VKC ScienceChemistry for written exams Telegram
VKC Notes · Biopolymers · Civil Services P-II · IFoS P-II

10.1 Biopolymers: Proteins, Peptides, DNA and RNA

★★★ 2021–2025: 18 parts, 135 marks (Civil Services 7 parts / 80 m · IFoS 11 / 55 m). Base pairing with H-bonds drawn, protein secondary and tertiary structure, and N-terminal analysis (Sanger, Edman) carry almost all of it.

Syllabus lines. Civil Services: polymeric systems, biopolymers: “structure of proteins, DNA and RNA”. IFoS: biopolymers, “basic bonding in proteins, DNA and RNA”. Synthetic polymers are in 9.1.

Two-page short notes for revisionAll VKC notes
Download PDF PLAN
PDF edition, print-ready. It opens with the VKC plan, together with every locked answer, note and test on the site.

CSE 2024 Q7(a) = asked there; tap to open the solved answerSN = line kept in the short notes

10.1.1 Amino acids ★★

Twenty α-amino acids, H₂N–CHR–COOH, build proteins; all except glycine are chiral and natural ones are L (S, except cysteine, which is R). In water they exist as zwitterions, ⁺H₃N–CHR–COO⁻: high melting, water-soluble, insoluble in ether.SN

pH < 2: cation pH ≈ pI: zwitterion pH > 10: anionpKₐ1 2.3pKₐ2 9.6
Fig. 10.1.1 Three charge states of an amino acid.
Draw it in 60 s: three structures in a row: +H3N–CHR–COOH, +H3N–CHR–COO−, H2N–CHR–COO−; write pKₐ1 ≈ 2.3 and pKₐ2 ≈ 9.6 over the arrows.
(10.1.1)
ClassResidues (3-letter)Role in the fold
Non-polarGly, Ala, Val, Leu, Ile, Met, Phe, Trp, Prohydrophobic core; Pro breaks helices
Polar, neutralSer, Thr, Tyr, Asn, Gln, CysH-bonds; Cys forms S–S bridges
AcidicAsp, Glu (pI ≈ 3)COO⁻ in salt bridges
BasicLys, Arg, His (pI 7.6–10.8)NH₃⁺ / guanidinium⁺ in salt bridges

10.1.2 The peptide bond ★★★

⟷ C–N ≈ 40 % double bond:planar, no free rotation, transONCαCαHC1.231.331.521.461.0116°123°121°six atoms in one plane; lengths in Å
Fig. 10.1.2 Resonance makes the peptide unit planar; the bond lengths prove it.
Draw it in 60 s: amide with the lone-pair arrow into C–N and the C=O arrow to O, then the zwitterion form; beside it the six-atom plane with 1.23, 1.33, 1.46, 1.52 Å.
  • The N lone pair is delocalised into C=O: C–N 1.33 Å (between C–N 1.47 and C=N 1.27), C=O 1.23 Å, partial double-bond character, rotation barrier ≈ 80 kJ mol⁻¹. Cα, C, O, N, H and the next Cα lie in one plane IFoS 2024 Q5(d) 5m.SN
  • The unit is almost always trans (ω ≈ 180°: the two Cα on opposite sides of C–N); cis peptides occur mainly before proline. Freedom comes only from rotation about N–Cα (φ) and Cα–C (ψ).SN
  • The N–H is a donor and the C=O an acceptor in every backbone H-bond (10.1.5); the C–N does not protonate (the lone pair is not available), so the peptide N is not basic.

10.1.3 Peptide synthesis ★

  1. Protect the N of the first amino acid (Boc, removed by CF₃COOH; Fmoc, removed by piperidine; Cbz, removed by H₂/Pd) and the COOH of the second (methyl or benzyl ester).
  2. Activate and couple with DCC (dicyclohexylcarbodiimide): the COOH becomes an O-acylisourea, the free NH₂ attacks it, dicyclohexylurea is lost.
  3. Deprotect and repeat. Merrifield's solid-phase method anchors the C-terminal residue to a polystyrene bead, so excess reagent is simply washed away; HF finally frees the peptide.SN

10.1.4 Sequencing: the N-terminus by Sanger and Edman ★★★

Sanger: 1-fluoro-2,4-dinitrobenzene (FDNB) labels the free N-terminal NH₂ by nucleophilic aromatic substitution (the two NO₂ groups stabilise the Meisenheimer anion); total hydrolysis then frees the yellow DNP-amino acid, identified by chromatography. The peptide is destroyed, so only one residue is learnt; Lys side-chain NH₂ is labelled too IFoS 2023 Q7(f) 5m.SN

