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How, on a physical level, does ATP confer energy?

How, on a physical level, does ATP confer energy?


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When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction


ATP + H2O → ADP + Pi ΔG˚ = −30.5 kJ/mol (−7.3 kcal/mol)


that 30.5 kJ/ mol is conferred by ATP molecules physically bumping around the reactants X and Y, the kinetic energy of the above reaction being what does it?

I mean, is the energy coin of ATP conferred to reactions by molecular collisions, or is it an electric field effect in the spatial geometry the way the ATP molecule tends to break apart?


Usually in biology (and being ATP, it most probably is biology), it's one of two things.

The gamma-phosphate (the third one, the one farthest from the adenosine) is very unstable, meaning the phosphoanhydride bond is easy to break. The cell "allows" it to break, but only at the cost of moving the phosphate to some other molecule, such as a serine or glycerol or fructose or whatever. This phosphorylation creates a bond with lower energy than the phosphoanhydride, and so is overall favored. Imagine the personification: the gamma phosphate hates being attached to anything, but hates being attached to an ADP the most.

Alternatively, if ATP hydrolysis is coupled via an enzyme, it is usually done through transient storage of the energy is protein conformation. An enzyme binds ATP, which makes the protein structure "bend" or conform around the ATP. This puts loads of strain (energy = A) on the protein which is offset by the stabilization of binding the ATP (energy = B). This strain can make an enzymatic surface open up on the protein which itself takes a lot of energy to make (energy = C). The surface can catalyze some reaction (X+Y->Z in your example) that costs some energy (energy = D). The completion of that reaction alters the enzyme's catalytic site to something new and higher energy (energy = E), which can be alleviated by cleavage of the ATP (-7.3 kcal/mol). Alas, ADP and P do not fit well into that site of the enzyme, so they float out, restoring that original ATP-binding surface to it's original state. Provided A>B>C>D>E>-7.3, the cycle will continue until the ATP is exhausted or you have no more Z to make.

Typing "enzyme catalysis cycle ATP" gives a few examples. Here's a few:
DNA gyrase
Actin-myosin cycle


Chemical reactions are based on collisions, but only those with the right amount of energy and the proper orientation give rise to them. If just one of these parameters deviates enough, the reactants will just bounce off. Within a cell, collisions between reactants are likely to happen, as one molecule is likely to collide with its enzyme within a second,[1, p. 6] but not in the right orientations. Enzymes through a moderate affinity to the reactants, place them in the right orientations.

Now, where does the energy come from? The molecular "storm" of water molecules around does have quite a bit of kinetic energy, but as collisions with them come from all directions, they usually cancel each other. When ATP hydrolyzes, about 0.36 eV of energy are released (5.8·10^-20 J),[2] and the molecules around it vibrate. I suppose that this is because once the chemical bond is broken, the repulsive force between ADP and phosphate is very strong at such a close distance, violently pushing whatever molecule they find on their way. The amount of energy released has 14 times the average kinetic energy of the molecules around it, so it is the equivalent of locally heating a molecule to 3,900 ºC.[2] Naturally, if the hydrolysis happens within an enzyme, it vibrates like crazy and induces a conformational change. If the enzyme has reactants bound to it, they are likely to collide with the right amount of energy.

Interestingly, the molecular storm is powerful enough at 150 ºC to break down ATP. This is why scientists do not expect to find any hyperthermophile living at such warm temperatures. Currently, the archeon Pyrolobus fumarii holds the record, being able to survive up to 122 ºC, but its optimal temperature is 113 ºC and "freezes to death" at temperatures lower than 90 ºC [Wikipedia].

[1] Goodsell, D. "The Machinery of Life". 2nd edition. Springer. 2009.

[2] Hoffmann, P. "Life's Ratchet: How molecular machines extract order from chaos" Basic Books. 2012.


Researching quantum constituents in ADP energy transfer gives this page which describes the ATP reaction with some geometry, aside from electrical/proton transfer of the many energy-expensive reactions like of cells like F-actin filament molecule treadmill lengthening process:

https://pubs.rsc.org/-/content/articlelanding/2016/cp/c6cp01364c/unauth#!divAbstract

This page describes F-actin length and reconstitution using ADP: https://m.phys.org/news/2014-09-scientists-uncover-clues-atp-mystery.html

Video actin treadmilling simulation: https://m.youtube.com/watch?v=VVgXDW_8O4U

Two parallel F-actin strands must rotate 166 degrees join correctly together. This creates the double helix structure of the microfilaments found in the cytoskeleton. ATP is well described on wiki in at that level.

It seems to imply that there is a "static/magnetic" electrical charge differential surrounding the actin molecules and transferred in the minuscule H2O medium which attracts rotates and bonds them.

The electrical differential of Actin is described as heterogenous with surrounding salt bridges and protonationdeprotonation, by this general research: https://www.google.com/amp/s/www.researchgate.net/figure/The-charge-distribution-on-the-surface-of-F-actin-is-highly-heterogeneous-leading-to_fig5_7090136/amp

I'll try to synthesise some quantim articles of that kind for a coherant sequence of events, ill have to pause because im writing on a phone.

Some info on the H2O alignment involving a different view of ATP is here : https://www.google.com/amp/s/phys.org/news/2017-03-atp-hydrolysis-energy-large-scale-hybrid.amp


How Is Energy Released From ATP?

Energy is released from ATP by the breaking of the phosphate bond, states the University of Illinois at Chicago. Adenosine triphosphate, or ATP, consists of a sugar called ribose, the molecule adenine and three phosphate groups. During the hydrolysis of ATP, the last phosphate group is transferred to another molecule, thus breaking the phosphate bond. This reaction causes energy to be released to power other activities within the cell.

ATP is made by breaking down glucose, as stated by Dr. Dawn Tamarkin at Springfield Technical Community College. By breaking down the bonds in glucose in the presence of oxygen, energy is produced in order to add a phosphate group to ADP to form ATP. In this way, 38 ATPs are formed. This process is called cellular respiration.

