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You know what’s even better than the GRE?

The Chemistry GRE!

I had the opportunity (read:  obligation) to take this test recently, and unlike many, I found I had a really great time.  For those who have yet to take it, the Chem GRE is a 3 hour long test where you are asked a variety of questions on all branches of chemistry, with the major focuses on Organic and Physical, with some inorganic, transition-metal, and analytical chem thrown in for good measure.  In case you thought you read that wrong, you didn’t.  The test is, in fact, three hours long.  It is a very long three hours, and can be intimidating. Here are some tips and tricks to being successful on the GRE:

First, concentrate on the stuff you don’t know.  Unless you finished all of your chemistry classes by the end of junior year (unlikely?), you probably won’t know some of the concepts outlined on the GRE.  Pick up a review book and at least familiarize yourself with some of the basic concepts.  For example, I had no idea what the 18-electron rule was for metal complexes before taking the GRE. It’s a startlingly easy concept to learn, and will earn you a couple easy points.

Second, take a day or two and review the stuff you haven’t looked at in a while.  For me, that was P-Chem.  A GRE book will help with this.  Just remember that the GRE sometimes will go into absurdly small detail on some material you learned in sophomore year, so just stay on top of your chemistry knowledge.  You’ll be surprised with how much you remember.

Third, remember to get some sleep.  My test started at 8:30, which meant I had to leave the house at 7:45.  I’m not really used to waking up that early, so it was really no fun.  I’m sure all of you have taken enough standardized exams to know this, but just reminding you.  Also, eat breakfast and get hydrated before the exam.  It’s around 3 hours long and the exam proctors will not let you drink or eat anything while you’re taking it.

Lastly, and anecdote.  This summer I started lifting weights with a friend of mine as a way to stay in shape (and secretly to be able to carry those 20 gal jugs of DMF around the lab and not hurt myself).  He is an economics/philosophy major who is also a varsity swimmer, and has a lot of really interesting things to say about life.  His philosophy on exams is this:  treat it like a game!  You win the game if you get the most points, and you’re playing against everyone else in the room.  Games are fun.  Therefore, treat the test as a game, and you’ll have a blast.  I took this philosophy in with me, and really enjoyed all the really tough questions – they’re just chemistry, right?

Yup, still in Kansas.

A mitotic kinase - oncoprotein!

Your protein of the day! Aurora A Kinase is protein involved in mitosis, and is generally upregulated in cancerous tumors. It is very difficult to target because of its highly conserved C-terminal Kinase domain. (See inset for ADP) From PDB: 4mq1

Wow!  It has certainly been a long time.  I guess a blog can sometimes be like a google reader account.  You can get into the rhythm and read all your articles for a week, but then you forget about it and you get 620 items into your unread folder.  Oops.  Anyhow, here’s just a little post to get y’all updated with what’s going on with me.

Senior year is going pretty well  - I’ve been spending 20-30 hours in lab a week.  I would like to be spending more, but I have these silly things called requirements to fulfill.  Oh well, I guess my 45-50 hours weeks can wait until I start graduate school.  Research is definitely on a better rhythm than it has been in the past.  I feel like I’ve stopped making some of the small mistakes, and can now actually execute the science at a high level, and pretty efficiently.  My only limit now is how much time I have (and how quickly I can get reagents mailed in).  I’m sure once I start working in cells or doing some more serious organic chemistry my pace will bog down a bit, but for now it’s pretty nice to be working efficiently.

I’ve started work on a thesis, which is going on nicely so far.  Unfortunately, keeping procrastination to a minimum is harder than I anticipated.  The plan right now is to really start working on the methods, and hopefully be up to date by winter break (when I really) have to start writing.

As for the blog, you’ll get in the near future my ruminations on the Chem GRE, some more talk of Chemical Biology, and a little bit on the application process, or what little of it I’ve gone though.  Stick around for a whole lot more content in the coming weeks!


We’re not in Kansas anymore.

