MCB Lecture 3 Bonding in Proteins

Question 0

What are four types of representations of proteins?

Answer 0

Ribbon
Snake/line
Space filling
Ball and stick

Question 1

What is special about the tertiary structure of proteins?

Answer 1

The folding up into tertiary structure is built into the code of the protein.
Self assembling

Question 2

Relate the size of a protein to the size of a water molecule.
In angstroms, how big is the average protein?

Answer 2

Water: ping pong ball
Protein: pool toys

Question 3

What types of bonds have free rotation, and which don’t (in general) ?

Answer 3

Double bonds or resonance bonds do not have free rotation

Single bonds have free rotation

Question 4

What is the ionic status of amino acids at biological conditions?

Answer 4

The molecule is neutral,

Ionised N and C terminus

Question 5

Describe peptide bond formation, and between which two atoms they form.

Answer 5

This is a condensation reaction (H2O produced)

It forms between the carbon of the C terminus and the N of the amino group of another residue

Question 6

Describe the characteristics of the peptide bond

Answer 6

The peptide bond (omega) is a resonance bond
Thus, there is no rotation about this bond

Partial double bond character

Sorter than single bond, longer than double

Planar

Question 7

Describe peptide bond isomerisation

Answer 7

The bond can be cis: alpha carbons on same side

Trans: alpha carbons on opposite sides

Question 8

What is the more common conformer of a dipeptide?

Why?

Answer 8

Trans

Less steric hindrance

Question 9

What are the names of the dihedral angles in amino acids?

Answer 9

These are phi and psi

Question 10

What are the torsion angles of cis and trans peptide bonds?

Answer 10

Cis: 0
Trans: -180

Question 11

Describe the character of the omega bond

Answer 11

Resonant

Planar

Question 12

Describe the character of the Phi bond

Answer 12

Single bond
Rotatable
Tetrahedral

Question 13

Describe the character of the Psi bond

Answer 13

Single
Rotatable
Tetrahedral

Question 14

Which is the Phi bond?

Answer 14

Phi is between the N and the alpha carbon within a residue

Question 15

Which is the Psi bond?

Answer 15

The psi bond is between the alpha carbon and the carbonyl carbon in a residue

Question 16

Which is the omega bond?

Answer 16

This is the peptide bond:

Between the carbonyl carbon and Nitrogen of two residues

Question 17

Describe what is meant by positive and negative dihedral angles

Answer 17

Positive: rotated clockwise

Negative: rotated anticlockwise

Question 18

What is a Ramachandran plot?

Answer 18

This is a probability plot of all the dihedral/torsion angles in many proteins

It shows pattern and the most likely angles that you will see in protein

Question 19

Describe what the three clusters on a Ramachandran plot represent

Answer 19

Beta sheets: -130 +130

Alpha helices: around -60, -60

Left handed turns