The energy of the ATP molecule lies in the bonds between the phosphate groups, or pyrophosphate bonds, states Dr. Mike Farabee of Estrella Mountain Community College. The bond between the second phosphate and last phosphate groups yields the most energy, about seven kilocalories per mole. When this bond is broken, adenosine diphosphate, or ADP, is formed.

Because ATP is constantly being used, it needs to be replenished. A single muscle cell, probably one of the greatest users of ATP, uses and replenishes 10,000,000 ATP molecules per second, according to the University of Illinois at Chicago.


Role of ATP

#ATP# is a carrier of energy, and it keeps it when it is not needed and releasing it when it is.

Explanation:

When energy is released, #ATP# loses one of its phosphate groups and turns to #ADP# (ADENOSINE DI-PHOSPHATE). #ADP# is present in cells and has two phosphate groups firmly attached. The energy from respiration is used to form another phosphate group to each molecule to form #ATP# .

#ATP- ADP + "phosphate" + "energy"# , and here is an image for this chemical reaction is given. Observe how in #ADP# , the #gamma# - #PO_4# group is removed and results in release of tremendous energy.

Answer:

ADP provides one of the building blocks for ATP, the source of cellular energy.

Explanation:

Adenosine diphosphate could be compared to a partially-charged battery. Both ATP (adenosine triphosphate) and ADP (adenosine diphosphate) consist of the nucleotide adenine, a sugar called ribose, and either two or three phosphate groups. The bonds holding the three phosphate groups together require great energy to build, and when these bonds are broken, a great amount of energy is released.

When ATP is used to provide energy for cellular activities, the bond between the second and the third phosphate groups is broken and energy is released. Through the process of cellular respiration, glucose provides the energy to rebuild ADP and a phosphate group into ATP.


How Exercise Works

For your muscles -- in fact, for every cell in your body -- the source of energy that keeps everything going is called ATP. Adenosine triphosphate (ATP) is the biochemical way to store and use energy.

The entire reaction that turns ATP into energy is a bit complicated, but here is a good summary:

  • Chemically, ATP is an adenine nucleotide bound to three phosphates.
  • There is a lot of energy stored in the bond between the second and third phosphate groups that can be used to fuel chemical reactions.
  • When a cell needs energy, it breaks this bond to form adenosine diphosphate (ADP) and a free phosphate molecule.
  • In some instances, the second phosphate group can also be broken to form adenosine monophosphate (AMP).
  • When the cell has excess energy, it stores this energy by forming ATP from ADP and phosphate.

ATP is required for the biochemical reactions involved in any muscle contraction. As the work of the muscle increases, more and more ATP gets consumed and must be replaced in order for the muscle to keep moving.

Because ATP is so important, the body has several different systems to create ATP. These systems work together in phases. The interesting thing is that different forms of exercise use different systems, so a sprinter is getting ATP in a completely different way from a marathon runner!

ATP comes from three different biochemical systems in the muscle, in this order:


DNA and RNA Synthesis

When cells divide and undergo the process of cytokinesis, ATP is used to grow the size and energy content of the new daughter cell. The ATP is used to trigger DNA synthesis, where the daughter cell receives a complete copy of the DNA from the parent cell.

ATP is a key component in the DNA and RNA synthesis process as one of the key building blocks used by RNA polymerase to form the RNA molecules. A different form of ATP is converted to a deoxyribonucleotide, known as dATP, so that it can be incorporated into DNA molecules for DNA synthesis.


Meat and Fish

One type of food that provides a source of ATP is meat and fish. These foods contain several animal cells, with each cell containing preformed ATP. The nutrients found within meats and fish may also provide a source of ATP within your body. Upon consumption, the fatty acids and proteins in meats and fish are digested and absorbed. If your body requires an immediate source of energy, these nutrients are used to make ATP within your own cells, helping to fuel your body. When selecting meats and fish as a source of ATP, the Harvard School of Public Health recommends selecting poultry and fresh fish and avoiding fatty cuts of red meat that contain high levels of saturated fat.

Nuts also provide a source of ATP for your body, as each cell within the nut contains a reserve of ATP used as cellular fuel. In addition to their ATP content, nuts provide energy to your body through their fat, carbohydrate and protein content, which can be converted into ATP following digestion. Nuts also contain dietary fiber, plant material that passes through your gastrointestinal tract unchanged. Consuming fiber each day helps promote a healthy digestive tract, allowing your intestines to work efficiently to absorb the nutrients and ATP from the food you eat. The Linus Pauling Institute at Oregon State University recommends consuming five, 1-oz. servings of nuts weekly as a healthy source of several nutrients, including ATP.


Aerobic Respiration

There are four stages of aerobic cellular respiration that occur to produce ATP (the energy cells need to do their work):

Stage 1 Glycolysis (also known as the breakdown of glucose)

This occurs in the cytoplasm and involves a series of chain reactions known as glycolysis to convert each molecule of glucose (a six-carbon molecule) into two smaller units of pyruvate (a three-carbon molecule). During the formation of pyruvate, two types of activated carrier molecules (small diffusible molecules in cells that contain energy rich covalent bonds) are produced, these are ATP and NADH (reduced nicotinamide adenine dinucleotide).This stage produces 4 molecules of ATP and 2 molecules of NADH from glucose but uses 2 molecules of ATP to get there,- so it actually results in 2 ATP + 2 NADH and pyruvate. The pyruvate then passes into the mitochondria.

Stage 2 The Link reaction

This links glycolysis with stage 3 the Citric acid/ Krebs cycle, which is explained below. At this point, one carbon dioxide molecule and one hydrogen molecule are removed from the pyruvate (called oxidative decarboxylation) to produce an acetyl group, which joins to an enzyme called CoA (Coenzyme A) to form acetyl-CoA, which is then ready to be used in the Citric acid/Krebs cycle. Acetyl-CoA is essential for the next stage.

Stage 3 The Citric Acid/Krebs Cycle

Taking place in the mitochondria, the acetyl-CoA (which is a two-carbon molecule) combines with oxaloacetate (a four-carbon molecule) to form citrate (a six-carbon molecule). The citrate molecule is then gradually oxidized, allowing the energy of this oxidation to be used to produce energy-rich activated carrier molecules. The chain of eight reactions forms a cycle because, at the end, the oxaloacetate is regenerated and can enter a new turn of the cycle. The cycle provides precursors including certain amino acids as well as the reducing agent NADH that are used in numerous biochemical reactions.

