nitrogen metabolism Flashcards
the atmosphere is __% nitrogen
78%
the the 4 forms of nitrogen that are useful
nitrate, nitrite, ammonia, ammonium
nitrate
NO3-
nitrite
NO2-
ammonia
NH3
ammonium
NH4+
NO3-
nitrate
NO2-
nitrite
NH3
ammonia
NH4+
ammonium
N2
atmospheric nitrogen
which organism can convert nitrogen to biologically useful forms
nitrogen fixing prokaryotes
nitrogen fixing prokaryotes fix over ___ kg of nitrogen per year
10^11
what does it mean to “fix” something
take it out of the atmosphere and make it an organic compound
when fixing N2, what form is it converted to?
NH3 (ammonia), and then will be converted to organic forms of nitrogen
out of the usable forms of nitrogen, which is the most oxidized?
nitrate (NO3-)
out of the usable forms of nitrogen, which is the most reduced?
ammonia (NH3)
what does nitrogen fixation produce
NH3, which is then converted to organic forms of nitrogen
what does nitrogen fixation use to make NH3
N2
T or F: most organisms can do nitrogen fixation
true
what does nitrification start with
NH3
what does nitrification produce
NO3-
is nitrogen fixation an oxidation or reduction
reduction
is nitrification an oxidation or reduction
oxidation
what does assimilation start with
NO2- or NO3-
what does assimilation produce
NH3
is assimilation an oxidation or reduction
reduction
what organisms use assimilation
plants
explain why plants use assimilation + what benefit this has for the plant
they take up nitrate and nitrite from the soil and convert it back to ammonia, which is used to build amino acids and nucleotides
in regards to the nitrogen cycle, what happens when an organism dies
decomposers return ammonia to the soil to be reused by nitrifying bacteria. Animals ingest these amino acids when they ingest plants or animals that ate plants
what does denitrification start with
NO3-
what does denitrification produce
N2
in what conditions does denitrification occur
anaerobic
does denitrification occur under aerobic or anaerobic conditions
anaerobic
in denitrification, what is the final electron acceptor instead of oxygen
NO3- or NO2-
is assimilation an oxidation or reduction
reduction
is denitrification an oxidation or reduction
reduction
in the nitrogen cycle, which step completes the cycle
denitrification
other than denitrification, which step can complete the cycle
anammox
what does anammox start with
NH3
what does anammox produce
N2
what electron acceptor does anammox use
NO2-
which organisms use anammox
anammox bacteria
does anammox happen aerobically or anaerobically
anaerobicaly
what makes anammox bacteria weird?
they create their ETC across an organelle membrane called the anammoxosome (weird that bacteria have an organelle)
what is the anammoxosome
an organelle in anammox bacteria where the ETC is located
what reaction does the nitrogenase complex mediate
reduction of atmospheric nitrogen to ammonia
T or F: converting N2 to NH3 (via nitrogenase complex) is spontaneous
true
T or F: converting N2 to NH3 (via nitrogenase complex) is easy to do
false; it’s very hard to do
why is the conversion of N2 to NH3 using the nitrogenase complex hard to do?
the N≡N triple bond is very stable, and this nitrogen fixation has such a high activation energy that it’s basically inert under normal temp/pressure
since N2–> NH3 via nitrogenase complex is so hard to do, how do prokaryotes manage it?
ATP plays a role! (this is odd considering the reaction is exergonic)
making 2 ammonia from N2 costs __ ATP
16
which organisms can fix nitrogen
diazotrophs
list 3 examples of diazotrophs
cyanobacteria, methanogens, rhizobia
what are rhizobia
gram negative anaerobic bacteria living in the root nodules of legumes
what two enzymes make up the nitrogenase complex
dinitrogenase and dinitrogenase reductase
describe why the legume-rhizobium interaction is mutualistic
the plant provides sugars and phosphates, the bacteria provides nitrogen
in the legume-rhizobium interaction, in what form do the bacteria give nitrogen to the plant
ammonium (NH4+)
describe how the nitrogenase complex interacts with air
it’s rapidly inactivated in air due to instability around the presence of oxygen (it’s anaerobic)
list 4 things that a bacteria with the nitrogenase complex might do
live anaerobically, inhibit complex activity when O2 is present, balance enzyme inactivation with enzyme synthesis, block O2 binding site by conformational changes
describe how a bacteria (with the nitrogenase complex) living in the root nodule can solve the problem of oxygen toxicity
the plant provides the nodule with a hemoglobin-derivative called leghemoglobin, which binds and sequesters the oxygen in the nodule away from the anaerobic bacteria
what hemoglobin derivative do plants have
leghemoglobin
benefit of a plant providing its root nodule with leghemoglobin?
it binds and sequesters the oxygen in the nodule, keeping it away from the anaerobic bacteria
structure of dinitrogen reductase (3)
homodimer, has an Fe-S redox center, and an ATP binding site on each subunit
structure of dinitrogenase? (3)
tetramer, each with a P cluster and Fe-Mo cofactor
list the 4 cofactors that dinitrogenase might have
Fe, S, molybdenum, vanadium
in order to produce 2NH4+ from one N2, how many electrons are required
8
where does dinitrogenase get the 8 electrons required for NH4+ formation?
