Dani’s Cerebrum

Simple complexity.
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Amino Acid Tales

with apologies to G. ChaucerRandom APS Picture


When fall hath come, and days grow short and cool, 
Then eager students hasten back to school; 
And freshmen who would gladly doctors be 
Begin to study biochemistry, 
And memorize a host of useless structures 
Because they know that pleases their instructors,
But also so that they their boards might pass, 
And go to practice medicine at last; 
For they would fain restore the sick to health, 
And also would win fame, respect, and wealth. 
As first to teach in biochemistry, 
The section treating structures falls to me. 
With the amino acids we begin, 
The building blocks of muscle, enzymes, skin.


For R-group glycine has an H, that’s all. 
It boasts no isomers and is so small; 
But when in protein structure space is tight, 
Then glycine’s chosen because it is slight; 
And this, dear students, is the reason why 
In collagen the glycine content’s high.


Draw glycine, then with pen a methyl add, 
And alanine will be there on your pad. 
The methyl group, apolar as you know, 
Gives alanine a hydrophobic glow. 
If alanine you now should modify 
And to its methyl various groups apply, 
All the amino acids we will learn 
Can quickly be produced, each in its turn.


To valine learn, imagine, if you can, 
A structure with the outline of a man. 
He’s hydrophobic from the waist on down, 
And hydrophilic is from waist to crown.

Leucine and Isoleucine

To valine’s leg affix one carbon more, 
And isoleucine joins the growing corps. 
In valine’s trunk instead a C insert, 
And valine then to leucine does convert. 
Their R-groups are like little drops of oil; 
From water they with loathing do recoil. 
At isoleucine look now carefully; 
Two asymmetric carbons you will see.


Five carbon atoms fastened end to end, 
Just look, my students, notice how they bend 
Until, in sooth, the circle is perfected, 
And the last C is to the N connected 
To form a hydrophobic little ring, 
And the amino a substituent bring. 
Amino acid proline’s truly not, 
For an imino group instead it’s got.
Now polypeptide chains coil often round.
In many proteins are such spirals found. 
As alpha helices by scientists known, 
These coils are by H-bonds together sewn. 
But should the chain with proline be corrupted,
Then is the alpha helix interrupted.

Serine and Threonine

To alanine an OH group append, 
And serine’s what you’re left with in the end; 
And if you add a methyl group as well 
Then you have threonine, as chemists tell—
Indeed, a very hydrophilic pair, 
Because of the hydroxyls that they bear,
Check threonine most carefully and you’ll see 
A second center of asymmetry. 
Now serine oft is cleaved within the cell 
To glycine and a smaller piece as well. 
The latter’s then to synthesis remanded 
When a one-carbon fragment is demanded.


To alanine an extra carbon lend, 
And next attach a sulfur to the end, 
Then finally if you methylate the S 
Methionine is what you will possess. 
Examine now the R-group carefully, 
It’s truly hydrophobic, as you’ll see. 
Reactions which in living cells transpire 
Quite often do a methyl group require; 
And usually does the cell such units glean 
From the S-methyl of methionine.


Just add an SH group to alanine;
The compound that is formed is cysteine.
Its SH can a proton liberate,
The pK of this group being close to eight.
But more important, you should realize,
That the sulfhydryl group can oxidize,
And that, thereby, two cysteines are joined 
(For such a pair the name cystine is coined).
If cysteines are linked, it’s surely true,
The peptide chains they’re part of are joined, too.
Thus protein structures, full of folds and kinks,
Are held together by cystine cross-links.

Phenylalanine and Tyrosine

We now consider phenylalanine,
Whose name alone the structure does convene.
And tyrosine, in structure close related, 
Just phenyalalanine hydroxylated. 
When phenyl group has a hydroxyl gained 
Then are its properties substantially changed:
Decreased is its hydrophobicity; 
More strongly it absorbs in the uv. 
And should the pH over ten arise, 
Then does this new hydroxyl ionize. 
In proteins this OH is wont to form 
H-bonds, and these, and others, do transform
A random polypeptide, as a rule, 
To a precisely folded molecule. 
An enzyme found within each living cell 
Performs this same hydroxylation well; 
But should there in this enzyme lie a fault,
Phenylketonuria is the result.


