lecture 4

Question 1

four levels of protein structure

Answer 1

primary secondary tertiary quaternary

Question 2

are peptide bonds usually cis or trans

Answer 2

trans

Question 3

what does partial double bond character in the amide bond have implications for

Answer 3

protein structure
IR spectra
causes amide plane

Question 4

what causes double bond character

Answer 4

pi orbitals

Question 5

what number is the maximally extended phi and psi

Answer 5

0

Question 6

what allows folding into secondary structure

Answer 6

rotation at psi and phi

Question 7

what is a ramachandran plot

Answer 7

steric model of dipeptide showing non clashing values of phi and psi
top one beta sheet
bottom one alpha helix

Question 8

which bond is phi

Answer 8

C - N

Question 9

what bond is psi

Answer 9

C - C = O

Question 10

necessary structure of secondary structure

Answer 10

bond lengths and angles not distorted
no two atoms approach one another
the amide group must remain planar and in the trans configuration
some non-covalent bonding

Question 11

properties of alpha helix

Answer 11

3.6 residues per helical turn
backbone carbonyl oxygen H-bonds to the backbone N-H of 4th residue
H bonds 2.86 angstroms long
R group project outwards

Question 12

what is needed in tight turn

Answer 12

gly helix breaker

Question 13

what stabilises beta strand

Answer 13

hydrogen bonding between adjacent strands in beta sheet

Question 14

what causes right hand twist in beta pleated sheets

Answer 14

intrinsic tendencies of the backbone

Question 15

where are side chain beta pleated sheet

Answer 15

alternate above and below the chain