Each turn of the cycle produces two molecules of carbon dioxide, three molecules of NADH, one molecule of GTP (guanosine triphosphate) and one molecule of FADH2 (reduced flavin adenine dinucleotide).

Because two acetyl-CoA molecules are produced from each glucose molecule utilised, two cycles are required per glucose molecule.

Stage 4 Electron Transport Chain

In this final stage, the electron carriers NADH and FADH2, which gained electrons when they were oxidizing other molecules, transfer these electrons to the electron transport chain. This is found in the inner membrane of the mitochondria. This process requires oxygen and involves moving these electrons through a series of electron transporters that undergo redox reactions (reactions where both oxidation and reduction take place). This causes hydrogen ions to accumulate in the intermembrane space.

A concentration gradient then forms where hydrogen ions diffuse out of this space by passing through ATP synthase. The current of hydrogen ions powers the catalytic conversion of ATP synthase, which, in turn, phosphorylates ADP (adds a phosphate group) therefore producing ATP. The endpoint of the chain occurs when the electrons reduce molecular oxygen, which results in the production of water.

Although there is a theoretical yield of 38 ATP from the breakdown of one glucose molecule, realistically it is thought 30-32 ATP molecules are actually generated.

This process of aerobic respiration takes place when the body requires sufficient energy just to live, as well as to carry out everyday activities and perform cardio exercise. While this process yields more energy than the anaerobic systems, it is also less efficient and can only be used during lower-intensity activities.

So, if you have SLOW and STEADY energy requirements, your NET ENERGY PRODUCTION from aerobic respiration equals 30-32 Molecules of ATP.

Glucose + Oxygen → Carbon dioxide + Water + Energy (as 30-32 ATP)

The body releases carbon dioxide and water in this process. This will theoretically burn the highest number of calories.

Under other physiological conditions the body can still acquire its energy in other ways:

There are further energy processes the body uses to create ATP, they depend on the speed at which the energy is required and whether they have access to oxygen or not.

Anaerobic Respiration

Human muscle can respire anaerobically, a process that does not require oxygen. The process is relatively inefficient as it has a net energy production of 2 molecules of ATP.

This is effective for vigorous exercise of between 1-3 minutes duration, such as short sprints. If the intense exercise requires more energy than can be supplied by the oxygen available, your body will partially burn glucose without oxygen (anaerobic). Without the presence of oxygen, the electron transport chain cannot work. Therefore, the usual number of ATP molecules cannot be made. The anaerobic pathway uses pyruvate, the final product from the glycolysis stage. Pyruvate is reduced to lactic acid by NADH, leaving NAD + after the reduction. This reaction is catalysed by an enzyme (lactate dehydrogenase) and leads to the recycling of NAD + . This then allows the process of glycolysis to continue.

This glycolysis pathway yields 2 molecules ATP, which can be used for energy to drive muscle contraction. Anaerobic glycolysis occurs faster than aerobic respiration as less energy is produced for every glucose molecule broken down, so more has to be broken down at a faster rate to meet demands.

Lactic acid (the by-product from anaerobic respiration) builds up in the muscles causing the “burn” felt during strenuous activity. If more than a few minutes of this activity are used to generate ATP, lactic acid acidity increases, causing painful cramps. The extra oxygen you breath in following intensive exercise, reacts with the lactic acid in your muscles, breaking it down to make carbon dioxide and water.

So, summing up: Exercises that are performed at maximum rates for between 1 and 3 minutes depend heavily on anaerobic respiration for ATP energy. Also, in some performances, such as running 1500 meters or a mile, the lactic acid system is used predominately for the “kick” at the end of a race.

Therefore, if you are doing VIGOUROUS EXERCISE for 1-3 minutes, there will be NO TISSUE OXYGEN AVAILABLE so you will see a NET ENERGY PRODUCTION from anaerobic respiration equal to 2 molecules of ATP.

Beta Oxidation/Gluconeogenesis or Fat Burning (Aerobic Lipolysis)

A fat molecule consists of a glycerol backbone and three fatty acid tails. They are called triglycerides. In the body, they are stored primarily in fat cells called adipocytes making up the adipose tissue. To obtain energy from fat, the triglyceride molecules are broken down into fatty acids in a process called ‘Lipolysis’ occurring in the cytoplasm. These fatty acids are oxidized into acetyl- CoA, which is used in the Citric acid/Krebs cycle. Because one triglyceride molecule yields three fatty acid molecules with 16 or more carbons in each one, fat molecules yield more energy than carbohydrates and are an important source of energy for the human body (over 100 molecules of ATP generated per molecule of fatty acid). Therefore, when glucose levels are low, triglycerides can be converted into acetyl-CoA molecules and used to generate ATP through aerobic respiration.

This need arises after any period of not eating even with a normal overnight fast, mobilization of fat occurs, so that by the morning most of the acetyl-CoA entering the Citric acid/Krebs cycle comes from fatty acids rather than from glucose. Following a meal, however, most of the acetyl-CoA entering the Citric acid/Krebs cycle comes from glucose from food, with any excess glucose being used to replenish depleted glycogen stores or to synthesize fats.

This is a SLOW, NOT IMMEDIATE ENERGY SOURCE but has a NET ENERGY PRODUCTION of over 100 molecules of ATP.

ATP Phosphocreatine (ATP-PC)

This energy system consists of ATP (all muscle cells have a little ATP in them) and phosphocreatine (PC), which provide immediate energy from the breakdown of these high energy substrates.

Firstly, ATP that is stored in the myosin cross-bridges (within the muscle) gets broken down producing adenosine diphosphate (ADP) and one single phosphate molecule. Then, an enzyme, known as creatine kinase, breaks down phosphocreatine (PC) to creatine and a phosphate molecule. This breakdown of phosphocreatine (PC) releases energy, which allows the adenosine diphosphate (ADP) and phosphate molecule to re-join forming more ATP. This newly formed ATP can then be broken down to release energy to fuel activity. This will continue until creatine phosphate stores are depleted.

