Saturday, September 28, 2013

Famous quote (23)

"Science does not know its debt to imagination."
Ralph Waldo Emerson

Saturday, September 21, 2013

Noncovalent interactions (part 2)

As mentioned in my first post about the non-covalent bonds , they are something essential in biochemistry!

At one side, since they are weak forces, they allow dynamic communications between molecules or within the same molecule. In other words, since they are weak they may allow, for example, that two molecules interact temporarily with one another, or that certain macromolecules acquire specific conformations temporarily . But in either case, if you need to change this situation, it is not complicated as these are weak forces... Examples of the first situation are an interaction between a substrate and the active site of an enzyme (please note that in some cases the substrate can interact with the enzyme covalently!), an interaction between a receptor and its ligand, an interaction between two proteins , etc. . Examples of the latter are an enzymatic conformational changes induced by binding of a substrate or by binding of an allosteric modulator, a protein conformational changes in response to a pH change (which happens, for example, with phosphofructokinase -1 during lactic fermentation, and this is one of the factors associated with muscle fatigue...), etc.
But do not be fooled by the individual weakness of each non-covalent interaction. In fact, as in biochemistry we often deal with large molecules (polysaccharides, proteins, nucleic acids , for example) , there are numerous locations within those molecules that can interact with each other. Thus, they form a network of non-covalent interactions that is responsible for maintaining the 3D structure of these molecules. The sum of all forces becomes huge, giving a greater stability to biomolecules. This is why, for example, a protein acquires one or a few possible conformations, despite virtually there is an enormous number of protein conformations that could be present...
Finally, there is a very important aspect that is related to non-covalent forces that molecules may be involved with: its solubility! In fact, often when someone dissolves something in water (salt or sugar, for example), does not think on why the dissolution occured. The idea is quite simple... for a substance to dissolve in a particular solvent, the molecules that compose it must be able to interact with the molecules of the solvent, in an energetically way more favorable than their initial arrangement . For example, the sum of the network of interactions between the atoms of Na+ and Cl- in the salt is less than the sum of the interactions of such ions with water molecules. Thus, in the presence of water the salt dissolves. And the reasoning is valid for any solute and/or solvent. Therefore it is said that "Like dissolves like" , which in reality tells us that the dissolution occurs when there is chemical affinity between the molecules of solute and solvent .

Friday, September 13, 2013

Music about to study biochemistry (2)

The "despair" and "anguish" of having to study biochemistry, with all those complicated names, and concepts that are not always very easy to understand, inspired once again Dr. Ahern, who this time was based on the song She’ll Be Comin’ ‘Round the Mountain.

Download the music here

Anthem for BB 350

Oh the students taking BB 350 - 350
Have an awful lot of things that we must know - 350
With acetic acid buffer
Kevin Ahern makes us suffer
The exams could not be tougher 3-5-0 – 350

There’s amino acid side chains to recall - 350
And the things it takes to make cholesterol - 350
Anabolic catabolic
Kevin Ahern’s diabolic
I’m becoming alcoholic 3-5-0 -350

There must be a way to jam into my head - 350
All the metabolic enzyme names I dread - 350
Can you help me learn the spaces
Where the endonucleases
Cut the DNA in places 3-5-0 -350

I must find a way to make a better grade
Or my GPA will truly get waylaid
I shall overcome frustration
To achieve my aspiration
On the last examination 3-5-0, 350

Here’s the plan I made to help me to succeed
Fill the notecard with the knowledge I will need
I’ve put all of Ahern’s quotes
Along with what each one denotes
Onto a massive stack of notes for 3-5-0, 350

So there’s just one teensy problem I must fix
It requires some very skillful penman tricks
Squeezing info I must store
Onto the card he gave before
Will mean a font the size of zero point one four

Monday, September 9, 2013

Famous quote (22)

"Bad times have a scientific value. These are occasions a good learner would not miss."
Ralph Waldo Emerson

Tuesday, September 3, 2013

Non-covalent interactions (part 1)

Today I will dedicate a post to a type of weak interactions that is often overlooked in chemistry classes (probably because they are weaker than covalent bonds ...), but in biochemistry are equally or more important than the covalent bonds. I'm talking about the non-covalent interactions (or bonds). Before starting to talk about them, it should be highlighted the difference between non-covalent and covalent bonds. In the first there is no sharing of electrons between the atoms participating in the bond, while in the second type there is sharing of the electrons (bonding electrons). Because there is no sharing of electrons, the resulting bond is significantly weaker.
There are different types of non-covalent interactions that collectively are known as van der Waals forces. The main types are:
- Ion interactions
- Dipole-dipole interactions
- Ion-dipole interactions
- Hydrogen bonds
- London dispersion forces

Often these interactions are referred to intermolecular forces, that means, forces that exist between molecules. In fact, it is the existence of interactions of this type that allows the molecules to interact with each other, thus justifying the existence of substances in liquid or solid state. Despite all the intermolecular forces are of this kind, they are also often responsible for interactions that occur between different regions within one molecule, being designated intramolecular forces. This is particularly frequent in the case of biochemistry, where one often deals with macromolecules (large molecules). Therefore, the non-covalent bonds can be intra-or intermolecular.