Protein Structure & Denaturation

CHEAmino Acids & Proteins

Proteins are organised in up to four structural levels, each held by characteristic bonds, and denaturation is the disruption of all but the primary level. This subtopic tests the four-level description, denaturation, fibrous-vs-globular proteins, and enzymes as biocatalysts.

Primary structure: the sequence of amino acids joined by peptide (covalent amide) bonds — the most stable level.
Secondary structure: regular local folding ( $\alpha$ -helix or $\beta$ -pleated sheet) held by hydrogen bonds between backbone $>C=O$ and $\text{-}NH$ groups.
Tertiary structure: the overall 3-D folding held by H-bonds, ionic (salt) bridges, disulphide ( $\text{-}S\text{-}S\text{-}$ ) bonds and hydrophobic/van der Waals interactions; quaternary structure: the assembly of two or more polypeptide subunits.
Denaturation: loss of secondary, tertiary and quaternary structure (by heat, acid, alcohol, heavy-metal ions) while the primary sequence stays intact, so biological activity is lost — e.g. boiling an egg, curdling of milk.
Fibrous proteins are long, thread-like, insoluble in water and structural (keratin, collagen, myosin); globular proteins are folded, roughly spherical, water-soluble and functional (insulin, albumin, enzymes).
Enzymes are globular protein biocatalysts; key features are high specificity (lock-and-key for a particular substrate) and very high catalytic efficiency under mild body conditions (about 37 degrees Celsius, near-neutral pH).
The $\alpha$ -helix is stabilised by intra-chain H-bonds (a coiled rod), whereas the $\beta$ -pleated sheet is stabilised by inter-chain H-bonds between adjacent extended strands.
In the $\alpha$ -helix each backbone $>C=O$ hydrogen-bonds to the $\text{-}NH$ of the amino acid roughly four residues further along the chain.
Denaturation is usually irreversible (a boiled egg does not un-boil) because the unfolded chains aggregate; only the non-covalent and disulphide interactions break, never the peptide bonds.
On denaturation a protein loses its specific 3-D shape and hence its biological function (e.g. an enzyme loses catalytic activity), while still yielding the same amino acids on hydrolysis.
Enzymes work by lowering the activation energy of a reaction and are extremely efficient, increasing reaction rates by very large factors under mild conditions.
Enzyme activity depends on shape, so it is sensitive to temperature and pH: extremes denature the enzyme and destroy its activity.

Where the marks go

Saying peptide bonds break during denaturation — only secondary/tertiary/quaternary interactions are lost; the primary peptide-bonded sequence is retained.
Mixing up the H-bonding pattern: $\alpha$ -helix uses intra-chain H-bonds, $\beta$ -pleated sheet uses inter-chain H-bonds.
Listing disulphide bridges as a feature of primary structure — they form within tertiary structure (cross-links), not the peptide backbone sequence.
Swapping fibrous/globular properties: fibrous = insoluble, structural (keratin, collagen); globular = soluble, functional (enzymes, insulin).
Claiming denaturation changes the amino-acid composition or sequence — it changes only the 3-D shape, so hydrolysis still gives the same amino acids.

How the board asks it

Define / statedenaturation and the structural levels it affects
Define denaturation of proteins. Name two physical or chemical agents that can bring it about, and state which structural levels are affected.
Distinguishfibrous vs globular proteins
Distinguish between fibrous and globular proteins on the basis of shape, solubility in water and biological role, giving one example of each.
Give reasonsprimary sequence is retained during denaturation
Account for the fact that a boiled egg yields the same amino acids on hydrolysis as a raw egg, even though it has lost its biological activity.
Assertion–Reasonpeptide bonds not broken on denaturation
Assertion: On denaturation a protein loses its biological activity. Reason: During denaturation the peptide bonds of the primary structure are hydrolysed. State whether the assertion and reason are true and whether the reason correctly explains the assertion.
Give reasons $\alpha$ -helix vs $\beta$ -pleated sheet hydrogen bonding
Give reasons: the $\alpha$ -helix of a protein is stabilised by intra-chain hydrogen bonds whereas the $\beta$ -pleated sheet is stabilised by inter-chain hydrogen bonds.
Define / stateenzymes as biocatalysts; sensitivity to temperature and pH
State two characteristic features of enzymes as biocatalysts, and explain why their catalytic activity is destroyed at very high temperature or extreme pH.

Practise this topic

PreviousAmino Acids & Proteins: Structure & Terms NextNucleic Acids: Components & Structure

Written for Sublevo. Question text quoted anywhere in these notes is the Council’s and carries its year and paper; the board’s own diagrams are not reproduced.