Breathing in greater depth than you ever cared to know

What you may know

Breathing is controlled by pH and the following reaction

Also, hemoglobin (Hb) is the oxygen transporting protein carried by red blood cells (RBCs).
Fun fact: RBCs eject their nucleus as part of their normal life cycle and become little more than sacks of Hb. :D

Onto what you likely don't know:

Hemoglobin

is made of four protein chains, two alpha and two beta chains. Each chain holds one heme, giving each Hb a total of four hemes.

What is a heme, you ask? A heme is a large, planar, geometric molecule that stabilizes one iron(II) atom. This is where oxygen binds to Hb.

Histidine is an amino acid that plays a HUGE role in the way Hb is able to bind oxygen. The histidine in Hb alpha or beta is associated with the iron(II) atom in a heme due to an ionic intermolecular force using the highlighted hydrogen projecting from HIS' sexy, sexy face.

When oxygen is not bound to the iron(II), the atom hangs below the plane of the heme. This is called the relaxed (R) form.

When oxygen binds to the iron(II) it pulls the atom up and into the plane of the heme. This tugs on the histidine and changes the shape of the entire chain (subunit). We call this the taut (T) form of a chain. If one chain (alpha or beta) is in the T conformation it also tugs on the adjacent chains, making it slightly easier for the next iron(II) to bind with another oxygen molecule.

Super cool, right? This is called cooperation. Go figure.

 

Haldane Effect

When the concentration of carbon dioxide in the blood is high (in venous blood) it is easier for the carbon dioxide to bind to its own binding site on the Hb subunit. When carbon dioxide binds to Hb it causes an opposing structural change that helps to release oxygen!

When the concentration of carbon dioxide is low, like in the lung capillaries, oxygen binds again and causes a structural change that releases carbon dioxide. Neat, right?

Wait! There is more!

 

At high altitudes

Hb must bind oxygen especially well because tehr eis less of it available. One of the ways that the bodies of people who are acclimated to the altitude ope with how "grabby" the Hb is with oxygen is to increase levels of a chemical called 2, 3 bisphosphoglycerate (2, 3-BPG). This is anotehr allosteric ligand, similar to the way carbon dioxide works. In venous blood, 2, 3-BPG will "muscle" into the very center of tan Hb protein, among the four subunits and release the oxygen! When it reaches the lungs it dissociates from the Hb and allows oxygen to bind again!

 

 

Fetal Hb

binds oxygen more tightly so that it can take oxygen from the mother's blood and transport it to the fetus.

 

Myoglobin

Is a singular subunit (one alpha, one beta) that is used to store, but not transport oxygen. It doesn't form sites for allosteric binding to release the oxygen. It is found most in muscle tissue!

 

Bringin' it together

When carbonic anhydrase (best dive around) catalyzes the reaction laid out at the beginning of this section, blood pH increases and stimulates chemoreceptors in the carotid and aortic blood vessels as well as receptors in the medulla oblongata. This stimulates the phrenic and thoracic nerves and contracts the diaphragm.

 

 

SUPER COOL! YEAH! :D

The Tale of Carbonic Anhydrase

The Tale of Carbonic Anhydrase

In a divey bar(spelling says it all) where we set out scene, we find Sodium working the corner. For Sodium is the gigolo of the cations and is forever going in and out of random cells.

Carbon Dioxide is a well renowned uni-cyclist, I am sure all are aware.

Now, H2O and CO2 walk into a bar. Heh...heh...heh...

H2O is getting jealous because she has crazy eyes for CO2's bad boy uni-cycle skilzzzzzz. Histidine (sigh), the bouncer, is relegated to restraining H2O to keep the peace.

H2O is, however, a whiley little lass. With little effort on her own part, she escapes! In the struggle Histidine accidentally broke off one of H2O's proton pigtails. OH NO!

Poor Histidine has no idea what to do with the casualty of H2O's war of love.

Most people do not know this bit of adventure I am about to share with you. Even weird chemists are unaware. When H2O loses a proton pigtail, bitch gets scrappy. It is kind of like going Super Saiyan but with less hair product.

H2O becomes so scrappy, in fact, that she gets a whole new moniker:

Hydroxide (A.K.A Hyd-Roxie)!

If we are being honest, and what else would be be, Hyd-Roxie is trashy, too. She will make out with anything positive. If nothing positive is around, she will make something!

Like so:

In the carnage, CO2 loses a leg and is stuck to crazy, scrappy Hyd-Roxie! Poor guy!

Histidine, still left with the proton pigtail finds a happy home for the appendage by wedging it into the wheel of the once great uni-cyclist, CO2.

The Dating Game, Amino Acid Edition

The Dating Game, Amino Acid Edition

A quick preface for this week’s post: A gentleman caller of mine asked me a really great question early in the wee beginnings of conversation. It surprised me a little because I had never thought of it. The question was, “what is your favorite amino acid?” It was absurd to me that I have never considered this question before. The answer, however, was clear.

