Biochem Chap 3 Pt. 2B - AA Acid/Base Chemistry

What's the general pattern for a weakly acidic group's ionization?

HA ⇌ A⁻ + H⁺ (acid → conjugate base + proton); examples

What's the general pattern for a weakly basic group's ionization?

HA⁺ ⇌ A⁰ + H⁺ (protonated acid form → neutral conjugate base + proton); examples

Is the amide group in Asn/Gln side chains basic?

No — despite containing nitrogen, the amide group is NOT basic.

What's the "big picture" charge rule for weak acid groups (HA/A⁻)?

HA form = 0 charge; A⁻ form = −1 charge; if exactly half-and-half (pH = pKa), average charge = −½.

What's the "big picture" charge rule for weak base groups (HA⁺/A⁰)?

HA⁺ form = +1 charge; A⁰ form = 0 charge; if exactly half-and-half (pH = pKa), average charge = +½.

What are the 3 rules of thumb for determining charge on a weakly acidic group at a given pH?

If pH is 1+ below pKa → charge = 0; if pH = pKa → charge = −½; if pH is 1+ above pKa → charge = −1.

What are the 3 rules of thumb for determining charge on a weakly basic group at a given pH?

If pH is 1+ below pKa → charge = +1; if pH = pKa → charge = +½; if pH is 1+ above pKa → charge = 0.

How do you calculate the net charge on Alanine at pH 2.5 (easy method)?

α-carboxyl (pKa 2.5)

How do you calculate net charge using the Henderson-Hasselbalch equation (the "difficult way")?

pH = pKa + log([A⁻]/[HA]) (or [A⁰]/[HA⁺] for bases) — solve for the ratio of forms present, then determine predominant species and assign charge accordingly.

How do you calculate the net charge on Glutamic acid at pH 4?

α-COOH (pKa 2.5)

How do you calculate the net charge on Glutamic acid at pH 9.5?

α-COOH (pKa 2.5)

How does being part of a polypeptide chain shift an amino acid's terminal group pKa's?

The α-NH3⁺ pKa drops from ~9.5 to ~8.5, and the α-COOH pKa rises from ~2.5 to ~3.5, once incorporated into a peptide bond (only the very end residues have these free groups).

How do you calculate net charge on a full polypeptide (e.g., Ala-Glu-Gly-Lys at pH 12.5)?

Write out N-terminal amine (pKa ~8.5), C-terminal COOH (pKa ~3.5), and all side chain pKa's (Glu ~4.0, Lys ~10.5); apply the charge rules to each group individually at the given pH, then sum. At pH 12.5

What does a titration curve of an amino acid without a side-chain pKa (like Gly) look like?

Two inflection points corresponding to pK1 (α-COOH, ~2.5) and pK2 (α-NH3⁺, ~9.5), with the isoelectric point (pI) as a flat midpoint between them.

What is the isoelectric point (pI)?

The pH at which an amino acid or polypeptide carries zero net charge (found between the +1 and −1 charge states).

What's the formula for pI of an amino acid with NO extra ionizable side chain (plus Tyrosine)?

pI = ½(pKa1 + pKa2) — the average of the α-COOH and α-NH3⁺ pKa's.

Why is Tyrosine an exception even though it has an ionizable side chain (phenol)?

Because its ±1/−1 charge transition still only involves the α-COOH and α-NH3⁺ groups, not the phenol — so the standard formula still applies.

What's the formula for pI of amino acids with a weakly basic side chain (Arg, His, Lys)?

pI = ½(pKa2 + pKaR) — average of the α-amino pKa and the side chain pKa.

What's the formula for pI of amino acids with a weakly acidic side chain (Asp, Glu, Cys)?

pI = ½(pKa1 + pKaR) — average of the α-carboxyl pKa and the side chain pKa.

Why do you always average the two pKa's flanking the +1/−1 charge states to get pI?

Because pI is defined as sitting exactly between the +1 and −1 net charge states, so it's the midpoint (average) of the two relevant pKa's.

What is the pI of Glutamic acid, and how is it calculated?

pI = (pKa1 + pKaR)/2 = (2.5 + 4)/2 = 3.25 — averaging the α-COOH pKa and the acidic side chain pKa (since Glu goes from +1 to −1 across this range).

What is the pI of Lysine, and how is it calculated?

pI = (pKa2 + pKaR)/2 = (9.5 + 10.5)/2 = 10 — averaging the α-amino pKa and the basic side chain pKa.

How do you calculate the pI of a polypeptide (e.g., Ala-Glu-Gly-Lys)?

First find net charge at very low pH (should be maximally positive), then "titrate" upward through each pKa in order, tracking how charge decreases by 1 at each pKa crossed; pI = the average of the two pKa's that flank the 0 net charge state. For Ala-Glu-Gly-Lys

What does "polyampholytic behavior" mean for a peptide?

A molecule with multiple acidic and basic groups that can each gain or lose protons — giving a titration curve with multiple distinct inflection points, one per ionizable group.