Secondary Structure

What are the four levels of protein structure?

Primary = amino acid sequence; secondary = local structures; tertiary = 3D fold of one chain; quaternary = arrangement of multiple folded chains.

What determines secondary protein structure?

Repeated local backbone conformations and hydrogen bonding produce alpha-helices, beta-sheets, and turns.

Why are peptide bonds planar?

Resonance gives the C–N peptide bond partial double-bond character, restricting rotation.

Why are peptide bonds usually trans?

The trans arrangement minimizes steric clashes between groups on adjacent residues.

Which backbone bonds can rotate, and what angles describe them?

N–Cα rotates by phi (φ); Cα–C=O rotates by psi (ψ).

Why are protein backbone conformations restricted?

Peptide bonds are rigid and many φ/ψ combinations cause steric clashes between atoms.

What is a Ramachandran plot?

A graph of φ versus ψ showing sterically allowed and unfavorable backbone conformations.

What do the favored regions on a Ramachandran plot correspond to?

Backbone conformations associated with alpha-helices, beta-sheets, and some turns.

Why does glycine have more allowed Ramachandran angles?

Its side chain is only hydrogen, producing less steric hindrance.

How do repeated φ and ψ angles produce secondary structure?

Repeating favorable backbone angles creates regular, repeating structures such as helices and sheets.

What are the approximate φ and ψ angles of a right-handed alpha-helix?

φ = −57° and ψ = −47°; both are negative.

What are the approximate φ and ψ angles of antiparallel beta-sheets?

φ = −139° and ψ = +135°.

What are the approximate φ and ψ angles of parallel beta-sheets?

φ = −119° and ψ = +113°.

What two requirements make alpha-helices and beta-sheets favorable?

Sterically allowed backbone conformations and extensive backbone hydrogen bonding.

Which backbone groups form hydrogen bonds in secondary structures?

The backbone carbonyl C=O acts as an acceptor, and the amide N–H acts as a donor.

What is the hydrogen-bond pattern in a right-handed alpha-helix?

The C=O of residue i hydrogen-bonds with the N–H of residue i+4.

What are the important geometric properties of an alpha-helix?

Right-handed; about 3.6 residues per turn; pitch of 5.4 Å per turn.

Why can an alpha-helix form without many steric clashes?

Side chains project outward and backward away from the helical backbone.

Why are glycine and proline generally unfavorable for alpha-helices?

Glycine is highly flexible; proline is rigid and lacks the backbone N–H needed for normal helix hydrogen bonding.

What sequence characteristics tend to favor alpha-helix formation?

Non-beta-branched residues, limited steric crowding, and favorable nearby side-chain interactions.

Which amino acid positions are near one another in an alpha-helix?

Residues i and i+3 or i+4; their side chains may interact.

How do charged side chains affect alpha-helix formation?

Nearby opposite charges can stabilize through attraction; nearby like charges repel and can destabilize.

What is a helical wheel?

A diagram looking down the axis of an alpha-helix that shows the arrangement of side chains.

How do you draw a helical wheel?

Place successive residues around a circle about 100° apart, following their order from N to C.

How do you identify an amphipathic helix using a helical wheel?

Hydrophobic residues cluster on one face while polar or charged residues cluster on the other.

What is a heptad repeat and which positions are important?

A repeating seven-residue a–g pattern; positions a and d often form a hydrophobic face.

How do coiled-coils form?

Two amphipathic alpha-helices pack together through hydrophobic interactions between their matching faces.

How can you distinguish parallel from antiparallel beta-sheets?

Parallel strands run in the same N→C direction; antiparallel strands run in opposite directions.

How do hydrogen bonds differ in parallel versus antiparallel beta-sheets?

Parallel sheets have non-linear H-bonds; antiparallel sheets have more linear H-bonds.

What do arrows indicate when drawing beta-sheets?

The N→C direction of each strand; same arrows = parallel, opposing arrows = antiparallel.

How are side chains arranged in a beta-sheet?

They alternate above and below the sheet, away from the hydrogen-bonded backbone.

Why can bulky and beta-branched residues favor beta-sheets?

The extended structure separates their side chains and minimizes steric clashes.

What is a mixed beta-sheet?

A sheet containing both parallel and antiparallel neighboring strands; extended sheets also twist in 3D.

What are random coils, loops, and beta-hairpins?

Random coils lack detectable regular structure; loops connect structures; beta-hairpins connect antiparallel beta-strands.

What distinguishes Type I and Type II beta-turns?

Both can have an H-bond between residues 1 and 4. Type I often has Pro at position 2; Type II often has Gly at position 3.