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- AMINO ACID TALES
- (by Leroy Kuehl, abridged by Michael Ya e with apologies to G. Chaucer)
- PROLOGUE
- When fall hath come, and days grow short and cool,
- Then eager students hasten back to school
- And those who would gladly Scientists 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 exams might pass
- And go to practice biochemistry at last;
- For they would fain restore the sick to health,
- And also would win fame, respect and wealth.
- As rst to teach in biochemistry,
- The section treating structures falls to me.
- With amino acids we begin,
- The building blocks of muscle, enzymes, skin.
- GLYCINE
- For R-groups 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 so slight;
- And this, dear students, is the reason why
- In collagen the glycine content's high.
- ALANINE
- 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.
- VALINE
- 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 a x 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.
- PROLINE
- 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, so 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.
- METHIONINE
- To alanine an extra carbon lend,
- And next attach a sulfur to the end.
- Then nally, if you methylate the S
- Methionine is what you will possess.
- Examine now the R-group carefully.
- It's truly hydrophobic, as you 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.
- CYSTEINE
- Just add an SH group to alanine;
- The compound that is formed is cysteine.
- Its SH can a proton liberate
- The pKa of this group being close to eight.
- But more important, you should realize
- 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
- When we consider phenylalanine
- Whose name alone the structure does convene,
- And tyrosine, in structure close related
- Just phenylalanine hydroxylated.
- When phenyl groups as a hydroxy 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 therein this enzyme lie a fault
- Phenylketonuria is the result.
- TRYPTOPHAN
- Let alanine an indole function gain,
- And from the two arises tryptophan.
- (The indol group, in case you don't remember,
- Has a benzene ring and a 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 captivate
- 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 pKa's near two.
- So it may come as a surprise to you,
- The pKa 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.
- ARGININE
- 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 pKa high,
- At nearly 12.5 it's known to lie.
- (Now the guanido group, my student 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 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.
- LYSINE
- 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 pKa value over ten.
- HISTIDINE
- 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 a x
- Its R-group has a pKa close to six.
- Dear students, this is, as you know full well,
- Not far from the pH within the cell.
- And since the pKa of a group may change
- In uenced by other groups lying at close range
- So histidine within a protein structure
- Shows sometimes one ion form, sometimes the other.
- EPILOGUE
- 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 "A" in 7.05x that will be your reward.
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