Short, sharp explosive bursts of exercise (10-30 secs) use this system. It doesn’t require oxygen but is very limited to short periods of explosive exercise, such as a sprint or weight/power lifting. This is why creatine supplementation helps this sort of exercise, ensuring there is adequate creatine phosphate to provide those required phosphates. The ATP-CP system usually recovers 100% in 3 mins so, the recommended rest time in between high intensity training is 3 minutes.

In short, for sharp explosive bursts of exercise needing FAST, IMMEDIATE energy this system produces COPIUS AMOUNTS OF ATP until the creatine phosphate in muscles runs out.

Different forms of exercise use different systems to produce ATP

  • For short distance sprinters/ weight lifters the energy system used would be ATP-PC as its fast and only few seconds
  • During intense, intermittent exercise and throughout prolonged physical activity the energy system used would typically be via the glycogen route (fat burning /no oxygen) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019055/
  • In endurance events like marathon running or rowing etc., which lasts for unlimited time would use the energy process of aerobic respiration.

Role of gut bacteria in energy regulation

Gut bacteria plays an important role in nutrient and energy extraction and energy regulation. The bacteria makes a multitude of small molecules (known as metabolites) that can act as signals that can modulate appetite, energy uptake, storage and expenditure, something which is explored in the review article Gut Microbiota-Dependent Modulation of Energy Metabolism.

Gut bacteria influences the bioavailability of polysaccharides and how this occurs is unclear but it is an increasing area of research, with this 2016 paper, on the causality of small and large intestinal microbiota in weight regulation and insulin resistance, investigating the subject at length.

Side effects with low energy levels

Not properly managing your energy levels can result in both physical and cognitive functions being affected.

Physical signs can include: reduced stamina, reduced strength and less ability to recover from exercise.

Performance related effects can include: loss of focus, slow reaction times, low mood, poor working memory, poor decision making and decreased reaction times.


1. Phosphagen System

During short-term, intense activities, a large amount of power needs to be produced by the muscles, creating a high demand for ATP. The phosphagen system (also called the ATP-CP system) is the quickest way to resynthesize ATP (Robergs & Roberts 1997).

Creatine phosphate (CP), which is stored in skeletal muscles, donates a phosphate to ADP to produce ATP: ADP + CP = ATP + C. No carbohydrate or fat is used in this process the regeneration of ATP comes solely from stored CP. Since this process does not need oxygen to resynthesize ATP, it is anaerobic, or oxygen-independent. As the fastest way to resynthesize ATP, the phosphagen system is the predominant metabolic energy system used for all-out exercise lasting up to about 10 seconds. However, since there is a limited amount of stored CP and ATP in skeletal muscles, fatigue occurs rapidly.


When you consume foods, your intestine absorbs the nutrient molecules into the bloodstream. Cells then take up these nutrients and chemically burn them to liberate energy. For instance, one of the most important sources of cellular energy is glucose, a molecule that comes from starch and many dietary sugars. As the cells break down glucose, they produce the waste products carbon dioxide and water. They use the energy liberated from breaking down a single molecule of glucose to make approximately 30 molecules of ATP.

Once a cell has made ATP, it can use the ATP to fulfill any of its energy needs. Cells need energy to make large molecules, like hormones. Muscle cells use ATP to produce movement. As a cell makes a hormone molecule, it breaks down molecules of ATP and uses the energy to make new bonds between smaller molecules in order to produce a larger one, explain Drs. Garrett and Grisham. When a muscle cell contracts, it uses large quantities of ATP to fuel the contraction.


How, on a physical level, does ATP confer energy? - Biology


ATP: The Perfect Energy
Currency for the Cell

Jerry Bergman, Ph.D.
© 1999 by Creation Research Society. All rights reserved. Used by permission.
This article first appeared in Vol. 36, No. 1 of the Creation Research Society Quarterly ,
a peer-reviewed journal published by the Creation Research Society.

Abstract

The major energy currency molecule of the cell, ATP, is evaluated in the context of creationism. This complex molecule is critical for all life from the simplest to the most complex. It is only one of millions of enormously intricate nanomachines that needs to have been designed in order for life to exist on earth. This motor is an excellent example of irreducible complexity because it is necessary in its entirety in order for even the simplest form of life to survive.

Introduction

Fig. 1. Views of ATP and related structures.

A critically important macromolecule—arguably &ldquosecond in importance only to DNA&rdquo—is ATP . ATP is a complex nanomachine that serves as the primary energy currency of the cell (Trefil, 1992, p.93). A nanomachine is a complex precision microscopic-sized machine that fits the standard definition of a machine. ATP is the &ldquomost widely distributed high-energy compound within the human body&rdquo (Ritter, 1996, p. 301). This ubiquitous molecule is &ldquoused to build complex molecules, contract muscles, generate electricity in nerves, and light fireflies. All fuel sources of Nature, all foodstuffs of living things, produce ATP, which in turn powers virtually every activity of the cell and organism. Imagine the metabolic confusion if this were not so: Each of the diverse foodstuffs would generate different energy currencies and each of the great variety of cellular functions would have to trade in its unique currency&rdquo (Kornberg, 1989, p. 62).

ATP is an abbreviation for adenosine triphosphate , a complex molecule that contains the nucleoside adenosine and a tail consisting of three phosphates. (See Figure 1 for a simple structural formula and a space filled model of ATP.) As far as known, all organisms from the simplest bacteria to humans use ATP as their primary energy currency. The energy level it carries is just the right amount for most biological reactions. Nutrients contain energy in low-energy covalent bonds which are not very useful to do most of kinds of work in the cells.

These low energy bonds must be translated to high energy bonds, and this is a role of ATP. A steady supply of ATP is so critical that a poison which attacks any of the proteins used in ATP production kills the organism in minutes. Certain cyanide compounds, for example, are poisonous because they bind to the copper atom in cytochrome oxidase. This binding blocks the electron transport system in the mitochondria where ATP manufacture occurs (Goodsell, 1996, p.74).

