protein structures-lecture 8

What is a peptide bond?

A covalent bond between the carboxyl group of one amino acid and the amino group of another, formed by a condensation reaction.

Which ends define a polypeptide?

N-terminal has the free amino group, C-terminal has the free carboxyl group.

What is the chemical nature of a peptide bond?

Has partial double-bond character, planar, rigid, restricts rotation.

Why is protein conformation important?

The 3D shape determines biological activity; misfolding leads to loss of function or disease.

What is steric hindrance?

Restriction of bond rotation or position due to bulky groups interfering with each other.

What is primary structure of a protein?

Linear sequence of amino acids.

What is secondary structure of a protein?

Local folding such as α-helix and β-sheet.

What is a supersecondary structure (motif)?

Combination of α-helices and β-sheets, e.g., helix-turn-helix.

What is tertiary structure of a protein?

Overall 3D structure of one polypeptide chain.

What is quaternary structure of a protein?

Assembly of multiple polypeptide subunits.

What is a protein domain?

An independently folded, functional region of a protein.

What is denaturation?

Loss of 3D structure due to heat, pH, or chemicals → loss of function.

What hydrogen bond pattern stabilizes an α-helix?

H-bonds between backbone C=O of residue i and N–H of residue i+4.

What hydrogen bond pattern stabilizes a β-sheet?

H-bonds between backbone groups of adjacent strands (parallel or antiparallel).

Which amino acids form hydrogen bonds in proteins?

Ser, Thr, Tyr, Asn, Gln, His.

Which amino acids form ionic bonds in proteins?

Asp⁻, Glu⁻ with Lys⁺, Arg⁺, His⁺.

Which amino acids cluster in the hydrophobic interior of proteins?

Val, Leu, Ile, Phe, Trp, Met.

Which amino acids are usually on the surface of proteins?

Polar or charged residues.

Which amino acid forms disulfide bonds?

Cysteine (Cys).

What determines protein conformation?

The amino acid sequence.

Describe the structure of collagen.

Triple helix of Gly-X-Y repeats (X often Pro, Y often hydroxyproline); stabilized by hydroxylation requiring vitamin C.

What is the biological role of collagen?

Provides tensile strength in connective tissues, skin, bone, tendons.

How do proteins interact with ligands?

Through complementary binding sites stabilized by weak forces (H-bonds, ionic, hydrophobic, van der Waals).