition of a third phosphate group forms adenosine tri phosphate (ATP).

Figure 4.14 ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken.

The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy.

Even exergonic, energy-releasing reactions require a small amount of activation energy to proceed. However, consider endergonic reactions, which require much more energy input because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule, but within its bonds contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.


Results

A Mechanism for Robust Input–Output Relation.

A mechanism for a robust input–output relation can be suggested based on biochemical features that are found in a class of bacterial two-component signaling systems. Table 1 lists six such systems, each of which is composed of two proteins, an input-sensitive sensor denoted X and a response regulator denoted Y. The sensor X senses the input signal and acts to phosphorylate the diffusible response-regulator Y. The phosphorylated form of Y, denoted YP, activates the expression of relevant genes (16). Thus, the input signals of these systems affect gene expression by setting the output, which is the concentration YP.

Bacterial two-component signaling systems that underlie the present model

One well studied example is the EnvZ/OmpR two-component signaling system of E. coli. Its primary input is the osmolarity of the medium in which the bacterium grows, and its output is the concentration of phosphorylated response-regulator OmpR, which controls the expression level of genes. In this system, a correlate of the output is the ratio between the transcription levels of two genes controlled by Y P. This correlate, which is a continuous function of the input signal, has been experimentally shown by Batchelor et al. (17) to have a high degree of robustness at a given input level, the correlate changes by <5% when protein levels are varied by 2-fold and by ≈20% for 10-fold changes (5). This approximate robustness breaks down only at high over- or underexpression of the proteins.

The signaling systems of Table 1 all share certain specific biochemical features (Fig. 2 a).The first feature concerns the sensor kinase activity. In these systems, the sensor is not a simple kinase that binds Y and ATP to phosphorylate Y. Rather, the sensor works in two steps. First, it phosphorylates itself by binding and hydrolyzing ATP (16). The rate constant of this autophosphorylation, v a(s), is controlled by the input signal s. The phosphorylated sensor, denoted XP, then performs a phosphotransfer step it transfers the phosphoryl group to Y, thereby forming YP (16).

Mechanism for robust signaling based on a class of bacterial signaling systems. (a) Sensor X bound to ATP phosphorylates itself to form XP. The phosphorylated sensor XP then transfers the phosphoryl group to the response-regulator Y, thereby forming YP, which is the output of the system. The sensor bound to ATP also dephosphorylates YP. (b) Mechanism reactions and some of their rate constants, where the first reaction is autophosphorylation, the second is phosphotransfer, and the third is dephosphorylation. (c) Steady-state level of the output Y P as a function of the input-signal-modulated function ƒ(s)=(va(s)/vp)(k′ 3+vp/k 3. In the region ƒ(s)≤YT, the curve is invariant to changes in the total concentrations XT and YT of the sensor and the response regulator, as well as to changes in the concentration of ATP.

This two-step process is found in virtually all bacterial two-component systems. The following features, however, appear to be particular only to a class of systems, such as those in Table 1. In these systems, the sensor X is a bifunctional enzyme it catalyzes not only the phosphorylation of Y but also the dephophosphorylsphorylation of YP (16). Finally, ATP, which is used as the phosphoryl donor for the autophosphorylation reaction, is also required as a cofactor for the dephosphorylation reaction (18–20). This ATP dependence occurs despite the fact that ATP is not used as an energy source in the dephosphorylation step.

The features above were used to construct a signaling mechanism whose reactions are shown in Fig. 2 b. To find the input–output relation of the mechanism and study its robustness, it is necessary to solve for the fixed points of the seven nonlinear differential equations that describe the mass-action kinetics of the model. This is done in the supporting information (SI). However, another way to obtain the input–output relation presents itself when the system is viewed as a black box that breaks down ATP and releases phosphoryl groups. Consider the fluxes of phosphoryl into and out of the system. The influx of phosphoryl groups from the cell's ATP pool is equal to the rate of the autophosphorylation reaction: The outflux of phosphoryl groups is equal to the rate of the dephosphorylation reaction: To proceed, one can compute the concentration of the complex X·ATP·YP. This complex is formed in the model by the binding of X·ATP to YP and is lost when the constituents dissociate or when the dephosphorylation reaction takes place: Thus, at steady state, the concentration of the complex is proportional to the product of its component concentrations: Using this in Eq. 2 yields At steady state, J i = J o using Eqs. 1 and 5 , one finds that: When [X·ATP] is nonzero, one can divide it out from both sides of Eq. 6 . This results in a robust input–output relation, in which Y P depends only on kinetic rate constants: Hence, the output Y P does not depend on the level of any of the proteins in the system, or on the level of ATP. The output is responsive to the input signal via the rate constant v a(s). This mechanism thus shows a robust input–output relation (Fig. 2 c).