Let alanine an indole function gain,
And from the two arises tryptophan. 
(The indole group, in case you don’t remember, 
Has benzene ring and pyrrole fused together. 
And pyrrole—is it hard remembering?—
Has four carbons and an N joined in a ring.) 
Now indole is a planar residue; 
Aside from this, it’s hydrophobic, too. 
The indole group so strongly resonates 
That it impinging photons captivates —
To an absorption spectrum this gives rise 
Which is presented for you to apprise.

Aspartic and Glutamic Acids

Now aspartate has carbon atoms four; 
And glutamate has these and then one more. 
Carboxyl groups at each extremity 
Make these compounds acidic, you’ll agree. 
Alpha carboxyls have pK’s near two, 
So it may come as a surprise to you, 
That pK values close to four attend 
Carboxyl groups placed at the other end. 
And now about an enzyme I’ll relate 
Which the amino cleaves from glutamate 
To yield ammonia, there inside the cell, 
And alpha ketoglutarate as well. 
A second enzyme then the latter takes,
And from it glutamate regenerates. 
For this amino groups are now required,
And from amino acids they’re acquired. 
Thus using glutamate, as you can see, 
The cell has this broad capability: 
Diverse amino acids can it take, 
And every one of them deaminate. 
And residues which then are left behind, 
To metabolic pathways are consigned.

Asparagine and Glutamine

Aspartate’s amide is asparagine, 
And glutamate’s is known as glutamine 
. The two are neutral—amides have no charge, 
But polar still with dipole moments large.


If alanine’s two carbons more extended,
And a guanido’s to the end appended, 
A compound’s formed which arginine we call—
Most base amino acid of them all; 
For the guanido group has pK high; 
At nearly 12.5 it’s known to lie. 
(Now the guanido group, my freshmen friends, 
Is but a C surrounded by three N’s.) 
A liver enzyme, arginase by name, 
Does act on arginine and cleaves the same 
By hydrolysis, for water comes between, 
To yield urea and also ornithine. 
The latter converts back to arginine 
By a complex, but key, reaction scheme 
In which excess ammonia is consumed, 
Except for this the cell were surely doomed. 
Thus arginine—you should remember this— 
Is source of the urea in your piss.


This unbranched basic molecule is lysine. 
It has four carbons more than are in glycine,
And an amino group on its tail end 
Which has a pK value over ten.


The residue which histidine we call 
Is alanine with an imidazole. 
The latter is—now listen closely, please—
A pentagon with two N’s and three C’s. 
To histidine a proton can affix; 
Its R-group has a pK close to six 
Dear students, this is, as you know full well. 
Not far from the pH within the cell, 
And since the pK of a group may change, 
Influenced by other groups lying at close range,
So histidine within a protein structure, 
Shows sometimes one ion form, sometimes the other.


With the amino acids we are through. 
The learning of them now is up to you. 
Do not despair, but work industriously; 
And you will have them mastered presently; 
And think, when it is late and you grow bored,
Of the M.D. that will be your reward.

(via themedicalchronicles)


Informal infographic depicting evolution 

(via fyeahbiologymemes)

Robin Williams isn’t dead. He’s just waiting in the jungle until someone rolls a 5 or 8.

(via kristwrrrryyn)


The Evolution Of The Batman Logo till 2012. Check out all about the Batman’s 75 Anniversary on the corresponding DC Comics page.

(Image via Imgur)


Vegans, please do not do this. Cats are not omnivores like us, they are obligate carnivores and cannot survive on a meat-free diet.
Edit: a lot of people commenting on this are arguing that the owners of this cat just “didn’t know what they were doing”, that protein is protein, and that any animal can survive on a vegan diet if done properly. NO. Cats are OBLIGATE CARNIVORES. They will die on a vegan diet. Some animals can do perfectly well on a vegan diet - dogs for example can be fed a vegan diet, if you’re careful. Cats ABSOLUTELY CAN NOT.
Via I Fucking Love Science


Vegans, please do not do this. Cats are not omnivores like us, they are obligate carnivores and cannot survive on a meat-free diet.

Edit: a lot of people commenting on this are arguing that the owners of this cat just “didn’t know what they were doing”, that protein is protein, and that any animal can survive on a vegan diet if done properly. NO. Cats are OBLIGATE CARNIVORES. They will die on a vegan diet. Some animals can do perfectly well on a vegan diet - dogs for example can be fed a vegan diet, if you’re careful. Cats ABSOLUTELY CAN NOT.

Via I Fucking Love Science

(via pizza)




Wear one.


