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Why is ATP the preferred choice for energy carriers?

Why is ATP the preferred choice for energy carriers?


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Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?


I really like this question as it is such a fundamental underpinning of all life on the planet, yet there is such sparsity of actual information on its origins and why selection rewarded ATP use over anything else. Here I am talking generally since no specific studies exist in ATP vs other candidates.

A lot of the below information is taken from a relatively old article mentioned in the comments by TomD that discusses: "Why nature chose phosphates." by Westheimer, 1987. The article is very influential and has been cited over a thousand times since publication. Another article that came out in the same year that this question was asked "Why nature really chose phosphate." by Kamerlin et al., 2013

Some of the below arguments are more convincing than others, but all of them should be thought of when attempting to answer this question.

Summary.

  • ATP has ancestral dominance. Most other reasons derive from this.

  • Alternative phosphate groups or other molecules may not provide enough energy.

  • Alternatives may be toxic.

  • Other molecules, particularly phosphates, are used for inefficient high energy bursts.

  • Pi is a "good" leaving group.

  • Phosphates are fundamentally able to be regulated through electrostatic manipulation.

  • ATP synthase can efficiently reattach the Pi to ADP.

  • Lots of Pi available to organisms because of it's ancestral dominance ("if it ain't broken, why fix it?" is at play).

  • ATP can provide more energy if needed; it's scalable to the situation. (ADP becomes AMP + Pi)

  • Easily usable by a variety of proteins.

Why ATP?

ATP is an efficient and relatively easily biosynthesised molecule that can fulfil multiple biochemical roles. Cells do have alternative energy carriers, some with more specialised roles, however, ATP is ubiquitous throughout our cells and inter-cellular spaces. There aren't a wealth of resources explaining why ATP is any better than other compounds, however, there is plenty of reasons why the phosphates are required.

Why not the alternatives?

Citric acids and their derivatives are a good candidate, with deductible groups and high bioavailability but they simply don't give enough energy to stabilise genetic material.

Another tribasic candidate is arsenic acid. This is a fundamentally toxic compound, though, which isn't particularly great for living things.

There are other phosphates too, and they are used in many organisms. In biology, they have specific functions, and not used as the general energy carrier. For example, creatine triphosphate provides a high energy phospho- anhydride bond, that is often used to quickly and anaerobically regenerate ATP, useful during high rate muscle activity for contraction.

GTP is structurally very similar to ATP. GTPases are used more to initiate cellular signalling pathways. It is sometimes used as an energy source. This is a good example of an alternative energy carrier.

Over the years, many proteins have specialised with a specific shape, and this chance is the primary reason behind ATP over GTP. In other words, the choice of ATP over GTP is primarily down to cellular preference of molecular shape. One of them had to emerge as being more widely used, and it was ATP that 'won'.

Efficiency and simplicity.

The reaction was once thought to be a relatively simple nucleophilic displacement. From the 2013 paper:

… this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalysed reactions.

Traditionally one will be taught that ATP is such a chemically efficient way of storing and transporting energy. This is due to the ATP->ADP & Pi hydrolysis reaction. The phosphate groups in ATP are full of negative charges and these are repelling one another. This means that the third phosphate is a great leaving group and breaking the phospho- anhydride bond is a favourable reaction…

… But the story is a lot more complicated than that. The above explanation isn't really satisfying because those same negative charge forces are repulsive of the nucleophile that is attempting to complete ATP->ADP & Pi. A more comprehensive explanation would go along the lines of 'although a negative charge repulsion exists between the nucleophile of the protein and the phosphate, that high energy barrier can be overcome by electrostatic manipulation'. This allows an "on-off switch" for the hydrolytic reaction by tweaking the electrostatic environment. This is another great regulatory tool that the phosphates provide. This regulatory feature is important for signal and metabolic/catabolic cascades.

