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Where is ATP used in Phosphorylation?

Where is ATP used in Phosphorylation?


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In the section describing the Calvin Cycle, under the subheading "Reduction", my textbook states that:

The steps involve utilisation of 2 molecules of ATP for Phosphorylation…

I could not get where is ATP used in Phosphorylation (ATP synthesis by cells)? Please help me to understand.


In biology phosphorylation marks the addition of inorganic phosphate groups to proteins or other organic molecules. The phospho-group usually comes from ATP which is converted into ADP in this process.

In the context of the Calvin Cycle there are two positions where molecules get phosphorylated. The first is the phosphorylation of 3-phosphogylcerate to 1,3-bisphosphoglyerate, the other is the phosphorylation of Ribulose 5-phosphate to Ribulose 1,5-bisphosphate.

See the image (from here):


Production of ATP in Respiration

Summary of respiration to see how much ATP is made from each glucose molecule. ATP is made in two different ways:

  • Some ATP molecules are made directly by the enzymes in glycolysis or the Krebs cycle. This is called substrate level phosphorylation (since ADP is being phosphorylated to form ATP).
  • Most of the ATP molecules are made by the ATP synthase enzyme in the respiratory chain. Since this requires oxygen it is called oxidative phosphorylation. Scientists don’t yet know exactly how many protons are pumped in the respiratory chain, but the current estimates are: 10 protons pumped by NADH 6 by FADH and 4 protons needed by ATP synthase to make one ATP molecule. This means that each NADH can make 2.5 ATPs (10/4) and each FADH can make 1.5 ATPs (6/4).

Two ATP molecules are used at the start of glycolysis to phosphorylate the glucose, and these must be subtracted from the total.

The table below is an “ATP account” for aerobic respiration, and shows that 32 molecules of ATP are made for each molecule of glucose used in aerobic respiration. This is the maximum possible yield often less ATP is made, depending on the circumstances. Anaerobic respiration only produces the 2 molecules of ATP from the first two rows.

Other substances can also be used to make ATP. Glycogen of course is the main source of glucose in humans.

Triglycerides are broken down to fatty acids and glycerol, both of which enter the Krebs Cycle. A typical triglyceride molecule might make 50 acetyl CoA molecules, yielding 500 ATP molecules. Fats are thus a very good energy store, yielding 2.5 times as much ATP per g dry mass as carbohydrates. Proteins are not normally used to make ATP, but in starvation they can be broken down and used in respiration.

They are first broken down to amino acids, which are converted into pyruvate and Krebs Cycle metabolites and then used to make ATP.


What Is Phosphorylation? (with pictures)

Phosphorylation is a chemical process in which a phosphate group (PO4 3- ) is added to a compound. It normally applies to organic chemistry and is crucial to all living organisms. The process is involved in protein synthesis and in the production of adenosine a molecule that stores and supplies energy. It also plays a crucial role in various chemical signaling and regulatory mechanisms within the cell by modifying the structure of various proteins and altering their activities.

Normally, energy is required for the biochemical reactions that involve the addition of a phosphate group to a molecule. Often, this energy comes from ATP molecules. ATP contains three phosphate groups, one of which is easily removed. The removal of this group releases considerable energy, which can be used to enable a phosphorylation reaction in which the phosphate group is added to another molecule — for example, glucose. Thus, phosphate groups can easily be transferred from ATP to other molecules.

These reactions, however, require that ATP and the receptor molecule be brought together so that the transfer can take place. This is achieved by enzymes known as kinases. These are large, complex proteins, which may contain several hundred amino acids. The shape of the enzyme is crucial: the structure of a kinase enzyme is such that both the ATP and the receptor molecule can be accommodated in close proximity to allow the reaction to proceed. An example is glycerol kinase, which facilitates the transfer of a phosphate group from ATP to glycerol this is part of the process that produces phospholipids, which are used in cell membranes.

ATP is itself produced by a well-known phosphorylation process called oxidative phosphorylation, in which a phosphate group is added to adenosine diphosphate (ADP) to produce ATP. The energy for this process ultimately comes from the food we eat, but more specifically the oxidation of glucose. It is a very complex process with many steps, but in simple terms, the energy from glucose is used to form two compounds, known as NADH and FADH2, which provide the energy for the rest of the reaction. The compounds are reducing agents that easily part with electrons, so that they can be oxidized. Phosphate groups are added to ATP molecules using the energy released by the oxidation of NADH and FADH2 this reaction is facilitated by the enzyme ATP synthetase.

