Happy New Year

I want to wish to all the readers of World of Biochemistry a 2013 full of profissional and personal success! :)

Tattoo - quantum physics

Merry Christmas!

Metabolic map about the transport of proteins to the nucleus

Video about the nucleic acids

Cartoon about male pregnancy

Enantiomers

Enantiomers are a class of isomers belonging to the optical isomers, taht means, they are characterized by differencies in regions containing at least one chiral carbon.
The enantiomers are considered as the mirror image of one another, like it happens with our hands. Therefore, they are symmetric, non-superimposable molecules.

However, when trying to compare two potential enantiomers, it is not always easy to imagine the rotation of the molecules in space, in order to check whether one is dealing with mirror images of one another. So, the best thing to do is to use the definition of enantiomer. This definition tells us that the enantiomers are molecules that differ in the configuration of ALL chiral carbons. Thus, what should be done is:
1. Identify all the chiral carbons present in the molecule.
2. Verify if the configuration of each one differs or stands in the possible enantiomer.
When I speak in different configuration, I am referring to the situation where it is impossible to overlap all substituents of a chiral carbon in the two molecules. If the configuration of ALL chiral carbons is different, they are enantiomers. If there is at least one chiral carbon with the same configuration in both molecules, they are no longer enantiomers.
Finally, by definition, when there is only one chiral carbon in a molecule, and the corresponding configuration is different in the two isomers, these are enantiomers.

Music about biochemistry

This song made by Dr. Ahern (www.davincipress.com/metabmelodies.html) is one of those that everyone likes. It is based on the music If You're Happy and You Know It, Clap Your Hands, and it covers several issues of biochemistry. Come on, everybody singing...:)

If You're Molecular and Know It, Clap Your Hands

Instructor sings regular text, class sings bold text

If you want to have a lot of energy (En-er-gy)
You had better make a lot of ATP (A-T-P)
I will only tell you once
You need proton gradients
And a bunch of starting stuff like ADP (A-D-P)

If you hanker for a sweet thing you can taste (You can taste)
And your Atkins diet book has been misplaced (been misplaced)
You should know adrenalin
Is an aid to getting thin
Putting phosphates onto enzymes trims your waist (trims your waist)

If you're feeling kind of achy in your ways (in your ways)
And that hangover has hung around for days ('round for days)
You should know you silly dear
Pain does not come from your beer
Prostaglandin's made by PGH synthase (H synthase)

There are acids in the bile that make up gall (make up gall)
Which emulsify triacylglyerol (glycerol)
If your health is gone to hell
You should blame the LDLs
'Cause they carry all of that cholesterol (lesterol??)

Some phosphates and a sugar on a base (on a base)
Make up C's and G's and U's or T's and A's (T''s and A's)
You can make a DNA
Or a strand of RNA
If you add a template and polymerase (lymerase??)

If you want to ace this test with utmost ease (utmost ease)
You don't really have to get down on your knees (on your knees)
And you need not say a prayer
So please don't pull out your hair
Just go download QuickTimes or the MP3s (MP3s)

Famous sentence (16)

Concerning levers:
Give me a place to stand, and I will move the Earth. (Archimedes)

Video about the name of a protein

Titin is the biggest protein that exists in our body. It is composed by almost 27000 aminoacid residues and has a molar mass of about 3tons/mol!!! As you can imagine, it should be hard to pronounce its name according tot the rules of organic chemistry numenclature. Here it is a video of someone brave enough to spend more than 3 hours saying the name of this protein, which has "only" 189819 letters. You can even notice that during the video his beard grows. eheheh

Thanks to Hélder Pimenta for this contribution! :)

Metabolic map about phospholipase C signalling pathway

Tattoo - Genetics

Video about DNA structure and replication

Cartoon about nanoscience

With nanoscience will it be possible to create new "nanofunctions"? eheheh

Geometric isomers

The geometric isomers belong to the family of the stereoisomers, more precisely, the configurational isomers. So, as the name indicates, they differ in the configuration of one or more carbons. The particularity of this kind of isomerism is the fact that it involves non-tetraedric carbons, that means, carbons that do not establish 4 single bonds. Putting it more simply, it involves carbons that establish double bounds. 