When it comes to 'rebinding' the Pi to ADP, it is fairly easy since ADP seldom covalently binds to anything, which would require a lot of energy to recover the ADP. This also helps the bioavailability of free ADP to ATP synthase, an incredibly efficient enzyme, that uses membrane proton gradient to drive the production of ATP. Talking about actual numbers is difficult here as there is only data available from Rat hepatocytes. Who is to say mammals are representative of all organisms? The estimates of energy of hydrolysis range from ΔG˚ = -48 kJ mol-1 to -30.5 kJ mol-1. Note that these are considerable, but not exceptional values, so it's easy for many different proteins, that need not be very specialized, to break the bond all over the body. I couldn't even find the numbers for the synthase reaction per ATP, but a single ATP synthase can produce up to 600 ATP per minute.

The final point of this efficiency is that the elements in ATP are very abundant and established in the biosphere making it readily available. This makes the phosphates a convenient biomolecule.

Multi-functionality.

ATP is ubiquitous in the body, but in some cases more energy is needed than there are ATP available. In these times of need, ATP can be used to produce more energy, breaking another phosphoanhydride bond to become AMP+2Pi. AMP however is typically a signalling molecule.

With the low activation energy required to break the phosphoanhydride bond, a multitude of enzymes, far too many to list here, can make use of ATP in order to gain energy towards the activation energy for many other functions.


I don't like this sort of question because I don't think it can really be answered and I'm very suspicious of arguments that seem to claim ATP is the only or even the best solution to the problem. Nature generally demonstrates that there is more than one way to kill a cat, but if one way works adequately you don't always need to look for another.

This is not necessarily the case, of course, if we consider an example from the postulated RNA World - which I shall presently - catalysis using RNA was supplanted in most cases by catalysis using proteins. So sometimes a better solution provides an evolutionary advantage, and sometimes if things work well enough they stick as the limiting factor is elsewhere.

So I tend to the view that ATP worked, so it stuck. It was probably chance it wasn't GTP or CTP or UTP, as these work as energy sources in signal transduction, phospholipid synthesis, and glycogen synthesis, respectively.

But this raises the question of the function or necessity of the purine or pyrimidine ring in the nucleoside triphosphates. As far as I can see the answer is this serves no indispensible function. (Sure, it binds to enzymes - but all sorts of other structure are able to do this.) So I would like to fly the following kite (which must have been flown before, although I am not aware of a reference).

A nucleotide triphosphate (ATP) became the preferred energy source in metabolism after a mechanism of RNA synthesis evolved that used NTPs as substrates.

When the synthesis of RNA evolved to use the free energy of hyrolysis of a 'diphosphorylated extension' of its structural building block (NMP), a system of using a related hydrolysis was extended to metabolism. Note that I say 'related', as RNA synthesis (like other macromolecular syntheses) hydrolyses the alpha-beta phosphodiester bond (releasing pyrophosphate), whereas in metabolism it is generally the beta-gamma bond that is hydrolysed (releasing orthophosphate).

The hydrolysis of ATP would have displaced what it is thought to have been a pre-replication system(s) of energy generation because it would presumably have been better and allowed integrated energy metabolism. (The energy demands of replication would have been large.) But that doesn't mean it's the best conceivable method - working well and being convenient could have been enough.

Footnote

Although not part of my argument, there is another key molecule in metabolism that has what may be considered a 'useless' adenosine component - NAD (and NADP). The redox guts of this is the nicotinamide ring. Did this evolve from a form that was initially part of a ribozyme - perhaps involved in the formation of deoxyribose when the RNA genome was being displaced by the DNA genome?


Preface

I have already provided an answer to this question, addressing one aspect of it: why a nucleotide triphosphate - rather than any other molecule - was the choice for an energy carrier. In that answer I suggest that the choice of ATP, rather than any GTP, CTP or UTP, was mere chance.

This second question has, in fact, been posed, but was regarded - incorrectly in my opinion - as a duplicate. I have recently become aware of research that suggests to me a possible reason for the preference of ATP over other NTPs, and, as it is independent of my previous answer, I would like to present it as a separate answer.

Why ATP rather than other NTPs?

