proteolysis Flashcards
what do proteases, proteinases, peptidases and cathepsins do?
enzymes that cleave peptide bonds
what are cathepsins?
lysosomal proteins
why do proteases in the small intestine need to be non specific?
so they can degrade any type of protein that is ingested
what is a proprotein?
the precursor of the active form
how does chymotrypsin get activated?
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.
what is the activation of factor 12 in the clotting cascade activated by?
damaged surfaces
how does HIV-1 protease work?
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.
What are the two pathways for protein degradation?
Lysosomal degradation and the other is the ubiquitin proteasome pathway
What are ubiquitins?
small regulatory proteins that are attached covalently to the substrate protein.
What is the proteasome?
a large protease complex the active sites all point towards the center of the inner cavity.
How many peptides is ubiquitin made from?
76
what does ubiquitin do?
acts like a marker for proteins that need to be broken down.
what does formation of the isopeptide bond require?
ATP
describe ubiquitylation
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)
How many ubiquitin molecules need to be added to the bound ubiquitin?
4
What is a half life of a protein?
The amount of time taken to degrade half the amount of protein that was present in the beginning
What is the mechanism that is responsible for the differences in half life?
N-end rule pathway
describe what the N-end rule pathway is
βthe first amino acid is methionine
βthis is sometimes cleaved off by methionine aminopeptidases which exposes the second amino acid after the methionine at the N terminus
βit is the nature of the second amino acid which determines the stability of the protein.
what determines how stable the protein is?
βThe affinity of the ubiquitin ligase (kM) to the amino acid that comes after methionine.
if the affinity of the ubiquitin ligase to the amino acid after methionine is high what does this mean?
βthat the protein has a higher chance of being ubiquitylated and being degraded
what is one stable second amino acid to have after methionine?
βany one of : methionine, glycine, alanine, serine, threonine or valine
why is the liver the only organ that can get rid of cholesterol completely?
βit can convert cholesterol into bile acids
how do statins work?
βblock cholesterol biosynthesis
How do we classify proteases based on the manner in which they bind to and cleave their targets?
βENDOPEPTIDASES: they break peptide bonds of non-terminal amino acids (ie. within the molecule)
βEXOPEPTIDASES: they break peptide bonds of terminal amino acids (ie. cleaves at the end of a polypeptide chain)
What are the two subdivisions of exopeptidases?
βAMINOPEPTIDASES: cleaves peptide bonds at the N-terminal (amine terminus)
βCARBOXYPEPTIDASES: cleave peptide bonds at the C-terminal (carboxy terminus)
What are some examples of cysteine proteases?
βBromelain
βPapain Both can be used a meat tenderisers.