Nor are we in Boston anymore, either. It’s certainly been a while, but I’m back! And after:

-a very busy summer
-packing up all of my worldly possessions into a U Haul
-driving nearly 600 miles and 10+ hours (traffic and rain were terrible!) with only a cat as my co-pilot
-leaving an old home
-establishing a new one
-beginning grad school
-beginning research (already?! I know!)
-getting to know the new boss
-all the while wondering if this will be worth the effort,

I’m here. I’m officially a grad student, and they’re paying me¹ to be here. I’ve been collecting new ‘data’ to write about, and letting previous data stew for a while. I think I’ve reached a good point of stewing, steeping, and fermenting, and I should be able to distill out what Transition States is all about.

[1a] Well, not paying much, but they are paying. We’ll see how things go, because…

[1b] I haven’t been paid yet. We get paid at the end of each month we work. Although I’ve been here since the middle of August, of course orientation didn’t count as time worked. It’s been a very long month and a half, and although the weather’s been alright, I’ve dubbed this the ‘coldest September.’

What a GREat experience!

Hey everyone!

If you were following along, you’d know that I took the GRE last monday.  It was an… interesting experience.  This was my first computer test, so it was a little refreshing to not have a moderator or be in a room with a bunch of my stressed peers taking the same test at the same time.  Instead, I was sitting in a cubicle with noise-canceling headphones concentrating on my own exam.  I found it pretty fun, actually.  I was in the minority, however, as the tension in the waiting room was so thick you could probably cut it with a knife.  Finding out my score immediately after the exam was very refreshing as well, and made for a very fun afternoon (as I didn’t have to worry about how I did – I already knew!).

The test itself was in some ways challenging.  The prompts for the writing section I found to be topical and interesting to write on – I had no lack of examples to cite, though I may have used far too many from science, and I was able to choose positions I was passionate about.  A word of advice that was passed on to me:  read up on your utopian novels (1984, The Handmaid’s Tale, and Fahrenheit 451 to name a few) because they end up being great examples to use for these essays.  I think I might have used them on both.

I can’t really comment too much on the verbal section for several reasons.   The vocabulary was very challenging, and I had a hard time with the analogies.  However, if you’re taking the GRE any time after July, 2011 the verbal section will contain no analogies or antonyms.  This is nice, as those two questions are likely the most difficult on the test.  Also, I’m not entirely sure how important it is for chemistry graduate schools for the verbal section.  But, as I am neither a graduate student or on any admissions boards, I can only speculate.

Quantitative was a dream.  I enjoy math, and it was fun to be able to get lots of points on a test by using my knowledge of arithmetic and algebra.  Really fun stuff.  The only thing I wish I did differently was time myself while working through problems.  I ended up rushing at the very end.  But it was really fun.  The fact that if you do well, the problems get harder (another thing they’re getting rid of in the new GRE) made it very exciting to get to some really tough questions in the final minutes.  Well, I enjoyed it.

Overall, I had a pretty fun time with the GRE.  I didn’t take it too seriously, and got scores in the ranges I was expecting, if even a little higher.  If I were to do it all over again, I would do a little more vocab prep for the verbal and spend some more time in the books doing some practice problems, if just to get set with the test directions.  I hope this is helpful to any intrepid undergrads hoping to take the GRE.  If any of you (undergrad, grad, postgrad, ect.) have any advice or fun GRE memories, feel free to post below!  I’m returning in a few short days with a new installment of “What is Chemical Biology” – get pumped!

How has your week been? Mine has been GREat!

Hey everyone!

Sorry for the inexcusably long absence from the blog.  Summer time is research time for me, and I’ve (finally) gotten the chance to put in the long hours that I really don’t have the time for during the semester.  Maybe this is just my undergraduate naivete speaking, but to me there’s nothing like working full time in the lab.  It’s just nice to have no distractions.  The warm weather probably helps too.  Anyway, I apologize for my lack of posting.  Organic synthesis can, as many of you know, can be very distracting.

ooOOOoo... Rapamycin!

