Chapter 26: Biomolecules: Amino Acids, Peptides, and Proteins
One scaffold, twenty side chains, five families
An alpha-amino acid is a carboxylic acid with an amino group on the carbon adjacent to the carboxyl carbon. The Greek letter is doing real work: in the older nomenclature the carbon bearing the carboxyl group is C1, the next one along is alpha, the one after that beta, and so on, so beta-amino acids and gamma-amino acids are perfectly respectable compounds that simply are not what proteins are made of. Every one of the twenty amino acids specified by the genetic code is an alpha-amino acid, and each is the same four-substituent arrangement around one carbon: an amino group, a carboxyl group,…
Nineteen are S, cysteine is R, and nothing moved
Look at the alpha carbon of any amino acid and count its substituents: an amino group, a carboxyl group, a hydrogen, and a side chain R. Provided R is not itself a hydrogen, those four are all different and the carbon is a stereocenter. Glycine is the one place this fails, because its side chain is a hydrogen and the alpha carbon therefore holds two of them; glycine is achiral, has no D or L form, and does not rotate plane-polarized light. The other nineteen standard amino acids are chiral, and biology uses one enantiomer of each with near-total consistency. That enantiomer is designated L,…
The zwitterionic nature of amino acids
The structure most often drawn for an amino acid, with a neutral NH₂ at one end and a neutral COOH at the other, is a convenient fiction. Use it to predict physical properties and every prediction fails. A neutral molecule of that size and polarity should melt somewhere below 150 °C, dissolve in ether or dichloromethane, and have a dipole moment of a couple of debye. Glycine instead decomposes above 230 °C without ever melting cleanly, is highly soluble in water, is effectively insoluble in every nonpolar solvent, and has a dipole moment several times larger than the neutral structure allows.…
Locating the pH at which net charge vanishes
Everything an amino acid does in an electric field, on an ion-exchange column, or at the point where it drops out of solution is governed by one number, and that number is not any of its pKa values. It is the pH at which the molecule carries, on average, no net charge at all — the isoelectric point, written pI. Start from the titration curve, because reading it backwards is how the whole idea is built. Dissolve alanine hydrochloride in water, so that the amino acid begins as its fully protonated cation with a neutral COOH and a positive NH₃⁺, and add sodium hydroxide slowly while monitoring…
Four laboratory routes to an alpha-amino acid, and why every one of them gives a racemate
Every alpha-amino acid poses the same synthetic question in a different disguise: how do you place an amino group and a carboxyl group on the same carbon, with an arbitrary side chain also attached? Four classical answers cover most of the ground, and it is worth sorting them by which fragment carries the side chain into the synthesis, because that is what determines the starting material you have to buy. Bromination and ammonolysis. The shortest route starts from the carboxylic acid that already contains the side chain. Hell-Volhard-Zelinskii bromination — Br₂ with a catalytic amount of…
The peptide bond is a planar, partially double amide, and the backbone bends only between them
A peptide bond is formed, at least on paper, by dehydration: the carboxyl group of one amino acid and the amino group of another lose H₂O and become an amide. In a cell the reaction requires activation and a ribosome, and in the flask it requires the coupling reagents of the next section, because carboxylic acids and amines simply form a salt when mixed. But the product is an ordinary amide — Chapter 21's least reactive derivative, made by its one mechanism of nucleophilic acyl substitution — and understanding it is almost entirely a matter of understanding amide resonance. The bond is partly…
Taking a peptide apart: composition by hydrolysis, sequence by Edman, disulfides by separate bookkeeping
Frederick Sanger's determination of the insulin sequence took roughly a decade and established that a protein has one definite, reproducible sequence rather than some statistical distribution of residues. The methods have been automated since, but the logic he used is still the logic: establish composition, establish the ends, cut the chain into overlapping pieces, sequence the pieces, and account separately for the disulfides. Composition: total hydrolysis. Every peptide bond is an amide, and amides hydrolyze in hot aqueous acid. Sealing the peptide in 6 M HCl at 110 °C for about twenty-four…
Building a peptide on purpose: protecting groups, DCC, and the solid phase
The peptide bond is an amide, and Chapter 21 already showed how to make an amide: activate a carboxylic acid and let an amine attack. The complication with amino acids is that each starting material carries both halves of that reaction. Stir alanine and glycine together with a condensing agent and every activated carboxyl is available to every amine in solution. Four dipeptides result — Ala-Gly, Gly-Ala, Ala-Ala, and Gly-Gly — and because each of them still presents a free NH₃⁺ and a free COO⁻, the mixture goes on to tripeptides and beyond. The desired compound is a minor component of an…
Four levels of protein structure
A polypeptide of a hundred residues has an astronomical number of conformations available to it, and yet in solution it adopts essentially one. Describing that one structure is conventionally organized into four levels, and the most useful thing to notice at the outset is that only the first level is covalent. Everything above it is held by hydrogen bonds, hydrophobic effects, ion pairs, and van der Waals contacts — individually weak, collectively decisive, and collectively fragile. Primary structure is the sequence of residues, written from the N-terminus on the left to the C-terminus on the…
Enzymes: rate acceleration from geometry and proximity
Almost every reaction in a cell is catalyzed, most of them by proteins, and the rate enhancements involved are outside ordinary laboratory experience — between 10⁶ and 10¹⁷ relative to the uncatalyzed reaction in water at the same pH and temperature. Before accounting for that, it is worth being exact about what a catalyst is not permitted to do. A catalyst lowers ΔG‡ and leaves ΔG° alone. It offers an alternative pathway whose highest point is lower than that of the uncatalyzed path, and it emerges unchanged at the end. It does not alter the free energy of the starting material or of the…
Part of Organic Chemistry, a free and open textbook licensed CC BY-SA 4.0.