Monday, December 23, 2013

Merry Christmas!


Sunday, November 24, 2013

Famous quote (24)

Seven Deadly Sins:
1. Wealth without work
2. Pleasure without conscience
3. Science without humanity
4. Knowledge without character
5. Politics without principle
6. Commerce without morality
7. Worship without sacrifice.
(Mahatma Gandhi)
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Thursday, October 24, 2013

Electronegativity



In order to understand the concept of electronegativity, it is necessary to take into account the following idea... The molecules are highly dynamic, and electrons are in constant motion around the atoms, representing the so-called "electron cloud". The movement of electrons around an atoms is directly conditioned by its characteristics. That is, if an atom has a greater ability to take over the electronic cloud, the electrons will be located predominantly on him. Electronegativity concerns exactly with this capability. Therefore, the more electronegative an atom is, the greater the portion of the electron cloud on it. Consequently, the more electronegative atoms tend to have negative partial charges, because at every moment there will be more electrons on them than on other atoms .

It is this asymmetry that is created in the distribution of the electron cloud that causes the molecules to become polar. Thus, in general , the presence of different atoms with different electronegativities in a molecule causes the molecule becomes polar, or at least the region where this happens to become polar .
In the case of biochemistry , since carbon and hydrogen have similar electronegativities, the regions of the molecules that contain only these two atoms are nonpolar , while the presence of oxygen, nitrogen , fluorine , phosphorus , etc., tend to render that region polar .

Wednesday, October 16, 2013

Music about the study of biochemistry (3)

What do you think about the idea to listen Frank Sinatra singing about biochemistry? Well, it is not the real Frank Sinatra that sings, but Dr. Ahern has adapted the famous song My Way and made another music about the study of biochemistry. It is for sure one of my favourite songs of Dr. Ahern! :)

Download the music here

My 'A'

And now, the course is done
Except for all that final testing
Dear friends, let’s have some fun
There surely won’t be much protesting

We’ve had a busy term
Addressing all the content swiftly
And so I sit and squirm
B-B three fif-ty

Exams, there’s been a few
Our averages were somewhat lower
The grades are all askew
I wish that Ahern would go slower

I studied hard each time
And even though my grades were iffy
Oh no, I did not whine
B-B three fif-ty

Yes it was tough
You knew it too
I memorized
My knowledge grew
And through it all
I did not frown
I thought it up
And wrote it down
I fought the fight
I hope it’s right
B-B three fif-ty

I laughed, I cried, I swore
Just as I did here on the first day
But since, the term is o’er
Let’s all go out for thirsty Thursday

I guess I have to face
The fact that I am not a swifty
But oh, I need to ace
B-B three fif-ty

The end arrives
Our grades are out
As I log in
To my account
I say some things
I truly feel
I hope I don’t
Have to appeal
There’s no dismay
I made my ‘A’

B-B three fif-ty
.

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.

Tuesday, June 25, 2013

Music about to study biochemistry

As it seems obvious, Dr. Ahern made a music about the exams of Biochemistry, and about the hard work that is to study for them. He got inspiration in the song The Yellow Rose of Texas. And by the way... for all that are at this moment studying Biochemistry... Good luck! ;)

Download the music here

The Mellow Woes of Testing

The term is almost at an end
Ten weeks since it began
I worried how my grade was ‘cause
I did not have a plan
The first exam went not so well
I got a fifty three
‘Twas just about the average score
In Biochemistry

I buckled down the second time
Did not sow my wild oats
I downloaded the videos
And took a ton of notes
I learned about free energy
And Delta Gee Naught Prime
My score increased by seven points
A C-plus grade was mine

I sang the songs, I memorized
I played the mp3s
I learned the citrate cycle
And I counted ATPs
I had electron transport down
And all of complex vee
I gasped when I saw my exam
It was a ninety three

So heading to the final stretch
I crammed my memory
And came to class on sunny days
For quizzing comedy
I packed a card with info and
My brain almost burned out
‘Twas much to my delight I
Got the ‘A’ I’d dreamed about

So here’s the moral of the song
It doesn’t pay to stew
If scores are not quite what you want
And you don’t have a clue
The answers get into your head
When you know what to do
Watch videos, read highlights and
Review, review, review
.

Tuesday, April 30, 2013

Famous quote (21)

“Science without religion is lame, religion without science is blind.” - Albert Einstein

Sunday, April 21, 2013

Cellular respiration - an overview

Today I will dedicate a post to some general considerations about cellular respiration. This process occurs in the mitochondria More precisely, in the mitochondrial inner membrane. To put it in a simple way, it is an oxidation-reduction process that involves the transport of electrons, from NADH and FADH2 to oxygen. In fact, it is mainly because of this process that we need to breathe oxygen. During the process, the O2 molecules are reduced to H2O, which is the main reason for us to breathe out water vapor. Thus, in fact most of our pulmonary respiration is not more than a consequence of our cellular respiration!
But back to the cellular respiration process... The electrons are received and transported over four complexes, designated I, II, III and IV. These complexes are not more than sets of electron transport proteins, many of which with cofactors specialized in the transport of electrons, such as iron-sulfur centers, heme and flavoproteins. A key element in this process is the presence of transition metals (iron and copper, for example) because, due to the fact that they can oscillate between two oxidation states, they are able to temporarily capture or donate electrons.
For electrons to pass from complex I or II to complex III, there is a lipophilic molecule that will carry them, which is called ubiquinone. For the electrons to move from complex III to IV there is an intermembrane space protein that carries them, designated cytochrome c.
As the electrons move along the complexes, in some of them ther will be a coupled process, which is the proton (H +) pumping from the matrix to the intermembranar space. That means, it will be created a H+ gradient, designated electromotive force , which will accumulate enough energy to drive ATP synthesis via a process called oxidative phosphorylation. The intervening in this process is the mitochondrial ATP synthase.
In future posts I will devote some attention to a detailled explanation of how cellular respiration works...

