Start of Winter 2025 Semester
Table of Contents
Sunday, January 5
163.2 lbs (Day 9, starting from 162.6 lbs on Dec 28)
woke up around 8 AM and prepared to go to the gym. My friend from the UCSF-UCB joint Bioengineering PhD program joined me, and we focused on similar exercises as before but targeted different muscle groups(hit triceps instead of biceps towards the end of the workout). After the gym, we headed to Costco for groceries. I bought a large pack of 36 small cans of chicken breast😄, which should last about six weeks. We also tried to find gym clothes but couldn’t, so we decided to look on Amazon or Uniqlo instead. It is unfortunate for me that there is only one Uniqlo in SF(I loved Uniqlo U line and it is way easier to get items in Korea)
I picked up a two-liter bottle of extra virgin olive oil(there was no 1L…2L is too many for a single😵). Even though I initially wanted a smaller one, considering the expiration date, I thought I could use it in time. After grocery shopping, I had a brunch-like meal and then cut my hair. This time, it only took an hour, a big improvement from the previous attempts. My haircut ended up shorter haha, with the top at 1 3/4 inches and the sides and back at 6 mm, tapering them for a natural blend. Someday, I might reach Buzz cut…?
I thoroughly cleaned my house and bought a smaller portion of gim at Costco, which is more convenient because the larger container(previous one) tends to lose quality due to moisture absorption. In the evening, I worked on a blog post in English, which I’ve been doing since January 3rd. It’s been challenging and time-consuming, but I’m sure I will gradually get used to it. I finished writing around 11 PM, then had a quick dinner. I prepared some overnight oats for breakfast and went to bed around 1 AM, aiming to maintain my gym routine!
Monday, January 6
164.0 lbs (Day 10, starting from 162.6 lbs on Dec 28)
New Start! After arriving at the lab, I talked with my mentor about the meaning of the rotation project (what we want to see and check) and possible application if our assumption is correct. Thanks to the thorough reading of the review paper regarding eIF4E, we discussed biology and our project way better than before I began. And then I ate lunch and went to the new class of this semester!
CHEM 244: Reaction Mechanisms
Winter
3 units
This course is designed to develop knowledge of organic reaction mechanisms. This interactive course involves some lectures but enforces student learning through intensive arrow-pushing sessions with students at the board. Current topics include: electrocyclic reactions, Woodward-Hoffman rules, sigmatropic reactions, migration reactions, neighboring group effects, carbanions and free radicals, carbenes, carbenoids, nitrenes, six-membered heterocyclic rings, five-membered heterocyclic rings.
It was easy because I took almost six organic synthesis classes. Furthermore, we don’t have to worry about the results of quizzes and exams because TAs say there would be opportunities for us to resubmit our assignments or tests when we think our grades are not good, haha… so it is a low-key class for me.
After taking a class, we take the NMRs of two samples. I haven’t had a chance to convert my NMR account’s payment method from the previous rotation lab into the current one. So, I had to be along with my mentor. It was a hassle, but seeing different processing methods and the NMR pattern was good. But again, it is so inconvenient that the NMR facility doesn’t have an auto-sampler, which means the tester should be in front of the computer. Considering how often we use these instruments, I hope we have a decent one that can reduce a significant amount of time. We jumped into the next task, purifying crude mixture using prepartive HPLC. Learning instruments is always fascinating. It is so powerful that we can do many things by virtue of new instruments, which can broaden our perspective on the research we can initiate. Somewhat late, I got off work and had dinner, cleaned my room thoroughly, and literally passed out😵🛌
Tuesday, January 7
162.4 lbs (Day 11, starting from 162.6 lbs on Dec 28)
I woke up around 8:30, so I failed to go to the gym in the morning…🤪 I quickly ran a reaction and took a class (CHEM 297: QBC Journal Club, same as the one in the Fall quarter). The latter presentation was about the paper from Jack Taunton and was presented by a lab member in my current rotation lab, so I tried to focus on it, and it was great! (Mutant-selective AKT inhibition through lysine targeting and neo-zinc chelation – Craven GB, et al. Nature (6 November 2024)) As much as I have learned about chemical biology, especially small molecules, drug discovery has been driven by serendipity. Haha. At the beginning of the experiment design, they didn’t expect zinc chelation in this paper. Come to think of science, it might be natural. Zinc chelation in this paper.
