Thursday, September 27, 2012

Constitutional isomers

In the coming weeks I will devote a few posts to the different types of isomers that molecules can present. I'll start with the constitutional isomers...
This type of isomerism involves changes in the pattern of the covalent bonds that exist in a molecule. That is, when we compare two isomers in order to try to understand what kind of isomerism exists between them, the first thing to do is to look at their covalent bonds skeleton. Basically the idea is this ... we have to see if each atom of a molecule establishes exactly the same kind of bonds with the same substituents, than the corresponding isomer. If there is at least one difference in those bonds, these are constitutional isomers.

In this context, there are several situations that can occur, being the most common:
1. Changes in the identity of the functional groups
In some cases, changing the pattern of covalent bonds may lead to changes in the identity of functional groups such as the following examples.

2. Changes in the position of the functional groups
In this particular case, the isomers are designated as positional isomers.

3. Changes in the localization of double bonds
In this situation the double bonds of the molecules remain in the same amount, the only change is their localization within the molecule.

4. Cyclization of alkenes
Sometimes, constitutional isomers appear when the alkenes undergoes cyclization, losing the double bond during the process.

Sunday, September 23, 2012

Music about proteins

Dr. Ahern ( has created a march of proteins, inspired by The Ants Go Marching One by One.

March of the Proteins

Oh there's a method you should know that's very huge
It's spinning round and round inside the centrifuge
The supernatant, pellet too
You choose the one that's right for you
And from there we pu-ri-fy
What's inside

To size exclude filtration is the way to go
The beads have pores small proteins can go in you know
The largest ones, they come out fast
The smallest ones eluting last
And the proteins purified
By their size

Electrons power gel e-lec-tro-pho-re-sis
The protein is denatured thanks to SDS
Proteins in a minus state
Get sorted by atomic weight
Smaller ones in speedy mode
To the anode

Ion exchange is special chromatography
To switch cations, you must have a minus bead
Upon this bead, the proteins bind
They're positive, not any kind
And the others wash right through
Out to you

Oh my this song has given you a mighty list
Perhaps we'll just skip over ol' dialysis
So study HPL and C
If you have questions, talk to me
You will get through protein hell
You'll do well.

Saturday, September 15, 2012

Famous sentence (13)

The best doctor is the one who knows the worthlessness of most medicines. (Benjamin Franklin)

Friday, September 7, 2012

Conformation vs. configuration

Before I start posting on the different types of isomers, I will devote a post to an aspect that is very important when studying the isomerism of molecules. Despite its great importance, this can be sometimes confusing ... I'm talking about the difference between conformation and configuration. J
These two concepts are often used interchangeably, but represent very different things. The conformation regards the relative spatial orientation of a portion of a molecule relative to another. Thus, it is an aspect that is not directly related to the covalent bonds that are established within the molecule, but with their possible rotation.

When we talk about rotation around covalent bonds, we are only referring to the single bonds, as they are the only ones that can suffer rotation. Basically this concept is easily understood if we think that the bounds work as an axis...

It should be noted that when we speak of different conformations, it does not necessarily involve all the covalent bonds of a molecule, it can account only for one or few of them.

Taken together, it is possible to convert one conformation to another without cleaving or forming chemical bonds, simply by rotating some simple covalent bonds.

The configuration is a concept that is related to the order by which different substituents linked to the same central atom establish covalent bonds. That means, in this case it is clearly an aspect that is a direct consequence of the covalent backbone of molecules.

To change the configuration, you must always cleave and form new covalent bonds...

In conclusion, the concept conformation encompasses portions of a molecule which are not directly linked to the same atom and do not involve the covalent backbone of the molecules, while the configuration comprehends parts of the molecule which are bound to the same atom, which means that there is a direct involvement of the covalent bounds of the molecule.

Wednesday, September 5, 2012

Music about the ribosome

This music made by Dr. Ahern ( is about a little big organelle, the ribosome. It was inspired on the song  American the Beautiful.

The Ribosome

O beautiful with R-N-A
That makes the peptide bonds
You hold t-RNA so it
Can pair up with co-dons

The Ribosome! The Ribosome!
Translate m-RNA
Initiate and translocate
From start to U-G-A