Module 2: V5 - V9

Question 1

Why are phi and psi so important?

Answer 1

because all conformational freedom in the backbone of a polypeptide is due to these two rotations
everything else is fixed

Question 2

What is a Ramachandran plot and what does it show?

Answer 2

describes the backbone conformation of a protein in terms of the phi and psi values
shows the distribution of phi and psi dihedral angles that are found in a protein (shows common secondary structure elements and reveals the presence of unusual backbone structures)

Question 3

Why are all phi/psi pairings not equally probable?

Answer 3

because Ramachandran plots are never filled with data points evenly

Question 4

What determines the favorability of phi and psi combinations?

Answer 4

steric crowding of backbone atoms with other atoms in the backbone or side chains and because of the chance to form favourable H-bonding interactions along the backbone

Question 5

What are the regions of a Ramachandran plot?

Answer 5

alpha (bottom left), beta (top left), left-handed turn (top right) and disallowed (bottom right)

Question 6

What does ‘disallowed’ mean in the case of the Ramachandran plot?

Answer 6

means unfavourable or uncommon, but not impossible

Question 7

What does secondary structure refer to?

Answer 7

a local spatial arrangement of the polypeptide backbone

Question 8

What are two common regular arrangements?

Answer 8

the ɑ helix (stabilised by hydrogen bonds between residues nearby in the sequence) and the β sheet (stabilised by hydrogen bonds between adjacent segments that may not be nearby in the sequence)

Question 9

What is a random coil?

Answer 9

irregular arrangement of the polypeptide chain

Question 10

What must any polar group buried in a protein do?

Answer 10

form a hydrogen bond

Question 11

Why do hydrogen bonds increase the compactness and stability of a protein?

Answer 11

this is because the atoms of a hydrogen bond can approach much closer than a VDW interaction (2.7 A compared to 1.9 A) due to covalent character of the hydrogen bond

Question 12

What type of interactions occur within a protein?

Answer 12

backbone-backbone interactions, backbone-side chain interactions and side chain-side chain interactions

Question 13

Do side chains project outwards or inwards from alpha helix axis?

Answer 13

outwards

Question 14

Which type of interactions are occurring in an alpha helix?

Answer 14

NH (residue i) hydrogen bonding to C=O (residue i-4)

peptide bond dipoles which add together to give a macrodipole

Question 15

Are alpha helices left or right handed?

Answer 15

right handed

Question 16

What does amphipathic mean in a protein?

Answer 16

having both hydrophilic and hydrophobic character but separated onto different faces of the helix

Question 17

What is the inner diameter of the alpha helix? Can anything fit into this hole?

Answer 17

4-5 A

no, not even water molecules are able to fit inside an alpha helix

Question 18

What is a heptad repeat?

Answer 18

a repeating pattern of amino acid residues that corresponds to an alpha helix with hydrophobics all on one face

Question 19

What amino acid residues are strong helix formers?

Answer 19

small hydrophobic residues such as Ala and Leu

Question 20

Which amino acid residues act as helix breakers?

Answer 20

Pro because it lacks the NH hydrogen bond donor and Gly because the tiny R group doesn’t contribute to the stability of the helix

Question 21

How are alpha helices stabilised?

Answer 21

by attractive or repulsive interactions between side chains 3 to 4 amino acids apart (e.g. stabilised by oppositely charged residues 3-4 away in sequence)

Question 22

What creates a pleated sheet-like structure?

Answer 22

the planarity of the peptide bond and tetrahedral geometry of the ɑ carbon (held together by hydrogen bonds between the backbone amides in different strands)

Question 23

How do side chains protrude from β strand?

Answer 23

in an alternating up-and-down direction

Question 24

What forms a β sheet?

Answer 24

multiple parallel/antiparallel strands which undergo hydrogen bonding

Question 25

Are parallel or antiparallel β sheets more stable? Why?

Answer 25

antiparallel β sheets because the H-bonded strands run in opposite directions resulting in less of an angle between neighbouring N-H and C=O groups allowing for stronger hydrogen bonding

Question 26

What are reverse turns (β turns)?

Answer 26

a turn which frequently occurs when strands in β sheets change direction

Question 27

How are reverse turns stabilised?

Answer 27

by a hydrogen bond from a carbonyl oxygen of position 1 to amide hydrogen of position 4 in the turn (i and i+3)

Question 28

What is common in reverse turns?

Answer 28

proline in position 2 (i+1) or glycine in position 3 (i+2)

Question 29

What is the difference between a type-1 turn and a type-2 turn?

Answer 29

the oxygen atom on the carbonyl of residue 2 in a type-1 turn points away from us into the page and the oxygen atom on the carbonyl of residue 2 in a type-2 turn points towards us out of the page (dictated by phi and psi values)

Question 30

What are supersecondary structural elements?

Answer 30

simple ways of arranging secondary structures
more than half of all of protein structure is composed of three very simple arrangements of structural elements (ɑɑ-hairpin, ββ-hairpin and βɑβ)

Question 31

What would the Ramachandran plot look like for a planet where the naturally occurring amino acids are D-amino acids?

Answer 31

since d-amino acids differ from l-amino acids by 180˚ the Ramachandran plot of a d-amino acid will be the inverse of an l-amino acid plot