My related essay on Photosynthesis is here: Photosynthesis
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        Here is an essay on how eukaryotic (animal and plant) cells use energy (from imported high energy glucose molecules) to control their ion concentrations, membrane voltage, water, and do various specialized jobs.
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Reference
        1 ) 1 ev = 23.1 kcal/mol = 96.5 kj/mol
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Introduction
        Learning about photosynthesis with its specialized membrane processes powered by photon energy made me curious about how cells (in general) handle energy. Amazingly no reference I have found gives the big picture on energy, it's all details. As I have learned more about cells, there does appear to be a relatively simple big picture about how from an energy viewpoint cells function.

Big, big picture -- cell energy and photosynthesis
            The ways in which energy in a cell is used has a lot in common with the ways plant chloroplasts capture the energy from solar photons. Consider

In a cell
          *  local regions in the cell (mitochondria) use energy from imported glucose to make
                    a proton gradient
          *  energy from the proton gradient is transferred (by ATP synthase) to (recycled)
                    ATP molecules
                         -- glucose (C6H12O6) has atoms of only carbon, oxygen and hydrogen. The
                                oxidation of glucose releases its hydrogen and oxygen as a water byproduct
                                and imported oxygen (from respiration) combines with the carbon of
                                glucose to form CO2 byproduct. The oxidization of glucose releases
                                2,870 kJ/mole of energy (which went into making it) about half of which
                                is transferred to the ATP molecules (50% conversion efficiency).
          *  energy extracted from ATP molecules powers the major ion pump of the cell
                     (generates K+ and Na+ gradients), and runs many cellular functions, like
                      generating heat, powering muscles and flagella
           *  energy from the K+/Na+ gradient is used by many other membrane pumps and
                     transporters

In a chloroplast
         * local regions in the chloroplast (photosystems) use electrons energized by photons
                  to make a proton gradient
          *  energy from the proton gradient is transferred (by ATP synthase) to (recycled)
                   ATP molecules
          *  energy extracted from ATP molecules run local cellular functions, like ion pumps
                    to make ion gradients
          *  local regions of chloroplasts use energy from ATP to make glucose which is exported
                    as an energy source to the rest of the plant
                        -- glucose (C6H12O6) has atoms of only carbon, oxygen and hydrogen. The
                                carbon and oxygen come from CO2 (pulled from the air) and the hydrogen
                                from water (pulled up by the roots). Excess oxygen (from the water) is
                                released into the air as a byproduct. Synthesis of glucose requires an input
                                of 2,870 kJ/mole of energy, all of which comes from captured solar
                                photons.

Cell energy overview
        All animal and plant cells (eukaryotic cells) take in fuel in the form of sugar (glucose) and bring it into microchondria, which are separate, isolated regions of the cell (organelles), where it is burned (oxidized) producing by-products CO2 and H2O. The microchondria use the energy obtained from the sugar to make the energy rich molecule ATP that is exported into the cell.

        ADP/ATP is an energy carrier molecule within the cell. Energy is stored in the molecule by attaching (via a covalent bond) an extra phosphate (phosphorus atom with oxygens), and energy is extracted by popping off a phosphate. It cycles between having two phosphate groups (ADP is Adenosine Di-Phosphate) and three phosphate groups (Adenosine Tri-Phosphate). So microchondria take in ADP and add energy by adding a phosphate group creating ATP. Various processes in the cell, like ion pumps in the membrane, get the energy they need by popping of a phosphate group from ATP, taking it back to ADP.

        The cell uses a lot of the ATP stored energy to run ion pumps. The cell pumps in potassium, and pumps out salt (sodium and chloride) and calcium. The pumps regulate the concentration of the major ions in the cell fluid,  keeping potassium ion concentration always high and the sodium, calcium, and chloride ion concentration always low. The big, main pump of the cell is the Na+/K+ ATPase transporter, which pumps potassium (in) and sodium (out), other pumps handle calcium and chloride ions. The pumps are large complex proteins that span the cell membrane.

        The enzymes that use ATP for energy (ATPases) perform what the chemist call a coupled reaction. Some of the energy released when the phosphate bond is broken (exothermic reaction) is captured to perform work and the rest goes into heat. One 'turn' of the Na+/K+ ATPase pump uses the energy of one ATP (ATP => ADP + Pi) to pump 3 Na+ out of the cell and 2 K+ in.  (net charge flow outward)

        Most of the energy that the pumps expend building up the concentration gradients is not lost, it is stored in the concentration gradients that the pumps create. This energy is available to other proteins that live in the membrane. By opening an ion diffusion channel across the membrane energy can be extracted from ions diffusing down their concentration gradient. One example of this is the Na+/glucose pump. The energy it needs to pump glucose into the cell comes from it providing a channel for Na+ ions to diffuse into the cell, down their concentration gradient.

        Another (classic) example of using concentration gradients for energy occurs in chloroplasts doing photosynthesis. Here a high gradient (10,00 to 1) of protons (H+) pumped up by the energy from captured light photons is used as a source of energy to make ATP in the chloroplast's membrane. This process is called chemiosmosis (by analogy with osmosis) and the enzyme that makes ATP is called ATP synthase. The understanding of this has been called one of the seminal discoveries in biology in the 20th century and won Mitchell Nobel prize for Chemistry in 1978.

        Mitochondria organelles in cells also make ATP using a proton gradient and the enzyme ATP synthase. In this case the proton gradient is only about 10 to 1 and the energy needed to create it comes from the oxidization of glucose. The protons just circulate around, pumped in and then diffusing back out. The potential across the mitochondria membrane is -200 mv (inside negative).   (Bacteria make ATP using chemiosmosis too.)

Synthesis of ATP by ATP synthase in mitochondria

          In mitochondria the PMF (proton motive force) is almost entirely made up of the electrical component but in chloroplasts the PMF is made up mostly of the pH gradient. In either case the PMF needs to be about 50 kJ/mol for the ATP synthase to be able to make ATP.

        The energy used by human cells requires the hydrolysis of 50 to 75 kg of ATP daily, which means a human typically will use up their body weight of ATP over the course of the day!  However, the total quantity of ATP in the human body (at any one time) is about 50 mg. This means that each ATP molecule is recycled 1,000 to 1,500 times during a single day (50 kg/50 mg  = 1000). (1,000 times a day is each ATP being recycled every 86 sec). ATP cannot be stored, hence its consumption closely follows its synthesis.

               ATP (combined with water)                          30.5 kj/mole (7.3 kcal/mole)
               Energy (0.1 mole ATP)                                 3.05 kj
               Power  (0.1 mole every 86 sec)                   3,050 j/86 sec
                                                                                        35 watt

        I found a reference that states the efficiency of energy transfer from glucose to ATP (in mitochondria) is approximately 50%. This means 70 watts of food energy are needed to get 35 watts into ATP.

Check
           If you eat 2,000 (nutritional) calories/day, this is (2,000 kcal/day x 4.18 j/cal) =  8.36 million j/day. A day has 86,400 sec, so the power provided by eating 2,000 cal/day is about 100 watts. Hence, about 75% of 2,000 food calories is used in the ATP synthesis process with about half of this energy making its way into ATP.  Checks.

        Another interesting, related topic is how the body cools itself, How does it dump the 100 watts or so that it is continually extracting from oxidizing food. There are three major routes for heat to leave the body: convection, radiation, and respiration. Here some estimates I found which look reasonable (for low activity):

                Convection (heat transfer from skin to air)            65 watt
                Radiation  (skin 6F warmer than ambient)              24 watt
                Respiration (exhaled warmed air & H2O)             11 watt
                                                                               ------------------------
                                                                                total           100 watt

Organelles
        Organelles in eukaryotic cells (cells of everything except bacteria and archaea) are sort of like cells within cells. Wikipedia says, "an organelle is to the cell what an organ is to the body." Organelles are small regions of the cell, isolated from the rest of the cell with a membrane, that do specific jobs for the cell, and even have their own DNA.

        Examples of organelles are microchondria, which oxidize fuels to make energy for the cell and chloroplasts, which do photosynthesis. There can be a huge number of organelles in a cell. A typical eukaryotic cell contains about 2,000 mitochondria (about 20% of its volume).  A good case can be make that organelles chloroplasts and microchondria were originally free living bacteria (cynobacteria) that got captured (a process called endosymbiosis) by plant and animal cells.

Cell membrane voltage (overview)
        All cells normally maintain a voltage across their cell membranes (-80mv or so). They use this voltage to pull molecules they need (like sugars) into the cell from the outside. The E field across the cell membrane points inward, so the cell can only pull in (via this mechanism) positively charged outside molecules or ions. Glucose (sugar) get pumped in with positive sodium ions (Na+) though channels where energy is available from the sodium ions that feel an inward force from both the E field and the sodium concentration gradient.

        Cells generate the membrane potential by a two step process. First they do work ('burning' fuel ATP) pumping ions (mostly potassium K+) into the cell. This pumping does not (directly) produce a membrane potential, because (somehow) the inside of the cell is initially neutral with a balancing negative charge residing on proteins in the cell. (Are electrons being pumped in too?) It's important to note that the positive charge resides on something tiny and mobile (nucleus of an atom) compared to the carrier of the negative charge (protein) that is large and relatively immobile.

