Structure

Question 1

Peptide bond

Answer 1

Planar, rigid, strong dipole moment

Question 2

Peptide H bond

Answer 2

C=O proton acceptor, N-H proton donor. Directional (needs orientation)

Question 3

Alpha helix

Answer 3

H bond 4 residues up strand, right handed, 3.6 residues per turn, side chains point out

Question 4

Beta sheets

Answer 4

Parallel or anti-parallel, extended structure, slight curvature

Question 5

Amino acid bond angles

Answer 5

Ca-C(=O) (psi, w), C-N (omega), N-Ca (phi ø)

Question 6

Ramachandran plot

Answer 6

psi vs phi
alpha -57, -47
beta -135, 135
disallowed regions

Question 7

Glycine

Answer 7

no side chain = flexible

Question 8

Proline

Answer 8

cyclic - limits phi to 60º

Question 9

Cysteine

Answer 9

has sulfur (disulphide bonds), more nucleophilic than O

Question 10

Secondary structure

Answer 10

mediated by backbone atoms not side chains (freedom to change but have similar function but also achieve many functions by varying residues)

Question 11

Protein diagrams

Answer 11

Topology, cartoon/ribbon, ball & stick, surface, spheres

Question 12

Techniques to find structure

Answer 12

NMR (small proteins, dynamics), X-ray crystallography (electron density, crystals, common), cyroelectron-microscopy (big proteins, images)

Question 13

Anfinsen experiment

Answer 13

ribonuclease A -> proteins encode info -> folding
reducing agent BME-> expose disulfide bonds
remove urea and low BME = native structure

Question 14

Denaturants

Answer 14

chaotropic salts (expose hydrophobic), disulphide bond disruption, heat, organic solvents, detergent

Question 15

tracking folding/unfolding

Answer 15

activity, circular dichroism, heat capacity, light scattering, trp abs/fluorescence (environment)

Question 16

circular dichroism

Answer 16

spectroscopy technique -> rotating plane of polarised light -> gives characteristic spectrum

Question 17

molten globule

Answer 17

partly folded structure made after hydrophobic collapse

Question 18

protein folding assistance

Answer 18

foldases (slow steps), chaperones (destabilise unproductive states)

Question 19

Chaperonin example

Answer 19

GroEL-GroES (lid), control exposure of hydrophobic residues -> refolding cycle