Thursday, September 16, 2010

There's Always Room for JELL-O

Any halfway decent cook knows that you can't put certain fresh fruits -- kiwi, pineapple, and papaya, to be exact -- into gelatin (commonly known as JELL-O). Well, you can ... but the gelatin won't set. Which rather defeats the purpose of making JELL-O, doesn't it?

Any halfway decent scientist knows why. And after Monday's biology lab, all of the students in Dominican University's Biology class (including myself) do too.

I will explain. But to do so, we must zoom in to what's called the "particulate" world, the world we can't see with our own eyes ...

The failure of the gelatin to set has to do with a type of enzyme (protein) called "gelatinase" found in those tropical fruits. (In case you were wondering: Yes, these fruits do contain protein.) If active, gelatinase breaks down the gelatin protein found in your typical packet of JELL-O, preventing the JELL-O from setting.

How does this work? Understanding this phenomenon requires a bit of biology and a bit of chemistry. (But don't be scared! It's actually really cool how this works.) Proteins, such as the gelatinase found in the tropical fruit mentioned, are organic molecules that have very important roles in the function of living cells (including our own cells). One role that many proteins have is that of an enzyme, or biological catalyst. These catalysts basically facilitate chemical reactions in living cells by reducing the amount of energy required for those reactions to take place. Without these chemical reactions, life would cease. So proteins (as enzymes) are pretty important to us, and to other living things.

Enzymes function as a result of a very specific three-dimensional structure. This structure is determined by the DNA that "spells out" the instructions for making the enzyme. Each enzyme, then, has its own unique structure. Because of this individualized three-dimensional structure, each enzyme usually fits, in the same manner as a lock and key, with only one other molecule (called a "substrate") and catalyzes a reaction there. So each enzyme does one specific job. The enzyme will not function (act as a catalyst) if a different molecule is present. This property is called "enzyme specificity" or "substrate specificity."

However, proteins are very sensitive. If they get too warm, or the solution around them changes in pH (how acidic/basic the solution is), then the protein can lose its three-dimensional structure. And when that happens, the protein can no longer bind with its substrate -- the key doesn't fit into the lock anymore. This is called "denaturing" of a protein.

Now let's return to the "macroscopic" world, the world we can see unaided by microscopes and chemical models. The world of the lovely, green, sweet-and-sour kiwi ...

Like all good scientists, once we learned the principles of how enzymes work, we tested them out. Using (yes) kiwis and (yes) gelatin. Raspberry gelatin, actually. The experiment was simple, yet elegant, explanatory, and enlightening. Here is my data chart. I will explain it below.

Assay of Gelatinase From Fresh Kiwi Fruit
Tube No. Contents of Tube Gelatin set? Active Enzyme present? Is the tube a control or test sample?
1 gelatin + water Y negative control
2 gelatin + water Y negative control
3 gelatin + known gelatinase N X positive control
4 gelatin + known gelatinase N X positive control
5 gelatin + fresh kiwi extract N X test sample
6 gelatin + fresh kiwi extract N X test sample
7 gelatin + boiled kiwi extract Y negative control
8 gelatin + boiled kiwi extract Y negative control
9 agar + fresh kiwi extract Y test sample
10 agar + fresh kiwi extract Y test sample

We tested 10 tubes of solutions (five different mixtures, each mixture done twice to see if we got the same result). After mixing the solutions, we set them all in an ice bath to find out whether they would set into hard gelatin, or remain as liquids.

Tubes 1 and 2 had only gelatin + water (no gelatinase). These tubes were what is called a "negative control" -- they had a known negative test in an experiment (no enzyme activity). Tubes 3 and 4 had gelatin + a "known gelatinase" -- an enzyme from a pineapple prepared by our lab professor. So as predicted, they did NOT set because there was active enzyme present. These tubes were "positive controls"-- a known positive test (enzyme acting on the gelatin). Tubes 5 and 6 were test samples -- tubes we were interested in the results of. And they behaved as predicted -- the gelatinase from the kiwi extract did interact with the gelatin and prevent the gelatin from setting! Contrast this with tubes 7 and 8, which contained gelatin and boiled kiwi extract. Remember that heat will "denature," or unfold, an enzyme. That's exactly what happened -- boiling the kiwi rendered the gelatinase ineffective, so tubes 7 and 8 did set (more negative controls). Tubes 9 and 10 were filled with agar, another jello-y substance, and fresh kiwi extract. This time, we were testing the "enzyme specificity" concept -- would the kiwi's gelatinase also work on agar, as well as the gelatin? The answer, we found, was "no." The gelatinase is specific to the gelatin, and would not work on a different substrate (agar).

As I said, simple yet elegant, and very hands-on. My kind of learning.

Thursday, September 9, 2010

An End To The Silence

The few of you following my blog (thank you, by the way) will have noticed that I did not post at all during August. Or if you did not notice that fact specifically, you probably did observe that a good while went by without so much as a whisper from me. No worries, nothing is wrong. I'm not sick, I'm not dying, and as you saw from my two recent posts, I have not changed my mind about becoming a doctor.

So why the silence? Reason #1: busyness. August was the-month-to-get-everything-done-before-school. And when you have a family, a house, a husband, and other such life elements, figuring out how to manage them on a totally different schedule takes some time, juggling, and preparation.

Reason #2: business. Yes, I have my own business, called The Artful Diner. As with most artists, I won't be able to retire off my income from it, but the extra money helps, and I enjoy it. As the name implies, my work has to do with dining. And indeed, I make decoupaged dishware and beaded / wire-wrapped utensils to sell online and at art shows. At the end of July, I heard about a local art fair that I really wanted to participate in. I signed up, paid my fee ... and then realized I needed more inventory. So I spent the next several weeks in full production mode. (My dining room -- aka my "studio" -- still looks like a hurricane swept through it, much to my husband's delight.) Here is a link to my storefront, and a few photos of my recent work.