I am starting from the assumption of an RNA world in which some sort of RNA genome had developed the ability to replicate and exhibit enzymic activity. The ribosome, and especially ribosomal RNA, can be regarded as a fossil of such a world. Harry Noller, in a review of this topic in Science in 2005, considers the bases that are involved in base-pairing in the many RNA double-helical loops, and those that are unpaired in such loops. Many of the latter are involved in ternary interactions in the rRNA, which has an overall protein-like structure. A significant fact that he mentions about the bases that are unpaired in the helical secondary structures is their skewed distribution:

“However, the unpaired bases are not distributed evenly among the four bases. In Escherichia coli 16S rRNA, for example, the proportions of unpaired bases for G, C, and U are 31%, 29%, and 33%, respectively, whereas 62% of As are unpaired, a tendency that extends to other functional RNAs.

It transpires that many of these 'unpaired As' are involved in what are called Type II A-minor nucleoside interactions, which are illustrated in Fig 3. of that paper, below:

In the legend to this figure Noller points out that:

These precise lock-and-key minor-groove interactions between (usually) an adenosine and a Watson-Crick base pair are found extensively in 16S and 23S rRNA. They were first observed in crystal packing of the hammerhead ribozyme and in the P4-P6 domain of the group I ribozyme. A-minor interactions play an important functional role in monitoring codon-anticodon interaction by the ribosome via their unique stereo-chemical fit to Watson-Crick base pairs.

From this I conclude that adenine has unique structural properties that would allow it to form a more precise and stronger interaction to base-pairs in a ribozyme RNA than the other three bases. One of the features of any ribozyme involved in using an NTP to drive chemical reactions would have been to bind the NTP. (We see this in contemporary proteins with the Rossman Fold which binds adenine.)

The greater suitability of the adenine of ATP for this role may be why it, rather then GTP, CTP or UTP, became the major (I would assume initial) choice for energy carrier.


Biology OER

Glucose is the preferred carbohydrate of cells. In solution, it can change from a linear chain to a ring. Energy is stored in the bonds of the carbohydrates. Breaking these bonds releases that energy. Crushing sugar crystals creates tiny electrical fields that give off invisible ultraviolet light. The wintergreen chemical (methyl salicylate) gets excited by these excited electrons and fluoresces in a visible blue wavelength. This phenomenon is called triboluminescence.


Why should I measure/care about it?

Since Adenosine Triphosphate is present in all living and active microbial cells, it is an excellent indicator of overall microbiological content in fluids or deposits. To measure it we turn to a well known example of bioluminescence the tail of a firefly! Through a chemical reaction, ATP reacts with luciferase and light is produced. The amount of light can be quantified in a luminometer and the amount of ATP present can then be calculated. Because this reaction happens instantly, the amount of microbiological content can be quantified immediately.

Standard microbiological monitoring methods often require culturing microbes on media and waiting for them to reproduce and form visible colonies. It takes days or weeks to obtain results depending on the species, and these methods only capture <1% of the total population present.

In contrast, LuminUltra’s patented 2nd Generation ATP® Testing provides data to help you know what is happening in your system and represents a major upgrade over other microbiological tools. When combined with our myLuminUltra software, you gain a true total measurement of all microorganisms contained in your sample in just a few minutes.

Having rapid information allows you to take action at the earliest possible moment, saving time and money in the battle against microorganisms. By measuring ATP regularly, and being able to differentiate between cellular ATP inside active microorganisms and dissolved ATP released from dead cells, cause & effect relationships can be identified helping you solve microbiological challenges before it’s too late.


Types of Carrier Proteins

Active Transport

Active transport carrier proteins require energy to move substances against their concentration gradient. That energy may come in the form of ATP that is used by the carrier protein directly, or may use energy from another source.

Many active transport carrier proteins, such as the sodium-potassium pump, use the energy stored in ATP to change their shape and move substances across their transportation gradient.

Pumps which practice “secondary active transport,” are sometimes referred to as “coupled carriers.” These pumps use the “downhill” transport of one substance to drive the “uphill” transport of another.

“Coupled carriers” like the sodium-glucose cotransport protein do end up costing the cell energy, because the cell must use ATP to maintain the sodium concentration gradient that this carrier uses as its energy source. But the carrier protein does not use ATP directly.

