protein degradation Flashcards
Distinguish between nitrogen balance, negative nitrogen balance, and positive nitrogen balance.
Nitrogen balance in the ratio of nitrogen ingested to nitrogen excreted.
Negative balance: more excreted than ingested. This can occur during starvation, injuries, and some diseases
Positive balance: taking in more than we excrete. Seen in growing children and pregnant women
Explain why essential amino acids cannot be made in humans.
We cannot form the carbon skeleton of the amino acid, or we just can’t make enough
Which amino acids are essential in kids but not adults?
Cysteine and arginine
Specify two methods by which the protein quality of foods can be assessed.
Chemical score: based on essential amino acid content of food
Net protein utilization looks at the ratio of amino acids retained vs supplied
Explain why serine and glycine are not considered essential amino acids.
Serine: we can make serine from 3-phosphoglycerate (glycolytic intermediate)
Glycine: we can make glycine from serine
Explain how we degrade dietary proteins
We begin breaking it down with mechanical digestion in the mouth. In the stomach we use pepsin to form peptides. These peptides encounter bicarb in the small intestine to neutralize the acidic environment. They also encounter various activated proteolytic enzymes. This leaves us with amino acids and oligopeptides. Aminopeptidase makes the oligopeptides into di and tri peptides in the intestine. We then have free amino acids that can enter the blood stream.
What is the rate limiting enzyme of cholesterol synthesis?
HMG-CoA reductase
Describe how protein degradation regulates cholesterol biosynthesis
If we have high cellular cholesterol, we degrade HMG CoA reductase faster by tagging it with ubiquitin to target it to the ubiquitin-proteasome pathway. If we have low cellular cholesterol, we will not degrade HMG-CoA reductase and cholesterol synthesis will continue.
What are the two important amino acids in ubiquitin? What do they do?
Lysine 48: when we link more ubiquitin at the gly76 here to make chains, the protein is targeted for degradation.
Glycine 76: forms an isopeptide bond between the target protein and ubiquitin
Describe the steps involved in protein ubiquitination and the subsequent degradation by proteasomes
-E1 adds an AMP to the ubiquitin molecule, then we hydrolyze the AMP and connect the ubiquitin to the active site of E1 on a cysteine residue
-E2 covalently links to the active site via a cysteine residue
-E3 coordinates the E2 carrying ubiquitin and the target protein and allows the ubiquitin and the protein to bond
What is the general structure of proteosome?
It has a barrel and two caps. The caps recognize the ubiquitin chain and starts to unfold the target protein and send it into the barrel. In the barrel, the protein will be chewed up. Peptidases outside the proteosome can finish breaking the pieces into free amino acids
What is bortezomib? What is its significance?
A proteosome in cancer cells; If we inhibit bortezomib (proteosome in cancer cells), we build up misfolded proteins and conflicted signals in the cancer cells. These can result in death of the cancer cell
What are DUBS? What is their significance?
The are deubiquitinating enzymes; they can be targeted for use in cancer treatments. If a cancer cell can’t use these to remove ubiquitin they cannot prevent degradation of their proteins.
What conditions are associated with mutations in ubiquitin-proteosome pathways
Cancers (breast, kidney), neurodegenerative diseases, cardiovascular disease