 The classic example of this kind of isomerism is the cis and trans isomers, where the configuration of one of the carbons involved in the double bound changes. It is important to note that these isomers are not conformational ones, because the double bonds cannot rotate. 

Finally, it is noteworthy that one should be careful when comparing two molecules that differ in a region that contains double bonds. In this case, the molecules are geometric isomers only if the constitutional isomerism is not applicable to the molecules. For example, in the following image the first two molecules are geometric isomers, while the molecules 1 and 3, or 2 and 3 are constitutional isomers.

Music about PCR

PCR is present in the daily routine of many investigators. Due to Dr. Ahern (www.davincipress.com/metabmelodies.html), it can also be present in the form of a music. This sob was base on the famous She’ll Be Comin’ Around the Mountain.

PCR Woes

First you must design the primers- PCR!
Make sure that they won't form dimers - PCR!
Then you check the melting T's
A's and T's are two degrees
And it's four for G's and C's in PCR!

Oh the thermocycler's set for PCR!
If this fails you'll be upset with PCR!
First you melt and did I mention
It's anneal and then extension
Copying is the intention - PCR!

Many times the protocol you've tried to fix
Checking all your tubes and then your mastermix
Looking for contamination
As you build up your frustration
If there's no amplification - PCR!

You can use reverse transcription - PCR!
Surely you'll throw a conniption - PCR!
Other types may give you trouble
Oh there's inverse and there's bubble
Your anxiety will double - PCR

Oh you've really got to amplify this strand
Hope that when you run your gel you've got a band
Didn't get what you expected
Damn this project you selected
Now you're feeling quite dejected - PCR!

Famous sentence (15)

Only two things are infinite, the universe and human stupidity, and I'm not sure about the former. (Albert Einstein)

Tattoo - Schrodinger's equation

Metabolic map about apoptosis induced by free radicals

Cartoon about the brain

Video about carbohydrates

Happy Halloween

Conformational isomers

Today I will post about conformational isomers, a class that belongs to the family of stereoisomers. This type of isomerism is somehow controversial, since there are people that consider it, indeed, as a particular type of isomerism, while others consider that we are talking about different structures of the same molecule.

In order to understand the concept of conformational isomer, it is recommended to highlight a property that is observed only in single bounds – its capacity to rotate, functioning as an axis.

In this context, regions of a molecule that contain single bounds are characterized by their high rotational flexibility.

When two molecules are compared, if it is possible to convert one in the other through rotation on one (or more) single bounds, they are conformational isomers.

Since, in fact, the two molecules are converted without the need to break or create new covalent bonds (this is the definition of conformation, as it was explained here in a previous post…), there are people that claim that those molecules don’t have to be considered isomers.

Music about codons

This music was bsed on the famous When I'm Sixty Four, and talks about codons. It was made by Dr. Kevin Ahern (www.davincipress.com/metabmelodies.html).

The Codon Song

Building of proteins, you oughta know
Needs amino A's
Peptide bond catalysis in ribosomes
Triplet bases, three letter codes
Mixing and matching nucleotides
Who is keeping score?
Here is the low down
If you count codons
You'll get sixty four

Got - to - line - up - right
16-S R-N-A and
Shine Dalgarno site

You can make peptides, every size
With the proper code
Start codons positioned
In the P site place
Initiator t-RNAs
UGA stops and AUGs go
Who could ask for more?
You know the low down
Count up the codons
There are sixty four

Famous sentence (14)

Ignorance affirms or denies, science questions. (Voltaire)

Metabolic map about fibrinolysis

Tattoo - Neuron

Video about isomers

Cartoon about animal experiments

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.

Music about proteins

Dr. Ahern (www.davincipress.com/metabmelodies.html) 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.

Tattoo - chemical elements "ThInK"

Metabolic map about the mechanism of action of anthrax

Famous sentence (13)

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

Video about isomerism

Cartoon about experiments

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.