        Second step is open (potassium) ion channels allow K+ ions (only) to begin to passively diffuse down the concentration gradient toward the outside. K+ ions actually diffuse through the ions channels in both directions, but because the concentration of K+ inside the cell is much higher than outside the net result is diffusion of positive ions out of the cell. The negative charge, unlike the positive charge, is unable to get out of the cell, because it resides on proteins, which are far too large to fit into the small, open, ion channels. The (net) diffusion down these ion channels soon stops, because the net negative charge inside the cell cause an inward pointing E field to appear that opposes the outward diffusion pressure of the positive ions.

        A slightly more technical (& obscure) explanation I found puts it this way:

        There are two forces acting on a given ionic species. The driving force of the chemical concentration gradient tends to move ions down this gradient (chemical potential). On the other hand the electrostatic force due to the charge separation across the membrane tends to move ions in a direction determined by its particular charge. Eventually an equilibrium can be reached so that the actual ratio of intracellular and extracellular concentration ultimately depends on the existing membrane potential.

Ion transport across membranes
        Cells normally keep ion levels inside (relative to fluid outside) as shown below.  The second column lists the permeability (which looks like a diffusion constant). These values are for mammalian cells.

                             ion                                    concentration                    diffusion rate
                    ----------------                        ------------------                 -------------------
                      potassium (K+)                      high (x 20)                      5x 10^-7 cm/sec
                       chloride (Cl-)                        low (1/10)                       1x 10^-8 cm/sec
                        sodium (Na+)                       low (1/10)                        5x 10^-9 cm/sec
                       calcium (Ca2+)                     very low (1/10,000)

        Note cells normally pump up their (internal) potassium concentration and pump down the concentrations of all the other ions (sodium, chloride and calcium).

        These ion flows do not imply a (substantial) charge imbalance. I'm not sure how this is managed but (apparently) electron (?) and proton concentrations are adjusted too. A small charge imbalance, say due to a loss of positive internal charge, is able to produce a (typical) -70mv internal voltage. All that is needed is to open a potassium diffusion channel. After a small quantity of potassium ions (positive charge) diffuse out a voltage and electric field then develops across the membrane pointing inward, which pushes the positive ions inward stopping the diffusion. (Well really what happens is that diffusion currents outward are canceled by electric drift currents inward.)

        Also note that (rapid) flows down the concentration gradient of either (or both) of the lower two ions (Na+ and Ca2+) can (rapidly) 'flip' the membrane voltage, driving the inside of the cell positive, and that concentration gradient flows of K+ and/or Cl- can reverse the flip. This is in fact how so called 'active cells' like nerve and muscle cells work, followed by recovery period (refractory period) while the cell's ion pumps restore the concentration gradients.

Na+/K+ ATPase transporter
        Cells (eukaryote cells of animals and plants) have ion pumps in their membrane (powered by burning ATP) that pump potassium ions (K+) into the cell and pump sodium ions (Na+) out of the cell. In fact the same pump does both jobs (Na+/K+ ATPase transporter), and it changes concentration levels about a factor of 10. References say for every two K+ pumped in, three Na+ are pumped out. (Is this ratio fixed? Does this lead to a loss of charge in the cell?)  Below is a link to a neat animation that shows the Na+/K+ ATPase transporter working (inside of cell is below).

        http://www.stolaf.edu/people/giannini/flashanimat/transport/secondary%20active%20transport.swf

        The crucial roles of the Na+/K+ ATPase are reflected in the fact that almost one-third of all the energy generated by the mitochondria in animal cells is used just to run this pump. It looks (to me) that the Na+/K+ ATPase pump is the primary engine of the cell. The potential energy that this (fuel burning) pump stores up in the concentration gradients (of K+ and Na+) and in the membrane electric field is available to be tapped by other (secondary) engines that do work in the cell, for example, the Na+/glucose transporter (below) that brings in glucose.

         Mitochondria are organelles in cells that make ATP (used for energy in the membrane and throughout the cell) by oxidizing food molecules (glucose) breaking them down into CO2 and water. The sugars are the external source of energy to the cell. The 'eating' of sugars (food molecules) by mitochondria inside cells is sometimes called (misleadingly) cellular respiration.

Na+/glucose transporter
        One the right side of the (above) animation some of the pumped out Na+ ions are shown diffusing back in bringing in glucose molecules with them. In the long term, of course, all ions pumped one way must later diffuse back (generally through other paths) to keep the cell's ion concentration and charge in steady state. Here is a more technical description of the Na+/glucose pathway:

Na+/glucose transporter --- This transmembrane protein allows sodium ions and glucose to enter the cell together. The sodium ions flow down their concentration gradient while the glucose molecules are pumped up theirs. Later the sodium is pumped back out of the cell by the Na+/K+ ATPase. Note an ion flowing down its concentration gradient can do work. The energy needed to pump the glucose is being extracted from the sodium, which is why their paired. Technically this pairing is called 'Indirect Active Transport'.

"Na+/Ca2+ exchanger uses the energy that is stored in the electrochemical gradient of sodium (Na+) by allowing Na+ to flow down its gradient across the plasma membrane in exchange for the countertransport of calcium ions (Ca2+).

Ion channel conductances
        Across the membrane there are channels for specific ions (mainly K+, Na+, Ca++, Cl-). Ions move across the cell membrane through these channels (when open) under the influence of concentration gradients (chemical potential) and the electric field, which depends on the membrane voltage. For K+ and Cl- the force from the inward pointing E field tends to cancel (much of) the pressure from the concentration gradient. However, for Na+ and Ca++ the E field and concentration gradient are aligned in the same direction, both pushing the ions into the cell. A consequence of this (I think) is that normally Na+ and Ca++ channels must be closed, whereaas K+ channels (and maybe Cl- channels) can (probably) remain open.

        To an electrical engineer these channels are like a bunch of resistors in parallel each ion channel having its own resistance (conductance). The flow of ions (which are charged) is, of course, a current. So ohms law applies, and each ion current = (membrane voltage)/(its channel resistance). The voltage required to stop diffusion down an ion channel is called the Nernst potential, and its formula (for K+) at human body temperature (37C) is below.

                            E = - 61 mv x log (K+ inside/K+ outside)

        Since the log function is base 10, a 10:1 concentration ratio yields 61 mv and a 100:1 ratio 2 x 61 mv = 122 mv. For a typical potassium concentration of K+ inside the cell x20 higher than outside its Nernst potential is E = - 61 mv x log (20) = - 79 mv.

        The polarity of the Nernst potential depends on both the polarity of the ion and on whether the inside concentration is higher or lower than outside.  For potassium, which is a positive ion with a higher concentration inside, the membrane voltage is negative (inside relative to outside). For sodium, also a positive ion but with higher concentration outside, the voltage is positive.

        It turns out that in animal cells the membrane voltage is pretty much set by the potassium ion (K+). The reason for this is that the conductance of the K+ ion channel is much higher (by about a factor of 20) than the other ion channels. (In simple terms --- the potassium channels are open and the other ion channels are closed.) This results in a cell's resting membrane voltage being usually just a little lower (in magnitude) than the voltage needed to stop K+ from diffusing down its ion channel and out of the cell. Typical numbers (for a heart cell) are membrane resting potential -90 mv, whereas its K+ Nernst potential is -96 mv. This less than complete cancellation (6 mv) leads to a slow, but steady, 'potassium leakage' out of the cell, which is compensated for by pumping K+ back in using the main Na+/K+ ATPase pump.

        For Na+ and Ca++  the E field and concentration gradient are aligned and pushing inward. The flow rate of these ions is low only because these ion channels have a very high resistance, in other words these channels are basically closed..

Circuit model of the membrane
        To me, as an electrical guy, what I really wanted to understand the membrane voltage was a circuit model of the membrane. It could (it seemed to me) include pumps (sources), ion flows (currents), chemical potentials (batteries due to concentration gradients), ion channel conductances (resistances) all connected to the membrane capacitance. A good circuit diagram with these elements would really show (at least to an electrical engineer) how the voltage across the membrane capacitance is controlled, and would be especially helpful in understanding how active cells rapidly change their membrance voltage.

        Unfortunately nearly everything written on this subject is written by biologists, who generally describe all this complexity only in words, making it nearly impossible to really understand. I looked through a textbook on the eukaryotic cell (1,000 pages), and no circuit diagram. After much searching on the web, I finally found that membrane circuit diagrams do exist (though to date I have found only one). It's in a Univ of New Mexico biology exam (with answers). Here is a link to it: http://www.unm.edu/~toolson/435_samp1_2001_key.html. Below is a membrane ciruit diagram I have drawn. It's like the Univ of New Mexico diagram, but more complete.

More membrane circuit models
        I finally stumbled on a book reference for membrance circuit models. It's handbook like with definitions and general equations, but nothing as detailed as I have above. The link below opens a Biomedical Engineering Handbook (Ch11 -- Membrance Models).

        http://www.cmu.edu.cn/jcyxy/upl_files/2008112218461948.pdf

        My sketch above seems to be called by the biologists a Hodgkin-Huxley resistor battery model.

        -- Hodgkin-Huxley is the frequently used model. It models the passive flow of ions across the membrane.
        -- resistance in the model can be non-linear and time varying (think nerve cells)
        -- battery voltage is the Nerst Potential (for the ion modeled)
                                  E = (1/z) x (RT/F) x ln{ion concentration inside/ion concentration outside}
                                              z is valence of ion
        -- most cell membranes are lipid and act as a capacitor (C = 1 uf/cm^2) or (1 pf for (10um x 10um))
        -- at dilute concentrations ions in aqueous solution behave like a gas (this is why the gas constant R appears in the equations)

Active cells
        The voltage reversal figure below is from the same Univ of New Mexico exam. This type of cell is called an active cell because it modulates (by gating on/off its ion channels) its cell membrane voltage. The most common active cells are muscle and nerve cells, but interestingly the female egg cell membrane is active too, changing the membrane potential (from negative to positive) after a sperm enters to block further sperm. Still another type of active cell is the photoreceptor cells of the eye where photons trigger (via modulation of Na+ flows) cell voltage changes.