N-terminal NH2FDNB (Sanger), pH 8–9addition: Meisenheimeranion, the negativecharge on the C–NO2 − F−− H+ DNP-peptide (yellow)6 M HCl, heat: the peptide bonds break, the aryl–N bond survives:DNP-amino acid (the N-terminal residue) + free amino acids
Fig. 10.1.3 Sanger’s method: addition–elimination (SNAr) on FDNB, then acid hydrolysis.
Draw it in 60 s: peptide NH2 with a lone-pair arrow to the C–F carbon, ring arrow to the C–NO2; then the Meisenheimer anion with its pair re-forming the ring and F− leaving; finish with the DNP-peptide.

Edman: phenyl isothiocyanate (PhN=C=S) adds to the N-terminal NH₂ at pH 9 (PTC-peptide). Anhydrous CF₃COOH makes the sulfur attack the first peptide C=O and cuts off only the first residue as an anilinothiazolinone (ATZ), which aqueous acid turns into the stable phenylthiohydantoin (PTH), identified by HPLC against standards. The shortened peptide is intact, so the cycle repeats (automated sequenator, ≈ 50 residues) IFoS 2025 Q5(a) 5m.SN

PhN=C=S (Edman), pH 9H+ shiftphenylthio-carbamoyl (PTC)peptide CF3COOH (dry): C=O protonated; S attacks C C=O re-forms, peptide N leaves ATZ (thiazolinone)+H2N–peptide(n − 1): next cycleaq. H+ PTH-amino acid → HPLC
Fig. 10.1.4 Edman degradation: one residue per cycle, the rest of the peptide survives.
Draw it in 60 s: PhN=C=S + H2N–peptide: arrow from N to the central C, C=N arrow to N. PTC-peptide: S lone pair to the next C=O. Tetrahedral ring: C=O re-forms, peptide N leaves. Then ATZ → PTH.
  • C-terminus: carboxypeptidase removes the C-terminal residue. Fragments: trypsin cuts after Lys and Arg, chymotrypsin after Phe, Tyr and Trp, CNBr after Met; overlap the fragments to get the whole sequence.

10.1.5 Secondary structure ★★★

1 turn:3.6 residues,pitch 5.4 Årise 1.5 Å/resα-helix: right-handedC=O(i)···H–N(i+4), along the axisCαRCONHCαRCONHCαRNHCOCαRNHCONCNCantiparallel β-sheetH-bonds between strands; R alternate up/down
Fig. 10.1.5 α-Helix (H-bonds along the axis, inside one chain) and antiparallel β-sheet (H-bonds across, between chains).
Draw it in 60 s: a right-handed coil with dashed lines from residue i to i+4; beside it two zigzag strands with arrows N → C in opposite directions, C=O above H–N, dashed between.
  • α-Helix (Pauling and Corey): right-handed, 3.6 residues per turn, pitch 5.4 Å, rise 1.5 Å per residue. C=O of residue i H-bonds to N–H of residue i + 4 (a 13-atom ring); all backbone N–H and C=O are used, the bonds lie almost parallel to the axis and the side chains point outward. Stabilised by these intrachain H-bonds, close packing (van der Waals) inside the coil and the aligned peptide dipoles; Pro (no N–H, rigid ring) and Gly (too flexible) break it, as do runs of like charges CSE 2025 Q4(b)(iii) 5m IFoS 2022 Q6(c) 5m.SN
  • β-Pleated sheet: extended strands (≈ 3.4 Å per residue) side by side, interchain H-bonds perpendicular to the strands; side chains alternate above and below the pleat. Antiparallel sheets have straighter, stronger H-bonds than parallel ones. Silk fibroin (Gly-Ala rich) is β-sheet; α-keratin of hair is α-helix IFoS 2022 Q6(c).SN
  • Secondary vs tertiary: secondary structure is the local backbone conformation, fixed by backbone C=O···H–N bonds (helix, sheet, β-turn, random coil); tertiary structure is the whole chain folded in 3-D, fixed mainly by side-chain interactions (10.1.6) CSE 2022 Q7(a) 15m.

Part of VKC Basic

Read all 14 sections of this topic, its short notes and the PDF with VKC Basic

VKC Basic (₹999 for 6 months) opens every solved answer, the notes, the handbook and the daily answer archive. Every Mains test series includes it.

See what is included Already a member? Sign in

Solved PYQs, short notes and books: vkcscience.comTelegram: t.me/upsc_chemistry_vkc