Information

Which enzymes use ATP?


It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well there are enzymes that simply work spontaneously and do not require such an influx of energy. However I can't seem to find any sort of list, however brief, that contains examples of enzymes that use ATP and ones that do not, or any indication of their prevalence. I could go one by one through each of the commonly encountered enzymes in the cell, but that would be tedious.

Is there any source where I could find what I am looking for? Or at the very least which of the major enzymes in the protein transcription/synthesis chain require ATP?


D-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations

The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, d-alanine-d-alanine ligase (Ddl), catalyzes ATP-dependent formation of the d-alanyl-d-alanine dipeptide essential for bacterial cell wall biosynthesis and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K + , but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize MVC activation. We found that TtDdl is a type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ∼20-fold in the presence of activating MVCs, and it was maximally activated by K + and Rb + ions. A strict dependence on ionic radius of the MVC was observed, with Li + and Na + providing little to no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K + , Rb + , or Cs + Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.

Keywords: ATP-grasp X-ray crystallography d-alanine–d-alanine ligase (Ddl) enzyme catalysis enzyme kinetics enzyme mechanism enzyme structure metal activation metal ion–protein interaction monovalent cation structural biology.

Conflict of interest statement

Conflict of interest—The authors declare that they have no conflicts of interest with the contents of this article.


Introduction

In Part 4 of this text, we will address how living things manage their energy needs. Many autotrophs (organisms able to form biological macromolecules from simple inorganic compounds) are photosynthetic, and obtain energy from light. Both autotrophs and heterotrophs (organisms that have to eat complex organic substances to live) can break down biological macromolecules to release useable energy. Consider the oxidation of one molecule of glucose:

If this reaction occurs in a single step, combustion occurs, with energy released as the light and heat of a flame. Obviously, this single-step reaction is not compatible with life. Fortunately, evolution has resulted in a slower way to release energy from glucose and harness that energy in a safe form for the cell’s use: ATP.

Meeting a cell’s energy needs is one of the functions of metabolism. Technically speaking, metabolism is the sum of all reactions occurring in a living organism. More explicitly, metabolism deals with how an organism manages its material and energy resources, including:

In this course, we focus on the first two roles of metabolism, and only a portion of those. If you take an advanced biochemistry course, you will delve further into the pathways that allow organisms to function. To understand the basics of metabolism, you need an understanding of how living things manage energy and how enzymes allow them to do so.


Contents

Most eukaryotic cells have mitochondria, which produce ATP from products of the citric acid cycle, fatty acid oxidation, and amino acid oxidation. At the inner mitochondrial membrane, electrons from NADH and FADH2 pass through the electron transport chain to oxygen, which is reduced to water. [3] The electron transport chain comprises an enzymatic series of electron donors and acceptors. Each electron donor will pass electrons to a more electronegative acceptor, which in turn donates these electrons to another acceptor, a process that continues down the series until electrons are passed to oxygen, the most electronegative and terminal electron acceptor in the chain. Passage of electrons between donor and acceptor releases energy, which is used to generate a proton gradient across the mitochondrial membrane by "pumping" protons into the intermembrane space, producing a thermodynamic state that has the potential to do work. This entire process is called oxidative phosphorylation since ADP is phosphorylated to ATP by using the electrochemical gradient established by the redox reactions of the electron transport chain.

Mitochondrial redox carriers Edit

Energy obtained through the transfer of electrons down the electron transport chain is used to pump protons from the mitochondrial matrix into the intermembrane space, creating an electrochemical proton gradient (ΔpH) across the inner mitochondrial membrane. This proton gradient is largely but not exclusively responsible for the mitochondrial membrane potential (ΔΨM). [4] It allows ATP synthase to use the flow of H + through the enzyme back into the matrix to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. Complex I (NADH coenzyme Q reductase labeled I) accepts electrons from the Krebs cycle electron carrier nicotinamide adenine dinucleotide (NADH), and passes them to coenzyme Q (ubiquinone labeled Q), which also receives electrons from complex II (succinate dehydrogenase labeled II). Q passes electrons to complex III (cytochrome bc1 complex labeled III), which passes them to cytochrome c (cyt c). Cyt c passes electrons to complex IV (cytochrome c oxidase labeled IV), which uses the electrons and hydrogen ions to reduce molecular oxygen to water.