        Biologists call the voltage reversal shown in the figure (below) a membrane depolarization,which I find a little misleading. Note it's very fast, an ion current pulse and resulting voltage reversal can happen in less than 1 msec. The reversal in this (unspecified) cell is caused by the cell opening positive Na+ ion channels (blue) in its membrane. This allows a large pulse of N+ ions to flow into the cell (down the Na+ concentration gradient). This (positive ion) current charges the membrane capacitance causes the cell membrane voltage to change from -65 mv to +40 mv. A msec or so later as the sodium channels are closing, the cell opens potassium ion (K+) channels (green) for a few msec. This allows potassium ion (K+) current to flow out of the cell (down the K+ concentration gradient) restoring the original negative charge on the membrane capacitance. (In some cells like heart muscle cells there is a delay of a msec or two before the K+ ion channel opens to repolarize the cell making the voltage pulse wider than shown in this figure.).

        These ion flows reduce the K+ and Na+ concentration gradients, but only a little, and over time they are restored to their original concentrations by the K+/Na+ pumps in the membrane (pumping Na+ out and K+ in). (Wikipedia at this link (http://en.wikipedia.org/wiki/Membrane_potential) works some back of the envelope numbers showing that the change in concentration gradients is only about 0.1%.)

        From the curves above we can work some numbers. The charge flows of K+ and Na+ must balance since the membrane voltage starts and ends at the same voltage. The current is equal to the conductance x voltage (version of ohms law). Looking at the blue curve above we can make estimates of current, charge, and capacitance.

Current is the (rectangular equivalent) voltage (across the Na+ conductance) x (rectangular equivalent) conductance.

                        i = (av) voltage x (av) conductance
                          = 1/2 x (65 + 45) mv x 1/2 x 28 x 10^-12 x siemen
                          = 0.77 x 10^-12 A          (0.77 pa)

                        q = current x time
                           = 0.77 x 10^-12 amp x 0.8 msec
                           = 0.62 x 10^-15 coulomb

Membrance capacitance is charge flow divided by voltage change

                        C = charge/voltage
                            = 0.62 x 10^-15 coulomb/(65 +40) mv
                            = 5.9 x 10^-15 farad    (5.9 ff or femto farad)

One coulomb is the amount of electrical charge carried by 6.24 x 10^18 electrons (or single ions), so the number of ions flowing into (and out) of the cell during each pulse

                        # of ions = q x 6.24 x 10^18 ions/coulomb
                                        =  0.62 x 10^-15 coulomb x 6.24 x 10^18 ions/coulomb
                                        = 3.87 x 10^3 ions
                                        = 3,870 ions

Check --- Maybe. Kimball's online biology reference says a measured value for (some type of) nerve cell is 7,000 Na+ ions in one msec for one ion channel. So it could be that the vertical scaling in the figure above is for a much smaller cell than Kimball referenced (very possible, since large cells are usually measured), or it might be for only one channel, or it might just be wrong.

In rectangular equivalent time (0.8 msec) the Na+ charge flows in, so the Na+ ion (diffusion) flow rate is

                    Na+ ion flow rate = # of ions/0.8 msec
                                                   = 3,870 ions /0.8 msec
                                                   = 4.8 million ion/sec

How cells communicate
        For nerve signals to propagate and muscles to contract adjoining nerve cells and muscle cells need to 'talk' to one another. They (apparently) do this by flipping (pulsing) their membrane voltages. Sections of the membrane in the same cell communicate this way too.

        The (Na+) ion flow channels across the membrane respond directly to the voltage of adjoining regions. When a section of membrane 'sees' a voltage more positive than its threshold voltage (about -50 mv in mammal cells), it opens briefly its Na+ ion channels allowing diffusion down concentration gradients, driving the cell voltage fully positive (+40 mv). The biologist speak of this as a "wave of (de)polarization" sweeping across the membrane.

Voltage 'flip'
        Cell voltages in active cells are able to change rapidly (1 msec or so) by allowing transient ion flows across concentration gradients previously set up in the cell by ion pumps. Then there is a recovery period (refractory period) while the pumps restore the original ion concentrations. The voltage 'flip' is really a three step process. First an ion flow drives the cell voltage up, then immediately following a second (different) ion flow drives the voltage back down again. Thirdly, there is a recovery time while all the (slightly) disturbed ion concentrations are restored by the cell pumps.

        To 'flip' the voltage up (drive it positive) one (or more) of the positive ions that have been pumped out of the cell are allowed to flow back in. The candidates are sodium (Na+) and calcium (Ca2+). To do the second part of the 'flip', i.e. drive the membrane voltage negative again, some of the positive potassium ions (K+), whose concentration is pumped up in the cell, can be allowed to diffuse out, or the negative ion chloride (Cl-), whose concentration is low inside the cell, can be allowed to diffuse in. In practice in nearly all active cells it is flows of Na+ in followed by K+ out that cause the voltage flip, which is just what is shown in the figure above. This is nicely consistent with the fact that the major pump in cell membranes is a combo Na+ (out) and K+ (in) pump, called the Na+/K+ ATPase transporter.

        To put some numbers on it (see above) a voltage 'flip' is a fast ion flow (diffusion) into the cell of (about) 1 pa for 1 msec of positive Na+ ions, which changes the cell membrane voltage (about) +100 mv (from -70 mv to +40 mv), followed by a similar ion pulse flow out of the cell of positive K+ ions. Recovery time (refractory period), where the Na+/K+ pump restores the concentration gradients, is typically another msec or two. Here is a figure of an active cell voltage 'flip' from Wikipedia.

        In muscle cells the time it takes for the cell to 'twitch' (contract & relax) is 50 msec or so, much longer than the time it takes for its membrane voltage 'flip' and its ion concentrations to recover (refractory period), hence rapidly stimulating the cell (every 20 msec or so) can keep a muscle cell fully contracted. A sustained muscle contraction caused by rapid triggering goes by the weird name of 'tetanus'.  It's the opposite for heart cells, refractory (recovery) time exceeds twitch/contraction time, so they cannot stay contracted. (One reference comments that this is a good thing!)

Nerve cells
        Nerve cells normally have a negative voltage across their membranes too (-70 mv or), but unlike other cells they are able to change their membrane voltage rapidly and to do so when the cell is stimulated in some way externally. This is the mechanism they use to transmit information (on/off, binary information) from one nerve cell to another nerve cell.

        Nerve cells have many ion channels that are gated, i.e. they can be triggered open or closed. When these ion channels trigger open (in sequence), the voltage rises and then falls quickly ('flips') in a msec or so. This is not because the ion concentrations change much, but because the conductivity (resistance) across the membrane is modulated. When Na+ channels open strongly, the membrane voltage is driven toward the Nernst potential of Na+. This is positive (reversed from K+), because the Na+ concentration in the cell is low. A cell with a collapsed (or reversed) membrane voltage is said to be 'depolarized'. This depolarization can be sensed by adjoining nerve cells, allowing signals to propagate from nerve cell to nerve cell through the body.

Light sensitive cells
        Like all cells the photoreceptor cells of the eye have pumps which pump up the concentration of K+ (inside the cell) and pump down the concentration of all other ions like Na+ and Ca2+. In the dark photoreceptor cell membranes have open channels for K+ (ungated) and Na+ (light gated off) and Ca2+ (voltage gated). Since these channels are to some degree (in the dark) open, the ions diffusing (and drifting) down their channels are recycled and concentrations maintained by a high density of K+/Na pumps.

        Wikipedia calls photoreceptor cells "strange" because in their dark state (normal state) the cell voltage is 'depolarized' (due to the leaky Na+ ion channels) causing the cell voltage to be (partially) collapsed at -40 mv. Photon hits trigger the Na+ and Ca2+ channels to close allowing the cell voltage to fully polarize (or hyperperpolarize, which just means to increase the potential) to -70mv, set by the open, ungated, K+ channels. It is this light induced voltage change that activates the next cell and sends an excitatory signal down the neural pathway. The Na+ ion diffusion flow into a dark cell is called the 'dark current'. In an (unspecified) time after a photon hit, the Na+ channels reopen, the cell voltage drops back to its depolarized -40mv, and the cell is  ready for another photon hit.

Ion transport controls a cell's water pressure
        Control of ion concentration inside cells indirectly (via osmosis) controls water pressure in the cell. Osmosis is a special term used for the diffusion of water through cell membranes. Water is never transported actively; that is, it never moves against its concentration gradient. Water passes by diffusion from a region of higher to a region of lower concentration, meaning the concentration of water.

        When ion pumps and diffusion channels produce a high concentration of ions inside the cell (relative to outside), it means the concentration of water inside the cell is lowered, so water will diffuse into the cell (building up pressure). Conversely low ion concentration inside causes water in the cell to diffuse out of the cell, lowering pressure.

