Wednesday, August 31, 2011

Metabolic map on the synthesis of sphingolipids

Tuesday, August 30, 2011

Scientific jokes (6)

What is the most abundant functional group in the space?
Is the ether.

Monday, August 29, 2011

Krebs cycle (general ideas) - part 2

For each round of the Krebs cycle, three molecules of NADH, 1 FADH2, 1 ATP (GTP) are produced.

The passage of electrons from a molecule of NADH to O2 on oxidative phosphorylation leads to the formation of 2.5 molecules of ATP. If the donor electron is the FADH2 only 1.5 molecules of ATP are formed. Therefore, one molecule of glucose that is completely oxidized to CO2 via glycolysis, pyruvate dehydrogenase, Krebs cycle and oxidative phosphorylation, produces 32 ATP molecules.

The Krebs cycle plays a central role in cellular metabolism, because all the nutrients that may play a role "energy" generated in its catabolism acetyl-CoA.In addition to oxidize acetyl-CoA to CO2 and to produce ATP, NADH and FADH2, also receives several intermediaries arising from several catabolic pathways. Oxaloacetate and α-ketoglutarate, for example, are the products of decomposition of aspartate and glutamate. In addition to receiving several intermediates from catabolic processes, it also provides various intermediates for anabolic pathways. Because of this feature (involvement on both anabolic and catabolic processes) the Krebs cycle is an amphibolic process.
Oxaloacetate and α-ketoglutarate are also precursors of amino acids and purine and pyrimidine bases. Oxaloacetate is converted to glucose in gluconeogenesis, succinyl-CoA intermediate in the synthesis of the porphyrin ring of heme groups.
When the Krebs cycle intermediates are diverted to biosynthetic processes, their stock quantity is replenished by anaplerotic reactions. The most important reaction in the liver and kidneys is the reversible carboxylation of pyruvate to oxaloacetate. The enzyme that catalyzes this reaction is pyruvate carboxylase and is stimulated by acetyl-CoA. Another important reaction is the carboxylation of phosphoenolpyruvate to oxaloacetate. The enzyme that catalyzes this reaction is phosphoenolpyruvate and is stimulated by fructose-1,6-bisphosphate. Other important anaplerotic reactions are transaminations, to obtain amino acids (the intermediate of cycle provides the carbon skeleton). The cycle also provides intermediates in the synthesis of glucose (gluconeogenesis) and fatty acids.

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, August 28, 2011

Biochemistry quiz

Here it is a link to a very complete quiz about many different biochemistry concepts.

Saturday, August 27, 2011

Thursday, August 25, 2011

Scientific jokes (5)

What is the most violent chemical element?
It is the Cesium (Cs).

What is the most musical chemical element most musical?
It is the Silicon (Si).

Wednesday, August 24, 2011

Animation on the size of virus

Indeed, the size is a very relative concept. Do you think that a nail is something small? See the following animation...

Monday, August 22, 2011

Music about lipoproteins

One more music of Dr. Kevin Ahern (, this time about lipoproteins, based on the God Rest Ye Merry Gentlemen. Here goes the link to download it...

God Rest Ye Merry Lipoproteins
Instructor Sings
God rest ye merry dieters
With high cholesterol
Your chylomicrons all contain
And move from lymph to capillaries
Where their progress stalls

Everyone sings
Tha-anks lipo protein li-pase,
Protein lipase
O-oh thank you lipo protein li-pase

Instructor Sings
And after their fat goodies
Have been hydrolyzed away
The chylomicron remnants
Go along their merry way
The liver grabs them from the blood
And puts them all away

Everyone sings
Just as we should do with Kenneth Lay,
Kenneth Lay
O-oh just as we should do with Kenneth Lay
(Note - He's the Enron guy)

Instructor Sings
And when the liver gets a message
From the body's cells
It makes up little packages
We call VLDLs
They seem like chylomicrons, but turn
In to something else

Everyone sings
Please don't become the LDLs ,
O-oh please don't become the LDLs

Instructor Sings
For LDLs cause chaos
When their insides oxidize
The macrophages bind to them
And foam cells can arise
You'd better watch your diet
Or your blood flow will downsize

Everyone sings
And that would not be very wise,
Very wise
No-oh that would not be very wise

Instructor Sings
So if you take some lessons from
This little comic bit
Your diet should be healthy
And you should try to stay fit
Eat greens and drink red wine but try
Not to overdo it

Everyone sings
And your heart will never ever quit
Want to quit
No, no your heart will never ever quit

