ATP: The Perfect Energy Currency for the Cell

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 In order to function, every machine requires specific parts such as screws, springs, cams, gears, and pulleys. Likewise, all biological machines must have many well-engineered parts to work. Examples include units called organs such as the liver, kidney, and heart. These complex life units are made from still smaller parts called cells which in turn are constructed from yet smaller machines known asorganelles. Cell organelles include mitochondria, Golgi complexes, microtubules, and centrioles. Even below this level are other parts so small that they are formally classified as macromolecules (large molecules). Fig. 1. Views of ATP and related structures. A critically important macromolecule—arguably “second in importance only to DNA”—is ATP. ATP is a complexnanomachine 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 “most widely distributed high-energy compound within the human body” (Ritter, 1996, p. 301). This ubiquitous molecule is “used 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” (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).

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The Aufbau Principle

The electron configuration of an atom gives the distribution  of electrons among atomic orbitals in the atom.  Two general methods are used to show electron configurations.  The subshell notation uses numbers to designate the principal shells and the letters s, p, d, and f to identify the subshells.  A superscript following the letter indicates the number of electrons in the designated subshell.  The ground state electron configuration for nitrogen would be   1s²2s²2p³.  A drawback to this method of showing the electron configuration is that it does not tell us how the three 2p electrons are distributed among the three 2p orbitals.  We can show this by using an orbital diagram in which boxes are used to indicate orbitals within subshells and arrows to represent electrons in these orbitals.  The direction of the arrows represent the directions of the electron spins.  The orbital diagram for nitrogen is

1s	2s		2p

The way we arrive at electron configurations such as the one for nitrogen above is to use a set of rules collectively called the aufbau principle. 

• Electrons occupy orbitals of the lowest energy available
• No two electrons in the same atom may have all four quantum numbers alike
• When entering orbitals of the same energy, electrons initially occupy them singly ant with the same spin
• Electrons fill orbitals in order of the quantum number sum (n + l). For equal (n + l) sums, fill levels in order of increasing n.

A mnemonic diagram for the aufbau principle known as the diagonal rule is shown here

The aufbau principle is really a thought process in which we think about building up an atom from the one that preceeds it in atomic number, by adding a proton and neutrons to the nucleus and one electron to the appropriate atomic orbital.  

There are some exceptions to the to the aufbau principle.  The first is chromium (Z = 24), the aufbau principle predicts the an electron configuration of  [Ar]3d⁴4s² but experimentally we find it to be  [Ar]3d⁵4s¹.  The next exception found is that of copper (Z = 29), the predicted electron configuration is  [Ar]3d⁹4s² but experimentally we find it to be  [Ar]3d¹⁰4s¹.  The reason for these and other exceptions are not completely understood, but it seems that a half-filled 3d subshell in the case of chromium or a completely-filled  3d subshell in the case of copper lend a special stabilty to the observed electron configurations.  There is no need to dwell on these exceptions, the point to remember is that the aufbau principle predicts the correct electron configuration most of the time and that the energy of the predicted electron configuration is very close to the ground state energy.

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Dipolar Bonding in Water

The dipolar interaction between water molecules represents a large amount of internal energy and is a factor in water's large specific heat. The dipole moment of water provides a "handle" for interaction with microwave electric fields in a microwave oven. Microwaves can add energy to the water molecules, whereas molecules with no dipole moment would be unaffected.

The polar nature of water molecules allows them to bond to each other in groups and is associated with the high surface tension of water. The polar nature of the water molecule has many implications. It causes water vapor at sufficient vapor pressure to depart from the ideal gas law because of dipole-dipole attractions. This can lead to condensation and phenomena like cloud formation, fog, the dewpoint, etc. It also has a great deal to do with the function of water as the solvent of life in biological systems.

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Dipole Moment of Water

The asymmetry of the water molecule leads toa dipole moment in the symmetry plane pointed toward the more positive hydrogen atoms. The measured magnitude of this dipole moment is Treating this system like a negative charge of10 electrons and a positive charge of 10e, the effective separation of the negative and positivecharge centers is

This is 0.0039 nm compares with about .05 nm for the first Bohr radius of a hydrogen atom and about .15 nm for the effective radius of hydrogen in liquid form, so the charge separation is small compared to an atomic radius.
The polar nature of water molecules allows them to bond to each other in groups and is associated with the high surface tension of water.

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Venom Chemistry

Venoms contain many components that have beenrecognized. They contain proteins, lipids, steroids,aminopolysaccharides, amines, quinines, neurotransmitters, andother compounds, and are capable of causing many effects. Elapidvenom is the least complex, while pit vipers have the mostcomplex venoms. Elapid venoms have higher concentrations ofesterases, such as acetylcholinesterase, while viper venoms havehigher concentrations of endopeptidases. This difference isimportant because it helps understand why elapid venom exertseffects on the nervous system while viper venom is mainly asomatic toxin.

To better understand the diverse effects ofvenom, let us examine several of the common components found insnake venoms. Proteolytic enzymes are trypsin like and accountfor much of the digestive reactions of snake venoms. Theseenzymes break the peptide bonds between amino acids and denatureproteins. Arginine ester hyrdolases break carbon-oxygen bondsthat are not neurotransmitter related (neurotransmitter esteraseswill be explained in greater detail later), but rather causebreakup of certain proteins where arginine residues are frequent.Collagenase degrades collagen, which is a major component ofconnective tissue, skin and flexible vascular tissue. This enzymeis found in crotalid and viperid venoms and this explains thenecrosis often seen following viper bites. Phospholipases A and Bdegrade lipids to free fatty acids and can cause damage to thecell membrane causing lysis and apoptosis. Phosphodiesterasesbreak the phosphate bonds that provide the backbone for nucleicacids, thus rendering DNA and RNA useless in the effected cell,eventually causing apoptosis. Acetylcholinesterase is aneurotransmitter esterase that breaks the acetate ester bondfound in acetylcholine. The main site of action is in thesynapse, although some vesicle-contained acetylcholine may bedegraded as well. The end result of this action is an inabilityto enervate smooth muscle and the inability to relax striatedmuscle resulting in spasmodic paralysis and sometimes aconcurrent drop in blood pressure and difficulty breathing. Somevenoms also contain highly competitive antagonists that preventacetylcholine from binding at the postsynaptic membranereceptors, also causing neurotoxic symptoms and often apnea andasphyxiation will result. DNase and Rnase are enzymes thatdegrade DNA and RNA respectively. NAD Nucleotidase degradesnicotinamide, which is an important part of the cellularmetabolism machinery. Cellular respiration is interrupted andcell death may ensue. L-Amino acid oxidase is found in all knownsnake venoms. Procoagulants cause blood coagulation to occur;conversely Anticoagulants prevent blood from clotting. Bothchemicals may be found in the same venom, which is perplexingsince they may antagonize each other. Anticoagulant action ismore frequent and will cause bleeding at the site of envenomationas well as internal bleeding and tissue edema.

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