3D, primary and secondary

Question 1

what kind of double bond do peptide bonds feature and why

Answer 1

partial double bond due to resonance

Question 2

describe the length of the C=O bond in a peptide bond

Answer 2

longer than usual

Question 3

describe the length of the C-N bond in a peptide bond

Answer 3

shorter than usual

Question 4

what configuration are most peptide bonds in in proteins

Answer 4

trans

Question 5

which bonds can rotate in an polypeptide

Answer 5

the ones attached to alpha carbons only, phi and psi

Question 6

which atoms define torsion

Answer 6

central 2 and the 2 on either side

Question 7

draw trans 180 newman conformations for phi and psi

Answer 7

see slide 13

Question 8

why is L-proline restricted in rotation? which bond is this around?

Answer 8

phi bond restricted because cyclic side chain

Question 9

what kind of bonds are found in regular secondary structure?

Answer 9

repeating phi and psi angles for sequential amino acids

Question 10

what kind of H-bonding patterns do stable forms of secondary structures feature?

Answer 10

repeating

Question 11

what are 3 examples of regular secondary structure

Answer 11

alpha helix, beta sheets, collagen helixes

Question 12

what kind of bonds are found in irregular secondary structures

Answer 12

non repeating phi and psi angles

Question 13

what are 3 types of irregular secondary structure

Answer 13

beta turns, coils, loops

Question 14

what kind of twist is in the alpha helix

Answer 14

right handed

Question 15

where are the H-bonds in an alpha helix

Answer 15

c=o of i and NH of i+4

Question 16

where do the sidechains project in an alpha helix

Answer 16

away from core

Question 17

what is the bond angle for phi and psi in an alpha helix

Answer 17

(-57,-47)

Question 18

how many residues per turn of alpha helix

Answer 18

3.6

Question 19

which R-groups from the primary sequence interact favourable in alpha helix

Answer 19

3-4 residues apart

Question 20

what are atoms in the alpha helix backbone stabilized by

Answer 20

van der waals and H-bonding

Question 21

which terminus in the alpha helix is negatively charged

Answer 21

C-terminus

Question 22

which terminus in the alpha helix is positively charged

Answer 22

N-terminus

Question 23

which direction is the C=O bonds pointing towards in an alpha helix

Answer 23

C-terminus

Question 24

what is found at each end of the alpha helix

Answer 24

4 unpaired amino acids not involved in H-bonds

Question 25

which amino acids are usually found ar the N-terminus of an alpha helix? what about the C-terminus

Answer 25

glu and asp lys and arg

Question 26

which end of an amino acid would interact with phosphates or nucleotides

Answer 26

the N terminus

Question 27

what are the 3 kind of beta sheets

Answer 27

parallel antiparallel mixed

Question 28

what is phi and psi for parallel beta sheets what is phi and psi for antiparallel beta sheets

Answer 28

(-120, +120) (-140, +140)

Question 29

what are beta sheets formed by

Answer 29

H-bonds between strands

Question 30

what are the 2 types of situations involving strands for beta sheets

Answer 30

separated within primary structure or coming from different peptides

Question 31

compare the repeat period for parallel vs antiparallel beta sheets

Answer 31

shorter for parallel

Question 32

T or F: the hydrogen bonding pattern for antiparallel vs parallel beta sheets is the same

Answer 32

false

Question 33

T or F: individuals strands in a beta-sheet always follow each other in the primary sequence

Answer 33

false

Question 34

are beta sheets planar

Answer 34

no they are not planar

Question 35

what can beta sheets twist into

Answer 35

saddle shapes or barrels

Question 36

where are the H-bonds between in beta turns

Answer 36

C=O of residue 1 to NH of residue 4

Question 37

what is the degree change in the direction of the polypeptide in a beta turn

Answer 37

180 degrees

Question 38

how are the types of beta turns characterized

Answer 38

combinations of phi and psi angles

Question 39

which amino acids are often found in beta turns

Answer 39

proline and glycine

Question 40

what is always the third residue in a type II beta-turn? why is this? what is the name/ designation for this third residue?

Answer 40

glycine geometry (80,0) i+2

Question 41

which amino acids have the highest propensity for alpha helix formation

Answer 41

ala glu and met