Ion channels compared to pn junctions
        Inside the common silicon diode there is a zone (pn junction) not unlike the ion channels in cell membranes. Highly doped silicon is electrically neutral, but has an interesting property. One polarity of charge is mobile and the other polarity is immobile, and (importantly) in p and n type silicon which charge type is mobile and which fixed is reversed. So at the interface between the p and n materials (pn junction), a diffusion gradient exists tending to cause net diffusion of mobile charges across the pn junction. When some of the mobile charges do diffuse over to the other side, however, the fixed charges in the silicon are (in effect) exposed and an electric field develops across the pn junction that opposes further diffusion.

        The diffusion gradient in silicon is far higher than in cells, so the potential across pn junction is typically 800 mv (about x10 higher than across cell membranes), however, the basic mechanism generating the voltage (mobile and fixed charges self-cancelling a diffusion gradient) is the same as it is in the cell.

 Footnote ---- A diode just sitting on a table, totally unpowered, has internally an electric field with 800 mv potential across its pn junction. (An unpowered diode is like a 'resting' cell.) The flow of charge talked about above essentially occurs once when the diode is manufactured. When the diode is used in a circuit, slight modulations externally of the voltage across the junction control current flowing (by diffusion) through the diode.

        The analogy is made that the voltage across a pn junction (or cell membrane) is like a height of dam with a spillway. Slight modulations in the height of the dam (voltage) cause large variations in the flow of water (charge) through the spillway.

        Ion channel proteins create paths across cell membranes through which ions can passively diffuse without expenditure of energy. Most cells have potassium-selective ion channel proteins that remain open all the time.

        While most descriptions of the genesis of membrane potential begin with the concentration gradients already in place, as if by magic (therefore ignoring the principle of conservation of energy), these gradients can only be created at the expense of putting energy into the system. This work is done by the ion pumps (ion transporters or exchangers) and generally is powered by ATP.  The resting membrane potential is not an equilibrium potential as it relies on the constant expenditure of energy (for ionic pumps as mentioned above) for its maintenance.???

        One of the key roles of the membrane is to maintain the cell potential. In most cells the resting potential has a negative value, which by convention means that there is excess negative charge inside compared to outside. For most animal cells potassium ions (K+) are the most important for setting the resting potential. Due to the active transport of potassium ions, the concentration of potassium is higher inside cells than outside. (Note, the high concentration of positive potassium ions inside the cell is (initially) charge balanced by immobile?? negative (An-) ions (free electrons?)

        The outward movement of positively-charged potassium ions is due to random molecular motion (diffusion) and continues until enough excess positive charge accumulates outside the cell to form a membrane potential which can balance the difference in concentration of potassium between inside and outside the cell. 'Balance' means that the electrical force (qE) that results from the build-up of ionic charge increases until it is equal in magnitude but opposite in direction to the tendency for outward diffusive movement of potassium.

        The typical membrane potential of a cell arises from the separation of potassium ions from intracellular immobile (meaning unable to move through the ion channels?) anions across the membrane of the cell. If the membrane were to become permeable to a type of ion that is more concentrated on one side of the membrane, then that ion would contribute to membrane voltage because the permeant ions would move across the membrane with net movement of that ion type down the concentration gradient.

        (Wikipedia figure shows) K+ diffusing out of the cell. (initially inside of cell is neutral with as many K+ and An- ions) As positive charge builds up outside the membrane and negative (due to loss of K+) inside the membrane an E field pointed inward develops. This E field pushes K+ ions back toward the inside of the cell. Steady state is reached when the E field is strong enough to bring (net) K+ diffusion across membrane to a halt.  (energy is transferred from the concentration gradient to the electrical energy (voltage) across the membrane capacitance).

What's the purpose of the cell potential?
        While cells expend energy to transport ions and establish a transmembrane potential, they use this potential in turn to transport other ions and metabolites such as sugar. (The cell E field will pull any positive ion from the outside into the cell if the cell provide an open channel for the ion.)
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Electrochemical gradient
        -- electrochemical potential is the mechanical work done in bringing 1 mole of an ion from a standard state to a specified concentration and electrical potential.

        --  In mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force. This potential energy is used for the synthesis of ATP by oxidative phosphorylation

        - An electrochemical gradient has two components. First, the electrical component is caused by a charge difference across the lipid membrane. Second, a chemical component is caused by a differential concentration of ions across the membrane. The combination of these two factors determines the thermodynamically favorable direction for an ions movement across a membrane.

        -- With respect to a cell, organelle, or other subcellular compartments, the inclined tendency of an electrically charged solute, such as a potassium ion, to move across the membrane is decided by the difference in its electrochemical potential on either side of the membrane, which arises from three factors:
                * difference in the concentration of the solute between the two sides of the membrane
                * charge or "valence" of the solute molecule
                * difference in voltage between the two sides of the membrane (i.e. the transmembrane potential)

        -- A solute's electrochemical potential difference is zero at its "reversal potential". The transmembrane voltage to which the solute's net flow across the membrane is also zero. This potential is predicted theoretically either by the Nernst equation (for systems of one permeant ion species)  In physiology the Nernst equation is used for finding the electric potential of a cell membrane with respect to one type of ion.

        -- The potential level across the cell membrane that exactly opposes net diffusion of a particular ion through the membrane is called the Nernst potential for that ion.

        -- Nernst equation for cell membrane voltage. Note 'ln' arises because the ratio of oxidized to reduced molecules, [Ox]/[Red], is equivalent to the probability of being oxidized (giving electrons) over the probability of being reduced (taking electrons). And these are describe with Bozmann statistics  e^-(volt treshold/KT) . Also  -- Dividing by e converts from chemical potentials to electrode potentials, and (kT/e) = (RT/F)

                            E = E0 - (RT/nF) ln (reduced concetration/oxided concentration)
                                        + (59mv/n) log (ion outside of cell/ion inside of cell)

Osmosis overview
            Inside a cell there is water with stuff (larger molecules) dissolved in it. The small water molecule is able to diffuse though the cell wall and membrane. If the cell is placed in an water with less stuff dissolved in it (it doesn't matter what the stuff is!) and the pressure inside the cell is the same as outside, what happens is that net water molecules travel into the cell raising the pressure of the cell against its cell wall.

        Water diffuses into the cell, because inside the cell fewer water molecules per sec hit the barrier than on the outside since inside the water molecules are spaced further apart due to the stuff dissolved in it. (From an entropy point of view the water moves to try an equalize the solute concentrations.) As water diffuses in, the pressure inside the cell builds up, eventually stopping the net inflow of water.  (The higher pressure must either increases the speed of the water molecules or the number of water molecules/sec hitting the barrier.)

        Osmotic pressure a very important to cells. For example, it builds up high pressure in the cells of plant leaves giving the leaf structure. If you drink sea water, (apparently) there is more salt in the sea water than solutes in your cells, so water diffuses out of your cells. Reverse osmosis, which is used to desalinate sea water, is simply applying pressure higher than the osmotic pressure to cause water to diffuse from the side with lots of solutes to the side with fewer.

        -- (osmosis) Water is never transported actively; that is, it never moves against its concentration gradient. However, the concentration of water can be altered by the active transport of solutes and in this way the movement of water in and out of the cell can be controlled.

Energy conversion
        Reaction energy is often given in Kcal/mole (where mole = 6 x 10^23) or Kj/mole. These can be converted into electron-volts. (1 Kcal = 4.2 x 10^3 joule) (1 Kj = 1 Kcal/4.2) (A mole of photons (6.2 x 10^23) is called an Einstein.)

             100 Kcal/mole = 100 x 4.2 x 10^3 joule}/(6.2 x 10^23) = 68 x 10^-20 joule
                                1 ev = 1.6 x 10^-19 joule
                         68 x 10^-20 joule /1.6 x 10^-19 = 4.25 ev
so
                            100 Kcal/mole <=> 4.25 ev
                                100 Kj/mole <=> 1 ev

        -- Cells need energy to drive reactions. The molecule that supplies the energy is ATP (This reaction is called ATP hydrolysis). When the third phosphate is removed by hydrolytic cleavage, 7 kcal of energy is released per mole of ATP.

        ATP + H2O ---> ADP + Phosphate + Energy (7 kcal)

When the second phosphate is removed, the same amount of energy is released.

      ADP + H2O ---> AMP + Phosphate + Energy (7 Kcal)

        The bonds between the two phosphates are not strong bonds.  In fact, these bonds are easily broken releasing 7Kcal of energy per mole.  7 Kcal of energy is enough to drive endergonic reactions in the cell. All the energy does not come from the moving of electrons to a lower energy level. In fact, the rearrangement of electrons in other orbitals (i.e..ATP ---> ADP) result in a structure with less energy.

ATP
        ATP is made up of the nitrogenous base adenine, the five-carbon sugar ribose and three phosphate groups. Three phosphate units (triphosphate), each made up of one phosphorus atom and four oxygen atoms, are attached to the ribose. The two (covalent) bonds between the three phosphate groups are relatively weak and yield their energy readily when split by enzymes.

        Wikipedia formula --- C10 H16 N5 O13 P3

  ATP consists of three phosphates (blue), a sugar, ribose (magenta), and a nitrogen base, adenine (red).
Removal of the left phosphate (PO4) converts ATP to ADP and releases energy.

