Proteolysis

Question 1

What are the different classes of proteases?

Answer 1

Metallo proteases
Serine Proteases
Cysteine Proteases
Aspartyl Proteases

Question 2

What is an endopeptidase?

Answer 2

Cleaves substrate protein in the middle of the chain

Question 3

What is an exopeptidase?

Answer 3

Cleave substrate protein at the end of the chain

Question 4

What are examples of exopeptidases?

Answer 4

Amino and carboxypeptidases - this is because this is the C-terminal and the N-terminal of the amino acid

Question 5

What is specific proteolysis?

Answer 5

Protein activation the protease will activate a certain protein e.g preproinsulin to proinsulin

Question 6

What is non-specific proteolysis?

Answer 6

Protein degradation enzymes do not need to be specific. e.g stomach enzymes to digest the proteins in ingestion

Question 7

What are inactive forms of a protein known as?

Answer 7

Zymogen
Proenzyme
Proprotein

Question 8

What is the digestive example of protein activation?

Answer 8

Chymotrypsinogen and trypsinogen is converted to chymotrypsin and trypsin

Question 9

What is an example of protein activation in clotting factors?

Answer 9

Prothrombin is converted to thrombin

Question 10

What us the famous HIV-1 aspartyl protease

Answer 10

The HIV genome produces two proteins called Gag and Pol however they are inactive and need to be activated by specific proteolysis. The activator is the HIV-1 aspartyl protease. HIV protease inhibitors were produced to prevent the production of these two proteins.

Question 11

How is protein degradation compartmentalised?

Answer 11

The breakdown can be targeted to different areas for example lysosomes or by ubiquitylation to the proteasome which then breaks the protein down into amino acids

Question 12

What is the proteasome?

Answer 12

Proteasome is a large protease complex where the active sites will point into an inner cavity. The ubiquitin-substrate complex is targeted to this cavity and degraded into amino acids and small peptides

Question 13

What does ubiquitin do?

Answer 13

Target proteins for degradation and guides them to the proteasome

Question 14

What are the enzymes that are involved in ubiquitylation?

Answer 14

E1 = ubiquitin activating 
E2 = ubiquitin conjugating 
E3 = ubiquitin ligase

Question 15

What is the process of ubiquitylation

Answer 15

1) Ubiquitin -COOH terminus forms a thioester bond with a cysteine residue on E1 this activates ubiquitin. This process requires ATP. Ubiquitin is conjugated to E1.
2) Activated ubiquitin will be transferred onto a cysteine molecule on E2.
3) Ubiquitin is then transferred from E2 to lysine on the target protein using E3.

Question 16

What amino acid does ubiquitin bind to on the target protein? (Last stage of ubiquitylation)

Answer 16

Lysine

Question 17

What is the N-end rule?

Answer 17

E3 Ubiquitin Ligase will have a poor affinity for the N -terminal of stabilizing amino acid residues therefore they are less likely to be guided to the proteasome

Question 18

How does the nature of an amino acid determine its half life?

Answer 18

Amino acids can either be stabalizing or destabalizing. Destabalzing amino acid residues will have a higher affinity for E3 resulting in a greater interaction between the N-terminal and E3. This means that the protein is more likely to be targeted to the proteasome and broken down resulting in a shorter half life.

Question 19

Example of destabilizing amino acid

Answer 19

Isoleucine, Tyrosine, Leucine, Arginine, Phenylalanine, Aspartic acid

Question 20

Examples of stabilizing amino acids

Answer 20

Methionine, Glycine, Alanine, Serine, Threonine

Question 21

What is an example of protein activation?

Answer 21

When blood cholesterol levels are too low

Question 22

What is the SREBP pathway in the regulation of cholesterol?

Answer 22

SREBP is a transcription factor involved in the regulation of cholesterol.
At low levels cholesterol binds to SCAP causing it to undergo a conformational change binding to INSIG which will anchor SCAP and SREBP into the ER.

At low levels cholesterol will no longer bind to SCAP causing the conformational change to be reversed and SCAP and SREBP will leave the complex and go to the Golgi. At the Golgi there will be proteases which will cleave SREBP by N-terminal proteolysis. This forms N-SREBP which will then travel to the nucleus and activate specific genes e,g LDL receptors and cholesterol biosynthesis pathway

Question 23

How do statins work?

Answer 23

Statins will lower blood cholesterol levels by blocking the enzyme HMG-CoA reductase involved in the synthesis of AcetylCoA to cholesterol. This will lower the blood cholesterol concentration and the SREBP pathway is activated to increase levels to normal if necessary