This guy thinks about synthesis all the time too! (Credit to Sidechain and Flickr user Glockoma)

In the midst of my synthesis-induced bliss, I came to a realization.  I want to get into graduate school, and in order to get into graduate school, it is important to take the Graduate Record Exam, or GRE.  Luckily, I had signed up for the test several months ago, for July 18th.  I figured that it was probably time to go ahead and start studying.  This realization came on Monday.

If you’re sitting at home doing the math, this would mean that I have a week to study for the GRE.  It turns out that a week is more than enough time, if you budget it correctly.  I had already purchased some good GRE review books, and got to work right away.  In my experience (which should not be mistaken for an expert’s), as long as you know how the text works

, you’ll be okay.  GRE questions, much like the SAT ones, come in very specific formats that, once you can recognize the pattern, are pretty easy to figure out.

So how am I studying if I only have a week?  Pretty carefully, actually.  Here’s how I’ve been doing it:  (Disclaimer:  DON’T wait until the last week to study for the GRE.  It’s not a good idea.)

  1. Figure out the format.  I’ve found the GRE workbook series to be very helpful, as they go over test-taking strategies for each question type on the exam, and give an hour’s worth of practice for each, so you can focus on one type of question at a time.  Another good source I’ve been using is the website Syvum to be very helpful in test prep questions.  They have some pretty tough ones there, and (so far) has been good in prepping for the verbal portion.
  2. Practice, Practice, Practice.  (This is where I’m at).  Use a book, use your friends, use the internet.  I’ve been looking at practice problems while reactions have been running, and at night before bed, which I hope is enough.  I’ll let you all know how it goes, I guess.
  3. Practice Tests.  Time yourself!  Because you only get to do one question at a time, it is important that you time each and every question.  Use all the time allotted, as well.  Be sure of the answer.

I hope this is helpful for all those procrastinators out there.  I’ll check back next Monday and give you all a play-by-play of how the test went!

Shipping Assay Samples: The FedEx Paradox

There is nothing that takes the wind out of your sails quite like when you think you’re being clever, and later find out how totally lame your attempts were. Synthesizing some precursor by a route you think is super streamlined, only to later find a simple, one-pot prep. Driving and taking a ‘short cut,’ only to wind up hopelessly lost. Making eyes at the cute girl in the neighboring lab, only to realize your fly was down. Stuff like that…

Recently, my PI asked me to prepare a few aliquots of a compound to be shipped out for biological testing. Of course, I put the samples on the back burner, because hey, I already had the compounds made… how hard could it be to stick a few mgs in a few vials and ship them? (That’s not rhetorical. The answer for this circumstance is “harder than one would expect.”)

When I finally got around to checking everything out, and preparing to pack and ship everything, I noticed the HPLC of one of the compounds was a bit iffy looking. After a quick purification, rotovapping down, weighing out, administering aliquots to HPLC vials, and rotovapping them down, all samples were on dry ice and finally ready to ship. The biochemist I’m working with and I grabbed a box, crossed over the labels (it had obviously been shipped a few times before), and loaded the styrofoam cooler into it. However, by this time, we’d missed the 4 PM FedEx pickup at our shipping and receiving.

No problem, I thought. “I can just walk it over to the local FedEx store. Their last pickup is at least 6 PM.” So, down the street I walked, with box under one arm, and shipping label in hand. Upon arriving, I felt like a boss. “Here’s this, shipping to here, overnight, and here’s the account number.” As the clerk picked up the box and went to weigh it, the dry ice started to rattle.

“Whats in here?” she asked.

With minimal thinking I replied, “Oh, a few vials of solid material, over dry ice.” In my head, it made perfect sense – FedEx ships dry ice, it should be no problem. The samples are solid powder, not volatile liquids or anything. No problem, right?

The clerk – “Nope. I can’t take this.”

Myself – “Uh. What?”

“Yeah, we cannot accept anything on dry ice here, we have nowhere to put it.”

“It’s… just dry ice? In a styrofoam cooler? In a box? Isn’t that the point that you don’t necessarily need a place to put it?”