Wednesday, April 17, 2013

Music about hormones (epinephrine)


Simon and Garfunkel have immortalized many songs, among which is the famous "The sound of silence". Dr. Ahern adapted this beautiful music and created a song about the hormone apinephrine. You can download it in www.davincipress.com/metabmelodies.html.
 
The Tao of Hormones

Biochemistry my friend
It's time to study you again
Mechanisms that I need to know
Are the things that really stress me so
"Get these pathways planted firmly in your head,"
Ahern said
Let's start with ep-inephrine

Membrane proteins are well known
Changed on binding this hormone
Rearranging selves without protest
Stimulating a G alpha S
To go open up and displace its GDP
With GTP
Because of ep-inephrine

Active G then moves a ways
Stimulating ad cyclase
So a bunch of cyclic AMP
Binds to kinase and then sets it free
All the active sites of the kinases await
Triphosphate
Because of ep-inephrine

Muscles are affected then
Breaking down their glycogen
So they get a wad of energy
In the form of lots of G-1-P
And the synthases that could make a glucose chain
All refrain
Because of ep-inephrine

Now I've reached the pathway end
Going from adrenalin
Here's a trick I learned to get it right
Linking memory to flight or fright
So the mechanism that's the source of anxious fears
Reappears
When I make ep-inephrine

Saturday, April 13, 2013

Famous quote (20)

The saddest aspect of life right now is that science gathers knowledge faster than society gathers wisdom. (Isaac Asimov)

Tuesday, April 2, 2013

Regulation of the Krebs cycle

The Krebs cycle plays a central role in our metabolism. In all the classes I give about metabolism, the Krebs cycle is present...
As I mentioned in previous posts, this process is composed by 8 steps, 3 of which are catalyzed by regulatory enzymes. These enzymes are citrate synthase (1st reaction), isocitrate dehydrogenase (3rd Reaction) and alpha-ketoglutarate dehydrogenase (4th reaction).
In this post I will talk a little about the main activators and inhibitors of each. As you will see, there are many modulators that are common to more than one enzyme, which makes life easier for those who have to study this metabolic pathway. :)

Citrate synthase:
Inhibitors
Succinyl-CoA - it is an intermediate of Krebs cycle. More specifically, it is the 4th intermediate of Krebs cycle, that means, it is formed in a reaction after the reaction that we are considering. So if we have an accumulation of intermediates formed in further reactions, it makes sense that these may inhibit the initial reactions of the pathway in question, in this case the first.
Citrate - it is the product of the reaction, so it makes sense that it might inhibit its own synthesis.
ATP - the Krebs cycle is a catabolic pathway, ie, its main goal is to produce energy (ATP). If the cell already has energy, the process is inhibited.
NADH - The reasoning is equivalent to that made for the ATP. That is, the NADH has a high energy potential, since in cellular respiration it can lead to the production of ATP, therefore it is logical that NADH functions as an inhibitor of Krebs cycle.
Long Chain fatty acid-CoA - it is not completely understood the inhibitory role of the long chain fatty acids in the Krebs cycle, but it is believed that this property is related to the fact that they behave as detergents because they are amphipathic compounds consisting of one polar part (carboxylic group) and one part apolar part (hydrocarbon chain). Oleic acid (18 carbons and one double bond at carbon 9) appears to be the major fatty acid inhibitor of citate synthase.

Activators
ADP - ADP signals an energy deficit in the cell because it is produced when ATP is spent for energy. So it makes sense that it activates the Krebs cycle, because the main objective of this pathway is the production of energy.

Isocitrate dehydrogenase:

Inhibitors
Succinyl-CoA - the reasoning that was made for the citrate synthase applies in this situation.
ATP - the reasoning that was made for the citrate synthase applies in this situation.
NADH - the reasoning that was made for the citrate synthase applies in this situation.

Activators
ADP - the reasoning that was made for the citrate synthase applies in this situation.
Ca2 + (muscle) - as I mentioned in a previous post, about the regulation of pyruvate dehydrogenase complex, Ca2+ is an intracellular messenger whose concentration increases during muscle contraction. Therefore, in this context contracting cells will require energy, so catabolic processes and, in particular, the Krebs cycle, is activated.

Alpha-ketoglutarate dehydrogenase:
 Inhibitors
Succinyl-CoA - it is the product of the reaction so, it makes sense that this molecule may inhibit its own synthesis.
ATP - the reasoning that was made for the citrate synthase applies in this situation.
NADH - the reasoning that was made for the citrate synthase applies in this situation.

Activators
Ca2 + (muscle) - the reasoning that was made for isocitrate dehydrogenase applies in this situation.