After spotting the happy sign of billowing bubbles below her SDS-PAGE gel, the bumbling biochemist knew something was finally going well (one of those days…). And after an exhausting day of protein purification strategy scout-outing, she was nearing time when she could recharge her brain battery – so here’s a post about rechargeable batteries – and how they’re similar yet “opposite” to gel electrophoresis!
I wrote this post a few months ago when my car battery wouldn’t start – so the story starts there….You might be a biochemist if your car won’t start and, while waiting for a jump start you start thinking about how it relates to gel electrophoresis… And how “dead” rechargeable batteries are kinda like U-haul rental truck companies where all the trucks are stuck at the popular destination! How can we get the trucks to go the other way? What would Le Chatlier have to say?
Warning – I’m not a physicist or an electrochemist, just a biochemist stranded and curious. Electricity is the movement of charged things. Often the charged things we’re talking about are electrons, which are negatively charged subatomic particles that whizz around the positively-charged nuclei of atoms. The atoms that live on the outskirts of the “electron clouds” are held less tightly and can come & go more easily. Especially if there’s a lot of them really far away from the positive pull of the nucleus as is the case with some transition metals. More here: http://bit.ly/2XDSLjd
Because they’re negatively charged, electrons are attracted to positively charged things, so they have a “desire” to go there, and when they move there, you have the movement of charged things (an electrical current) so you have electricity and its associated energy.
But you need a route between the – thing and the + thing (without the route, you just have potential energy). And you need a way to make the – thing – & the + thing +. And that’s where the chemistry comes in, getting atoms to give and take electrons. If you think batteries are just for physicists, think again. Chemistry’s what makes them work to begin!
Specifically, REDOX reactions. When molecules transfer electrons we call it oxidation (taking electrons) and reduction (giving electrons).
to help us remember this we have a helpful mnemonic: OIL RIG: Oxidation Is Loss (of electrons (e-)); Reduction Is Gain of electrons
And to help us remember what happens where, we have another mnemonic: RED CAT; AN OX: REduction occurs at the CAThode
Sometimes the electron pass-off is direct from the initial giver to the final taker. But if you make the electrons travel to get to their final destination you make a current. And generate an electric field between the negative place electrons are fleeing from & the positive place they’re fleeing to.
You think of things in terms of of a shipping problem. When there’s demand, the thing getting oxidized “produces” electrons that it wants to ship out. But the electrons need a route! In a battery, the highway’s closed – there’s a barrier preventing the electrons from going anywhere, so it’s like an electron factory in the middle of nowhere. What if you hook a wire to it? Like building a road, there’s now there’s a travel route out but it’s a road to nowhere – there’s no “customer” on the other end – so there’s no demand and nothing attractive at the end, so there’s no reason to waste the electron goods!
But if you hook the other end of the wire to an electron acceptor (the thing getting reduced, the cathode), you’ve connected electron supplier (reducing agent) to electron consumer (oxidizing agent). So the electrons travel through the wire, and since electrons are negatively charged, and electricity is the movement of charge, you’ve generated electricity! And you don’t have to make the shipping route direct – you can make it travel through different “cities” and the cities can use the energy it provides to do things – like power your car starter.
But electron goods are kinda like U-Haul rental trucks. They often let you rent a truck from one location and drop it off at another. So each location has to be able to both provide trucks (act as a reducing agent and get oxidized) and receive trucks (act as an oxidizing agent and get reduced).
Some locations are really popular for people to move to and less likely for them to leave from. This is analogous to a strong oxidizing agent, which wants to get reduced (gain electrons). Whereas, less popular living places are more likely to have people renting trucks than returning them. This is like a strong reducing agent, which wants to be oxidized (lose electrons). The “popularity” rankings can be found in redox potential tables. More here: http://bit.ly/2NFOeHL
This imbalance can lead to a buildup of trucks at the popular place and not enough trucks at the unpopular place. So, even if the popular place is still really attractive, there aren’t any trucks to send there. So you need to get the trucks back to the unpopular place. But no one wants to go there! So it’s not going to happen spontaneously – you’re going to have to put in some energy to “push” the trucks back to the unpopular place.
So you can use energy from electricity from another battery. When you recharge a battery, you’re basically doing a massive tow of trucks from the more popular destination to the less popular one. And because you’re actually getting the atoms to change (give up electrons) you’re doing chemical reactions. And when you use electricity to drive a chemical reaction, we call it an ELECTROLYTIC CELL. This is basically the reverse of what the battery “normally” works as – a GALVANIC (aka VOLTAIC) cell, which use chemical reactions to create electricity
And the U-haul trucks aren’t the only things attracted to the popular place. Anything that’s negatively charged will be attracted to it. (and positively-charged things to the “unpopular” place). We take advantage of this when we use GEL ELECTROPHORESIS to separate molecules by size. Wes set up a charge gradient and take molecules that are negatively charged and get them to move towards a positive charge. But their “travel route,” instead of being a nice insulated wire is a gel mesh that they get tangled up in (bigger ones getting tangled more and thus traveling more slowly).
