Tag Archives: electron


Substrate Level Phosphorylation

Several processes occur during normal eukaryotic metabolism to create ATP. During glycolysis (the breaking of sugar) both prokaryotes and eukaryotes use energy from the chemical bonds in the sugar to make ATP by directly transferring phosphates from the substrate molecule to ADP, resulting in ATP. Predictably, this process became known as ‘substrate-level phosphorylation. Both Cell Respiration, occurring in the mitochondria, and the light reactions of photosynthesis, occurring in the chloroplasts, also made ATP, however, no one understood how this occurred as no intermediate substrate molecule bearing the phosphates groups was known.


1978 Nobel Prize in Chemistry winner

The Peter Mitchell, working at his own, privately funded research foundation, tackled this problem and determined that the power to make ATP came from two processes linked indirectly. For his work in this area, Mitchell won the 1978 Nobel Prize in Chemistry “for his contribution to the understanding of biological energy transfer through the formulation of the chemiosmotic theory”.

Model diagram of electron transport and H+ translocation across the membrane


Electron flow carries H+ across the membrane

Process#1: One of these processes is the electron transport chain (E.T.C.) during which a high-energy, excited electron is passed down a series of membrane proteins. As the electron is passed, it sometimes pulls hydrogen ions (H+) along and passes them across the membrane (see the cartoon illustration of this model by Mitchell). As a result, this process creates an electrochemical gradient across the membrane with more H+ on one side compared to very few on the other.

Process #2: As we know, these gradients will ‘want’ to resolve themselves and move towards equilibrium (by diffusion). There exists a special channel protein that H+ may pass through from the side of the membrane with a high concentration of these ions to the other.

“Each chemical species (for example, “water molecules”, “sodium ions”, “electrons”, etc.) has an electrochemical potential (a quantity with units of energy) at any given location, which represents how easy or difficult it is to add more of that species to that location. If possible, a species will move from areas with higher electrochemical potential to areas with lower electrochemical potential; in equilibrium, the electrochemical potential will be constant everywhere for each species”

                         -from the wiki page on electrochemical potential

I prefer to imagine the membrane and ions as a hydroelectric dam with water building up on one side and a relief passage through the dam.Image

Just as energy is captured when water rushes through the dam, H+ ions coming through the channel protein are used to power an enzymatic subunit that synthesizes ATP.

Sigma-Aldrich provides an excellent animation illustrating how ATP Synthase operates as both a H+ channel and an enzyme making ATP.

A conceptually simple set of experiments provides the evidence supporting this model. Here, an artificial membrane is made incorporating ATP synthase and bacteriorhodopsin. The rhodopsin molecule is capable of transporting H+s across the cell membrane when it is struck by light. Given sufficient supplies of H+ ions, ADP and Pi, ATP will be formed when a light source is present. In the absence of light, no H+ is transported and no ATP is made.

When a H+ carrier molecule that can diffuse through the membrane is introduced, this carrier maintains equal amounts of H+ on both sides of the membrane. Further, even when light is present, H+ is pumped across the membrane and then re diffuses back creating little or no ATP. This is illustrated in a cartoon from Albert’s Essential Cell Biology:


Chemiosmosis defined experimentally

Chemiosmosis and the work of Peter Mitchell

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Posted by on October 5, 2013 in Uncategorized


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All I know about is a bunch of damn gangs that live in a round neighborhood

Professor Venus schools Arnold on the Pros, the New Boys and the Elected Ones – the three gangs who rule the neighborhood.

Now, get back to school.

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Posted by on August 26, 2013 in Uncategorized


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Getting Oxygen Where It’s Needed

Oxygen is required by many organisms for survival, luckily it is plentiful in the air, but how does it get into all the tiny cells all over the body?

periodicFirst, Oxygen is a highly electronegative atom. This means that it attracts electrons very well and can pull them away from other molecules. Only one other atom is more electronegative and that’s the most reactive element in the periodic table, Fluorine. Electronegativity becomes useful biologically because electrons are capable to storing energy that can be passed along from one molecule to the next. But , to do this, each molecule must be more electronegative than the last. Therefore, it is not surprising that Oxygen is used as the final electron acceptor in the electron transport chain of cellular respiration. This reaction is required by many organisms, and can be highly beneficial even to some organisms that can live without Oxygen. An electron transport chain is a process by which molecules in a membrane pass en electron down the line using its energy in a controlled way to extract even more energy from sugar.

But how does Oxygen get to the cells that need it? Two molecules account for much of this action, myoglobin and hemoglobin, both illustrated below:


Hb- hemoglobin, Mb-myoglobin.

What this image also elegantly portrays is the amazing similarity between the molecules that belies their evolutionary relationship.

