My journey as a scientist has led me to discovering new and exciting areas of research that I had never come across before. Science is a broad term, encapsulating multiple fields and areas of interest. To be a scientist, one needs to find something they’re interested in and begin to study it. In this series of questions and answers, I hope to outline my experience in science and help others discover their own passions or learn more about protein biochemistry.
In your own words, what is protein biochemistry?
First of all, biochemistry is just as it sounds: it is a combination of chemistry and biology and uses chemistry concepts to explain biological processes. When I say protein biochemistry, I am referring to the processes carried out by proteins that use small molecules to produce a chemical reaction. Proteins play a role in many biological functions, and they are the enzymes that catalyze biological reactions. This means that they increase the rate of chemical reactions and by providing the energy necessary to exceed the activation energy of a particular chemical reaction. So proteins play a role in almost all chemical reactions in the body, and should be studied from the perspective of being biological components serving a chemical purpose.
How did you become a protein scientist?
When I started college at UCSD, I was unsure what I wanted to study. I enrolled in a chemistry class as the first class that I took, and was instantly hooked. During high school, I took AP Chemistry which had been a big challenge for me, but was also taught by one of my favorite teachers. One of the things that got my attention in my college chemistry class was when the professor would admit that there were still a lot of unknowns that weren’t just beyond the scope of the class, but beyond current scientific understanding. I really wanted to make a difference, and I was so interested in the topic that I decided to join a research lab as soon as possible. I reached out to a number of labs looking to hire undergraduate students, but most required more experience or more coursework prior to entry. One professor was intrigued by my willingness to start early and learn while in the lab, and took me on as a volunteer working for a graduate student. This graduate student studied proteins, in particular the way that proteins in bacteria produce the fatty acids that make up the cell wall. He described all of the things that proteins are capable of, and how most of chemistry in our body is carried out by proteins that we don’t even know about. This was exciting to me and just what I wanted to learn, but I still didn’t understand how we could get these proteins that are used in different tissues in all different types of species. That’s when I learned about cloning, and it’s just as cool and futuristic as it sounds! The sequence of proteins are encoded in our DNA and in the DNA of every species, and once you know the sequence, or gene, that codes for the protein, you can recreate it outside of the genetic material in any form you want. This means that the gene can be encoded in the DNA of another organism, such as bacteria cells, and then millions of these bacteria act as little factories to grow and produce the protein that can then be purified and studied one by one. I learned a lot while working in the lab, and while my experience may have been a bit backwards, it inspired me to read a lot about the concepts behind what I was doing. By the time I studied this in a classroom setting, I was well-versed enough to teach it to others. It was around this time, towards the end of my undergraduate career, that I realized I was a protein scientist.
What was the first project that you worked on?
The first protein project that I was a part of was the fatty acid biosynthesis process in E. coli bacteria. Every cell is surrounded by a cell wall composed of phospholipids, made from lipids, or fats, and a phosphate group. How do the lipids form in the cell to the right length and saturation necessary to build a cell wall? Fatty acid biosynthesis starts with the byproduct of glycolysis, an acetyl-CoA molecule, that contains a short chain carbohydrate that can be extended in a series of reactions. There are multiple proteins, or fatty acid enzymes, that work in concert with one another to add carbons and hydrogens onto the end of the acetyl-CoA molecule to extend it into a fatty acid chain of up to 16 carbons. This may sound complicated, but think of it as each protein bringing two puzzle pieces together, then keeping two puzzle pieces and adding a third, and so one until it makes the full picture, or in this case a fatty acid of the desired length. I worked on the proteins that extended the fatty acid in the chain, and how they interacted with each other to continue the cycle. A protein’s structure indicates its function, and we as a lab discovered the structure of multiple proteins in this process. This was how I became interested in studying the structures of proteins and how they do what they were designed to do.
What classes helped you learn the background to become a protein biochemist?
Most of my training was through laboratory techniques I learned while on the job, working as a research assistant. I learned many of the concepts behind the techniques on my own through reading textbooks and papers (see Book and Article Reviews). Course offerings will be slightly different between universities, but those that helped me the most focused on biochemistry metabolism and general concepts, laboratory classes that taught experiments with DNA such as PCR and cloning, laboratory classes that taught protein biochemistry specifically, and chemistry classes that outlined reaction mechanisms. I found what helped me to learn was through doing the experiments and repetition of the same concepts until it was second nature, and I could focus on the cool things the proteins themselves were involved in.