photorespiration
breakdown of ribulose-1,5-P2 into 3P-glycerate and phosphoglycolate (then glyoxylate)
causes eventual shutdown of Calvin Cycle, runs dry
reductive TCA
used to fix CO2 for gluconeogenesis
chlorobii, hyperthermophilic archaea
uses 3 NADPH, 3 CO2, 2 ATP, 2 FDH2 –> 1 pyruvate
pyruvate synthase
acetyl-CoA + NADPH + CO2 —> pyruvate
reverse reaction of pyruvate dehydrogenase
used in reductive TCA
PEP synthase
pyruvate + ATP —> PEP + AMP + Pi
3-hydroxypropionate pathway
fixes 2 CO2 into glyoxylate, then 1 more to make pyruvate
uses 3 NADPH, 4 ATP, 3 CO2 —> 1 pyruvate
acidophilic bacteria, mesophiles, chloroflexi
best sources of nitrogen
proteins/AAs NH4+ N2 NO3- last 2 go thru NH4+
anammox
ammonia to N2
denitrification
nitrate to N2
nitrification
ammonia to nitrate/nitrite
ammonia oxidation
glutamate dehydrogenase
2-ketoglutarate + NH4+ + NADPH —> glutamate
GDH
low affinity
only used in high NH4+
glutamine synthase
glutamate + NH4+ + ATP —> glutamine
GS
high affinity
only used in low NH4+ with GOGAT
glutamate synthase
glutamine + 2-ketoglutarate + NADPH —> 2 glutamate
GOGAT
only used in low NH4+
low ammonia enzymes
GS and GOGAT
high ammonia enzymes
GDH, use ammonia directly
transaminase
2-ketoglutarate + amino acid glutamate + ketoacid
regulation of phosphoribulokinase
-: AMP, PEP
+: NAD(P)H
regulation of rubisco
-: PEP
+: NADPH
cyanobacteria
use PSI and PSII
obligate photoautotrophs
H2O as electron donor
use Calvin cycle for CO2 fixation
calvin cycle
begins with rubisco 3PG kinase GAP DH regeneration phosphoribulokinase fixes CO2 for gluconeogenesis
purple bacteria
sulfur and non-sulfur are the same only PSII = cyclic electron transport H2S, H2, organic C as electron donor calvin cycle for C fixation bacteriochlorophyll a,b
chloroflexi
green non-sulfur bacteria only PSII = cyclic electron transport chemoheterotroph H2S, H2 as electron donor Calvin cycle bacteriochlorophyll a, c, d
chlorobium
green sulfur bacteria obligate photoautotrophs only PSI, non-cyclic electron transport bacteriochlorophyll a,c,d,e H2S and H2 as electron donor reductive TCA to fix C
CO2 transporters
low affinity constitutive transporter CO2 –> HCO3-
high affinity inducible CO2 –> HCO3-
high A symporter, uses Na motive force, HCO3- + Na+ –> HCO3- + Na+
high A ATPase, uses ATP inside cell to move HCO3- in
carboxysomes
densely packed protein structures with high levels of rubisco for carbon fixation
can use .037% CO2, need at least 5% without
carbonic anhydrase
HCO3- –> CO2
assimilatory nitrate reduction and enzymes
using nitrate for biomass
NO3- + XH2 —> NO2- + X (nitrate reductase)
NO2- + 3 NADH + 4 H+ —-> NH3 + 3 NAD+ (nitrite reductase)
haber process
chemical method of fixing nitrogen into ammonia, increases overall nitrogen bioavailability
N2 + 3 H2 + 2 H+ —> 2 NH4+
exergonic but requires high activation energy
nitrogenase reaction
N2 + 8 H+ + 8 e- + 16 ATP —-> 2 NH3 + H2 + 16 ADP+Pi
4 ATP used to free e- from FdH2
electrons continuously added to N2 to yield 2 NH3
2 H+ —> H2
anammoxasome
membrane structure containing ladderanes for ammonia oxidation to N2
ladderane
fatty acid structure present in anammoxasomes, stabilizes intermediates like hydrazine
hydrazine synthase
NO + NH4+ + 1 e- —> N2H4
hydrazine dehydrogenase
N2H4 —-> 4 e- + N2 + 4H+
1 e- goes to hydrazine synthase
2 e- go to ETC
1 e- goes to nitrite reductase
nitrite reductase
NO + 1 e- —> NO2- + 2H+
leghemoglobin
in root nodules of legumes
regulate O2 levels for nitrogen-fixing bacteria
heterocysts
specialized cyanobacteria cells for nitrogen fixation
fix nitrogen to ammonia, then put it into glutamate and send to regular cells
regular cells do photosynthesis and send carbohydrates to heterocyst for energy, make NADH then FdH2 for nitrogenase
cyclic electron transport
regulation of nitrogen fixation
NtrB phosphorylated by ATP in low NH4+
NtrB passes P to NtrC, which activates transcription of nifL and nifA and glutamine synthase (glnA)
NifL inactivates NifA in high O2, NifA active in low O2
NifA activates transcription of nitrogen fixation (nif) genes
cyclic amino acids
tryptophan, phenylalanine, tyrosine
regulation of cyclic amino acid synthesis
first product after chorismate inhibits its own enzyme to prevent overproduction
making chorismate
erythrose-4P + PEP + NADPH + ATP –>–>–> shikimate
shikimate + PEP –> chorismate
tryptophan biosynthesis
chorismate –>–>–> tryptophan
uses serine, PRPP, glutamine
produces GAP, PP, pyruvate, glutamate
tyrosine biosynthesis
chorismate –>–>–> tyrosine
uses glutamate
makes 2-ketoglutarate
phenylalanine biosynthesis
chorismate –>–>–> phenylalanine
glutamate –> 2-ketoglutarate
making PRPP
ribose-5P + ATP —> 5P-ribosyl-1PPi + AMP
UTP synthesis
aspartate + carbonoyl-P + PRPP –>–>–> UTP
CTP synthesis
UTP –> CTP
TTP synthesis
UTP –> dUTP –> dUMP –> dTTP
AMP and GMP synthesis
PRPP + glutamine + glycine + aspartate –> IMP (inosimic acid) + fumarate
IMP –> AMP or GMP
ribonucleotide reductase
reduces ribonucleotides to deoxyribonucleotides using thioredoxin
XTP + TR (red.) —> dXTP + TR (ox)
TR reduced by NADH/thioredoxin reductase
thioredoxin reductase
TR (ox) + NADH –> TR (red.) + NAD+
desaturase
palimityl-ACP + NADPH + O2 —> palmitoyl-ACP + NADP+ + H2O
elongase
palmitate —> long FA