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.
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.