Ribozymes are catalytic RNAs!

I’m studying for my second qualifying exams (the exam which, should I pass, will officially qualify me as a PhD candidate). In an effort to bolster my general knowledge of all things RNA-related, I’m reading a textbook called the “Molecular Biology of RNA.”

This book as an entire chapter devoted to catalytic RNAs. Since my days as an AP Biology student I’ve known that some RNA molecules can behave as enzymes and catalyze reactions, but this chapter opened up the world of ribozymes as I’ve never understood them before.

A Ribozyme is an RNA molecule that can catalyze a reaction. The ribosome is probably the most famous ribozyme, which catalyzes peptide bond formation, but other RNAs exist that also behave as true catalysts. A true catalyst is not destroyed or changed by the reaction it speeds up.

Some RNAs with enzymatic activity ARE exhausted by the reactions they catalyze, and the chemistry here is equally fascinating. These include self-splicing RNA introns and self-cleaving viral genomes.

Most catalytic RNAs use acid-base chemistry and leverage the heightened reactivity of the ribose sugar via the 2′-OH functional group.

Let’s take a step back. To understand how RNA can act as an RNA-cutting enzyme, we need to know two things. 1) how structure and function are intimately related in biology, and 2) how generally unstable RNA is as a polymer.

1) Structure and Function:

This is something I also learned in high school biology that I took for granted until late in college. Primary sequences of proteins and RNAs are closely tied to secondary or tertiary structures, and these are intimately related to how a molecule functions. In the case of RNAs, primary sequence influences base-pairing or secondary structure, and RNA molecules can fold up into tertiary structures that bring reactive groups into close proximity. All you need is an environment that encourages this folding and can stabilize the reactive groups in this close proximity.

2) RNA instability

RNA is less stable than DNA. The namesake ribose sugar has an extra functional group (-OH) attached to carbon #2. This functional group is reactive, and particularly so when de-protonated. The partially-negatively charged oxygen can attack the phosphate in RNA’s phosphate backbone, triggering cleavage of the backbone.

(I understand pictures would be greatly useful here…I’ll get on that)

So for enzymatic RNAs to function, all we need is creation of an active site by RNA-folding, and then stable acid-base chemistry to trigger cleavage. This can occur within the RNA sequence itself (self-cleavage) or by sequence-recognition in a separate RNA molecule (site-specific cleavage).



Why women still can(‘t) have it all ?!!!

We are back from break.

We decided to reread Anne-Marie Slaughter’s article “Why Women Still Can’t Have It All” published in the Atlantic in the summer of 2012.  One of her arguments is that the difference between the maternal and paternal bond is the reason that a woman is more likely than a man to sacrifice career for family.

It is often claimed that “biology” is the reason for the difference between the maternal and paternal bond.  This is only a hypothesis and we don’t see how it can ever be proven.  This is because we cannot separate nature from nurture.

Many factors could be considered as parents decide how to balance their career and family responsibilities.  They might consider career flexibility, career trajectory, and income as well as the preferences of the individuals.  We believe that the construction of gender in our society affects all of these variables and we that this construction is manmade.


[insert title that someone wants and is completely inappropriate]

We are sitting around our breakfast table, drinking warm apple cider and de-stressing with a very intense conversation:

1. Can you be a feminist if you are economically dependent on a man?

2. What if we had artificial wombs? Would it make the world more feminist? Is there something wrong with wanting men and women to be more equal with respect to child-bearing (perhaps somewhat literally)?

3. How do you separate biology from society? Paternal instincts, maternal instincts…how real are these things in modern society?

4. Isn’t it weird that women can’t go shirtless and men can [yes, we know it is weird, but why???]?

5. Do women on average need more positive feedback than men? Is this something to feel ashamed of or need to fix?

6. Would anyone watch Big Bang Theory if Penny was actually a “dumb blonde” male and the lead scientists were all <badass> nerdy women? Why not? [actually, we could totally pull this off….just need to find a dumb blonde male – please post applications 🙂 ]