Saturday, August 20, 2011

Krebs cycle (general ideas) - part 1

The Krebs cycle is also called the citric acid cycle or the tricarboxylic acids cycle. It is a catabolic process that occurs in mitochondria, specifically in the mitochondrial matrix (as I will highlight in a next post, there is just a reaction that occurs in association with the inner membrane of mitochondria). In the cycle, cells oxidize acetyl-CoA molecules to CO2, and the energy released is conserved in the form of NADH and FADH2. The Krebs cycle is exclusively aerobic, because although O2 does not participate directly in the cycle, the NAD + and FAD can only be regenerated in the mitochondria by transferring electrons to O2 (in the post on the regulation of the Krebs cycle, which will place soon, it will be possible to see that if NADH accumulates, that is what happens in the absence of O2, the Krebs cycle is inhibited ...).
We oxidize in the Krebs cycle many moles of acetyl-CoA per day. The oxidants, NAD+ and FAD, are reduced to NADH and FADH2. In the cell there are only a few micromoles of NAD + and FAD and within the mitochondria (where the cycle occurs) the regeneration of NAD+ and FAD depends on the respiratory chain, so the Krebs cycle does not occur under anaerobic conditions. The Krebs cycle is like a "mill" where the "grain" (the substrate) is the acetyl group of acetyl-CoA and the "flour" (products) are CO2 and electrons (NADH and FADH2), the "millstone" are the enzymes and intermediate compounds.
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, August 18, 2011

Biochemical curiosities (2)

1. If you put a steak in a bowl with Coca-Cola, it will disappear within two days.
2. To remove rust spots from chrome bumpers of old cars, the ideal is to rub them with a piece of
crumpled aluminum foil dipped in Coca-Cola.
3. Coca-Cola is a great plunger of pipes because dissolves fat.

As you can seeCoca-Cola is much more than a drink ... :)

Wednesday, August 17, 2011

Tuesday, August 16, 2011

Sunday, August 14, 2011

Music about glycolysis (2)

Dr. Ahern ( has based on the song A Few of My Favorite Things to dedicate a music to glycolysis. Here it is the link for the download.

Instructor sings
Aldehyde sugars are always aldoses and
If there's a ketone we call them ketoses
Some will form structures in circular rings
Saccharides do some incredible things

Onto a glucose we add a 'P' to it
ATP energy ought to renew it
Quick rearranging creates F6P
Without requiring input energy

Everyone Sings
At a high rate
Add a phosphate
With PFK
F1,6BP is made up this way
So we can run and play

Instructor sings
Aldolase breaks it and then it releases
DHAP and a few G3Pieces
These both turn in to 1,3 BPG
Adding electrons onto NAD

Phosphate plus ADP makes ATP
While giving cells what they need - en-er-gy
Making triphosphate's a situa-shun
Of substrate level phosphoryla-shun

Lose a water
PEP gets a high energy state
Just to make py-ru-vate

Instructor sings
So all the glucose gets broken and bent
If there's no oxygen cells must ferment
Pyruvate / lactate our cells hit the wall
Some lucky yeast get to make ethanol

This is the end of your glucose's song
Unless you goof up and get it all wrong
Break it, don't make it to yield ATP
You'll save your cells from fu-til-i-ty

Everyone Sings

The Sound of Glucose

Saturday, August 13, 2011

Scientific jokes (4)

What is the acid which has a reversible and cyclic ionization?
It is the periodic acid.

Wednesday, August 10, 2011

Oxidation of pyruvate

Under aerobic conditions, most eukaryotic cells and various bacteria oxidize the pyruvate, produced in glycolysis, to CO2 and H2O, instead of reducing it to lactate or ethanol.
Production of acetyl-CoA from pyruvateThe molecules of acetyl-CoA are the form in which the Krebs cycle accepts most of its fuel. Pyruvate is oxidized to acetyl-CoA and CO2 by an enzyme complex (3 enzymes) called pyruvate dehydrogenase complex. This complex is located in the mitochondria (eukaryotes) or cytosol (prokaryotes).
The oxidation of pyruvate to acetyl-CoA is an example of an irreversible oxidative decarboxylation. The irreversibility of the reaction was demonstrated by proving that when radiolabelled CO2 was used, pyruvate  with radioactive carbon was not be obtained.
In addition to acetyl-CoA and CO2, this reaction produces a molecule of NADH from NAD+.The pyruvate dehydrogenase complex requires the action of five cofactors: thiamine pyrophosphate (TPP), flavin adenine dinucleotide (FAD), coenzyme A (CoA), nicotinamide adenine dinucleotide (NAD +) and lipoate. 4 necessary vitamins in human nutrition are vital components of this system: thiamine (for TPP), riboflavin (for FAD), niacin (to NAD) and pantothenate (for CoA).

The enzymes that compose the pyruvate dehydrogenase complex are pyruvate dehydrogenase, and dihydrolipoyl transacetilase dihydrolipoyl dehydrogenase. Each of these enzymes is present in multiple copies.
Animals deprived of thiamine are usually unable to oxidize pyruvate. This has implications especially in the brain that usually gets all its energy from glucose oxidation, a process that necessarily involves the oxidation of pyruvate. Beriberi is a vitamin deficiency caused by thiamine deficiency. It is characterized by a loss of neuronal function. This disease is more common in populations that eat predominantly white rice (polished), because it is in rice husks that most of its thiamine is found.
Mutations in genes that encode subunits of this enzyme complex, as well as a diet deficient in thiamine can have serious consequences.

