Primers

Overall, my husband found what I had to share about programmed cell death to be very interesting, but he had a few observations. "When you say 'protein,' I think about meat. I think 'amino acids' are kind of like vitamins? I sort of know what a 'catalyst' is, but the 'enzyme' just makes me think about saliva."

I don't want to bog down my sciencey posts by stopping to explain everything from the ground up. But I do want them to be understood. So as I go along, I'm going to try to identify terms and concepts that a person really needs to grasp to get anything out of what I'm writing, and then give them their own page that I can link to as needed. I'm going to label them "primers" and include the word "primer" in the title so they can be easily found and identified.

So far I have written primers for amino acids and proteins and catalysts and enzymes. I have edited the post about programmed cell death to link to those pages.

Please keep in mind that I'm not an expert in what people do and don't know. I'm open to suggestions for topics that need a primer. Right now those suggestions are coming from my husband, but there's no reason why he needs to be the only one.

Next post: Thursday, 15 November, 2018 (ish)

In the meantime, please enjoy this glass of hydrogen peroxide solution (I was a bad chemist; I didn't label it!):

Primer: catalysts and enzymes

If you pour a glass of hydrogen peroxide (H₂O₂) solution and watch it for a while, not much happens. It sits there, looking very similar to a glass of water. If you get distracted for a while and come back later, you might see a few bubbles on the surface of the glass, but that's about it.

If you know a little bit about chemistry, you know that hydrogen peroxide is not a very stable molecule. Oxygen is one of the biggest electron hogs on the periodic table, and two electron hogs are not going to like being that close together. Oxygen (O₂) and water (H₂O), on the other hand, are very stable molecules. If you know a little more about chemistry, you know that less stable molecules tend to react to form more stable ones. So, where's my water and oxygen?

Molecules don't just react willy-nilly. They need to orient themselves properly for the atoms to interact in new ways. They also need to bring enough energy to form an unstable, temporary, intermediate arrangement of atoms between the reactants and products - a transition state. In our example, the hydrogen peroxide molecules can tumble around in the glass for hours before enough of them meet those conditions for us to actually see oxygen bubbles. But if we drop a little steel wool into the glass, there will be oxygen bubbles everywhere!

The iron in the steel wool is acting as a catalyst. Catalysts increase the probability of molecules reacting by guiding them into the proper orientation, lowering the energy requirements of the transition state, or often both. What catalysts do not do is contribute to the net result of the reaction. Even with the steel wool, our hydrogen peroxide reaction is still only producing oxygen and water. The iron temporarily interacts with the peroxide to form a different, more attainable transition state than the peroxide would form by itself. Since the iron is left behind after the peroxide has reacted, one atom of iron can catalyze any number of hydrogen peroxide reactions.

The chemistry of living things uses catalysts all the time! Life as we know it would be impossible without them. When catalysts appear in a living system, they are called enzymes. Let's look at our hydrogen peroxide example again. Peroxides are damaging to living tissues, so many organisms utilize a protein called catalase, which converts hydrogen peroxide into water and oxygen. Catalase is acting as an enzyme, and similar to our non-biological example, it incorporates iron in its molecular structure.

Primer: amino acids and proteins

Amino acids are a family of molecules that contain an amine group (NH₂) and a carboxyl group (COOH). The ones you'll hear about the most in the context of biochemistry are alpha amino acids. An alpha amino acid has the amine group on one end, the carboxyl group on the other end, and a carbon atom between them. Attached to that middle carbon atom is the molecular structure that gives that particular amino acid its unique properties. It could be a hydrocarbon chain, an benzene ring, an alcohol. For example, the simplest alpha amino acid, glycine, has the structure H₂NCHCOOH. The possibilities are nearly endless, but we tend to focus on the twenty amino acids that are encoded in our gene sequences.

The useful thing about amino acids is that the amine group of one can react with the carboxyl group of another, forming water (H₂O) and two amino acids joined together by an amide link (...NHCO...). This can be done over and over again, with the amino acids becoming the links in a long molecular chain that can bend and coil into a unique shape. This is called a protein. Proteins provide structure, transport needed (or unneeded) materials, transmit signals, and facilitate chemical reactions in living things. Aside from water, proteins make up more of our mass than any other type of substance.

There is a small group of amino acids that we humans have to get from our diet. Since all living things utilize proteins in one way or another, we get those amino acids by breaking down the proteins of the organisms we eat. That's why you hear about needing to eat protein to stay healthy. From those "essential amino acids," our bodies can synthesize all the other amino acids we need, and we can make proteins of our own.