Protein Structure And Folding

Front 1

What are the non-covalent forces that stabilise protein structure?

Back 1

1. Hydrogen bonds

2. Hydrophobic effect

3. Ionic interactions

4. Van der Waals forces

Front 2

What type of bond are disulphide bridges between proteins?

Back 2

Covalent bonds

Front 3

How come there is an increase in entropy when a protein folds due to the hydrophobic effect?

Back 3

The entropy of water, not the protein increases. This is because when the protein is in its unfolded state, it forces water molecules to form highly ordered structures. However when the protein fold, water molecule are less ordered .

Front 4

In the unfolded state of a protein, are there any VdW interactions?

Back 4

No

Front 5

Where are the hydrogens bonds present in a proteins?

Back 5

Between side chains (so within the chain) of alpha helices and B pleated sheets.

e.g N-H ---- O=C

Front 6

Can water molecules that are in contact with a hydrophobic side-chain form any types of covalent bond with that side chain?

Back 6

No.

So they form tighter bonds with each other.

Front 7

Why do hydrogen bonds not contribute 3kcal/mol to the free energy of folding?

Back 7

No-only 1 kcsl/mol because they can also form (weak) H-bonds with water molecules in the unfolded state.

When NH2 and COOH groups aren't together, they form H bonds with water.

The hydrogen bond that NH2 makes on its own with water is about 1kcal/mol

The hydrogen bond that COOH makes with water is about 1kcal/mol.

3-1-1 =1 kcal/mol

Front 8

Do electrostatic interactions each contribute 5kcal/mol to the free energy of folding?

Why?

How does the entropy of water change?

Back 8

No-because the charges are fully solvated (neutralised) by water in the unfolded state. The entropic contribution of 1kcal/mol remains.

When the charges are brought together, they are neutralised by each other rather than by water molecules.

The entropy of water increases when they are brought together

Front 9

Entropy can be related to the number of states, or degrees of freedom of a system. This is the entry equation

S=klnW

What does the k stand for and what does the W stand for?

Back 9

k stands for the Bolzmann's constant

W stands for the number of states

Front 10

How many conformations does the native state of a protein have?

Back 10

1 ( this is the folded state)

Front 11

For a mole of protein, how can we calculate the ΔS of folding?

Back 11

ΔS folding = S(native) - S (unfolded)

Front 12

What is the entropy of folding for a protein that has 100 residues and for every residue there are 10 conformations?

Back 12

Front 13

What does this show?

Back 13

The energy of non-covalent bonds (just) enough to outweigh the positive entropy of chain folding

Front 14

Why favours protein folding?

Back 14

The enthalpy of each hydrogen bond and the other non covalent forces favour folding

Front 15

What favours protein unfolding?

Back 15

Entropy of the polypeptide chain greatly favours unfolding

Front 16

The free energy of folding a protein is typically around (-) 10kcal/mol. What does this suggest?

Back 16

Proteins are very easily destabilised e.g by mutation or by a change in their environment

Front 17

What does the hydrophobic effect drive?

Back 17

Protein-protein interactions

Front 18

What is the principle driving force for protein folding (or protein-protein interactions) in aqueous solution?

Back 18

The increased entropy of the water molecules that results from burying hydrophobic amino-acid side chains.

Front 19

Is protein folding fast or slow?

Back 19

Fast

Front 20

Is protein folding spontaneous or induced?

Back 20

Spontaneous

Front 21

Does protein folding follow a defined pathway or is it trial and error?

Back 21

Defined pathways

Front 22

What does the amino acid sequence encode?

Back 22

Protein structure and folding pathway

Front 23

Describe the typical stages in going from a protein in the unfolded state, to a protein in the folded state.

Back 23

1. B turns form

2. Alpha helices form

3. B sheet form

4. Protein folds

Front 24

In vivo, what assists with protein folding?

Back 24

Chaperone proteins. They pick up the

unfolded protein and enclose it in an isolated box that provides an environment favourable to protein folding, and then let it out once this is achieved.

Front 25

In the closed state, what surfaces are exposed on the chaperone protein?

Back 25

Hydrophobic surfaces

Front 26

In the open state, what surfaces are exposed on the chaperone proteins and what surfaces are hidden?

Back 26

Hydrophilic residues exposed

Hydrophobic surfaces hidden

Front 27

In sickle cell anaemia, which amino acid mutates (to what) and what does this cause?

Back 27

Glutamate (glutamic acid) goes to valine.

This causes proteins to aggregate.

Front 28

Diseases can be transmitted through a protein. An example of this is the PrP protein. The protein exits in two possible conformations. What two forms does this protein exist in?

Back 28

The normal cellular form ( PrP c) which is benign

The pathogenic form (Prp Sc) which is disease causing

Front 29

What happens when the normal cellular form of PrP is converted to the pathogenic form?

Back 29

It aggregates

Front 30

What is the differences between PrP c and PrP Sc?

Back 30

PrP c cannot polymerise but PrP Sc can

Front 31

What do the prion proteins have in common?

Back 31

Identical amino acid sequences and are coded for by the same gene

Front 32

As the polypeptide chain is synthesised, what do sections of the polypeptide rapidly assume?

Back 32

Their secondary structure

Front 33

What is an example of a disease in humans caused by protein misfolding?

Back 33

Creutzfeldt-Jakob disease (CJD)

Alzheimers

Front 34

What are amyloids and what diseases are they associated with?

Back 34

B strand rich rich aggregates

They cause cell and tissue destruction

Alzheimers disease

CJD

Front 35

As the polypeptide is synthesised, what happens?

Back 35

Sections of the polypeptide rapidly assume their secondary structure

Front 36

Chaperones enclose the unfolded protein in an environment that is favourable for protein folding, and then let it out once it is activated. True or false.

Back 36

True

Front 37

Can chaperones give directions on how a protein folds?

Back 37

No.

Chaperones simply make it more likely the the protein will fold according to its amino acid sequence by stopping it interacting with other folded proteins.

Front 38

In the alpha-helix, the length of a hydrogen bond, measured from the donor N atom to theacceptor O atom is:

Back 38

0.28 nm