Cogito et scio invicem . . .








A Treatise: On the Chemistry of Living Things

                                                            By Marilynn Stark     


         In pure chemistry empirical observations  of changes in matter can be studied when these changes fit into discrete categories of combinations of compounds.  When these compounds undergo reactions, these reactions yield products which can be quantitatively predicted as balanced with their original reactants.  Various  universal-level laws  have been observed in regards to these chemical reactions, such as the conservation of energy.  Much of the understanding of the chemical events which actually comprise a living cell, or affect a given molecular structure or inter-molecular event, indeed, which allow the empirical truth of life itself at all levels of ordination to be sought after, arises from the simple chemical event, the balanced chemical equation, or the chemical interactions which can be inferred from the fundamentals of chemical reactions known to arise from the periodic nature of over one hundred categorized elements.

     For example, a given enzyme may act as a catalyst in the metabolism of a cell, which lowers the activation energy needed to drive a given mechanism in that metabolism.  These energetics are quite indirect as compared to the probability of a sheer chemical reaction which would occur according to the known reactivity of elements as derived and tabulated in the Periodic Table, and in controlled conditions predetermined by an empiricist, an experimenter.  Yet, imagine how carefully such energetic mediators as catalysts guard the preservation of life in a cell, and how they mediate by lending a certain harmony.  Biological norms, such as temperature [37 degrees C], must be maintained.  A reaction might be caused by an input of heat, yet, heat has the power to denature protein.  And protein, all protein, has a structure whose precision is vital to the inner workings of the chemistry of the cell, and this can be expanded also unto the system's level of the living organism.  The most wondrous intricacy of life-supporting chemistry arises out of the sheer structure of the material of life, wherein and whereupon, as well as in and through, do chemical events occur, mediate, and simply direct everything in a thriving manner.  Yet this manner of living things can only thrive  because of the precision of the structure, the multi-faceted  and complex structure, of the constituents of  living matter; for function derives its utility from the nature and perfection  of matter in quite a fundamental way.  Ongoing life, even as we observe growth and general characteristics of living things, is nothing  more than  organized function.

     Many of the imbalances and imperfections which crop up in medical science and in various other disciplines in the sciences concerned with human physiology and biology in general, teach us how to better inquire after normative behavior in certain considerations of function as it relates to structure.  These questions inevitably and always  concern themselves with the building blocks of chemistry.  The expanse of chemistry as derived from empirical work in the laboratory is thus quite totally relevant and vital to a more full grasp of living things at any level of inquiry, from molecule to cell to organism to even effects of the atmosphere on the longevity of the planet's climates and seasons, if not even the planet,  if one pursues the argument completely.   

     Thus, to form a treatise which concerns itself with the functions of biological activities and topics, which finds its source in the plethora of chemical reactions based upon sheer chemical structure, should allow a thinking biologist a better grasp of the basics which are essential to fully understanding the living being, and how that being relates to ongoing life, procreation, preservation, vitality and its environment, to the fullest extent possible.  Chemical bonding has elucidated the profoundly challenging question of structure at the molecular level.   Since the function which occurs interfaced with this structural universe of molecules is dynamic,  it naturally involves complex chemical changes at many levels of observation.  And further, most of this chemistry, whether at the cellular, organelle, tissue, systemic or organismic level, is actually roundabout in comparison to the straightforward chemical interactions derivable from mere elements  and compounds reacting in a test tube or in a clinical laboratory for research.  The most accurate way to unravel and fully understand this indirect chemistry, whose conditions, reactants, energetics and functional success rely upon the miraculous power of ordered life;  whose preservation and nature rely upon the precise structure and inter-relatedness of functioning substructures, superstructures, and internal systems and milieus whose chemical constituents and constancy must be known; whose destiny also as topics in research for a growing span of knowledge by scientific man;  for all of this, the indirect nature of the chemistry thus sought after in studying the mysteries of life, lends itself to the prerequisite knowledge of pure chemistry and chemical fact: compounds by structure, name, characteristics and bonding; compounds by functional groups, and interactions thereby, their syntheses and also their element comprise, even as to the question at certain instances of constituent particles and the very nature of subatomic matter and energy.  These chemistry building blocks must be built in the working knowledge of a biological entrepreneur who sets out upon the dimensionally multivariate inquiry, 'What is this', in reference to living things.  For if the simpler chemical nature of sheer elements and compounds is explored  first for its dynamic possibilities, then the potential of that simpler chemical understanding can be brought to bear upon the more diffuse and indirect questions and challenges which are inherent to the  structure/function couplet in biological questions.  For it is this structure/function couplet which  complexifies biological science, until basic though elaborated chemical knowledge simplifies it once again into a one-to-one correlation of structure-to-function, as the unknown field of objective fact is empiricized successfully through the chemistry of life.


