Protein DLA -Structure And Function

Question 1

What is protein folding?

Answer 1

Folding allows formation of the native(functional) protein form

Question 2

What processes do protein folding depend on?

Answer 2

Folding is a trial and error process that depends on :

1. Composition of side chains
2. Hydrogen bonding
3. Disulfide bonds
   The
4. Ionic interactions
5. Hydrophobic effect
6. All in the context of repulsion of some shapes(steric, charge, bond angle constraints)

Question 3

What is the purpose of protein folding?

Answer 3

To result in the most stable or favorable structure

Question 4

Outline the process of protein folding

Answer 4

1. Formation of secondary structures
2. Formation of domains
3. Formation of final protein monomer

Question 5

Denaturation is usually….

Answer 5

Irreversible

In rare cases, denaturation is reversible (RNAse A)ribonuclease A

Question 6

What is lost due to denaturation?

Answer 6

• loss of biological activity

- all other shape / conformational structure

Question 7

How does denaturation affect primary structure?

Answer 7

Primary structure stays intact

Question 8

List some denaturation agents

Answer 8

• heat
• organic solvents
• mechanical shearing
• heavy metals
• detergents
• chaotropic
• drastic change in pH

Question 9

Where can RNAse be found?

Answer 9

On the hand

Question 10

What happens if denaturing agents are removed from RNAse after it is denatured?

Answer 10

RNAse, forms right back

Question 11

What are Chaperones?

Answer 11

Molecules that prevent inappropriate protein to protein interactions by:

• keeping unfolded proteins separate
• enhance folding rate
• Protect side chains from inappropriate interactions

Question 12

What are Heat Shock Proteins?

Answer 12

A special type of chaperone

Question 13

What is the purpose of Heat Shock Proteins?

Answer 13

Their synthesis increases in response to high temperature and other conditions which increase protein denaturation in the cell e.g. HSP70

Question 14

What are proteases?

Answer 14

Enzymes that degrades the protein

Question 15

How do protease break down proteins?

Answer 15

Breaking the peptide bond

Question 16

What may cause non-enzymatic protein degradation?

Answer 16

• Very low pH or very high pH
• Heat
• Time
• doesn’t happen naturally

Question 17

Does protein degradation occur in the stomach? Why?

Answer 17

Does not occur in the stomach.

The pH is not low enough, Heat is not high enough and not enough time

Question 18

What happens to dietary protein in the stomach?

Answer 18

Dietary protein is not degraded, but it is denatured

• denatured means the proteins unfolds
• loss of conformation/shape

Question 19

What is the job of the stomach?

Answer 19

To denature proteins, so they are easier to degrade by digestive enzymes

Question 20

What are chemicals and conditions that promote protein denaturation, giving a reason for each

Answer 20

• Heat, pulls stuff apart
• stuff that alters changes ionic bonds and hydrogen bonding( e.g. salt, acid, base)
• detergent which allows hydrophobic areas to interact with water
• reducing agents which can break disulfide bonds

Question 21

Detergents are _________ molecules

Answer 21

Amphipathic

Question 22

Give an example of a detergent that can denature proteins

Answer 22

SDS- sodium dodecyl sulfate

Question 23

What is sodium dodecyl sulfate used for?

Answer 23

SDS is in toothpaste

Question 24

What is another name for beta-mercaptoethanol?

Answer 24

Ethanol thiol

Question 25

How can mercaptoethanol be used to remove disulfide bridges and restore cysteine molecules?

Answer 25

Addition of urea and mercaptoethanol break cystine bridges and acts as a reducing agent

Removal of urea and mercaptoethanol restores disulfide cross-links correctly

Question 26

Give two examples of misfolded proteins that are resistant to degradation, causing diseases

Answer 26

• Prion disease

- Alzheimer disease

Question 27

What may increase protein misfolding?

Answer 27

Some genetic variants(mutation) might increase likelihood

Question 28

Explain how protein misfolding leads tho Ahlzeimers

Answer 28

• Amyloid-B protein undergoes proteolytic cleavage as a part of normal degradation
  - A non-toxic fragment may be created, which is cleared and disposed of
  - A neurotoxic form may be created, this accumulates and will eventually lead to Ahlzeimer’s which is degrade-resistant
  
  • this accumulation causes aggregation with other proteins, such as tau, which cause neurofibrillary tangles and death of brain regions

Question 29

Describe the structure and effect of the fibrous Amyloid protein

Answer 29

The twisted B-pleated sheet fibrils have 3d structure that resembles silk fibrils

Supposed to be globular protein but becomes fibrous which the brain cannot degrade fast enough

Question 30

Give prison disease examples

Answer 30

• Scrapie in sheep(sheep scraping flesh and hair)
• creutzfeldt-Jacob disease in humans
• mad cow disease

Question 31

All mammals have…

Answer 31

The prion protein (PrP)as a normal brain protein(unknown function)

Question 32

What does prion stand for?

Answer 32

Protianacious infectious particle

Question 33

What is the normal shape of the prion protein?

Answer 33

The normal protein is the PrPc(prion protein cellular)

Question 34

How can PrPc indirectly cause Scrapie in sheep?

Answer 34

The PrPc can change shape to become a disease causing form called, PrPSc (Prion protein-scrapie)

Question 35

What happens when PrPc become PrPSc?

Answer 35

• Predominant beta sheet
• Super-duper resistant to degradation
• damages neuron (scrapie in goats)

Question 36

Why is PrPSc called transmissible/ one of the transmissible spongiform encephalopathies?

Answer 36

Because if you ate someone’s brain who had PrPSc it would cause your normal PrPc into PrPSc

Question 37

How much PrPSc to convert your PrP into the disease state?

Answer 37

Only one, because it’s accumulation will cause damage to brain tissue

Formation of one PrPSc cause conversion of all PrPc to take the form of PrPSc

“Catalytic conversion”