Four membrane-bound complexes have been identified in mitochondria. Each is an extremely complex transmembrane structure that is embedded in the inner membrane. Three of them are proton pumps. The structures are electrically connected by lipid-soluble electron carriers and water-soluble electron carriers. The overall electron transport chain:

Complex I Edit

In complex I (NADH ubiquinone oxireductase, Type I NADH dehydrogenase, or mitochondrial complex I EC 1.6.5.3), two electrons are removed from NADH and transferred to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH2), freely diffuses within the membrane, and Complex I translocates four protons (H + ) across the membrane, thus producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of the main sites of production of superoxide. [5]

The pathway of electrons is as follows:

NADH is oxidized to NAD + , by reducing Flavin mononucleotide to FMNH2 in one two-electron step. FMNH2 is then oxidized in two one-electron steps, through a semiquinone intermediate. Each electron thus transfers from the FMNH2 to an Fe-S cluster, from the Fe-S cluster to ubiquinone (Q). Transfer of the first electron results in the free-radical (semiquinone) form of Q, and transfer of the second electron reduces the semiquinone form to the ubiquinol form, QH2. During this process, four protons are translocated from the mitochondrial matrix to the intermembrane space. [6] As the electrons become continuously oxidized and reduced throughout the complex an electron current is produced along the 180 Angstrom width of the complex within the membrane. This current powers the active transport of four protons to the intermembrane space per two electrons from NADH. [7]

Complex II Edit

In complex II (succinate dehydrogenase or succinate-CoQ reductase EC 1.3.5.1) additional electrons are delivered into the quinone pool (Q) originating from succinate and transferred (via flavin adenine dinucleotide (FAD)) to Q. Complex II consists of four protein subunits: succinate dehydrogenase, (SDHA) succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial, (SDHB) succinate dehydrogenase complex subunit C, (SDHC) and succinate dehydrogenase complex, subunit D, (SDHD). Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also direct electrons into Q (via FAD). Complex II is a parallel electron transport pathway to complex 1, but unlike complex 1, no protons are transported to the intermembrane space in this pathway. Therefore, the pathway through complex II contributes less energy to the overall electron transport chain process.

Complex III Edit

In complex III (cytochrome bc1 complex or CoQH2-cytochrome c reductase EC 1.10.2.2), the Q-cycle contributes to the proton gradient by an asymmetric absorption/release of protons. Two electrons are removed from QH2 at the QO site and sequentially transferred to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons sequentially pass across the protein to the Qi site where the quinone part of ubiquinone is reduced to quinol. A proton gradient is formed by one quinol ( 2 H 2 + e − >> ) oxidations at the Qo site to form one quinone ( 2 H 2 + e − >> ) at the Qi site. (In total, four protons are translocated: two protons reduce quinone to quinol and two protons are released from two ubiquinol molecules.)

When electron transfer is reduced (by a high membrane potential or respiratory inhibitors such as antimycin A), Complex III may leak electrons to molecular oxygen, resulting in superoxide formation.

This complex is inhibited by dimercaprol (British Antilewisite, BAL), Napthoquinone and Antimycin.

Complex IV Edit

In complex IV (cytochrome c oxidase EC 1.9.3.1), sometimes called cytochrome AA3, four electrons are removed from four molecules of cytochrome c and transferred to molecular oxygen (O2), producing two molecules of water. The complex contains coordinated copper ions and several heme groups. At the same time, eight protons are removed from the mitochondrial matrix (although only four are translocated across the membrane), contributing to the proton gradient. The exact details of proton pumping in complex IV are still under study. [8] Cyanide is an inhibitor of complex 4.