 Please note, there will be a short story featuring my one true residue shortly.

 The big question, how do you decide? There are all of these friendly protein building blocks (and these are just the super common ones):

 

We will start out with the hydrophobes.

These fellas are all auto-ruled out in my book any –phobes are a little sketch if you ask me.

 Anyway, in the list we have Tryptophan (you may know this fella from recollections like, Thanksgiving, Christmas, any holiday in which you eat a bunch of crap and feel bad about yourself)

 

Disclaimer: The tryptophan/turkey assertion

 is not actually founded in science.

Please refrain from judging the reference.

 

There is Tyrosine the tyrant and twin sister, Phenyl alanine. Pictured also is Methionine, the friend who likes to start shit (which would be funny if you know anything about start codons).

Next we have Leucine and Isoleucine. Isoleucine being the older, more put-together sibling.

 

To round out this group, we have the basic bitches, Valine and Alanine.

 

Next group to immediately omit, The Polars.

From hot to cold, super reactive. Polars are certainly not long-term relationship material.

We have the not-so-serene, Serine and Threonine who is presently going through an identity crisis (three or nine?).

 

Rumor has it that Asparagine is the heir of a large asparagus fortune.

 

To round this group out we have a great energy source in a pinch. He is the one, the only Glutamine.

 

Next we have the Special Cases.

These are the artists, the beautiful, torrid, magnificent creatures one simply cannot tie down.

Cystine and Selenocysteine, are well known for forming the strongest bonds among those similar enough to be graced by their presence. Their inevitable split is tragic, dramatic, passionate.

Glycine, the most basic of the bitches, has nothing going for him. He is incapable of forming strong bonds or participating in really cool structures. He is void of any interesting tidbits. Seriously. Nothing. How does Glycine even belong in this group?

 

Proline always feels a little inbred; he is sort of like the banjo kid from Deliverance. Eugh.

I present to you the Charged Amino Acids.

Onto the best proteins have to offer, the movers and the shakers, the doers.  They are electric. Cue ‘80s music.

 

 

Which of these fine bachelors have stolen my heart?

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Despite their drive and Ability to get shit done (think NMDA receptors and ions moving across a cell membrane or MSG and the fall of the Asian food empire), Aspartic Acid and Glutamic Acid are a bit too negative for my taste. I need someone with drive, ambition, stability.

 

A girl like myself needs someone who is well rounded, has hobbies, has dreams and is down to earth. Residues like Lysine and Arginine seem to be headed strongly in one direction and have a hard time wrapping their head around the big picture.

 

 

So I guess that settles it. The one remaining residue, brilliant, maker of change, handsome, a great breadth of experience has to be none other than Histidine.

 

Sophocles in Short- Oedipus the King

Sophocles in Short

 

Oedipus the King, also known as Oedipius Rex is the first of three Theban plays which detail the initial instance that cursed Thebes and the fallout thereafter. It is a mess, as all Greek tragedy is.

Anyway, here goes:

 

 

Enter Oedipus, we will call him “Oeddy.”

 

“All you silly geese,

What is it you’re dong

Strewn about my step?”

 

 

 

 

 

 

In the play the speak of plague is ambiguious—is it the people, themselves, sick with some disease? Is the city plagued by barren fields and misfortune? I like to assume it is disease and that Oeddy is exposing himself because he is a headstrong sillypants.

 

“From the sphinx and her

Tribute you saved us. We rose,

Do not let us fall.”

 

 

 

“Just kidding, I know

Illness brought you here. I sent

Creon already.”

Enter Creon. Note his big shoes.

 

 

“The oracle said

Laius must be avenged to

save your lovely Thebes!

-------------------------------

We’re screwed Oeddy!

Our previous king was killed;

No one knows by whom.”

 

So, Oeddy pledges to avenge Laius (king previous to Oeddy) despite there being zero chance in hell of finding the killers. As a starting point, Oeddy summons (he does quite a bit of this summoning thing. Perhaps he is working toward a level in wizard?) a prophet.

 

“… … … … …

… … … … … … …

… … … … …”

 

 

 

 

Oeddy gets pissed when the prophet wont tell him anything. Words are exchanged and Oeddy decides tat Creon (shoes) paid the prophet to suit his own interests. More arguments and the prophet leaves (with an angry hobble) mumbling something:

 

 

“The murderer is 

Native to Thebes. Father and

Brother to his kids.”

Creon comes to face Oeddy’s accusations. Oeddy is about to shank a bitch (Creon) when Jocasta (bad '90s JLo ponytail), Oeddy’s wife shows up.

 

“Pish, posh! Oracles

Are full of shit! Laius was

To die by his son

------------------------

E’ryone knows he

Was killed by highwaymen, right?