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

Tuesday, August 9, 2011

Video about the transport of fatty acids to the mitochondria

Here it is a video about the transport of fatty acids to the mitochondria, where they are degraded.

Monday, August 8, 2011

Animation about feedback inhibition

Here it is the link to download a flash animation about feedback inhibition, also called negative feedback or retro-inhibition.

Sunday, August 7, 2011

Band with a biochemical name...

Today I have decided to post something different... a video of a band called Ketone Bodies! :)

Saturday, August 6, 2011

Scientific jokes (3)

What is the better informed chemical element?
It is the francium because it is next to the radio.

Wednesday, August 3, 2011

Music about Biochemistry

This Dr. Kevin Ahern's music ( is dedicated to all who have studied or are studying biochemistry. It is an adaptation of the famous American Pie. Here is the link to download the mp3 file.

Biochemistry Pie

A long nine weeks ago
I can still remember
How the lectures sometimes made me smile
I pushed myself to study lots
So I could fill my head with thoughts
And then I'd find the effort all worthwhile

But mid-term one, it left me jaded
I worried as exams were graded
Sad news came from Kevin
The average - forty seven

It was so bad I went in shock
I couldn't stand to hear the talk
Of Henderson and Hasselbalch
And bi-o-che-mis-try

So why why biochemistry why
Does percent misrepresent that
My attention is high?
And all the students have a rallying cry
Singin' I will be a studious guy
I will be a studious guy

Did you draw an alanine?
And can you titrate a histidine?
If you know its p-K-a
Now do you believe you'll have it made
If you can pull a decent grade
And can recitation lead me to an 'A'?

Well we learned that protein structure is
A bunch of pleats and helixes
True beauty to behold
Man I dig how proteins fold!

There are seniors in pre-pharmacy
Learning all that chromatography
Gel filtration / HPLC
For bi-o-che-mis-try

I started Singin'
Why why biochemistry why
Must performance be enormous for
My grade to be high?
And all the students have a rallying cry
Singin' I will be a studious guy
I will be a studious guy

Now for ten weeks we've been crammin' in
The fact that nuc-le-i have spin
But that's not all there is to see
There are six enzyme classes from EC
A cat-a-lytic triad three
And a voice that whispers Delta G

Oh, with enzymes there are lots of facts
Like low Kms and high Vmax
Some zymogens break down
If trypsin is around
And while Kevin lectured Milam Hall
His camera captured movies small
Sometimes they had no sound at all
In bi-o-che-mis-try

We were singing
Why why biochemistry why
Should I lament my last percent
If my incentive was high?
And all the students have a rallying cry
Singin' I will be a studious guy
I will be a studious guy

R state, T state metabolic soul mates
Protein forms that we appreciate
ATCase binding siiii----iiiites
They grab a C-T-P upright
The enzyme gets itself uptight
With aspartate on the sidelines out of sight

Then the stage was set for ex-am two
And some of us were feeling blue
I almost lost my nerve
Whoa, 'til I moved up on the curve
'cause my memory to me revealed
The answers that had been concealed
As if the key had been unsealed
For bi-o-che-mis-try

I'm always Singin'
Why why biochemistry why
Must a student be so prudent
Just to qua-a-lify?
And all the students have a rallying cry
Singin' I will be a studious guy
I will be a studious guy

(two stanzas skipped here)

We all pulled down the MP
And memorized the older keys
Then I just smiled and carried on
I went down to the class web site
To download ev-e-ry highlight
But the server said the pages were all gone

And in their rooms, the students stayed
The chemists crammed and the pre-meds prayed
There was no indecision
The end was in our vision
And the section that had made me fret
The questions for the problem set
I nailed them all without a sweat
In bi-o-che-mis-try

And I was singin'
Bye bye biochemistry bye
You can debit all my credit
'Cause my grade is so high
And all the students have a rallying cry
Singin' there'll be a party tonight
There'll be a party tonight

And I was singin'
Bye bye biochemistry bye
You can debit all my credit
'Cause my grade is so high
And all the students have a rallying cry
Singin' there'll be a party tonight

Tuesday, August 2, 2011

Monday, August 1, 2011

Alcoholic fermentation

The first reaction requires the presence of Mg2 + and the second reaction regenerates NAD+ from NADH (one molecule per molecule of pyruvate). As I mentioned in the post of lactic fermentation, this is the aim of fermentation, the regeneration of NAD+ so that glycolysis can continue to occur.
The pyruvate decarboxylase enzyme is normally present in yeast used in the manufacture of beverages and bread. The gasification of champagne and other alcoholic beverages, as well as the bubbles present in the bread crumbs are originated by the decarboxylation of pyruvate.
The alcoholic fermentation does not occur in our bodies. Bear in mind that when I say this, I am not saying that we can not metabolize ethanol, as this is an independent process of fermentation. What I am saying is that it is impossible for our body to convert glucose into ethanol.

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