WARNING: Digressions may occur. Wee knight illustration courtesy of the magnificent Jon Hoehn II.

Friday, October 24, 2014

Bioremediation by bacterial badasses part 2: How do bacteria digest toxic waste?

If you haven't checked out part 1, you should! Unless you know how heavy metals are poisonous, then you're already caught up.

Ok, so stuff like radioactive waste and oil are bad for the environment. Thus, it might be a good idea to clean that stuff up if it gets where it's not supposed to be. Unfortunately, you can't just mop it up with a paper towel like that time you spilled wine all over your grandmother's new carpet (you drunkard, you). There are some very smart people trying to design materials that can act like paper towels and sop up bad stuff, and I'll include some links at the end if you want to read more about that business. However, I promised you bacteria, and bacteria you shall have! Let me introduce you to my friend Geobacter. You can call him Geo.
Don't mind me. I'm just chillin', saving the environment and stuff.
Geo is kind of an oddball. Like many bacteria (and higher organisms such as ourselves), Geo likes to eat sugars and/or small, sugar-like molecules (e.g., acetate, malate), because sugar is delicious.
Take a break if you need to and go find some candy.
But, Geo also eats metal and petroleum, because he doesn't care about your rules.
Imagine a bacterium sitting in that swing seat, if you would.
You see, most (possibly all) organisms make high-energy molecules using what is called an electron transport chain. We can think of it this way: in general, organisms receive energy (eat) from a lot of different sources. That is apparent just by looking around us. Humans eat pretty much anything that stands still long enough; chickens, broccoli, termites (check this out!) Dogs are so anti-picky, they eat their own puke--among other things...

But wouldn't it be kind of a pain if we had to build cars that ran on gasoline, natural gas, electricity, hydrogen, solar power, wind power, etc.? That would be pretty silly, so most cars are powered by just gasoline.

Cells are the same as cars. A lot of proteins--our handy-dandy molecular machines--are powered by ATP (adenosine triphosphate).
You have about 250 grams of me right now. Picture--Ben Mills
Alright, back to the electron transport chain (ETC). The basic idea isn't really intuitive to me, even though I've worked in biological sciences for several years now, so I'm going to do my best to break it down into something simple but still fairly accurate.

ATP is a way for you to store energy. Returning to the car analogy, you probably fill up your tank when it starts getting low, but most of the time you don't use all that gas at once. You drive to work, you go to the grocery store, you visit your friend's house a few minutes away. And you can do this because gasoline is a source of energy that can be stored. Sunlight is a form of energy, too, but if you don't have a solar panel to soak it up and put it inside a battery, you can't use the sunlight later. So, ATP is one of the reasons why you don't need to constantly eat to power your body.

The way the ETC works is kind of like this: you have a vehicle that you want to drive down a hill at midnight. The vehicle can only run when the sun is shining on it. So, you drive the vehicle to the top of the hill during the day, then later that night you can just give it a little nudge and it will roll down the hill. ETC is how your cells get the vehicle up the hill.

That's great, but what does this have to do with our old friend Geo? Geo has the neat ability to use nasty stuff like oil and uranium as steps in the ETC. It can bounce electrons through them to other molecules to make ATP.

Why can't we do that? We just don't have the machinery! Like I said earlier, proteins do everything for us. We don't have the same proteins that Geo uses to eat up toxic waste.

Geo has already been useful in cleaning up the streets, and a lot of people are trying to figure out how he does his job and maybe how to help him do it better, like a bunch of Commissioner Gordons rooting for Batman.
I am the night!
Some people are even thinking about using him to make batteries! But let me not leave you thinking that Geo is the only quicker-picker-upper out there. He has friends like Pseudomonas putida and Deinococcus radiodurans. I've heard they like to have parties and talk about all the seagulls they've saved.
Like a boss.


Pictures!

Tuesday, October 14, 2014

Bioremediation by bacterial badasses part I: Why are heavy metals toxic?

We all know that heavy metals like uranium and arsenic, as well as hydrocarbons such as crude oil and plastics are pretty bad for the environment, since they have this weird tendency to kill things. Most people know how oil kills innocent critters: it gets all over their feathers, gills, fur and fins, weighing them down so that they can't use their locomotory method of choice, which often results in them drowning. They probably get eaten sometimes, too, since they're slow, easy prey, and I'm sure that gives some unlucky predator a lingering foul (or fowl, ha) taste and a nasty bout of indigestion.

But how are heavy metals toxic? And what the heck is a heavy metal? Are there metals that aren't heavy? I think those are questions not many folks know the answers to. I didn't, until my junior (senior? It's been a while) year of college.

It all comes down to proteins. Proteins are not, contrary to bodybuilder popular opinion, just a post-workout necessity. Actually, we are all made up of a vast number and diversity of proteins that basically do everything for us. Yes, even plants. Don't be racist, plants are people too. Here are a few examples of cool proteins:

actin keeps your cells in their proper shape, and makes those sexy muscles contract
They look weird, but they're supposed to. That green stuff is actin, and the blue is DNA.

DNA polymerase copies your DNA, in conjunction with DNA helicase, which unzips your genes

Hank Green is my hero. Watch all of his videos.


I'm a little disappointed that I'm already in a relationship and can't use this pickup line on somebody.
trypsin breaks up them food proteins
amylase breaks up them food sugars
rhodopsin eyeballs! I'm actually not 100% sure what this one does, but I do know it's important for seein'.
Pretty. I got this from Petr Novák, Wikipedia - Own work.
I learned what rod and cone cells are from this. I never knew! You should look it up if you don't know already.

Proteins are great. Wouldn't it be sad if they stopped working? Or if something stopped them from working? Like heavy metals?

That's right, sports fans, that huge tangent had a purpose. Coming back around, let's talk about metalloproteins. A lot of super important proteins require metals to function.

Most metalloproteins use lighter metals like sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca). Some use slightly heavier metals like manganese (Mn), cobalt (Co), or zinc (Zn). Heavy metals are elements like silver (Ag), gold (Au), and mercury (Hg). Those metals like proteins, too. They actually like them more than the lighter metals. You can think of heavy metals as bullies. Gold comes up and sees magnesium playing with a DNA polymerase, and he's like "I want to play with that protein!" Since he's bigger, he pushes magnesium in the dirt and takes the polymerase.

Of course, it's not quite that simple, but that's the general idea. You can also imagine that sticking a bigger blob where a smaller one used to be would change the shape of something. Since a protein needs to have a certain shape to work, heavy metals cause problems and basically break whichever protein they attach to.

The title of this post mentions bacteria. Odd, I didn't mention bacteria at all in this article, did I? I guess that will be in part 2!
This is like a trailer, except it's not a video!



I can't do art, so let me tell you where I got all those neat pictures, in order of appearance: