secondary protein structure

Question 1

in amino acids where does H bonding occur in secondary structure, how big are the H bonds

Answer 1

between the H of the N-H and the O of the O=C, about 3.5 angstroms

Question 2

what is the distance between each turn in an alpha helix, each residue in an alpha helix and how many residues per turn?

Answer 2

5. 4 angstroms between turns
6. 5 angstroms between residues
7. 6 residues per turn

Question 3

are alpha helices right or left handed

Answer 3

right handed

Question 4

how does H bonding occur in alpha helices?

Answer 4

full set of H bonds between residues parallel to helix (H bonding between residues above/below each other)

Question 5

how are side chains projected in respect to an alpha helix, and how are they arranged

Answer 5

R groups project away from helix, side chains tend to come as pairs; 2 hydrophilic then 2 hydrophobic (since one side faces aqueous and one side faces organic environment)

Question 6

how are oxygen and nitrogen in the backbone arranged in alpha helix

Answer 6

nitrogens are bonded in as part of carbon backbone, oxygens are bonded downward from the beta carbons

Question 7

how do beta strands differ to alpha helices

Answer 7

alpha helices are like compact version of beta strand, beta strands are close to most extended form of polypeptide chain possible

Question 8

what is distance between nitrogen to nitrogen and alpha carbon to alpha carbon in beta strands

Answer 8

between neighbouring nitrogens; 3.6 angstroms

between neighbouring alpha carbons; 3.8 angstroms

Question 9

what do beta sheets consist of?

Answer 9

h bonded beta strands from different regions of the protein, they are arranged antiparallel so that C and N terminus of neighbouring strands hand opposite ends

Question 10

what is arrangement of hydrophobic/philic residues in anti parallel beta sheets

Answer 10

neighbouring R groups side chains alternate, but are same direction as corresponding R group on neighbouring strand

on same strand alternate one by one between hydrophilic and hydrophobic

Question 11

do parallel beta sheet exist

Answer 11

yes, however H bonds are at angles, side chains still point to same side as on neighbouring strands

Question 12

can mixed (parallel and antiparallel) beta sheets occur?

Answer 12

yes

Question 13

are beta sheets flat

Answer 13

no, they have a right handed twist

Question 14

in beta strands where does the arrow head point towards

Answer 14

C terminus

Question 15

what connects beta strands?

Answer 15

loops

Question 16

what is minimum number of residues for a loop

Answer 16

2

Question 17

what is difference between what long/short loops connect

Answer 17

short/hairpin loops connect beta strands to each other

long loops connect beta sheets and alpha helices