Question 5 of 6: Protein Structure and Eukaryotic Organelles

Question 5: Protein Structure and Eukaryotic Organelles (20 marks)

Question text not reproduced: the examination questions are © Engineers and Geoscientists BC. Open the official past paper (linked at the top of this page) to read the question, then follow the worked solution below.

(i) Levels of protein structure

Primary structure is the linear sequence of amino acids joined by peptide bonds along the polypeptide backbone, read N-terminus to C-terminus — it is entirely determined by the genetic code and uniquely dictates every higher level of folding.

Secondary structure is the local, regular folding pattern stabilised by hydrogen bonds between backbone N–H and C=O groups (not side chains). Four principal types:

1. α-helix. The backbone coils into a right-handed helix (≈3.6 residues/turn) stabilised by H-bonds between each residue's C=O and the N–H four residues ahead; side chains project outward. Common in membrane-spanning segments and structural proteins (e.g. keratin).
2. β-sheet (pleated sheet). Extended backbone strands (β-strands) line up side-by-side and H-bond to each other across strands, either parallel (strands run the same direction) or antiparallel (opposite directions, generally more stable H-bond geometry); the sheet "pleats" because alternating Cα atoms sit slightly above/below the plane.
3. β-turn (reverse turn). A tight, roughly 180° direction change over just 4 residues, stabilised by a single H-bond between residue 1's C=O and residue 4's N–H; turns let a polypeptide reverse direction so β-strands can pack into sheets and globular domains can form.
4. Random coil (and 3₁₀-helix). Segments with no regular, repeating H-bond pattern — irregular but not necessarily disordered in the folded protein; a related, tighter helix variant (3₁₀-helix, 3 residues/turn) occurs at helix termini and in short helical segments.

Tertiary structure is the overall three-dimensional fold of a single polypeptide chain, built from the packing and orientation of its secondary-structure elements against each other, stabilised by side-chain interactions: hydrophobic collapse of nonpolar residues to a solvent-shielded core, hydrogen bonds, ionic (salt-bridge) interactions, and covalent disulfide bonds between cysteines.

Quaternary structure is the assembly of two or more independently-folded polypeptide chains (subunits) into a single functional multi-chain complex, held together by the same non-covalent (and occasionally disulfide) interactions as tertiary folding, but between chains rather than within one — e.g. haemoglobin's four subunits, or many industrial enzymes that are only active as dimers/tetramers.

(ii) Eukaryotic organelles

(a) Mitochondria. Double-membrane organelles (own circular DNA, a relic of their prokaryotic endosymbiotic origin) that house the TCA cycle (matrix) and the electron transport chain + ATP synthase (inner membrane, folded into cristae to maximise surface area) — the site of oxidative ATP production described in Question 3(ii).

(b) Golgi bodies (Golgi apparatus). A stack of flattened membrane sacs (cisternae) that receives proteins/lipids from the ER, chemically modifies them (glycosylation, proteolytic processing), sorts them by destination tag, and packages them into vesicles for secretion, the plasma membrane, or lysosomes — the cell's "post office."

(c) Endoplasmic reticulum. A continuous network of membrane tubules/sacs extending from the nuclear envelope. Rough ER is studded with ribosomes and is the site of synthesis and initial folding of secreted and membrane-bound proteins (which are threaded into the ER lumen as they are translated). Smooth ER lacks ribosomes and instead synthesises lipids/steroids, and in liver cells detoxifies drugs and other lipophilic compounds via cytochrome P450 enzymes.

(d) Chloroplast. Found in plant cells and algae (not fungi, not animal cells); like mitochondria it is a double-membrane organelle with its own circular DNA (also endosymbiotic in origin), but it captures light energy in the thylakoid membranes (light reactions, producing ATP/NADPH and O₂ from water) and fixes CO₂ into sugar in the stroma (Calvin cycle) — the converse energy flow to a mitochondrion's oxidative breakdown.

(e) Flagella. Long, whip-like appendages used for cell motility. Eukaryotic flagella are built from a 9+2 arrangement of microtubules (axoneme) driven by dynein motor proteins and powered by ATP, undulating in a wave-like beat; this is structurally and mechanistically distinct from a bacterial flagellum, which is a rigid, hollow protein (flagellin) filament rotated like a propeller by a membrane-embedded motor driven by the proton-motive force, not ATP directly.