Monday, October 31, 2011

Cartoon about strong acids and bases

Wednesday, October 26, 2011

Carboxyl group

The carboxyl group is composed of two oxygen atoms bound to a carbon, one by a double bond and the other through a single bond. The latter is also covalently bonded to a hydrogen atom (R-COOH). Put simply, it can be seen as a functional group comprising a carbonyl group and a hydroxyl group.
The carboxyl group is the main acidic group in organic chemistry, and therefore can lose an H+, resulting in an anionic carboxylate group (R-COO-). Carboxylate ions are stabilized by electronic resonance, which allows the carboxyl group to present a significant acidic behavior. Carboxyl groups are highly polar and can act as H donors and acceptors in hydrogen bonds.
In biochemistry, the carboxyl groups are sometimes removed from biomolecules in the so-called decarboxylation reactions (they are released in the form of CO2).
The presence of carboxyl groups in the molecules can be detected by infrared spectroscopy, showing a characteristic vibration between 1680 and 1725 cm-1. Alternatively, it can be identified by nuclear magnetic resonance, appearing in the region of 10-13 ppm.

Tuesday, October 25, 2011

Famous sentence (2)

“People are DNA’s way of making more DNA.” - Edward O. Wilson.

Sunday, October 23, 2011

Animation about a weak acid

Here it is a link to download a very simple animation about what happens to a weak acid in solution.

Thursday, October 20, 2011

Biochemical curiosities (5)

To prevent odors in the refrigerator it can be used an open box of baking soda. It completely absorbs all the odors from stored food.

Monday, October 17, 2011

Hydroxyl group

The hydroxyl group is a functional group characterized by the presence of an oxygen atom covalently bonded to a hydrogen atom (R-OH). It is also called alcohol group, and the molecules that contain it have in their names the suffix "ol". In biochemistrythis group is particularly important because it can act both as donor and acceptor of H in hydrogen bonds. Therefore, their presence in biomolecules increases their water solubility and hydrophilic character.
This is a non-charged polar group. However, in some biochemical contexts it can function as a weak acid, losing one H+. This behavior is particularly important in the case of phenolic hydroxyl groups, i.e., in the case of hydroxyl groups bounded to benzene rings. As the main example of this situation, we have the amino acid tyrosine, which in some proteins may have an acidic behaviour.

Sunday, October 16, 2011

Music about protein translation (2)

The music Maria from West Side Story has inspired Dr. Ahern ( to create of a music about protein translation.


The most intricate thing I ever saw
From five prime to three prime, translation, translation
The final step that we know about the central dog-ma
Amino, carboxyl, translation, translation. . . .

Translation, translation, translation . .
I just learned the steps of translation
And all the things they say
About tRNA
Are true

To form peptide bonds in translation
The ribosomal cleft
Must bind to an E-F

A-U-G binds the f-met's cargo
16S lines up Shine and Dalgarno

I'll never stop needing translation
The most intricate thing I ever saw

Thursday, October 13, 2011

Animation about buffers

Buffers are very important for biochemistry. Here it is a link to download an animation about the way buffers work.

Saturday, October 8, 2011

Carbonyl group

The carbonyl group is characterized by the presence of an oxygen atom covalently linked via a double bond to a carbon atom. Depending on the position within the molecule to which it belongs, it can be called aldehyde group or ketone group. The first concerns the carbonyl groups that are located at an end of the molecule, that is, includes groups that are located on the first or the last carbon in the molecule. The ketone group refers to a carbonyl group which is at an internal position within the molecule. If the carbonyl is an aldehyde group, the molecule name ends with the suffix "al". If it is a ketone, it ends with "one".

Oxygen is more electronegative than carbon, which causes the carbonyl group to present a high polarity. As it is more electronegative, oxygen tends to relocate the electronic cloud, pulling it towards it. Consequently, carbon displays a partial positive charge and oxygen a partial negative charge.
Finally, it should also be noted that the term "carbonyl" can also be applied to carbon monoxide, when acting as a ligand in an inorganic or organometallic complex.
In the analysis of the composition of molecules, the carbonyl group can be identified by infrared spectroscopy (it absorbs between approximately 1600-1900 cm-1) or nuclear magnetic resonance (about 160-220 ppm).

Thursday, October 6, 2011

Music about enzyme catalysis

This music is about enzyme catalysis and is an adaptation made by Dr. Ahern ( of the song Close to You.

My enzymes
Truly are inclined
To convert
Things they bind
Turn the key

How do cells
Regulate these roles?
Allo-ster-ic controls
Two forms, see
States R and T
Competing inhibition keeps
The substrates from the active site
They raise Km, but leave Vmax and shirk
While the non-competers bind elsewhere
And lift the plot made on Lineweaver-Burk

Other ways
Enzymes can be blocked
When things bind
Then get locked
Stuck not free
Tied to the key

Penicillin’s action stops
Peptidoglycan cross-links in
Bacterial cell walls in awesome ways
Beta lactam ring’s reactive site
Starts bonding with D-D-transpeptidase
So there are
Several enzyme states
Counteract-ing substrates
Now you see
Blocking the key
Have to be controlled
Some get slowed
Put on hold
It's sublime
How the enzymes
(slow) Cat-a-lyze
ahhhhhhhhhhhhhhhhhhh - cat-a-lyzeahhhhhhhhhhhhhhhhhhh - cata-
lyzeahhhhhhhhhhhhhhhhhhh - cat-a-lyze

Monday, October 3, 2011

Animation about the action of epinephrine on hepatocytes

The liver is a central organ in our metabolism. There are many hormones that act on it, being epinephrine (also called adrenaline) one of them. Here it goes an animation that explain the action of that homone on liver cells.