How ATP Transfers Energy

Energy is usually liberated from the ATP molecule to do work in the cell by a reaction that removes one of the phosphate-oxygen groups, leaving adenosine di phosphate (ADP). When the ATP converts to ADP, the ATP is said to be spent . Then the ADP is usually immediately recycled in the mitochondria where it is recharged and comes out again as ATP. In the words of Trefil (1992, p. 93) &ldquohooking and unhooking that last phosphate [on ATP] is what keeps the whole world operating.&rdquo

The enormous amount of activity that occurs inside each of the approximately one hundred trillion human cells is shown by the fact that at any instant each cell contains about one billion ATP molecules. This amount is sufficient for that cell&rsquos needs for only a few minutes and must be rapidly recycled. Given a hundred trillion cells in the average male, about 10 23 or one sextillion ATP molecules normally exist in the body. For each ATP &ldquothe terminal phosphate is added and removed 3 times each minute&rdquo (Kornberg, 1989, p. 65).

The total human body content of ATP is only about 50 grams, which must be constantly recycled every day. The ultimate source of energy for constructing ATP is food ATP is simply the carrier and regulation-storage unit of energy. The average daily intake of 2,500 food calories translates into a turnover of a whopping 180 kg (400 lbs) of ATP (Kornberg, 1989, p. 65).

The Structure of ATP

ATP contains the purine base adenine and the sugar ribose which together form the nucleoside adenosine . The basic building blocks used to construct ATP are carbon, hydrogen, nitrogen, oxygen, and phosphorus which are assembled in a complex that contains the number of subatomic parts equivalent to over 500 hydrogen atoms. One phosphate ester bond and two phosphate anhydride bonds hold the three phosphates (PO 4 ) and the ribose together. The construction also contains a b-N glycoside bond holding the ribose and the adenine together.

Fig. 2. The two-dimensional stick model of the adenosine phosphate family of molecules, showing the atom and bond arrangement.

Phosphates are well-known high-energy molecules, meaning that comparatively high levels of energy are released when the phosphate groups are removed. Actually, the high energy content is not the result of simply the phosphate bond but the total interaction of all the atoms within the ATP molecule.

Because the amount of energy released when the phosphate bond is broken is very close to that needed by the typical biological reaction, little energy is wasted. Generally, ATP is connected to another reaction—a process called coupling which means the two reactions occur at the same time and at the same place, usually utilizing the same enzyme complex. Release of phosphate from ATP is exothermic (a reaction that gives off heat) and the reaction it is connected to is endothermic (requires energy input in order to occur). The terminal phosphate group is then transferred by hydrolysis to another compound, a process called phosphorylation , producing ADP, phosphate (P i ) and energy.

The self-regulation system of ATP has been described as follows:

The high-energy bonds of ATP are actually rather unstable bonds. Because they are unstable, the energy of ATP is readily released when ATP is hydrolyzed in cellular reactions. Note that ATP is an energy-coupling agent and not a fuel. It is not a storehouse of energy set aside for some future need. Rather it is produced by one set of reactions and is almost immediately consumed by another. ATP is formed as it is needed, primarily by oxidative processes in the mitochondria. Oxygen is not consumed unless ADP and a phosphate molecule are available, and these do not become available until ATP is hydrolyzed by some energy-consuming process. Energy metabolism is therefore mostly self-regulating (Hickman, Roberts, and Larson, 1997, p.43). [Italics mine]

ATP is not excessively unstable, but it is designed so that its hydrolysis is slow in the absence of a catalyst. This insures that its stored energy is &ldquoreleased only in the presence of the appropriate enzyme&rdquo (McMurry and Castellion, 1996, p. 601).

The Function of ATP

The ATP is used for many cell functions including transport work moving substances across cell membranes. It is also used for mechanical work , supplying the energy needed for muscle contraction. It supplies energy not only to heart muscle (for blood circulation) and skeletal muscle (such as for gross body movement), but also to the chromosomes and flagella to enable them to carry out their many functions. A major role of ATP is in chemical work , supplying the needed energy to synthesize the multi-thousands of types of macromolecules that the cell needs to exist.

ATP is also used as an on-off switch both to control chemical reactions and to send messages. The shape of the protein chains that produce the building blocks and other structures used in life is mostly determined by weak chemical bonds that are easily broken and remade. These chains can shorten, lengthen, and change shape in response to the input or withdrawal of energy. The changes in the chains alter the shape of the protein and can also alter its function or cause it to become either active or inactive.

The ATP molecule can bond to one part of a protein molecule, causing another part of the same molecule to slide or move slightly which causes it to change its conformation, inactivating the molecule. Subsequent removal of ATP causes the protein to return to its original shape, and thus it is again functional. The cycle can be repeated until the molecule is recycled, effectively serving as an on and off switch (Hoagland and Dodson, 1995, p.104). Both adding a phosphorus (phosphorylation) and removing a phosphorus from a protein (dephosphorylation) can serve as either an on or an off switch.

How is ATP Produced?

ATP is manufactured as a result of several cell processes including fermentation, respiration and photosynthesis. Most commonly the cells use ADP as a precursor molecule and then add a phosphorus to it. In eukaryotes this can occur either in the soluble portion of the cytoplasm (cytosol) or in special energy-producing structures called mitochondria. Charging ADP to form ATP in the mitochondria is called chemiosmotic phosphorylation . This process occurs in specially constructed chambers located in the mitochondrion&rsquos inner membranes.

Fig. 3. An outline of the ATP-synthase macromolecule showing its subunits and nanomachine traits. ATP-synthase converts ADP into ATP, a process called charging. Shown behind ATP-synthase is the membrane in which the ATP-synthase is mounted. For the ATP that is charged in the mitochondria, ATP-synthase is located in the inner membrane.

The mitochondrion itself functions to produce an electrical chemical gradient—somewhat like a battery—by accumulating hydrogen ions in the space between the inner and outer membrane. This energy comes from the estimated 10,000 enzyme chains in the membranous sacks on the mitochondrial walls. Most of the food energy for most organisms is produced by the electron transport chain. Cellular oxidation in the Krebs cycle causes an electron build-up that is used to push H + ions outward across the inner mitochondrial membrane (Hickman et al., 1997, p. 71).

