4.5.3 · D5Biomolecules
Question bank — Peptide bond; primary, secondary, tertiary, quaternary protein structure
True or false — justify
The peptide bond is a normal single bond that rotates freely.
False — resonance (see Amides — resonance & planarity) gives it partial double-bond character, locking the six-atom amide unit flat and rigid.
Denaturation destroys the primary structure of a protein.
False — it only breaks the weak forces (H-bonds, ionic, hydrophobic); the covalent peptide bonds stay intact, so the sequence is unchanged. See Denaturation of proteins.
A protein with a single polypeptide chain still has a quaternary structure.
False — quaternary structure means ≥2 chains assembled together; one chain can only reach up to tertiary.
Every protein must have a secondary structure.
True in practice for folded proteins — but some regions are "random coil" with no regular helix/sheet, so not every stretch of backbone is α or β.
The α-helix and β-sheet are both held together by the same type of bond.
True — both use backbone hydrogen bonds; they differ only in geometry (coil vs. flat sheet).
Disulphide bridges are a feature of secondary structure.
False — links side-chains, so they belong to tertiary (or between chains, quaternary) structure, not the backbone-only secondary level.
Forming a dipeptide from two amino acids releases two water molecules.
False — amino acids release waters, so a dipeptide () releases exactly one .
Haemoglobin loses its ability to carry oxygen if boiled.
True — heat denatures it, collapsing the tertiary/quaternary fold that shapes the -binding pocket. See Haemoglobin & oxygen transport.
Spot the error
"A peptide bond is an ester between and ."
Wrong — it is an amide between and ; nitrogen sits in the link, not oxygen. An ester would need an alcohol.
"Primary structure is held by hydrogen bonds."
Wrong — primary structure (the sequence) is held by covalent peptide bonds (and ); H-bonds hold the secondary level.
"The N-terminus is the end with the free group."
Reversed — the N-terminus has the free ; the free end is the C-terminus. Sequences are read N→C.
"Glycine + Alanine (Gly first) is named Alanylglycine."
Wrong — the N-terminal residue takes the "-yl" ending first, giving Glycylalanine (Gly-Ala), read N→C.
"Fibrous proteins are water-soluble and act as enzymes."
Wrong — fibrous proteins are thread-like, insoluble, and structural; globular proteins are soluble and functional (enzymes, insulin). Compare Enzymes — globular proteins as biocatalysts.
"The peptide bond forms by hydrolysis."
Wrong — it forms by condensation (loss of water); hydrolysis (addition of water) does the reverse, breaking it.
"Hydrophobic groups sit on the outside of a globular protein."
Wrong — non-polar R-groups hide inside, away from water; polar/charged groups face the aqueous outside.
"Sickle-cell anaemia is caused by a broken hydrogen bond."
Wrong — it's a primary-structure change: one Glu→Val substitution in the sequence, which then alters the fold.
Why questions
Why does the peptide bond being planar help proteins fold into regular shapes?
Because the rigid, flat units can only pivot at the atoms, the backbone has limited freedom — it naturally settles into repeating helices/sheets instead of a floppy tangle.
Why are secondary/tertiary structures broken by heat but the primary is not?
Secondary/tertiary rely on weak forces (H-bonds, ionic, hydrophobic) that gentle heat easily shakes apart; peptide bonds are strong covalent bonds that survive.
Why does changing one amino acid sometimes ruin the whole protein?
The sequence (primary) dictates all higher folding; swapping one residue can alter local charge/size and disrupt the R-group interactions that hold the 3D shape.
Why do amino acids react with each other at all?
They are bifunctional — each carries an acid and a base — so one's acid attacks the next's amine, exactly like acid + amine → amide. See Amino acids — structure, classification, zwitterion.
Why is the peptide bond shorter than an ordinary single bond?
Resonance delocalises N's lone pair into the , adding double-bond character; more bonding electron density pulls the atoms closer, shortening the bond.
Why can't the peptide bond be an ionic bond even though amino acids form zwitterions?
Zwitterions are electrostatic states of a single amino acid; the peptide link is a genuine shared-electron covalent amide bond formed by condensation, not attraction of ions.
Why does silk (β-sheet) feel different from wool/hair (α-helix)?
β-sheets are flat, extended and packed side-by-side (strong, inextensible); α-helices are coiled springs that can stretch — so wool is springy, silk is not.
Edge cases
A "peptide" made of exactly one amino acid — how many peptide bonds?
Zero — with , bonds ; you need at least two residues to form a single peptide bond.
Is a glycosidic bond in a carbohydrate the same as a peptide bond?
No — a glycosidic bond joins sugars via an oxygen bridge (an acetal), while a peptide bond is an amide joining amino acids. See Carbohydrates — glycosidic bond.
Can a protein have tertiary structure but no quaternary structure?
Yes — a single folded chain (e.g. myoglobin, insulin's mature form) has full tertiary structure; quaternary only appears once multiple chains assemble.
If you break every bond but leave peptide bonds intact, is primary structure lost?
No — the amino-acid sequence (the backbone order) is defined by peptide bonds and remains; you have only removed cross-links stabilising the higher folds.
What is the "structure level" of a free, unbonded single amino acid?
None of the four — the levels describe polypeptides; a lone amino acid is just a monomer (a zwitterion) with no peptide bond yet.
Does adding water back to a peptide restore two separate amino acids?
Yes — hydrolysis reverses condensation, inserting across the bond to regenerate the free and ends.
At what level does haemoglobin's "2α + 2β" description belong?
Quaternary — it describes how four separate chains assemble; each individual chain's own fold is its tertiary structure.
Recall One-sentence self-test
If you can state, for any given force, which structural level it stabilises and why that level survives or dies under heat, you've mastered this bank. Force → level, and does heat break it? ::: Covalent peptide/S–S → primary/tertiary cross-links (heat-resistant); H-bonds, ionic, hydrophobic → secondary/tertiary/quaternary (heat-sensitive).