Exam II

Primary Structure

Linear sequence of aa in a polypeptide.

• connected by (covalent) peptide bonds

Secondary Structure

Folding of polypeptide backbone

• stabilized by H-bonds between C=O and N-H

• alpha helix & beta pleated

Tertiary Structure

3D folding of one polypeptide chain
- interactions between side chains

Interactions:

• Hydrophobic interactions

• Hydrogen bonds

• Ionic bonds

• Disulfide bridges

• Van der Waals forces

• Weak attractions between closely packed atoms

Quaternatry Structure

Assembly of multiple polypeptide chains

• dimer

• trimer

• tetramer

What is the protein folding funnel?

• what is the most stable (functional) state called?

A model showing how a protein moves from many unfolded, high-energy conformations toward fewer, lower-energy conformations until reaching its stable, functional native state.

• Native state

What are the WEAK protein stabilizing interactions? (strongest to weakest)

• Ionic

• Hydrogen

• Hydrophobic Interactions

• Van der waals

What is a salt bridge.

• why might the energy gain be lower than expected

Ionic interations + & - amino acid side chain

• Desolvation (bonds were stabilized by water must be broken)

What are van der waals effects

e weak attractions between atoms caused by temporary or permanent dipoles (uneven distributions of electrons).

They help stabilize proteins by allowing closely packed atoms to attract one another.

Psi & Phi Torsion angle

Psi: Rotation around the Cα–C' (carbonyl carbon) bond.

Phi (φ): Rotation around the N–Cα bond.

• allows rotation

Omega angles

peptide bonds (cis or trans)

• partial double bond character = very RIGID

96% trans due to sterics

Alpha Helix

Polypeptide backbone right handed spiral around helical axis.

• side chains protrude

• 3.5 residues/ turn

• 7 residues/ integral turn

• Phi: -60

• Psi: 45 to -50

• H-bonds between backbone atoms

What is the n-4 rule

Donor is n (N-H)

Acceptor is n-4 (C=O)

What is a helical wheel diagram

Helical Stability

• bulkiness of side chains → steric hinderance = instability

• Interactions between side chains 3-4 residues apart (hydrophobic / electrostatic)

• Proline & Glycine = instability

• Terminal AA electrostatic attraction/ repulsion

How does Proline change Helical Stability?

Proline is too rigid & can’t function as a H-bond donor

• can still be in a helix

BENDS → local instability

How does Glycine change Helical Stability?

Decreases stability

Alpha helices require relatively consistent φ and ψ angles. Glycine's flexibility makes it easier for the helix to bend or lose its regular structure.

How does Electrostatic attraction/ repulsion with terminal amino acids affect helical stability?

Beta Strands → Sheets

• created by H-bonds between strands

• pleated sheets comes from planarity of peptide bonds

• side chains alternate directions

• ± 120 degrees

Anti parallel B sheets

Strands run in opposite directions.

OPTIMAL H-bonding (STRAIGHT)

• alternates H-bond donors/ acceptors

Parallel B-sheets

• Strands run in the same direction.

• Hydrogen bonds are angled.

B-Turn

4 residues connecting AP B -strands

Typically, a hydrogen bond forms between:

• The C=O group of amino acid 1.

• The N-H group of amino acid 4.

IMPORTANT Amino Acids:

Proline - rigid ring restricts backbone movement, bends the chain

Glycine - Small side chain allows it to fit in tight turn

Super Secondary Structures (Motifs)

Commonly observed, stable arrangements of 2ary structures

recognizable arrangement of multiple secondary structure elements (alpha helices, beta strands, and turns) that come together to form a recurring pattern.

What is a Globular Protein?

compact, rounded proteins with hydrophobic cores.

Protein Domains

Independently forming & folding region of a protein.