[nerual]

This is an integrated lab course designed for students in chemical biology. It consists of seven labs that can be grouped into two parts.

The first three labs are the first part of the course, which deals mostly with protein extraction and purification. The first lab (2 weeks) involves extracting a protein (ovalbumin) from an egg, and using size exclusion chromatography to purify it and determine its molecular weight. In the second lab (1 week), you take the ovalbumin and run it on SDS-PAGE along with several other samples, and determine the identity/molecular weight of an unknown sample. The third lab (2 weeks) uses a fluorescence-based assay to analyze how dansyl amide binds to BSA, and uses tryptophan fluorescence to analyze how the structure of BSA changes as it denatures. A ten-page (double spaced, including figures and references) report will encompass these first three labs.

The fourth and fifth labs take 3-4 weeks each, and are done simultaneously. I thought this was the most enjoyable part, and it's really the "meat and potatoes" of the course. The fourth lab involves extracting a natural product from a source of your choosing (everyone extracts a different product, and no more than two people can have the same plant/source). You must provide the source yourself. The goal is to extract a molecule that will be a good inhibitor of acetylcholinesterase (AChE). AChE inhibitors are important Alzheimer's drugs, thus you're attempting to "discover" a potential drug. There is a liquid-liquid extraction, running a column, lots and lots of rotovaping and TLC plates, and when you finally have your (hopefully) pure product, you analyze it using IR, H-NMR, and MS and hope that you actually isolated the molecule you set out to get. In our year, out of 25 people in the course, somewhere around 6-7 were successful. The rest of us got something, we just don't actually know what it is

While the fourth lab is drug discovery by extracting a natural product, the fifth lab is drug discovery using combinatorial chemistry. Combi chem is introduced in the chembio unit in chem 1AA3--taking a library of similar substances and seeing what functional groups are important for activity with a certain protein. Each person will synthesize a unique member of the chalcone class of chemicals, using the Claisen-Schmidt reaction. Some of the combinations have never ever ever been tested/created before, so they actually had no idea how exactly it would work, which was kind of cool. You had to pick starting products out of a hat and figure out what chalcone you would make, and research it. There was lots of troubleshooting in the lab, since different chalcones would require slightly different procedures in order to get them to solidify and recrystallize. Once your chalcone is synthesized and purified (this required more TLC plates...) you characterize it using IR, H-NMR and MS, to make sure you actually synthesized the right molecule. Some chalcones are known inhibitors of AChE, depending on what functional groups it has--you're required to research what functional groups make a chalcone a good inhibitor.

The 6th lab (one week) uses a colourimetric assay (the Ellman Assay) to analyze the activity of AChE using Michaelis-Menten kinetics (figuring out the Km, IC50, etc).

The 7th lab (one week) only works if the enzymes are not in varying stages of death. This is very important. If your enzyme is warm, DON'T USE IT. In this lab, you use the Ellman Assay to see if your natural product and your chalcone are actually inhibitors of AChE.

The final lab report is 20 pages (double spaced, including figures and references) and encompasses the entire class' results for natural products and chalcones. You have to find structural similarities between inhibitors, and draw conclusions from this. I literally didn't leave my room for two days, doing this report--and I had already done a good chunk of it by the time I got to this point.

Marking Scheme:
Pre-labs: 3% x 7 labs = 21%
Lab notebook neatness and keeping it updated during the lab: 3% x 11 weeks = 33% (your lab notebooks are checked between 1-2 times each week).
Weekly skills assessment: 16% overall (averaged from each week, you're marked on lab skills such as how well you pipette, do you use the right equipment/waste container, etc etc)
Lab report #1: 10%
Lab report #2: 20%

The profs for this course in Jan 2010 were Dr McKenzie & Dr Brennan. Both profs were present for every lab. For the first three labs, 3 TAs were present, but for the more busy labs, all 6 TAs were present. 6 TAs + 2 profs for 25 people is practically a 3:1 student:instructor ratio!