ATP, well it almost agrees with stick figure above
Count here agrees with Wikipedia formula --- C10 H16 N5 O13 P3
Notice ribuse here has 8 H whereas in figure above there is 6 H
source -- http://biology.clc.uc.edu/Courses/bio104/photosyn.htm

        Inside a cell the ATP molecule is split at one of the high energy bonds, releasing the energy to power cellular activities. Adenosine diphosphate (ADP) and phosphorus (P) are produced in the process. With the release of the end phosphate group, 7 kilocalories per mole (under laboratory conditions, about 11 kilocalaries per mole in cell) of energy become available for work.

                        ATP + H2O --> ADP + Phosphate + energy

        ATP needs to be regenerated continuously by the recombining of ADP and P. But note the synthesis of ATP requires that ADP be available. The burning of food to make ATP is regulated by the levels of 'spent' ATP (ADP) in the cell. ATP is made only as needed, the process is self-limiting.
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(atomic bonding isn't really cell biology. Does this below with Atoms, or its own essay?)

Atomic Bonding Overview (4/08)
        All chemical energy (including explosives) comes from a rearrangement of (shared) electron bonds that changes their potential energy. Potential energy lost is released, and conversely potential energy gained must be input to drive the reaction.

Pairs
        Electrons always want to pair up (one spin up, one spin down), it's the heart of bonding. An up spin electron can share the same space as a down spin electron. When electrons pair up by forming covalent (etc) bonds, the electrons lose potential energy and this energy is released.

Pulling (shared) electrons toward the nucleus -- Electronegativity
        Electrons that move closer to a nucleus lose potential energy, so energy is released. This is the 'secret' of how reactions with atoms that have high electronegativity, like oxygen, put out energy. In other words why burning things makes heat!

        Electronegativity is measure of how strongly a (shared) electron pair is attracted to an atom's nucleus. The cause of electronegativity is really quite simple. It's a measure of the electrical attraction between the fraction of the positive nucleus that is unshielded and the shared (negative) electron pair. It's higher if the nucleus has more protons and higher if the (shared) electrons are in a lower orbit, and thus closer to the nucleus.

        And -- key concept --  if (shared) electrons do in fact end up closer to the nucleus, then (net) energy is released as the potential energy of the electrons drops.

            * Fluorine (element 9) has the highest electronegativity of any element in the periodic chart. The shared electron pair are in level 2 and they  'see' a (net) positive charge of 7 ( = 9 protons - 1s inner pair shielding). Electronegative value = 3.98.

            * Oxygen (element 8) electronegativity is high, but not quite as high as fluorine because it's (net) positive charge is 6 ( = 8 protons - 1s inner pair shielding). Electronegative value = 3.44.

            * Chlorine (element 17) shared pair, like fluorine, also see a net positive charge of 7 (= 17 protons - 10 electron shielding in levels 1 and 2), but the shared pair is in level 3 so it's a little further from the nucleus than in fluorine, this the attraction is a little weaker. Electronegative value = 3.16

            * Hydrogen (element 1) has a very low net positive charge (1) because it only has one proton, but it's electronegativity is increased by the fact that the shared electrons 'orbit' quite close to the nucleus in the 1s orbit. Electronegative value = 2.2.

How oxygen bonding (oxidation) releases (net) energy
        When oxygen is able to pull the shared electrons it wants from another atom with a lower electronegativity (which includes carbon and hydrogen and just about every other atom), it pulls the shared electrons in closer to its nucleus. This lowers their potential energy, and this energy is released. Of course, to get an unattached oxygen atom (from the atmosphere) some energy must be expended, since oxygen in air is already bonded to another oxygen (O2), so an oxygen-oxygen covalent bond (of molecular oxygen) needs to be broken.  But the energy needed to break an oxygen-oxygen covalent bond is not as high as will later be released when the oxygen combines with carbon or hydrogen. The reason is an oxygen bond in O2, being between identical atoms, is symmetrical; it's a true covalent bond. The shared electrons are located (on average) right between the two oxygen nuclei. Here's the electronegativity values of oxygen, carbon, and hydrogen.

                        Oxygen                          3.44
                        Carbon                           2.55
                        Hydrogen                       2.20

        There's actually a pretty linear relationship between electronegativity and bond energy. The graph below shows that making bonds with oxygen typically outputs about 40% more energy than is required to break carbon and  hydrogen bonds and the oxygen-oxygen bond too (2,000 vs 1,300 -1,500 KJ/mole). Vertical scale is the usual Pauling electronegativity values (from 0.7 to 4) and horizontal is bond energy in KJ/mole.

Working some numbers --- Oxidation of methane
        Methane (CH4) is the simplest hydrocarbon. It's just one carbon surrounded by four hydrogen, each hydrogen attached to the carbon by a single covalent bond. Since the electronegativity of carbon is a little higher than hydrogen (2.66 vs 2.2), the shared electrons are a little closer to the carbon nucleus than the hydrogen.

        Burning methane (in air) yields CO2 and water. The reaction breaks the oxygen-oxygen covalent bonds, then half of the oxygen bonds covalently with the hydrogen (making water, H2O) and the other half with the carbon (making carbon dioxide, CO2). Here's the chemical formula (you adjust quantities so atoms out = atoms in):

                            CH4 + 2 O2 = CO2 + 2 H2O

        To find the (net) energy released in the burning of methane (to what degree of accuracy?) you just find the energy released in the newly made bonds (on the right) and subtract off the energy required to break the bonds (on the left side). Atomic bond energies are tabulated. (a double covalent bond is two shared electrons whereas a single covalent bond is one shared electron)

CO2                  2  O=C double covalent             2 x 799
2 H2O               4  O-H single covalent              4 x 460
CH4                  4  C-H single covalent                               - 4 x 410
2 O2                 2  O=O double covalent                             - 2 x 494
                                                            ------------------------------------
                                                                                    3438     -  2628 = 810 kJ/mole (released)

        So adding (& subtracting) the bond energies tells us that burning a mole of methane (16 grams) releasees 810 kJ = (194 kcal/mole, 8.39 ev) of energy.

Some useful molecule total bond energies:

         H2O          2 O-H single covalent         2 x 460 = 920 Kj/mole = 220 kcal/mole = 9.53 ev
        CO2          2  O=C double covalent      2 x 799 = 1,598 Kj/mole = 382.5 kcal/mole = 16.56 ev
        O2             1 O=O double covalent      1 x 494 = 494 Kj/mole = 118.3 kcal/mole = 5.12 ev
        H2             1 H-H single covalent         1 x 460 = 460 Kj/mole = 110 kcal/mole = 4.76 ev

Covalent, polar, & ionic
        A covalent bond is just a shared electron pair. If the electronegativity of the two atoms are (significantly) different, i.e. if the electrostatic 'pull' of the two nuclei are (significantly) different, then the electron pair moves closer (on average) to the stronger pulling nucleus.

            * The electron pair moving closer to one nucleus makes that atom acquire a (net) negative charge and the other atom (from which the electron pair is more distant) acquires a (net) positive charge. A molecule with positive and negative atoms is called a polar molecule, and these plus and minus 'ends' causes some attraction between molecules. Water is polar and each water molecules pulls on four others. This raises its boiling point because (extra) heat is required to break all molecule to molecule (polar) attraction.

            * If the electron pair is much closer to one nucleus than another, then the covalent bond is called ionic. The classic case is NaCl. The shared electron pair is in level 3. Sodium (element 11) on the left side of the periodic chart only has a (net) positive attraction of 1 ( = 11 protons - 10 electron shielding in levels 1 and 2), whereas chlorine on the right side of the periodic chart has a (net) positive charge of 7 (= 17 protons - 10 electron shielding in levels 1 and 2). When salt disolves in water, the sodium and chlorine separate with chlorine keeping the extra electron resulting in ions Na+ and Cl-.

            * (I think) Pulling of the shared electron pair closer to one nucleus (quasi-ionic) also reduces the electron's potential energy and thus releases energy.

        This link is by far the best bonding tutorial I have found. Very clear discussion of orbit changes of many different bond types (worth studying in detail):

         http://www.chemguide.co.uk/atoms/bondingmenu.html#top
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(This is an earlier treatment of the same material when I understood it less well)

Atomic bonds -- Electronegativity
        Atoms bond into molecules by overlapping their electronic orbitals. Whether this is called 'sharing'  or 'donating/accepting' electrons, it's really the same thing. Wikipedia link on Electronegativity (see below) is a good introduction to atomic bonding. Electronegativity is a measure of the ability of an atom or molecule to attract electrons in the context of a chemical bond. The link has a periodic chart showing the electronegativity value of every element (ranges from about 1 to 4) with oxygen at 3.44 having the 2nd highest value (fluorine is highest at 3.98). (Electronegativity is so important even my supermarket sells it!  Yes indeed, I was able to buy a periodic chart with all the negativity values in my supermarket -- part of a plastic 'crib notes' series for students).

        When bond is made between only two atoms, it's typically an atom from the left side of the periodic table, which have a few excess (outside a full shell) electrons, joining an atom from the right side of the table, which are just a few electrons shy of completing an electron shell. When multiple atoms bond, there are a lot of different ways to fill a shell. For example, in CH4 (methane) carbon gets the four extra electrons it needs to fill its shell by sharing with four hydrogen. From the hydrogen perspective it gets the one extra electron it needs to fill its shell by sharing one of the carbon electrons. (Note, shell filling is just a set of 'rules of thumb' that make it easy to remember the lower energy orbit states.)