Other carrier proteins, such as some that are found in bacteria and in organelles such as mitochondria and chloroplasts, might use energy sources directly from the environment without requiring ATP.

Facilitated Diffusion

Carrier proteins can also carry substances in a “downhill” direction – that is, carry them down their concentration gradient, in the direction that the substance “wants” to go.

One example is the valinomycin potassium carrier, which binds to potassium ions and changes shape to release them on the other side of the membrane.


Protein Complexes in the Chain

There are four protein complexes that are part of the electron transport chain that functions to pass electrons down the chain. A fifth protein complex serves to transport hydrogen ions back into the matrix. These complexes are embedded within the inner mitochondrial membrane.


Multiple Choice

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

  1. ATP : glucose
  2. an anabolic molecule : catabolic molecule
  3. glucose : ATP
  4. 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?

  1. This is an anabolic process
  2. This is a catabolic process
  3. This is both anabolic and catabolic
  4. This is a metabolic process but is neither anabolic nor catabolic

Why is ATP the preferred choice for energy carriers? - Biology

ATP (adenosine triphosphate) is a high energy molecule that is hydrolysed to provide [energy] for many reactions within cells. It is very important versatile activated carrier, ATP is mainly synthesised in an energetically unfavourable phosphorylation reaction in the mitochondria of a cell, in a process called oxidative phosphorylation, via electron transfer chain (sometimes alternatively known as chemiosmosis) [2] . A small amount of ATP is synthesised in the cytoplasm during glycolysis, and during the Krebs cycle in the Mitochondria. ATP is a very important source of energy for many cellular functions, including in muscle contraction, active transport and condensation reactions. The molecular structure of ATP constists of three phosphate groups linked to an adenosine core. These phosphate groups are linked in series by two phosphoanhydride bonds [3] .

Formation during aerobic respiration

The first stage of respiration is glycolysis, where there is a net gain of two ATP molecules. At first, glucose is phosphorylated by the addition of two phosphates, provided from the hydrolysis of 2ATP ↔ 2ADP + 2Pi, creating two molecules of triose phosphate. This is then oxidised, losing one hydrogen per molecule of triose phosphate, forming two molecules of pyruvate. During this step, four molecules of ATP are synthesised from 4ADP + 4Pi. This stage of respiration occurs in the cytoplasm, but the product, pyruvate, moves to the matrix of the mitochondria where the next 3 stages occur.

The next stage of aerobic respiration is the link reaction, however, no ATP is produced during this step.

The third stage, the Krebs cycle, produces one molecule of ATP per cycle. Since this cycle happens once per pyruvate molecule, it occurs twice per molecule of glucose and so a total of 2 ATP molecules are produced per glucose.

The final stage of aerobic respiration, oxidative phosphorylation, is where the vast amount of ATP is synthesised. Hydrogen atoms in the mitochondrial matrix, released from reduced FAD and reduced NAD, split into protons (H + ) and electrons (e - ). The electrons move along the electron transport chain, losing energy at each carrier. This energy is used to pump protons into the intermembrane space, forming and electrochemical grandient. The protons diffuse down this electrochemical gradient via ATP synthase, which drives the synthesis of ATP from ADP and Pi. This process is called chemiosmosis. Another 28 molecules of ATP are produced during oxidative phosphorylation, totalling to 32 molecules of ATP per molecule of glucose [4] .

ATP Hydrolysis

Hydrolysing ATP to ADP (adenosine diphosphate) or further to AMP (adenosine monophosphate) releases a large amount of free energy, because the phosphoanhydride bonds in the molecule are broken [5] . ATP is, however, a very stable molecule and will only release its energy in the presence of ATPase.

ATP Cycle

The formation of ATP requires an input of energy, therefore it must be coupled to energy-generating processes, such as photosynthesis or oxidation of food molecules. Hydrolysis of ATP releases a lot of free energy, therefore it must be coupled to energy-requiring processes such as muscle contraction and active transport [6] .