Each of these molecules is capable of binding Oxygen, but each occurs in a different tissue. ImageHemoglobin is present in Red Blood Cells, making them capable of transporting oxygen from the lungs to other tissues. Myoglobin occurs in these ‘other’ tissues, particularly muscle cells.

Despite the fact that they both bind oxygen, they do not bind it equally well under all conditions. While hemoglobin is just as good at binding Oxygen in high concentration environments (like the lung after inhalation), it is not as good at retaining oxygen when found in less Oxygen-rich environments (such as tissues like muscle).  Under these conditions, myoglobin is much better at binding Oxygen and can pull the molecules away from hemoglobin.

Recently, several groups have published new data about how subtle differences amongst proteins involved in Oxygen transport through blood and muscle result in different binding properties. In turn, the variability in these properties underlie the amazing diversity of lifestyles found in nature, from humans to birds to giant whales capable of holding their breath for up to an hour.

Image That brings us back to the electron transport chain and Oxygen’s electronegativity, where Ois used as a ‘magnet’ for the electron traveling down the pathway from one molecule to the next. As it goes it loses some of its energy, which is converted into a new form that the cell can use. Once the electron, now at a lower energy state, gets to O2, the Oxygen splits  and takes up a Hydrogen ion to form water.

So, electronegativity and binding affinity are the forces that both transport Oxygen through the body and pulls electrons from one molecule to another. Together, the movement of electrons, like that of water through a mill, powers processes that lead to the synthesis of ATP, the energy currency of the cell (see below).



Note the electron traveling down the chain (in pink)

Given what we’ve discussed here, how do you think a baby ever gets to pull the Oxygen away from its mother’s blood / hemoglobin?


Posted by on June 26, 2013 in Uncategorized


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The Bohr atom at 100


Bohr and Einstein having a smoke

One hundred years ago, in 1913, Niels Bohr published a trilogy of papers describing the atom in ways that we are still referring to today. These papers synthesized several previous ideas into one and presented the atom as a positive nucleus encircled by a cloud of electrons that stayed in very distinct orbits that were proportional to their energy (i.e.  electrons in low orbitals were lower energy than those that inhabited higher orbitals). 

This sounds like a simple concept, but it has some very important ideas nested in it. Probably most importantly is the idea that the orbitals are distinct. That is, there is no ‘between’ orbitals. Electrons are in one orbital or another, but never in between. Also, it takes energy input to raise an electron into a higher orbital and energy is released (as light) when an electron drops into a lower orbital. As a biologist, I find this most interesting and useful to think of when contemplating photosynthesis and considering how photons are absorbed by atoms in the reaction centers of chloroplasts. This is done by raising an electron to a higher … let’s say ‘energy level’. Once this happens, we have energy stored (at least for a while) in this electron. That energy can be used to do work, passed on to another atom or it can release the energy into the environment as light.


Bohr Model

Here’s a good representation of Bohr’s model with the different energy levels / orbitals indicated by the dotted lines labeled n=1, n=2 and n=3 .

Until now, this model has been a good, workable theory that seemed to fit  mathematically with what was observed indirectly. However, two really cool papers came out recently that have provided the first direct observations of atoms / molecules. In the first, Hydrogen atoms were observed using photoionization microscopy. This was done with a hydrogen at resting state (it’s lone electron in the lowest orbital), and in several higher energy states attained by providing energy to the atom using a laser. Below is a figure from the paper presented in Physical Review Letters 110, 213001 (2013). In each subsequent panel the electron can be seen in increasingly higher (distinct) orbitals.



Ok, I’m just going to come out and say it, ‘This is totally f’n cool.’ This means that Bohr’s totally theoretical model of a century ago has just been directly shown to be completely accurate.

But wait, there’s more. 

We’ve been using Bohr’s model and others’ ideas to model how multiple atoms come together to form molecules. Again, these structures have always been imagined from indirect observation. But, in the May 30 Science, this too has been directly observed using non-contact atomic force microscopy. Here we can see atoms in a molecule as well as the covalent bonds between them. 



Here’s to you Niels. Bang up work!! ImageNot to mention Dimas G. de Oteyza1,2,*,Patrick Gorman3,*Yen-Chia Chen1,4,*Sebastian Wickenburg1,4,Alexander Riss1Duncan J. Mowbray5,6Grisha Etkin3Zahra Pedramrazi1Hsin-Zon Tsai1,Angel Rubio2,5,6Michael F. Crommie1,4,,  and Felix R. Fischer3,4, for imaging the covalent bonds.

And A. S. Stodolna1,*A. Rouzée1,2F. Lépine3S. Cohen4F. Robicheaux5A. Gijsbertsen1J. H. Jungmann1C. Bordas3, and M. J. J. Vrakking for visualizing the orbitals of Hydrogen atoms.


Posted by on June 6, 2013 in Uncategorized


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