A few stuff about molecular biology.

I wanted to talk about a few of the really cool stuffs that one can find out by studying molecular biology.

These can be really neat and often are living witnesses of our most distant evolutionary past, carried deep in the heart our own cells.

But, yeah, when I started about thinking how to write up the coolest ones, I realized that I’d probably do a small recap of the bases, so here it comes.

Recap, the central dogma of molecular biology:

What we refer to as ‘the central dogma of molecular biology’ was first proposed by one Francis Crick of doubly helical fame. In short, it describes how genetic information is contained into DNA, how this DNA is transcribed into RNA and how this DNA is then translated into proteins.

One could, with a little smirk, describe it as the product of a simple time, because quite a few exceptions to this dogma have since been found, as always, Nature is a messy place. Still, it works well enough.

Now, the four DNA bases tend to bind to each other in pair: cytosine tends to bind guanine and thymine tends to bind adenine (in RNA, thymine is absent and instead another closely similar molecule, uracil, binds adenine). That means that complementary sequences will naturally tend to bind each other: CGTACGTA will naturally tend to bind GCATGCAT sequences, in fact, this is the combined forces of all these tiny base-to-base liaisons that bind together the two branches of the double helix (in fact, two complementary sequences of DNA).

Here you see the two helices bound together by the meeting of the nucleotide pairs

(image ruthlessly pilferaged from Genomes -third Edition- by T. A. Brown; University of Manchester)

Another point worth mentioning is that both lesion are not equal, cytosine that interacts with guanine through three hydrogen bonds will form stronger bonds than adenine that only interacts with thymine or uracil through two hydrogen bonds.

Here are the formula of the five nucleotide bases, also showing the interaction between the DNA base pairs, weaker between adenine and thymine or uracil than between cytosine and guanine.

The transcription and transcription termination in prokaryotes.

Now, imagine, if you will, the single lonely chromosome of a simple bacterium. Getting closer, we can discern the long flowing chain of this double stranded chain of DNA. Floating by is the bulky shape of a RNA polymerase, a complex of 5 different sub-units. Another molecule, the Sigma factor 70, pass by and start interacting with the RNA polymerase. These interaction slowly nudge the RNA polymerase toward the chromosome, and more precisely toward the -35 box (a sequence located 35 nucleotide upstream from the gene of interest). Then, the RNA polymerase finally bind the DNA, forming the ‘promoter complex’. It then starts pulling the DNA toward it, in the process, separating the two branches downstream and accumulating the energy it will need (imagine unwinding two rubber bands, tightly wound one on to the other). This lead to the formation of a ‘open promoter complex’ where, just uphead from the transcription complex, one may observe a short region where the two strings of DNA are separated (we call it the transcription bubble), a bit like the zipper of an overloaded bag, where the two half of the zipper start to break apart.

Inside the bubble, base pairs are added on after the other that match the ones on the DNA strand and, slowly, the RNA messenger is constructed that form a sequence complementary to the DNA. The two strands interact with each other, forming an ephemeral liaison that help stabilizing the transcription complex.

Here is a nice schema to illustrate this (taken from Principle of Biochemistry, Lehninger et al., 2000: get it, it’s a standard).

But now, it’s when it becomes really cool. At this point, the RNA arrives at the end of the gene. How does the transcription complex ‘know’ where to stop?

Well, there are two big ways in bacteria and the coolest part is common in both. You see, by the end of the gene there is what we call a ‘palyndromic sequence’. In English, a palindrome is a word or a sentence that can be read from both left to right and right to left, like the word, ‘radar’ for example. In molecular biologist English, a palindrome is a sequence that is identical when read in one direction to the one on the complementary strand when read in the opposite direction: for example CGTTAACG is palindromic, its complementary sequence would be GCAATTGC which, read from right to left, become CGTTAACG.

The importance of this palyndromic sequence is that it is complementary with itself. Look at it, the first pair (C) will bind the last one (G), the second pair (G) will bind the second to last (C) and the two Ts will bind the two As

Now, if we have a long palindromic sequence, the left and right portion of the sequence will tend to bind with each other, forming what is called a ‘hairpin loop’.

This hairpin loop fold onto itself, instead of interacting with the DNA sequence, which would stabilize the transcription complex. This destabilize the whole complex and slow down the transcription process.

Then, two things can happen. In about half the genes, this sequence is followed by a long sequence of adenine. As we mentioned, the adenine-thymine and adenine-uracil pairs are weaker than the cytosine guanine ones. This further weaken the binding of the mRNA on the DNA strain to the point where the two strands break up, interrupting the transcription process.

The other relies on what is call a Rho factor which is another helicase (it breaks bond between nucleotide pair). Essentially, he Rho binds the transcribed DNA sequence a bit upstream from the RNA polymerase and start moving in the same direction at roughly the same speed. Normally, the RNA polymerase own migration along the DNA strand allows it to stay ahead. But, as we mentioned, the RNA polymerase is slowed down at the hairpin level, this allows the Rho factor to catch up and start breaking up the pair lesions at the level of the RNA polymerase. This, in turn, leads to the breaking up of the transcription complex and the end of the transcription…

Conclusion

So, there you go, it’s certainly not complete, but reading that should give you the basis for understanding the really cool stuff I’d like to talk about next (starting with small interfering RNAs).