“We can’t accept it here. The closest place you could take it is our main distribution center on Summer St, they can accept dry ice, and they’ll have to authorize it. It’s at 775 Summer. Do you know where 775 Summer is? It’s in South Boston. If you head into downtown and go… Hey,” she turned to her co-worker, “How do you get to the distribution center on Summer?”

“Oh, it’s in South Boston. If you head into downtown and…” The co-worker started.

“I know where 775 Summer is. Thanks though,” I interrupted.

I took my box, and headed to an early dinner. While sitting at the window of the pizza place, my box tagging along next to me, I called FedEx’s 800 number to see if there were any other options. They weren’t the most helpful here, either, but let me know that on-call pickup was still available in my area until 7:30 PM, and that they could pick up the package from me, at my business or residence. Herein lies the FedEx Paradox: They may take it from you, but you may not give it to them. Ah… Zen-like, is it not?

Of course, being after 5 at this point, shipping & receiving in my building was closed… see where this is going?

I ran home, and handed the package off to my roommate, explained the situation to him, and went back to lab. I explained the admittedly half-baked and hair-brained circumstances to my biochemist co-worker, and she was like “That’s weird, but whatever works…” In a bit, the roommate confirmed FedEx had picked up the package. Ah ha! I had won!

Of course, the next morning, the box had been Return-To-Sender’ed, as we had crossed over one of the two “Dry Ice” labels, which FedEx did not seem to appreciate. We re-boxed the shipment, labeled it extra carefully, and let shipping and receiving work their magic. It was received the next day, safe and sound.

Moral of the story? In chemistry, there are times when clever, simple innovation can triumph over minor, but obnoxious inconveniences (I’m working on a series of posts entitled “Stupid Solutions to Stupid Problems” to celebrate just this kind of innovation!). In shipping, this does not apply. There are people in your department whose sole responsibility is to ship and or receive. Your job is chemistry. Go talk to the Art Vandelay (the importer-exporter, not the architect) of your department, and let them handle it.

Next time, I’m just going to adsorb the compounds on filter paper, and send them in a standard envelope via the USPS, the good, old fashioned way…

The rumors of my death have been greatly something something…

Why hello there,

It’s been quite a while since I’ve posted, and my apologies to all readers. I’ve been every flavor of busy, and unfortunately I’ve had less time that I’d prefer to write. In the meantime, my co-blogger has had some space to stretch his legs, and I’m very proud of his work.

Regular updates will resume shortly, with tales of large scale chemistry for large scale people, GRE gripes, nitpicking, and calls for overhaul, along with the chilling realization that in two months, I’ll be in a new city, and officially a grad student.

Oh boy!

Water, Wine, Milk or Beer? Perhaps none of the above.


Don't drink anything in this demo, or you'll end up sleeping, like this cute baby! (flickr user sat spade)

Hello everyone!

It’s time for another edition of Sidechain’s favorite chem demos.  The one I’ll be describing today holds a place near and dear to my heart.  When I was a young high schooler (a shorter polypeptide… get it?), my high school chem teacher showed this to our class.  She had a glass of what looked like water.  She poured it into a wine goblet, and the water turned to wine (cool, right!).  She then poured the ‘wine’ into another glass, where it became ‘milk’, which when poured into the final glass turned into ‘beer.’  When I first saw this, I really thought it was magic.  It turns out that the chemical principles are pretty simple!  All the student really needs to understand is acid-base chemistry, indicators, and precipitates.  Anyway, here’s what you’ll need:

  • Glass #1:  0.1 M Sodium Carbonate (NaHCO3).  What I did was make 100mL of a stock solution and add around 50mL to a clear water glass.
  • Glass/Goblet #2:  A few drops of phenophtalein in the bottom of a long-necked wine glass.  I usually use a plastic one and put some tape on the bottom to cover the indicator solution.
  • Glass #3:  5mL 1.0M BaCl in the bottom of a clear glass with some tape on the bottom.
  • Glass #4:  5mL 12M HCl and 5mL of bromothymol blue indicator, at the bottom of a pint glass/plastic clear solo cup

So if you can’t guess, the science behind this is pretty simple.