Variations in the concentrations of the sensor or ATP do not affect the input–output relation. The only loss of robustness occurs if the total level of protein Y, denoted Y T, falls below the expected Y P level for a given input signal (Fig. 2 c). In this case, there is not enough Y protein to reach the Y P value given by Eq. 7 . If this happens, a complete analysis of the model (see SI) shows that all of the Y molecules are phosphorylated, and Y P = Y T. Hence, the system cannot respond at all to the input signal. It therefore follows that both robustness and responsiveness to the signal require that Y T exceeds a certain threshold, given by the maximal desired output level Y P in expected physiological conditions ¶ .

Note that all three biochemical features of the mechanism are required for input–output robustness. First, ATP dependence of dephosphorylation is essential. Indeed, in a model without this feature, one finds that Y p∼ATP (ref. 5 see SI). Hence, the output is sensitive to fluctuations in the level of ATP (4). Similarly, if the sensor was not bifunctional, and dephosphorylation was carried out by a separate phosphatase protein Z, the balance of phosphoryl influx and outflux would require that [X·ATP] ∼ [Z·YP] ∼ ZYP. This would result in a steady-state level YP ∼ [X·ATP]/Z that depends on the intracellular levels of both the sensor X and phosphatase Z. Robustness would be lost.

Finally, the two-step nature of the kinase is also essential for robustness. If the sensor was a simple kinase that directly transfers a phosphoryl group from ATP to the substrate without first phosphorylating itself, the ATP breakdown rate would depend on the concentration of the complex X·ATP·Y, which at steady state is proportional to [X·ATP]Y. This would balance with the dephosphorylation flux, so that [X·ATP]Y ∼ [X·ATP]YP. As a result, the output YP would be proportional to the level Y of free response regulator and would thus depend on the total level of response-regulator YT, thereby abolishing robustness. In summary, robustness over a wide range of parameters in the present mechanism seems to require the combined effects of all three biochemical features.

We also studied the effect of adding reactions to the model. For example, spontaneous dephosphorylation of YP is known to occur on a much slower timescale than the response time of the system (Table 1), and accordingly we find it has a negligible effect on robustness (SI). As a second example, we find that adding ADP as a cofactor for the dephosphorylation activity of the sensor [in addition to ATP and with similar efficiency (21)] has a negligible effect on robustness (SI). This is primarily because the ADP concentration is much lower than the ATP concentration in the cell (22). We also studied other reactions, including spontaneous dephosphorylation of XP, reverse autophosphorylation, phosphotransfer, and dephosphorylation steps, as well as an alternative way to form the ternary complex in the system. In the supporting information (SI), we show that when the rates of these additional reactions are small compared with the rates of the present model reactions, they have only a small effect on robustness.

Remarks on the Black Box Approach.

To analyze the properties of the mechanism presented above, the system was considered as a black box that breaks down ATP. More generally, the black box approach can be used to suggest a class of systems that have the potential to show robust input–output relations. It can also point to system characteristics that may rule out such robustness.

Consider a system with one reaction that breaks down ATP at rate J i and another reaction that releases phosphoryl ions at rate J o (Fig. 3 a). Under what conditions might component Y in the system be robust? This can happen if, at steady state, J i and J o depend in the same way on the concentrations of all components except Y but depend in different ways on the concentration of Y itself. Thus, the steady-state influx and outflux can be expressed as follows: J i = f(X 1…, X N, Y, ATP)g(Y) and J o = f(X 1X N,Y, ATP)h(Y), where g(Y) and h(Y) are different functions of Y that intersect at only one point. These functions also depend on kinetic rate constants, some of which are signal-sensitive. If the system reaches a stable steady state, then J i = J o, and one has fg = fh. Assuming the fluxes are nonzero, the function f can be eliminated from both sides of the equation, which results in g = h. This can be solved to yield Y as a function of rate constants only, which makes the relation between the input signal and the output Y robust with respect to all component concentrations.

Black box approach and conditions that prohibit robust input–output relations. (a) Considering a system as a black box that breaks down ATP at rate J i and releases phosphoryl groups at rate J o suggests that the concentration of component Y is robust to the concentrations of all other components X1, X2, …, XN, if at steady state J i and J o depend in the same way on all components except Y but depend differently on Y. (b) Robustness cannot hold if there are two or more influxes that supply phosphoryl groups to the system. Similarly, robustness cannot hold if there are two or more outfluxes that drain phosphoryl groups from the system. Robustness can sometimes hold approximately, however, if the secondary fluxes J′I and J′o are small compared with the main fluxes.

Note that such robust systems can include any number of reactions within the black box, such as multiple phospho-transfer cascades, as long as a stable steady state is reached, and the influx and outflux of phosphoryl groups are as described above. Thus, many variants of the model of Fig. 2 b, which add reactions inside the black box, can in principle be formed, and all such variants can display the robustness property.

It can also be seen that robustness of the present type cannot generally occur if there is more than one reaction that introduces phosphoryl groups into the system. If two different influxes J i and J′i exist (Fig. 3 b), they generally cannot be canceled out with J o (in the sense of Eq. 6 above), leading to a loss of robustness. Similar considerations apply to cases where there is more than one way for phosphoryl groups to exit the system.