Atomic bonds -- Covalent vs ionic
       There are two (idealized) types of chemical bonds, Covalent and Ionic, but really they shade into each other with the key parameter being the relative electronegativity. This is nicely shown pictorially in this link:

        http://www.chem.ox.ac.uk/vrchemistry/electronsandbonds/bondsperatom1.htm

        Covalent --- If  electronegativity values are close, in a sense the atoms pull on (shared) electrons equally. When the difference in the relative electronegativity is not too great (< 1.7), the electron bond formed is called a covalent bond. This type of bond is conventionally described as the atoms sharing electrons. If the relative electronegativity values is < 0.4, then the bond is balanced, so these are non-polar covalent bonds. If the relative electronegativity values is 0.4 to 1.7, then the bond is unbalanced, so these are polar covalent bonds. Obviously bonds between identical atoms, like diatomic oxygen, are perfectly balanced, so these bonds are pure (non-polar) covalent.

        Ionic --- If  electronegativity values are far apart ( > 1.7),  then one atoms pulls on (shared) electrons much harder than the other. This type of bond is called an ionic bond. This type of bond is conventionally described as one atom donating an electron to another atom that accepts it. The force between the atoms created by this bond is then spoken of as being an electrostatic attractive force between the positive (donating) ion and the negative (accepting) ion.

        A dipole moment is an electrical force that is generated because of the unequal distribution of the bonding electrons between the two bonded atoms. In the case of an ionic bond that unequal distribution is extreme. The dipole moment of an ionic bond is quite large compared to polar bonds of the covalent bond. Ionic bonds (can be) about as strong as covalent bonds.

        Salt (sodium chloride) is a classic ionic bond. Most metals (like sodium) have only a few valence electrons hence relatively low ability to attract electrons and low electronegativity values. Sodium (atomic number 11) has only one valence electron, so it has a very low electronegativity value of 0.93. Many non-metals like nitrogen, chlorine, oxygen, fluorine have nearly full shells missing one or two electrons (nitrogen is missing three), so have high electronegativity values. Chlorine (atomic number 17) has a seven valence electrons, so it has a very high electronegativity value of 3.16.

        When salt dissolves in water,  the sodium and chlorine atoms come apart (why? see below) as charged ions, so here (at least) the sharing & loss of the electron must be 100%.

        --    Hydrogen and oxygen in water are covalently bonded. Water is a polar molecule, because it has partial positive and partial negative ends. The hydrogen atoms of the water molecule can now form bonds with other slightly negative (polar) compounds. Each hydrogen of this water molecule can form hydrogen bonds with oxygen atom of other water molecules. Hydrogen bonds are 20 times weaker than covalent bonds. But hydrogen bonding between molecules is very important with organic compounds.

        -- Water is able to dissolve anything polar due to polarity. Water separates ionic substances. Many covalently bonded compounds have polar regions, the covalent compounds dissolve in water and are called hydrophilic (water loving) compounds. Nonpolar substances do not dissolve in water and are called hydrophobic (water fearing).

        --  Due to hydrogen bonds water is attracted to itself (more than the air above it) forming surface tension. To change water from a liquid to a gas (boil it), a lot of energy must be added to break the hydrogen bonds between the water molecules.

        -- The bond strengths are expressed in terms of energy (kilocalories or kilojoules per mole) that must be supplied to break the bonds under standard conditions of temperature and pressure.

        -- Carbon backbone  Carbon can form covalent bonds directly with one to four atoms since it as four valence electrons. In many biological molecules carbon atoms form long chains. Carbon is unique in that it can form single, double, and triple covalent bonds with itself and other atoms.

         http://en.wikipedia.org/wiki/Electronegativity

Nitrogen
        Nitrogen has two stable isotopes: N14 (7 neutrons, 99.6%) and N15 (8 neutrons, 0.4%). Nitrogen is atomic number 7, between carbon (6) and oxygen (8). It has five electrons in its outer shell and is therefore trivalent in most compounds. Nitrogen is a nonmetal, with an electronegativity of 3.0.

        The triple bond in molecular nitrogen (N2) is the strongest in nature. The resulting difficulty of converting (N2) into other compounds, and the ease (and associated high energy release) of converting nitrogen compounds into elemental N2, have dominated the role of nitrogen in both nature and human economic activities.

Oxidation
        Oxidation is a slippery term. From its name you would think it means adding oxygen, but this is only one type of oxidation. Oxidation is also used in a loose sense to mean 'burn'. But there is an electrochemistry definition and it appears to be totally different. So what is oxidation really? And why does oxidizing something yield energy?

        (My thinking now is this)
         Oxidize --- A molecule is oxidized when an atom from the right side of the periodic table (an oxidant like oxygen, fluorine, or chlorine) bonds to the molecule causing electrons to be sucked (to some degree) from the molecule to the oxidant atom using them to fill the oxidant's shell. The energy stored in the combined molecule is less than the sum of its parts (due to the filled shell), so this reaction (always?) puts out energy.

        Oxidation example: In a fuel cell gaseous oxygen (O2) is used to oxidize gaseous hydrogen (H2) forming water. This puts out useful work in the form of electricity + some heat.

         Reduce --- A molecule is reduced when an atom from the left side of the periodic table (a reductant like hydrogen, or sodium) bonds to the molecule causing electrons to be added (to some degree) to the molecule from the reducer. The energy stored in the combined molecule is more than the sum of its parts (even though the reductant is down to a filled shell), so this energy need to added to make this reaction go.

        Reduction example: Electrolysis of water into gaseous oxygen and hydrogen. This is the reduction of hydrogen (putting back the electrons that the oxygen sucked away), and for it to occur energy must be added in the form of running electricity through the water.

As stated in Wikipedia:
        "Oxidation is the loss of electrons by a molecule, atom or ion"
        "Reduction is the gain of electrons by a molecule, atom or ion"

        When a carbon atom 'loses' (shares) two electrons to each of two oxygen atoms it bonds with, Wikipedia speaks of this as 'oxidation' of carbon to yield CO2. Yet when carbon joins with four hydrogen, Wikipedia refers to this as 'reduction' of carbon by hydrogen to yield methane (CH4).

       Is it oxidation of carbon when it joins with an atom with a higher electronegativity value (like oxygen), and reduction when it joins with an atom with a lower electronegativity value (like hydrogen)?

        Yes!   Here (I think) is the key --- When electrons are shared, they are pulled spatially toward the atom with the higher electronegativity value. So higher electronegativity atoms (oxidants) suck away electrons from the bonding molecule, and it is the loss of electrons by the molecule that is (technically) the definition of oxidation. It is correct (if confusing) to speak of carbon being reduced by hydrogen, because carbon being the higher electronegativity atoms sucks the electrons from the hydrogen to itself, thus technically since carbon has gained electrons it has been reduced! It's clearer I think to speak of it as carbon oxidizing the hydrogen.

              element                  electronegativity
            -------------             ---------------------
                oxygen                            3.44
                carbon                             2.55
                hydrogen                         2.20

        My guess is that oxygen's so-called high affinity for attracting electrons (its high electronegativity value) means that the oxygen atom when it bonds with other atoms that bring two electrons to share with it, drops into a lower energy state and (somehow) releases energy in the form of heat and useful work like current (fuel cells), electrons flows, and ion pumping.

         My model is gravity. When an object is attracted to a body by gravity, energy is released either as useful work or as heat. Is the oxygen atom like this? Is energy released when two electrons 'fall into' orbitals of oxygen allowing it to complete its electron shell?

Wikipedia excerpts on oxidation/reduction
        -- Oxidant removes electrons from another substance, and is thus reduced itself.
            (mnemonic) "OIL RIG" -- Oxidation Is Loss, Reduction Is Gain.

        -- Oxygen is an oxidant, but not the only one. Despite the name, an oxidation reaction does not necessarily need to involve oxygen.

        -- The gain of oxygen, loss of hydrogen and increase in oxidation number is also considered to be oxidation, while the inverse is true for reduction.

        --  Oxidants are usually chemical substances with elements in high oxidation numbers (e.g., H2O2, MnO4-, CrO3, Cr2O72-, OsO4) or highly electronegative substances that can gain one or two extra electrons by oxidizing a substance (O, F, Cl, Br).

        -- The oxidation state of an ion is the number of electrons it has  donated (+) or accepted (-) compared to its neutral state (which is defined as having an oxidation state of 0).

       -- A reaction in which both oxidation and reduction is occurring is called a redox reaction. These are very common; as one substance loses electrons the other substance accepts them.

        -- Electrochemical process are redox reactions where energy is produced by a spontaneous reaction which produces electricity, otherwise electrical current stimulates a chemical reaction. In a redox reaction, an atom's oxidation state changes as a result of an electron transfer.

        -- A spontaneous electrochemical reaction can be used to generate an electrical current, in electrochemical cells. This is the basis of all batteries and fuel cells. For example, gaseous oxygen (O2) and hydrogen (H2) can be combined in a fuel cell to form water and energy (a combination of heat and electrical energy, typically).

        -- Conversely, non-spontaneous electrochemical reactions can be driven forward by the application of a current at sufficient voltage. The electrolysis of water into gaseous oxygen and hydrogen is a typical example.

        -- NADPH a universal reductant used to reduce CO2 into sugars as well as for other biosynthetic reductions.

        -- The three-dimensional tertiary structure of bacteriorhodopsin resembles that of vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal, however the functions of rhodopsin and bacteriorhodopsin are different and there is no homology of their amino acid sequences.

        -- The electron transfer reactions concentrate protons inside the membrane vesicle and create an electric field across the photosynthetic membrane.