                                Raw Elements As Derived from Nature


      As  one contemplates the elements, the fundamental physical entities whose distinct properties and atomic structure make them discernable as collectives of matter now individuated into identities non-subdivisible for gross-level observable changes, one is actually defining in this day the superstructure of the natural world.  For instance, an iron skillet used in cooking may require constant lubrication with cooking oil in order to prevent the formation of iron oxide.  Although this metal may be an alloy of iron, the raw element of iron makes its presence known as it presents  rust to challenge the cook.

     The elements found in nature, in the Earth's store primarily in the crust, are reflected also in the material composition of living things, wherein the selfsame seemingly inert matter at the microcosmic juncture of  the living being displays the activity which works collectively to comprise none other than life's leading, distinguishing characteristic at the macrocosmic juncture: action.  This should be observed as the supportive principle of life for its vitality, its dynamic interest.  Such action may be self-willed as in the animal kingdom, or it can be even growth movement, or motion of the plants in their natural surround.   In either case, the distinct chemical elements of the physical  world as categorized for their periodic chemical properties  are hypostatic to what we can perceive  and empirically know of the world of living beings.  What we know and learn as scientists can work to preserve in the best interests of all  in both the plant and animal kingdoms--and of the entire ecosphere.  

     Indeed, the word element is taken from the Latin  elementum, which has the meaning of literally, usually in the plural, 'the physical elements.'  Then metaphorically the idea of 'the first principle' implicit in the physical element is extended to mean, according to Cassell's New Latin Dictionary, 'the beginnings of other things.'  How is it that the ancients could discern the true essence of matter as it relates to composition, such that an observation of how things are ordinated by basic building blocks of substance known to be elements, could guide their understanding?  This is a didactic query, for it is upon that conceptual foundation that our current-day knowledge was even built through the power of empirical science.  Early alchemists contributed to the growth of the science we now regard as chemistry, and this is the study of how elements which can be combined into compounds, through the interlocking of their shared atomic-level characteristics in the formation of those compounds, actually interact and comprise the chemistry of the living world in us and about us. However, the discovery of the myriad elements of the chemical panoply at our current command in the science of living things was derived largely from nature's raw materials, which were separated out into the respective elements, named and characterized for their properties.  This was inanimate matter, found in nature's raw materials, which began to make possible deeper biological sciences.

     The driving need to survive in life is awarefully brought into the study of living things, and is often therefore sought after in the stead of the internal biochemical conditions which normally mediate in the harmony of ongoing life's activities.  However, unless the basic elements are understood in the raw chemical sense for how and even why they form compounds,  and which compounds react with one another, then the complex biochemistry of living systems and processes will be less well understood, even to the point of deficit, given the challenge which ecologically presents humankind at the world-level interface in this day of technology and nuclear science.   Simple chemistry  complexifies out into the world of living things, where proper analysis can only revert back to  how elements combine and interact and under what conditions.  Once again, the premise of this treatise on the chemistry of living things is to build a working perspective for any empiricist who approaches the intricacies of biological cells and organisms and collectives with the desire to learn more of them, from first chemical principles up.


                                      Hydrogen : The First Element


     Hydrogen allows a vector-type relationship in electrochemical events in the universe of chemistry, in both living reactions and inert reactions of the physical world.  Since the preponderance of hydrogen atoms have no neutron, these atoms just work in a very labile fashion in the world of elements and molecules, as if mediating from a dialectical lever the exchange of  energy in the form of electrons, the transposition of charge much as bare protons.  This type of dynamic activity stands contraposed to the power of radioactive decay in elements of greater atomic weight, whose isotopic variations in neutrons set forth mutagenic and potentially lethal energy change events.

     Thus, when considering the energetics of the chemical reactivity and ubiquity of the hydrogen atom and the hydrogen ion for their intermediacy in chemical events, the lack of a neutron in their nuclei confers upon these hydrogen species the  unique and distinctive role of sheer electrochemical vector, whose fundamental and unit level work set them apart.  Hence, hydrogen is a uniquely distinctive unifying element.  Indeed, hydrogen, although the lightest element of all, comprises the vast preponderance by weight in the entire universe, let alone a similarly vast prevalence by elemental abundance in that universe.  Even so, hydrogen comprises less than one percent of the Earth's crust by weight.