Robustness of the present type thus depends on a single route for uptake and release of phosphoryl groups. However, in the SI, we find that in the case of the present model one can come close to robustness if the influx and outflux due to secondary reactions J′i and J′o are small in magnitude relative to Ji and Jo. If the relative magnitude of the secondary to primary fluxes is of order ε and steady-state stability is maintained, robustness is generally lost by only a factor of order ε.


Contents

ATP consists of an adenine attached by the 9-nitrogen atom to the 1′ carbon atom of a sugar (ribose), which in turn is attached at the 5' carbon atom of the sugar to a triphosphate group. In its many reactions related to metabolism, the adenine and sugar groups remain unchanged, but the triphosphate is converted to di- and monophosphate, giving respectively the derivatives ADP and AMP. The three phosphoryl groups are referred to as the alpha (α), beta (β), and, for the terminal phosphate, gamma (γ).

In neutral solution, ionized ATP exists mostly as ATP 4− , with a small proportion of ATP 3− . [4]

Binding of metal cations to ATP Edit

Being polyanionic and featuring a potentially chelating polyphosphate group, ATP binds metal cations with high affinity. The binding constant for Mg 2+
is ( 9 554 ). [5] The binding of a divalent cation, almost always magnesium, strongly affects the interaction of ATP with various proteins. Due to the strength of the ATP-Mg 2+ interaction, ATP exists in the cell mostly as a complex with Mg 2+
bonded to the phosphate oxygen centers. [4] [6]

A second magnesium ion is critical for ATP binding in the kinase domain. [7] The presence of Mg 2+ regulates kinase activity. [8]

Salts of ATP can be isolated as colorless solids. [9]

ATP is stable in aqueous solutions between pH 6.8 and 7.4, in the absence of catalysts. At more extreme pHs, it rapidly hydrolyses to ADP and phosphate. Living cells maintain the ratio of ATP to ADP at a point ten orders of magnitude from equilibrium, with ATP concentrations fivefold higher than the concentration of ADP. [10] [11] In the context of biochemical reactions, the P-O-P bonds are frequently referred to as high-energy bonds. [12]

The hydrolysis of ATP into ADP and inorganic phosphate releases 30.5 kJ/mol of enthalpy, with a change in free energy of 3.4 kJ/mol. [13] The energy released by cleaving either a phosphate (Pi) or pyrophosphate (PPi) unit from ATP at standard state of 1 M are: [14]

ATP + H
2 O → ADP + Pi ΔG° = −30.5 kJ/mol (−7.3 kcal/mol) ATP + H
2 O → AMP + PPi ΔG° = −45.6 kJ/mol (−10.9 kcal/mol)

These abbreviated equations can be written more explicitly (R = adenosyl):

Production, aerobic conditions Edit

A typical intracellular concentration of ATP is hard to pin down, however, reports have shown there to be 1–10 μmol per gram of tissue in a variety of eukaryotes. [15] The dephosphorylation of ATP and rephosphorylation of ADP and AMP occur repeatedly in the course of aerobic metabolism.

ATP can be produced by a number of distinct cellular processes the three main pathways in eukaryotes are (1) glycolysis, (2) the citric acid cycle/oxidative phosphorylation, and (3) beta-oxidation. The overall process of oxidizing glucose to carbon dioxide, the combination of pathways 1 and 2, known as cellular respiration, produces about 30 equivalents of ATP from each molecule of glucose. [16]

ATP production by a non-photosynthetic aerobic eukaryote occurs mainly in the mitochondria, which comprise nearly 25% of the volume of a typical cell. [17]

Glycolysis Edit

In glycolysis, glucose and glycerol are metabolized to pyruvate. Glycolysis generates two equivalents of ATP through substrate phosphorylation catalyzed by two enzymes, PGK and pyruvate kinase. Two equivalents of NADH are also produced, which can be oxidized via the electron transport chain and result in the generation of additional ATP by ATP synthase. The pyruvate generated as an end-product of glycolysis is a substrate for the Krebs Cycle. [18]

Glycolysis is viewed as consisting of two phases with five steps each. In phase 1, "the preparatory phase", glucose is converted to 2 d-glyceraldehyde -3-phosphate (g3p). One ATP is invested in Step 1, and another ATP is invested in Step 3. Steps 1 and 3 of glycolysis are referred to as "Priming Steps". In Phase 2, two equivalents of g3p are converted to two pyruvates. In Step 7, two ATP are produced. Also, in Step 10, two further equivalents of ATP are produced. In Steps 7 and 10, ATP is generated from ADP. A net of two ATPs is formed in the glycolysis cycle. The glycolysis pathway is later associated with the Citric Acid Cycle which produces additional equivalents of ATP.