The presentations ended earlier than I expected so I hit the gym quickly and grab lunch and purify the reaction. but that time I don’t know, for some reason, suddenly I wanted to try wet loading instead of using extra catrige that can contatin celite. But due to carelessness ㅠㅠㅠ, I spilled almost the reaction mixture, so I ended up doing the same reaction again around 5 pm and purified., lyophilized. I got off work around 20:30. It was so tiring, but I successfully separated it, and I think not using an extra cartridge is more convenient and can give a higher yield. So it was worth it haha. Between experiment I realized I have to study thoroughly how to exactly interpret the LC-MS pattern (there are three different spectra when we acquire a sample), because It is the one we used literally everyday. So, I took a picture of the instrument for a more detailed catalog or usage!
Wednesday, January 8
162.6 lbs (Day 12, starting from 162.6 lbs on Dec 28)
I was happy, thanks to the excellent weather these days. It is a little bit chill in the morning, but throughout the day, it is so clear. Today was quite busy. I had Reaction mech. at 1-2:30 pm, and I had to do two reactions. I synthesized one more warhead and ran a backup reaction to make starting material for synthesizing various cysteine reactive warheads. It was easy to set up but difficult to check the reaction progress. LC-MS doesn’t work for this chemotype, and the usual TLC also didn’t give us a clue about the conversion of the starting material. After several trials and errors, we used an AcOH additive in the eluent, making checking conversion visible. I used the same additive for the flash column, but the product had some impurities. We were planning to check NMR to confirm. I think we should(all scientists🧑🔬) write supporting material more thoroughly. Quite Frequently, repetition doesn’t give the same result.. many writers didn’t incorporate important information from the experiment. I don’t know if they did it intentionally or not.
I tried to use my evening to study the principles behind the techniques I have learned today and practice English. Still, I often found it difficult, especially since I worked hard these days, and after I arrived home, I was literally exhausted. Taking a shower and eating dinner made me sleepy, and I fell asleep immediately. I hope the weekend comes soon so that I can use some time to study and fully rest from work.
Thursday, January 9
162.4 lbs (Day 13, starting from 162.6 lbs on Dec 28)
I woke up around 8 a.m. but didn’t feel fresh or energetic. I think it was because I woke up briefly at around 4 a.m. last night. I went to bed at 8 p.m. because I was so tired I couldn’t help but sleep, but even so, I didn’t feel quite right when I finally got up. I decided to sleep for 30 more minutes😅, and then I quickly took a shower. After that, I checked my schedule for the day. I was determined to finish all my tasks by 6 p.m. (or maybe 5 p.m.) to keep my daily routine on track. Since I barely had time for breakfast, I just ate a protein bar before heading to the lab.
Last night, I worked on purifying a boronic acid derivative. I checked the fractions using LC-MS and TLC, but I’m unsure which ones contain the desired product. I collected two separate fractions based on their different peaks in LC-MS and different spots in TLC. I’ll analyze them further using NMR. Suddenly, I became curious about the vacuum strength of a rotary evaporator compared to a Schlenk line. Typically, chemists remove residual solvent after purification using a Schlenk line with a high-vacuum pump. However, our rotary evaporator can reach pressures as low as 10 millibar, which is quite powerful. I wondered whether that might be sufficient to remove the solvent without needing the high-vac setup.
- I searched and found that a high-vacuum pump can achieve pressures in the range of 10^-3 to 10^-7 mbar, which is better!
After collecting my fractions in scintillation vials, I took a class(BBC Seminar Series), the same one in the Fall semester. During a previous rotation, I often skipped it because I felt it didn’t align perfectly with my research interest(It deals with broad areas of science, not just chemical biology). However, this time, the lecturer was a chemical biologist (Philip A. Cole from Harvard), so I decided to go. I didn’t capture all the details, of course, but It was a good talk to learn about the biology of histone and the function of specific lysines on that. After class, I went home for lunch(so hungry) and then returned to the lab.
My mentor and I discussed another part of my rotation project(biology). We must express and purify a recombinant eIF4E protein with a specific amino acid mutation. We reviewed the method for designing forward and reverse primers for site-directed mutagenesis and how to get the protein we desired. The first attempt is usually challenging, but I’m sure I’ll get better with practice. I’m excited to try something different from chemical synthesis.
