Protein Structure and Function Questions and Answers

Q: The amino acid that interrupts α-helix conformation in protein by developing kinks in the structure :

The amino acid is proline.In proline the side chain is bonded back to the backbone nitrogen, forming a ring. Its nitrogen therefore has no hydrogen to donate to the hydrogen bond that holds the α-helix together, and the ring fixes the phi angle. Where proline occurs inside a helix, it breaks the pattern and puts a kink in the chain; it is a well-known helix breaker.Leucine is a strong helix former, and valine and serine weaken helices somewhat but do not cause kinks the way proline does.

Q: A Ramchandran plot describes, for a particular amino acid in a polypeptide chain, stearically allowed angles for :

The plot describes the allowed angles for the Cα-C and Cα-N bonds.The Ramachandran plot maps the two backbone torsion angles of each residue: phi (rotation about the N-Cα bond) and psi (rotation about the Cα-C bond). The peptide bond itself is planar, so these two rotations fix the backbone conformation, and the plot shows which combinations avoid steric clashes, the regions of alpha-helix and beta-sheet.The Cα-CB bond leads into the side chain, and Cα-H bonds carry a hydrogen; rotations about neither are plotted, so every option naming them is wrong.

Q: Which of the following bonds in proteins have a partial double bond character ?

The bond with partial double bond character is C – N, the peptide bond.In the peptide bond between the carbonyl carbon of one residue and the amide nitrogen of the next, the nitrogen's lone pair is delocalised into the carbonyl. Resonance gives the C-N bond about 40% double bond character, so it is shorter than a normal C-N single bond, planar and does not rotate freely. This planarity is why backbone conformation is described only by the phi and psi angles.The Cα-C, Cα-Cβ and Cα-N bonds are ordinary single bonds. Rotation about Cα-N (phi) and Cα-C (psi) is what lets the chain fold.

Q: How many different linear tripeptides can be made from three different L-α neutral amino acids, using each amino acid only once in the chain ?

6 different linear tripeptides can be made.A linear peptide has direction, from N-terminus to C-terminus, so Ala-Gly-Ser and Ser-Gly-Ala are different molecules. Using three different amino acids once each, the number of tripeptides is the number of orderings of three items:\[ 3! = 3 \times 2 \times 1 = 6 \]3 counts only which amino acid is first, or treats the chain as a ring. 27 is \(3^{3}\), the count if each position could use any of the three with repetition, which the stem excludes. 12 has no matching rule.

Q: NMR is a very important technique for determination of biopolymer structure. NMR experiments are not limited to the study of protons only. Which of the following represents a correct group of isotopes used to obtain resonance signals ?

The correct group is \(^{1}\)H, \(^{13}\)C, \(^{15}\)N, \(^{19}\)F.An NMR signal needs a nucleus with non-zero spin, and sharp lines in biopolymer work come from spin-1/2 nuclei. \(^{1}\)H, \(^{13}\)C, \(^{15}\)N and \(^{19}\)F all have spin 1/2, which is why proteins are labelled with \(^{13}\)C and \(^{15}\)N for multidimensional NMR.\(^{12}\)C has spin 0 and gives no signal, which rules out the options containing it. \(^{14}\)N, the common nitrogen isotope, has spin 1 and a quadrupole moment that broadens its lines, so the biomolecular work uses \(^{15}\)N instead.

Q: Indicate the ionic species that predominates at pH 4, 8 and 11 for ammonia :

The species are \(\mathrm{NH}_{4}^{+}\) at pH 4, \(\mathrm{NH}_{4}^{+}\) at pH 8 and \(\mathrm{NH}_{3}\) at pH 11.The ammonium ion has a pKa of about 9.25. By the Henderson-Hasselbalch relation, the protonated form dominates below the pKa and the base form above it:\[ \begin{aligned} \mathrm{pH} &= \mathrm{p}K_a \\ &+ \log\frac{[\mathrm{NH_3}]}{[\mathrm{NH_4^+}]} \end{aligned} \]At pH 4 and pH 8 the pH is below 9.25, so \(\mathrm{NH}_{4}^{+}\) predominates; at pH 8 the ratio is still about 1 to 18 in its favour. At pH 11, above the pKa, \(\mathrm{NH}_{3}\) predominates.The other options put \(\mathrm{NH}_{3}\) at low pH or \(\mathrm{NH}_{4}^{+}\) at pH 11, the reverse of this rule.

11.

The amino acid that interrupts α-helix conformation in protein by developing kinks in the structure :

A.Serine
B.Valine
C.Proline
D.Leucine

Exam Year(s)

MH SET - 2019, SET Exam - 2019,

Answer: C

The amino acid is proline.

In proline the side chain is bonded back to the backbone nitrogen, forming a ring. Its nitrogen therefore has no hydrogen to donate to the hydrogen bond that holds the α-helix together, and the ring fixes the phi angle. Where proline occurs inside a helix, it breaks the pattern and puts a kink in the chain; it is a well-known helix breaker.

Leucine is a strong helix former, and valine and serine weaken helices somewhat but do not cause kinks the way proline does.

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12.

A Ramchandran plot describes, for a particular amino acid in a polypeptide chain, stearically allowed angles for :

A.Cα-C and Cα-CB bonds
B.Cα-C and Cα-N bonds
C.Cα-C and Cα-H bonds
D.Cα-N and Cα-H bonds

Exam Year(s)

MH SET - 2020, SET Exam - 2020,

Answer: B

The plot describes the allowed angles for the Cα-C and Cα-N bonds.