     And since hydrogen combines so famously with oxygen to form water,  which is both universal solvent and universal purifier,  hydrogen at this molecule level also expresses as an agent of purification.  Further, this purificatory trait can be extended beyond the realm of water in both the broad hydrosphere and aqueous parts of the living cell to include its place as reducing agent and unit-level bearer of positive charge in the world of living  physical matter, where it is also quite free of harmful energetic properties. 

     Thus, the first element of the Periodic Table, hydrogen, becomes the great divide in chemical bonding, as its likeness to a bare proton in prevalent chemical events brings about a certain non-individuation with respect to its actual status as an element expressing as  an atom.  Hydrogen is an atom whose single positive composite charge  can couple it in reactions essentially to a sheer electron of opposite and negative charge, yes, and which distinguishes the hydrogen atom, or ion, as the only element whose simplicity of structure or particle comprise, a simple proton bearing a unit positive charge, causes it to behave in such a manner of a highly non-individuated  element.  Indeed, it is as if hydrogen works as an atom now in transition chemically with other atoms and molecules, yet  in transition with a sheer atomic particle status, thus motivating in a peculiar though familiar way the biochemical energetics of living processes through its coupling with electron loss in covalent bonds.  As such a bare substance, then, hydrogen nonetheless acts as a powerful agent of change in the realm of all living substance much more  complex in atomic structure through this oxidation-reduction coupling.  Let us explore conceptually this trait of hydrogen to so obscond with its identity  through the loss of a electron, and thus exert so much wide leverage chemically among atoms and molecules in their dynamic changes.  Such a conceptual hold might prove strategically sound for any biological inquirer in the realm of the nature of living things, as hydrogen bonds typically with carbon to form much of the substance of the living world.  Since water is the actual medium of life, and water is yet hydrogen dioxide, knowing more of the nature, the properties and the typical behavior of  hydrogen, should become useful.  Nor can any aqueous environment be properly understood except for determining  how prevalent its pH, or 'power of hydrogen ion', its acidity or basicity.   

     Hydrogen is distinct for its tendency to combine ubiquitously and in most prevailing conditions, and this is so true, that it is virtually never found except in a gaseous state, and as in a vacuum where other particles are not present for so easy combination.  To wit, hydrogen gas at constant volume undergoing  an expansion due to a decrease in pressure at room temperature actually increases its kinetic activity or temperature.  This is true only of hydrogen gas, since other gases given the same change in conditions display a decrease in temperature.  The repulsive forces of diatomic hydrogen come to full avail in this instance, as they exceed the attractive intermolecular forces.  In an element of higher atomic number, such as oxygen, for example, the diatomic bond is formed by satisfying the octet rule.  The core electrons shield the respective nuclei from repulsive force effects which could otherwise occur, and the covalent bond force is in good prevailing effect. 

     However, hydrogen as a molecule has but two electrons in mutual bond.  Lacking other electrons to so shield the two nuclei from one the other, the repulsive effects between these two yet bonded nuclei are significant, and the intermolecular repulsion due to the highly unshielded nuclei are there  also, if latent.

      Indeed, most of the activities of living organisms are invested of hydrogen not as a gaseous presence.  Rather, hydrogen is found in the C--H bond of organic molecules, and especially also in the various functional groups whose ready susceptibilities to chemical exchanges actually form dynamically the internal, living milieu, and this against the backdrop of the pH of that aqueous environment.  To better understand hydrogen for its properties as a gas, however, will enhance the understanding of the full ambit of hydrogen's chemical capabilities.

     Furthermore, within the realm of the watery cell and living systems, consider that hydrogen gas can even be liberated from water in the presence of sodium or lithium, two electropositive metals which are powerful reducing agents.  Accordingly,


     Eq.1                    2Na[g] + 2H2O[l]  -->  2NaOH[aq]  +  H2[g]   .


     Eq.2                   2Li[s]  +  2H2O[l] -->  2LiOH[aq]  +  H2[g]   .


     Both reactions are exothermic; however, the sodium experiences a significant rise in temperature on the order of a flame [orange in color] in the laboratory beaker. 

     Figure 1 depicts the diatomic hydrogen molecule with its mutual sharing of two electrons, one from each hydrogen atom shared equally in a non-polar covalent bond. 


[Note: figures and diagrams to follow ...]


     Eq.3                             H  +  H  -->  H2  .