Regulation Edit

In glycolysis, hexokinase is directly inhibited by its product, glucose-6-phosphate, and pyruvate kinase is inhibited by ATP itself. The main control point for the glycolytic pathway is phosphofructokinase (PFK), which is allosterically inhibited by high concentrations of ATP and activated by high concentrations of AMP. The inhibition of PFK by ATP is unusual since ATP is also a substrate in the reaction catalyzed by PFK the active form of the enzyme is a tetramer that exists in two conformations, only one of which binds the second substrate fructose-6-phosphate (F6P). The protein has two binding sites for ATP – the active site is accessible in either protein conformation, but ATP binding to the inhibitor site stabilizes the conformation that binds F6P poorly. [18] A number of other small molecules can compensate for the ATP-induced shift in equilibrium conformation and reactivate PFK, including cyclic AMP, ammonium ions, inorganic phosphate, and fructose-1,6- and -2,6-biphosphate. [18]

Citric acid cycle Edit

In the mitochondrion, pyruvate is oxidized by the pyruvate dehydrogenase complex to the acetyl group, which is fully oxidized to carbon dioxide by the citric acid cycle (also known as the Krebs cycle). Every "turn" of the citric acid cycle produces two molecules of carbon dioxide, one equivalent of ATP guanosine triphosphate (GTP) through substrate-level phosphorylation catalyzed by succinyl-CoA synthetase, as succinyl- CoA is converted to Succinate, three equivalents of NADH, and one equivalent of FADH2. NADH and FADH2 are recycled (to NAD + and FAD, respectively), generating additional ATP by oxidative phosphorylation. The oxidation of NADH results in the synthesis of 2–3 equivalents of ATP, and the oxidation of one FADH2 yields between 1–2 equivalents of ATP. [16] The majority of cellular ATP is generated by this process. Although the citric acid cycle itself does not involve molecular oxygen, it is an obligately aerobic process because O2 is used to recycle the NADH and FADH2 and provides the chemical energy driving the process. [19] In the absence of oxygen, the citric acid cycle ceases. [17]

The generation of ATP by the mitochondrion from cytosolic NADH relies on the malate-aspartate shuttle (and to a lesser extent, the glycerol-phosphate shuttle) because the inner mitochondrial membrane is impermeable to NADH and NAD + . Instead of transferring the generated NADH, a malate dehydrogenase enzyme converts oxaloacetate to malate, which is translocated to the mitochondrial matrix. Another malate dehydrogenase-catalyzed reaction occurs in the opposite direction, producing oxaloacetate and NADH from the newly transported malate and the mitochondrion's interior store of NAD + . A transaminase converts the oxaloacetate to aspartate for transport back across the membrane and into the intermembrane space. [17]

In oxidative phosphorylation, the passage of electrons from NADH and FADH2 through the electron transport chain releases the chemical energy of O2 [19] to pump protons out of the mitochondrial matrix and into the intermembrane space. This pumping generates a proton motive force that is the net effect of a pH gradient and an electric potential gradient across the inner mitochondrial membrane. Flow of protons down this potential gradient – that is, from the intermembrane space to the matrix – yields ATP by ATP synthase. [20] Three ATP are produced per turn.

Although oxygen consumption appears fundamental for the maintenance of the proton motive force, in the event of oxygen shortage (hypoxia), intracellular acidosis (mediated by enhanced glycolytic rates and ATP hydrolysis), contributes to mitochondrial membrane potential and directly drives ATP synthesis. [21]

Most of the ATP synthesized in the mitochondria will be used for cellular processes in the cytosol thus it must be exported from its site of synthesis in the mitochondrial matrix. ATP outward movement is favored by the membrane's electrochemical potential because the cytosol has a relatively positive charge compared to the relatively negative matrix. For every ATP transported out, it costs 1 H + . Producing one ATP costs about 3 H + . Therefore, making and exporting one ATP requires 4H +. The inner membrane contains an antiporter, the ADP/ATP translocase, which is an integral membrane protein used to exchange newly synthesized ATP in the matrix for ADP in the intermembrane space. [22] This translocase is driven by the membrane potential, as it results in the movement of about 4 negative charges out across the mitochondrial membrane in exchange for 3 negative charges moved inside. However, it is also necessary to transport phosphate into the mitochondrion the phosphate carrier moves a proton in with each phosphate, partially dissipating the proton gradient. After completing glycolysis, the citric acid cycle, the electron transport chain, and oxidative phosphorylation, approximately 30–38 ATP molecules are produced per glucose.