  • Sodium Carbonate is a basic solution that looks like water
  • Adding phenothalein will make the solution purple, and look like wine
  • Adding Barium ions will precipitate out a suspension of Ba(OH)2, which will look like an opaque white liquid (milk!)
  • In the last cup, the concentrated acid will (a) acidify the remaining base, eliminating the Ba(OH) (b) result in the evolution of CO2 gas and (c) make a beer-like color with the indicator

If you've done everything correct, it should look like this!

This demonstration is pretty easy to explain to a group of first-year chemists, and is a great application of the skills they have already learned!  Just remember not to drink any of these liquids, especially the “beer” (no matter how tempting it may be!)

Everybody Needs A: Brain


Even if you have one of these, you may forget to label a vial. Be careful to remember! (Flckr user Liz Henry)

In a post several weeks ago, I examined the debate of synthesis or purchasing of commercially-made compounds.  If you recall, it appeared that I could not synthesize the correct compound, and the compound I had bought did not appear to have been synthesized correctly.  I took the advice of one of a reader and decided to call the company from which I had bought my compound.  Luckily, I had a great conversation with customer support, and they said that they’d run some tests on the batch that they had sent me.

Shortly after this call, I realized that I had taken the wrong compound from the wrong vial, and had labeled my aliquot wrong. I ended up finding the vial I needed and the positive control worked as expected. The lesson is pretty clear here.    Make sure that you label everything!

Feel free to share embarrassing stories like mine in the comments below.  Might just make me feel better about making such a rookie mistake.

What is chemical biology? Native Chemical Ligation!

Disclaimer: I am not an expert. In fact, this series of blog posts is as informative  to me as it is to you. Probably even more so. My views and the views of people interviewed for this blog do not, in fact, reflect what exactly “chemical biology” is, but only a snapshot.  Please direct any comments or suggestions below!

The two subunits were synthesized separately

HIV-1 Protease, one of the first proteins synthesized via chemical ligation (PDB 3CDR)

On the last “What is Chemical Biology” post, several readers had comments that Chemical Biology was nothing more than a relabeled version of Pharmacology.  To be honest, they do have a point.  A lot of Chemical Biology that I have investigated so far has been drug discovery, which falls squarely in the realm of Pharmacology.  To that end, I have decided to find something that fits in this field that is more “pure science.”  Enter Native Chemical Ligation.

Native Chemical Ligation was born of the effort of the total synthesis of proteins.  Solid phase peptide synthesis (SPPS), as most of you probably know, is limited to around 50 residues as the peptide begins to form secondary/tertiary structure around  the resin bead it is attached to.  This secondary structure could reduce the (already not so great) efficiency of the coupling reactions.  In addition, by this point in a peptide synthesis, the overall yield is very low as well.  This results in some very major problems in the total synthesis of proteins.  How did bio-organic chemists solve this problem?  You can probably guess the answer by now.

Native Chemical ligation is born from Chemical Ligation, a method to connect two synthesized peptides together without the use of protecting groups on each and every side chain.  Chemical ligation used chemistries involving the formation of thioester or thioether bonds among other linkages.  While Chemical ligation resulted in the total synthesis of several peptides, there are several disadvantages to this technique, including the replacement of a nitrogen with a sulfur atom.  This is the equivalent of placing a soccer ball in the place of a tennis ball.  Naturally, this can result in problems in protein folding.  Native Chemical Ligation is a method by which a native peptide bond can be “installed” into a synthetic peptide structure.

Look! Modification!

Native Chemical Ligation Mechanism (Credit: American Physiological Society)

The chemistry is surprisingly simple.  A S to N acetyl transfer upon ligation of the two peptide fragments results in a native peptide bond and an easily purified thioester side product.  This reaction is shown in the figure.  Native chemical ligation can also be used to synthesize glycerolized peptides at specific sites.  This was described in an article out of Nature.  Overall, a pretty cool mechanism for synthesizing whole proteins, and making slight alternations without using recombinational techniques.

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