Download BioMI 2900

BioMI 2900
Dr. Hay
Fall 2016
09/30/16
Week 6: Lecture 3 of 3 (Lecture 15)
Title: Nitrogen Fixation and Assimilation
Keywords: Modularity, Biosynthesis, Nitrogen Cycle, Nitrification (Nitrogen Fixation), Nitrogenase, NifH, Protection from Oxygen, Heme, Heterocysts, Bacteroids, Gas Chromatograph,
Ammonia, Ammonium, Hydrozene, Tetrapyrroles, Amino Acid Biosynthesis, Activated Sugars, Peptidoglycan Generation, Lysozyme
Review the second part of Lecture 11 (Panopto on Blackboard)!!!
What is a Module?
●
A molecule which can be used for a plethora of different pathways
●
The basic, central machinery of many energy production processes is conserved
●
Makes HGT simple and conserves genes
●
Evolution is thus accelerated
Overview of Biosynthesis:
Overview of the Nitrogen Cycle:
Nitrification (Nitrogen Fixation)
●
It is both lithotrophy and respiration
●
The challenge of this cycle is to reduce the inert N2 into organic forms
●
Learn Horizontal Transfer of Nitrogenase Genes (NifH) Slide!!
●
Takeaway: there is a lot of HGT of this gene, making it differ GREATLY from the 16s rRNA
phylogeny
●
Why is nitrogen fixation so common? 99.99% of Nitrogen in nature is inert!
●
Here is a table of some common nitrogen-fixing organisms:
●
The coupling of photosynthesis with N-fixation allows a wide environmental range (e.g. for
cyanobacteria)
●
N-fixation needs protection from O2:
○
some structures to protect it from oxygen are heterocysts in cyanobacteria, nodule formation in legumes/plants (Rhizobia), slime layers (Azotobacter)
○
Bacteroids in plant nodules are differentiated bacteria which fix nitrogen for the plant.
They are red in color due to a heme molecule. There environments are largely anoxic,
due to the heme molecule.
Fixation with Nitrogenase:
●
Requires unusual cofactors
●
Learn net reaction
●
Relies on reduction of NADH
●
Having a HYDROGENASE can recuperate energy lost in N-fixation.
●
Hydrozene is a toxic byproduct, so it is reduced again to form ammonia and ammonium
●
There is a high energy investment to make ammonia
Measuring N-Fixation:
●
Where does reducing power come from? Glycolysis!
Assimilation of NH4+ ●
It is condensed
Ammonia Assimilation:
Amino Acid Biosynthesis
●
Carbon comes from Glycolysis, Pentose Phosphate, and TCA
●
Very modular process:
○
●
Very complicated processes have a common, relative origin in the simple backbones of
respiration
The molecule Chorismate is associated with Aromatic amino acids (Trypophan, Tyrosine,
Phenylalanine)
Tetrapyrroles are modular structures used to make heme, chloropyll, vitamin Band many
other ringed structures:
●
Lead Poisoning directly affects tetrapyrrole formation
Nucleotide Biosynthesis
●
Sugar from Pentose Phosphate Pathway is activated
●
PRPP is gateway molecule, affecting the speed of the pathway
●
2 Phosphates are released, making the process irreversible (nucleotide biosynthesis is important and central)
●
Again, this process is modular, in that it has many different diverse outcomes
Peptidoglycan Biosynthesis
●
Starts with activated sugar (UDP)
●
UDP-NAM joins UDP-NAG to make chains and added to bactoprenol, which is then cleaved
by Bacitracin
●
Vancomycin and Penicillin directly inhibit this synthesis with lysozyme
●
Neomycin has Bacitracin (in addition to protein synthesis inhibitors), which also cleaves the
cell wall