        -- Protons pass through the ATP-Synthase protein complex that transforms electrochemical free energy into a type of chemical free energy known as phosphate group-transfer potential (or a high-energy phosphate bond). The energy stored in ATP can be transferred to another molecule by transferring the phosphate group.

        --  The oxidation- reduction midpoint potential (Em,7) of water is +0.82 V (pH 7). In photosystem II this reaction is driven by the oxidized reaction center, P680+ (the midpoint potential of P680/P680+ is estimated to be +1.2 V at pH 7)
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Life is right handed
        Some molecules, like sugars, come in both left handed and right handed versions. When made in the laboratory from symmetric non-organic sources, you get roughly an even mixture of right and left handed molecules, which are chemically identical. Feed this sugar mixture to sugar eating bacteria and you find the bacteria eat only half the sugar. The bacteria eat the right handed sugar and leave the left handed sugar. Amazingly all life, everything living on earth, at the molecular level is right handed.

        The reason bacteria can't eat left handed sugars is because many of the cells' complex key molecules, proteins and especially enzyme proteins, which act as catalysts greatly speeding biological operations, fold up in a way that reflects their handedness. The simple picture of how enzymes work is 'lock and key'. The enzyme orients the reacting molecule and keeps in position to react because the reacting molecule fits within a nook (fold) of the enzyme.

        So even though life is based on chemistry and right and left handed sugars are chemically identical, the lack of fit between left handed sugars and right handed enzymes means that cells can't process left handed sugars.

Evolutionary consequences
       As far as is known, the choice of handedness when life begins is random. If this is right, then clearly the fact that all life that has ever seen on earth has the same handedness is strong evidence that life on earth probably originated (or arrived !) just once, or more accurately, that it did not independently originate (or arrive) many times.
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        --    ATP is the chemical equivalent of a loaded spring; the close packaging of the three negatively charged phosphate groups ia an unstable, energy-storing arrangement (like charges repel).  The chemical “spring” tends to “relax” from the loss of terminal phosphate.  The cell taps this energy source by using enzymes (kinases) to transfer phosphate groups from ATP to other compounds, which are then said to be phosphorylated.  Adding the phosphate primes a molecule to undergo some kind of change that performs work, and the molecule loses its phosphate group in the process.

        -- ATP (Adenosine triphosphate)  It is the most important "molecular currency" of intracellular energy transfer. (C10H16N5O13P3).  It is produced as an energy source during the processes of photosynthesis and cellular respiration and consumed by many enzymes. This large release in energy makes the decomposition of ATP in water extremely exergonic (-20.5 kJ / mole, with a change in free energy of 3.4 kJ/mole). The overall process of oxidizing glucose to carbon dioxide is known as cellular respiration and can produce up to 30 molecules of ATP from a single molecule of glucose

        -- The system of ATP and water under standard conditions and concentrations is extremely rich in chemical energy; the bond between the second and third phosphate groups is loosely said to be particularly high in energy. Strictly speaking, the bond itself is not high in energy (like all chemical bonds it requires energy to break), but energy is produced when the bond is broken and water is allowed to react with the two products. Thus, energy is produced from the new bonds formed between ADP and water, and between phosphate and water.

        -- The phosphate ion is a polyatomic ion with the empirical formula PO4 and a molar mass of 94.973 g/mol; it consists of one central phosphorus atom surrounded by four identical oxygen atoms in a tetrahedral arrangement. It has a charge of -3.

        -- This gradient is composed of both the pH gradient and the electrical gradient. The pH gradient is a result of the H+ ion concentration difference. Together the electrochemical gradient of protons is both a concentration and charge difference and is often called the proton motive force (PMF).

        -- In mitochondria the PMF (proton motive force) is almost entirely made up of the electrical component but in chloroplasts the PMF is made up mostly of the pH gradient. In either case the PMF needs to be about 50 kJ/mol for the ATP synthase to be able to make ATP.
 

    ** -- Mitchell (1978 Nobel prize for Chemistry) realized that the movement of ions across an electrochemical membrane potential could provide the energy needed to produce ATP. He knew that living cells had a membrane potential; interior negative to the environment. The movement of charged ions across a membrane is thus affected by the electrical forces (the attraction of plus to minus charges). Their movement is also affected by thermodynamic forces, the tendency of substances to diffuse from regions of higher concentration. He went on to prove that ATP synthesis was coupled to this electrochemical gradient.

        -- Mitchell's theory was confirmed by the discovery of ATP synthase, a membrane-bound protein that uses the potential energy of the electrochemical gradient to make ATP. Mitchell's chemiosmotic theory turned out to be one of the two seminal discoveries in biology in the 20th century (DNA being the other)

        -- Hydrogen ions (protons) will diffuse from an area of high proton concentration to an area of lower proton concentration. Peter Mitchell proposed that an electrochemical concentration gradient of protons across a membrane could be harnessed to make ATP. He likened this process to osmosis, the diffusion of water across a membrane, which is why it is called chemiosmosis.

        -- ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

        -- Equation for diffusion of gas across a cell membrane (Ficks first law)
                    Rate of Diffusion  = k (A/d) (pressure difference)
                        Note this is like a current equation (i = V/R = V/(resistivity x length/area),
                        so flow x pressure diff must be power
 

        -- Osmosis is the net movement of a solvent across a semipermeable membrane from a region of high solvent potential to an area of low solvent potential. (Note it is the solvent that moves not the solute!) It is a physical process in which a solvent moves, without input of energy, across a semipermeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations. Osmosis releases energy, and can be made to do work. In plant cells, water enters the cell until the inside and outside water potential is equal.

       -- Cellular respiration is a process that describes the metabolic reactions and processes that take place in a cell to obtain chemical energy from fuel molecules. Energy is released by the oxidation of fuel molecules and is stored as "high-energy" carriers. The reactions involved in respiration are catabolic reactions in metabolism. Fuel molecules commonly used by cells in respiration include glucose, xx, and a common oxidizing agent (electron acceptor) is molecular oxygen (O2).

        -- The energy released in respiration is used to synthesize molecules that act as a chemical storage of this energy. One of the most widely used compounds in a cell is adenosine triphosphate (ATP). Most of the ATP produced by cellular respiration is by oxidative phosphorylation??   Chemiosmotic hypothesis (1961) --- The theory suggests essentially that most ATP synthesis in respiring cells comes from the electrochemical gradient across the inner membranes of mitochondria.

        --  The energy available in the electrons is used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The electrons and protons at the last pump in the ETC are taken up by oxygen to form water.

        -- Chemiosmosis is the diffusion of ions across a membrane. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

        -- (the proton circulate in and out of the cell. In driven by the electrochemical potential to make ATP and then some of the energy available is used to pump them out again restoring the potential. And some protons inside are oxidized to water). The energy available in the electrons (from metabolized glucose) is used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The protons move back across the inner membrane through the enzyme ATP synthase

        -- ATP is made by an enzyme called ATP synthase. The structure of this enzyme and its underlying genetic code is remarkably similar in all known forms of life. ATP synthase is powered by a transmembrane electrochemical potential gradient, usually in the form of a proton gradient. The function of the electron transport chain is to produce this gradient.
 

        -- The potential energy that an electron has is determined by its distance from the nucleus.  The more energy the electron contains, the further it will be from the nucleus; an electron with low energy will be closer to the nucleus. Electrons can move to a higher energy level by having added to it (sunlight and light energy). When this electron moves back to its original position, the same amount of energy that it took to move the electron is released.

        -- Most carbohydrates have the empirical formula C(H2O)n. Carbohydrates are composed of covalently bonded atoms of carbon, hydrogen, and oxygen.

            -- The basic unit of a carbohydrate is a monosaccharide or simple sugar. Monosaccharides can be burned (oxidized) to yield carbon dioxide, water, and energy. The principle source of energy for organisms is glucose ( C6H12O6). Structurally a sugar consists of a carbon backbone of three or more carbon atoms with either an aldehyde or carbonyl group on one carbon and hydroxyl groups on each of the other carbons.

        -- Electron carriers  Some compounds can accept and donate electrons readily, and these are called electron carriers in organisms. NADP is an electron carrier used in photosynthesis. These molecules readily give up 2 electrons (oxidized) and gain two electrons (reduced). Along with the electrons the molecules accept 2 hydrogens to offset the negative charge of the electrons.

        --  Oxidation Losing electrons, hydrogen or the gaining of oxygen.  An electron loses potential energy when it shifts from a less eletronegative atom towards a more electronegative one.  A redox reaction that relocates electrons closer to oxygen realeases chemical energy which can be put to work.

        -- Changing in Covalent Status  Usually, organic molecules that have and abundance of hydrogen are excellent fuels because their bonds are a source of electrons with high  potential energy.  They also have the potential to drop the energy when they  move closer to oxygen.  The important point in aerobic respiration is the change in covalent status of electrons as hydrogen is transferred to oxygen.This is what liberates the energy.

        --  At key steps in aerobic respiration, hydrogen atoms are stripped from glucose, but they are not directly transferred to oxygen.  They are passed to a coenzyme called NAD+ (nicotinamide adenine dinucleotide) which  functions as the oxidizing agent. Enzymes called dehydrogenases remove a pair of hydrogen atoms from the substrate.  These enzymes deliver two electrons along with one proton to NAD+, forming NADH.  The other proton is released as a hydrogen ion into the surrounding solution.

