proteolysis

Question 1

what do proteases, proteinases, peptidases and cathepsins do?

Answer 1

enzymes that cleave peptide bonds

Question 2

what are cathepsins?

Answer 2

lysosomal proteins

Question 3

why do proteases in the small intestine need to be non specific?

Answer 3

so they can degrade any type of protein that is ingested

Question 4

what is a proprotein?

Answer 4

the precursor of the active form

Question 5

how does chymotrypsin get activated?

Answer 5

trypsin cleaves amino acids from chymotrypsinogen and it becomes active chymotrypsin, and three amino acids are removed so three separate peptide chains are made which are joined by disulfide bonds.

Question 6

what is the activation of factor 12 in the clotting cascade activated by?

Answer 6

damaged surfaces

Question 7

how does HIV-1 protease work?

Answer 7

HIV genome produces two proteins called Gag and Pol that need to be processed by proteolysis. HIV-1 cleaves these two proteins and activate them.

Question 8

What are the two pathways for protein degradation?

Answer 8

Lysosomal degradation and the other is the ubiquitin proteasome pathway

Question 9

What are ubiquitins?

Answer 9

small regulatory proteins that are attached covalently to the substrate protein.

Question 10

What is the proteasome?

Answer 10

a large protease complex the active sites all point towards the center of the inner cavity.

Question 11

How many peptides is ubiquitin made from?

Answer 11

76

Question 12

what does ubiquitin do?

Answer 12

acts like a marker for proteins that need to be broken down.

Question 13

what does formation of the isopeptide bond require?

Answer 13

ATP

Question 14

describe ubiquitylation

Answer 14

1) ACTIVATION: formation of a thioester bond between the COOH terminus of ubiquitin and a cysteine in E1 (requires ATP)
2) CONJUGATION: transfer of ubiquitin from cysteine onto E2
3) LIGATION: transfer of ubiquitin from E2 to a lysine in the target protein, or to the other ubiquitin molecules already attached to a target (polyubiquitination)

Question 15

How many ubiquitin molecules need to be added to the bound ubiquitin?

Answer 15

4

Question 16

What is a half life of a protein?

Answer 16

The amount of time taken to degrade half the amount of protein that was present in the beginning

Question 17

What is the mechanism that is responsible for the differences in half life?

Answer 17

N-end rule pathway

Question 18

describe what the N-end rule pathway is

Answer 18

→the first amino acid is methionine

→this is sometimes cleaved off by methionine aminopeptidases which exposes the second amino acid after the methionine at the N terminus

→it is the nature of the second amino acid which determines the stability of the protein.

Question 19

what determines how stable the protein is?

Answer 19

→The affinity of the ubiquitin ligase (kM) to the amino acid that comes after methionine.

Question 20

if the affinity of the ubiquitin ligase to the amino acid after methionine is high what does this mean?

Answer 20

→that the protein has a higher chance of being ubiquitylated and being degraded

Question 21

what is one stable second amino acid to have after methionine?

Answer 21

→any one of : methionine, glycine, alanine, serine, threonine or valine

Question 22

why is the liver the only organ that can get rid of cholesterol completely?

Answer 22

→it can convert cholesterol into bile acids

Question 23

how do statins work?

Answer 23

→block cholesterol biosynthesis

Question 24

How do we classify proteases based on the manner in which they bind to and cleave their targets?

Answer 24

→ENDOPEPTIDASES: they break peptide bonds of non-terminal amino acids (ie. within the molecule)

→EXOPEPTIDASES: they break peptide bonds of terminal amino acids (ie. cleaves at the end of a polypeptide chain)

Question 25

What are the two subdivisions of exopeptidases?

Answer 25

→AMINOPEPTIDASES: cleaves peptide bonds at the N-terminal (amine terminus)

→CARBOXYPEPTIDASES: cleave peptide bonds at the C-terminal (carboxy terminus)

Question 26

What are some examples of cysteine proteases?

Answer 26

→Bromelain

→Papain Both can be used a meat tenderisers.