Amino Acid Tales
with apologies to G. Chaucer
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.
EpilogueWith 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.
No matter what anybody tells you, words and ideas can change the world.
We don’t read and write poetry because it’s cute. We read and write poetry because we are members of the human race. And the human race is filled with passion. And medicine, law, business, engineering, these are noble pursuits and necessary to sustain life. But poetry, beauty, romance, love, these are what we stay alive for.
(Dead Poets Society, 1989)Me
— (via emtvacation)
"Someone is dying aline in the night.
The hospital hums like a consciousness.”
I am not a poet.
I am a scientist.
I can measure the exact frequency
of your voice when you speak my name,
but I cannot explain how it resonates
with such perfect clarity down my spine.
I can describe the process by which you inherited
your mother’s hair
and your father’s smile,
but I cannot explain where the twinkling galaxies
in your eyes came from.
I am baffled by the apparent gravitational anomaly
that draws me to you
with a force far too great for your size.
I know of no way to quantify
the volume of your presence
in a room.
I am not a poet.
I am a scientist.
Prose is not my specialty.
I will never be able to combine words
to craft sonorous verses
as easily as I combine chemicals in a flask,
but know this — to me, you are every bit as fascinating
as the view through a microscope.
To me, you are a mystery greater
than any cat in a box,
and are fraught with as much uncertainty.
Each day brings new understanding of you,
and the knowledge
that there is still far more
I am not a poet.
I am a scientist,
and there is nothing a scientist loves more
than the the pursuit
For the Cute Boy.
wondering why i’ve got this urgency,
all that i yearn to be is right in front of me,
i’ve maintained courtesy to nth degree,
and now it’s my turn to go out and get it,
so i run full speed like towards the 45 kipling bus
when we were seventeen, and we saw it rolling up,
yeah i’ve got issues with trust,
yeah i’ve got issues with lust,
spontaneously combust, need no lighter
for this fire, we aim higher
than thought possible,
white coats, donned in hospitals,
expectations, we’ve got lots to fill,
we get lost at will, i’ve seen lots of real
turn fake, pile too much onto plates,
too much emphasis on fate,
this is our place, this our time,
this is our shine, and it’s not
dependent on jewelery or sunlight,
this is within, this is from soul,
this is from cell, this is nucleus,
this is realness, i can’t appeal to this
demographic, i used to think i couldn’t hack it,
but the fact is we’re all actin,
they’re all actors, where we act sure,
when we lack cures, where we act like
we all rap tight, when we lack right,
this aint black and white, this is real life,
this is the discarded blue boxes
of blockbuster videos, this is
thrown out mixtapes containing
high school flows, this is home phones,
this is loonies spent on speakers corner segment,
this is respite, these are my confessions
there are still lessons to learn,
used to burn all my mistakes,
but the only way to elevate
is to criticize, so now i analyze,
realize that our demise
is ongoing, foreclosing, impending,
but the ending is still under revision,
make each decision, with finality
don’t underestimate gravity,
levity and brevity are dead to me,
we grew up on mase and diddy,
so forgive me if i act hypocritically,
you’ve yet to see, the best of me,
this isn’t just a test to me,
this is everything, this is all of me,
all i want to be, is satisfied,
keep these struggles in perspective
with the end in mind.
"Coats" - Jane Kenyon
I saw him leaving the hospital
with a woman’s coat over his arm.
Clearly she would not need it.
The sunglasses he wore could not
conceal his wet face, his bafflement.
As if in mockery the day was fair,
and the air mild for December. All the same
he had zipped his own coat and tied
the hood under his chin, preparing
for irremediable cold.