     However, this picture of a typical hydrogen molecule represents actually the most prevalent of forms possible according to valence bond theory.  For in the probability range of electron placement in a valence bond, although the most likely distribution constitutes even sharing as depicted in Figure 1, wherein the energy of the bond is lowest and therefore the molecule is most stable, the ionic-level electron distribution possibilities must also occur.  Therein, a resonance between the most probable equal electron cloud distribution and those of the less probable ionic placements of electrons will actually give greater moment to the repulsive force between the two yet bonded hydrogen nuclei, unshielded as they are.  It is important to realize that these ionic extremes in the resonating bond do not constitute an actual breaking of the H--H bond.  That is another question.  But since the ionic bond-level electron distribution possibilities do exist, when hydrogen gas at a given constant temperature isochorically expands due to an induced pressure decrease, these ionic-covalence resonant forms, whose repulsing nuclei are even more disposed to one another's repulsion, must further translate that electrostatic effect into kinetic energy from intermolecular nucleus-to-nucleus axes with other similar resonating forms.

     See the diagram below in Figure 2: 

[Note: sorry for the current blank here--will follow]


Eq.4                              H+H-  <-->  H--H  <-->  H-H+


Fig.2.  Ionic-covalent resonance of diatomic hydrogen, where the dotted lines indicate that the H--H bond is still in effect in the ionic bond extreme forms.


     In order to understand the multivariate  ways of hydrogen as it interacts chemically in living systems, review the diagram [Figure 3], which visually depicts the profound consequence of a unit positive charge, the hydrogen ion H+, which works among the most prevalent covalent bonds found in nature:


[to be posted]...


Fig.3.  The  Interaction Fundamentally of Hydrogen/Hydrogen Ion with Atoms of Partial Charge in the Covalent Bond  

     The partial charges between atoms of differing electronegativities in heteronuclear molecules formed by the electron-sharing of covalent bonds sets up a charge-based leverage for hydrogen, whether it acts in leaving or in addition.  Much of the activity in the cell, for instance, occurs in an aqueous environment, so that hydrogen as present in oxide form, H2O, is available for chemical events. Not only is it so available, it is energetically favorable for water to hydrolyze into its ionic components.  Viewing the ions of water as in a deprotonation event, 


Eq.5                              OH-  +  H+  =   H--O--H


the D(r)G=+1607.1kJ/mol for this reaction, where D(r)G is the Gibbs free energy of reaction.  (Ref.: NIST Chemistry WebBook)

     Thus, the presence of hydrogen as a cation is typically expected, even if weakly, since the thermodynamic likelihood is there for it with such a positive Gibbs free energy value for the formation of water from its ions.  These hydroxide ions and hydrogen ions further carry out the energetically favorable hydrolysis of organic macromolecules, as well, which dominate in the molecular events that energetically favor catabolism over biosynthesis.  (See ahead in Figure 4a).  Yet hydrogen acts as a vital assist in the tendency of the bio-universe to oxidize, to give up energy in the form of electrons  which can accomplish work when harnessed molecularly, or even electrochemically, and in the form of heat.  This free energy, or the energy available to do work, expresses more directly through the element oxygen, whose ability to attract electrons  contradisposes  hydrogen's ability to give up its lone electron.  Thus, in the great biosphere  where oxygen gas is available, oxidizing  occurs, as it does as well in the cell and in the living systems comprised of cells.  Here the basic equation for both realms in words amounts to:


Eq.6.              matter  + oxygen  -->  carbon dioxide  +  water   .


Whether it is wood burning in the air and forming smoke, ashes, CO2 and H2O, or iron oxidizing into ferric oxide, Fe2O3; or glucose entering into the glycolytic pathway in the cytosol of a eucaryotic cell; the respiration of substance, of matter, is an energy-yielding process.  The energy is made available for such yield fundamentally in the form of electrons.  Hydrogen works as an assist to those electrons by virtue of its opposite charge to electrons.    Hydrogen ions also contribute to the electrochemical gradient in cells by posing the force of collective charge while at the same time constituting a concentration gradient across cell membranes.  In the vital metabolic events of cell respiration the chemical energy of hydrogen is first sent into the electron transport system of the mitochondrial inner membrane as NADH loses a hydride ion, H-.  This interesting hydrogen species had arisen out of  the resonating characteristics of the nicotinamide ring, wherein the less stable, non-resonating  reduced form easily contributes a hydride ion in favor of the more stable resonating form, NAD+.( See Diagram 1.)  The two high- energy electrons from the hydride ion are separated from it and sent into the electron carrier protein chain, while the remaining H+ ion, or proton, is pumped outward into the intermembrane space where it contributes to the proton-rich gradient so formed across this inner mitochondrial membrane.  Even though the protons of these hydrogens separate from their electrons at several steps along the way down the multi-step electron carrier system, they do transiently recombine with electrons.  The energy made available by successive exchanges between the electrons with resonating metal complexes in these protein passages actually pumps the protons back out into the intermembrane space.  Then finally, the protons, if in a high enough concentration, will be enzymatically taken up by the transmembrane-protein ATP synthase.  They will further  combine with the electrons through the chemical bonding  available with oxygen as oxygen is reduced through the cytochrome oxidase complex by the acceptance of the electrons having been so passed.  This forms water, and the proton movement inward also causes the formation of ATP from ADP plus Pi through the action of ATP synthase.   See Equation 6 and Equation 7 :