Coupling with oxidative phosphorylation Edit

The chemiosmotic coupling hypothesis, proposed by Nobel Prize in Chemistry winner Peter D. Mitchell, the electron transport chain and oxidative phosphorylation are coupled by a proton gradient across the inner mitochondrial membrane. The efflux of protons from the mitochondrial matrix creates an electrochemical gradient (proton gradient). This gradient is used by the FOF1 ATP synthase complex to make ATP via oxidative phosphorylation. ATP synthase is sometimes described as Complex V of the electron transport chain. [9] The FO component of ATP synthase acts as an ion channel that provides for a proton flux back into the mitochondrial matrix. It is composed of a, b and c subunits. Protons in the inter-membranous space of mitochondria first enters the ATP synthase complex through a subunit channel. Then protons move to the c subunits. [10] The number of c subunits it has determines how many protons it will require to make the FO turn one full revolution. For example, in humans, there are 8 c subunits, thus 8 protons are required. [11] After c subunits, protons finally enters matrix using a subunit channel that opens into the mitochondrial matrix. [10] This reflux releases free energy produced during the generation of the oxidized forms of the electron carriers (NAD + and Q). The free energy is used to drive ATP synthesis, catalyzed by the F1 component of the complex. [12]
Coupling with oxidative phosphorylation is a key step for ATP production. However, in specific cases, uncoupling the two processes may be biologically useful. The uncoupling protein, thermogenin—present in the inner mitochondrial membrane of brown adipose tissue—provides for an alternative flow of protons back to the inner mitochondrial matrix. Thyroxine is also a natural uncoupler. This alternative flow results in thermogenesis rather than ATP production. [13]

Reverse electron flow Edit

Reverse electron flow, is the transfer of electrons through the electron transport chain through the reverse redox reactions. Usually requiring a significant amount of energy to be used, this can result in reducing the oxidised form of electron donors. For example, NAD+ can be reduced to NADH by complex I. [14] There are several factors that have been shown to induce reverse electron flow. However, more work needs to be done to confirm this. One such example is blockage of ATP production by ATP synthase, resulting in a build-up of protons and therefore a higher proton-motive force, inducing reverse electron flow. [15]

In eukaryotes, NADH is the most important electron donor. The associated electron transport chain is

NADHComplex IQComplex IIIcytochrome cComplex IVO2 where Complexes I, III and IV are proton pumps, while Q and cytochrome c are mobile electron carriers. The electron acceptor is molecular oxygen.

In prokaryotes (bacteria and archaea) the situation is more complicated, because there are several different electron donors and several different electron acceptors. The generalized electron transport chain in bacteria is:

Electrons can enter the chain at three levels: at the level of a dehydrogenase, at the level of the quinone pool, or at the level of a mobile cytochrome electron carrier. These levels correspond to successively more positive redox potentials, or to successively decreased potential differences relative to the terminal electron acceptor. In other words, they correspond to successively smaller Gibbs free energy changes for the overall redox reaction Donor → Acceptor.

Individual bacteria use multiple electron transport chains, often simultaneously. Bacteria can use a number of different electron donors, a number of different dehydrogenases, a number of different oxidases and reductases, and a number of different electron acceptors. For example, E. coli (when growing aerobically using glucose as an energy source) uses two different NADH dehydrogenases and two different quinol oxidases, for a total of four different electron transport chains operating simultaneously.

A common feature of all electron transport chains is the presence of a proton pump to create an electrochemical gradient over a membrane. Bacterial electron transport chains may contain as many as three proton pumps, like mitochondria, or they may contain only one or two. They always contain at least one proton pump.

Electron donors Edit

In the present day biosphere, the most common electron donors are organic molecules. Organisms that use organic molecules as an electron source are called organotrophs. Organotrophs (animals, fungi, protists) and phototrophs (plants and algae) constitute the vast majority of all familiar life forms.

Some prokaryotes can use inorganic matter as an energy source. Such an organism is called a lithotroph ("rock-eater"). Inorganic electron donors include hydrogen, carbon monoxide, ammonia, nitrite, sulfur, sulfide, manganese oxide, and ferrous iron. Lithotrophs have been found growing in rock formations thousands of meters below the surface of Earth. Because of their volume of distribution, lithotrophs may actually outnumber organotrophs and phototrophs in our biosphere.

The use of inorganic electron donors as an energy source is of particular interest in the study of evolution. This type of metabolism must logically have preceded the use of organic molecules as an energy source.