        -- Electrons lose very little potential energy when they are transferred by dehydrogenases from glucose (organic molecules) to NAD+.  Thus, each NADH molecules formed during respiration represents stored energy that can be used to make ATP when the electrons complete their journey from NADH to oxygen.

        --  (Electrons can lower their energy by pairing {canceling magnetic moment??} This explains a lot of bonding and chemistry) --- Two atoms of hydrogen, each with one proton and one orbiting electron, will join into a dumbbell-shaped hydrogen molecule. With the two electrons now paired, the molecule has a lower energy state than the two separate hydrogen atoms. For this reason molecules with an odd number of electrons are highly unstable, likely to react with the first molecule that passes by.

**     -- Compared to the inner membranes of mitochondria, which have a significantly higher membrane potential due to charge separation, thylakoid membranes lack a charge gradient. To compensate for this, the 10,000 fold proton concentration gradient across the thylakoid membrane is much higher compared to a 10 fold gradient across the inner membrane of mitochondria.

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(This section on pn junction may be out of date)

pn junctions ---electric field and diffusion gradients
        A pn junction is formed in a semiconductor when the fixed dopant atoms in the crystal change (over a very short distance) from acceptor (P type) to donar (N type). The resultant pn junction has steep charge gradients of mobile positive (holes) and negative (electrons) carriers across the junction and an intrinsic voltage across the junction that opposes charge flow along the gradients. This voltage across the junction is initially set up by a small amount of positive charge (holes) from the P side diffusing to the N side, and a small amount of negative charge (electrons) diffusing from the N side to the P side. The holes and electrons that cross the junction annihilate each other (electrons fall into holes) expose in a thin region (depletion region) spanning the junction the underlying non-mobile charge in the crystal, which is positive on the N side of the junction and negative on the P side.

        The non-mobile exposed charge forms an electric field that points from the N to the P side. This electric field in the depletion region sweeps holes back to the P side and electrons back to the N side, thus keeping the depletion region free of mobile charge and (in effect) preventing charge from moving along the diffusion gradients. Summarizing, across a pn junction there exists two strong charge moving mechanisms, diffusion and an E field, that are opposed, and if undisturbed quickly come into balance preventing any net charge motion across the junction.

        Small changes to the junction field by an external voltage can induce large diffusion of charge carriers across the junction. For example: current in a diode increases exponentially if the voltage across the diode (P side positive with respect to N) is increased even slightly above the what is known as the diode forward voltage (typ 700 mv for a silicon diode). An analogy (from a 50's Scientific American article) is a dam with an overflow spillway. A slight lowering of the dam height (junction voltage) causes a large flow of water (diffusing charges) across the dam.

        Consider what happens when light falls on a pn junction (solar cell). Electron/hole pairs are generated by each photon of light and the charges are accelerated (in opposite directions) by the voltage across the junction. The holes driven by the electric field to the P side and the electrons to the N side. This raises the potential of the P side with respect to the N side, so if wires are attached to the P and N materials and resistor connected between them current will flow from the P material through the resistor to the N material. The power dissipated in the resistor has come from the energy of the photons via the electric field across the junction.
        I wonder --- Does understanding the energy physics of pn solar cells help us understand how photosynthesis works, how a plant is able via photosynthesis to capture the energy of solar photons?

Here is a link to lectures on basic semiconductor physics -- (discussion of why voltage is proportional to logarithm of charge densities)

        http://inst.eecs.berkeley.edu/~ee130/sp03/lecture.html

Do cell membranes act like semiconductor pn junctions?
        Question: Do cell membranes act like pn junctions? ---  Yes, somewhat. Cell membranes usually have across them ion gradients and if the membrane pores are 'open' (to diffusion), then an electric field soon forms that blocks further ion (potassium, sodium, hydrogen) diffusion through the membrane.

        In a common case the resting potential across a membrane is set up by (a few) potassium (K+) ions diffusing out of the cell (and negative ions diffusing in). The tendency of K+ to flow down the diffusion gradient out of the cell is balanced by the voltage across the membrane driving K+ into the cell. The membrane is spoken of a have a membrane capacitance and the voltage across it is due to the excess charges next to the membrane. The diffusion channel of a membrane is modeled as a resistor with a different ohms for each type of ion. Note the ion channel in the membrane must be open for the voltage to appear. The resting membrane voltage generated by potassium is -80 mv. Typical capacitance is 66 pf and typical resistance is 33 Mohm (RC = about 2 msec). A neuron cell fires for 2 msec passing a current of 3.3 na. (see 'membrane potential')
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ATP
        ATP is to the cell what hydrogen might someday be to cars. It is not really a fuel, it's an energy transport molecule. It's used in the cell to power basic functions like ion pumps and muscle cells use it to power a contraction, but ATP is not transported through the body, it's made locally in each cell. Energy is transported around the body via sugars, fats, etc. The cell's mitochondria organelles take in these sugars, oxidized them, and use the energy released to build up an energy store called, a 'proton motive force', which is later used to make ATP.

        The energy from burned sugar, in the form of an electron transport chain (similar to photosynthesis!), runs proton pumps in the mitochondria that pump protons out of the center region of mitochondria into a small inter-membrane space. This proton pumping drives the inner mitochondria membrane voltage negative (-190 mv), storing energy in the membrane capacitor, and some energy is also stored in a small H+ gradient. When ATP needs to be made, the 'proton motive force', meaning the membrane voltage and proton gradient, cause a flow of protons through the membrane into the center of the mitochondria. The protons flow in through the ATP synthase machine, which is a (9 nm dia) 'turbine', causing it to actually spin (up to 12,000 RPM) and with each 120 degree rotation an ADP is recombined with a Pi to make an ATP. The ATP then (apparently) diffuses out of the mitochondria into other parts of the cell to do work.

        -- If an enzyme is going to "push" two molecules together until they bond covalently, the energy to do that has to come from somewhere. That "somewhere" is frequently provided by a molecule of ATP.  The enzyme, DNA polymerase, not only has binding sites for the molecules it is going to join together, but another binding site for a molecule of ATP. Once the enzyme has bound all the players in the reaction, then the molecule of ATP is partially broken down; one covalent bond in the ATP is broken.

        Breaking that covalent  bond releases the energy that was put into it during its formation. The energy released when this particular bond in the ATP is broken is "caught" and harvested by the enzyme. The energy causes the enzyme to change shape in a small way, so that the OTHER things it is holding onto are forced together and covalently bonded together. SO, one covalent bond is broken in ATP, and a new covalent bond is formed in the other molecules the enzyme is binding. All that is left is for the enzyme to release everything and start all over.

        -- A critically important macromolecule—arguably “second in importance only to DNA”—is ATP.

        -- As far as known, all organisms from the simplest bacteria to humans use ATP as their primary energy currency.
        -- 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 diphosphate (ADP)

        -- 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.

        -- 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 makes 3 ATP and requires the energy of about nine hydrogen ions (more likely 12 H+ ions since latest thinking is H+/ATP = 4 or maybe 4.47) 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 (12,000 RPM per second, producing 600 ATPs during that second.

        --  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 ATP molecule is composed of three components. At the centre is a sugar molecule, ribose (the same sugar that forms the basis of RNA). Attached to one side of this is a base (a group consisting of linked rings of carbon and nitrogen atoms); in this case the base is adenine. The other side of the sugar is attached to a string of phosphate groups. These phosphates are the key to the activity of ATP.

        --  Modern fertilizers often contain phosphorus compounds that have been extracted from animal bones. These compounds are used by plants to make ATP. We then eat the plants, metabolise their phosphorus, and produce our own ATP.

        --- ATP is made by the enzyme ATP synthase. A Nobel prize for work on ATP synthase was given only recently (1997).

        -- Under certain conditions, protons can re-enter the mitochondrial matrix without contributing to ATP synthesis. This process is known as proton leak or mitochondrial uncoupling and is due to the facilitated diffusion of protons into the matrix. This process results in the unharnessed potential energy of the proton electrochemical gradient being released as heat. (This heat can be desired if the body needs to be warmed.)
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Fundamentals of life (1/30/15)
          Here's an interesting speculation of the minimum set of characteristics that are shared by every living thing on earth. The author, a biology professor, calls it a list of 'minimum characteristics of the last common ancestor of all life' from the book "Beginnings of Cellular Life" (by Prof Harold Morowitz, 1992, Yale University Press).

         All life is cellular.
         All living things are from 50 to over 90% water, which is the source of protons, hydrogen and oxygen in photosynthesis and the solvent of biomolecules.
         The major elements of covalently bound biomolecules are carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur.
         There is a universal set of small molecules: (i.e. sugars, amino acids, nucleotides, fatty acids, phospholipids, vitamins and coenzymes.)
         The principle macromolecules are proteins, lipids, carbohydrates and nucleic acids.
         There is a universal type of membrane structure (i.e. the lipid bilayer).
         The flow of energy in living things involves formation and hydrolysis of phosphate bonds, usually ATP.
         The metabolic reactions of any living species is a subset of a universal network of intermediary metabolism (i.e. glycolysis; the Krebs cycle, the electron transport chain)
         Every replicating cell has a genome made of DNA that stores the genetic information of the cell which is read out in sequences of RNA and translated into protein.
         All growing cells have ribosomes, which are the sites of protein synthesis.
         All living things translate information from nucleotide language through specific activating enzymes and transfer RNAs.
         All replicating biological systems give rise to altered phenotype due to mutated genotypes.
         Reactions that proceed at appreciable rates in all living cells are catalyzed by enzymes.