The Ramachandran plot maps the two backbone torsion angles of each residue: phi (rotation about the N-Cα bond) and psi (rotation about the Cα-C bond). The peptide bond itself is planar, so these two rotations fix the backbone conformation, and the plot shows which combinations avoid steric clashes, the regions of alpha-helix and beta-sheet.

The Cα-CB bond leads into the side chain, and Cα-H bonds carry a hydrogen; rotations about neither are plotted, so every option naming them is wrong.

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13.

Which of the following bonds in proteins have a partial double bond character ?

A.Cα – C
B.Cα – Cβ
C.Cα – N
D.C – N

Exam Year(s)

MH SET - 2021, SET Exam - 2021,

Answer: D

The bond with partial double bond character is C – N, the peptide bond.

In the peptide bond between the carbonyl carbon of one residue and the amide nitrogen of the next, the nitrogen's lone pair is delocalised into the carbonyl. Resonance gives the C-N bond about 40% double bond character, so it is shorter than a normal C-N single bond, planar and does not rotate freely. This planarity is why backbone conformation is described only by the phi and psi angles.

The Cα-C, Cα-Cβ and Cα-N bonds are ordinary single bonds. Rotation about Cα-N (phi) and Cα-C (psi) is what lets the chain fold.

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14.

How many different linear tripeptides can be made from three different L-α neutral amino acids, using each amino acid only once in the chain ?

A.3
B.6
C.12
D.27

Exam Year(s)

MH SET - 2021, SET Exam - 2021,

Answer: B

6 different linear tripeptides can be made.

A linear peptide has direction, from N-terminus to C-terminus, so Ala-Gly-Ser and Ser-Gly-Ala are different molecules. Using three different amino acids once each, the number of tripeptides is the number of orderings of three items:

\[ 3! = 3 \times 2 \times 1 = 6 \]

3 counts only which amino acid is first, or treats the chain as a ring. 27 is \(3^{3}\), the count if each position could use any of the three with repetition, which the stem excludes. 12 has no matching rule.

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15.

NMR is a very important technique for determination of biopolymer structure. NMR experiments are not limited to the study of protons only. Which of the following represents a correct group of isotopes used to obtain resonance signals ?

A.\(^{1}\)H, \(^{12}\)C, \(^{15}\)N, \(^{19}\)F
B.\(^{1}\)H, \(^{13}\)C, \(^{14}\)N, \(^{19}\)F
C.\(^{1}\)H, \(^{12}\)C, \(^{14}\)N, \(^{19}\)F
D.\(^{1}\)H, \(^{13}\)C, \(^{15}\)N, \(^{19}\)F

Exam Year(s)

MH SET - 2021, SET Exam - 2021,

Answer: D

The correct group is \(^{1}\)H, \(^{13}\)C, \(^{15}\)N, \(^{19}\)F.

An NMR signal needs a nucleus with non-zero spin, and sharp lines in biopolymer work come from spin-1/2 nuclei. \(^{1}\)H, \(^{13}\)C, \(^{15}\)N and \(^{19}\)F all have spin 1/2, which is why proteins are labelled with \(^{13}\)C and \(^{15}\)N for multidimensional NMR.

\(^{12}\)C has spin 0 and gives no signal, which rules out the options containing it. \(^{14}\)N, the common nitrogen isotope, has spin 1 and a quadrupole moment that broadens its lines, so the biomolecular work uses \(^{15}\)N instead.

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16.

Indicate the ionic species that predominates at pH 4, 8 and 11 for ammonia :

A.\(\mathrm{NH}_{4}^{+}\) at pH 4, \(\mathrm{NH}_{4}^{+}\) at pH 8 and \(\mathrm{NH}_{3}\) at pH 11
B.\(\mathrm{NH}_{4}^{+}\) at pH 4, \(\mathrm{NH}_{3}\) at pH 8 and \(\mathrm{NH}_{4}^{+}\) at pH 11
C.\(\mathrm{NH}_{3}\) at pH 4, \(\mathrm{NH}_{4}^{+}\) at pH 8 and \(\mathrm{NH}_{4}^{+}\) at pH 11
D.\(\mathrm{NH}_{3}\) at pH 4, \(\mathrm{NH}_{4}^{+}\) at pH 8 and \(\mathrm{NH}_{3}\) at pH 11

Exam Year(s)

MH SET - 2021, SET Exam - 2021,

Answer: A

The species are \(\mathrm{NH}_{4}^{+}\) at pH 4, \(\mathrm{NH}_{4}^{+}\) at pH 8 and \(\mathrm{NH}_{3}\) at pH 11.

The ammonium ion has a pKa of about 9.25. By the Henderson-Hasselbalch relation, the protonated form dominates below the pKa and the base form above it:

\[ \begin{aligned} \mathrm{pH} &= \mathrm{p}K_a \\ &+ \log\frac{[\mathrm{NH_3}]}{[\mathrm{NH_4^+}]} \end{aligned} \]

At pH 4 and pH 8 the pH is below 9.25, so \(\mathrm{NH}_{4}^{+}\) predominates; at pH 8 the ratio is still about 1 to 18 in its favour. At pH 11, above the pKa, \(\mathrm{NH}_{3}\) predominates.

The other options put \(\mathrm{NH}_{3}\) at low pH or \(\mathrm{NH}_{4}^{+}\) at pH 11, the reverse of this rule.

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