DNA & RNA come negatively-charged, but for proteins, some, but not all are – charged and the ones that are can be charged to different extents so we coat them all in a nice negative charge using a detergent called SDS, which also denatures (unfolds) them so they run based on length of their amino acid chains not their overall shape.
The running module we use to set up the gradient is an ELECTROLYTIC CELL – it uses a power box to provide electricity to power chemical reactions, in this case water-splitting (hydrolysis).
At the top of the gel, ▪️cathode: power box sends e- to cathode ⏩ water “gains” e- (is reduced) 👉 4H2O + 4e- ➡️ 4H2 + 4OH-
And at the bottom, 🔺anode: power box removes e- from anode ⏩ water “gives 🔙/loses” e- (is oxidized) 👉 4 H2O ➡️ O2 + 2H2O + 4e-
As you know if you’ve ever opened a soda bottle, gases like to ⬆️ in liquids, & anode’s at ⬇️ of tank, so O2 it releases floats ⬆️ as bubbles (pockets of trapped gas). (the H2’s also a gas, but you only have half as much so the bubbles are less obvious)
more on this here: http://bit.ly/2XMLMbG
It helps me to think about it as you need the power source to keep the popular destination popular. Because unless you have such high demand that a little neutralization’s just a drop in the bucket, when the negative charged things move towards the positive charge things, the positive charged thing becomes neutralized. So in order to maintain the gradient you need an external energy source.
For physicists, it might be easier to think of things in terms of currents & volts and watts and stuff, but I find it easier to, at least for a basic understanding, think of things from a chemistry point of view.
Say you have a reversible reaction A + B <-> C + D that will eventually reach some equilibrium where the ratio of reactants (A & B) and products (C and D) is constant. It doesn’t have to be 1:1, and the reaction can still go back and forth but it goes forward as much as it goes backwards, so it cancels out.
Le Chatlier’s principle basically says that you make the forward direction more favorable by removing some C or D or adding A or B because this skews the balance. You can learn more about it here: http://bit.ly/2pSmg2l
Red & ox go together (the electron has to go somewhere) but it’s easier to look at the “1/2 reactions” RED & OX separately – especially since they’re physically separated in a battery. In these 1/2 reactions, there are electrons in the reactants and products, so you can add or remove electrons to get things to go the other way.
Lead-acid car batteries have lead Pb(s) & lead dioxide (PbO2) electrodes. You might see plate 1 labeled as the anode & plate 2 as the cathode, but I don’t like this terminology here because when you switch directions if you still called plate 1 the anode you’d have reduction happening at the anode which by definition is backwards. So I’m going to use negative and positive electrodes. And in a car battery they’re metal plates.
Car batteries can have multiple cells & each cell has 1 of each electrode & they’re in a bath of “battery acid” – sulfuric acid (HSO4-) and water to serve as an electrolyte that allows ions (charged atoms or groups of atoms) but not individual electrons to travel through it, so the electrons have to go through an external circuit that’s more conductive. So if there’s nowhere to go, you don’t “discharge.” But when there’s a way there’s a will! When you hook up a circuit, there’s “demand” so it supplies -> it does discharge and here’s what happens
At the negative plate, lead gets oxidized, giving off electrons: Pb(s) + HSO4–(aq) → PbSO4(s) + H+(aq) + 2e–
At the other plate, the lead dioxide gets reduced, accepting electrons: PbO2(s) + 4H+(aq) + 2e– + SO42-(aq) → PbSO4(s) + 2H2O(l)
Overall reaction: Pb(s) + PbO2(s) + 2H+(aq) + 2HSO4–(aq) → 2PbSO4(s) + 2H2O(l)
Both reactions give you lead sulfate (PbSO4 ) as a product, but you have to “get there” from different directions.
You can see see that electrons are reactants at the anode & products at the cathode. So to charge the battery, where we want to make the reverse reaction more favorable, we want to add electrons to the anode to force the reaction “backwards” and you can do that with an external electricity source.
The reason you don’t constantly have to consciously recharge your battery is because the battery gets recharged while you drive and the battery itself really only powers the “small stuff” like the radio & lights. But you need it to start the car because it helps the gas engine get going. So, things like accidentally leaving the lights on are a common reason car batteries “die.” That wasn’t the case here – instead I got screwed over by a loose screw that cut off the travel route!