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27 Cards in this Set

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Describe the relative number of E genes for the ubiquitin system and why its set up that way.
1. About 10 E1 genes.
2. About 100 E2 genes
3. About 600-700 E3 genes.
E3 proteins have fine specificity for specific proteins. E2 binds with less, but significant specificity to various E3 molecules. E1 is quite promiscuous and binds to most E2 proteins and is the link between target proteins and proteasome.
Describe the proteasome the structure of the proteasome.
There's a cap and a lid on both ends that recognize the Ubiquinated protein. There are two alpha rings, each composed of 7 enzymes (total 14) that straighten the protein, break disulfide bonds, and regulate. Their are two central Beta rings that each have 7 enzymes (total 14) with different specificities.
How large are the fragments of ubiquitin degradation? What happens to them after that?
7-9 aa long. These are subject to amino- and carboxy- terminal degradation that produces free amino acids.
What's wrong in 12yo patients with Parkinsons?
Parkin, an E3-ubiquitin-ligase is defective and does not recognize target proteins. The protein accumulates, aggregates, and destroys dopaminergic neurons in the CNS substantia nigra pars compacta region of the brain - resulting in the characteristic tremors associated with Parkinson's Disease.
Describe how HPV interferes with the ubiquitin system to cause carcinoma. (p292)
HPV encodes for a E3-ubiquitin ligase that recognizes p53. p53 suppresses tumors in mammalian cells. Bc p53 is incorrectly degraded, cancers arise.
How does htt (huntingtin) protein interfere with the ubiquitin system to cause neurodegenerative disease?
A mutation in htt cause it to be an inhibitor of the proteasome instead of being degraded. Proteins accumulate and deposition within the brain causes degeneration.
dietary proteins are degraded in the: by:
Stomach by endo- and exo-proteases.
What do chief cells secrete?
Pepsinogen
Before proteins can be degraded, pepsinogen must be activated. To what is it degraded to and by what?
Pepsinogen is degraded to pepsin by low pH in stomach
What types of cells secrete HCl?
Parietal cells.
The N-terminal region of Pepsinogen blocks the active site. How is it removed?
When the protein experiences low pH, it undergoes a conformational change that allows the N-terminal region to be cleaved and released - unblocking the active site.
What does pepsin cleave?
N-terminal side of large hydroPHOBIC amino acids such as Isoleucine, Phenylalanine, Valine.
The acinar cells of the pancreas synthesize three protease zymogens:
1. Trypsinogen
2. Proelastase
3. Chymotrypsinogen
How/where are the pancreatic zymogens activated? And at what pH? (p293)
In the duodenum at pH7:
1. Trypsinogen is degraded to Trypsin by enteropeptidase located on the surface of the small intestine and active when cleaved from the membrane
2. Trypsin is then used to degrade Proelastase to Elastase and;
3. Chymotrypsinogen to Chymotrypsin
What neutralizes the pH of stomach acids as it enters the duodenum?
Bicarbonate.
Describe the activity of Trypsin:
1. What is characteristic of the AA it cleaves?
2. What two examples were given in class?
(p294)
1. Cleaves long-chain residues
2. Lysine and Arginine.
Describe the activity of Elastase:
1. What is characteristic of the AA it cleaves?
2. What examples were given in class and which side of the aa does it prefer to cleave?
3. What sequence requirement does it have/prefer
1. The aa have short chains
2. Glycine and Alanine - prefers to cleave after its target sequence
3. It also prefers to cut after two aa in a row.
Describe the activity of Chymotrypsin:
1. What is characteristic of the AA it cleaves?
2. What examples were given in class.
1. They have large side chains
2. Phenylalanine, Tyrosine, Tryptophan
What is the difference between Endo- and Exo-peptidases? (p294)
Endopeptidases cleave at specific locations anywhere along a peptide chain.
Exopeptidases cleave at only the amino or carboxy terminal ends to produce free, di- or tri-peptides.
What produces Carboxypeptidases? Aminopeptidases?
**What activates carboxypeptidase?
Carboxypeptidases are made by the pancreas (activated by Trypsin)
Aminopeptidases are made by the intestine
What are class transporters? (p295)
They are specific for different types of amino acids. They pick up Di- and Tri-peptides and free amino acids. Free amino acids are picked up by Acidic, Basic, Neutral, Small, Di- and Tripeptide, and Aromatic transporters.
When di- and tripeptides are picked up the cells, how are further degraded to free amino acids? (p295)
Via amino- and carboxypeptidases.
**NOTE: Dysfunctional absorption transporters can result in disease.
What three amino acids are released into the serum by the liver as a source of energy (10% of the energy usage, in fact)
LIV: Leucine, Isoleucine, Valine
Since amino acids are not stored, how are they used?
For energy
As amino acids are degraded, what is the fate of the ammonia? (297)
It is transferred to alpha-ketoacids to form amino acids that function as ammonia transport molecules, to take ammonia to the liver for urea synthesis.
In PKU, what enzymes are deficient? What is used instead?
Deficiency in Phenylalanine Hydroxylase or Dihydrobiopterin Reductase. Instead, Aminotransferase is used but this creates toxic products.
Aromatic amino acid transporter deficiency causes symptoms similar to:
Why and what are the symptoms
Pellagra. This is a deficiency in tryptophan and symptoms include the four D's: Diarrhea, dementia, dermatitis, death