As the charge builds up, it provides an electrical potential that releases its energy by causing a flow of hydrogen ions across the inner membrane into the inner chamber. The energy causes an enzyme to be attached to ADP which catalyzes the addition of a third phosphorus to form ATP. Plants can also produce ATP in this manner in their mitochondria but plants can also produce ATP by using the energy of sunlight in chloroplasts as discussed later. In the case of eukaryotic animals the energy comes from food which is converted to pyruvate and then to acetyl coenzyme A (acetyl CoA). Acetyl CoA then enters the Krebs cycle which releases energy that results in the conversion of ADP back into ATP.

How does this potential difference serve to reattach the phosphates on ADP molecules? The more protons there are in an area, the more they repel each other. When the repulsion reaches a certain level, the hydrogens ions are forced out of a revolving-door-like structure mounted on the inner mitochondria membrane called ATP synthase complexes. This enzyme functions to reattach the phosphates to the ADP molecules, again forming ATP.

The ATP synthase revolving door resembles a molecular water wheel that harnesses the flow of hydrogen ions in order to build ATP molecules. Each revolution of the wheel requires the energy of about nine hydrogen ions returning into the mitochondrial inner chamber (Goodsell, 1996, p.74). Located on the ATP synthase are three active sites, each of which converts ADP to ATP with every turn of the wheel. Under maximum conditions, the ATP synthase wheel turns at a rate of up to 200 revolutions per second, producing 600 ATPs during that second.

ATP is used in conjunction with enzymes to cause certain molecules to bond together. The correct molecule first docks in the active site of the enzyme along with an ATP molecule. The enzyme then catalyzes the transfer of one of the ATP phosphates to the molecule, thereby transferring to that molecule the energy stored in the ATP molecule. Next a second molecule docks nearby at a second active site on the enzyme. The phosphate is then transferred to it, providing the energy needed to bond the two molecules now attached to the enzyme. Once they are bonded, the new molecule is released. This operation is similar to using a mechanical jig to properly position two pieces of metal which are then welded together. Once welded, they are released as a unit and the process then can begin again.

A Double Energy Packet

Although ATP contains the amount of energy necessary for most reactions, at times more energy is required. The solution is for ATP to release two phosphates instead of one, producing an adenosine monophosphate (AMP) plus a chain of two phosphates called a pyrophosphate . How adenosine monophosphate is built up into ATP again illustrates the precision and the complexity of the cell energy system. The enzymes used in glycolysis, the citric acid cycle, and the electron transport system, are all so precise that they will replace only a single phosphate. They cannot add two new phosphates to an AMP molecule to form ATP.

The solution is an intricate enzyme called adenylate kinase which transfers a single phosphate from an ATP to the AMP, producing two ADP molecules. The two ADP molecules can then enter the normal Krebs cycle designed to convert ADP into ATP. Adenylate kinase requires an atom of magnesium—and this is one of the reasons why sufficient dietary magnesium is important.

Adenylate kinase is a highly organized but compact enzyme with its active site located deep within the molecule. The deep active site is required because the reactions it catalyzes are sensitive to water. If water molecules lodged between the ATP and the AMP, then the phosphate might break ATP into ADP and a free phosphate instead of transferring a phosphate from ATP to AMP to form ADP.

To prevent this, adenylate kinase is designed so that the active site is at the end of a channel deep in the structure which closes around AMP and ATP, shielding the reaction from water. Many other enzymes that use ATP rely on this system to shelter their active site to prevent inappropriate reactions from occurring. This system ensures that the only waste that occurs is the normal wear, tear, repair, and replacement of the cell&rsquos organelles.

Pyrophosphates and pyrophosphoric acid, both inorganic forms of phosphorus, must also be broken down so they can be recycled. This phosphate breakdown is accomplished by the inorganic enzyme pyrophosphatase which splits the pyrophosphate to form two free phosphates that can be used to charge ATP (Goodsell, 1996, p.79). This system is so amazingly efficient that it produces virtually no waste, which is astounding considering its enormously detailed structure. Goodsell (1996, p. 79) adds that &ldquoour energy-producing machinery is designed for the production of ATP: quickly, efficiently, and in large quantity.&rdquo

The main energy carrier the body uses is ATP, but other energized nucleotides are also utilized such as thymine, guanine, uracil, and cytosine for making RNA and DNA. The Krebs cycle charges only ADP, but the energy contained in ATP can be transferred to one of the other nucleosides by means of an enzyme called nucleoside diphosphate kinase . This enzyme transfers the phosphate from a nucleoside triphosphate, commonly ATP, to a nucleoside diphosphate such as guanosine diphosphate (GDP) to form guanosine triphosphate (GTP).

The nucleoside diphosphate kinase works by one of its six active sites binding nucleoside triphosphate and releasing the phosphate which is bonded to a histidine. Then the nucleoside triphosphate, which is now a diphosphate, is released, and a different nucleoside diphosphate binds to the same site—and as a result the phosphate that is bonded to the enzyme is transferred, forming a new triphosphate. Scores of other enzymes exist in order for ATP to transfer its energy to the various places where it is needed. Each enzyme must be specifically designed to carry out its unique function, and most of these enzymes are critical for health and life.

The body does contain some flexibility, and sometimes life is possible when one of these enzymes is defective—but the person is often handicapped. Also, back-up mechanisms sometimes exist so that the body can achieve the same goals through an alternative biochemical route. These few simple examples eloquently illustrate the concept of over-design built into the body. They also prove the enormous complexity of the body and its biochemistry.

The Message of the Molecule

Without ATP, life as we understand it could not exist. It is a perfectly-designed, intricate molecule that serves a critical role in providing the proper size energy packet for scores of thousands of classes of reactions that occur in all forms of life. Even viruses rely on an ATP molecule identical to that used in humans. The ATP energy system is quick, highly efficient, produces a rapid turnover of ATP, and can rapidly respond to energy demand changes (Goodsell, 1996, p.79).

