Friday, September 30, 2011

Metabolic map on the synthesis of leucine

Thursday, September 29, 2011

Scientific jokes (8)

In a lecture of physiology...
"Who can tell me how these cells communicate with one another?" asked the instructor, expecting someone to explain the phenomenon of neurotransmission.
After a few muffled whispers, one student finally spoke up. "With cellular phones?"

Wednesday, September 28, 2011

Functional groups (general ideas)

All substances have properties that impart specific physical and chemical characteristics. I'm talking about simple things like color, taste, smell, physical state, solubility, etc..
But how do these different features are explained at the molecular/atomic level? What makes a substance liquid at room temperature and other solid, for example? The answer involves the composition of molecules. But I'm not just talking about size, which, of course, is a very important parameter. I am also speaking about the presence of certain atoms, and the relative proportions of the atoms that constitute the molecule... Features such as smell, color or taste, are a direct consequence of the atomic composition of molecules. But other characteristics, for example, physical state, boiling point and melting point also relates to the composition, although in this case the relationship is more indirect.
In general, the characteristics of a substance depend on the presence of certain functional groups in it. But what are functional groups? Basically, they refer to atoms arranged in submolecular structures that alter the properties of substances. They determine the interactions established within the molecules and with neighboring molecules. Moreover, they are responsible for the reactivity of molecules. That is, a functional group always reacts the same way with another (for example, a carboxylic group always originates an ester when it reacts with an alcohol...), regardless of the remaining composition of the molecule where it is inserted. At the same time, it is the presence of functional groups that will make a molecule more or less reactive. Therefore, one can say that the functional groups determine the reactivity and the types of chemical reactions that molecules can suffer.
When it comes to functional groups, there is always some ambiguity about what can be considered  to belong or not to that class. Some authors argue that the functional groups must have at least one atom other than C or H (except for the phenyl group), while others include also groups such as methyl, ethyl, etc.
Soon I will start posting details about the main functional groups ...

Friday, September 23, 2011

Music about the fatty acids

This music is about the roles of fatty acids in our cells and is based in the song Halls of Montezuma. It was made by Dr. Ahern
(www.davincipress.com/metabmelodies.html).


http://www.mediafire.com/?2exx92e6264493c


Fatty Acids in Our Cells


From the fatty acids in our cells
To the lipids in our brains
We are made of biochemicals
Built in metabolic chains

Using glycolytic ATP
And electron energy
We can synthesize most everything
With the help of Delta G

A cell will tend to pump out sodium
But potassium it imports
It accomplishes this magic with
ATPase antiports

Our bilayer lipid membranes
Protect the cells' insides
Partly made of sphingolipids
We know as gangliosides

When it comes to regulation
The little cell has got it made
It phosphorylates a lot of things
With its own kinase cascade

Stimulated at a hormone site
Metabolic yang and yin
That's turned on by epinephrine
And turned off by insulin

Wednesday, September 21, 2011

Video about the Krebs cycle (3)

This video is different... it is a Legos's version of the Krebs cycle! :)

Tuesday, September 20, 2011

Monday, September 19, 2011

Krebs cycle (reactions) - part 2

Reaction 5: conversion of succinyl-CoA to succinate This reaction requires Mg2+. The enzyme that catalyzes this reaction, succinyl-CoA synthetase, breaks the thioester bond (S-CoA), releasing a large amount of energy that is used to phosphorylate GDP to GTP. It is another example of an energy coupling.








Reaction 6: oxidation of succinate to fumarate
Succinate is oxidized to fumarate, leading to the production of FADH2 from FAD. The reaction is catalyzed by succinate dehydrogenase, which is the only Krebs cycle enzyme that is not present in the matrix, but instead is strongly associated with the inner membrane of mitochondria.











Step 7: Hydration of fumarate to malate
This enzyme is highly stereo-specific, producing only the stereoisomer L-malate. The reaction is reversible in cellular conditions.



