Amino acids, nucleic acids, and proteins

The zwitterion is the resting state, not an exception. A standard $\alpha$-amino acid, $\text{H}_2\text{N–CHR–COOH}$, carries a carboxylic acid ($\text{p}K_a\approx2$) and an amine ($\text{p}K_a\approx9$–$10$) on the same carbon. At any pH between those two values — which includes neutral water — the acid has already given up its proton and the amine has already taken one, so the molecule exists as $\text{H}_3\text{N}^+\text{–CHR–COO}^-$: net neutral, but doubly charged internally. This is not a special case reserved for exam questions; it is simply what happens when you plot which species dominates at each pH, exactly the way any diprotic-looking acid-base system behaves.

Side chains sort amino acids into four behavioural families. The identity of R decides everything about how a residue behaves once built into a protein:

• Non-polar/hydrophobic (glycine, alanine, valine, leucine, phenylalanine, proline, tryptophan) — these bury themselves away from water.
• Polar, uncharged (serine, threonine, cysteine, asparagine, glutamine, tyrosine) — these sit comfortably at a water interface and hydrogen-bond with it.
• Acidic (aspartate, glutamate) — carry an extra $\text{–COOH}$ that ionises to $\text{–COO}^-$ near physiological pH.
• Basic (lysine, arginine, histidine) — carry an extra amine-type group that stays protonated near physiological pH.

This classification is why a folded protein looks the way it does: hydrophobic residues cluster into a solvent-shielded core, and charged/polar ones sit exposed on the surface where they bind, catalyse, or dissolve.

The peptide bond locks the backbone into a predictable shape. Amino acids condense head-to-tail — one residue's $\text{–COOH}$ with the next residue's $\text{–NH}_2$, losing water — to form the amide (peptide) bond. Because the nitrogen lone pair delocalises into the neighbouring carbonyl, this bond has partial double-bond character: it is planar and cannot rotate. The only conformational freedom per residue is two flanking dihedral angles, $\phi$ and $\psi$, whose allowed combinations form the Ramachandran plot. Regular, repeating $(\phi,\psi)$ choices, stabilised by a fixed backbone hydrogen-bonding pattern, generate the two classic secondary structures: the $\alpha$-helix (C=O of residue $n$ hydrogen-bonds to N–H of residue $n+4$) and the $\beta$-sheet (extended strands H-bonded side by side).

Nucleic acids repeat the same logic with a different alphabet. A nucleotide is a base (purine A, G; pyrimidine C, T/U) on a pentose sugar (deoxyribose in DNA, ribose in RNA) on a phosphate; phosphodiester bonds chain nucleotides into a directional ($5'\to3'$) backbone. Two DNA strands run antiparallel and pair through fixed hydrogen-bond counts — A–T with two H-bonds, G–C with three — coiling into the right-handed double helix. RNA swaps thymine for uracil, keeps a reactive 2′-OH, and is usually single-stranded.

One number captures an amino acid's overall charge behaviour: the isoelectric point, $\text{pI}$, the pH at which the average net charge is zero. Because it is built entirely from the same $\text{p}K_a$ values that fix the zwitterion, it is:

where: $\text{p}K_{a,\text{low}}$ and $\text{p}K_{a,\text{high}}$ are the two ionisable-group $\text{p}K_a$ values that immediately bracket — one just below, one just above — the pH window in which the molecule's net charge is zero (for glycine-type amino acids these are the $\alpha$-COOH and $\alpha$-NH$_3^+$; for acidic/basic side chains, the correct pair shifts, as the derivation below works out).

Continuing with glutamic acid ($\alpha$-COOH $\text{p}K_a\approx2.2$; side-chain COOH $\text{p}K_a\approx4.3$; $\alpha$-NH$_3^+$ $\text{p}K_a\approx9.7$): confirm its net charge at physiological pH ($7.4$) and then find its isoelectric point, checking the two results are consistent.

Step 1. Compare each group's $\text{p}K_a$ to pH $7.4$. The $\alpha$-carboxyl ($2.2$) and the side-chain carboxyl ($4.3$) are both far below $7.4$, so both are essentially fully deprotonated: two $\text{–COO}^-$ groups. The $\alpha$-amino group ($9.7$) is well above $7.4$, so it stays essentially fully protonated: $\text{–NH}_3^+$.

Step 2. Sum the charges at pH $7.4$: one $+1$ (the ammonium) plus two $-1$'s (the two carboxylates) gives a net charge of $-1$ — glutamate behaves as an anion in the body, consistent with its "acidic amino acid" label.

Step 3. Apply the derivation's result to find $\text{pI}$: the zero-charge window lies between the two carboxyl $\text{p}K_a$'s, so $\text{pI}=\tfrac{1}{2}(2.2+4.3)=3.25$.

Step 4. Check consistency: physiological pH ($7.4$) is well above $\text{pI}$ ($3.25$), and raising pH above $\text{pI}$ always pushes net charge negative (more deprotonation), which matches the $-1$ found in Step 2 directly. A glutamate residue carries a net charge of approximately $-1$ at pH $7.4$, and its isoelectric point is $\text{pI}\approx3.25$.

• Drawing an amino acid with neutral $\text{–NH}_2$/$\text{–COOH}$ groups at physiological pH instead of the zwitterionic $\text{–NH}_3^+/\text{–COO}^-$ form that actually dominates.
• Averaging the wrong pair of $\text{p}K_a$ values for $\text{pI}$ — for an acidic side chain, the correct pair is the two acidic $\text{p}K_a$'s, not the amine value; for a basic side chain the pair shifts the other way.
• Treating the peptide backbone as freely rotatable everywhere; the peptide bond itself is planar and locked, so only $\phi$ and $\psi$ vary.
• Forgetting G–C (three H-bonds) is stronger than A–T (two H-bonds), or writing a DNA complement without reversing it to respect antiparallel $5'\to3'$ directionality.

Ask the tutor: if picking the right pair of pKa values for an amino acid with a basic side chain (like lysine or histidine) feels confusing, ask the AI tutor to walk through the charge-region tracking step by step.