BS1030 Topic 1 Lecture 3 Primary and Secondary structure

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary structure.

What does the primary structure of a protein describe?

The linear sequence of amino acids in a polypeptide chain.

What does the secondary structure of a protein describe?

The local folding or coiling of regions of the polypeptide chain, often into α-helices or β-sheets.

What does the tertiary structure of a protein describe?

The overall 3D shape of a single folded polypeptide chain.

What does the quaternary structure of a protein describe?

The association of two or more folded polypeptide chains into a multi-subunit complex.

What is the N-terminus of a polypeptide?

The end of the chain with a free amino group (NH₃⁺).

What is the C-terminus of a polypeptide?

The end of the chain with a free carboxyl group (COO⁻).

In which direction are proteins synthesized?

From the N-terminus to the C-terminus.

What type of bond links amino acids in a polypeptide chain?

A peptide bond.

What atoms are involved in a peptide bond?

The carbon of one amino acid's carboxyl group and the nitrogen of another's amino group.

Are peptide bond side chains involved in peptide bonding?

No, side chains (R groups) are not involved in peptide bond formation.

Why does the peptide bond have partial double-bond character?

Because of resonance between the carbonyl oxygen and the amide nitrogen.

What are the consequences of peptide bond partial double-bond character?

The C-N bond is shorter and rigid, allowing no rotation around the bond.

What is the typical configuration of a peptide bond?

Trans configuration, which reduces steric clashes.

Which atoms in the peptide bond can form hydrogen bonds?

The carbonyl oxygen and the amide hydrogen.

What allows proteins to fold despite rigid peptide bonds?

Rotation occurs around the phi (φ) and psi (ψ) bonds of the α-carbon.

What are phi (φ) and psi (ψ) angles?

Torsion angles around the N-Cα and Cα-C bonds in a polypeptide chain.

What is a torsion (dihedral) angle?

The angle between two planes defined by four atoms; describes rotation around a bond.

Why are only certain φ and ψ angle combinations allowed?

Because some combinations cause steric clashes between atoms.

What does a Ramachandran plot show?

Allowed and disallowed φ and ψ angle combinations for amino acids in proteins.

Who created the Ramachandran plot?

Dr. G.N. Ramachandran.

What secondary structures are predicted by the Ramachandran plot?

The α-helix and the β-sheet.

What forces stabilize secondary structure?

Hydrogen bonds.

What is an α-helix?

A right-handed helical structure stabilized by hydrogen bonds within the same polypeptide chain.

How are hydrogen bonds arranged in an α-helix?

Between the carbonyl oxygen of one peptide bond and the amide hydrogen four residues ahead.

How many amino acid residues per turn are in an α-helix?

3.6 residues per turn.

What is the pitch (height per turn) of an α-helix?

0.54 nanometers.

Where are the R groups located in an α-helix?

On the outside of the helix.

Who discovered the α-helix?

Linus Pauling, Robert Corey, and Herman Branson (1950-1951).

What shape does the α-helix form?

A rigid, right-handed cylinder that supports protein architecture.

What is a β-sheet?

A structure made of extended peptide chains connected by hydrogen bonds between backbone atoms.

How are R groups arranged in a β-sheet?

They alternate above and below the plane of the sheet.

What is the difference between parallel and antiparallel β-sheets?

In parallel sheets, strands run in the same direction; in antiparallel, they run in opposite directions.

Which β-sheet arrangement is more stable?

Antiparallel, due to more linear hydrogen bonds.

What is a β-hairpin bend?

A turn connecting two antiparallel β-strands; common in globular proteins.

What type of bonds stabilize β-sheets?

Hydrogen bonds between neighboring strands.

How does hydrogen bonding differ in α-helices and β-sheets?

In α-helices, H-bonds form within one chain; in β-sheets, H-bonds form between chains.

What percentage of haemoglobin's structure is α-helical?

Approximately 60%.

What type of secondary structure predominates in silk fibroin?

β-sheets.

What property does β-sheet structure give silk fibroin?

High tensile strength but little elasticity.

Why are hydrogen bonds crucial for protein structure?

They stabilize both secondary and tertiary structures.