Furthermore, the ATP molecule is so enormously intricate that we are just now beginning to understand how it works. Each ATP molecule is over 500 atomic mass units (500 AMUs). In manufacturing terms, the ATP molecule is a machine with a level of organization on the order of a research microscope or a standard television (Darnell, Lodish, and Baltimore, 1996).

Among the questions evolutionists must answer include the following, &ldquoHow did life exist before ATP?&rdquo &ldquoHow could life survive without ATP since no form of life we know of today can do that?&rdquo and &ldquoHow could ATP evolve and where are the many transitional forms required to evolve the complex ATP molecule?&rdquo No feasible candidates exist and none can exist because only a perfect ATP molecule can properly carry out its role in the cell.

In addition, a potential ATP candidate molecule would not be selected for by evolution until it was functional and life could not exist without ATP or a similar molecule that would have the same function. ATP is an example of a molecule that displays irreducible complexity which cannot be simplified and still function (Behe, 1996). ATP could have been created only as a unit to function immediately in life and the same is true of the other intricate energy molecules used in life such as GTP.

Although other energy molecules can be used for certain cell functions, none can even come close to satisfactorily replacing all the many functions of ATP. Over 100,000 other detailed molecules like ATP have also been designed to enable humans to live, and all the same problems related to their origin exist for them all. Many macromolecules that have greater detail than ATP exist, as do a few that are less highly organized, and in order for life to exist all of them must work together as a unit.

The Contrast between Prokaryotic andEukaryotic ATP Production

An enormous gap exists between prokaryote (bacteria and cyanobacteria) cells and eukaryote (protists, plants and animals) type of cells:

. prokaryotes and eukaryotes are profoundly different from each other and clearly represent a marked dichotomy in the evolution of life. . . The organizational complexity of the eukaryotes is so much greater than that of the prokaryotes that it is difficult to visualize how a eukaryote could have arisen from any known prokaryote (Hickman et al., 1997, p. 39).

Some of the differences are that prokaryotes lack organelles, a cytoskeleton, and most of the other structures present in eukaryotic cells. Consequently, the functions of most organelles and other ultrastructure cell parts must be performed in bacteria by the cell membrane and its infoldings called mesosomes.

The Four Major Methods of Producing ATP

A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP. All life produces ATP by three basic chemical methods only: oxidative phosphorylation, photophosphorylation, and substrate-level phosphorylation (Lim, 1998, p. 149). In prokaryotes ATP is produced both in the cell wall and in the cytosol by glycolysis. In eukaryotes most ATP is produced in chloroplasts (for plants), or in mitochondria (for both plants and animals). No means of producing ATP exists that is intermediate between these four basic methods and no transitional forms have ever been found that bridge the gap between these four different forms of ATP production. The machinery required to manufacture ATP is so intricate that viruses are not able to make their own ATP. They require cells to manufacture it and viruses have no source of energy apart from cells.

In prokaryotes the cell membrane takes care of not only the cell&rsquos energy-conversion needs, but also nutrient processing, synthesizing of structural macromolecules, and secretion of the many enzymes needed for life (Talaro and Talaro, 1993, p. 77). The cell membrane must for this reason be compared with the entire eukaryote cell ultrastructure which performs these many functions. No simple means of producing ATP is known and prokaryotes are not by any means simple. They contain over 5,000 different kinds of molecules and can use sunlight, organic compounds such as carbohydrates, and inorganic compounds as sources of energy to manufacture ATP.

Another example of the cell membrane in prokaryotes assuming a function of the eukaryotic cell ultrastructure is as follows: Their DNA is physically attached to the bacterial cell membrane and DNA replication may be initiated by changes in the membrane. These membrane changes are in turn related to the bacterium&rsquos growth. Further, the mesosome appears to guide the duplicated chromatin bodies into the two daughter cells during cell division (Talaro and Talaro, 1993).

In eukaryotes the mitochondria produce most of the cell&rsquos ATP (anaerobic glycolysis also produces some) and in plants the chloroplasts can also service this function. The mitochondria produce ATP in their internal membrane system called the cristae. Since bacteria lack mitochondria, as well as an internal membrane system, they must produce ATP in their cell membrane which they do by two basic steps. The bacterial cell membrane contains a unique structure designed to produce ATP and no comparable structure has been found in any eukaryotic cell (Jensen, Wright, and Robinson, 1997).

In bacteria, the ATPase and the electron transport chain are located inside the cytoplasmic membrane between the hydrophobic tails of the phospholipid membrane inner and outer walls. Breakdown of sugar and other food causes the positively charged protons on the outside of the membrane to accumulate to a much higher concentration than they are on the membrane inside . This creates an excess positive charge on the outside of the membrane and a relatively negative charge on the inside.

The result of this charge difference is a dissociation of H 2 O molecules into H + and OH – ions. The H + ions that are produced are then transported outside of the cell and the OH – ions remain on the inside. This results in a potential energy gradient similar to that produced by charging a flashlight battery. The force the potential energy gradient produces is called a proton motive force that can accomplish a variety of cell tasks including converting ADP into ATP.

In some bacteria such as Halobacterium this system is modified by use of bacteriorhodopsin , a protein similar to the sensory pigment rhodopsin used in the vertebrate retina (Lim, 1998, p. 166). Illumination causes the pigment to absorb light energy, temporarily changing rhodopsin from a trans to a cis form. The trans to cis conversion causes deprotonation and the transfer of protons across the plasma membrane to the periplasm.

The proton gradient that results is used to drive ATP synthesis by use of the ATPase complex. This modification allows bacteria to live in low oxygen but rich light regions. This anaerobic ATP manufacturing system, which is unique to prokaryotes, uses a chemical compound other than oxygen as a terminal electron acceptor (Lim, 1998, p. 168). The location of the ATP producing system is only one of many major contrasts that exist between bacterial cell membranes and mitochondria.

