The BE&HM Series ~ Part VIII: Electron "Ownership" & Non-Reversible Oxidation

Previous posts in this series: Biophysical Electrochemistry and Human Metabolism, Part II: Atoms & The Periodic Table, Part III: The Main Group Elements, The Octet Rule and Ions, Part IV: Ionic Compounds, Elements & Oxidation State Defined, Part V: Covalent Bonding & Molecules, Part VI: Electron "Ownership" & Polarity, Part VII:  Chemical Reactions

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In a lot of the discussions of mitochondria and the various metabolic pathways in general, the term "redox" gets thrown around a lot.  Redox is a contraction of the terms reduction and oxidation.  This generally applies to reversible reactions where one species is oxidized and the other reduced, but it actually applies to all reactions wherein electrons are "transferred" from one element to another.  Where I'm going here (and I don't know when I'll get there, but I will)  is to discuss redox couples and basically how we are electrochemical machines where one chemical reaction is coupled with another -- the energy released from  the favorable reaction drives the otherwise unfavorable chemical reaction to which it is coupled.

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The BE&HM Series ~ Part VII: Chemical Reactions

It's been a while here, and I'd really rather move forward on some other topics, but I had most of this already in the "hopper" and wish to refer to it in a coming post on calories, so a couple of shorties here.  Also since it's been a while, here are links to the other posts in this series (in order): Biophysical Electrochemistry and Human Metabolism, Part II: Atoms & The Periodic Table, Part III: The Main Group Elements, The Octet Rule and Ions, Part IV:  Ionic Compounds, Elements & Oxidation State Defined, Part V:  Covalent Bonding & Molecules, Part VI: Electron "Ownership" & Polarity.

Most of this is copied from another post here at the Asylum, so if it seems familiar to any regular readers, that's why.  I'm going to be using the combustion of methane as an example in the next post on oxidation, so I might as well use it as an example here.  

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The BE&HM Series ~ Part VI: Electron "Ownership" & Polarity

Back to our regular programming ...

In the last post in this series I discussed covalent bonding, the type of bonding involved in most biologically relevant compounds.  Covalent bonds:

• Are formed between non-metals
• Are formed such that each constituent atom "feels complete" with 8 e's in its valence shell (H = 2e's)
• Involve the overlap of valence orbitals
• Involve the sharing of unpaired electrons to form bonding pairs
• Can involve one, two or three pairs of shared electrons to form single, double or triple covalent bonds

In this post we'll discuss one of the concepts that makes the world go round.  Well, it's not responsible for the rotation of the earth, but in terms of properties of compounds -- how they behave  with other compounds, react, have a propensity towards oxidation, etc. and molecular structure (e.g. think protein folding), polarity plays a key role.   And it all starts with the unequal sharing of electrons in covalent bonds.

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The BE&HM Series ~ Part V: Covalent Bonding & Molecules

In the last installment I discussed how atoms in Groups IA and IIA have only 1 and 2 e's in their valence shells respectively. These atoms satisfy the Octet Rule by losing those electrons to become +1 and +2 cations.  On the other side of the periodic table, Groups VIA and VIIA have almost filled valence shells containing 6 and 7 e's respectively.  One way these atoms can satisfy the Octet Rule is to take on 2 or 1 electron to become -2 or -1 anions.  Ionic compounds are formed between at least one cation and one anion so that the substance formed is electrically neutral, held together by the electrostatic force of attraction between oppositely charged ions.  Ionic compounds must contain at least one metal (cation) and one non-metal (anion).

Covalent compounds are bound by means of electron-sharing.  Covalent compounds are formed from non-metals only.

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The BE&HM Series ~ Part IV: Ionic Compounds, Elements & Oxidation State Defined

In the last post, I discussed the Group A, aka the Main Group, elements.  The chemical behavior of atoms  -- how they react/combine with other atoms in "the environment" -- is determined by the way electrons are configured orbiting about the nucleus.  All Main Group elements (with the biochemically relevant exception of hydrogen) share a valence shell (outermost shell) with 8 "vacancies" for electrons.  Having a filled valence shell with 8 electrons is the preferred energy state for these atoms -- this is called the Octet Rule -- and these atoms react/combine in order to satisfy this rule.  The atoms in each group (or column) contain the number of electrons in the group number, thus Na is in Group IA has 1e, C in Group IV has 4 e's, and Br in Group VII has 7 e's.

The Group IA and IIA elements lose electrons to form cations to meet the Octet Rule when the next lower filled shell now becomes the valence shell.  The Group VIA and VIIA elements have mostly filled shells and will gain electrons to completely fill them.

In this installment I'll discuss how different atoms combine to form unique substances called compounds.   One type of compound, ionic, will be discussed in detail, and the formation of an ionic compound shall be used to introduce the concept of oxidation state.

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The BE&HM Series ~ Part III: The Main Group Elements, The Octet Rule and Ions

In the previous part of this series, Atoms & The Periodic Table, I went into how the structure of atoms is related to the construction of the Periodic Table of elements.  Some take home points:

• The mass of an atom is highly concentrated in the central nucleus made up of protons and neutrons
• The volume of an atom is determined by the space "swept out" by the essentially massless electrons orbiting the nucleus.

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The BE&HM Series ~ Part II: Atoms & The Periodic Table

As I outlined in the introductory post, Biophysical Electrochemistry and Human Metabolism, many of the reactions involved in human metabolism might well be better understood by understanding electrochemistry which deals with redox chemistry and the physical chemistry of ionic gradients and diffusion.  But in order to get to that, I think it is important to lay the groundwork of the chemical nature of all matter.  And while I could send you to any number of tutorials about the net, I thought it worth my while to put the content here.  

Atomic Structure

The basic unit of all matter is the atom.  While there have been all manner of subatomic particles and such in the news, we really don't need to "go there" and the most simplistic model of the atom holds up fairly well for discussions of both biochemistry and electrochemistry.  Atoms are comprised of three particles:

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• Protons:  mass 1 amu, +1 charge
• Neutrons:  mass 1 amu, 0 charge
• Electrons:  massless* , -1 charge

The number of protons tells you what you have, and is called the atomic number.  For example the simplest atom is hydrogen, H, atomic number 1 meaning it has one proton.  The next atom is helium, He, with two protons, atomic number 2.  We can't add a proton to an H atom to make it a He atom or remove one from He to make H (we're not going into fission/fusion land here). 

* mass e <<< mass P or N, so negligible in the context of the atomic mass. 

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Biophysical Electrochemistry and Human Metabolism

Oxidation is a word that gets tossed around a LOT in discussions of nutrition and metabolism.  And for good reason -- it is integral to how our bodies "burn" fuels for energy and how that energy is harnessed to drive all manner of chemical reactions.    I spent my graduate years studying oxidation -- in metals -- but in many ways the principles are the same.  A little while ago I came across the following paper:  The Pecking Order of Free Radicals and AntiOxidants: Lipid Peroxidation, α-Tocopherol and Ascorbate.  In it we find the following chart:

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