Moore section post midterm Flashcards
is there a protein whose sole job is to act as a storage depot for amino acids?
nope.
What is the main source for amino acid input to the pool?
Cellular protein turnover
What is the weight of proteins recycled in a day due to cellular turnover?
300/400g of protein in a day
What are some examples of protein halflife being variable?
regulatory proteins degrade in minutes to hours
- collagens or eye lens proteins take months or years
What is the major protein degradation pathway?
ubiquitin-proteasome pathway
Give an overview of the ubiquitin proteasome pathway
Ubiquitin molecules are linked to a specific lysine residue in the target protein
- protein becomes polyubiquinated which is recognized by the proteosome
- protein is processed into peptides , ubiquitin is cleaved and re utilized.
What links the ubiquitin to the target protein? type of linkage?
isopeptide bond - to lysine not amino terminus
Why do we have to degrade proteins to peptides?
because they fat as fuck
What is proteolysis?
breakdown of protein by hydrolysis, cleavage of proteins by digestive proteinases - enzymes are secreted into stomach and small intestine
What is the benefit of the gastric environment for proteolysis?
gastric acid environment denatures proteins and thus enhances proteolysis - due to low pH
- gastric acid also acts as an antiseptic, killing bacteria and viruses
what is the important pump in the stomach?
K/H pump in membrane of specialized stomach cells pump protons into the stomach in exchange for K at the expense of ATP hydrolysis - generates acidic environment
What is GERD?
gastroesophageal reflux disease
- K/H pump is overactive which results in reflux
what are proteinase zymogens?
inactive proteolytic enzymes - activated by proteolysis
- proteinases are synthesized and stored as zymogens so they dont break down proteins in the cells where they are made stored and dont digest themselves prior to secretion
What can pepsin cleave?
preferentially cleaves peptide bonds between hydrophobic amino acids or aromatic amino acids
What can trypsin cleave?
cleaves bonds following an Arg or Lys residue
What can chymotrypsin cleave?
preferentially cleaves peptide bonds after an aromatic amino acid
What can elastase cleave?
not as specific - cuts amino acids with smaller hydrophobic side chains such as glycine, alanine or valine
Proteases eventually self _____
inactivate - digest themselves
What are endopeptidases?
proteolytic enzymes that cleave internal peptide bonds in a substrate
What are aminopeptidases and carboxypeptidases?
can only cleave amino or carboxy residue of a peptide - works further down in the intestine - chew up one by one until only amino acids are left
What happens to excess amino acids?
not excreted or stored, must be converted to other molecules that can be excreted or repurposed
What is the transamination reaction?
- transfers amino group to aKG
— donor - L amino acids
— acceptor - a KG - funnels amino groups to glutamate
- obligatory step in degradation of amino acids except for Lys and Thr
- Reversible reaction
- Enzymes - aminotransferases - specific amino group donor and acceptor
What are the two different aminotransferases? And what tissues / cell locations
Aspartate aminotransferase - liver mitochondria - see urea cycle
- Alanine aminotransferase - muscle cytosol - muscle amino groups converted to alanine which is transported to liver via blood
What is the ultimate acceptor of donated amino groups - what does this lead to?
alpha ketoglutarate - glutamate
what converts glutamate into alphaketoglutarate?
mitochondrial glutamate dehydrogenase
What is PLP?
Pyridoxal Phosphate - cofactor for transaminases
- amino group acceptor
Pyridoxamine phosphate is an aketo group acceptor
- bound by default in active site to lys side chain NH3 group
What does the amino group of incoming amino acids do with PLP?
forms covalent linkage with aldehyde group - a-keto group leaves
What does the ketone group of incoming a-keto acids do with pyridoxamine phosphate?
forms covalent linkage with amino group
- amino group displaves by active site lysine amino group
- glutamate leaves
What is a Schiff base / aldimine?
chemical term that defines an imine C—N group derived from an aldehyde
Aminotransferases are important molecules for what?
liver or heart damage
What are the fates of glutamate when it enters the mitochondria in the liver/
Enters liver - acted on by glutamate dehydrogenase
- some is converted to NH4 and goes to urea cycle
- some is converted back to aKG and goes into TCA cycle
Is NH3 or NH4 odorless?
NH4
Go back and look at second lecture of stan
yes maam
What are the three ways of removing nitrogen / ammonia?
NH4+ - ammonium in aquatic vertebrates and fish
Urea - most terrestrial vertebrates
Uric acid - reptiles and birds
What happens in the urea cycle?
converts NH4 to urea
- occurs in liver
- urea is secreted into blood, filtered by kidney and excreted in urine
What are the three precursors of urea?
NH4, CO2, Aspartate
What is a major regulation point of urea cycle?
Carbamoyl Phosphate Synthetase I
(not actually part of the cycle)
What occurs in step 1 of the urea cycle? forming carbamoyl phosphate?
- Bicarbonate turns into carboxyphosphate using ATP
-Carboxyphosphate turns into carbamic acid - carbamic acid goes to carbamoyl phosphate using ATP
- effectively NH2, Co2 and phosphate
- occurs in mito matrix
- enzyme is CPS1
- Allostericaly regulated
-uses 2 ATP - N-acetylglutamate is a required allosteric activator
What is N-Acetyl-Glutamate and how is it formed?
Required allosteric activator of CPSI
- Acetyl coa plus glutamate
- forms amide bond
- only occurs with excess amino acids in liver
What occurs in step 2 - forming citrulline in the urea cycle?
- formed in mito
- Ornithine (basically Lys) amide bonds with Carbamoyl phosphate using ornitihine transcarbamoylase
- makes citrulline
What occurs in step 3 - forming argininosuccinate in the urea cycle?
occurs in cytosol so citrulline has to exit mito
- citrulline and aspartate - aspartate is thedonor of the second NH3 group to urea
- uses 1 ATP
- forms arginosuccinate via arginosuccinate synthetase
- also forms L-citrulline intermediate
What happens in step 4 - forming arginine in the urea cycle?
Arginosuccinate gets broken down to arginine and fumarate by arginosuccinase
- fumarate goes to TCA
- arginine continues in urea cycle
Do we need arginine in our diet?
No, we make enough in the urea cyc;e
What happens in the 5th step, hydrolysis or arginine in the urea cycle?
Arginine is converted into ornithine and urea via arginase
- ornithine is regenerated and goes back to the start
How many ATP are used in the urea cycle?
3 - 2ATP, one AMP (whatever the activated form is)
What is a common treatment for deficiencies in Urea cycle enzymes?
supplement diet with benzoate phenybutyrate
- these molecules can form enzyme catalyzed amide linkages with glycine or glutamine
- can help deplete liver nitrogen eventually lowering ammonia levels in blood
Give a summary of the major sources of free NH4+? 4
- Major source is dietary and body protein
- glutamate dehydrogenase activity in liver leads to free NH4 - urea
- Ser and Thr dehydratase in liver generates NH4- urea
-glutaminase in liver releases NH4+ - urea
- Amino groups from other tissues come to liver in the form of alanine and glutamine- nh4 is released by transanimation/glutamate dehydrogenase and glutaminase - Kidney
- Amines
- purines in pyrimidines
In the liver, free ammonium can also be produced from the breakdown of what two amino acids?
Serine and threonine by respective dehydratases
- serine turns to pyruvate + NH4
- threonine turns to aketobutyrate + NH4