Regulation Edit

The citric acid cycle is regulated mainly by the availability of key substrates, particularly the ratio of NAD + to NADH and the concentrations of calcium, inorganic phosphate, ATP, ADP, and AMP. Citrate – the ion that gives its name to the cycle – is a feedback inhibitor of citrate synthase and also inhibits PFK, providing a direct link between the regulation of the citric acid cycle and glycolysis. [18]

Beta oxidation Edit

In the presence of air and various cofactors and enzymes, fatty acids are converted to acetyl-CoA. The pathway is called beta-oxidation. Each cycle of beta-oxidation shortens the fatty acid chain by two carbon atoms and produces one equivalent each of acetyl-CoA, NADH, and FADH2. The acetyl-CoA is metabolized by the citric acid cycle to generate ATP, while the NADH and FADH2 are used by oxidative phosphorylation to generate ATP. Dozens of ATP equivalents are generated by the beta-oxidation of a single long acyl chain. [23]

Regulation Edit

In oxidative phosphorylation, the key control point is the reaction catalyzed by cytochrome c oxidase, which is regulated by the availability of its substrate – the reduced form of cytochrome c. The amount of reduced cytochrome c available is directly related to the amounts of other substrates:

which directly implies this equation:

[ c y t c r e d ] [ c y t c o x ] = ( [ N A D H ] [ N A D ] + ) 1 2 ( [ A D P ] [ P i ] [ A T P ] ) K e q

Thus, a high ratio of [NADH] to [NAD + ] or a high ratio of [ADP][Pi] to [ATP] imply a high amount of reduced cytochrome c and a high level of cytochrome c oxidase activity. [18] An additional level of regulation is introduced by the transport rates of ATP and NADH between the mitochondrial matrix and the cytoplasm. [22]

Ketosis Edit

Ketone bodies can be used as fuels, yielding 22 ATP and 2 GTP molecules per acetoacetate molecule when oxidized in the mitochondria. Ketone bodies are transported from the liver to other tissues, where acetoacetate and beta-hydroxybutyrate can be reconverted to acetyl-CoA to produce reducing equivalents (NADH and FADH2), via the citric acid cycle. Ketone bodies cannot be used as fuel by the liver, because the liver lacks the enzyme β-ketoacyl-CoA transferase, also called thiolase. Acetoacetate in low concentrations is taken up by the liver and undergoes detoxification through the methylglyoxal pathway which ends with lactate. Acetoacetate in high concentrations is absorbed by cells other than those in the liver and enters a different pathway via 1,2-propanediol. Though the pathway follows a different series of steps requiring ATP, 1,2-propanediol can be turned into pyruvate. [24]

Production, anaerobic conditions Edit

Fermentation is the metabolism of organic compounds in the absence of air. It involves substrate-level phosphorylation in the absence of a respiratory electron transport chain. The equation for the reaction of glucose to form lactic acid is:

Anaerobic respiration is respiration in the absence of O
2 . Prokaryotes can utilize a variety of electron acceptors. These include nitrate, sulfate, and carbon dioxide.

ATP replenishment by nucleoside diphosphate kinases Edit

ATP can also be synthesized through several so-called "replenishment" reactions catalyzed by the enzyme families of nucleoside diphosphate kinases (NDKs), which use other nucleoside triphosphates as a high-energy phosphate donor, and the ATP:guanido-phosphotransferase family.

ATP production during photosynthesis Edit

In plants, ATP is synthesized in the thylakoid membrane of the chloroplast. The process is called photophosphorylation. The "machinery" is similar to that in mitochondria except that light energy is used to pump protons across a membrane to produce a proton-motive force. ATP synthase then ensues exactly as in oxidative phosphorylation. [25] Some of the ATP produced in the chloroplasts is consumed in the Calvin cycle, which produces triose sugars.

ATP recycling Edit

The total quantity of ATP in the human body is about 0.2 moles. The majority of ATP is recycled from ADP by the aforementioned processes. Thus, at any given time, the total amount of ATP + ADP remains fairly constant.

The energy used by human cells in an adult requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. A human will typically use up their body weight of ATP over the course of the day. Each equivalent of ATP is recycled 1000–1500 times during a single day ( 100 / 0.2 = 500 ). [26]

Intracellular signaling Edit

ATP is involved in signal transduction by serving as substrate for kinases, enzymes that transfer phosphate groups. Kinases are the most common ATP-binding proteins. They share a small number of common folds. [27] Phosphorylation of a protein by a kinase can activate a cascade such as the mitogen-activated protein kinase cascade. [28]

ATP is also a substrate of adenylate cyclase, most commonly in G protein-coupled receptor signal transduction pathways and is transformed to second messenger, cyclic AMP, which is involved in triggering calcium signals by the release of calcium from intracellular stores. [29] This form of signal transduction is particularly important in brain function, although it is involved in the regulation of a multitude of other cellular processes. [30]

DNA and RNA synthesis Edit

ATP is one of four monomers required in the synthesis of RNA. The process is promoted by RNA polymerases. [31] A similar process occurs in the formation of DNA, except that ATP is first converted to the deoxyribonucleotide dATP. Like many condensation reactions in nature, DNA replication and DNA transcription also consume ATP.