Eq.6.                              H2 + 1/2O2 --->  H2O

Eq.7.                              ADP + Pi  --->  ATP

     Thus, hydrogen ions regain atomic status in the process cited above, which is known as 'oxidative' phosphorylation due to the stepwise loss of energy in the electron transport system, yet this status is regained by hydrogen only after


                                      AD--P(OH)/////Pi -->  AD--P(OH)...Pi  ,     where /////represents schematically a hydrogen bond between the oxygen of P=O of Pi  and the hydrogen of an OH of ADP, and ...represents ithe breakage of that hydrogen bond.  (See Diagram 2 for elaboration).

     It can be seen further that any such hydrogen held in a hydrogen bond by the powerful electronegativity of oxygen will experience the ionic extreme valence bond state, wherein its electron cloud distribution will leave its nucleus with its positive charge open to the repulsive force of a travelling hydrogen ion coming down its gradient.  Such nucleus-level repulsive force  between the actual hydrogen ion or proton and the hydrogen of the hydroxyl group as shown above and in Diagram 2, will be likely to cause the hydrogen bond to break and the hydrogen of the hydroxy group to even hydrolyse.

     Even before considering the reverse case, wherein ATP in different conditions in the cell hydrolyses instead, the utility of hydrogen to work as an intermediary between the more rarefied energy of a sheer electron, whose mass is 1/1836 the mass of hydrogen, and mass itself no matter the amount, is unfolded in this case of the conversion of electrical potential to chemical formation.  The function of hydrogen in the physical universe is to be a go-between in the question of the conversion of mass to energy.  By interacting through charge attraction with its complement, the smaller electron, whose mass becomes negligible in electrochemical frameworks of activity in biochemical systems, the hydrogen ion bridges the tendency of matter to catabolize by thermodynamic principles, back to a continuation of the state of matter.  For mass and energy are conserved and equivalent according to the First Law of Thermodynamics, such that when matter is oxidized, its loss of electrons is the beginning of its transformation potentially into sheer energy if even through the giving off of heat in the process of combustion.  Things tend to greater disorder.  And because the structure of hydrogen lies in a balance between mass and energy through single values by number for protons and electrons, and through a single positive charge in its cationic form, hydrogen will work physico-chemically to regroup the rarer energy changes made possible by the energy attributes of labile electrons, the actual "stuff" of chemical bonds, which constantly abandon matter.  This coupling of the element hydrogen with the loss of electrons has a double-agency about it, since when hydrogen leaves a molecule, it also oxidizes that molecule, taking with it more mass of course than does its complement, the electron.

     It is hydrogen that comes full circle in the world of biological matter, for it as an ion re-enters through charge attraction to the negative partial charge of the typical covalent bond, and reorganizes, calls back to matter through such activity as a reduction equivalent, and brings about a significant balance in the favor of structure over function first, since it carries more mass than an electron, and which dialectical coupling generates the likely expression of function through the integrity thus retained of structure, of prevailing mass or substance. Consider the simple energetics of the equation  1/2 O2  +  H2  =  H2O.  If this were to occur in a laboratory situation, there would be an explosive event wherein most of the chemical energy would be expressed as heat given off.  Yet, in the living cell, oxidative phosphorylation allows the stepwise process of the electron carrier chain to take down the energy of the electrons in a roundabout way through the chemiosmotic coupling discussed here, and finally gently combine electrons with oxygen and hydrogen ions to form water.  See Figure 4B for a schematic of this discussion.

In apologies...please be patient...Marilynn   

2001 By Marilynn Stark


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