Step 8: oxidation of malate to oxaloacetate
This reaction produces a molecule of NADH from NAD+. At the intracellular conditions, the reaction is mainly driven in the opposite direction, but as the oxaloacetate is continuously removed (by the reaction of synthesis of citrate, by gluconeogenesis or by transamination to originate aspartate), the equilibrium is shifted in the forward direction. The oxaloacetate used in the first reaction of the Krebs cycle is then regenerated, so, theoretically, one molecule of oxaloacetate may be involved in the oxidation of an infinite number of molecules of acetyl-CoA (playing a kind of "catalytic" role) and, therefore, the oxaloacetate is present in cells at very low concentrations.
  
Main bibliographic sources:
- Quintas A, Freire AP, Halpern MJ, Bioquímica - Organização Molecular da Vida, Lidel
- Nelson DL, Cox MM, Lehninger - Principles of Biochemistry, WH Freeman Publishers

Sunday, September 18, 2011

Biochemical curiosities (4)

The clothes pressing iron glides easily over your clothes if you put a little toothpaste on the bottom of the iron.

Saturday, September 17, 2011

Friday, September 16, 2011

Music about fermentation

I like very much this music made by Dr. Ahern (www.davincipress.com/metabmelodies.html)... :)
It is about fermentation and is based in the famous Oh Susannah!

Here it is the link to download it:
http://www.mediafire.com/?zhbfbz91u70ca10


Oh, late last night I went to jog
when everything was still
I came upon a gravel road
a-windin’ up the hill
I don’t know why I did it but
I played a game with death
Ran up that hill in double time
And held in all my breath

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP

‘bout half way up I felt the burn
My hip down to my knee
if only I had stayed awake
In biochemistry
then I’d have had a warning, but
regrets were just too late
I stood in pain - my body was
reducing pyruvate!

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP
Well up came my professor who
was trailin’ close behind
he told me how fermenting was
a process most unkind
Oh ATP is energy
It’s keeping you alive
It’s mostly made by protons mov- ing
through the complex five

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP

In making ATP a pro- ton gradient is key
to ADP’s phosphoryla- tion, oxidatively
Electrons pass through complex four
And oxygen, you know
picks up four more electrons and

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP

I hope that you can clearly see
Exactly what I meant
That oxygen is needed for
The proton gra-di-ent
your muscles work in overdrive
And use up ATP
you might be breathin’ hard but lack sufficient energy
Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP

You’re in a heap o’ trouble and
this breath may be your last
if you can’t make some ATP
and NAD+ real fast
It’s lactate dehydrogenase
To save the day, you see
Turn pyruvate to lactate and
Produce more NAD+!

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP

The NAD+’s important,
Are You gettin’ all of this?
it gets fed back into the pathway
of glycolysis”
It hit my ear, it was so clear
and all made sense to me
Although I had no oxygen
I still made ATP

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP
For all he’d done I took my prof
to sit down for a drink
admitting that his lesson earlier
had made me think
I took a swig of ale
And grinning wide, I said with glee
Oh, fermentation hurts but all in all
It’s fine by me

Fermentation!
I need some NAD+
my cells are lackin’ oxygen
But using ATP
makes double H2O

Fermentation!

Wednesday, September 14, 2011

Video about the Krebs cycle (2)

Here it goes one more video about the Krebs cycle, this time in a karaoke version. :)

Tuesday, September 13, 2011

Scientific jokes (7)

Why do you should keep aboslute science in the laboratory?
To avoid that the reagents become unconcentrated.

Sunday, September 11, 2011

Friday, September 9, 2011

Krebs cycle (reactions) - part 1

Reaction 1: formation of citrate
This irreversible reaction is the 1st regulatory point of the Krebs cycle. It is a reaction in which an oxaloacetate molecule reacts with acetyl-CoA. In this process it is formed a very energetic intermediate (citroil-CoA) that rapidly converts into citrate. The molecule of CoA-SH liberated is recycled to participate in a new oxidative decarboxylation of pyruvate (catalyzed by pyruvate dehydrogenase complex).

