Feb 25 Flashcards
Nitrogen is the ______ factor in the growth of many organisms, not all, in their normal environments.
Limiting
All organic nitrogen is ultimately derived from ______ through reduction to _______ by the bacterial enzyme ________.
atmospheric N2, ammonia NH3, nitrogenase
What is the anammox reaction? Where occur (organelle)?
It is when bacteria turn fixed nitrogen back to N2 gas, happens in side special MB bound compartment called anammoxosome, it is where there is no oxygen present
What is the rough nitrogen cycle?
Have nitrogen fixing bacteria use nitrogenase to fix it into NH3, then nitrifying bacteria reduce it further into NO2- (nitrites), then nitrates NO3-. Then denitrifying bacteria use NO3- as acceptor of electrons instead of O2, turns it back to N2. Also have anammoz bacteria that turn NH2 and NO2 back to N2.
Where is nitrogenase located in plant cells and in cyanobacteria?
In plant cells, in the root nodules have bacteria in them. In cyanobacteria, they have special cells called heterocysts, they are enlarged cells
What rough mechanism used by nitrogenase?
It has Fe-S cluster that will accept electon from ferridoxin (plants) or NADH, then pass it to Fe-Mo center, then passed to N2 to make 2 HN3
What 2 amino acids are produced by incorporation of NH3?
Glutamate from alpha amino nitrogen provides it to other amino acids, and glutamine provides side chain nitrogen to many compounds
What is amino acid precursor before adding NH3? What cycle is theis precursor from, what enzyme and electron source?
It is a-ketoglutarate/2-oxoglutarate from the TCA cycle. Adding NH3 turns it into glutamate. Done by glutamate dehydrogenase (GDH) using NADPH.
How is glutamine made, from what precursor, what enzyme and what powers the reaction?
It is from glutamate, glutamine synthetase uses ATP to add ammonia to make glutamine.
Summarize the reactants and products and what enzymes to make more glutamate from 1 glutamate?
Glutamate and NH3 become Glutamine using glutamine synthetase.Then Glutamine and a-ketoglutarate reacted by glutamine 2-oxoglutarate aminotransferase (GOGAT) to make 2 glutamates. 1 will feed back to become glutamine again, other will enter cellular pool.
Glutamine synthetase (GS) is inhibited by what 4 metabolites, what happens if use all 4 at once?
Each metabolite partially inhibits, all 4 completely do it (cumulative feedback inhibition). All end products of glutamine metabolism, histidine, trp, 5’AMP, CTP.
What modification to glutamine synthetase (GS) makes it sensitive to end products of glutamine metabolism? ON what AA of the protein, what enzyme does this?
It is if cells grown in N rich media, GS has AMP covalently attached to a Tyr from ATP, done by adenylyltransferase.
How were glutamine synthetase deadenylation factors found, what are these 2 things?
If kinetic assay done after gel filtration, there are 2 groups of fractions that contain an adenylyltransferase (ATase) and a protein called P2. Both need to be present to deadenylate GS.
How is the adenylation and deadenylation done on Glutamine synthetase (GS)?
Have Adenylyltransferase, it has 2 active sites.
1. Uridyltrasferse/uridylyl-removing enzyme (UT/UR) is bifunctional, it allosterically senses Gln.
- Protein 2 (PII) will bind to ATP and 2-ketoglutarate and sense their levels in the cell.
- If [ATP] is high enough, then PII will change conformation, will now bind to 2-ketoglutarate, now a good substrate for UT/UR.
- Now for UT/UR, if Gln is low it will add UMP to PII bound to Adenylyltransferase which will deadenylate GS. If Gln is high, then PII does not have UMP put on by UT, so ATase will add AMP to GS.
What does Snf3/Rgt2 sense in terms of nutrients? What organisms?
It is in plasma MB, senses glucose levels outside of cells. Only in fungi, so like yeast, other single celled eukaryotes
What is Snf1, what does it sense, present in what?
It is AMP activated kinase, so energy sensor. It is in all eukaryotes
What does TOR sense? Present in which organisms?
It will sense AA’s, glucose and energy, it is present in all eukaryotes.
How do riboswitches work?
May be if ligand bound or not, but one of those options will have the ribosome binding site as part of dsRNA loop, or as part of ssRNA (available). This will allow transcription only if ligand is bound/unbound.
