Bree's dad's notebook

by meepers anonymous

This is to describe the structures that were found in Bree's dad's notebook

The structures in Bree's dad's labbook describe the cleavage reaction of a
hairpin ribozyme . Ribozymes cleave RNA (see
http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0020028&id=4283


There are 3 classes of ribozymes, hairpin, group 1 introns and hammerhead,
the one Bree's dad was looking at is called hairpin.

http://employees.csbsju.edu/hjakubowski/classes/ch331/catalysis/hairpinribozyme1.gif

For those who don't know any biochemistry, think of RNA as a necklace. RNA
is made up of nucleotides. Nucleotides are like the beads of the necklace.
Bree's dad's picture shows 2 nucleotides (2 beads and the string
inbetween) and how the ribozyme (scissors) can cut the RNA necklace.

Nucleotides are made of a sugar called ribose (the pentagons in the diagram)
a phosphate group (the P with all the O's hanging off it)
a base (the N+1 and N-1).

If we look at the picture, the 2 sugars(pentagons) are 2 beads on
the RNA necklace. The bases (N+1/N-1) are pendants which hang off the
beads. The phosphate group (P with 4 O's) is string between the 2 beads.
If you look closely you can see that the line between the P and the lower
pentagon disappears between the first and last structure. This is where
the ribozyme scissors cuts the RNA necklace.

There are four bases, Adenine, Guanine, Cytosine, Thymine or A,G,C,T. In
other words, there are 4 different pendants for our necklace. Depending on
the length of the necklace we could ge many pendants combinations.
Ribozymes don't just cut anywhere, they cut at particular sequences. In
other words, the scissors will only cut inbetween 2 beads when it sees a
particular row of pendants.

Unfortunately Bree's dad did not give the sequence or any indication of
which specific hairpin ribozyme Bree may be overexpressing. The only
sequence given is TCC which codes for serine, an amino acid and building
block for protein. It is unlikely this is the sequence which the ribozyme
targets as it is too short to be specific.

Below the diagram it says substition of the nucleophilic 2'OH. This is
describing the reaction mechanism. Its pretty complicated but its
basically saying at the OH group on the 2nd carbon (each point of the
pentagon represents a carbon atom) there will be a change in electron
distrubition which is how the reaction takes place.