2. Protein Folding and Function

Question 1

What is the primary structure of a protein?

Answer 1

The linear amino acid sequence of the polypeptide chain.

Question 2

What is the secondary structure of a protein?

Answer 2

The local spatial arrangement of the polypeptide backbone.

Question 3

What is the tertiary structure of a protein?

Answer 3

The 3-dimensional arrangement of all atoms in a polypeptide chain.

Question 4

What is the quaternary structure of a protein?

Answer 4

The 3-dimensional arrangement of protein subunits.

Question 5

What bonds are present in the primary structure of a protein?

Answer 5

Covalent (peptide) bonds.

Question 6

How many amino acids are there in one turn of the a-helix secondary structure?

Answer 6

3.6

Question 7

How big is one turn of the a-helix?

Answer 7

0.54nm.

Question 8

Does the helix have a left or right handed twist?

Answer 8

Right handed.

Question 9

What is an anti parallel B-sheet?

Answer 9

Adjacent B-strand running in opposite direction, with multiple inter-stranded H-bonds stabilising the structure.

Question 10

What is a parallel B-sheet?

Answer 10

Adjacent B-strand running in the same direction, with multiple inter-stranded H-bonds stabilising the structure.

Question 11

What are the three main differences between fibrous and globular tertiary structure proteins?

Answer 11

Fibrous proteins’ roles are to provide support, shape and protection, whereas globular proteins’ roles are to catalyse and regulate.
Fibrous proteins are made of long strands or sheets but globular proteins have a compact shape.
Fibrous proteins have a single type of repeating secondary structure but globular proteins have several types of repeating secondary structure.

Question 12

What type of arrangement are collagen chains in?

Answer 12

Triple helical arrangement.

Question 13

What is the repeating sequence if collagen a-chains?

Answer 13

Gly-X-Y

Question 14

What bonds form between the three a-helical chains of collagen?

Answer 14

Hydrogen bonds.

Question 15

What are motifs?

Answer 15

Folding patterns containing one or more elements of secondary structure.

Question 16

What are domains?

Answer 16

Part of a polypeptide chain that folds into a distinct shape, often with a specific functional role.

Question 17

How do water soluble proteins fold?

Answer 17

The polypeptide chains fold so the hydrophobic side chains are buried under the hydrophilic, charged chains, which are on the surface.

Question 18

What bonds are present in the secondary structure of a protein?

Answer 18

Hydrogen bonds.

Question 19

What bonds are present in the tertiary structure of a protein?

Answer 19

Covalent/ disulphide, ionic, hydrogen, van der Waals bonds and hydrophobic interactions.

Question 20

What bonds are present in the quaternary structure of a protein?

Answer 20

Covalent/ disulphide, ionic, hydrogen, van der Waals bonds and hydrophobic interactions.

Question 21

What do covalent/ disulphide bonds form between?

Answer 21

Cysteine residues.

Question 22

How can covalent/ disulphide bonds be broken?

Answer 22

By using reducing agents.

Question 23

What do electrostatic interactions form between?

Answer 23

Between charged groups.

Question 24

What do hydrogen bonds form between?

Answer 24

Between an electronegative atom and a hydrogen bound to another electronegative atom.

Question 25

Why does the hydrophobic effect happen?

Answer 25

Because of interactions between hydrophobic side chains, also due to the displacement of water.

Question 26

What are van der Waals forming a result of?

Answer 26

Dipole-dipole interactions.

Question 27

Explain three possible causes of protein denaturation?

Answer 27

Heat - increases vibrational energy so much that the secondary structure bonds are broken.
pH - alters the ionisation states of amino acids.
Detergents/ organic solvents - disrupt hydrophobic interactions.

Question 28

What can help assist protein folding?

Answer 28

Chaperones.

Question 29

What is the result of some misfolding?

Answer 29

Disease.

Question 30

What are amyloid fibres?

Answer 30

Mis folded, insoluble forms of normally soluble proteins.

Question 31

How are amyloid fibres formed?

Answer 31

The core B-sheet forms before the rest of the protein.