Protein Structure

What is primary protein structure?

The linear sequence of amino acids in a polypeptide chain.

What is secondary protein structure?

Localized, regular folding patterns like \alpha -helices and \beta -pleated sheets, stabilized mainly by hydrogen bonds between backbone amide and carbonyl groups.

What is tertiary protein structure?

The overall 3D folding of a single polypeptide chain, including secondary structures, loops, and irregular regions, stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and sometimes disulfide bridges.

What is quaternary protein structure?

The association of multiple polypeptide subunits into a functional protein complex (e.g., hemoglobin's \alpha2\beta2 structure).

Describe the key characteristics and rotational freedom of a peptide bond.

The peptide bond is planar and has a partial double-bond character due to resonance between the carbonyl C=O and the C–N bond. It also has a permanent dipole (carbonyl C\delta^{+}-O\delta^{-} and amide N\delta^{-}-H\delta^{+} ). Rotation is restricted across the peptide bond (C–N) but is possible around the C\alpha-N ( \phi ) and C\alpha-C ( \psi ) bonds.

What is the structure of an \alpha -helix?

Right-handed coil of backbone.

What is the structure of a \beta -sheet?

Extended zigzag strands.

Where do hydrogen bonds form in an \alpha -helix?

Between C=O of residue i and N–H of residue i+4 (within the same chain).

Where do hydrogen bonds form in a \beta -sheet?

Between backbone atoms in different strands (can be parallel or antiparallel).

How are side chains oriented in an \alpha -helix?

Side chains project outward from the helix.

How are side chains oriented in a \beta -sheet?

Side chains alternate above and below the sheet.

What factors stabilize an \alpha -helix?

Intrachain H-bonds, optimal \phi/\psi angles, often amphipathic.

What factors stabilize a \beta -sheet?

Interchain H-bonds; stability affected by sheet twist.

Where are \alpha -helices commonly found?

Common in membrane-spanning domains, keratin.

Where are \beta -sheets commonly found?

Common in silk fibroin, \beta -barrels.

Which amino acid residues typically form \alpha -helices?

Ala, Leu, Met.

Which amino acid residues typically form \beta -sheets?

Val, Ile, Tyr.

How would you design a 15-residue \alpha -helix with 4 nonpolar residues on one face, and what is its functional significance?

In an \alpha -helix, there are 3.6 residues per turn, so residues i and i+3 or i+4 will be on the same face. To design a 15-residue \alpha -helix with 4 nonpolar residues on one face, you would place nonpolar residues every 3rd or 4th position along the sequence to align them on one side. The remaining residues would be polar/charged to create an amphipathic helix.

Example sequence (N \to C):
Ala–Lys–Glu–Leu–Ala–Lys–Glu–Leu–Ala–Lys–Glu–Leu–Ala–Lys–Glu

Here, Leucine (Leu) is nonpolar and appears at positions i, i+4, i+8, i+12 , creating a hydrophobic face. The amphipathic nature makes it suitable for interacting with hydrophobic environments like membrane surfaces or protein cores.

What type of four-residue sequence is likely to form a reverse turn and why?

Reverse turns (or \beta -turns) often contain Glycine (flexible) and Proline (rigid kink) at specific positions. A common example is Pro–Gly–Ser–Asp. Proline at position 2 (or 1) helps create the bend, Glycine allows a tight turn angle, and polar residues help stabilize the turn through hydrogen bonds.

Describe the classic experiment that demonstrated spontaneous protein folding and its implications, along with modifications in cellular folding.

Christian Anfinsen’s ribonuclease A study (1960s). He denatured purified ribonuclease A with urea (to disrupt noncovalent interactions) and \beta -mercaptoethanol (to reduce disulfide bonds), causing the protein to lose catalytic activity. Upon removal of the denaturants and allowing oxidation in aqueous buffer, the protein spontaneously refolded and recovered its enzymatic activity. This concluded that all information for correct folding is contained in the primary amino acid sequence.

However, in cells, folding often requires molecular chaperones (e.g., Hsp70, chaperonins) to prevent aggregation, guide folding, and sometimes requires ATP, due to crowded cellular environments and co-translational folding.

What is the major thermodynamic driving force for protein folding, and how does it work?

The hydrophobic effect is the dominant thermodynamic driving force. Nonpolar side chains disrupt the hydrogen-bonded network of water. Burying these nonpolar groups inside the protein reduces the number of ordered water molecules, significantly increasing the entropy ( \Delta S ) of the solvent, which is a large favorable contribution to the overall free energy change of folding.

Early in folding, this leads to a hydrophobic collapse, forming a 'molten globule'—a compact but still dynamic intermediate—which then rearranges into the final stable tertiary structure via secondary structure stabilization and fine-tuning of side-chain packing.