(a) Discuss the different types of secondary structures of proteins and compare these structures with tertiary structure of…

(a) Secondary structures of proteins compared with tertiary structure

Protein secondary structures are local, regularly repeating backbone conformations stabilized mainly by C=O...H-N hydrogen bonds. The alpha-helix is a right-handed helix with 3.6 residues per turn, a rise of 1.5 Å and a pitch of 5.4 Å; each carbonyl oxygen accepts a hydrogen bond from the N-H group four residues ahead. The beta-pleated sheet is formed by extended strands linked by interstrand or interchain hydrogen bonds; antiparallel sheets have nearly linear hydrogen bonds, while parallel sheets have slightly angled bonds and a different spacing. Beta-turns are short four-residue reversals that change the direction of the chain, often involving proline or glycine, and may contain a hydrogen bond between residues i and i+3. Random coils or loops are irregular segments without a fixed hydrogen-bond pattern; they connect helices, sheets and turns. In globular proteins, alpha-helices and beta-sheets are often separated by turns and loops, while in fibrous proteins beta-sheets may form long, stable fibres. Tertiary structure is the overall three-dimensional folding of the entire polypeptide chain, in which these secondary elements pack into a compact native shape. It is controlled by side-chain interactions: hydrophobic residues cluster in the interior, disulfide bridges form between cysteine residues, ionic or salt bridges link charged side chains, and hydrogen bonds and van der Waals contacts further stabilize the fold. Thus secondary structure is local, regular and backbone-driven, whereas tertiary structure is global, side-chain-driven and determines the final biological shape; secondary elements are the building blocks organized by tertiary interactions.

(b)(i) Butanoyl chloride with NaBH₄

Butanoyl chloride, CH₃CH₂CH₂COCl, is reduced by NaBH4. Borohydride delivers hydride to the carbonyl carbon; the tetrahedral intermediate collapses, expelling chloride and giving butanal. The aldehyde formed is still readily reduced, so a second hydride adds, and H3O+ protonates the alkoxide to give butan-1-ol, CH3CH2CH2CH2OH.

(b)(ii) But-2-yne with Na in liquid NH₃

But-2-yne undergoes dissolving-metal reduction with Na in liquid NH₃. Sodium transfers an electron to the alkyne to form a radical anion; protonation by NH₃ gives a vinyl radical, which takes up the less crowded trans geometry. A second electron gives the trans vinyl anion, and a second protonation gives trans-but-2-ene, (E)-but-2-ene. The anti relationship of the two added hydrogens explains the trans alkene.

(c)(i) Identification of A, B and C

A contains C, H and O, has molecular weight 102, and shows 1H NMR signals at delta 1.1 (doublet, 6H) and 3.55 (septet, 1H). The formula C6H14O is consistent with M=102. The 6:1 doublet-septet pattern indicates two equivalent isopropyl groups, so A is diisopropyl ether, (CH3)2CHOCH(CH3)2. The septet at 3.55 is the methine proton coupled to six equivalent methyl protons; the doublet at 1.1 is the six methyl protons coupled to that methine. With 1 mol HI, the ether oxygen is protonated and iodide attacks the more accessible carbon, cleaving the C-O bond to give isopropanol B, (CH3)2CHOH, and isopropyl iodide C, (CH3)2CHI. C shows the corresponding isopropyl iodide pattern at delta 1.9 and 4.25. B has a strong IR band at 3330 cm-1 for O-H, 1H NMR signals at delta 1.05 (d, 6H) and 3.6 (septet, 1H), and a D2O-exchangeable singlet at delta 4.4. With excess HI, the alcohol is converted further to iodide, so only C remains: (CH3)2CHOCH(CH3)2 + HI gives (CH3)2CHOH + (CH3)2CHI, and (CH3)2CHOH + HI gives (CH3)2CHI + H2O.

(c)(ii) The three C₅H₁₀O carbonyl isomers

The C₅H₁₀O compounds giving a positive 2,4-DNP test are carbonyl compounds. The NMR patterns distinguish ethyl, tert-butyl and isopropyl environments attached to the carbonyl carbon. (1) Pentan-3-one, CH₃CH₂COCH₂CH₃: two equivalent ethyl groups give only a triplet (CH₃, δ 1.05) and a quartet (CH₂ next to C=O, δ 2.47). (2) 2,2-Dimethylpropanal, (CH₃)₃CCHO: a 9H singlet near δ 1.1 for the tert-butyl group and a 1H singlet near δ 9.5 for CHO, since neither has neighbours to couple with. (3) 3-Methylbutan-2-one, CH₃COCH(CH₃)₂: a 6H doublet (δ 1.0), a 3H singlet for the acetyl CH₃ (δ 2.1) and a 1H septet for the methine (δ 2.2). Among these, 2,2-dimethylpropanal, which has no α-hydrogen, is the isomer that, on treatment with concentrated KOH, undergoes the Cannizzaro reaction to give 2,2-dimethylpropan-1-ol, (CH3)3CCH2OH, and potassium 2,2-dimethylpropanoate, (CH3)3CCOOK. In the mechanism, OH⁻ adds to one aldehyde, and the tetrahedral anion transfers a hydride to a second aldehyde, which is reduced while the first is oxidised. Pentan-3-one and 3-methylbutan-2-one have α-hydrogens and enolise instead.