Module 1: V13 - V15

Question 1

What is the folded shape of a protein (conformation) specified by?

Answer 1

the protein’s amino acid sequence

Question 2

The ‘native’ conformation of a protein is the fold with the…

Answer 2

…lowest free energy

Question 3

What is the size difference between a protein and a water molecule?

Answer 3

a protein is about 15x bigger than a water molecule

a similar comparison is inflatable pool toys and ping pong balls

Question 4

How are peptide bonds formed?

Answer 4

formed when the carboxylate group of one amino acid reacts with the amine group of another amino acid
an amide (peptide) bond is formed with the removal of water (condensation reaction)

Question 5

Where is the N-terminus and C-terminus?

Answer 5

the N-terminus is located at the end of the protein with the amine group and the C-terminus is located at the end of the protein with the carboxylate group

Question 6

What determines the conformation freedom of a molecule?

Answer 6

the bonding between atoms (e.g. single or double bonds)

Question 7

Why is there limited rotation about peptide bonds?

Answer 7

this is because the peptide bond has partial double-bond character due to resonance caused by the C=O bond

Question 8

What is the evidence of double bond character in peptide bonds?

Answer 8

the peptide bond is shorter than the average C-N single bond and longer than the average C=N double bond

Question 9

What determines whether a peptide linkage is trans or cis?

Answer 9

the orientation of Ca atoms

Question 10

Why is the trans form energetically favoured?

Answer 10

there is less steric hindrance (van der Waals repulsion) than there is in the side chain of the cis form

Question 11

What is an example of an amino acid in which the cis form is more energetically favoured in comparison to the trans form?

Answer 11

proline can be found at a 4:1 ratio between its trans and cis form instead of the normal ratio of 1000:1 in most other amino acids

Question 12

What is the omega angle of a residue in the trans form?

Answer 12

either 180˚ or -180˚ when viewing the peptide bond directly

Question 13

What is the omega angle of a residue in the cis form?

Answer 13

0˚ when viewing the peptide bond directly

Question 14

Which bonds are able to undergo free rotation in the amino acid sequence?

Answer 14

N-Ca and Ca-C bonds

associated with the phi and psi angles respectively

Question 15

What is the phi angle defined by?

Answer 15

the four atoms C(i-1)-N-Ca-C(i) (not all in the same residue) with rotation about the N-Ca bond
the phi angle is a dihedral angle
take the shortest path to determine if the angle is positive or negative

Question 16

What is the psi angle defined by?

Answer 16

the four atoms N(i)-Ca-C-N(i+1) (not all in the same residue) with rotation about the Ca-C bond
the psi angle is a dihedral angle
take the shortest path to determine if the angle is positive or negative

Question 17

Why are phi and psi so important?

Answer 17

because: assuming all peptide bonds are trans all the conformational freedom in the backbone of a polypeptide is due to these two rotations
everything else in this diagram is fixed

Question 18

How is the backbone conformation of a protein displayed?

Answer 18

on a Ramachandran plot using the values for the phi and psi angles

Question 19

How are side chain conformations described?

Answer 19

they are described as chi (χ) angles χ1, χ2, χ3

generally prefer staggered rotamers (not eclipsed)