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All 20 amino acids, named and grouped in 25 seconds.
The groups come from the side chains: which ones carry a charge at pH 7.4, and at what pKa, and which ones bend the chain. That is what the questions ask you to use.
Glutamic acid has pKa values of 2.2 (α-carboxyl group), 4.3 (side-chain carboxyl group), and 9.7 (α-amino group). What is its isoelectric point (pI)?
Pick one. The red pen does the rest.
The deciding lineThe pI of an amino acid is the average of the two pKa values on either side of its neutral (zwitterionic) form; for an amino acid with an acidic side chain, these are the α-carboxyl and side-chain pKa values.
Why A: Glutamic acid is neutral (α-COO−, side-chain COOH, α-NH₃+) only between pH 2.2 and 4.3, so pI = (2.2 + 4.3)/2 = 3.25.
Why each choice fails
AThe neutral form lies between the first two ionizations, so pI = (2.2 + 4.3)/2 = 3.25. Above 4.3 the side chain is deprotonated and the molecule carries a net charge of −1.
BOne step short: the pI averages the two pKa values that flank the neutral form, not all three. (2.2 + 4.3 + 9.7)/3 = 5.40 has no physical meaning here.
CConditions ignored: (2.2 + 9.7)/2 = 5.95 is the rule for an amino acid whose side chain does not ionize. Glutamic acid's side chain loses its proton at 4.3, long before the amino group does at 9.7.
DLook-alike terms: averaging the two highest pKa values, (4.3 + 9.7)/2 = 7.00, is the rule for a basic amino acid such as lysine. Between pH 4.3 and 9.7, glutamic acid carries a net charge of −1, not zero.
Using pKa values of 9.0 (α-amino), 2.2 (α-carboxyl), 10.5 (lysine side chain), 6.0 (histidine side chain) and 4.2 (glutamate side chain), what is the approximate net charge of the tripeptide Lys–His–Glu at pH 7.4?
Pick one. The red pen does the rest.
The deciding lineA basic group is mostly protonated (positive) when the pH is below its pKa and mostly neutral above it; an acidic group is mostly deprotonated (negative) when the pH is above its pKa.
ADirection reversed: −2 treats the amino groups as deprotonated because their pKa is above 7.4; below its pKa a group keeps its proton, so both amines are +1.
BOne step short: −1 counts the side chains and the C-terminus but drops the N-terminal α-amino group, which is +1.
CHolds: two positive amines balance two negative carboxylates; histidine is mostly neutral.
DConditions ignored: +1 counts histidine as protonated, but at pH 7.4, 1.4 units above its pKa of 6.0, only about 4% is.
A proline placed in the middle of an α-helix usually breaks the helix. The main reason is that proline:
Pick one. The red pen does the rest.
The deciding lineAn α-helix is held by hydrogen bonds from each backbone N–H to the C=O four residues earlier; proline’s side chain is bonded back to its own backbone nitrogen, so it has no N–H to donate and its ring locks the backbone angle.
Why B: The helix is held by backbone N–H···O=C hydrogen bonds. Proline’s ring bonds to its own backbone nitrogen, so that nitrogen carries no hydrogen to donate, and the ring also restricts rotation: the helix is interrupted.
Why each choice fails
ARight effect, wrong mechanism: helix side chains point outward, not inside, and proline’s side chain is small; the problem is its backbone nitrogen.
BHolds: no amide hydrogen, so the helix loses a backbone hydrogen bond (and the ring restricts rotation).
CLook-alike terms: disulfide bonds form between cysteines and stabilize tertiary structure; proline has no thiol.
DSays more than the data: proline’s side chain is nonpolar and uncharged.
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