Determinants of protein structure

Question 1

What is the range of different environments that proteins work in?

Answer 1

Intracellular aqueous
Extracellular aqueous
Lipid membranes

Question 2

What determines a proteins shape?

Answer 2

The sequence of amino acids is the main determinant of a proteins shape - which is encoded within the nucleic acid.
A proteins function is determined by its shape.

Question 3

What are the levels of protein structure?

Answer 3

Primary
Secondary
Tertiary
Quaternary
Supramolecular

Question 4

What are the limitations of amino acid sequence determining protein shape?

Answer 4

The chemical properties of atoms and the peptide bonds restricts the number of possible shapes.
Non-covalent bonds between amino acid side chains also constrain folding.

Question 5

What are hydrophobic associations?

Answer 5

Non-polar amino acid side chains are repelled by water and tend to cluster together in the centre of the protein - so influence protein folding.

Question 6

What is the affect of hydrophobic interactions?

Answer 6

Clustering of hydrophobic side chains in the centre of the protein allows residues involved in non-covalent interactions to come close enough for these interactions to occur.

Question 7

What are the two regular folding patterns of secondary structure?

Answer 7

Alpha helixes.
Beta sheets.

Question 8

What is the alpha helix?

Answer 8

Driven by hydrophobic interactions.
It is an amino acid backbone coil, with side chains protrubing out, which interact with water and drive the shape.
Side chains then form bonds between different regions of the backbone, as the folding means they are now closer together.

Question 9

What is a beta-pleated sheet?

Answer 9

Hydrophobic associations drives the folding, and new interactions happening between regions that are now close together.

Question 10

How do a-helices form larger secondary structures?

Answer 10

BAR domains - numerous a-helices form together to form rod-shaped proteins.
They bind to membranes and cause them to curve.

Question 11

How do beta sheets cause larger secondary structures?

Answer 11

Forms beta-barrels - common in membrane pores, and in protective environments.
e.g. in chloroplasts.

Question 12

What are non-covalent interactions?

Answer 12

Hydrogen bonds
ionic bonds
van der Waals interactions
Hydrophobic association

Question 13

Which bonds are in which levels of protein structure?

Answer 13

Peptide bonds - primary onwards.
Hydrogen bonds - secondary onwards.
Ionic, Van der Waals, hydrophobic interactions and disulphide bridges are tertiary structure.

Question 14

Why are hydrogen bonds important for structure?

Answer 14

Hydrogen bonds are specific for certain atom types - in Nitrogen and Oxygen.
N and O are common in proteins, so have lots of influence

Question 15

How do ionic bonds influence protein structure?

Answer 15

Ionic bonds can form between carboxylic acid side groups and amine groups, which helps stabilise protein structure.
These are ionisable groups, so the pH of the environment is important for their formation.

Question 16

How do Van der Waals interactions influence protein structure?

Answer 16

While the interactions are individually very small, the sum of all the forces in the protein are significant for maintaining protein structure.

Question 17

What are Van der Waals forces?

Answer 17

The electron cloud around an atom is constantly fluctuating.
These small charge differences give rise to attraction or repulsion between atoms.

Question 18

What is a leucine zipper?

Answer 18

For DNA binding
Regions with lots of leucines that line up on an axis.
This comes together with another region so 2 proteins join together to remove water and forms a binding site.

Question 19

How do disulphide bridges form?

Answer 19

Formed between adjacent amino acids with a sulphur in its side chain, because S can either be reduced or oxidised.
The oxidation of sulfhydryl groups on the amino acid cysteine forms disulphide bridges.

Question 20

How are disulphide bridges important in antigens?

Answer 20

They form the binding site, and holds the heavy and light chains together.

Question 21

How does temperature cause protein denaturation?

Answer 21

Increased thermal energy disrupts hydrogen bonds and other bonds holding proteins together.

Question 22

How does pH cause protein denaturation?

Answer 22

Changing the pH affects the charge of the amino acids and disrupts ionic bonds.

Question 23

How do salts cause protein denaturation?

Answer 23

Chaotropic agents such as urea, imidazole and guanidinium disrupt hydrogen bonding and the hydrophobic effect.

Question 24

What factors cause protein denaturation?

Answer 24

Temperature
pH
Salts
These disrupt protein structure but do not break the peptide bond and therefore primary structure is unaffected.

Question 25

What is the law of increasing entropy?

Answer 25

States that the universe is always moving towards a greater state of disorder.

Question 26

How does protein folding seem to break the law of increasing entropy?

Answer 26

Protein folding requires peptide chains going from disorganised random structure to a highly ordered one.

Question 27

What is the Gibb’s equation?

Answer 27

ΔG =ΔH - TΔS

Question 28

What is enthalpy?

Answer 28

The energy content.
Enthalpy change is the energy released or required due to non-covalent interactions:
Ionic bonds
Electrostatic bonds
Hydrogen bonds
Van der Waals interactions

Question 29

What is entropy change?

Answer 29

The change in molecular disorder associated with the processes - water and the hydrophobic effect.

Question 30

How does protein folding not actually break the law of enthalpy?

Answer 30

In an unfolded protein, water forms hydration spheres around hydrophobic amino acid side chains. As the water is ordered, the entropy is decreased.
Hydrophobic interactions between amino acid side chains releases the water from the spheres.
So water molecules gain entropy as they are more disorganised, so entropy increases.