Chloroplasts

Chloroplasts are double membraned ATP-producing organelles found only in plants. Inside their outer membrane is a set of thin membranes organized into flattened sacs stacked up like coins called thylakoids (Greek thylac or sack, and oid meaning like). The disks contain chlorophyll pigments that absorb solar energy which is the ultimate source of energy for all the plant&rsquos needs including manufacturing carbohydrates from carbon dioxide and water (Mader, 1996, p. 75). The chloroplasts first convert the solar energy into ATP stored energy, which is then used to manufacture storage carbohydrates which can be converted back into ATP when energy is needed.

The chloroplasts also possess an electron transport system for producing ATP. The electrons that enter the system are taken from water. During photosynthesis, carbon dioxide is reduced to a carbohydrate by energy obtained from ATP (Mader, 1996, p. 12). Photosynthesizing bacteria (cyanobacteria) use yet another system. Cyanobacteria do not manufacture chloroplasts but use chlorophyll bound to cytoplasmic thylakoids. Once again plausible transitional forms have never been found that can link this form of ATP production to the chloroplast photosynthesis system.

The two most common evolutionary theories of the origin of the mitochondria-chloroplast ATP production system are 1) endosymbiosis of mitochondria and chloroplasts from the bacterial membrane system and 2) the gradual evolution of the prokaryote cell membrane system of ATP production into the mitochondria and chloroplast systems. Believers in endosymbiosis teach that mitochondria were once free-living bacteria, and that &ldquoearly in evolution ancestral eukaryotic cells simply ate their future partners&rdquo (Vogel, 1998, p. 1633). Both the gradual conversion and endosymbiosis theory require many transitional forms, each new one which must provide the animal with a competitive advantage compared with the unaltered animals.

The many contrasts between the prokaryotic and eukaryotic means of producing ATP, some of which were noted above, are strong evidence against the endosymbiosis theory. No intermediates to bridge these two systems has ever been found and arguments put forth in the theory&rsquos support are all highly speculative. These and other problems have recently become more evident as a result of recent major challenges to the standard endosymbiosis theory. The standard theory has recently been under attack from several fronts, and some researchers are now arguing for a new theory:

Scientists pondering how the first complex cell came together say the new idea could solve some nagging problems with the prevailing theory. &ldquo[the new theory is]. elegantly argued,&rdquo says Michael Gray of Dalhouisie University in Halifax, Nova Scotia, but &ldquothere are an awful lot of things the hypothesis doesn&rsquot account for.&rdquo In the standard picture of eukaryote evolution, the mitochondrion was a lucky accident. First, the ancestral cell—probably an archaebacterium, recent genetic analyses suggest—acquired the ability to engulf and digest complex molecules. It began preying on its microbial companions. At some point, however, this predatory cell didn&rsquot fully digest its prey, and an even more successful cell resulted when an intended meal took up permanent residence and became the mitochondrion. For years, scientists had thought they had examples of the direct descendants of those primitive eukaryotes: certain protists that lack mitochondria. But recent analysis of the genes in those organisms suggests that they, too, once carried mitochondria but lost them later ( Science , 12 September 1997, p. 1604). These findings hint that eukaryotes might somehow have acquired their mitochondria before they had evolved the ability to engulf and digest other cells (Vogel, 1998, p. 1633).

Summary

In this brief review we have examined only one cell macromolecule, ATP, and the intricate mechanisms which produce it. We have also looked at the detailed supporting mechanism which allows the ATP molecule to function. ATP is only one of hundreds of thousands of essential molecules, each one that has a story. As each of those stories is told, they will stand as a tribute to both the genius and the enormously complex design of the natural world. All the books in the largest library in the world may not be able to contain the information needed to understand and construct the estimated 100,000 complex macromolecule machines used in humans. Much progress has been made in understanding the structure and function of organic macromolecules and some of the simpler ones are now being manufactured by pharmaceutical firms.

Now that scientists understand how some of these highly organized molecules function and why they are required for life, their origin must be explained. We know only four basic methods of producing ATP: in bacterial cell walls, in the cytoplasm by photosynthesis, in chloroplasts, and in mitochondria. No transitional forms exist to bridge these four methods by evolution. According to the concept of irreducible complexity, these ATP producing machines must have been manufactured as functioning units and they could not have evolved by Darwinism mechanisms. Anything less than an entire ATP molecule will not function and a manufacturing plant which is less than complete cannot produce a functioning ATP. Some believe that the field of biochemistry which has achieved this understanding has already falsified the Darwinian world view (Behe, 1996).

Jerry Bergman has seven degrees, including in biology, psychology, and evaluation and research, from Wayne State University, in Detroit, Bowling Green State University in Ohio, and Medical College of Ohio in Toledo. He has taught at Bowling Green State University, the University of Toledo, Medical College of Ohio and at other colleges and universities. He currently teaches biology, microbiology, biochemistry, and human anatomy at the college level and is a research associate involved in research in the area of cancer genetics. He has published widely in both popular and scientific journals. [RETURN TO TOP]


What Is the ATP-PC Energy System?

The ATP-PC energy system is the system by which the body fuels 10 to 20 seconds of intense exercise by using stored ATP, the high-energy molecule that fuels muscles, and then through phosphocreatine, which is quickly converted to ATP to further fuel muscle contractions. This system is also sometimes called the ATP-CP energy system, because phosphocreatine is also known as creatine phosphate.

A small amount of ATP and phosphocreatine is stored in the muscle cells, so the ATP-PC energy system isn't related to food or beverage intake directly before or during exercise. The ATP-PC energy system also doesn't require the presence of oxygen, so it's said to be anaerobic. Alactic exercise utilizes the ATP-PC energy system to increase its efficiency. This type of exercise includes 10-second bursts of high intensity followed by 30-second recovery periods.

After both the stored ATP and the stored phosphocreatine in the muscle cells are used up, the body needs to produce more ATP to continue fueling the muscles. First, the body produces ATP directly from carbohydrates through glycolysis. This produces lactic acid as a waste product. After about 10 minutes, the lactic acid builds up to levels that cause pain and fatigue. During longer exercise periods the body relies on aerobic metabolism, which produces ATP from carbohydrates, fats and proteins with the help of oxygen from the circulatory system.