My Etsy storefront link: The Artful Diner

Here are some coaster sets I have painted and decoupaged with marbled paper (this is a new thing I am doing now):

Another new item for my online store this season is pillar candle stands. These are flat pieces of glass, with paper (and often vintage ephemera) decoupaged on the underside, on which you can put a tall pillar candle. The wax drips onto the flat, glass surface, and you just scrape it off. Here are a couple photos of those:

A set of six small decoupaged bowls:

A decoupaged serving tray, complete with a stand:

So rest assured: I have not been idle with my time. Between the life busyness and my business, posting on my blog fell between the cracks. But I missed writing during that time, and especially writing about science and medicine, so you may also rest assured that I will not let that happen again.

Wednesday, September 8, 2010

The Genetics Of Synthesis

"Synthesize." When I worked as a textbook editor at McGraw-Hill, we used that word all the time in our literature textbooks. (Usually in the context of asking -- rather, telling -- students to synthesize a number of elements.)

And now here I am, a student myself. And yes, I am synthesizing, too. But I will get to that shortly.

First, what is synthesizing and synthesis? It is, according to Merriam-Webster's online dictionary, "the combining of often diverse conceptions into a coherent whole." In other words, taking different pieces of evidence, material, readings, experiences, and so on and making sense of them when put together. It is an incredibly complex cognitive process, far beyond mere comprehension, even above analysis.

At the university level, it is rather taken for granted that students are capable of synthesis. Homework, quizzes, and exams require it. So to do well, it is necessary. But what is really exciting is the synthesis that happens independently of all of that required work. It may not boost your grade, but it should boost your confidence that you are understanding -- and connecting with -- the material. 

At least, that's what it does for me. It also encourages me that I am on the right track with what I am doing. Because making these kinds of connections (when it's not required by a professor, that is) requires not only knowledge, but interest. And a little passion doesn't hurt, either.

For me, the lightbulb flared this morning as I was reading my biology textbook. I will be honest -- reading that monstrous (read: insanely heavy) book was not what I felt like doing at 7:30 a.m. But I wanted to be prepared for my morning lecture, so read I did. While the whole selection -- relating the evolution of mammals -- was fascinating, the true reward lay in a nugget on the very final page: a one-paragraph blurb on a gene called FOXP2, thought to play an important role in human language. (And since language is one thing that sets us apart from our ape cousins, this gene is also thought to play a role in the evolution of Homo sapiens). 

"FOXP2 ... FOXP2 ... FOXP2 ... where do I know that from?" I asked myself as I finished reading. I knit my brow, cocked my head, and pursed my lips as I searched my brain for a possible link. Because I knew I knew that gene from somewhere. And then it dawned on me: my summer research. Olga had been looking for evidence of FOXP2 expression in her lung cell samples. Because while FOXP2 is involved in language development, it is also involved in cell proliferation (growth) in the lungs, and hence could signal the presence of stem cells. 

My eyes lit up and I laughed out loud. Synthesis indeed.

As I write this, I realize that maybe it sounds strange to get all warm and fuzzy about genetics and research. But I just can't seem to help myself.

Note: Of course, I had to tell someone who would really appreciate this "discovery." (Telling my husband, Geoff, didn't quite do it -- merely the letters "D - N - A" make his eyes glaze over). So I headed to my bio professor's office hours after my last class and told him I'd had an "interesting encounter with our biology textbook." That sure got his attention. We had a nice talk. He knows me a little better, and vice versa. One of the best parts of my undergrad education was getting to know my professors well and being mentored by a handful of them. I hope for that same kind of experience this time around as well.

Tuesday, September 7, 2010

The Honeymoon Will Soon End ... but that's OK

I am officially a pre-med student.

Correction: I have been for just over a week now. But it hasn't really sunk in yet, because this is still the honeymoon stage. All love songs, hugs, and kisses -- no slammed doors, curse words, or broken dishes (yet).

Everybody is still in friend-making mode; there are few cliques or ways to feel excluded, if you make an effort to be social. Everything comes easily at the moment: I still remember all that we have "learned" so far, even though I've barely touched a biology, chemisty, or physics textbook in more than a decade. Every grade is an A right now -- we haven't had any assignments, exams, or quizzes on which to lose points. The sun is shining, the future is bright, and everyone still has a chance to get in to medical school.

Soon that honeymoon will end. There will be late nights up studying before exams. And then the actual exams. Weekends lost to lab reports after hours spent in the lab during the week. The anxiety of eventually applying to medical school. The dread of not getting in.

So why do it? Is the destination worth it?

Hell no.

Don't get me wrong -- I can't wait to be a doctor. I think I'll be a pretty good one, and I have a feeling I'll enjoy it. But getting there is a long road. Years, literally, of your life. Anyone who thinks they can just push through without having any appreciation for the journey there will be incredibly miserable for an incredibly long time. And, I think, become bitter and angry about it. Yeah, that bodes real well for a person's bedside manner, doesn't it?

I'm one of those crazy people who actually likes school. When I'm interested in something, learning about it is a pleasure (most of the time -- ask me at 3 a.m. and I might tell you a different story). I'm excited about where I'm going, but I'm also excited about what I'll be doing along the way. And to do this, you have to be.

That's why it's OK that the honeymoon will soon end. Because when it does, that signals the beginning of a deeper, richer relationship with the subject matter. (For this school year: biology, chemistry, and physics.)  Sure, it will be harder. And sure, I may complain about that sometimes. I may struggle. I may even use four-letter words (*gasp*). But I wouldn't trade places with anyone.

Stay tuned.