Later, we checked the NMR data on the two fractions I collected. Fortunately, one of the fractions had an NMR pattern almost identical to what’s reported in the supporting information for our target compound. It still contained some impurities, but we concluded it wasn’t critical for the following reaction. I learned that LC-MS is not 100% credible, and we must know other methods to check reaction progress and characterization.
Right after I got off work, I headed to the gym on campus because I’ve made a goal to work out six times a week! Even though I’m busy, I want to keep up with my routine. Once I negotiated, I thought I might become lazy, and getting back also became harder. I had a good workout and then went back home. I had a second meal, did the laundry, and did meal prep. Finally, I tried to finish some work I had postponed during the week. I’m also working on writing a blog in English and continuing to review various lab techniques I have learned.
Friday, January 10
164.4 lbs (Day 14, starting from 162.6 lbs on Dec 28)
I woke up around 6 a.m. feeling fresh and in a really good mood. I headed to the gym because I wanted to do some cardio—I haven’t done much lately. My goal was to run between three and five miles. After warming up with some active stretching, I spent about 35 to 40 minutes on the treadmill and covered around four miles, which felt great. When I headed home, I realized I used to take a picture of the sky, so I took one pretty picture.
Once I finished my workout, I went home, took a quick shower, and had breakfast before heading to the lab. I had two reactions to run that day. During lunchtime, some people brought their meals from home, while others ordered food. We all gathered on the 4th floor of the CVRI building and enjoyed a delicious lunch together. I ate two kinds of pie(one was ‘Baby Clam and Tomato Sauce’ and another was ‘Beef and Potato’) from Peasant Pies(550 Gene Friend Way, San Francisco, CA 94158). It was crispy outside and warm, with yummy filling; it was good! One of my cohort members brought a deck of cards to show us how to play blackjack, which reminded me of the movie 21. We played a few hands and had fun discussing using math skills to beat the casino. hands and had fun discussing the idea of using math skills to beat the casino.
After lunch, we moved to the Reaction Mechanisms class, where we learned to use a Scifinder to search for specific reactions, substrates, references, and pharmacological data. Then, I went back to the lab to check my two reactions. Unfortunately, one reaction showed no change in the starting material, so we added more reagents and let it run over the weekend. For the other, we didn’t have enough time to purify it, so we stored the reaction mixture at –20°C and left it for the weekend as well.
When the workday ended, about 12 to 15 of us—including some former rotation students and one person’s fiancée—went to a bar near campus, just a three-minute walk from the lab. It was a welcome party for the new rotation students: three from my program (CCB) and one from PSPG, so four new people in total. We spent nearly three hours chatting about all sorts of topics: graduate student life, soccer teams in Germany (since three of the group are from Germany🇩🇪), Korean🇰🇷 food, our subsequent possible lab rotations, and some research projects and thesis work from a postdoc in our lab. It was entertaining, and I tried my best to keep the conversation flowing by asking questions so things wouldn’t get awkward. Afterward, I went home to rest. I planned to go to bed early tonight to prepare for tomorrow’s symposium
Saturday, January 11
162.6 lbs (Day 15, starting from 162.6 lbs on Dec 28)
I woke up around 7:30, which was relatively early for a weekend because I planned to attend the KASBP-SF symposium in 2025. I went there with two fellow UCSF PhD students—one from the PSPG program and another from the Tetrad program—and we traveled by Caltrain. On the way, we discussed finding a good thesis lab with my friend from PSPG, who, like me, is also in his first year and looking for a lab.
It took about 40 minutes, including the walk to the station. When we arrived, we were disappointed that the event was not intended for graduate students. Most attendees were CEOs and employees hoping to connect with potential employers or customers. It felt more like a business networking event. Although a few people from academia and industry—such as senior scientists—presented their pipelines and technologies, the event didn’t seem academically focused. We also noticed that we were the only graduate students there😳, which confirmed that it wasn’t aimed at people like us but at postdocs or professionals actively seeking industry or academic jobs.
Still, I enjoyed some of the lectures and appreciated the chance to receive advice from a mentor who works at a large pharmaceutical company in the U.S. I especially liked the presentation by the CEO of LigaChem Biosciences(a story about changing the name of the company was so funny😆), which is why I decided to use the company’s business philosophy as my thumbnail! He was so humorous that everyone in the room laughed a lot and left many meaningful takeaways. We didn’t stay until the end since the later sessions were even less relevant for us as graduate students. After returning home, I did some meal prep and wrote a bit on my blog.