— Kenyon, Constance, 40.
there’s a lot to escape from,
within these pods
that which is ugly and sinister,
can hide beauty, can hold hope.
those that persevere,
learn to accept
each spectrum end,
it’s waking up from a restless night of sleep, bracing yourself to face the day.
it’s willing your body to make it two more steps, so you can brush your teeth.
it’s compromising looking decent for having a bit more energy.
it’s realizing how tired you are…and it’s only nine in the morning.
it’s trying desperately to focus on your professor’s words.
it’s constant shifting to try and get a bit more comfortable.
it’s holding back the tears as you remember that meeting.
it’s nap time, because without it you would collapse.
it’s telling people no, not because you don’t want to but because you can’t.
it’s always feeling like you’ve let someone down.
it’s nagging pressure to try and act normal.
it’s your body shutting down when you do that.
it’s a phone book’s worth of doctor’s office numbers.
it’s lab work every month.
it’s eight, ten, twelve pills a day (or more).
it’s hoping and praying that this new treatment is effective.
it’s looking normal but knowing you’re not.
it’s judgmental glares from strangers when you take the elevator, not the stairs.
it’s misunderstanding from friends who truly do care.
it’s not fair, but you deal.
it’s giving up the life you thought you’d have because you can’t physically do it.
it’s seeing other people happy and healthy and wanting it for yourself.
it’s emotional and physical pain, twenty-four seven.
it’s wishing it would all go away.
it’s hearing you’ll never be able to have children.
it’s feeling inadequate and invisible.
it’s wanting what you’ll never have.
it’s the worry that something else will pop up.
it’s fibro and lupus and hashimoto’s and crohn’s.
it’s CFS and PCOS and CAH and RA.
it’s endometriosis and celiac and cushing’s and MS.
it’s chronic illness, and it’s your life.
In honor of all the unseen and underestimated.
you won’t remember me.
fumbling to position my hands,
as i check in your ears and
shine lights in your eyes,
treating your body like fine china,
delicate to the point of fault.
you won’t recall the silly
questions, asked to your parent
out of order, lacking pattern
or structure, vaguely medical.
you won’t know of the
smile which you gave me
when your little hand
grasped my finger,
the warmth from which
melted morning frost
you won’t realize that
i held your entire body
in my palm, my other hand
ran along the segments
of your spine, checking
alignment and symmetry.
it was a week before your
eyes made contact with mine,
and i’ll never forget that second.
these lessons will be a foundation
from which i’ll build my skills,
future patients of your size,
will be familiar territory.
i might see you at age 2,
taking steps in a shopping mall,
and while you may smile at me again,
you won’t remember me.
“Is that her femoral artery?”
I met my lover late one night,
Stethoscope on my chest, BP cuff on my right,
And as he held my hand, on his resident’s command,
He summoned up all his might -
“I’m a doctor-in-training”, he said,
Resting his body against my bed
“And is it too soon to make you swoon?
Because I know we’ve just met -
But you make my heart thump so hard
That cardiac arrest is on the cards,
Fast my blood flows for my soul knows
That true love has caught me off-guard.”
What was there to say but yes?
To a lack of experience he had confessed,
Yet I was fine with the nerdy pick up lines
Because for me adoration he had professed -
But he’s rare with actual compliments
Instead choosing to thank my ‘rents
For their chromosomes, their centrosomes
…I think good will was meant?
And even when he finds the right words
It sounds completely absurd
To hear “My dear, your telomeres
They have never faltered!”
All my girlfriends think I’m single
Because I never bring him out to mingle -
He works long hours, rarely showers,
And in small talk, the only lingual
Skills he has pertain to nerves of the tongue,
And if there’s pathology he has the lungs
To speak and speak for a more than a week,
As if other meddies he were among!
Surgery sets his heart on fire
More than my wanton desire,
Causing a fuss with his bloodlust
Whenever I want my body admired,
So when he’s making love to me,
I know he’s thinking of anatomy
Not what goes where, or how he fares,
But is that her femoral artery?
“Found it!” he cries instead of my name,
As if our activity is not a game
Of take-a-peek but hide-and-seek
Where physiology is the aim!
