End of the Quarter

Finally! The end of my first quarter at OHSU. I took two major classes and one minor one where attendance was required, but there were no grades. The first class was EBHE, which I figured out a few weeks in stood for Environmental and Biomolecular History of Earth. It was a team taught course with three instructors. Each and every lecture was a crash course in a different subject. Prebiotic chemistry, paleontology, atmospheric chemistry, stable isotope analysis, thermodynamics, biomolecular systematics, phylogenetic analysis, elemental cycling, microbial metabolism, bioinorganic chemistry....just to name a few.

We'd get a crash course in one of these topics during every lecture and then have a technical paper assigned to read about the topic. During the next class we'd start with a new 30 minute lecture, and then spend the next two hours discussing the last lecture and the assigned paper. Because the lectures were just half hour tastes of the material, most of the learning came outside the class while doing outside research to understand the paper. All in all, it was a great class and I definitely learned a lot. Since the department is interdisciplinary, this course really helps put everyone on equal more equal footing with regards to what we've been exposed to subject wise. Everyone knew about at least one of the subjects from their past academic studies, but we all knew about different things. This course was great in that, though certainly not comprehensive in any area, we can all now at least speak using using the same language and terminology and understand each other. That's always a difficult thing to accomplish when throwing engineers, chemists, biochemists, microbiologists, biologists, geologists, hydrologists, environmental scientists, and ecologists together.

Though EBHE was definitely the more time consuming course for me this quarter, my Biochemistry course was the one I had the most trouble with. There were 8 of us in the class. Turns out 4 of them weren't even taking it for a grade, but were sitting through it for a second time, and not because it was entertaining or fun. At the end of everyone's first year, students need to take, and pass a qualifying exam. The exam is made of 4 sections which depend on which classes you've already taken. Apparently almost everyone failed last year's biochemistry section of the exam so they were sitting through it again in hopes of passing it the second time around. Not encouraging. Thankfully, I'm an ESE (Environmental Science and Engineering) major, and not an EBS (Environmental and Biomolecular Systems) major, so biochem isn't required to be on my qualifying exam. I only took it because the other ESE class offered this quarter was analytical chemistry, a course I've already taken in Reno.

Anyway, so of the four of us who were taking the course for the first time, I was the only student in the class who didn't have an undergraduate major in biochem. Lucky me. I had to do a TON of outside work to just understand what the terminology used in class. Biochem wouldn't be on my qualifying exam, but I still needed to pass. But graduate school isn't like working towards your undergraduate degree. When you're working on your PhD, anything lower than a B is failing and you have to retake the course! But hey, no pressure! The only grades for this class were two homework assignments (5% each) and two tests (45% each). I got B+ on the first test which I was mighty proud of, and an A- on the first homework. That first test was a lot of memorization so I was pretty sure I'd do better on it than on the second test which involved a ton of structural chemistry. After sitting for the second exam last week and only feeling comfortable with the answers to 2 of the 6 questions, I was pretty worried.

Questions looked like "draw the structural schematic of the catalytic triad of residues essential to the activity of serine proteases," or "draw the chemical structure of the covalent tetrahedral intermediate of the first stage of the turnover in serine proteases and explain the roll of the oxyanion hole." Uh...sure...what the heck is a serine protease again??? In regards to the second question...I knew the function had to do with the backbone chain of the monomer and not the side chains of the residues. I knew the intermediate was stabilized in terms of it's charge. But that's all I could come up with. Then I drew this:

By some miracle, I got a 6/10 on that question. No, that's not very good, but considering a 65% turned out to be a B, it's could have been worse. Below you can see what the professor wanted. To be fair, cartoon versions in the text book look like the image on the right, with the jelly bean-looking thing around the residues that make up the oxyanion hole. And though much much simplified, I oriented my tetrahedral intermediate in the hole properly.

Anyway, I somehow managed to pull off an A- on the final and wound up with an A- in the class. I still dislike structural biochem. I guarantee I'm never taking another class in it again. And hopefully next semester I can limit it to one class. It's been really hard to get any work done in the lab when I've had so much class work to do. In early February I have to have an abstract written and a poster and speach put together for a conference they might be sending me too. That mean's I have to seriously get busy in the lab. I also have a seminar to present for the department on Tuesday. It'll be the first time most students and faculty get introduced to the project I'm working on, so it's kind of a big deal. On that note, I should probably start working on that...