Metabolic map on the synthesis of leucine

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?"

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 ...

Game about carbohydrates

Here it is a link to a quizz about carbohydrates:

http://www.funtrivia.com/playquiz/quiz2768101fb0fb8.html

Tattoos - atom (1)

Animation on mitosis and meiosis

One more animation that compares mitosis and meiosis...

http://www.mediafire.com/?lspx4uu9sazcdv7

Cartoon about gene therapy

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

Metabolic map on the synthesis of lysine

Video about the Krebs cycle (3)

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

Animation on mitosis and meiosis

Here it goes a link to download an animation that compares mitosis and meiosis.

http://www.mediafire.com/?61b76085w0gg9s9

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

Biochemical curiosities (4)

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

Game about chemistry

Here it goes a link to crosswords about chemical issues...

Have fun!

http://www.creative-chemistry.org.uk/funstuff/xword/index.htm

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 ATPmakes double H2O

Fermentation!

Tattoo - Microscope

Video about the Krebs cycle (2)

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

Scientific jokes (7)

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

Metabolic map on the synthesis of valine

Animation about the PCR

Today I leave here a link to download a very nice animation about the PCR.

http://www.mediafire.com/?t0905c865va068x

Cartoon about transgenics

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

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

Biochemical curiosities (3)

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

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)

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

Tatuagens - DNA (5)

Animation on the degradation of glucose

Here it is a link to doawnload an animation about the degradation of glucose.

http://www.mediafire.com/?47pugrpueq4igby

Cartoon about cloning (4)

Video about the respiratory chain

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