Still I know he’ll never cheat
Because he never has the time to meet
Another girl to take for a whirl,
And besides, I know I have them beat
With my ample mitochondria, cranial hypertrophy,
A million neurotransmitters and long phalanges -
Subcutaneous tissue, it’s never an issue;
So I’ll let him study our mutual biochemistry
Because he gives me atrial fibrillation,
Ventricular contractions and palpitations,
Every single date my muscles fasciculate,
Forever he’ll be my doctor, and I, his patient.
[An old poem I had lying around. It never fails to amuse me.]
When they take the knife!
Underneath their fine incisions
Stirs the Culprit - Life!"
— Emily Dickinson (1830-1886)
To the 11-week-pregnant woman who came to the Urgent Care with vaginal bleeding, stomach cramps, and “little clots of tissue coming out”…
I wish I could’ve given you better news,
but there is nothing I or any human can do now.
I could see the acceptance of that fact in your tear-filled eyes,
even as your mouth and heart recited the expected objections:
“But I didn’t do anything wrong! I’ve been eating right! I quit smoking as soon as I found out I was pregnant! Isn’t there anything you can give me to stop this?”
I stammered a lot as I explained things to you, didn’t I?
It wasn’t because I was unsure. I am sure. Sure that you are having a miscarriage, and that the fetus inside your abdomen (and whom you have already imagined wearing a cute baby outfit and blowing spit bubbles on a diaper-changing table) is going to be leaving your body much sooner than you or I or anyone else would wish.
No, it was because I kept imagining that it was my wife sitting on that exam table, instead of you.
And it’s hard to keep from stammering when you are fighting back tears.
God bless you, lady.
Good news. I saw this woman in the clinic building today, almost a year after the incident when she had this miscarriage. She’s 6 months pregnant and doing great! I had to hug her from the joy of it all, and I really wish that I could’ve “let her in” on my secret Cranquis identity to share this poem with her.
By Natalie Nuzzo
I cry in buses
I have a Dr.
that is the twin
of Mr. Monopoly
white handlebar mustache
round bald head white
curled at the edges
varied length and fashion
today new tortoise
I have high blood pressure
and a tumor
I don’t know you tell me
feel about that
Dr. has a pretty tall
she compliments my outfits
I love her always stilettos
the most elegant
a glamorous nurse
diagnoses behind closed doors
analyzed over paper work
Dr. yells at me he’s strict
old and grumpy
the best around
Dr. gives me pills
says things like:
“no good deed goes unpunished”
“that’s the problem
I’m never here”
I don’t understand Dr.
he scolds me
I forget my dosage
“you should know this”
“I don’t trust my own records”
I swallow pills blindly pretend
the quantity the Rx
I imbibe every day orange
not white or yellow
my eyes forget
Dr. complains to me:
“I joined the gym
then I was sick
I went for two weeks
then I was traveling
is right in my building
and the gym
right in my building”
I don’t know what to say
so I fake laugh instead
always the expert
( at thirty I learn
how to hold back )
steel file cabinet-ed quantities
and expensive free samples
the “ america “n
modern medical machine
the best kept
secrets dangle above
in gold-plated premiums
and cushioned carpets
those sweet n sexy nurses
the flat screen arrogance
of the cardiovascular
“ america ”s most prolific legalized
white white haired men roam
work the counter
these few men hold the keys
white mustaches white walls
white halls white coats worn by all
these few men who invite you
to walk down our cash
walled halls ours
are the most expansive
and well-lit here we save
bodies but not minds
( university medicine
only comes with
a side of infection )
I cry in buses
I have a doctor
that is the twin
of Mr. Monopoly
I don’t know you tell me
feel about that
Typewriter Series #12 by Tyler Knott Gregson
I am more than the brittle bones
and creaking joints
that move me with purpose
and something that once
Rattle though they may
and ache where they will
I am more than bones.
I am made of magic things
and the left-over fire
of silently exploded
-Tyler Knott Gregson-
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