There is one 50min lecture a week, and it usually goes over what you do in the lab--the theory and the procedural nuts & bolts. The labs are scheduled to be 4hrs long every week, and I think the longest I was ever in the lab was for 5-ish hours. Usually you're out of there on timeish, but it's not a good idea to have a class right after the lab if you can avoid it. Very occasionally, the labs are shorter than 4hrs, but it feels weird and wrong to leave early If you have a long break during the lab, the profs let us go to Thode or to Thode room (the chem/chembio room in ABB) to play cards & whatnot.

Since I'm really interested in drug discovery/development, I really enjoyed this course! Most of the labs were fun/interesting. The post-lab analysis was probably the worst/most time-consuming part, but the actual experiments were good. They're still working on perfecting the procedures, so often you're troubleshooting/modifying the procedure as you go, but doing that gives you good experience and makes sure you understand the theory. Overall, this is a really good course, and definitely possible to get a 12 in!

So I've just finished taking this course, and the content of the course content remains the same as last years, although they revised the marking scheme slightly.

Prelabs - 1.5% x 7 = 10.5%
Lab Notebook - 1.5% x 11 = 16.5 (each week, you get a mark of out 5)
Weekly Skills Assessment - 2% x 11 = 22%
Natural Product Proposal - 5%
Lab Report 1 - 16%
Lab Report 2 - 30%

The found the weekly lectures to be very useful and well taught. Dr McKenzie (the only professor this year) makes the lessons straight to the point and clear. We also had a small class (less than 20 people), so we could ask a lot of questions along the way.

The labs themselves on the whole were rather interesting and well integrated. The first 3 labs went smoothly. However, the natural product (NP) isolation and chalcone synthesis was a lot more hectic than I think we expected. I found that I had a hard time finishing the expected portions in 4 hours and there were 2 weeks where most of us stayed for around 5 and a half hours. It was pretty exhausting, especially when you just can't seem to get the compound isolated. They were also done simultaneously, so you had to be organized and plan stuff ahead of time. However, be prepared for things not to work. For example, a couple people's chalcones would not precipitate after various attempts, even after going to the lab outside the assigned lab time. It was a pretty frustrating month, but it introduces us to the problems encountered in research, where you do not have a protocol to follow and must do some creative troubleshooting.

I would have liked to see the labs to be better organized so that we don't cram a lot of things into one lab. For example, in the first week of natural product isolation, all we did was grind/chop our sources and soak them in solvent and let them sit. We were out of there in 2 and a half hours max. But the next week, we were scrambling to extract the NP and do the chalcone reaction at the same time. So it would have been a better use of time if we did a bit of both the first week and avoided the hectic scramble afterwards.

Just a side note, I'd recommend that you choose a natural product that is relatively abundant in your source, so you have a higher chance of isolating it (TAs mentioned this too). It also makes the analysis much easier, as you can explain the obtained spectrum and why peaks showed up where they did. I didn't get the NP that I was going for, but luckily managed to isolate another NP in my source that I could identify. A lot of people couldn't figure out what they isolated, mainly because on the TLC, we just choose an arbitrary spot from the crude extract and hope that it's the substance you were aiming for. Ideally, you would run an NMR on all your spots (or use staining) to identify the spot you want before proceeding, but there wasn't enough time or equipments for that. It's incredibly frustrating to spend a month purifying something that you cannot identify at the end. :(

In terms of marking, this course has rather high standards and a fair amount of effort goes into the prelabs and maintaining the lab notebook. Since the TAs rotate every week (so you get marked by all of them at one point), the weekly assessment and notebook marks are prone to subjectivity. I found that my marks fluctuated a lot (more than they should to be honest) from week to week, so it just depends on which TA grades it.

As for the reports, start them early!! (Cannot stress this enough) They take a long time to write, and the week before, I spent almost all my time writing them. There's a lot of research involved in the discussion and introduction, so don't cram! They give feedback from the first report, so you get to a chance to fix stuff in the second one. They do mark it pretty meticulously, so it's worth the effort.

All in all, it was a tough course, but I learned a lot from it, so it's all good. It's different from the first year chem and orgo labs, as in 2L03, the labs are connected together instead of being independent of each other. After finishing the course, I learned how to budget my time more efficiently in the lab and be more organized/prepared before walking in. Definitely a good experience!