Complex I and II Edit

Bacteria can use a number of different electron donors. When organic matter is the energy source, the donor may be NADH or succinate, in which case electrons enter the electron transport chain via NADH dehydrogenase (similar to Complex I in mitochondria) or succinate dehydrogenase (similar to Complex II). Other dehydrogenases may be used to process different energy sources: formate dehydrogenase, lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, H2 dehydrogenase (hydrogenase), electron transport chain. Some dehydrogenases are also proton pumps others funnel electrons into the quinone pool. Most dehydrogenases show induced expression in the bacterial cell in response to metabolic needs triggered by the environment in which the cells grow. In the case of lactate dehydrogenase in E.coli, the enzyme is used aerobically and in combination with other dehydrogenases. It is inducible and is expressed when there is high concentration of DL- lactate present in the cell. [ citation needed ]

Quinone carriers Edit

Quinones are mobile, lipid-soluble carriers that shuttle electrons (and protons) between large, relatively immobile macromolecular complexes embedded in the membrane. Bacteria use ubiquinone (Coenzyme Q, the same quinone that mitochondria use) and related quinones such as menaquinone (Vitamin K2). Archaea in the genus Sulfolobus use caldariellaquinone. [16] The use of different quinones is due to slightly altered redox potentials. These changes in redox potential are caused by changes in structure of quinone. The Change in redox potentials of these quinones may be suited to changes in the electron acceptors or variations of redox potentials in bacterial complexes. [17]

Proton pumps Edit

A proton pump is any process that creates a proton gradient across a membrane. Protons can be physically moved across a membrane this is seen in mitochondrial Complexes I and IV. The same effect can be produced by moving electrons in the opposite direction. The result is the disappearance of a proton from the cytoplasm and the appearance of a proton in the periplasm. Mitochondrial Complex III uses this second type of proton pump, which is mediated by a quinone (the Q cycle).

Some dehydrogenases are proton pumps others are not. Most oxidases and reductases are proton pumps, but some are not. Cytochrome bc1 is a proton pump found in many, but not all, bacteria (it is not found in E. coli). As the name implies, bacterial bc1 is similar to mitochondrial bc1 (Complex III).

Cytochrome electron carriers Edit

Cytochromes are pigments that contain iron. They are found in two very different environments.

Some cytochromes are water-soluble carriers that shuttle electrons to and from large, immobile macromolecular structures imbedded in the membrane. The mobile cytochrome electron carrier in mitochondria is cytochrome c. Bacteria use a number of different mobile cytochrome electron carriers.

Other cytochromes are found within macromolecules such as Complex III and Complex IV. They also function as electron carriers, but in a very different, intramolecular, solid-state environment.

Electrons may enter an electron transport chain at the level of a mobile cytochrome or quinone carrier. For example, electrons from inorganic electron donors (nitrite, ferrous iron, electron transport chain.) enter the electron transport chain at the cytochrome level. When electrons enter at a redox level greater than NADH, the electron transport chain must operate in reverse to produce this necessary, higher-energy molecule.

Terminal oxidases and reductases Edit

When bacteria grow in aerobic environments, the terminal electron acceptor (O2) is reduced to water by an enzyme called an oxidase. When bacteria grow in anaerobic environments, the terminal electron acceptor is reduced by an enzyme called a reductase. In mitochondria the terminal membrane complex (Complex IV) is cytochrome oxidase. Aerobic bacteria use a number of different terminal oxidases. For example, E. coli (a facultative anaerobe) does not have a cytochrome oxidase or a bc1 complex. Under aerobic conditions, it uses two different terminal quinol oxidases (both proton pumps) to reduce oxygen to water.

Bacterial Complex IV can be split into classes according to the molecules act as terminal electron acceptors. Class I oxidases are cytochrome oxidases and use oxygen as the terminal electron acceptor. Class II oxidases are Quinol oxidases and can use a variety of terminal electron acceptors. Both of these classes can be subdivided into categories based on what redox active components they contain. E.g. Heme aa3 Class 1 terminal oxidases are much more efficient than Class 2 terminal oxidases [1]

Anaerobic bacteria, which do not use oxygen as a terminal electron acceptor, have terminal reductases individualized to their terminal acceptor. For example, E. coli can use fumarate reductase, nitrate reductase, nitrite reductase, DMSO reductase, or trimethylamine-N-oxide reductase, depending on the availability of these acceptors in the environment.