Right! I am pretty sure!”
 

Oeddy forces more info from her because he is uneasy for some reason (not sure why). To rest his suspicions he summons the last remaining witness and admits the following to Jocasta:

“A long time ago

Some lush in Corinth said I

Had been adopted.”

---------------------

An oracle said

I’d murder my father and

Sleep with my mother!

-------------------------------

So I left Corinth.

I came to the same crossroads

Where Laius was killed.

-----------------------------

Some dicks drove me off

The road. I was pissed! So, out

I got and killed them!

----------------------------

One of ‘em looked a

Whole lot like your despcription

Of Laius. I’m concerned.”

Rumor had it that Laius was killed by a slough of men, not just one. So, everyone writes it off as no big deal and moves on with their lives. Oeddy was ‘rull’ bothered by it. He immediately summons a ton of people to prove that the oracle was wrong. Seriously though, how many summon spells can one dude have?

 

“Your dad is dead, dude.

No big deal. Hope you didn’t like
Him much because, well…”

 

The messenger is sporting a cowboy hat and lasso, both are entirely appropriate in ancient Greece. Promise. Our cowboy friend isn’t the only cool breeze arriving from Corinth. Soon after, a letter arrives with some more telling information for Oeddy’s present situation:

 

 

 
Dear Oeddy, you scamp!

Polybus, yer dad.

Totally took you in when

You were found, exposed

Signed, sincerely, or something,

Telling you yer fucked

(insert “your mom” here)

By “exposed” I mean, “exposed to the elements.”

            Jocasta puts the pieces together and begs Oeddy to stop asking questions, operating on the idea that it is easier to ignore a huge problem that everyone already knows about than it is to accept it. That is a legitimate response, right? Denial? When Oeddy refuses she runs away, like a poorly written little girl, into the palace.

            Oeddy finally gets ahold of the shepherd wo saw Laius’ slaughter. He happened to also be the guy who brought Polybus a baby instead of killing it by the command of the baby’s father. Great family dynamic.

 

 

“So…that baby

I gave Polybus was the

Son of King Laius.

------------------------

Hope you don’t care. I

Mean, killin babies is bad.

Kinda worse than incest.”

 

“Why, Gods, why? I will

Curse myself then curse fate and

I’ll stomp off this stage!”

 

So he does.

 

 A servant comes up to explain what happened to the crowd.

 

 

 

“Turns out that Oeddy

Is incestuous. Huh. Maybe

Watch out for that.”

 

 

 

 

 

            We now find that Jocasta has hung herself. Oeddy, distraught by the death of his wife and knowledge that she is also his mother, commands that someone bring him a sword. When his staff, refuse he mills (by “mills” I mean “rages,” full-on, barbarian style rage) about the palace. He comes to Jocasta’s still hanging corpse, takes her down, pulls the pins that bind her clothing together from her person because now is the very best time to get naked. He proceeds to stab his own eyes out.

            Oeddy begs to be exiled due to his own shame and despair. Creon is unsure and consults the oracles. While he waits, Oeddy is comforted by his two daughter/sisters, Ismene and Antigone.

“I lament that I

Released my man juices in

Our mom and you’re here.

----------------------------------

Boo hoo hoo, boo hoo

Boo hoo! We are cursed, my dear

Sisterly-daughters!”

Oeddy asks Creon (despite having nearly killed him a few short scenes back) to care for his sister/daughters while he is in exile. The moral of Oedipus the King, as we find in the final chorus is,

“No man should be considered fortunate until he is dead.”

A Protein with a Propensity for Romance

Here is a little something short and simple to kick things off! Hope you enjoy it!

Albumin is a carrier protein that comprises roughly 50-60% of the protein in plasma.

Its function is to carry hydrophobic things (certain cations, hormones, fatty acids, drugs) through the blood by “hiding” them in a little cocoon that is hydrophobic (repel or “fear” water) on the inside and hydrophilic (an affinity for water) on the outside. This way, the hydrophobic things can be carried through the blood to places they are needed throughout the body.

General info aside, the kitschy thing about albumin is that it is heart-shaped! Moreover, the protein is held together by six cystine bonds. Cystine refers to two cysteine amino acids bound by an ultra-strong disulfur bridge. The disulfur bridge in cystine is the strongest intermolecular interaction involved in shaping a protein (beyond a long chain of amino acids). It is actually a covalent bond between two parts of the same amino acid chain or two separate chains of amino acids. Now, cystine is not uncommon in proteins, not at all. What makes it unique in albumin is the number of cystine. Five to six cystine exist within this one,  small to average-sized protein.

In short, albumin is an abundant, heart-shaped protein that bear-hugs molecules that are shy or awkward in the blood environment (I imagine the awkward person trying to –be- a lamp shade at a house party) and protects them on their journey in the blood. So sweet!