Protein structure

Question 1

how are peptide bonds formed in terms of orientation of the amino acids

Answer 1

one has to invert
reduce steric clashes between R groups

Question 2

why does the backbone of a polypeptide have high hydrogen-bonding potential

Answer 2

C=O hydrogen bond acceptor
NH hydrogen bond donor

Question 3

peptide

Answer 3

<50 amino acids

Question 4

mass of an amino acid

Answer 4

110 Da

Question 5

1Da

Answer 5

1g/mol

Question 6

why can polypeptides for tightly packed globular structures

Answer 6

peptide bonds are uncharged

Question 7

characteristics of peptide bonds

Answer 7

planar
cannot rotate freely due to partial double bond character that shortens the bond

Question 8

why do peptide bonds have double bond character

Answer 8

electrons in the nitrogen can be delocalised into the peptide bond

Question 9

why are trans isomers more common

Answer 9

cis isomers are unfavourable due to steric clashes

Question 10

proline isomers

Answer 10

both cis and trans have steric clashes as the side chain is bonded both to the alpha carbon and the amino group to form a five membered ring

Question 11

how can proteins fold if there is no rotation about the peptide bond

Answer 11

alpha carbon-carboxyl bond and alpha carbon-amine bond are single bonds that can freely rotate

Question 12

dihedral angles

Answer 12

phi
psi

Question 13

phi

Answer 13

angle of rotation about the bond between the nitrogen and the alpha carbon atom

Question 14

psi

Answer 14

angle of rotation about the bond between the carbonyl atom and the alpha carbon atom

Question 15

Ramachandran plot

Answer 15

shows which combinations of phi and psi do not cause steric clashes so are possible.

Question 16

secondary structures

Answer 16

alpha helix
beta sheet
loop

Question 17

alpha helix

Answer 17

rod like structure of a tightly coiled backbone and a helical array of side chains

Question 18

how many residues per helical turn?
distance of a turn?

Answer 18

3.6
5.4A

Question 19

dihedral angles of amino acids in an alpha helix

Answer 19

phi=-57
psi=-47

Question 20

why are left handed alpha helices rare

Answer 20

L amino acids would clash

Question 21

why do alpha helices have a dipole moment

Answer 21

all amino groups point up and all carbonyl groups point down: N terminus and C terminus

Question 22

how many degrees is each residue separated by

Answer 22

100

Question 23

structure of beta pleated sheets

Answer 23

2 or more polypeptide chains called beta strands
almost fully extended
Side chains of adjacent amino acids point in opposite directions

Question 24

distance between adjacent amino acids in beta strand

Answer 24

3.5A

Question 25

dihedral angles of amino acids in a beta strand

Answer 25

phi -120
psi+120

Question 26

why can large side chains be accepted on beta strands

Answer 26

7A between amino acids orientated the same way so chance of steric clashes is low

Question 27

how do beta sheets form

Answer 27

linking two or more beta strands by hydrogen bonds

Question 28

antiparallel beta sheet

Answer 28

adjacent chains run in opposite directions
H bonds between NH and CO connect each amino acid to a single amino acid on adjacent strand (one amino acid on one strand forms 2H bonds with another)

Question 29

parallel beta sheet

Answer 29

adjacent strands run in the same direction
each amino acid on one strand hydrogen bonds with two amino acids on the adjacent strand

Question 30

why dont beta sheets have a dipole

Answer 30

dipoles on adjacent amino acids cancel out as they are in opposite orientation

Question 31

why arent beta sheets perfectly planar?

Answer 31

twist slightly due to tug of war between conformational energies of the side chain (minimising steric clashes) and maximal H-bonding

Question 32

why don’t proline or glycine exist in these secondary structures

Answer 32

glycine is too flexible so not energetically favourable
proline forms kinks in the chain

Question 33

loops

Answer 33

join secondary structures together and change the direction of a polypeptide chain

Question 34

type 1 loop

Answer 34

proline in the second position- kink allows hydrogen bond between 1 and 4 amino acids

Question 35

type 2 loop

Answer 35

glycine in position 3- flexibility allows it to form different conformations, H bond between 1 and 4 amino acids