Most terminal oxidases and reductases are inducible. They are synthesized by the organism as needed, in response to specific environmental conditions.

Electron acceptors Edit

Just as there are a number of different electron donors (organic matter in organotrophs, inorganic matter in lithotrophs), there are a number of different electron acceptors, both organic and inorganic. In aerobic bacteria and facultative anaerobes if oxygen is available, it is invariably used as the terminal electron acceptor, because it generates the greatest Gibbs free energy change and produces the most energy. [18]

In anaerobic environments, different electron acceptors are used, including nitrate, nitrite, ferric iron, sulfate, carbon dioxide, and small organic molecules such as fumarate.

In oxidative phosphorylation, electrons are transferred from a low-energy electron donor such as NADH to an acceptor such as O2) through an electron transport chain. In photophosphorylation, the energy of sunlight is used to create a high-energy electron donor which can subsequently reduce redox active components. These components are then coupled to ATP synthesis via proton translocation by the electron transport chain. [8]

Photosynthetic electron transport chains, like the mitochondrial chain, can be considered as a special case of the bacterial systems. They use mobile, lipid-soluble quinone carriers (phylloquinone and plastoquinone) and mobile, water-soluble carriers (cytochromes, electron transport chain.). They also contain a proton pump. The proton pump in all photosynthetic chains resembles mitochondrial Complex III. The commonly-held theory of symbiogenesis believes that both organelles descended from bacteria.


5.1: Energy, Matter, and Enzymes

  • Contributed by OpenStax
  • General Biology at OpenStax CNX
  • Define and describe metabolism
  • Compare and contrast autotrophs and heterotrophs
  • Describe the importance of oxidation-reduction reactions in metabolism
  • Describe why ATP, FAD, NAD + , and NADP + are important in a cell
  • Differentiate between substrate-level and oxidative phosphorylation
  • Identify the structure and structural components of an enzyme and the roles of substrates and products in a reaction

The term used to describe all of the chemical reactions inside a cell is metabolism (Figure (PageIndex<1>)). Cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions called metabolic pathways. Reactions that are spontaneous and release energy are exergonic reactions, whereas endergonic reactions require energy to proceed. The term anabolism refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy, usually in the form of ATP (energy) and/or NAD(P)H (electrons). Conversely, the term catabolism refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules (usually in ATP (energy) and/or NADH (electrons)), which are used to drive anabolic pathways. Thus, in terms of energy and molecules, cells are continually balancing catabolism with anabolism.

Figure (PageIndex<1>): Metabolism includes catabolism and anabolism. Anabolic pathways require energy to synthesize larger molecules. Catabolic pathways generate energy by breaking down larger molecules. Both types of pathways are required for maintaining the cell&rsquos energy balance.

Oxidation and Reduction in Metabolism

The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy incrementally that is, in small packages rather than a single, destructive burst. Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reactions those that add electrons to acceptor molecules, leaving them reduced, are reduction reactions. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions, or redox reactions.

Energy Carriers: NAD+, NADP+, FAD, and ATP

The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carriers, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide. These compounds can be easily reduced or oxidized. Nicotinamide adenine dinucleotide (NAD + /NADH) is the most common mobile electron carrier used in catabolism. NAD + is the oxidized form of the molecule NADH is the reduced form of the molecule. Nicotine adenine dinucleotide phosphate (NADP + ), the oxidized form of an NAD + variant that contains an extra phosphate group, is another important electron carrier it forms NADPH when reduced. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2. Both NAD + /NADH and FAD/FADH2 are extensively used in energy extraction from sugars during catabolism in chemoheterotrophs, whereas NADP + /NADPH plays an important role in anabolic reactions and photosynthesis. Collectively, FADH2, NADH, and NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reactions.

A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the &ldquoenergy currency&rdquo of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP) the addition of a third phosphate group forms ATP (Figure (PageIndex<2>)). Adding a phosphate group to a molecule, a process called phosphorylation, requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate (called inorganic phosphate [Pi]) or two connected phosphate groups (called pyrophosphate [PPi]) from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions (Figure (PageIndex<3>)).