from dinitrogenase reductase
where does dinitrogenase reductase get the 8 electrons from required for NH4+ formation
came from pyruvate, which would then be oxidized to acetyl-CoA
NH4+ formation: how does pyruvate get the 8 electrons to give to dinitrogenase reductase
it’s oxidized to acetyl-CoA, which produces 8 electrons
NH4+ formation: how does pyruvate transfer the 8 electrons to dinitrogenase reductase
via ferredoxin or flavodoxin
NH4+ formation: what does dinitrogenase reductase do with the 8 electrons
gives them one at a time to dinitrogenase
NH4+ formation: T or F: dinitrogenase reductase gives all 8 electrons to dinitrogenase all at the same time
false; it gives them one at a time
NH4+ formation: passage of 1 electron from dinitrogenase reductase to dinitrogenase requires __ ATP
2 ATP
NH4+ formation: what is the result of ATP binding+hydrolysis to dinitrogenase reductase
causes a conformational change to bring DR and D cofactors together to promote electron transfer
NH4+ formation: what does dinitrogenase do with the 8 electrons
uses 6 to reduce N2 to 2NH4+, and uses 2 to make H2
NH4+ formation: what does dinitrogenase use 6/8 electrons for
reduction of N2 –> 2NH4+
NH4+ formation: what does dinitrogenase use 2/8 electrons for
to make H2
what is glutamate synthetase suppressed by? why?
low ATP, high NH4+
this is because the process is very costly (ATP), and it produces NH4+
NH4+ is incorporated into all biomolecules starting with ___ and ___
glutamate and glutamine
once in glutamate, what happens to NH4+ to generate most other amino acids
it can be transaminated
once in glutamine, what happens to NH4+
incorporated into other biomolecules
__ + ___ = glutamine
NH4+ and glutamate = glutamine
T or F: synthesis of glutamine from NH4+ and glutamate uses ATP
true
once glutamine is produced from NH4+ and glutamate, what can it combine with + what is produced
combines with a-ketoglutarate to make two glutamate molecules
how many glutamates are made from a-ketoglutarate and glutamine joining
2
what does glutamine join with to make glutamate
a-ketoglutarate
during glutamine + a-keto –> glutamate, what else is produced
NADPH
what is formed when a-keto gains a backbone amine
glutamate
what is formed when glutamate gains an R group amine
glutamine
how many amines does a-keto have
0
how many amines does glutamate have
1
how many amines does glutamine have
2
when pairing glutamine and glutamate synthesis, what are the net products?
glutamate, NADP+, ADP, Pi
how many types of glutamine synthetase are there
2
type I of glutamine synthetase is present in ____
bacteria
type II of glutamine synthetase is present in ____
eukaryotes
how many subunits does type I glutamine synthetase have
12
how many subunits does type II glutamine synthetase have
10
in glutamine synthetase, each subunit has an active site where __ and __ bind
ATP and glutamate
type I glutamine synthetase is regulated by __ other molecules
8
how is type I glutamine synthetase regulated
all 8 inhibitory molecules must be present to shut it down. The effects of each one are additive
define cumulative feedback inhibition
the downstream products act as inhibitors of an enzyme, but all of them are required in order to shut down the enzyme
other than the downstream products, which molecule is able to inhibit the activity of glutamine synthetase
AMP
how does AMP inhibit glutamine synthetase activity
it covalently binds to a tyrosine (adenylation) near the enzyme active site
which enzyme promotes adenylation and deadenylation of glutamine synthetase
adenylyltransferase (AT)
which regulatory protein modules adenylyltransferase activity
PII
result of PII binding to adenylyltransferase?
stimulates adenylation of glutamine synthetase
when glutamine synthetase is adenylylated, is it active or inactive
inactive
what regulates PII activity
uridylylation
how is glutamine synthetase deadenylylated
via UMP-PII binding to adenylyltransferase
which enzyme promotes uridylylation and deurifylylation
uridylyltransferase (UT)
UT uridylylation activity is inhibited by ___
glutamine
UT uridylylation activity is stimulated by __ and ___
a-keto and ATP
PII inhibits or promotes transcription of glutamine synthetase gene
inhibits
UMP-PII inhibits or promotes transcription of glutamine synthetase gene
promotes
which enzyme incorporates nitrogen in glutamine into other biological molecules
glutamine amidotransferases
after glutamine amidotransferase activity to incorporate nitrogen into other molecules, what happens to the glutamine that donated the N
it converts back to glutamate
how many active sites does glutamine amidotransferase have
2
what do the 2 active sites of glutamine amidotransferase fit
one fits glutamine, other fits various nitrogen acceptors
during the transfer of nitrogen from glutamine to other molecules, which enzyme acts as the nucleophile that cleaves the amide bond in glutamine
cysteine
after cysteine cleaves the amide bond in glutamine, what is released
NH3
after cysteine cleaves the amide bond in glutamine, where does the freed NH3 go
it’s transferred to a second product
after cysteine cleaves the amide bond in glutamine and the NH3 is transferred to a second product, what happens
the residual glutamate and new aminated product leave