Many different kinases are found in both plants and animals. Due to their importance in so many cellular processes, a phosphorylation assay has become a common laboratory procedure. This involves testing samples of cell material to check if protein phosphorylation has taken place and, in some cases, measuring its extent. There are a number of different methods used to check for phosphorylation, including labeling phosphate groups with radioisotopes, the use of antibodies specific to the phosphorylated protein and mass spectrometry.

As of 2011, extra signal-regulated kinases (ERKs) — enzymes that are involved in signaling activities within the cell — are an area of particular interest. ERK phosphorylation plays a role in regulating various cell functions, including mitosis and other processes related to cell division. This process is relevant to some areas of cancer research as it can be activated by carcinogenic substances and by virus infections, leading to uncontrolled cell division and other cancer-related effects. Research into possible cancer treatments that involve inhibiting this process is underway. A phosphorylation assay can be used to test different substances for their effectiveness in this role.


Energy, phosphorylation and ATP (CIE A-level Biology)

A Science teacher by trade, I've also been known to be found teaching Maths and PE! However, strange as it may seem, my real love is designing resources that can be used by other teachers to maximise the experience of the students. I am constantly thinking of new ways to engage a student with a topic and try to implement that in the design of the lessons.

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This lesson outlines the need for energy in living organisms, and describes how ATP is formed by phosphorylation in respiration and photosynthesis. The engaging and detailed PowerPoint and accompanying resources have been primarily designed to cover points 12.1 (a, b, c & e) of the CIE A-level Biology specification but can be used as a revision of topics 1, 4 and 6 as the students knowledge of cell structure, membrane transport and ATP is constantly challenged.

As this is the first lesson in topic 12 (respiration), it has been specifically planned to act as an introduction to this cellular reaction and provides important details about glycolysis, the Krebs cycle and oxidative phosphorylation that will support the students to make significant progress when these stages are covered during individual lessons. Photophosphorylation is also introduced so students are prepared for the light-dependent reaction of photosynthesis in topic 13.

The main focus of the start of the lesson is the demonstration of the need for energy in a variety of reactions that occur in living organisms. Students met ATP in topics 1 and 6, so a spot the errors task is used to check on their recall of the structure and function of this molecule. This will act to remind them that the release of energy from the hydrolysis of ATP can be coupled to energy-driven reactions in the cell such as active transport and a series of exam-style questions are used to challenge them on their knowledge of this form of membrane transport. They will also see how energy is needed for protein synthesis and DNA replication and the maintenance of resting potential, before more questions challenge them to apply their knowledge of cell structure and transport to explain how it is needed during the events at a synapse.

The rest of the lesson focuses on the production of ATP by substrate-level, oxidative and photophosphorylation and the students will learn when ATP is formed by each of these reactions and will see how the electron transport chain in the membranes in the mitochondria and chloroplast is involved

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Topics 12 & 13: Respiration and photosynthesis (CIE A-level Biology)

Respiration and photosynthesis are two of the most commonly-assessed topics in the terminal A-level exams but are often poorly understood by students. These 14 lessons have been intricately planned to contain a wide range of activities that will engage and motivate the students whilst covering the key detail to try to deepen their understanding and includes exam-style questions so they are fully prepared for these assessments. The following specification points in topics 12 and 13 of the CIE A-level Biology course are covered by these lessons: * The need for energy in living organisms * The features of ATP * The synthesis of ATP by substrate-level phosphorylation in glycolysis and the Krebs cycle * The roles of the coenzymes in respiration * The synthesis of ATP through the electron transport chain in the mitochondria and chloroplasts * The relative energy values of carbohydrates, lipids and proteins as respiratory substrates * Determining the respiratory quotient from equations for respiration * The four stages of aerobic respiration * An outline of glycolysis * When oxygen is available, pyruvate is converted into acetyl CoA in the link reaction * The steps of the Krebs cycle * Oxidative phosphorylation * The relationship between the structure and function of the mitochondrion * Distinguish between aerobic and anaerobic respiration in mammalian tissue and in yeast cells * Anaerobic respiration generates a small yield of ATP and builds up an oxygen debt * The products of the light-dependent stage are used in the Calvin cycle * The structure of a chloroplast and the sites of the light-dependent and light-independent stages of photosynthesis * The light-dependent stage of photosynthesis * The three stages of the Calvin cycle * The conversion of Calvin cycle intermediates to carbohydrates, lipids and amino acids * Explain the term limiting factor in relation to photosynthesis * Explain the effects of changes in light intensity, carbon dioxide concentration and temperature on the rate of photosynthesis * Explain how an understanding of limiting factors is used to increase crop yields in protected environments Due to the detail of these lessons, it is estimated that it will take up to 2 months of allocated A-level teaching time to cover the detail included in the slides of these lessons If you would like to sample the quality of the lessons, download the roles of the coenzymes, the Krebs cycle and the products of the Calvin cycle lessons as these have been shared for free

