Protein Structure

How is a peptide bond formed?

carboxyl group of one amino acid reacts with the amino group of another, releasing H₂O.

What reaction breaks a peptide bond?

Hydrolysis — addition of water breaks the peptide bond.

In what direction is an amino acid sequence written/read?

N-terminus → C-terminus.

What identifies the N-terminus of a peptide?

end containing free amino group.

What identifies the C-terminus of a peptide?

end containing free carboxyl group.

What is the repeating pattern of the peptide backbone?

α-carbon → carbonyl carbon → amide nitrogen.

Are amino acid R-groups part of the peptide backbone?

No, R-groups/side chains project from the backbone.

Which parts of the peptide backbone participate in hydrogen bonding?

N-H = hydrogen-bond donor;

C=O = hydrogen-bond acceptor.

Why is the peptide C-N bond relatively rigid?

does not freely rotate.

What conformation do peptide bonds usually adopt?

Trans.

What are the four levels of protein structure?

Primary = amino acid sequence

Secondary = local folding

Tertiary = 3D shape of one polypeptide

Quaternary = arrangement of multiple polypeptide subunits

What is primary protein structure?

linear amino acid sequence of a polypeptide.

What does Anfinsen's principle state?

protein's primary aa sequence contains info to determine final 3D structure

What is secondary protein structure?

Local recurring folding patterns of the polypeptide backbone, including

-α-helices

-β-strands/β-sheets

-loops and turns.

What primarily stabilizes secondary protein structure?

Hydrogen bonds.

What is tertiary protein structure?

complete 3D shape of ONE polypeptide chain.

What is quaternary protein structure?

2 or more polypeptide chains into functional protein complex

Homomeric vs heteromeric proteins?

Homomeric = identical subunits

Heteromeric = different subunits.

What are the major structural features of an α-helix?

Right-handed helix

R-groups project outward

Stabilized by hydrogen bonds

What hydrogen-bonding pattern stabilizes an α-helix?

carbonyl O of one residue H-bonds with the amide H of the amino acid 4 residues later.

Why is proline rarely found within an α-helix?

Its amide nitrogen cannot participate normally in the hydrogen bonding needed for the helix.

Where do the R-groups point in an α-helix?

Outward from the helix.

What is a β-sheet?

Extended β-strands arranged next to one another and stabilized by hydrogen bonds.

What are the two possible arrangements of β-strands in a β-sheet?

Parallel ; Antiparallel

Where do the R-groups point in a β-sheet?

Outward from the sheet.

What is a protein domain?

An independently folding, stable, compact 3D unit that acts as a building block of protein structure and function.

What is the helix-turn-helix motif commonly associated with?

DNA-binding proteins.

What is a coiled-coil, and what protein from the lecture uses it?

Two right-handed α-helices wrap around one another; Example: keratin.

What is an EF-hand motif?

A Ca²⁺-binding motif consisting of two α-helices separated by a loop that binds Ca²⁺.

What is the function of a zinc-finger motif?

Often allows proteins to bind DNA.

How does a leucine zipper promote protein-protein interactions?

Leucine side chains line one face of an α-helix, producing hydrophobic interactions.

What is the β-α-β motif?

Two parallel β-strands with an intervening α-helix.

What is the Greek-key motif?

A motif containing four β-strands arranged in a pattern resembling a Greek decorative key.

What do molecular chaperones do?

They assist proteins in folding.

What bond forms between two cysteine residues?

A disulfide bond.

What are ionic interactions in proteins?

Attraction between oppositely charged groups.

Which levels/interactions can hydrogen bonds contribute to?

Secondary structure, Tertiary structure, Protein-ligand interactions.

What is the hydrophobic effect in protein folding?

Nonpolar side chains tend to avoid water and cluster together.

Which major interactions stabilize tertiary protein structure?

Hydrophobic interactions

Hydrogen bonds

Ionic interactions

Disulfide bonds.

What happens during protein denaturation?

The protein loses its normal 3D shape.

Are peptide bonds usually broken during protein denaturation?

No, peptide bonds usually remain intact.

What is protein misfolding?

Failure of a protein to achieve its correct structure.

In a typical soluble protein, where are hydrophobic side chains usually found?

Inside the protein, away from water.

In a typical soluble protein, where are hydrophilic side chains usually found?

On the protein surface.

What could happen if a hydrophobic residue is replaced with a strongly hydrophilic residue?

It may destabilize protein folding.

What is collagen?

The most common protein in the body.

Which amino acid is especially abundant in collagen?

Glycine.

Which other amino acid is abundant in collagen?

Proline.

What is the handedness of an individual collagen chain versus the collagen triple helix?

Individual chain = LEFT-handed; Triple helix = RIGHT-handed.

Which collagen amino acids undergo hydroxylation?

Proline and lysine.

What vitamin is required for hydroxylation during collagen formation?

Vitamin C.

Why is hydroxylation important for collagen?

It helps collagen form strong cross-links.

What happens to collagen during severe vitamin C deficiency?

Impaired collagen strengthening leads to scurvy.