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Flashcards in MCB Lecture 3 Bonding in Proteins Deck (20)
0

What is special about the tertiary structure of proteins?

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

1

What are four types of representations of proteins?

Ribbon
Snake/line
Space filling
Ball and stick

2

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

Water: ping pong ball
Protein: pool toys

3

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

Double bonds or resonance bonds do not have free rotation

Single bonds have free rotation

4

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

The molecule is neutral,
Ionised N and C terminus

5

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

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

6

Describe the characteristics of the peptide bond

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

7

Describe peptide bond isomerisation

The bond can be cis: alpha carbons on same side
Trans: alpha carbons on opposite sides

8

What is the more common conformer of a dipeptide?
Why?

Trans
Less steric hindrance

9

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

These are phi and psi

10

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

Cis: 0
Trans: -180

11

Describe the character of the omega bond

Resonant
Planar

12

Describe the character of the Phi bond

Single bond
Rotatable
Tetrahedral

13

Describe the character of the Psi bond

Single
Rotatable
Tetrahedral

14

Which is the Phi bond?

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

15

Which is the Psi bond?

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

16

Which is the omega bond?

This is the peptide bond:
Between the carbonyl carbon and Nitrogen of two residues

17

Describe what is meant by positive and negative dihedral angles

Positive: rotated clockwise

Negative: rotated anticlockwise

18

What is a Ramachandran plot?

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

19

Describe what the three clusters on a Ramachandran plot represent

Beta sheets: -130 +130

Alpha helices: around -60, -60

Left handed turns

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