Figure (PageIndex<2>): The energy released from dephosphorylation of ATP is used to drive cellular work, including anabolic pathways. ATP is regenerated through phosphorylation, harnessing the energy found in chemicals or from sunlight. (credit: modification of work by Robert Bear, David Rintoul) Figure (PageIndex<3>): Exergonic reactions are coupled to endergonic ones, making the combination favorable. Here, the endergonic reaction of ATP phosphorylation is coupled to the exergonic reactions of catabolism. Similarly, the exergonic reaction of ATP dephosphorylation is coupled to the endergonic reaction of polypeptide formation, an example of anabolism.

There are two general mechanisms by which ATP is formed in cells: substrate-level phosphorylation and oxidative phosphorylation (Figure (PageIndex<4>)). Remember that a substrate is a molecule on which an enzyme acts. In substrate-level phosphorylation, ADP and a phosphorylated metabolite are both substrates in the same enzymatic reaction. During the exergonic enzymatic reaction, the phosphate on the metabolite is transferred to ADP to form the products ATP and an unphosphorylated metabolite. Any ATP produced in a typical metabolic pathway is through substrate-level phosphorylation.

Oxidative phosphorylation, on the other hand, is specifically the addition of inorganic phosphate to ADP by ATP synthase powered by a proton gradient across a membrane. This almost always occurs in conjunction with an electron transport chain in respiration.


Figure (PageIndex<4>): Substrate-level (top) and oxidative (bottom) phosphorylation (2021 Jeanne Kagle)

What is the function of an electron carrier?

Enzyme Structure and Function

A substance that helps speed up a chemical reaction is a catalyst. Catalysts are not used or changed during chemical reactions and, therefore, are reusable. Whereas inorganic molecules may serve as catalysts for a wide range of chemical reactions, proteins called enzymes serve as catalysts for biochemical reactions inside cells. Enzymes thus play an important role in controlling cellular metabolism.

An enzyme functions by lowering the activation energy of a chemical reaction inside the cell. Activation energy is the energy needed to form or break chemical bonds and convert reactants to products (Figure (PageIndex<5>)). Enzymes lower the activation energy by binding to the reactant molecules and holding them in such a way as to speed up the reaction.

The chemical reactants to which an enzyme binds are called substrates, and the location within the enzyme where the substrate binds is called the enzyme&rsquos active site. The characteristics of the amino acids near the active site create a very specific chemical environment within the active site that induces suitability to binding, albeit briefly, to a specific substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates, enzymes are known for their specificity. In fact, as an enzyme binds to its substrate(s), the enzyme structure changes slightly to find the best fit between the transition state (a structural intermediate between the substrate and product) and the active site, just as a rubber glove molds to a hand inserted into it. This active-site modification in the presence of substrate, along with the simultaneous formation of the transition state, is called induced fit (Figure (PageIndex<6>)). Overall, there is a specifically matched enzyme for each substrate and, thus, for each chemical reaction however, there is some flexibility as well. Some enzymes have the ability to act on several different structurally related substrates.

Figure (PageIndex<5>): Enzymes lower the activation energy of a chemical reaction. Figure (PageIndex<6>): According to the induced-fit model, the active site of the enzyme undergoes conformational changes upon binding with the substrate.

Enzymes are subject to influences by local environmental conditions such as pH, substrate concentration, and temperature. Although increasing the environmental temperature generally increases reaction rates, enzyme catalyzed or otherwise, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function. Enzymes are also suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature. Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH.

Another factor that influences enzyme activity is substrate concentration: Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate. Overall, enzymes are optimized to work best under the environmental conditions in which the organisms that produce them live. For example, while microbes that inhabit hot springs have enzymes that work best at high temperatures, human pathogens have enzymes that work best at 37°C. Similarly, while enzymes produced by most organisms work best at a neutral pH, microbes growing in acidic environments make enzymes optimized to low pH conditions, allowing for their growth at those conditions.

Many enzymes do not work optimally, or even at all, unless bound to other specific nonprotein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Two types of helper molecules are cofactors and coenzymes. Cofactors are inorganic ions such as iron (Fe 2+ ) and magnesium (Mg 2+ ) that help stabilize enzyme conformation and function. One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn 2+ ) to function.