What makes ATP an efficient energy source

ATP is the most common energy source in most cellular metabolism. However, some other cellular metabolism were not driven by ATP. Such an example of the other energy currency used in cellular metabolism is guanosine triphosphate (GTP), uridine triphosphate (UTP), and cytidine triphosphate (CTD). Nonetheless, ATP is the most efficient energy source used in cellular metabolism. The reasons that ATP is more reliable than the other nucleoside triphosphate in producing energy are:


Examples of Coenzymes

Most organisms cannot produce coenzymes naturally in large enough quantities to be effective. Instead, they are introduced to an organism in two ways:

Vitamins

Many coenzymes, though not all, are vitamins or derived from vitamins. If vitamin intake is too low, then an organism will not have the coenzymes needed to catalyze reactions. Water-soluble vitamins, which include all B complex vitamins and vitamin C, lead to the production of coenzymes. Two of the most important and widespread vitamin-derived coenzymes are nicotinamide adenine dinucleotide (NAD) and coenzyme A.

NAD is derived from vitamin B3 and functions as one of the most important coenzymes in a cell when turned into its two alternate forms. When NAD loses an electron, the low energy coenzyme called NAD + is formed. When NAD gains an electron, a high-energy coenzyme called NADH is formed.

NAD + primarily transfers electrons needed for redox reactions, especially those involved in parts of the citric acid cycle (TAC). TAC results in other coenzymes, such as ATP. If an organism has a NAD + deficiency, then mitochondria become less functional and provide less energy for cell functions.

When NAD + gains electrons through a redox reaction, NADH is formed. NADH, often called coenzyme 1, has numerous functions. In fact, it is considered the number one coenzyme in the human body because it is necessary for so many different things. This coenzyme primarily carries electrons for reactions and produces energy from food. For example, the electron transport chain can only begin with the delivery of electrons from NADH. A lack of NADH causes energy deficits in cells, resulting in widespread fatigue. Additionally, this coenzyme is recognized as the most powerful biological antioxidant for protecting cells against harmful or damaging substances.

Coenzyme A, also known as acetyl-CoA, naturally derives from vitamin B5. This coenzyme has several different functions. First, it is responsible for initiating fatty acid production within cells. Fatty acids form the phospholipid bilayer that comprises the cell membrane, a feature necessary for life. Coenzyme A also initiates the citric acid cycle, resulting in the production of ATP.

Non-Vitamins

Non-vitamin coenzymes typically aid in chemical transfer for enzymes. They ensure physiological functions, like blood clotting and metabolism, occur in an organism. These coenzymes can be produced from nucleotides such as adenosine, uracil, guanine, or inosine.

Adenosine triphosphate (ATP) is an example of an essential non-vitamin coenzyme. In fact, it is the most widely distributed coenzyme in the human body. It transports substances and supplies energy needed for necessary chemical reactions and muscle contraction. To do this, ATP carries both a phosphate and energy to various locations within a cell. When the phosphate is removed, the energy is also released. This process is result of the electron transport chain. Without the coenzyme ATP, there would be little energy available at the cellular level and normal life functions could not occur.

Here is an example of the electron transport chain. The vitamin-derived coenzyme NADH begins the process by delivering electrons. ATP is the final resulting product:


Introduction

ATP is an unstable molecule which hydrolyzes to ADP and inorganic phosphate when it is in equilibrium with water. The high energy of this molecule comes from the two high-energy phosphate bonds. The bonds between phosphate molecules are called phosphoanhydride bonds. They are energy-rich and contain a &DeltaG of -30.5 kJ/mol.

Figure 1: Structure of ATP molecule and ADP molecule, respectively. The adenine ring is at the top, connected to a ribose sugar, which is connected to the phosphate groups. Used with permission from Wikipedia Commons.