Amino acid activation in protein synthesis Edit

Aminoacyl-tRNA synthetase enzymes consume ATP in the attachment tRNA to amino acids, forming aminoacyl-tRNA complexes. Aminoacyl transferase binds AMP-amino acid to tRNA. The coupling reaction proceeds in two steps:

The amino acid is coupled to the penultimate nucleotide at the 3′-end of the tRNA (the A in the sequence CCA) via an ester bond (roll over in illustration).

ATP binding cassette transporter Edit

Transporting chemicals out of a cell against a gradient is often associated with ATP hydrolysis. Transport is mediated by ATP binding cassette transporters. The human genome encodes 48 ABC transporters, that are used for exporting drugs, lipids, and other compounds. [32]

Extracellular signalling and neurotransmission Edit

Cells secrete ATP to communicate with other cells in a process called purinergic signalling. ATP serves as a neurotransmitter in many parts of the nervous system, modulates ciliary beating, affects vascular oxygen supply etc. ATP is either secreted directly across the cell membrane through channel proteins [33] [34] or is pumped into vesicles [35] which then fuse with the membrane. Cells detect ATP using the purinergic receptor proteins P2X and P2Y.

Protein solubility Edit

ATP has recently been proposed to act as a biological hydrotrope [36] and has been shown to affect proteome-wide solubility. [37]

Biochemistry laboratories often use in vitro studies to explore ATP-dependent molecular processes. ATP analogs are also used in X-ray crystallography to determine a protein structure in complex with ATP, often together with other substrates.

Enzyme inhibitors of ATP-dependent enzymes such as kinases are needed to examine the binding sites and transition states involved in ATP-dependent reactions.

Most useful ATP analogs cannot be hydrolyzed as ATP would be instead, they trap the enzyme in a structure closely related to the ATP-bound state. Adenosine 5′-(γ-thiotriphosphate) is an extremely common ATP analog in which one of the gamma-phosphate oxygens is replaced by a sulfur atom this anion is hydrolyzed at a dramatically slower rate than ATP itself and functions as an inhibitor of ATP-dependent processes. In crystallographic studies, hydrolysis transition states are modeled by the bound vanadate ion.

Caution is warranted in interpreting the results of experiments using ATP analogs, since some enzymes can hydrolyze them at appreciable rates at high concentration. [38]

ATP is used intravenously for some heart related conditions. [39]

ATP was discovered in 1929 by Karl Lohmann [40] and Jendrassik [41] and, independently, by Cyrus Fiske and Yellapragada Subba Rao of Harvard Medical School, [42] both teams competing against each other to find an assay for phosphorus.

It was proposed to be the intermediary between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. [43]

It was first synthesized in the laboratory by Alexander Todd in 1948. [44]

The Nobel Prize in Chemistry 1997 was divided, one half jointly to Paul D. Boyer and John E. Walker "for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)" and the other half to Jens C. Skou "for the first discovery of an ion-transporting enzyme, Na+, K+ -ATPase." [45]


6.4 ATP: Adenosine Triphosphate

By the end of this section, you will be able to do the following:

  • Explain ATP's role as the cellular energy currency
  • Describe how energy releases through ATP hydrolysis

Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, from where does energy to power such reactions come? The answer lies with an energy-supplying molecule scientists call adenosine triphosphate , or ATP . This is a small, relatively simple molecule (Figure 6.13), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. Think of this molecule as the cells' primary energy currency in much the same way that money is the currency that people exchange for things they need. ATP powers the majority of energy-requiring cellular reactions.

As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure 6.13). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds ( phosphoanhydride bonds ) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. These bonds are “high-energy” because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place using a water molecule, it is a hydrolysis reaction. In other words, ATP hydrolyzes into ADP in the following reaction:

Like most chemical reactions, ATP to ADP hydrolysis is reversible. The reverse reaction regenerates ATP from ADP + Pi. Cells rely on ATP regeneration just as people rely on regenerating spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. This equation expresses ATP formation:

Two prominent questions remain with regard to using ATP as an energy source. Exactly how much free energy releases with ATP hydrolysis, and how does that free energy do cellular work? The calculated ∆G for the hydrolysis of one ATP mole into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, one would expect a different value exists under cellular conditions. In fact, the ∆G for one ATP mole's hydrolysis in a living cell is almost double the value at standard conditions: –14 kcal/mol (−57 kJ/mol).

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question we posed above discusses how ATP hydrolysis energy release performs work inside the cell. This depends on a strategy scientists call energy coupling . Cells couple the ATP hydrolysis' exergonic reaction allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na + /K + pump) drives sodium out of the cell and potassium into the cell (Figure 6.14). A large percentage of a cell’s ATP powers this pump, because cellular processes bring considerable sodium into the cell and potassium out of it. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K + ions), one ATP molecule must hydrolyze. When ATP hydrolyzes, its gamma phosphate does not simply float away, but it actually transfers onto the pump protein. Scientists call this process of a phosphate group binding to a molecule phosphorylation. As with most ATP hydrolysis cases, a phosphate from ATP transfers onto another molecule. In a phosphorylated state, the Na + /K + pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na + to the cell's outside. It then binds extracellular K + , which, through another conformational change, causes the phosphate to detach from the pump. This phosphate release triggers the K + to release to the cell's inside. Essentially, the energy released from the ATP hydrolysis couples with the energy required to power the pump and transport Na + and K + ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation.

