Student blogs

If you’ve been looking at the Chemical Biology course page with quizzical eyes, wondering how it differs from the very similar sounding Biochemistry, or want to have some nice ~student perspective~ about the course, you’ve come to right place! And if you’ve here hoping for an explanation for the title, skip to the final section 🙂

For this blog, I’ve had the pleasure of collaborating with my classmate Larissa Chia, who’s been fabulous in offering both fantastic content as well as great perspectives. We’re hoping that our collaboration will really enrich your reading experience!

Now without further ado: here we go!

The Content

According to our introduction lecture, the course can be broadly summarized in 3 categories. I’ve added the most succint explanations I can cook up along with them:

• Structural biology looked at the structures of macromolecules (DNA, RNA, proteins) as well as ways to determine and analyze them.
• Chemical biology looked at different ways to use chemical reactions and probes to reveal more about reactions, structures, genetics, etc.
• Drug discovery was about the process from an idea to a drug on the market, and the steps along the way like lead identification, development, testing, etc.

The Lectures

The lecturers were mostly researchers and clinicians who had used or researched what they were talking about, be it a particular technique or a concept. So they knew the subject matter very well. Perhaps a bit too well, as I would realize in the NMR and X-Ray crystallography lecture series.

Most lectures were concise and informative beyond the textbook, and hearing from scientists who gave comparisons of the methods and actual complications was a huge added bonus, even if they’re not tested in the exam.

Tip: use the book in conjunction with the lectures as much as you can: it will be enormously helpful in putting your new knowledge into context.

Labs, labs, labs <3

So there were two labs in this course:

1. The Computer Lab called for the use of protein structure manipulation software such as Chimera and Pose View to retrieve information of structures for drug discovery. Both Larissa and I are of the opinion that it was occasionally rather tedious but an awesome learning experience on the whole.

2. The Inhibitor Characterization Lab looked at characterizing the PTP1B enzyme that we worked with in the Biochemistry course (read the review for more info!). This was done in pairs (a vestige of our time in the lab while we were distance learning due to Covid-19), and analyzed a lot of data.

While we unfortunately, we didn’t do any practical work due to distance learning, I think the labs really gave us time to focus on the theory and data analysis.

Tips for the labs:

• Discuss your work and process friends, especially Chimera. We often sat on call with each other and gave each other moral support and advice.
• Ask the teaching assistants if you need help! They’re there to make it easier for you.
• Start early! Lots of graphing and calculation work was involved so do it for your own sanity.
• Save your work, especially in Chimera where the software on my computer was quite fond of freezing.

Project Work

The project work at the end of the course served both as a summary and an exploration of what we learned throughout the course. We were split up into groups and assigned a different disease as a starting point.

We had to pick a target protein of interest for the disease and then choose one of two paths to traverse: create and propose an experiment for discovering a drug or explore how existing drugs function on a chemical level. It’s a broad project aim so being a good team player is key!

Final Exam

Disclaimer: This describes the exam for Spring 2020, and may not apply to future sessions!

The final exam was split into 2 parts:

1. The Theory Part called upon knowledge mostly from the structural biology and chemical biology components. The questions were short and in a sort of MCQ style, which I quite liked! Knowing your amino acids and Ramachandran plot is indispensable.
2. Case study paper where we were expected form hypotheses and conclusions based on the findings as well as generate related PoseView structures and pharmacokinetic models.

The time constraint for the drug discovery case study may make it more challenging. Time went by fast during this exam, and a lot of us would’ve liked some extra buffer time for uploading our work. But I wager that you’ll do great if you keep an eye on the time and try to finish early!

A great tip from Larissa is to prepare using Introduction to Medicinal Chemistry by Graham Patrick, where similar case studies were examined by the author.

Highlights!

Inika: One of my favourite parts of this course was the project work. It was really great working with my teammates and brainstorming how to make our presentation work! I loved researching the drug target we picked (the Smoothened protein) and looking at how exactly different drugs affected it.

Larissa: I especially enjoyed the drug discovery part because of its clinical relevance; learning to construct and understand pharmacophores and pharmacokinetics was pretty cool!

Final Notes

I hope this has been useful and provided insight! Two heads are often better than one, and in the true spirit of studying at KI this blog is the result of some solid teamwork. As always, reach out to the Digital Ambassadors if you have any questions!

ATCG and More: The canonical pairings of the bases in DNA as proposed by Watson and Crick in 1953 are Adenine to Thymine, and Cytosine to Guanine. Since then, alternative base pairings such as Hoogsteen base pairs and Wobble base pairs have been discovered and also found to play a role in nucleic acid structures.

~An Inika and Larissa Collaboration~