Glucose and ATP

Energy-Carrying Molecules

You know that the fish you had for lunch contained protein molecules. But do you know that the atoms in that protein could easily have formed the color in a dragonfly&rsquos eye, the heart of a water flea, and the whiplike tail of a Euglena before they hit your plate as sleek fish muscle? Food consists of organic (carbon-containing) molecules which store energy in the chemical bonds between their atoms. Organisms use the atoms of food molecules to build larger organic molecules including proteins, DNA, and fats (lipids) and use the energy in food to power life processes. By breaking the bonds in food molecules, cells release energy to build new compounds. Although some energy dissipates as heat at each energy transfer, much of it is stored in the newly made molecules. Chemical bonds in organic molecules are a reservoir of the energy used to make them. Fueled by the energy from food molecules, cells can combine and recombine the elements of life to form thousands of different molecules. Both the energy (despite some loss) and the materials (despite being reorganized) pass from producer to consumer &ndash perhaps from algal tails, to water flea hearts, to dragonfly eye colors, to fish muscle, to you!

The process of photosynthesis, which usually begins the flow of energy through life, uses many different kinds of energy-carrying molecules to transform sunlight energy into chemical energy and build food. Some carrier molecules hold energy briefly, quickly shifting it like a hot potato to other molecules. This strategy allows energy to be released in small, controlled amounts. An example starts in chlorophyll, the green pigment present in most plants, which helps convert solar energy to chemical energy. When a chlorophyll molecule absorbs light energy, electrons are excited and "jump" to a higher energy level. The excited electrons then bounce to a series of carrier molecules, losing a little energy at each step. Most of the "lost" energy powers some small cellular task, such as moving ions across a membrane or building up another molecule. Another short-term energy carrier important to photosynthesis, NADPH, holds chemical energy a bit longer but soon "spends" it to help to build sugar.

Two of the most important energy-carrying molecules are glucose and adenosine triphosphate, commonly referred to as ATP. These are nearly universal fuels throughout the living world and are both key players in photosynthesis, as shown below.

Glucose

A molecule of glucose, which has the chemical formula C6H12O6, carries a packet of chemical energy just the right size for transport and uptake by cells. In your body, glucose is the "deliverable" form of energy, carried in your blood through capillaries to each of your 100 trillion cells. Glucose is also the carbohydrate produced by photosynthesis, and as such is the near-universal food for life.

Glucose is the energy-rich product of photosynthesis, a universal food for life. It is also the primary form in which your bloodstream delivers energy to every cell in your body.

ATP molecules store smaller quantities of energy, but each releases just the right amount to actually do work within a cell. Muscle cell proteins, for example, pull each other with the energy released when bonds in ATP break open (discussed below). The process of photosynthesis also makes and uses ATP - for energy to build glucose! ATP, then, is the useable form of energy for your cells. ATP is commonly referred to as the "energy currency" of the cell.

Why do we need both glucose and ATP?

Why don&rsquot plants just make ATP and be done with it? If energy were money, ATP would be a quarter. Enough money to operate a parking meter or washing machine. Glucose would be a ten dollar bill &ndash much easier to carry around in your wallet, but too large to do the actual work of paying for parking or washing. Just as we find several denominations of money useful, organisms need several "denominations" of energy &ndash a smaller quantity for work within cells, and a larger quantity for stable storage, transport, and delivery to cells. (Actually a glucose molecule would be about $9.50, as under the proper conditions, up to 38 ATP are produced for each glucose molecule.)

Let&rsquos take a closer look at a molecule of ATP. Although it carries less energy than glucose, its structure is more complex. The "A" in ATP refers to the majority of the molecule, adenosine, a combination of a nitrogenous base and a five-carbon sugar. The "TP" indicates the three phosphates, linked by bonds which hold the energy actually used by cells. Usually, only the outermost bond breaks to release or spend energy for cellular work.

An ATP molecule, shown in the Figure below, is like a rechargeable battery: its energy can be used by the cell when it breaks apart into ADP (adenosine diphosphate) and phosphate, and then the "worn-out battery" ADP can be recharged using new energy to attach a new phosphate and rebuild ATP. The materials are recyclable, but recall that energy is not!

How much energy does it cost to do your body&rsquos work? A single cell uses about 10 million ATP molecules per second, and recycles all of its ATP molecules about every 20-30 seconds.

An arrow shows the bond between two phosphate groups in an ATP molecule. When this bond breaks, its chemical energy can do cellular work. The resulting ADP molecule is recycled when new energy attaches another phosphate, rebuilding ATP.