Enzymes and the Problem with Cosmo Kramer’s Levels

If I were to ask you- yes, all of you out there- what you thought was the cornerstone method for assessing changes in metabolism, and metabolic regulation as a whole, what would your answer be?

.

Your choices

All those who were thinking of using RT-PCR to measure changes in gene transcription, raise your hand. Hey, you too, hiding back there- I know you’re a huge PCR nerd!

Now, those of you who were planning on using western blots to see changes occurring at the translational level, raise your hand. But wait; keep them up for a second. Which antibodies were you planning on using? Was it just a pan-specific antibody that would detect your protein no matter what state it were in? If so, you can go ahead and put your hand down. But, those of you who were planning on using an antibody specific to a post-translational modification- something like phosphorylation, acetylation, nitrosylation, glycosylation, or any of the others- you’ve got my attention.

One last one: were any of you planning on assaying any enzyme activity? Maybe using a colourimetric or spectrophotometric method? Great!

That lazy friend of yours…

Remember on Seinfeld when Kramer formulates a plan to completely reconfigure his apartment? He intends to get rid of all the furniture and just build a bunch of levels… with carpeting, and a lot of pillows, like ancient Egypt. Jerry figures that it won’t get done within the month that Kramer allots himself, and- surely enough- Kramer doesn’t even attempt the levels.

Cosmo Kramer. If this guy designed our cells, we'd all be in big, big trouble.

We all have them: the friends who make up big plans that never quite seem to materialize. What’s unfortunate, too, is that it’s not really even an all-or-nothing concept. There are various degrees to which Kramer’s plans might not have panned out. What if he hadn’t just dropped the idea entirely, but instead would’ve actually taken a few steps towards realizing his dream of levels? Let’s say he had bought all the lumber- would he have properly measured twice, cut once? If he had hammered together all the pieces and made the entirety of these wooden levels- would he have properly carpeted all of them? And if he had laid down the finest carpets and rugs- would he have made the effort to find the appropriate pillows to go with them? There were not just one, but many steps that Kramer would’ve needed to get through before his levels were truly complete.

Kramer told Jerry that he didn’t draw up any plans, that the blueprint was entirely in his head. Similarly, the blueprint for any would-be metabolic “levels” are stored right there in DNA. DNA stores the code for any molecular mechanism of metabolic regulation that could ever be needed. Just like building those levels, though, there are many steps to get through before any of those blueprints become functional. DNA could just sit there, tightly coiled around its histones, not doing terribly much- like that blueprint locked away in Kramer’s brain. Histones may be acetylated, unlocking that DNA- but would it be unwound by helicase? DNA may be transcribed into RNA- but will that RNA be processed before it is degraded? Capped, polyadenylated mRNA may exit into the cytoplasm- but would it be translated by ribosomes? And full-length, folded protein may be synthesized- but would it be active? After all, proinsulin isn’t that useful (or friendly, from an immunogenic point of view), and the unphosphorylated b form of glycogen phosphorylase isn’t especially active when there’s no AMP to be seen.

Where the (bio)chemistry happens

As an enzymologist, of course I’m biased. But as anyone in the biological sciences will easily admit, active enzymes are where the chemistry of life takes place. Without those glorious biological catalysts pushing those reactions along, life as we know it simply wouldn’t exist. Sure, many would argue that ribozymes have catalytic powers of their own- but they can’t compare to the complexity and vastness of their protein cousins.

There is, of course, absolutely nothing wrong with the steps that come before functional enzymes! DNA, transcription, mRNA, translation, degradation- all of these are golden within the Central Dogma. These are perfectly viable metabolic control sites, studied and focused upon by countless scientists around the world. The take home message that I’ve been thrusting upon you, overall, is that while steps before active enzymes have so much potential, it is those active enzymes themselves that have the function.

After all- earlier, I mentioned a few epigenetic control mechanisms. Acetylases to acetylate histones and unlock DNA? Helicase to unwind the double helix, and allow RNA polymerase access? RNA polymerase itself? All of these are enzymes… enzymes that make the biochemistry happen.

Did I mention that 2011 is the International Year of Chemistry?

What do you say? What is your bread and butter of metabolic control? Those of you who aren’t enzyme-centric, feel free to knock me on my posterior and put me in my place!

.

.

Chris is originally from Montreal, and is a Comparative Biochemist and Physiologist. His educational and postdoctoral experiences have taken him from Montreal to Ottawa ON, State College PA, and finally back to Montreal’s biotech industry. In his spare time- as you would expect from a Canadian- Chris enjoys watching hockey and is a stalwart fan of the Montreal Canadiens and Ottawa Senators. You can keep up to date with the latest from Chris on Twitter.

.

.

.