Visual Connection

One ATP molecule's hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na + across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule's hydrolysis move?

Often during cellular metabolic reactions, such as nutrient synthesis and breakdown, certain molecules must alter slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a sugar glucose molecule breaks down in the process of glycolysis. In the first step, ATP is required to phosphorylate glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to convert to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, ATP hydrolysis' exergonic reaction couples with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for phosphorylyzing another molecule, creating an unstable intermediate and powering an important conformational change.


INTRODUCTION

An understanding of a species' ecophysiological limits helps us identify the reasons underpinning species and population processes over different spatial scales. Whilst we have a relatively good understanding of how species distributions are shaped by temperature (see Bozinovic et al., 2011), for other emerging environmental drivers, such as increasing seawater partial pressure of CO2 (PCO2), which is causing the acidification of the oceans, we know relatively little (see Calosi et al., 2013 Kroeker et al., 2011 Maas et al., 2012). Shallow water, high CO2 vents have been used as analogues to investigate the potential ecological and evolutionary implications of ocean acidification. In particular, at the CO2 vent of Ischia the polychaete fauna have been characterised in relation to the venting activity (e.g. Kroeker et al., 2011). Based on their distribution patterns, species found inside and outside these naturally acidified areas can be considered to be either ‘tolerant’ (abundant both inside and outside the low pH/high PCO2 areas) or ‘sensitive’ (found outside the vents in similar habitat). Tolerant species include those that are able to maintain their metabolic rate levels unchanged during acute exposure to elevated PCO2, thus maintaining their energy metabolism and metabolic scope levels. In comparison, sensitive species show extreme decreases or increases in metabolic rates, corresponding to an extreme decrease of aerobic metabolism and an increase in metabolic costs, respectively, with both responses probably leading to a substantial decrease in metabolic scope (see Calosi et al., 2013 and references therein). In general, species that are poor regulators of metabolic rate under high PCO2 conditions have been shown to have lesser homeostatic control, with some undergoing metabolic depression (Melzner et al., 2009). The fan worm Sabella spallanzanii (Gmelin, 1791) (Sabellidae) is present in the waters around Ischia (including those near the vents M.-C.G. and P.C., personal observation), being especially abundant in areas with high nutrient levels, e.g. harbours (Bocchetti et al., 2004). It is absent from the high venting areas, despite showing the ability to increase its metabolic rates when exposed in situ to high PCO2 conditions (e.g. Calosi et al., 2013), and thus possibly maintain its metabolic scope, unless it undergoes a physiological trade-off between energy metabolism and other important functions (e.g. enzymatic activities, osmo-ionic or pH intracellular regulation). Thus, S. spallanzanii allows us to investigate the biochemical mechanism underpinning a type of sensitivity to high PCO2 not connected to metabolic depression, which may contribute towards explaining the distribution of this polychaete around the CO2 vent of Ischia.

To determine the extent to which the cellular physiological condition explains the sensitivity of S. spallanzanii to ocean acidification, we conducted in situ transplant experiments (e.g. Calosi et al., 2013), transferring specimens to either control pH/PCO2 or low pH/high PCO2 conditions, and examined the concentration of fundamental aerobic and anaerobic metabolites and of carbonic anhydrase. Carbonic anhydrase is an essential enzyme involved in an organism's acid–base and respiratory function (see Fehsenfeld et al., 2011), which are key to defining its tolerance to high PCO2. This approach allowed us to test for the effect of high PCO2 on this species' biochemical metabolic responses, enabling us to unravel possible functional trade-offs among different traits, which may help explain its sensitivity. Our use of an ‘individual approach’ allowed us to examine the significance of inter-individual variation in the metabolic versus enzymatic responses, which may otherwise remain masked by using an independent samples analysis (see discussion on ‘the golden mean’ in Bennett, 1987). Furthermore, our study is the first to provide mechanistic evidence for an alternative metabolic pathway of sensitivity to high PCO2 conditions, characterised by a significant reduction in metabolic rates and energy metabolism (e.g. Ivanina et al., 2013). This mechanism seems to be underlined by a regulatory trade-off between a fundamental enzyme and the maintenance of this species' metabolic homeostatic machinery upon exposure to high PCO2 conditions. This provides a possible explanation for the distribution of S. spallanzanii around the CO2 vent of Ischia, and further assists our understanding of the variety of mechanisms through which climate change may pose a threat to extant marine biodiversity.


CHAPTER SUMMARY

6.1 Energy and Metabolism

Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.

6.2 ATP: Adenosine Triphosphate

ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Pi is used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.

6.3 Enzymes

Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.

Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.

654 Energy in Living Systems

ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis.