Reaction 2: formation of isocitrate via cis-aconitate
This reaction occurs through the formation of an intermediate, cis-aconitate, obtained by dehydration of citrate. Thereafter, the cis-aconitate is hydrated, forming isocitrate. Thus, citrate and isocitrate are isomers. Despite that in cellular conditions the reaction produces only about 10% of isocitrate, the rapid consumption of this product in the following reaction shifts the equilibrium in the forward direction. The fluoroacetate is a toxic molecule because in physiological conditions it is transformed into fluoroacetil-CoA, which condenses with oxaloacetate to form fluorocitrate, that inhibits aconitase, causing accumulation of citrate.








Reaction 3: oxidation of isocitrate to α-ketoglutarate and CO2This reaction is an example of an irreversible oxidative decarboxylation, and it is the 2nd regulatory point in the Krebs cycle. In fact, this reaction is a set of three different reactions:
1. Dehydrogenation of isocitrate, creating oxalosuccinate and producing NADH.
2. Binding of Mn2+ to the carbonyl group of oxalosuccinate, stabilizing the enol and promoting the release of CO2.
3. Hydrogenation, with the arrangement of the resonance hybrid.





Reaction 4: Oxidation of α-ketoglutarate to succinyl-CoA and CO2This reaction, like the previous one, is another example of an irreversible oxidative decarboxylation. It is the 3rd (and the last one!) regulatory point of the Krebs cycle. This reaction is virtually identical to the oxidative decarboxylation of pyruvate, also leading to the formation of NADH. It is a very exergonic reaction due to the energy stored in the bond S-CoA.





Main bibliographic sources:
- Quintas A, Freire AP, Halpern MJ, Bioquímica - Organização Molecular da Vida, Lidel
- Nelson DL, Cox MM, Lehninger - Principles of Biochemistry, WH Freeman Publishers

Thursday, September 8, 2011

Scientific t-shirts

Here it goes the link to a site that sells many scientific t-shirts. There are some funny ones... :)

http://yellowibis.spreadshirt.com/chem/p4

Wednesday, September 7, 2011

Biochemical curiosities (3)

To make the lenses of the glasses to shine you can use vinegar. One drop in each lens is sufficient.

Tuesday, September 6, 2011

Music about enzymes

Here it goes a link to download another Metabolic Melody from Dr. Ahern (www.davincipress.com/metabmelodies.html), this time about enzymes. It was base on the song Downtown.

http://www.mediafire.com/?w0gd96oo6ecpymg


Enzymes
Reactions alone
Energy peaks
Are what an enzyme defeats
In its catalysis
Enzymes

Transition state
Is what an enzyme does great
And you should all know this
Enzymes

Catalytic action won't run wild - don't get hysteric
Cells can throttle pathways with an enzyme allosteric

You know it's true

So when an effector fits
It will just rearrange
all the sub-u-nits
Inside an
ENZYME!
Flipping from R to T
ENZYME!
Slow catalytically
ENZYME!
No change in Delta G
(Enzyme, enzyme)


You should relax
When seeking out the Vmax though
There are many steps
Enzymes

Lineweaver Burk
Can save a scientist work
With just two intercepts
Enzymes

Plotting all the data from kinetic exploration
Let's you match a line into a best fitting equation

Here's what you do

Both axes are inverted then
You can determine Vmax and
Establish Km for your ENZYMES!
Sterically holding tight
ENZYMES!
Substrates positioned right
ENZYMES!
Inside the active site
Enzymes (Enzymes, enzymes, enzymes)
Could starve your cells to the bone
Thank God we all produce
Enzymes

Units arrange
To make the chemicals change
Because you always use
Enzymes
Sometimes mechanisms run like they are at the races
Witness the Kcat of the carbonic anhydrases
How do they work?

Inside of the active site
It just grabs onto a substrate
and squeezes it tight
In an
ENZYME!
CAT-al-y-sis
In an ENZYME!
V versus S
In an
ENZYME!
All of this working for you
(Enzyme, enzyme)

Monday, September 5, 2011

Game about cholesterol

Pacman was one of the most successful games when computer games started to appear. Today I have found a biochemical adaptation of that game, namely, to cholesterol. :)

http://www.weightlossresources.co.uk/funandgames/cholesterol.htm

Saturday, September 3, 2011

Thursday, September 1, 2011

Video about the respiratory chain

Hey Soul Sister is a very well known song. Its biochemical version is not so famous...