Coenzymes are organic helper molecules that are required for enzyme action. Like enzymes, they are not consumed and, hence, are reusable. The most common sources of coenzymes are dietary vitamins. Some vitamins are precursors to coenzymes and others act directly as coenzymes.

Some cofactors and coenzymes, like coenzyme A (CoA), often bind to the enzyme&rsquos active site, aiding in the chemistry of the transition of a substrate to a product (Figure (PageIndex<7>)). In such cases, an enzyme lacking a necessary cofactor or coenzyme is called an apoenzyme and is inactive. Conversely, an enzyme with the necessary associated cofactor or coenzyme is called a holoenzyme and is active. NADH and ATP are also both examples of commonly used coenzymes that provide high-energy electrons or phosphate groups, respectively, which bind to enzymes, thereby activating them.

Figure (PageIndex<7>): The binding of a coenzyme or cofactor to an apoenzyme is often required to form an active holoenzyme.


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Pay off phase of glycolysis pathway (the exothermic phase)

Pay off phase of glycolysis is a sequence of exothermic reactions that provides energy for the cell.

Step 6: Glyceraldehyde-3-phosphate to 1,3-Bisphosphoglycerate (Glyceraldehyde 3-phosphate dehydrogenase)

Following preparatory phase of glycolysis, in the sixth step, each glyceraldehyde-3-phosphate (PGAL) is oxidized.

The transfer of electrons and a proton to the carrier molecule NAD + (nicotinamide adenine dinucleotide) creates NADH.

This is the point where the process of glycolysis can slow down or stop. The availability of the oxidized form of the electron carrier, NAD + , is a limiting factor. To keep this step going NADH must be oxidized back into NAD + without intermission. If oxygen is available in the system, the NADH will be oxidized in the final phase of cellular respiration - the stage of oxidative phosphorylation.

Without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD + .

The oxidized form of glyceraldehyde-3-phosphate is now able to attract a free phosphate ion in the cytosol, forming 1,3-biphosphoglycerate (PGAP).

Step 7: 1,3-Biphosphoglycerate to 3-Phosphoglycerate (Phosphoglycerate kinase)

Phosphoglycerate kinase catalyzes the seventh step of glycolysis.

Following the formation of 1,3-biphosphoglycerate (PGAP), two ADP molecules each remove one phosphate group from each PGAP to form 3-phosphoglycerate (PGA) and ATP.

At this point the net change in the number of ATP molecules is zero.

Next, the two 3-phosphoglycerate (PGA) molecules are each oxidized, forming two water molecules and two phosphoenolpyruvate (PEP) molecules.

Step 8: 3-Phosphoglycerate to 2-Phosphoglycerate (Phosphoglycerate mutase)

In the eighth step, moving the phosphate group in 3-phosphoglycerate from the third carbon to the second carbon, an isomerase creates 2-phosphoglycerate.

Step 9: 2-Phosphoglycerate to Phosphoenolpyruvate (Enolase)

The ninth glycolysis step is a dehydration reaction. Enolase forces 2-phosphoglycerate to lose water and produces phosphoenolpyruvate (PEP).

The rearrangement of some of the electrons causes the remaining phosphate group to become unstable.

Step 10: Phosphoenolpyruvate to Pyruvate (Pyruvate kinase)

Finally, in tenth step catalyzed by the pyruvate kinase, two ADP molecules each remove the remaining phosphate group from each phosphoenolpyruvate (PEP) molecule.

The result products of glycolysis are four ATP molecules, two NADH molecules and two pyruvate molecules.

Two ATP molecules are used in the first half of the pathway in the preparatory phase of glycolysis.

The entire glycolysis process, including preparatory and pay off phases of glycolysis, produces a net gain of two ATP molecules.

Pyruvate can be further oxidized in mitochondria.


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Ye, X. et al. Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails. ChemSusChem 2, 149–152 (2009).

Welch, P. & Scopes, R.K. Studies on cell-free metabolism: ethanol production by a yeast glycolytic system reconstituted from purified enzymes. J. Biotechnol. 2, 257–273 (1985).

Korman, T.P. et al. A synthetic biochemistry system for the in vitro production of isoprene from glycolysis intermediates. Protein Sci. 23, 576–585 (2014).

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Which enzymes use ATP? - 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]