Lightning Appreciation Post:

  • There are nearly 500 lightning strikes every second around the world.
  • Only about 100 of these strike the earth, the others are between and within the clouds themselves.
  • Lightning is very visible from space (last gif from Astronaut Reid Wiseman)
  • Besides regular storms (thunder storms, hurricanes, etc.) lightning can be found in volcanoes (gif 3) and even intense forest fires.

In conclusion: nature is fucking awesome!

(via physicsphysics)


i swear to god this is what they must be doing.  

(p.s. bonus panel here)

This happens to me all the time.



I know this is common knowledge to most of us, but for the new Spoonies, we need to educate :-)

This graphic has some good stuff — but here’s the not-so-good portions that I, as a physician, do not agree with (plus sources when applicable):

  • "Tylenol and Antibiotics" are NOT a “dangerous drug interaction to avoid" — in patients with bacterial infections + fever, we often use acetaminophen and an antibiotic together. However, since acetaminophen is primarily metabolized by liver, and most antibiotics undergo liver metabolism AT VARYING LEVELS, it is wise to be wary of taking both of these medication categories together — especially if you already have a pre-existing liver condition (in which case, you shouldn’t be taking acetaminophen at all, unless your liver doc said it’s ok!). But not all antibiotics are created equal, so don’t just lump "antibiotics" into this warning. In most cases, low/normal doses of acetaminophen, used for a few days of fever/pain control while concurrently undergoing standard-dose antibiotic therapy, will not nuke your liver.
  • Aspirin does NOT interact w/ “diabetes meds" to cause low blood sugar. The graphic doesn’t specify whether they mean insulin or oral meds such as glucophage, but regardless — aspirin is actually used often (and according to clinical studies, not ENOUGH) among diabetic patients, in order to help decrease their risk for cardiovascular disease. Aspirin can RARELY cause low blood sugar if given to children by itself, though. Sources: Epocrates.com, UpToDate.com
  • Birth Control (I assume they mean Hormonal Contraceptives — which are only one category of “birth control”) and Antibiotics do NOT interact… 99.98% of the time. I run into this flat-out medical myth all the time, and here’s the skinny: the ONLY antibiotic proven to decrease hormonal contraceptive efficacy (for “The Pill”, “The Patch” and “The Ring”) is Rifampin (which is used very rarely, mainly for treatment of tuberculosis). Planned Parenthood has addressed this beforeUpToDate.com has this to add: “In spite of anecdotal reports of oral contraceptive failure, other antibiotics [besides Rifampin] have not been proven to affect the pharmacokinetics of [oral contraceptives]. For women taking antibiotics other than rifampin with oral contraceptives, back-up contraception is not required.” [BONUS TIP: “Vaginal miconazole suppositories and creams (i.e. Monistat, etc) do not appear to affect serum steroid levels in women using the contraceptive vaginal ring.” That’s not an antibiotic at all, but an interesting fact I didn’t know before, so there you go.]

Incidentally, the interaction between St. John’s Wort and Antidepressants is true — but did you know that St. John’s Wort CAN also interact with hormonal contraceptives? (See the Planned Parenthood link above; also Epocrates.com). Since many more people take St. John’s Wort (an over-the-counter herbal treatment) than Rifampin, that would be a useful addition to this type of infographic. 

Besides all that: the other specific interactions on this graphic are correct to the best of my medical knowledge/training, and the “General Rules” section is terrific.

As a doctor who also thrives on social media, I love medical infographics — except when they mix in (unsourced) health mis-information. Infographics are powerful, and we must be careful to create mis-infographics which may pre-condition patients into incorrectly “avoiding”/ignoring a doctor’s recommended treatment, just because the pretty graphic they saw online had already labeled that treatment as a “dangerous drug interaction”.

You guys have to create a diversion. What do you want me to do, dress in drag and do the hula?

Every time the Disney Channel airs The Lion King, I always wait for this scene and then I sing along with Timon and Pumbaa.

(via yohoyohoadisneylifeforme)


my dad has a folder on his computer named Cool Dad and it’s just pictures of himself

(via rnarinadiamondis)


If you reblog this before July 1 2014, I will write your url down and stick it in a jar or whatever. Over the summer I will take the jar of urls and I will scatter them around. They may get taped to public loos, they may be thrown into crowds at festivals, or they may get put under napkins at restaurants.
Some one may find your url, and who knows, they could message you telling you where they found it.
You have until July 1 to reblog.

(via xscapechicago)

"Music has been my outlet, my gift to all of the lovers in this world. Through it — my music, I know I will live forever."

1958 -

(via crazyovermjforumsandfanfics)