Topic 12: Energy and respiration (CIE A-level Biology)

Topic 12 tends to be the 1st topic to be taught in the second year of the CIE A-level Biology course and these 9 lessons are filled with a wide variety of differentiated tasks that will immediately engage and motivate the students whilst ensuring that the detailed content is covered. It is critical that students understand how energy in the form of ATP is produced by aerobic and anaerobic respiration and are able to describe the energy-driven reactions like active transport that need this input. For this reason, the lessons contain multiple understanding checks which assess the students on their current knowledge as well as checking on their ability to link to previously-covered topics. The following specification points in topic 12 of the CIE A-level Biology specification are covered in these lessons: * The need for energy in living organisms * The features of ATP that make this molecule suitable as the energy currency * Substrate-level phosphorylation in glycolysis and the Krebs cycle * The role of the coenzymes in respiration * The involvement of the electron transport chain that's found in the mitochondria and chloroplast membranes in the production of ATP * The four stages of aerobic respiration * Glycolysis * The link reaction * The Krebs cycle * Oxidative phosphorylation * The structure of the mitochondrion * The differences between aerobic and anaerobic respiration * The oxygen debt If you would like to sample the quality of these lessons, then download the roles of the coenzymes and the Krebs cycle lessons as these have been uploaded for free


29 3.7 ATP: Adenosine Triphosphate

Almost all chemical reactions in human cells require energy. 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 1 ), 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.

Figure 1. ATP is the cell’s primary energy currency. It has an adenosine backbone with three phosphate groups attached.

As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure 1). 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:

ATP + H2O → ADP + Pi + free energy

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:

ADP + Pi + free energy → ATP + H2O

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + P i , and the free energy released during this process is lost as heat. Cells can harness the energy released during ATP hydrolysis by using energy coupling, where the process of ATP hydrolysis is linked to other processes in the cell. 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 2 ). 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 (a change in the shape of the protein.) 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 Figure 2. The sodium-potassium pump is an example of energy coupling. The energy derived from exergonic ATP hydrolysis pumps sodium and potassium ions across the cell membrane.

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 phosphorylze 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.


What is Substrate Level Phosphorylation?

Unlike oxidative phosphorylation, substrate-level phosphorylation does not couple phosphorylation with oxidation rather, the free energy required for phosphorylation is provided by the chemical energy released when a higher energy substrate is converted into a lower energy product. Substrate-level phosphorylation occurs in the cytoplasm of cells (glycolysis) and in the mitochondria (Krebs cycle). It can occur under both aerobic and anaerobic conditions and provides a quicker, but less efficient source of ATP compared to oxidative phosphorylation.

Diagram featuing the ATP-ADP Cycle in substrate level phosphorylation. Click for larger image.


Synopsis

The impact of oncogene activation and hypoxia on energy metabolism is analyzed by integrating quantitative measurements into a redox-balanced metabolic flux model. Glutamine-driven oxidative phosphorylation is found to be a major ATP source even in oncogene-expressing or hypoxic cells.

  • The integration of oxygen uptake measurements and LC-MS-based isotope tracer analyses in a redox-balanced metabolic flux model enabled quantitative determination of energy generation pathways in cultured cells.
  • In transformed mammalian cells, even in hypoxia (1% oxygen), oxidative phosphorylation produces the majority of ATP.
  • The oncogene Ras simultaneously increases glycolysis and decreases oxidative phosphorylation, thus resulting in no net increase in ATP production.
  • Glutamine is the major source of high-energy electrons for oxidative phosphorylation, especially upon Ras activation.

The Proton Gradient

The proton gradient is critical to the chemiosmotic coupling of electron transport and ATP synthesis. As electrons are moved along the respiratory chain, protons are pumped across the inner membrane, from the matrix into the intermembrane space this results in an electrochemical proton gradient. The force of this gradient drives protons back across the inner membrane into the matrix, through the F0 subunit of the ATP synthase, which results in activation of the F1 subunits and synthesis of ATP. On average, for each NADH, approximately 3 ATPs are synthesized, and for each FADH2, approximately 2 ATPs are synthesized. The lower ATP yield for FADH2 results from the smaller proton gradient generated when electrons are donated from FADH2. In this case, the electrons are donated to succinate dehydrogenase, which does not pump protons when electrons enter the ETC, thereby bypassing NADH dehydrogenase and the protons it would pump across the membrane.


Section Summary

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.