5.5 Glycolysis

Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD + . Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell.

5.6 Oxidation of Pyruvate and the Citric Acid Cycle

In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD + , and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs.

The citric acid cycle is a series of redox and decarboxylation reactions that remove high-energy electrons and carbon dioxide. The electrons temporarily stored in molecules of NADH and FADH2 are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one.

5.7 Oxidative Phosphorylation

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy, High-energy electrons donated to the chain by either NADH or FADH2 complete the chain, as low energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH2 to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways.

5.8 Metabolism without Oxygen

If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD + , ensuring the continuation of glycolysis. The regeneration of NAD + in fermentation is not accompanied by ATP production therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized.

5.9 Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.

5.10 Regulation of Cellular Respiration

Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD + , and FAD. Other intermediates of the pathway also affect certain enzymes in the systems.

5.11 Overview of Photosynthesis

The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, photosynthesis evolved to allow living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today.

Only certain organisms, called photoautotrophs, can perform photosynthesis they require the presence of chlorophyll, a specialized pigment that absorbs certain portions of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a waste product into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm.

5.12 The Light-Dependent Reactions of Photosynthesis

The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. A photon strikes the antenna pigments of photosystem II to initiate photosynthesis. The energy travels to the reaction center that contains chlorophyll a to the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of ions. The ions flow through ATP synthase via chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy and reducing power carrier for the light-independent reactions.

5.13 Using Light Energy to Make Organic Molecules

Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2 from the environment. An enzyme, RuBisCO, catalyzes a reaction with CO2 and another molecule, RuBP. After three cycles, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO2. Photosynthesis forms an energy cycle with the process of cellular respiration. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria.

REVIEW QUESTIONS

Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule.

an anabolic molecule : catabolic molecule

a catabolic molecule : anabolic molecule

DNA replication involves unwinding two strands of parent DNA, copying each strand to synthesize complementary strands, and releasing the parent and daughter DNA. Which of the following accurately describes this process?

This is an anabolic process

This is a catabolic process

This is both anabolic and catabolic

This is a metabolic process but is neither anabolic nor catabolic

Which of the following is not an example of an energy transformation?

Turning on a light switch

Formation of static electricity

The energy released by the hydrolysis of ATP is

primarily stored between the alpha and beta phosphates

harnessed as heat energy by the cell to perform work

providing energy to coupled reactions

An allosteric inhibitor does which of the following?

Binds to an enzyme away from the active site and changes the conformation of the active site,

increasing its affinity for substrate binding

Binds to the active site and blocks it from binding substrate

Binds to an enzyme away from the active site and changes the conformation of the active site, decreasing its affinity for the substrate

Binds directly to the active site and mimics the substrate

Which of the following analogies best describe the induced-fit model of enzyme substrate binding?

A key fitting into a lock

A square peg fitting through the square hole and a round peg fitting through the round hole of a children’s toy

The fitting together of two jigsaw puzzle pieces.

The energy currency used by cells is ________.

Chemiosmosis involves ________.

the movement of electrons across the cell membrane

the movement of hydrogen atoms across a mitochondrial membrane

the movement of hydrogen ions across a mitochondrial membrane

the movement of glucose through the cell membrane

Which of the following fermentation methods can occur in animal skeletal muscles?

The effect of high levels of ADP is to ________.

increase the activity of the enzyme

decrease the activity of the enzyme

have no effect on the activity of the enzyme

Which of the following components is not used by both plants and cyanobacteria to carry out photosynthesis?

What two main products result from photosynthesis?

oxygen and carbon dioxide

sugars/carbohydrates and oxygen

sugars/carbohydrates and carbon dioxide

CRITICAL THINKING QUESTIONS

Does physical exercise involve anabolic and/ or catabolic processes? Give evidence for your answer.

Name two different cellular functions that require energy that parallel human energy requiring functions.

Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy?

With regard to enzymes, why are vitamins necessary for good health? Give examples.

Why is it beneficial for cells to use ATP rather than energy directly from the bonds of carbohydrates? What are the greatest drawbacks to harnessing energy directly from the bonds of several different compounds?

Nearly all organisms on earth carry out some form of glycolysis. How does that fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways?

Red blood cells do not perform aerobic respiration, but they do perform glycolysis. Why do all cells need an energy source, and what would happen if glycolysis were blocked in a red blood cell?

What is the primary difference between fermentation and anaerobic respiration?

Why might negative feedback mechanisms be more common than positive feedback mechanisms in living cells?

What is the overall outcome of the light reactions in photosynthesis?

Why are carnivores, such as lions, dependent on photosynthesis to survive?

Adapted from:

OpenStax, Biology. OpenStax. May 20, 2013. <http://cnx.org/content/col11448/latest/>

“Download for free at http://cnx.org/content/col11448/latest/.”



Comments:

  1. Shijo

    than in result.

  2. Marchland

    This is power !!!!

  3. Corwin

    Bravo, what words ... wonderful thought



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